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Tsai YY, Ienes Lima J, Alvarez Narvaez S, Logue CM. Whole-genome analysis of five Escherichia coli strains isolated from focal duodenal necrosis in laying hens reveals genetic similarities to the E. coli O25:H4 ST131 strain. Microbiol Spectr 2025; 13:e0211024. [PMID: 40162772 PMCID: PMC12054123 DOI: 10.1128/spectrum.02110-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 03/10/2025] [Indexed: 04/02/2025] Open
Abstract
Focal duodenal necrosis (FDN) is an intestinal disease causing significant economic losses in the table-egg industry due to reduced egg production in laying hens. Its etiology and pathogenesis remain poorly understood. Between 2021 and 2023, 111 Escherichia coli isolates were collected from FDN lesions and screened for the presence of virulence genes using PCR panels. Five strains-FDN-4, FDN-9, FDN-11, FDN-24, and FDN-50-were selected for whole-genome sequencing due to their high virulence gene content. Core-genome analyses found that the five FDN E. coli belong to different phylogroups and strain types (ST), but they all share multiple complete operons involved in key pathogenic functions, including host cell adhesion and invasion, iron acquisition, motility, biofilm formation, and acid resistance. Comparative genomic analyses identified FDN-4 as the most genetically distinct strain, closely resembling EC958, an O25b:H4 ST131 uropathogenic E. coli (UPEC) commonly associated with extended-spectrum beta-lactamase production. FDN-4 and EC958 share unique chromosomal virulence genes absent in the other FDN strains, all located within genomic islands. This study provides the first complete genomic characterization of E. coli isolated from FDN lesions and highlights FDN-4 as a genetically distinct strain with similarities to O25b:H4 ST131 UPEC.IMPORTANCEThis study presents the first complete genomic characterization of Escherichia coli isolated from focal duodenal necrosis (FDN) lesions. Notably, FDN-4 is the first E. coli strain from a poultry disease (FDN) to show significant similarity to O25b:H4 ST131 strains, commonly classified as uropathogenic E. coli and often associated with extended-spectrum beta-lactamase production. However, caution is warranted when attributing direct transmission routes between poultry and humans.
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Affiliation(s)
- Yu-Yang Tsai
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Julia Ienes Lima
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Sonsiray Alvarez Narvaez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Catherine M. Logue
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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Guliy OI, Evstigneeva SS. Bacteria- and Phage-Derived Proteins in Phage Infection. FRONT BIOSCI-LANDMRK 2025; 30:24478. [PMID: 40018916 DOI: 10.31083/fbl24478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 03/01/2025]
Abstract
Phages have exerted severe evolutionary pressure on prokaryotes over billions of years, resulting in major rearrangements. Without every enzyme involved in the phage-bacterium interaction being examined; bacteriophages cannot be used in practical applications. Numerous studies conducted in the past few years have uncovered a huge variety of bacterial antiphage defense systems; nevertheless, the mechanisms of most of these systems are not fully understood. Understanding the interactions between bacteriophage and bacterial proteins is important for efficient host cell infection. Phage proteins involved in these bacteriophage-host interactions often arise immediately after infection. Here, we review the main groups of phage enzymes involved in the first stage of viral infection and responsible for the degradation of the bacterial membrane. These include polysaccharide depolymerases (endosialidases, endorhamnosidases, alginate lyases, and hyaluronate lyases), and peptidoglycan hydrolases (ectolysins and endolysins). Host target proteins are inhibited, activated, or functionally redirected by the phage protein. These interactions determine the phage infection of bacteria. Proteins of interest are holins, endolysins, and spanins, which are responsible for the release of progeny during the phage lytic cycle. This review describes the main bacterial and phage enzymes involved in phage infection and analyzes the therapeutic potential of bacteriophage-derived proteins.
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Affiliation(s)
- Olga I Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Stella S Evstigneeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
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3
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Sha S, Gao H, Zeng H, Chen F, Kang J, Jing Y, Liu X, Xu B. Adherent-invasive Escherichia coli LF82 disrupts the tight junctions of Caco-2 monolayers. Arab J Gastroenterol 2024; 25:383-389. [PMID: 39069423 DOI: 10.1016/j.ajg.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/14/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND AND STUDY AIMS Adherent invasive Escherichia coli (AIEC) are enriched in IBD (inflammatory bowel disease) patients, but the role and mechanism of AIEC in the intestinal epithelial barrier is poorly defined. We evaluated the role of the AIEC strain E. coli LF82 in vitro and investigated the role of Th17 in this process. MATERIAL AND METHODS After coincubation with AIEC, the epithelial barrier integrity was monitored by epithelial resistance measurements. The permeability of the barrier was evaluated by TEER (trans-epithelial electrical resistance) and mucosal-to-serosal flux rate. The presence of interepithelial tight junction proteins ZO-1 and Claudin-1 were determined by immunofluorescence and western blot analysis. Cytokines in the cell culture supernatant were assayed by enzyme-linked immunosorbent assay (ELISA). RESULTS AIEC infection decreased TEER and increased the mucosal-to-serosal flux rate of Lucifer yellow in the intestinal barrier model in a time- and dose-dependent manner. AIEC infection decreased the expression and changed the distribution of ZO-1 and claudin-1. It also induced the secretion of cytokines such as TNF-α and IL-17. CONCLUSION AIEC strain E. coli LF82 increased the permeability and disrupted the tight junctions of the intestinal epithelial barrier, revealing that AIEC plays an aggravative role in the inflammatory response.
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Affiliation(s)
- Sumei Sha
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Key Laboratory of Gastrointestinal Motility Disorders, Clinical Research Center of Gastrointestinal Diseases, Xi'an, Shaanxi Province 710004, PR China
| | - Huijun Gao
- Department of Gastroenterology, No. 988 Hospital of Joint Logistic Support Force, Jiaozuo, Henan Province 454000, PR China
| | - Hong Zeng
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Key Laboratory of Gastrointestinal Motility Disorders, Clinical Research Center of Gastrointestinal Diseases, Xi'an, Shaanxi Province 710004, PR China; Department of Gastroenterology, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, Shaanxi Province 710000, PR China
| | - Fenrong Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Key Laboratory of Gastrointestinal Motility Disorders, Clinical Research Center of Gastrointestinal Diseases, Xi'an, Shaanxi Province 710004, PR China
| | - Junxiu Kang
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Key Laboratory of Gastrointestinal Motility Disorders, Clinical Research Center of Gastrointestinal Diseases, Xi'an, Shaanxi Province 710004, PR China
| | - Yan Jing
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Key Laboratory of Gastrointestinal Motility Disorders, Clinical Research Center of Gastrointestinal Diseases, Xi'an, Shaanxi Province 710004, PR China
| | - Xin Liu
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Key Laboratory of Gastrointestinal Motility Disorders, Clinical Research Center of Gastrointestinal Diseases, Xi'an, Shaanxi Province 710004, PR China.
| | - Bin Xu
- Tangdu Hospital of the Air Force Medical University, Xi'an, Shaanxi, PR China; Department of General Surgery, the Chenggong Hospital Affiliated to Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen Fujian Province 361003, PR China.
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Zangara MT, Darwish L, Coombes BK. Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. EcoSal Plus 2023; 11:eesp00182022. [PMID: 37220071 PMCID: PMC10729932 DOI: 10.1128/ecosalplus.esp-0018-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 01/28/2024]
Abstract
The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of Enterobacteriaceae species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new Escherichia coli subtype called adherent-invasive E. coli (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original in vitro phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.
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Affiliation(s)
- Megan T. Zangara
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lena Darwish
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
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Majchrzak M, Sakowski S, Waldmajer J, Parniewski P. New Genetic Markers Differentiating IPEC and ExPEC Pathotypes-A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool. Int J Mol Sci 2023; 24:ijms24054681. [PMID: 36902111 PMCID: PMC10002601 DOI: 10.3390/ijms24054681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/08/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
The increasingly expanding genomic databases generate the need for new tools for their processing and further use. In the paper, a bioinformatics tool, which is a search engine of microsatellite elements-trinucleotide repeat sequences (TRS) in files of FASTA type-is presented. An innovative approach was applied in the tool, which consists of connecting-within one search engine-both mapping of TRS motifs and extracting sequences that are found between the mapped TRS motifs. Accordingly, we present hereby the tool called TRS-omix, which comprises a new engine for searching information on genomes and enables generation of sets of sequences and their number, providing the basis for making comparisons between genomes. In our paper, we showed one of the possibilities of using the software. Using TRS-omix and other IT tools, we showed that we were able to extract sets of DNA sequences that can be assigned only to the genomes of the extraintestinal pathogenic Escherichia coli strains or to the genomes of the intestinal pathogenic Escherichia coli strains, as well as providing the basis for differentiation of the genomes/strains belonging to each of these clinically essential pathotypes.
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Affiliation(s)
- Marta Majchrzak
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland
| | - Sebastian Sakowski
- Faculty of Mathematics and Computer Science, University of Lodz, Banacha 22, 90-238 Lodz, Poland
- Centre for Data Analysis, Modelling and Computational Sciences, University of Lodz, Scheibler Family Avenue 2, 90-128 Lodz, Poland
- Correspondence: (S.S.); (P.P.); Tel.: +48-42-272-36-20 (P.P.); Fax: +48-42-27-23-630 (P.P.)
| | - Jacek Waldmajer
- Institute of Computer Science, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Pawel Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland
- Correspondence: (S.S.); (P.P.); Tel.: +48-42-272-36-20 (P.P.); Fax: +48-42-27-23-630 (P.P.)
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Liao C, Santoscoy MC, Craft J, Anderson C, Soupir ML, Jarboe LR. Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution. PLoS One 2022; 17:e0276046. [PMID: 36227900 PMCID: PMC9560509 DOI: 10.1371/journal.pone.0276046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Miguel C. Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
| | - Julia Craft
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Chiron Anderson
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Laura R. Jarboe
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
- * E-mail:
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7
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Influence of Escherichia coli on Expression of Selected Human Drug Addiction Genes. Life (Basel) 2021; 11:life11121346. [PMID: 34947877 PMCID: PMC8705772 DOI: 10.3390/life11121346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/02/2022] Open
Abstract
The impact of enteric microflora on the expression of genes associated with cocaine and amphetamine addiction was described. Human genome-wide experiments on RNA transcripts expressed in response to three selected Escherichia coli strains allowed for significant alteration (p > 0.05) of the linear regression model between HT-29 RNA transcripts associated with the KEGG pathway:hsa05030:Cocaine addiction after 3 h stimulation with intracellular pathogenic E. coli strain UM146 versus non-pathogenic E. coli Nissle 1917. Among the features influenced by the UM146 bacterial strain were visual learning, response to the presence of morphine, response to hypoxia, behavioral fear response and cognitive functions.
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Comparative Pathogenomics of Escherichia coli: Polyvalent Vaccine Target Identification through Virulome Analysis. Infect Immun 2021; 89:e0011521. [PMID: 33941580 PMCID: PMC8281228 DOI: 10.1128/iai.00115-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Comparative genomics of bacterial pathogens has been useful for revealing potential virulence factors. Escherichia coli is a significant cause of human morbidity and mortality worldwide but can also exist as a commensal in the human gastrointestinal tract. With many sequenced genomes, it has served as a model organism for comparative genomic studies to understand the link between genetic content and potential for virulence. To date, however, no comprehensive analysis of its complete “virulome” has been performed for the purpose of identifying universal or pathotype-specific targets for vaccine development. Here, we describe the construction of a pathotype database of 107 well-characterized completely sequenced pathogenic and nonpathogenic E. coli strains, which we annotated for major virulence factors (VFs). The data are cross referenced for patterns against pathotype, phylogroup, and sequence type, and the results were verified against all 1,348 complete E. coli chromosomes in the NCBI RefSeq database. Our results demonstrate that phylogroup drives many of the “pathotype-associated” VFs, and ExPEC-associated VFs are found predominantly within the B2/D/F/G phylogenetic clade, suggesting that these phylogroups are better adapted to infect human hosts. Finally, we used this information to propose polyvalent vaccine targets with specificity toward extraintestinal strains, targeting key invasive strategies, including immune evasion (group 2 capsule), iron acquisition (FyuA, IutA, and Sit), adherence (SinH, Afa, Pap, Sfa, and Iha), and toxins (Usp, Sat, Vat, Cdt, Cnf1, and HlyA). While many of these targets have been proposed before, this work is the first to examine their pathotype and phylogroup distribution and how they may be targeted together to prevent disease.
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9
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Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals. Microorganisms 2021; 9:microorganisms9061299. [PMID: 34203637 PMCID: PMC8232093 DOI: 10.3390/microorganisms9061299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.
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10
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Elhenawy W, Hordienko S, Gould S, Oberc AM, Tsai CN, Hubbard TP, Waldor MK, Coombes BK. High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn's disease-associated Escherichia coli. Nat Commun 2021; 12:2032. [PMID: 33795670 PMCID: PMC8016931 DOI: 10.1038/s41467-021-22306-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) are pathogenic bacteria frequently isolated from patients who have Crohn's disease (CD). Despite the phenotypic differences between AIEC and commensal E. coli, comparative genomic approaches have been unable to differentiate these two groups, making the identification of key virulence factors a challenge. Here, we conduct a high-resolution, in vivo genetic screen to map AIEC genes required for intestinal colonization of mice. In addition, we use in vivo RNA-sequencing to define the host-associated AIEC transcriptome. We identify diverse metabolic pathways required for efficient gut colonization by AIEC and show that a type IV secretion system (T4SS) is required to form biofilms on the surface of epithelial cells, thereby promoting AIEC persistence in the gut. E. coli isolated from CD patients are enriched for a T4SS, suggesting a possible connection to disease activity. Our findings establish the T4SS as a principal AIEC colonization factor and highlight the use of genome-wide screens in decoding the infection biology of CD-associated bacteria that otherwise lack a defined genetic signature.
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Affiliation(s)
- Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Sarah Hordienko
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Steven Gould
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexander M Oberc
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Troy P Hubbard
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada.
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada.
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Costa RFA, Ferrari MLA, Bringer MA, Darfeuille-Michaud A, Martins FS, Barnich N. Characterization of mucosa-associated Escherichia coli strains isolated from Crohn's disease patients in Brazil. BMC Microbiol 2020; 20:178. [PMID: 32576138 PMCID: PMC7310525 DOI: 10.1186/s12866-020-01856-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Crohn’s disease (CD) is characterized by chronic inflammation of the human intestine. Several studies have demonstrated that the intestinal mucosa of CD patients in Western countries is abnormally colonized by adherent-invasive Escherichia coli (AIEC) strains. However, no studies to date have focused on the involvement of such E. coli strains in CD patients in Brazil. Here, we characterized E. coli strains associated with the ileal mucosa of Brazilian CD patients (ileal biopsies from 35 subjects, 24 CD patients and 11 controls). Results The colonization level of adherent Enterobacteriaceae associated with the ileal mucosa of CD patients was significantly higher than that of the controls. The proportions of E. coli strains belonging to phylogroups B1 and B2 were two-fold higher in strains isolated from CD patients than in those isolated from controls. CD patients in the active phase harbored 10-fold more E. coli belonging to group B2 than CD patients in remission. Only a few E. coli isolates had invasive properties and the ability to survive within macrophages, but 25% of CD patients in Brazil (6/24) harbored at least one E. coli strain belonging to the AIEC pathobiont. However, fimH sequence analysis showed only a few polymorphisms in the FimH adhesin of strains isolated in this study compared to the FimH adhesin of AIEC collections isolated from European patients. Conclusions Mucosa-associated E. coli strains colonize the intestinal mucosa of Brazilian CD patients. However, the strains isolated from Brazilian CD patients have probably not yet co-evolved with their hosts and therefore have not fully developed a strong adherent-invasive phenotype. Thus, it will be crucial to follow in the future the emergence and evolution of AIEC pathobionts in the Brazilian population.
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Affiliation(s)
- Rafaella F A Costa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRAE 2018, 28 place Henri Dunant, 63000, Clermont-Ferrand, France
| | - Maria L A Ferrari
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto Alfa de Gastroenterologia, Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marie-Agnès Bringer
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Arlette Darfeuille-Michaud
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRAE 2018, 28 place Henri Dunant, 63000, Clermont-Ferrand, France
| | - Flaviano S Martins
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRAE 2018, 28 place Henri Dunant, 63000, Clermont-Ferrand, France.
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Martinez-Medina M, Strozzi F, Ruiz Del Castillo B, Serrano-Morillas N, Ferrer Bustins N, Martínez-Martínez L. Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams. Antibiotics (Basel) 2020; 9:antibiotics9050251. [PMID: 32414140 PMCID: PMC7277491 DOI: 10.3390/antibiotics9050251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.
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Affiliation(s)
- Margarita Martinez-Medina
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
- Correspondence: ; Tel.: +34-972-418261
| | - Francesco Strozzi
- Data Science Departement, Enterome Biosciences S.A., 75011 Paris, France;
| | - Belén Ruiz Del Castillo
- Service of Microbiology, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain;
| | - Natalia Serrano-Morillas
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Nuria Ferrer Bustins
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Luis Martínez-Martínez
- Unit of Microbiology, University Hospital Reina Sofia, 14004 Córdoba, Spain;
- Maimonides Biomedical Research Institute, 14004 Córdoba, Spain
- Department of Agricultural Chemistry and Microbiology, University of Córdoba, 14004 Córdoba, Spain
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13
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Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics 2020; 21:162. [PMID: 32349661 PMCID: PMC7191737 DOI: 10.1186/s12859-020-3505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains of E. coli. As proteins are one of the main targets of oxidative damage, understanding how the genetic changes of different strains of a species relates to its oxidative environment can reveal hypotheses as to why these variations arise and suggest directions of future experimental work. RESULTS Creating a reference structural proteome for E. coli allows us to comprehensively map genetic changes in 1764 different strains to their locations on 4118 3D protein structures. We use metabolic modeling to predict basal ROS production levels (ROStype) for 695 of these strains, finding that strains with both higher and lower basal levels tend to enrich their proteomes with antioxidative properties, and speculate as to why that is. We computationally assess a strain's sensitivity to an oxidative environment, based on known chemical mechanisms of oxidative damage to protein groups, defined by their localization and functionality. Two general groups - metalloproteins and periplasmic proteins - show enrichment of their antioxidative properties between the 695 strains with a predicted ROStype as well as 116 strains with an assigned pathotype. Specifically, proteins that a) utilize a molybdenum ion as a cofactor and b) are involved in the biogenesis of fimbriae show intriguing protective properties to resist oxidative damage. Overall, these findings indicate that a strain's sensitivity to oxidative damage can be elucidated from the structural proteome, though future experimental work is needed to validate our model assumptions and findings. CONCLUSION We thus demonstrate that structural systems biology enables a proteome-wide, computational assessment of changes to atomic-level physicochemical properties and of oxidative damage mechanisms for multiple strains in a species. This integrative approach opens new avenues to study adaptation to a particular environment based on physiological properties predicted from sequence alone.
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Affiliation(s)
- Nathan Mih
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Jonathan M. Monk
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Xin Fang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Edward Catoiu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - David Heckmann
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Laurence Yang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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14
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Camprubí-Font C, Martinez-Medina M. Why the discovery of adherent-invasive Escherichia coli molecular markers is so challenging? World J Biol Chem 2020; 11:1-13. [PMID: 32405343 PMCID: PMC7205867 DOI: 10.4331/wjbc.v11.i1.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains have been extensively related to Crohn’s disease (CD) etiopathogenesis. Higher AIEC prevalence in CD patients versus controls has been reported, and its mechanisms of pathogenicity have been linked to CD physiopathology. In CD, the therapeutic armamentarium remains limited and non-curative; hence, the necessity to better understand AIEC as a putative instigator or propagator of the disease is certain. Nonetheless, AIEC identification is currently challenging because it relies on phenotypic assays based on infected cell cultures which are highly time-consuming, laborious and non-standardizable. To address this issue, AIEC molecular mechanisms and virulence genes have been studied; however, a specific and widely distributed genetic AIEC marker is still missing. The finding of molecular tools to easily identify AIEC could be useful in the identification of AIEC carriers who could profit from personalized treatment. Also, it would significantly promote AIEC epidemiological studies. Here, we reviewed the existing data regarding AIEC genetics and presented those molecular markers that could assist with AIEC identification. Finally, we highlighted the problems behind the discovery of exclusive AIEC biomarkers and proposed strategies to facilitate the search of AIEC signature sequences.
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Affiliation(s)
- Carla Camprubí-Font
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona 17003, Spain
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona 17003, Spain
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15
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Tang L, Zhou YJ, Zhu S, Liang GD, Zhuang H, Zhao MF, Chang XY, Li HN, Liu Z, Guo ZR, Liu WQ, He X, Wang CX, Zhao DD, Li JJ, Mu XQ, Yao BQ, Li X, Li YG, Duo LB, Wang L, Johnston RN, Zhou J, Zhao JB, Liu GR, Liu SL. E. coli diversity: low in colorectal cancer. BMC Med Genomics 2020; 13:59. [PMID: 32252754 PMCID: PMC7133007 DOI: 10.1186/s12920-020-0704-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. coli diversity with human health and diseases. METHODS Using genomic sequencing and pulsed field gel electrophoresis (PFGE) techniques, we analyzed E. coli from the intestinal microbiota of three groups of healthy individuals, including preschool children, university students, and seniors of a longevity village, as well as colorectal cancer (CRC) patients, to probe the commensal E. coli populations for their diversity. RESULTS We delineated the 2280 fresh E. coli isolates from 185 subjects into distinct genome types (genotypes) by PFGE. The genomic diversity of the sampled E. coli populations was so high that a given subject may have multiple genotypes of E. coli, with the general diversity within a host going up from preschool children through university students to seniors. Compared to the healthy subjects, the CRC patients had the lowest diversity level among their E. coli isolates. Notably, E. coli isolates from CRC patients could suppress the growth of E. coli bacteria isolated from healthy controls under nutrient-limited culture conditions. CONCLUSIONS The coexistence of multiple E. coli lineages in a host may help create and maintain a microbial environment that is beneficial to the host. As such, the low diversity of E. coli bacteria may be associated with unhealthy microenvironment in the intestine and hence facilitate the pathogenesis of diseases such as CRC.
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Affiliation(s)
- Le Tang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Departments of Ecosystems and Public Health, University of Calgary, Calgary, Canada
| | - Yu-Jie Zhou
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Present address: Department of Immunology, Capital Medical University, Beijing, China
| | - Songling Zhu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Gong-Da Liang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - He Zhuang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Man-Fei Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Xiao-Yun Chang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hai-Ning Li
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Zheng Liu
- Department of Colorectal Surgery of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Present address: Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhi-Rong Guo
- Department of Microbiology, Peking University Health Sciences Center, Beijing, China
| | - Wei-Qiao Liu
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Present address: Department of Clinical Neurosciences, University of Calgary, Calgary, Canada
| | - Xiaoyan He
- Department of Microbiology, Peking University Health Sciences Center, Beijing, China
| | - Chun-Xiao Wang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Dan-Dan Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Jia-Jing Li
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xiao-Qin Mu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Bing-Qing Yao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xia Li
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases of the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Li-Bo Duo
- Clinical Laboratory of Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Li Wang
- Clinical Laboratory of Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N Johnston
- Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Jin Zhou
- Department of Hematology of the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jing-Bo Zhao
- Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Gui-Rong Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
- Department of Microbiology, Peking University Health Sciences Center, Beijing, China.
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.
- Department of Infectious Diseases of the First Affiliated Hospital, Harbin Medical University, Harbin, China.
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16
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Barrios-Villa E, Martínez de la Peña CF, Lozano-Zaraín P, Cevallos MA, Torres C, Torres AG, Rocha-Gracia RDC. Comparative genomics of a subset of Adherent/Invasive Escherichia coli strains isolated from individuals without inflammatory bowel disease. Genomics 2019; 112:1813-1820. [PMID: 31689478 DOI: 10.1016/j.ygeno.2019.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/05/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
There is increased evidence demonstrating the association between Crohn's Disease (CD), a type of Inflammatory Bowel Disease (IBD), and non-diarrheagenic Adherent/Invasive Escherichia coli (AIEC) isolates. AIEC strains are phenotypically characterized by their adhesion, invasion and intra-macrophage survival capabilities. In the present study, the genomes of five AIEC strains isolated from individuals without IBD (four from healthy donors and one from peritoneal liquid) were sequenced and compared with AIEC prototype strains (LF82 and NRG857c), and with extra-intestinal uropathogenic strain (UPEC CFT073). Non-IBD-AIEC strains showed an Average Nucleotide Identity up to 98% compared with control strains. Blast identities of the five non-IBD-AIEC strains were higher when compared to AIEC and UPEC reference strains than with another E. coli pathotypes, suggesting a relationship between them. The SNPs phylogeny grouped the five non-IBD-AIEC strains in one separated cluster, which indicates the emergence of these strains apart from the AIEC group. Additionally, four genomic islands not previously reported in AIEC strains were identified. An incomplete Type VI secretion system was found in non-IBD-AIEC strains; however, the Type II secretion system was complete. Several groups of genes reported in AIEC strains were searched in the five non-IBD-AIEC strains, and the presence of fimA, fliC, fuhD, chuA, irp2 and cvaC were confirmed. Other virulence factors were detected in non-IBD-AIEC strains, which were absent in AIEC reference strains, including EhaG, non-fimbrial adhesin 1, PapG, F17D-G, YehA/D, FeuC, IucD, CbtA, VgrG-1, Cnf1 and HlyE. Based on the differences in virulence determinants and SNPs, it is plausible to suggest that non-IBD AIEC strains belong to a different pathotype.
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Affiliation(s)
- Edwin Barrios-Villa
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Claudia Fabiola Martínez de la Peña
- Posgrado en Microbiología, Laboratorio de Biología Molecular de Enteropatógenos, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Patricia Lozano-Zaraín
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico.
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17
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Renouf MJ, Cho YH, McPhee JB. Emergent Behavior of IBD-Associated Escherichia coli During Disease. Inflamm Bowel Dis 2019; 25:33-44. [PMID: 30321333 DOI: 10.1093/ibd/izy312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases are becoming increasingly common throughout the world, both in developed countries and increasingly in rapidly developing countries. Multiple lines of evidence point to a role for the microbial composition of the gastrointestinal tract in the etiology of IBD, but to date, attempts to define a specific microbial cause for IBD have proved unsuccessful. Microbial 16S rRNA profiling shows that IBD patients have elevated levels of Enterobacteriaceae, in particular Escherichia coli, and reduced levels of Faecalibacterium prausnitzii. The observed E. coli have been assigned to a specific pathovar, adherent-invasive E. coli (AIEC). Adherent-invasive E. coli are a genomically heterogenous group, and whereas many groups have attempted to identify specific genetic markers that differentiate AIEC from non-AIEC strains, very few concrete genetic associations have been uncovered. Here, we highlight the advantages of applying a phenotyping approach to the study of these organisms, rather than solely depending on a sequencing or genomic-based screening strategy because virulence-associated phenotypes exhibit behaviors of emergent systems. In this respect, attempts at genetic reductionism are prone to failure because there are numerous metabolic, regulatory or genetic paths that can underlie these virulence-associated behaviors. Here, we review these IBD-associated phenotypes in E. coli and make recommendations for experimental approaches to advance our understanding of IBD-associated bacteria more generally. With advances in high-throughput screening and nongenetically based metabolomic characterization of IBD-associated bacteria, we anticipate a fuller understanding of how altered microbial communities contribute to the development of IBD.
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Affiliation(s)
| | - Youn Hee Cho
- Department of Chemistry and Biology, Ryerson University, Toronto ON, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Ryerson University, Toronto ON, Canada
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18
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Tyakht AV, Manolov AI, Kanygina AV, Ischenko DS, Kovarsky BA, Popenko AS, Pavlenko AV, Elizarova AV, Rakitina DV, Baikova JP, Ladygina VG, Kostryukova ES, Karpova IY, Semashko TA, Larin AK, Grigoryeva TV, Sinyagina MN, Malanin SY, Shcherbakov PL, Kharitonova AY, Khalif IL, Shapina MV, Maev IV, Andreev DN, Belousova EA, Buzunova YM, Alexeev DG, Govorun VM. Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses. BMC Genomics 2018; 19:968. [PMID: 30587114 PMCID: PMC6307143 DOI: 10.1186/s12864-018-5306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated. METHODS We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability. RESULTS The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes. CONCLUSIONS The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.
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Affiliation(s)
- Alexander V. Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
- ITMO University, 49 Kronverkskiy pr, Saint-Petersburg, Russian Federation 197101
| | - Alexander I. Manolov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Alexandra V. Kanygina
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
| | - Dmitry S. Ischenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
| | - Boris A. Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Anna S. Popenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Alexander V. Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Anna V. Elizarova
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
| | - Daria V. Rakitina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Julia P. Baikova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Valentina G. Ladygina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Elena S. Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
| | - Irina Y. Karpova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Tatyana A. Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
| | - Andrei K. Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | | | - Mariya N. Sinyagina
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation 420008
| | - Sergei Y. Malanin
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation 420008
| | - Petr L. Shcherbakov
- Moscow Clinical Scientific Center, 86 Shosse Entuziastov St., Moscow, Russian Federation 111123
| | - Anastasiya Y. Kharitonova
- Clinical and Research Institute of Emergency Children’s Surgery and Trauma, 22 Bolshaya Polyanka St., Moscow, Russian Federation 119180
| | - Igor L. Khalif
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation 123423
| | - Marina V. Shapina
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation 123423
| | - Igor V. Maev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation 127473
| | - Dmitriy N. Andreev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation 127473
| | - Elena A. Belousova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation 129110
| | - Yulia M. Buzunova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation 129110
| | - Dmitry G. Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
| | - Vadim M. Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation 141700
- M.M. Shemyakin - Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, Russian Federation 117997
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Khan S, Imran A, Malik A, Chaudhary AA, Rub A, Jan AT, Syed JB, Rolfo C. Bacterial imbalance and gut pathologies: Association and contribution of E. coli in inflammatory bowel disease. Crit Rev Clin Lab Sci 2018; 56:1-17. [DOI: 10.1080/10408363.2018.1517144] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shahanavaj Khan
- Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, India
| | - Ahamad Imran
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Malik
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Pharmacology, College of Medicine, Al-Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdur Rub
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Arif Tasleem Jan
- School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jakeera Begum Syed
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- College of Medicine and Dentistry, Dar Al Uloom University, Riyadh, Saudi Arabia
| | - Christian Rolfo
- Phase I-Early Clinical Trials Unit, Oncology Department and Multidisciplinary Oncology Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
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20
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Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC SYSTEMS BIOLOGY 2018; 12:66. [PMID: 29890970 PMCID: PMC5996543 DOI: 10.1186/s12918-018-0587-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/21/2018] [Indexed: 01/04/2023]
Abstract
Background Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad comparative genomic analysis of E. coli B2 isolates, and identified virulence factors that allow B2 strains to reside within human intestinal mucosa. Metabolic capabilities of E. coli strains have been shown to be related to their colonization site, but remain unexplored in IBD-associated strains. Results In this study, we utilized pan-genome analysis and genome-scale models (GEMs) of metabolism to study metabolic capabilities of IBD-associated E. coli B2 strains. The study yielded three results: i) Pan-genome analysis of 110 E. coli strains (including 53 isolates from IBD studies) revealed discriminating metabolic genes between B2 strains and other strains; ii) Both comparative genomic analysis and GEMs suggested that B2 strains have an advantage in degrading and utilizing sugars derived from mucus glycan, and iii) GEMs revealed distinct metabolic features in B2 strains that potentially allow them to utilize energy more efficiently. For example, B2 strains lack the enzymes to degrade amadori products, but instead rely on neighboring bacteria to convert these substrates into a more readily usable and potentially less sought after product. Conclusions Taken together, these results suggest that the metabolic capabilities of B2 strains vary significantly from those of other strains, enabling B2 strains to colonize intestinal mucosa.The results from this study motivate a broad experimental assessment of the nutritional effects on E. coli B2 pathophysiology in IBD patients. Electronic supplementary material The online version of this article (10.1186/s12918-018-0587-5) contains supplementary material, which is available to authorized users.
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21
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Ma HQ, Yu TT, Zhao XJ, Zhang Y, Zhang HJ. Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease. World J Gastroenterol 2018; 24:1464-1477. [PMID: 29632427 PMCID: PMC5889826 DOI: 10.3748/wjg.v24.i13.1464] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze the alterations of fecal microbiota in Chinese patients with inflammatory bowel disease (IBD).
METHODS Fecal samples from 15 patients with Crohn’s disease (CD) (11 active CD, 4 inactive CD), 14 patients with active ulcerative colitis (UC) and 13 healthy individuals were collected and subjected to 16S ribosomal DNA (rDNA) gene sequencing. The V4 hypervariable regions of 16S rDNA gene were amplified from all samples and sequenced by the Illumina MiSeq platform. Quality control and operational taxonomic units classification of reads were calculated with QIIME software. Alpha diversity and beta diversity were displayed with R software.
RESULTS Community richness (chao) and microbial structure in both CD and UC were significantly different from those in normal controls. At the phyla level, analysis of the microbial compositions revealed a significantly greater abundance of Proteobacteria in IBD as compared to that in controls. At the genera level, 8 genera in CD and 23 genera in UC (in particular, the Escherichia genus) showed significantly greater abundance as compared to that in normal controls. The relative abundance of Bacteroidetes in the active CD group was markedly lower than that in the inactive CD group. The abundance of Proteobacteria in patients with active CD was nominally higher than that in patients with inactive CD; however, the difference was not statistically significant after correction. Furthermore, the relative abundance of Bacteroidetes showed a negative correlation with the CD activity index scores.
CONCLUSION Our study profiles specific characteristics and microbial dysbiosis in the gut of Chinese patients with IBD. Bacteroidetes may have a negative impact on inflammatory development.
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Affiliation(s)
- Hai-Qin Ma
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Ting-Ting Yu
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Xiao-Jing Zhao
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Yi Zhang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Hong-Jie Zhang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
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22
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Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel JF. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 2018; 67:574-587. [PMID: 29141957 DOI: 10.1136/gutjnl-2017-314903] [Citation(s) in RCA: 352] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/20/2017] [Accepted: 10/28/2017] [Indexed: 02/06/2023]
Abstract
Intestinal microbiome dysbiosis has been consistently described in patients with IBD. In the last decades, Escherichia coli, and the adherent-invasive E coli (AIEC) pathotype in particular, has been implicated in the pathogenesis of IBD. Since the discovery of AIEC, two decades ago, progress has been made in unravelling these bacteria characteristics and its interaction with the gut immune system. The mechanisms of adhesion of AIEC to intestinal epithelial cells (via FimH and cell adhesion molecule 6) and its ability to escape autophagy when inside macrophages are reviewed here. We also explore the existing data on the prevalence of AIEC in patients with Crohn's disease and UC, and the association between the presence of AIEC and disease location, activity and postoperative recurrence. Finally, we highlight potential therapeutic strategies targeting AIEC colonisation of gut mucosa, including the use of phage therapy, bacteriocins and antiadhesive molecules. These strategies may open new avenues for the prevention and treatment of IBD in the future.
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Affiliation(s)
- Carolina Palmela
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Caroline Chevarin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Zhilu Xu
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Gwladys Sevrin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Robert Hirten
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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23
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Camprubí-Font C, Lopez-Siles M, Ferrer-Guixeras M, Niubó-Carulla L, Abellà-Ametller C, Garcia-Gil LJ, Martinez-Medina M. Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. Sci Rep 2018; 8:2695. [PMID: 29426864 PMCID: PMC5807354 DOI: 10.1038/s41598-018-20843-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/24/2018] [Indexed: 01/19/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) have been involved in Crohn's disease (CD). Currently, AIEC are identified by time-consuming techniques based on in vitro infection of cell lines to determine their ability to adhere to and invade intestinal epithelial cells as well as to survive and replicate within macrophages. Our aim was to find signature sequences that can be used to identify the AIEC pathotype. Comparative genomics was performed between three E. coli strain pairs, each pair comprised one AIEC and one non-AIEC with identical pulsotype, sequence type and virulence gene carriage. Genetic differences were further analysed in 22 AIEC and 28 non-AIEC isolated from CD patients and controls. The strain pairs showed similar genome structures, and no gene was specific to AIEC. Three single nucleotide polymorphisms displayed different nucleotide distributions between AIEC and non-AIEC, and four correlated with increased adhesion and/or invasion indices. Here, we present a classification algorithm based on the identification of three allelic variants that can predict the AIEC phenotype with 84% accuracy. Our study corroborates the absence of an AIEC-specific genetic marker distributed across all AIEC strains. Nonetheless, point mutations putatively involved in the AIEC phenotype can be used for the molecular identification of the AIEC pathotype.
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Affiliation(s)
- Carla Camprubí-Font
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | | | - Laura Niubó-Carulla
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Carles Abellà-Ametller
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
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24
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Abstract
The human gut is home to trillions of bacteria and provides the scaffold for one of the most complex microbial ecosystems in nature. Inflammatory bowel diseases, such as Crohn's disease, involve a compositional shift in the microbial constituents of this ecosystem with a marked expansion of Enterobacteriaceae, particularly Escherichia coli. Adherent-invasive E. coli (AIEC) strains are frequently isolated from the biopsies of Crohn's patients, where their ability to elicit inflammation suggests a possible role in Crohn's pathology. Here, we consider the origins of the AIEC pathovar and discuss how risk factors associated with Crohn's disease might influence AIEC colonization dynamics within the host to alter the overall disease potential of the microbial community.
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Affiliation(s)
- Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada,Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Alexander Oberc
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada,Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada,Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada,CONTACT Brian K. Coombes , Department of Biochemistry and Biomedical Sciences, McMaster University, MDCL 2319, Hamilton, ON Canada L8S 4K1
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25
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Rakitina DV, Manolov AI, Kanygina AV, Garushyants SK, Baikova JP, Alexeev DG, Ladygina VG, Kostryukova ES, Larin AK, Semashko TA, Karpova IY, Babenko VV, Ismagilova RK, Malanin SY, Gelfand MS, Ilina EN, Gorodnichev RB, Lisitsyna ES, Aleshkin GI, Scherbakov PL, Khalif IL, Shapina MV, Maev IV, Andreev DN, Govorun VM. Genome analysis of E. coli isolated from Crohn's disease patients. BMC Genomics 2017; 18:544. [PMID: 28724357 PMCID: PMC5517970 DOI: 10.1186/s12864-017-3917-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/02/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. CONCLUSIONS Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.
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Affiliation(s)
- Daria V. Rakitina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I. Manolov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | - Sofya K. Garushyants
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Julia P. Baikova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry G. Alexeev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute for Physics and Technology, Moscow, Russia
| | - Valentina G. Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena S. Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrei K. Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A. Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Irina Y. Karpova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav V. Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ruzilya K. Ismagilova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Fundamental Medicine and Biology of Kazan Federal University, Kazan, Russia
| | - Sergei Y. Malanin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Fundamental Medicine and Biology of Kazan Federal University, Kazan, Russia
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Elena N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Roman B. Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Eugenia S. Lisitsyna
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Gennady I. Aleshkin
- The Gamaleya Research Institute for Epidemiology and Microbiology of the Russian Academy of Medical Science, Moscow, Russia
| | - Petr L. Scherbakov
- Central Scientific Institute of Gastroenterology, Moscow Clinical Research Centre, Moscow, Russia
| | - Igor L. Khalif
- State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Marina V. Shapina
- State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Igor V. Maev
- Moscow State University of Medicine and Dentistry named after A.I. Evdokimov, Ministry of Health of Russian Federation, Moscow, Russia
| | - Dmitry N. Andreev
- Moscow State University of Medicine and Dentistry named after A.I. Evdokimov, Ministry of Health of Russian Federation, Moscow, Russia
| | - Vadim M. Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute for Physics and Technology, Moscow, Russia
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26
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B. Bacteriophages and phage-derived proteins--application approaches. Curr Med Chem 2016; 22:1757-73. [PMID: 25666799 PMCID: PMC4468916 DOI: 10.2174/0929867322666150209152851] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Currently, the bacterial resistance, especially to most commonly used antibiotics has proved to be a severe therapeutic problem. Nosocomial and community-acquired infections are usually caused by multidrug resistant strains. Therefore, we are forced to develop an alternative or supportive treatment for successful cure of life-threatening infections. The idea of using natural bacterial pathogens such as bacteriophages is already well known. Many papers have been published proving the high antibacterial efficacy of lytic phages tested in animal models as well as in the clinic. Researchers have also investigated the application of non-lytic phages and temperate phages, with promising results. Moreover, the development of molecular biology and novel generation methods of sequencing has opened up new possibilities in the design of engineered phages and recombinant phage-derived proteins. Encouraging performances were noted especially for phage enzymes involved in the first step of viral infection responsible for bacterial envelope degradation, named depolymerases. There are at least five major groups of such enzymes – peptidoglycan hydrolases, endosialidases, endorhamnosidases, alginate lyases and hyaluronate lyases – that have application potential. There is also much interest in proteins encoded by lysis cassette genes (holins, endolysins, spanins) responsible for progeny release during the phage lytic cycle. In this review, we discuss several issues of phage and phage-derived protein application approaches in therapy, diagnostics and biotechnology in general.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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27
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Thompson AP, O'Neill I, Smith EJ, Catchpole J, Fagan A, Burgess KEV, Carmody RJ, Clarke DJ. Glycolysis and pyrimidine biosynthesis are required for replication of adherent-invasive Escherichia coli in macrophages. MICROBIOLOGY-SGM 2016; 162:954-965. [PMID: 27058922 DOI: 10.1099/mic.0.000289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Adherent-invasive Escherichia coli (AIEC) have been implicated in the aetiology of Crohn's disease (CD), a chronic inflammatory bowel condition. It has been proposed that AIEC-infected macrophages produce high levels of pro-inflammatory cytokines thus contributing to the inflammation observed in CD. AIEC can replicate in macrophages and we wanted to determine if bacterial replication was linked to the high level of cytokine production associated with AIEC-infected macrophages. Therefore, we undertook a genetic analysis of the metabolic requirements for AIEC replication in the macrophage and we show that AIEC replication in this niche is dependent on bacterial glycolysis. In addition, our analyses indicate that AIEC have access to a wide range of nutrients in the macrophage, although the levels of purines and pyrimidines do appear to be limiting. Finally, we show that the macrophage response to AIEC infection is indistinguishable from the response to the non-replicating glycolysis mutant (ΔpfkAB) and a non-pathogenic strain of E. coli, MG1655. Therefore, AIEC does not appear to subvert the normal macrophage response to E. coli during infection.
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Affiliation(s)
- Aoife P Thompson
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Ian O'Neill
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Emma J Smith
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - John Catchpole
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Ailis Fagan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Karl E V Burgess
- Glasgow Polyomics, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | | | - David J Clarke
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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28
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Munyaka PM, Sepehri S, Ghia JE, Khafipour E. Carrageenan Gum and Adherent Invasive Escherichia coli in a Piglet Model of Inflammatory Bowel Disease: Impact on Intestinal Mucosa-associated Microbiota. Front Microbiol 2016; 7:462. [PMID: 27092122 PMCID: PMC4820460 DOI: 10.3389/fmicb.2016.00462] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/21/2016] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD) including Crohn's disease (CD), and ulcerative colitis (UC), are chronic conditions characterized by chronic intestinal inflammation. Adherent invasive Escherichia coli (AIEC) pathotype has been increasingly implicated in the etiopathogenesis of IBD. In a 21-day study, we investigated the effects of AIEC strain UM146 inoculation on microbiota profile of the ileal, cecal, ascending and descending colon in a pig model of experimental colitis. Carrageenan gum (CG) was used to induce colitis in weaner piglets whereas AIEC strain UM146 previously isolated from a CD patient was included to investigate a cause or consequence effect in IBD. Treatments were: (1) control; (2) CG; (3) AIEC strain UM146; and (4) CG+UM146. Pigs in groups 2 and 4 received 1% CG in drinking water from day 1 of the study while pigs in groups 3 and 4 were inoculated with UM146 on day 8. Following euthanization on day 21, tissue mucosal scrapings were collected and used for DNA extraction. The V4 region of bacterial 16S rRNA gene was then subjected to Illumina sequencing. Microbial diversity, composition, and the predicted functional metagenome were determined in addition to short chain fatty acids profiles in the digesta and inflammatory cytokines in the intestinal tissue. CG-induced colitis decreased bacterial species richness and shifted community composition. At the phylum level, an increase in Proteobacteria and Deferribacteres and a decrease in Firmicutes, Actinobacteria, and Bacteroidetes were observed in CG and CGUM146 compared to control and UM146. The metabolic capacity of the microbiome was also altered in CG and CGUM146 compared to UM146 and control in the colon. We demonstrated that CG resulted in bacterial dysbiosis and shifted community composition similar to what has been previously observed in IBD patients. However, AIEC strain UM146 alone did not cause any clear changes compared to CG or control in our experimental IBD pig model.
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Affiliation(s)
- Peris M Munyaka
- Department of Immunology, University of ManitobaWinnipeg, MB, Canada; Department of Animal Science, University of ManitobaWinnipeg, MB, Canada
| | - Shadi Sepehri
- Children Hospital Research Institute of Manitoba Winnipeg, MB, Canada
| | - Jean-Eric Ghia
- Department of Immunology, University of ManitobaWinnipeg, MB, Canada; Children Hospital Research Institute of ManitobaWinnipeg, MB, Canada; Section of Gastroenterology, Department of Internal MedicineWinnipeg, MB, Canada; Inflammatory Bowel Disease Clinical & Research Centre, University of ManitobaWinnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of ManitobaWinnipeg, MB, Canada; Children Hospital Research Institute of ManitobaWinnipeg, MB, Canada; Department of Medical Microbiology, University of ManitobaWinnipeg, MB, Canada
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Forbes JD, Van Domselaar G, Bernstein CN. Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2016; 22:817-25. [PMID: 26937623 DOI: 10.1097/mib.0000000000000684] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND We aimed to contrast the mucosal microbiota in Crohn's disease (CD) and ulcerative colitis (UC). METHODS We assessed the concept of localized dysbiosis by comparing the bacterial communities of inflamed and noninflamed mucosa of patients with inflammatory bowel disease (IBD) and by analysis of the microbiota composition at distinct gut compartments (ileum, cecum, mid-colon, and rectum). We performed 16S rDNA sequencing to analyze population structures. Quality control and operational taxonomic unit classification of reads were performed using mothur with statistical analyses executed in the R package, phyloseq. RESULTS There was no variation in any phyla or genera comparing inflamed to noninflamed mucosa within CD (or UC) or when comparing different gut compartments within CD (or UC). There were differences between the inflamed and noninflamed mucosa between CD and UC: analysis of the inflamed IBD gut at the phylum level indicated that Bacteroidetes (P = 0.002) and Fusobacteria (P < 0.05) were detected more frequently in inflamed CD mucosa than in inflamed UC mucosa. Conversely, Proteobacteria and Firmicutes (P < 0.05) were more frequently observed in the inflamed UC mucosa. At the genus level, the abundance of Faecalibacterium (P ≤ 0.05), Bacteroides (P = 0.003), and Pseudomonas (P < 0.001) were significantly different between the inflamed CD and UC and the abundance of 13 genera were significantly different within the noninflamed mucosa. The noninflamed UC mucosa was the most different from non-IBD mucosa. CONCLUSIONS Dramatic shifts of microbial communities were not observed between the noninflamed and inflamed mucosa within CD (or UC) although both the inflamed (and noninflamed) mucosa was different between CD and UC.
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Affiliation(s)
- Jessica D Forbes
- *Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Canada; †Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; and ‡Department of Internal Medicine, IBD Clinical and Research Centre, University of Manitoba, Canada
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Abstract
BACKGROUND Adherent-invasive Escherichia coli (AIEC) associated with Crohn's disease target M cells lining Peyer's patches (PPs) through the expression of long polar fimbriae (LPF) and survive macrophage killing. Invasion of PPs constitutes a way to colonize the mucosa for bacteria able to escape or resist killing of underlying immune cells. We aimed to identify new virulence factors involved in PPs colonization by AIEC. METHODS The presence of gipA (Growth in PPs) gene was determined by polymerase chain reaction. In vivo experiments were performed using CEABAC10 transgenic mice. Intramacrophagic behavior of AIEC was assessed in murine bone marrow-derived macrophages and human monocyte-derived macrophages. Cytokines production was quantified by ELISA. RESULTS A higher prevalence of gipA-positive E. coli was observed in patients with Crohn's disease (27.3%) compared with controls (17.2%). Unlike non-AIEC strains, all gipA-positive AIEC strains also harbored lpfA. GipA deletion impaired AIEC translocation across M cells and their replication inside macrophages. GipA expression was induced by gastrointestinal (bile salts) and phagolysosomal (reactive oxygen species and acid pH) conditions. GipA deletion decreased lpfA mRNA level in AIEC bacteria. Survival of AIEC-ΔgipA bacteria was reduced in medium containing H2O2 or acidic pH. GipA deletion impaired AIEC colonization of PPs and dissemination to mesenteric lymph nodes in mice. CONCLUSIONS GipA is required for optimal colonization of mouse PPs and survival within macrophages by AIEC, suggesting that this factor plays a role in AIEC promotion of Crohn's disease. Detection of gipA and lpfA could be a predictor for the presence of AIEC.
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Deshpande NP, Wilkins MR, Mitchell HM, Kaakoush NO. Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group. FEMS Microbiol Lett 2015; 362:fnv193. [PMID: 26459886 DOI: 10.1093/femsle/fnv193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2015] [Indexed: 12/13/2022] Open
Abstract
The B2 phylogenetic group of Escherichia coli contains important pathogens such as extraintestinal pathogenic, adherent-invasive, and uropathogenic strains. In this study, we used comparative genomics and statistical methods to identify genetic variations that define a subset of pathogenic strains belonging to the B2 phylogenetic group. An initial proof of concept analysis indicated that five of the 62 E. coli strains available in the Kyoto Encyclopedia of Genes and Genomes database showed close association with B2 adherent-invasive E. coli, forming a subgroup within the B2 phylogenetic group. The tool, kSNP which uses a k-mer approach, and the statistical phenotype prediction tool PPFS2 were then employed to identify 29 high-resolution SNPs, which reaffirmed this grouping. PPFS2 analysis also provided indications that the clustering of this subgroup was highly consistent, and thus, could have a strong phenotypic basis rather than being only evolutionary. Protein homology analyses identified three proteins to be conserved across this subgrouping, two CRISPR-Cas proteins and a hypothetical protein. Functional analyses of these genetic and protein variations may provide insights into the phenotype of these strains.
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Affiliation(s)
- Nandan P Deshpande
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia Ramaciotti Centre for Gene Function Analysis, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Nadeem O Kaakoush
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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García-Gutiérrez E, Almendros C, Mojica FJM, Guzmán NM, García-Martínez J. CRISPR Content Correlates with the Pathogenic Potential of Escherichia coli. PLoS One 2015; 10:e0131935. [PMID: 26136211 PMCID: PMC4489801 DOI: 10.1371/journal.pone.0131935] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/08/2015] [Indexed: 12/15/2022] Open
Abstract
Guide RNA molecules (crRNA) produced from clustered regularly interspaced short palindromic repeat (CRISPR) arrays, altogether with effector proteins (Cas) encoded by cognate cas (CRISPR associated) genes, mount an interference mechanism (CRISPR-Cas) that limits acquisition of foreign DNA in Bacteria and Archaea. The specificity of this action is provided by the repeat intervening spacer carried in the crRNA, which upon hybridization with complementary sequences enables their degradation by a Cas endonuclease. Moreover, CRISPR arrays are dynamic landscapes that may gain new spacers from infecting elements or lose them for example during genome replication. Thus, the spacer content of a strain determines the diversity of sequences that can be targeted by the corresponding CRISPR-Cas system reflecting its functionality. Most Escherichia coli strains possess either type I-E or I-F CRISPR-Cas systems. To evaluate their impact on the pathogenicity of the species, we inferred the pathotype and pathogenic potential of 126 strains of this and other closely related species and analyzed their repeat content. Our results revealed a negative correlation between the number of I-E CRISPR units in this system and the presence of pathogenicity traits: the median number of repeats was 2.5-fold higher for commensal isolates (with 29.5 units, range 0-53) than for pathogenic ones (12.0, range 0-42). Moreover, the higher the number of virulence factors within a strain, the lower the repeat content. Additionally, pathogenic strains of distinct ecological niches (i.e., intestinal or extraintestinal) differ in repeat counts. Altogether, these findings support an evolutionary connection between CRISPR and pathogenicity in E. coli.
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Affiliation(s)
- Enriqueta García-Gutiérrez
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 Alicante, Spain
| | - Cristóbal Almendros
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 Alicante, Spain
| | - Francisco J. M. Mojica
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 Alicante, Spain
| | - Noemí M. Guzmán
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 Alicante, Spain
| | - Jesús García-Martínez
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 Alicante, Spain
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Matter LB, Spricigo DA, Tasca C, Vargas ACD. Invasin gimB found in a bovine intestinal Escherichia coli with an adherent and invasive profile. Braz J Microbiol 2015; 46:875-8. [PMID: 26413073 PMCID: PMC4568875 DOI: 10.1590/s1517-838246320140621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/19/2014] [Indexed: 11/22/2022] Open
Abstract
The invasin gimB (genetic island associated with human newborn
meningitis) is usually found in ExPEC (Extraintestinal Pathogenic Escherichia
coli) such as UPEC (uropathogenic E. coli), NMEC
(neonatal meningitis E. coli) and APEC (avian pathogenic E.
coli). In NMEC, gimB is associated with the invasion
process of the host cells. Due to the importance of E. coli as a
zoonotic agent and the scarce information about the frequency of
gimB-carrying strains in different animal species, the aim of
this study was to investigate the presence of gimB in isolates from
bovine, swine, canine and feline clinical samples. PCR was conducted on 196 isolates
and the identity of the amplicons was confirmed by sequencing. Of the samples tested,
only E. coli SB278/94 from a bovine specimen was positive (1/47) for
gimB, which represents 2.1% of the bovine isolates. The ability
of SB278/94 to adhere to and invade eukaryotic cells was confirmed by adherence and
gentamicin-protection assays using HeLa cells. This is the first study that
investigates for gimB in bovine, canine and feline E.
coli isolates and shows E. coli from the
intestinal-bovine samples harboring gimB.
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Affiliation(s)
- Letícia B Matter
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Denis A Spricigo
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Caiane Tasca
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Agueda C de Vargas
- Laboratório de Bacteriologia, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One 2015; 10:e0130902. [PMID: 26125937 PMCID: PMC4509574 DOI: 10.1371/journal.pone.0130902] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/25/2015] [Indexed: 12/30/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn’s disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)—CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p <0.05). These results support a comparative genomic/transcriptomic approach towards identifying candidate AIEC signature transcripts.
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Pathogenesis of human diffusely adhering Escherichia coli expressing Afa/Dr adhesins (Afa/Dr DAEC): current insights and future challenges. Clin Microbiol Rev 2015; 27:823-69. [PMID: 25278576 DOI: 10.1128/cmr.00036-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The pathogenicity and clinical pertinence of diffusely adhering Escherichia coli expressing the Afa/Dr adhesins (Afa/Dr DAEC) in urinary tract infections (UTIs) and pregnancy complications are well established. In contrast, the implication of intestinal Afa/Dr DAEC in diarrhea is still under debate. These strains are age dependently involved in diarrhea in children, are apparently not involved in diarrhea in adults, and can also be asymptomatic intestinal microbiota strains in children and adult. This comprehensive review analyzes the epidemiology and diagnosis and highlights recent progress which has improved the understanding of Afa/Dr DAEC pathogenesis. Here, I summarize the roles of Afa/Dr DAEC virulence factors, including Afa/Dr adhesins, flagella, Sat toxin, and pks island products, in the development of specific mechanisms of pathogenicity. In intestinal epithelial polarized cells, the Afa/Dr adhesins trigger cell membrane receptor clustering and activation of the linked cell signaling pathways, promote structural and functional cell lesions and injuries in intestinal barrier, induce proinflammatory responses, create angiogenesis, instigate epithelial-mesenchymal transition-like events, and lead to pks-dependent DNA damage. UTI-associated Afa/Dr DAEC strains, following adhesin-membrane receptor cell interactions and activation of associated lipid raft-dependent cell signaling pathways, internalize in a microtubule-dependent manner within urinary tract epithelial cells, develop a particular intracellular lifestyle, and trigger a toxin-dependent cell detachment. In response to Afa/Dr DAEC infection, the host epithelial cells generate antibacterial defense responses. Finally, I discuss a hypothetical role of intestinal Afa/Dr DAEC strains that can act as "silent pathogens" with the capacity to emerge as "pathobionts" for the development of inflammatory bowel disease and intestinal carcinogenesis.
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Nazareth N, Magro F, Machado E, Ribeiro TG, Martinho A, Rodrigues P, Alves R, Macedo GN, Gracio D, Coelho R, Abreu C, Appelberg R, Dias C, Macedo G, Bull T, Sarmento A. Prevalence of Mycobacterium avium subsp. paratuberculosis and Escherichia coli in blood samples from patients with inflammatory bowel disease. Med Microbiol Immunol 2015; 204:681-92. [PMID: 25994082 DOI: 10.1007/s00430-015-0420-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/13/2015] [Indexed: 12/31/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) and adherent-invasive Escherichia coli (AIEC) have been implicated as primary triggers in Crohn's disease (CD). In this study, we evaluated the prevalence of MAP and E. coli (EC) DNA in peripheral blood from 202 inflammatory bowel disease (IBD) patients at various disease periods and compared against 24 cirrhotic patients with ascites (CIR) (non-IBD controls) and 29 healthy controls (HC). MAP DNA was detected by IS900-specific nested PCR, EC DNA by malB-specific nested PCR and AIEC identity, in selected samples, by sequencing of fimH gene. CD patients with active disease showed the highest MAP DNA prevalence among IBD patients (68 %). Infliximab treatment resulted in decreased MAP detection. CIR patients had high individual and coinfection rates (75 % MAP, 88 % EC and 67 % MAP and EC), whilst HC controls had lower MAP prevalence (38 %) and EC was undetectable in this control group. EC DNA prevalence in IBD patients was highly associated with CD, and 80 % of EC from the selected samples of CD patients analyzed carried the fimH30 allele, with a mutation strongly associated with AIEC. Our results show that coinfection with MAP and AIEC is common and persistent in CD, although the high MAP and EC detection in CIR patients suggested that colonization is, at least, partially dependent on increased gut permeability. Nevertheless, facilitative mechanisms between a susceptible host and these two potential human pathogens may allow their implication in CD pathogenesis.
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Affiliation(s)
- Nair Nazareth
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
| | - Fernando Magro
- Institute of Pharmacology and Therapeutics, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
- Gastroenterology Department, Centro Hospitalar São João, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
- MedInUP -Center for Drug Discovery and Innovative Medicines, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Elisabete Machado
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
- REQUIMTE, Laboratory of Microbiology, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Teresa Gonçalves Ribeiro
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
- REQUIMTE, Laboratory of Microbiology, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - António Martinho
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
| | - Pedro Rodrigues
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
- Infection and Immunity Unit, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180, Porto, Portugal
| | - Rita Alves
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
| | - Gonçalo Nuno Macedo
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal
| | - Daniela Gracio
- Institute of Pharmacology and Therapeutics, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
- MedInUP -Center for Drug Discovery and Innovative Medicines, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Rosa Coelho
- Gastroenterology Department, Centro Hospitalar São João, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Candida Abreu
- Department of Infectious Diseases, Centro Hospitalar S. João, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
- Nephrology Research and Development Unit, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Rui Appelberg
- Infection and Immunity Unit, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180, Porto, Portugal
| | - Camila Dias
- Department of Biostatistics and Medical Informatics, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Guilherme Macedo
- Gastroenterology Department, Centro Hospitalar São João, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Tim Bull
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Amélia Sarmento
- FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Portugal.
- Infection and Immunity Unit, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180, Porto, Portugal.
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The IbeA invasin of adherent-invasive Escherichia coli mediates interaction with intestinal epithelia and macrophages. Infect Immun 2015; 83:1904-18. [PMID: 25712929 DOI: 10.1128/iai.03003-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/15/2015] [Indexed: 12/22/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) pathogroup isolates are a group of isolates from the intestinal mucosa of Crohn's disease patients that can invade intestinal epithelial cells (IECs) or macrophages and survive and/or replicate within. We have identified the ibeA gene in the genome of AIEC strain NRG857c and report the contribution of IbeA to the interaction of AIEC with IECs and macrophages and colonization of the mouse intestine. An ibeA deletion mutant strain (NRG857cΔibeA) was constructed, and the in vitro effect on AIEC adhesion and invasion of nonpolarized and polarized Caco-2 cells, the adhesion and transcytosis of M-like cells, the intracellular survival in THP-1 macrophages, and the contribution to intestinal colonization of the CD-1 murine model of infection were evaluated. A significant reduction in invasion was observed with the ibeA mutant in Caco-2 and M-like cells, whereas adhesion was not affected. Complementation of the mutant reestablished Caco-2 invasive phenotype to wild-type levels. Reduction in invasion did not significantly affect transcytosis through M-like cells at early time points. The absence of ibeA significantly affected AIEC intramacrophage survival up to 24 h postinfection. No significant changes associated with IbeA were found in AIEC colonization across the murine gastrointestinal tract, but a slight reduction of gamma interferon was observed in the ceca of mice infected with the ibeA mutant. In addition, a decrease in the pathology scores was observed in the ilea and ceca of mice infected with the ibeA mutant. Our data support the function of IbeA in the AIEC invasion process, macrophage survival, and inflammatory response in the murine intestine.
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Analysis of the σE regulon in Crohn's disease-associated Escherichia coli revealed involvement of the waaWVL operon in biofilm formation. J Bacteriol 2015; 197:1451-65. [PMID: 25666140 DOI: 10.1128/jb.02499-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Ileal lesions of patients with Crohn's disease are colonized by adherent-invasive Escherichia coli (AIEC), which is able to adhere to and to invade intestinal epithelial cells (IEC), to replicate within macrophages, and to form biofilms on the surface of the intestinal mucosa. Previous analyses indicated the involvement of the σ(E) pathway in AIEC-IEC interaction, as well as in biofilm formation, with σ(E) pathway inhibition leading to an impaired ability of AIEC to colonize the intestinal mucosa and to form biofilms. The aim of this study was to characterize the σ(E) regulon of AIEC strain LF82 in order to identify members involved in AIEC phenotypes. Using comparative in silico analysis of the σ(E) regulon, we identified the waaWVL operon as a new member of the σ(E) regulon in reference AIEC strain LF82. We determined that the waaWVL operon is involved in AIEC lipopolysaccharide structure and composition, and the waaWVL operon was found to be essential for AIEC strains to produce biofilm and to colonize the intestinal mucosa. IMPORTANCE An increased prevalence of adherent-invasive Escherichia coli (AIEC) bacteria was previously observed in the intestinal mucosa of Crohn's disease (CD) patients, and clinical observations revealed bacterial biofilms associated with the mucosa of CD patients. Here, analysis of the σ(E) regulon in AIEC and commensal E. coli identified 12 genes controlled by σ(E) only in AIEC. Among them, WaaWVL factors were found to play an essential role in biofilm formation and mucosal colonization by AIEC. In addition to identifying molecular tools that revealed a pathogenic population of E. coli colonizing the mucosa of CD patients, these results indicate that targeting the waaWVL operon could be a potent therapeutic strategy to interfere with the ability of AIEC to form biofilms and to colonize the gut mucosa.
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Wirth R, Bódi N, Maróti G, Bagyánszki M, Talapka P, Fekete É, Bagi Z, Kovács KL. Regionally distinct alterations in the composition of the gut microbiota in rats with streptozotocin-induced diabetes. PLoS One 2014; 9:e110440. [PMID: 25469509 PMCID: PMC4254516 DOI: 10.1371/journal.pone.0110440] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/18/2014] [Indexed: 12/19/2022] Open
Abstract
The aim of this study was to map the microbiota distribution along the gut and establish whether colon/faecal samples from diabetic rats adequately reflect the diabetic alterations in the microbiome. Streptozotocin-treated rats were used to model type 1 diabetes mellitus (T1D). Segments of the duodenum, ileum and colon were dissected, and the microbiome of the lumen material was analysed by using next-generation DNA sequencing, from phylum to genus level. The intestinal luminal contents were compared between diabetic, insulin-treated diabetic and healthy control rats. No significant differences in bacterial composition were found in the luminal contents from the duodenum of the experimental animal groups, whereas distinct patterns were seen in the ileum and colon, depending on the history of the luminal samples. Ileal samples from diabetic rats exhibited particularly striking alterations, while the richness and diversity obscured some of the modifications in the colon. Characteristic rearrangements in microbiome composition and diversity were detected after insulin treatment, though the normal gut flora was not restored. The Proteobacteria displayed more pronounced shifts than those of the predominant phyla (Firmicutes and Bacteroidetes) in the rat model of T1D. Diabetes and insulin replacement affect the composition of the gut microbiota in different, gut region-specific manners. The luminal samples from the ileum appear more suitable for diagnostic purposes than the colon/faeces. The Proteobacteria should be at the focus of diagnosis and potential therapy. Klebsiella are recommended as biomarkers of T1D.
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Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Nikolett Bódi
- Department of Physiology, Anatomy and Neuroscience, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Mária Bagyánszki
- Department of Physiology, Anatomy and Neuroscience, University of Szeged, Szeged, Hungary
| | - Petra Talapka
- Department of Physiology, Anatomy and Neuroscience, University of Szeged, Szeged, Hungary
| | - Éva Fekete
- Department of Physiology, Anatomy and Neuroscience, University of Szeged, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Kornél L. Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- Department of Oral Biology and Experimental Dentistry, University of Szeged, Szeged, Hungary
- * E-mail:
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Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation. Inflamm Bowel Dis 2014; 20:1919-32. [PMID: 25230163 DOI: 10.1097/mib.0000000000000183] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Perturbations of the intestinal microbiome, termed dysbiosis, are linked to intestinal inflammation. Isolation of adherent-invasive Escherichia coli (AIEC) from intestines of patients with Crohn's disease (CD), dogs with granulomatous colitis, and mice with acute ileitis suggests these bacteria share pathoadaptive virulence factors that promote inflammation. METHODS To identify genes associated with AIEC, we sequenced the genomes of phylogenetically diverse AIEC strains isolated from people with CD (4), dogs with granulomatous colitis (2), and mice with ileitis (2) and 1 non-AIEC strain from CD ileum and compared them with 38 genome sequences of E. coli and Shigella. We then determined the prevalence of AIEC-associated genes in 49 E. coli strains from patients with CD and controls and correlated genotype with invasion of intestinal epithelial cells, persistence within macrophages, AIEC pathotype, and growth in standardized conditions. RESULTS Genes encoding propanediol utilization (pdu operon) and iron acquisition (yersiniabactin, chu operon) were overrepresented in AIEC relative to nonpathogenic E. coli. PduC (propanediol dehydratase) was enriched in CD-derived AIEC, correlated with increased cellular invasion, and persistence in vitro and was increasingly expressed in fucose-containing media. Growth of AIEC required iron, and the presence of chuA (heme acquisition) correlated with persistence in macrophages. CD-associated AIEC with lpfA 154 (long polar fimbriae) demonstrated increased invasion of epithelial cells and translocation across M cells. CONCLUSIONS Our findings provide novel insights into the genetic basis of the AIEC pathotype, supporting the concept that AIEC are equipped to exploit and promote intestinal inflammation and reveal potential targets for intervention against AIEC and inflammation-associated dysbiosis.
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Ma Q, Chen X, Liu C, Mao X, Zhang H, Ji F, Wu C, Xu Y. Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective. SCIENCE CHINA-LIFE SCIENCES 2014; 57:1121-30. [DOI: 10.1007/s11427-014-4734-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/11/2014] [Indexed: 12/15/2022]
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Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: An update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol 2014; 5:213-227. [PMID: 25133024 PMCID: PMC4133521 DOI: 10.4291/wjgp.v5.i3.213] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/08/2014] [Accepted: 05/29/2014] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli (E. coli), and particularly the adherent invasive E. coli (AIEC) pathotype, has been increasingly implicated in the ethiopathogenesis of Crohn’s disease (CD). E. coli strains with similar pathogenic features to AIEC have been associated with other intestinal disorders such as ulcerative colitis, colorectal cancer, and coeliac disease, but AIEC prevalence in these diseases remains largely unexplored. Since AIEC was described one decade ago, substantial progress has been made in deciphering its mechanisms of pathogenicity. However, the molecular bases that characterize the phenotypic properties of this pathotype are still not well resolved. A review of studies focused on E. coli populations in inflammatory bowel disease (IBD) is presented here and we discuss about the putative role of this species on each IBD subtype. Given the relevance of AIEC in CD pathogenesis, we present the latest research findings concerning AIEC host-microbe interactions and pathogenicity. We also review the existing data regarding the prevalence and abundance of AIEC in CD and its association with other intestinal diseases from humans and animals, in order to discuss the AIEC disease- and host-specificity. Finally, we highlight the fact that dietary components frequently found in industrialized countries may enhance AIEC colonization in the gut, which merits further investigation and the implementation of preventative measures.
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Parent KN, Tang J, Cardone G, Gilcrease EB, Janssen ME, Olson NH, Casjens SR, Baker TS. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain. Virology 2014; 464-465:55-66. [PMID: 25043589 DOI: 10.1016/j.virol.2014.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 01/21/2023]
Abstract
CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the "HK97-fold" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain ("I-domain"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States.
| | - Jinghua Tang
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Giovanni Cardone
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Eddie B Gilcrease
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112, United States
| | - Mandy E Janssen
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Norman H Olson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Sherwood R Casjens
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112, United States.
| | - Timothy S Baker
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States; University of California, San Diego, Division of Biological Sciences, La Jolla, CA, 92093, United States.
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Smith EJ, Thompson AP, O'Driscoll A, Clarke DJ. Pathogenesis of adherent-invasive Escherichia coli. Future Microbiol 2014; 8:1289-300. [PMID: 24059919 DOI: 10.2217/fmb.13.94] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The etiology of Crohn's disease (CD) is complex and involves both host susceptibility factors (i.e., the presence of particular genetic alleles) and environmental factors, including bacteria. In this regard, adherent-invasive Escherichia coli (AIEC), have recently emerged as an exciting potential etiological agent of CD. AIEC are distinguished from commensal strains of E. coli through their ability to adhere to and invade epithelial cells and replicate in macrophages. Recent molecular analyses have identified genes required for both invasion of epithelial cells and replication in the macrophage. However, these genetic studies, in combination with recent genome sequencing projects, have revealed that the pathogenesis of this group of bacteria cannot be explained by the presence of AIEC-specific genes. In this article, we review the role of AIEC as a pathobiont in the pathology of CD. We also describe the emerging link between AIEC and autophagy, and we propose a model for AIEC pathogenesis.
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Affiliation(s)
- Emma J Smith
- Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Pathogenesis of human enterovirulent bacteria: lessons from cultured, fully differentiated human colon cancer cell lines. Microbiol Mol Biol Rev 2014; 77:380-439. [PMID: 24006470 DOI: 10.1128/mmbr.00064-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hosts are protected from attack by potentially harmful enteric microorganisms, viruses, and parasites by the polarized fully differentiated epithelial cells that make up the epithelium, providing a physical and functional barrier. Enterovirulent bacteria interact with the epithelial polarized cells lining the intestinal barrier, and some invade the cells. A better understanding of the cross talk between enterovirulent bacteria and the polarized intestinal cells has resulted in the identification of essential enterovirulent bacterial structures and virulence gene products playing pivotal roles in pathogenesis. Cultured animal cell lines and cultured human nonintestinal, undifferentiated epithelial cells have been extensively used for understanding the mechanisms by which some human enterovirulent bacteria induce intestinal disorders. Human colon carcinoma cell lines which are able to express in culture the functional and structural characteristics of mature enterocytes and goblet cells have been established, mimicking structurally and functionally an intestinal epithelial barrier. Moreover, Caco-2-derived M-like cells have been established, mimicking the bacterial capture property of M cells of Peyer's patches. This review intends to analyze the cellular and molecular mechanisms of pathogenesis of human enterovirulent bacteria observed in infected cultured human colon carcinoma enterocyte-like HT-29 subpopulations, enterocyte-like Caco-2 and clone cells, the colonic T84 cell line, HT-29 mucus-secreting cell subpopulations, and Caco-2-derived M-like cells, including cell association, cell entry, intracellular lifestyle, structural lesions at the brush border, functional lesions in enterocytes and goblet cells, functional and structural lesions at the junctional domain, and host cellular defense responses.
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Wurpel DJ, Totsika M, Allsopp LP, Hartley-Tassell LE, Day CJ, Peters KM, Sarkar S, Ulett GC, Yang J, Tiralongo J, Strugnell RA, Jennings MP, Schembri MA. F9 fimbriae of uropathogenic Escherichia coli are expressed at low temperature and recognise Galβ1-3GlcNAc-containing glycans. PLoS One 2014; 9:e93177. [PMID: 24671091 PMCID: PMC3966885 DOI: 10.1371/journal.pone.0093177] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 03/03/2014] [Indexed: 11/29/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the leading causative agent of urinary tract infections (UTI) in the developed world. Among the major virulence factors of UPEC, surface expressed adhesins mediate attachment and tissue tropism. UPEC strains typically possess a range of adhesins, with type 1 fimbriae and P fimbriae of the chaperone-usher class the best characterised. We previously identified and characterised F9 as a new chaperone-usher fimbrial type that mediates biofilm formation. However, the regulation and specific role of F9 fimbriae remained to be determined in the context of wild-type clinical UPEC strains. In this study we have assessed the distribution and genetic context of the f9 operon among diverse E. coli lineages and pathotypes and demonstrated that f9 genes are significantly more conserved in a UPEC strain collection in comparison to the well-defined E. coli reference (ECOR) collection. In the prototypic UPEC strain CFT073, the global regulator protein H-NS was identified as a transcriptional repressor of f9 gene expression at 37°C through its ability to bind directly to the f9 promoter region. F9 fimbriae expression was demonstrated at 20°C, representing the first evidence of functional F9 fimbriae expression by wild-type E. coli. Finally, glycan array analysis demonstrated that F9 fimbriae recognise and bind to terminal Galβ1-3GlcNAc structures.
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Affiliation(s)
- Daniël J. Wurpel
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Makrina Totsika
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- * E-mail: (MAS); (MT)
| | - Luke P. Allsopp
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Christopher J. Day
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Kate M. Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Sohinee Sarkar
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Glen C. Ulett
- School of Medical Sciences, Centre for Medicine and Oral Health, Griffith University, Southport, Queensland, Australia
| | - Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joe Tiralongo
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Mark A. Schembri
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- * E-mail: (MAS); (MT)
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Small CLN, Reid-Yu SA, McPhee JB, Coombes BK. Persistent infection with Crohn's disease-associated adherent-invasive Escherichia coli leads to chronic inflammation and intestinal fibrosis. Nat Commun 2013; 4:1957. [PMID: 23748852 PMCID: PMC3938456 DOI: 10.1038/ncomms2957] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/30/2013] [Indexed: 02/06/2023] Open
Abstract
Crohn’s disease is a chronic inflammatory condition of the gastrointestinal tract in which alterations to the bacterial community contribute to disease. Adherent-invasive E. coli (AIEC) are associated with human Crohn’s disease, however their role in intestinal immunopathology is unclear due to the lack of an animal model compatible with chronic timescales. Here we establish chronic AIEC infection in streptomycin-treated conventional mice (CD-1, DBA/2, C3HeN, 129e, C57BL/6), enabling the study of host response and immunopathology. AIEC induces an active Th17 response, heightened levels of proinflammatory cytokines and fibrotic growth factors, with transmural inflammation and fibrosis. Depletion of CD8+ T cells increases cecal bacterial load, pathology and intestinal fibrosis in C57BL/6 mice suggesting a protective role. Our findings provide evidence that chronic AIEC infections result in immunopathology similar to that seen in Crohn’s disease. With this model, research into the host and bacterial genetics associated with AIEC-induced disease becomes more widely accessible.
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Affiliation(s)
- Cherrie-Lee N Small
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada L8N 3Z5
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Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB. Recent advances in understanding enteric pathogenic Escherichia coli. Clin Microbiol Rev 2013; 26:822-80. [PMID: 24092857 PMCID: PMC3811233 DOI: 10.1128/cmr.00022-13] [Citation(s) in RCA: 895] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although Escherichia coli can be an innocuous resident of the gastrointestinal tract, it also has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases. Pathogenic variants of E. coli (pathovars or pathotypes) cause much morbidity and mortality worldwide. Consequently, pathogenic E. coli is widely studied in humans, animals, food, and the environment. While there are many common features that these pathotypes employ to colonize the intestinal mucosa and cause disease, the course, onset, and complications vary significantly. Outbreaks are common in developed and developing countries, and they sometimes have fatal consequences. Many of these pathotypes are a major public health concern as they have low infectious doses and are transmitted through ubiquitous mediums, including food and water. The seriousness of pathogenic E. coli is exemplified by dedicated national and international surveillance programs that monitor and track outbreaks; unfortunately, this surveillance is often lacking in developing countries. While not all pathotypes carry the same public health profile, they all carry an enormous potential to cause disease and continue to present challenges to human health. This comprehensive review highlights recent advances in our understanding of the intestinal pathotypes of E. coli.
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de Muinck EJ, Lagesen K, Afset JE, Didelot X, Rønningen KS, Rudi K, Stenseth NC, Trosvik P. Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche. BMC Genomics 2013; 14:81. [PMID: 23384204 PMCID: PMC3637554 DOI: 10.1186/1471-2164-14-81] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/30/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche. RESULTS Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles. CONCLUSIONS Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.
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Affiliation(s)
- Eric J de Muinck
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
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Leimbach A, Hacker J, Dobrindt U. E. coli as an All-Rounder: The Thin Line Between Commensalism and Pathogenicity. Curr Top Microbiol Immunol 2013; 358:3-32. [PMID: 23340801 DOI: 10.1007/82_2012_303] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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