• attachment
• holobiont
• interaction
• pathogen
• zooplankton

• FISH
• bacteria
• bony nonunion
• infected implant
• molecular diagnostics
• tissue culture

• bacterial pathogenesis
• comparative genomics
• pan-genome

• Algorithms
• Animals
• Bacterial Infections/microbiology
• Bacterial Physiological Phenomena
• Biodiversity
• Ecology
• Evolution, Molecular
• Genes, Bacterial
• Genetic Variation
• Genome, Bacterial
• Genome-Wide Association Study
• Genomics
• Genotype
• Humans
• Mice
• Molecular Biology
• Multigene Family
• Phenotype
• Phylogeny
• Symbiosis
• Whole Genome Sequencing

• P41 RR006009 NCRR NIH HHS
• R01 AI080935 NIAID NIH HHS
• R01 DC002148 NIDCD NIH HHS
• U01 DK082316 NIDDK NIH HHS

• Antibiotic resistance
• Biofilm inhibition
• Biotechnology
• Green tea polyphenols
• Immunology
• Microbiology
• Molecular biology
• Pharmaceutical science
• Quorum sensing
• Short-chain acyl homoserine lactone
• Waterways

Acinetobacter baumannii is a nosocomial pathogen which is establishing as a major cause of morbidity and mortality within the healthcare community. The success of this pathogen is largely due to its ability to rapidly gain resistance to antimicrobial therapies and its capability to persist in an abiotic environment through the production of a biofilm. Our tertiary-care hospital has showed high incidence of carbapenem-resistant Acinetobacter baumannii (CRAB) isolates.

In this study we explore both genotypic and phenotypic properties of 26 CRAB isolates: 16 isolates were collected from January 2010 to March 2011, and 10 were collected between February and May 2015.

We determined that all 26 CRAB isolates possessed multiple β-lactamase genes, including genes from Groups A, C, and D. Specifically, 42% of the isolates possesses the potentially plasmid-borne genes of OXA-23-like or OXA-40-like β-lactamase. The presence of mobile gene element integron cassettes and/or integrases in 88% of the isolates suggests a possible mechanism of dissemination of antibiotic resistance genes. Additionally, the location of insertion sequence (IS) ISAba1 in promotor region of of the OXA-51-like, ADC-7, and ampC genes was confirmed. Multilocus sequence typing (MLST) demonstrated that all 26 CRAB isolates were either sequence type (ST)-229 or ST-2. Interestingly, ST-2 went from being the minority CRAB strain in the 2010–2011 isolates to the predominant strain in the 2015 isolates (from 32 to 90%). We show that the ST-2 strains have an enhanced ability to produce biofilms in comparison to the ST-229 strains, and this fact has potentially led to more successful colonization of the clinical environment over time.

This study provides a longitudinal genetic and phenotypic survey of two CRAB sequence types, and suggests how their differing phenotypes may interact with the selective pressures of a hospital setting effecting strain dominance over a 5-year period.

The online version of this article (10.1186/s12941-017-0248-3) contains supplementary material, which is available to authorized users.

• Acinetobacter baumannii
• Biofilm
• CRAB
• Carbapenem resistance
• Colonization
• Integrase
• Integron cassette
• MLST
• Multilocus sequence typing
• Multiple drug resistance
• OXA-23
• OXA-40
• OXA-51
• Plasmid
• β-lactamase

• EPS
• biofilm
• confocal microscopy
• potassium permanganate staining

• Animals
• Biofilms/growth & development
• Biopolymers/analysis
• Coloring Agents/metabolism
• Extracellular Matrix/chemistry
• Humans
• Image Processing, Computer-Assisted/methods
• Microscopy, Confocal/methods
• Potassium Permanganate/metabolism
• Pseudomonas aeruginosa/physiology
• Rabbits
• Staining and Labeling/methods
• Staphylococcus/physiology
• Streptococcus/physiology

• R01 AI097511 NIAID NIH HHS
• R01 NR013898 NINR NIH HHS
• NR013898 NINR NIH HHS
• DC 02148 NIDCD NIH HHS
• AI097511 NIAID NIH HHS
• T32 AI112542 NIAID NIH HHS
• T32-AI-112542 NIAID NIH HHS
• DC 04173 NIDCD NIH HHS
• DC 05659 NIDCD NIH HHS

We previously carried out the design and testing of a custom-built Haemophilus influenzae supragenome hybridization (SGH) array that contains probe sequences to 2,890 gene clusters identified by whole genome sequencing of 24 strains of H. influenzae. The array was originally designed as a tool to interrogate the gene content of large numbers of clinical isolates without the need for sequencing, however, the data obtained is quantitative and is thus suitable for transcriptomic analyses. In the current study RNA was extracted from H. influenzae strain CZ4126/02 (which was not included in the design of the array) converted to cDNA, and labelled and hybridized to the SGH arrays to assess the quality and reproducibility of data obtained from these custom-designed chips to serve as a tool for transcriptomics. Three types of experimental replicates were analyzed with all showing very high degrees of correlation, thus validating both the array and the methods used for RNA profiling. A custom filtering pipeline for two-condition unpaired data using five metrics was developed to minimize variability within replicates and to maximize the identification of the most significant true transcriptional differences between two samples. These methods can be extended to transcriptional analysis of other bacterial species utilizing supragenome-based arrays.

The presence of viable Helicobacter pylori (H. pylori) in the environment is considered to contribute to the levels of H. pylori found in the human population, which also aids to increase its genetic variability and its environmental adaptability and persistence. H. pylori form biofilms both within the in vitro and in vivo environment. This represents an important attribute that assists the survival of this bacterium within environments that are both hostile and adverse to proliferation. It is the aim of this paper to review the ability of H. pylori to form biofilms in vivo and in vitro and to address the inherent mechanisms considered to significantly enhance its persistence within the host and in external environments. Furthermore, the dissemination of H. pylori in the external environment and within the human body and its impact upon infection control will be discussed.

• Helicobacter pylori
• Biofilm
• Coccoid forms
• Virulence
• Water

Helicobacter pylori (H. pylori) is a Gram negative pathogen that selectively colonizes the human gastric epithelium. Over 50% of the world population is infected with H. pylori reaching up to 90% of infected individuals in developing countries. Nonetheless the increased impact upon public health care, its reservoir and the transmission pathway of the species has not been clearly established yet. Molecular studies allowed the detection of H. pylori in various aquatic environments, even forming biofilm in tap water distribution systems in several countries, suggesting a role of water as a possible reservoir of the pathogen. The persistence of human infection with H. pylori and the resistance of clinical isolates to commonly used antibiotics in eradication therapy have been related to the genetic variability of the species and its ability to develop biofilm, demonstrated both in vivo and in vitro experiments. Thus, during the last years, experimental work with this pathogen has been focused in the search for biofilm inhibitors and biofilm destabilizing agents. However, only two anti- H. pylori biofilm disrupting agents have been successfully used: Curcumin - a natural dye - and N-acetyl cysteine - a mucolytic agent used in respiratory diseases. The main goal of this review was to discuss the evidences available in the literature supporting the ability of H. pylori to form biofilm upon various surfaces in aquatic environments, both in vivo and in vitro. The results published and our own observations suggest that the ability of H. pylori to form biofilm may be important for surviving under stress conditions or in the spread of the infection among humans, mainly through natural water sources and water distribution systems.

• Helicobacter pylori
• Biofilm, Water
• Infection

• Acetylcysteine/chemistry
• Anti-Bacterial Agents/therapeutic use
• Biofilms
• Curcumin/chemistry
• Environment
• Environmental Microbiology
• Gastric Mucosa/microbiology
• Helicobacter Infections/microbiology
• Helicobacter Infections/physiopathology
• Helicobacter pylori/physiology
• Humans
• Water Microbiology

• Biofilms
• Biopsy
• Chronic Disease
• Coculture Techniques
• DNA Primers/genetics
• Gene Expression
• Gene Expression Regulation
• Genes, Bacterial
• Haemophilus influenzae/metabolism
• Humans
• Models, Statistical
• RNA/metabolism
• RNA, Bacterial/metabolism
• RNA, Ribosomal, 16S/metabolism
• Sinusitis/microbiology
• Sinusitis/physiopathology
• Streptococcus pneumoniae/metabolism
• Time Factors
• Virulence

Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer (HGT) processes that occur during chronic polyclonal infections, to date there have been few studies that directly address this topic. We have characterized multiple HGT events that most likely occurred during polyclonal infection among nasopharyngeal strains of Streptococcus pneumoniae recovered from a child suffering from chronic upper respiratory and middle-ear infections. Whole genome sequencing and comparative genomics were performed on six isolates collected during symptomatic episodes over a period of seven months. From these comparisons we determined that five of the isolates were genetically highly similar and likely represented a dominant lineage. We analyzed all genic and allelic differences among all six isolates and found that all differences tended to occur within contiguous genomic blocks, suggestive of strain evolution by homologous recombination. From these analyses we identified three strains (two of which were recovered on two different occasions) that appear to have been derived sequentially, one from the next, each by multiple recombination events. We also identified a fourth strain that contains many of the genomic segments that differentiate the three highly related strains from one another, and have hypothesized that this fourth strain may have served as a donor multiple times in the evolution of the dominant strain line. The variations among the parent, daughter, and grand-daughter recombinant strains collectively cover greater than seven percent of the genome and are grouped into 23 chromosomal clusters. While capturing in vivo HGT, these data support the distributed genome hypothesis and suggest that a single competence event in pneumococci can result in the replacement of DNA at multiple non-adjacent loci.

Bacterial infections have long been studied using Koch's postulates wherein the paradigm is that a single clone leads to a given infection. Over the past decade, it has become clear that chronic bacterial infections often do not fit this paradigm. Instead these are associated with the presence of multiple strains or species (polyclonal) of bacteria that are organized into highly structured communities, termed biofilms, which can persist in the body and are recalcitrant to antibiotic treatment. In addition, there is extensive evidence that bacteria can incorporate genes from neighboring bacteria into their own genomes. This process can produce new strains and is known as horizontal gene transfer. In this study, we investigated for the first time, the tempo and relevance of gene transfer among bacterial strains of Streptococcus pneumoniae during a naturally occurring chronic childhood infection. We identified extensive gene transfer among multiple infecting strains, by sequencing of isolates recovered sequentially over a seven-month period. This gene transfer may serve as a counterpoint to the host's adaptive immune response and help explain the phenomenon of bacterial persistence, since, as occurs with some chronic viral and parasitic infections, the immune system may become overwhelmed by a set of related strains.

• Alleles
• Chronic Disease
• Gene Expression Regulation, Bacterial
• Gene Transfer, Horizontal/physiology
• Genetic Variation
• Genome, Bacterial
• Humans
• Infant
• Mucous Membrane/microbiology
• Phylogeny
• Pneumococcal Infections/genetics
• Pneumococcal Infections/microbiology
• Polymorphism, Single Nucleotide/genetics
• Recombination, Genetic
• Respiratory Tract Infections/genetics
• Respiratory Tract Infections/microbiology
• Streptococcus pneumoniae/classification
• Streptococcus pneumoniae/genetics

• R01 DC002148 NIDCD NIH HHS
• R01 DC005659 NIDCD NIH HHS
• DC05659 NIDCD NIH HHS
• P41 RR006009 NCRR NIH HHS
• R01 DC004173 NIDCD NIH HHS
• AI080935 NIAID NIH HHS
• DC04173 NIDCD NIH HHS
• DC02148 NIDCD NIH HHS
• Wellcome Trust
• R01 AI080935 NIAID NIH HHS

• chronic bacterial pathogenesis
• bacteria
• horizontal gene transfer
• distributed genome hypothesis
• supragenome
• pangenome

• Bacteria/genetics
• Bacterial Adhesion
• Bacterial Infections/microbiology
• Bacterial Physiological Phenomena
• Biofilms/growth & development
• Evolution, Molecular
• Gene Transfer, Horizontal
• Genome, Bacterial
• Humans

• R01 DC002148 NIDCD NIH HHS
• DC02118-16S1 NIDCD NIH HHS
• R01 AI080935 NIAID NIH HHS
• P41 RR006009 NCRR NIH HHS
• R01 DC004173 NIDCD NIH HHS
• AI080935 NIAID NIH HHS
• DC04173 NIDCD NIH HHS
• DC02148 NIDCD NIH HHS

A review of the evolution of microbial pathogenicity in the context of the 'symbiome' of microbes and their multicellular hosts.

Metazoans contain multiple complex microbial ecosystems in which the balance between host and microbe can be tipped from commensalism to pathogenicity. This transition is likely to depend both on the prevailing environmental conditions and on specific gene-gene interactions placed within the context of the entire ecosystem.