Microbiota decolonization of bacterial pathogens in pediatric surgery-related intestinal disorders: Insights on current strategies and future outlook

Abstract

The significance of gut microbiota (GM) in human health is being increasingly researched. An imbalance in GM composition, known as dysbiosis, is linked to various and other health issues. In addition, antibiotics are the primary and most significant factors leading to major changes in the composition and function of the GM, which may result in colonization by antimicrobial-resistant (AMR) pathogens. Therefore, alternative antibiotic strategies for combating AMR pathogens are urgently needed. This narrative review highlights current knowledge regarding various pertinent strategies for decolonizing bacterial pathogens from GM and emphasizes decolonization therapies’ critical role in pediatric surgical disorders. Strategies such as decontamination of the digestive tract utilizing antibiotics, the use of probiotics, and particularly fecal microbiota transplantation have introduced new options for clinical treatment. These treatments show the potential to restore GM balance and have demonstrated advantages for intestinal disorders related to pediatric surgery, including inflammatory bowel disease, neonatal necrotizing enterocolitis, Hirschsprung-associated enterocolitis, and short bowel syndrome. Despite GM therapeutics, recent strategies are still in their developmental phase and exhibit challenges that need further research. Thus, potential future directions for GM-targeted decolonization therapies are under consideration. Innovative alternative strategies to combat AMR though GM modulation in disorders related to pediatric surgery appear to be promising and should continue to be prioritized for further research and development.

Key Words: Gut microbiota; Intestinal disorders; Pediatric surgery; Decolonization; Prebiotics; Probiotics; Antibiotics; Fecal microbiota transplantation; Engineering methods; Combined therapies

Core Tip: Optimizing gut microbiota composition is a promising strategy for decolonizing bacterial pathogens in pediatric surgery-related intestinal disorders. The decolonization of bacterial pathogens in this condition is crucial for reducing complications and improving recovering. Current approaches include selective digestive decontamination, probiotics, and fecal microbiota transplantation. Future strategies should focus on microbiota-targeted precision therapies, including phage therapy and clustered regularly interspaced short palindromic repeat-based gene editing among others, to enhance pathogen eradication while preserving beneficial gut flora.

INTRODUCTION

The human gut microbiota (GM) comprises a vast array of commensal microorganisms, approximately 100 trillion (10¹⁴), that coexist harmoniously with the host and provide a variety of health benefits, including resistance against pathogenic bacteria, contributions to nutrition and metabolism, and modulation of the immune system[1]. This complex community encompasses a diverse of bacteria, viruses, protozoa, archaea, fungi, and other eukaryotic microorganisms[2]. Various factors, including diet, lifestyle, stress, and antibiotic exposure, can shape and influence this ecological system[2,3]. More specifically, repeated exposure to antibiotics, along with dietary and environmental changes, can disrupt microbial diversity, leading to a condition known as gut “dysbiosis”[4]. This imbalance, in turn, affects interactions between the host microbiota and the immune system.

Multi-drug resistant (MDR) bacteria are a major global health issue that has resulted in constant decrease of antibiotic effectiveness and increasing morbidity and mortality due to bacterial infection[5]. GM is a serious depository of antibiotic resistance bacteria and genes that can be spread to vulnerable bacteria and the habitat[6]. The colonization of GM from MDR is complex and it can be carried out through two different mechanisms, namely, the exogenous MDR bacteria or the existing GM due to the selection pressure of antibiotics or by antibiotic resistance genes (ARGs)[6]. ARGs constitute the so-called “resistome”, describing a group of bacterial genes that enable bacteria to develop mechanisms to resist death from antibiotics[7,8]. It is noteworthy that ARGs are not limited to adults; they also affect children and infants. For example, a neonate’s gut may harbor a diverse range of ARGs even without prior antibiotic treatment, possibly originating from the maternal microbiome[9].

The term "decolonization", often described in the literature as "loss of carriage", or "eradication", refers to the elimination of MDR strain carriage[10]. Several studies have shown that the presence of MDR bacteria in GM, is a major source of extraintestinal infections, such as pneumonia, urinary tract infection or acquired bloodstream infections[11]. To eliminate MDR bacteria from the gastrointestinal tract, various decolonization strategies have been proposed. These include antibiotics[12], probiotics, prebiotics, and symbiotics[13-15], fecal microbiota transplantation (FMT)[16,17], selective phages or phage mixtures[18,19], engineered clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems[20], and combination therapies[21]. Although some of the previously mentioned studies are still in the experimental phase[19-21], implementing new, innovative strategies to eliminate MDR bacteria are essential. Further experimental and clinical studies are needed to validate the efficacy and safety of these approaches.

Intestinal microecology refers to the dynamic ecosystem formed by the interaction between microorganisms residing in the human gut and the surrounding intestinal environment[22]. Recent advances in the dynamic of GM suggest an association between pediatric surgical disorders such as inflammatory bowel disease (IBD), necrotizing enterocolitis (NEC), Hirschsprung-associated enterocolitis (HAEC), short bowel syndrome (SBS), and intestinal microecology leading to an early recognition and management of these conditions[22].

The aim of this study is to evaluate and analyze existing and emerging strategies for the decolonization of bacterial pathogens in pediatric patients undergoing surgery for intestinal disorders. By assessing the effectiveness, safety, and feasibility of various interventions, this study seeks to identify optimal approaches for restoring GM balance, reducing post-surgical complications, and improving overall patient outcomes. Additionally, future directions in microbiome-based therapies, including precision medical approaches tailored to individual patient are highlighted.

LITERATURE SEARCH

We performed a literature search covering the period from January 1, 2000 to February 28, 2025. The studies included in this narrative review were sourced from the databases of PubMed, Google Scholar, Scopus, and Web of Science. The search strategy comprised the following terms/keywords: "pediatric surgery", "pediatric intestinal disorders", "necrotizing enterocolitis", “Hirschsprung’s disease-associated enterocolitis”, “inflammatory bowel disease”, “short bowel syndrome”, “gut microbiota", "microbiome", "intestinal dysbiosis", “gastrointestinal flora”, "bacterial decolonization", "probiotics", “prebiotics”, "fecal microbiota transplantation", "bacteriophage therapy", "microbiome engineering", and “combined therapies”. Only original research articles, reviews, and systematic reviews published in English that clearly discuss the deconolization of bacterial pathogens in microbiota related to pediatric surgery-associated intestinal disorders and specifically focus on children were considered for a thorough analysis. Additionally, the references from the selected studies were reviewed to find further research. Articles that were not peer-reviewed, poorly designed, did not provide date on the specified topics, and duplicates were omitted (Figure 1).

Figure 1 The study flow chart.

GM COMPOSITION

A healthy GM is primarily composed of two major phyla: Bacteroidetes and Firmicutes, alongside two minor but significant phyla: Actinobacteria and Proteobacteria. Together, these four key divisions shape the typical human GM, with Bacteroidetes and Firmicutes collectively accounting for approximately 90% of the total microbial population. Although this profile remains consistent, the GM exhibits variations both spatially and temporally, with diversity and abundance differing significantly; for instance, the distal esophagus contains approximately 10¹ bacteria per gram, while the colon and distal gut can harbor up to 10¹² bacteria per gram[23]. Firmicutes and Bacteroidetes are the dominant phyla found in the large intestine. Furthermore, experimental studies in mice have revealed significant differences between the bacterial populations in the lumen and those at the outer mucosal barrier of the intestine. While the most common luminal bacteria include Bacteroides, Bifidobacterium, Streptococcus, Enterococcus, Enterobacteriaceae, Clostridium, Lactobacillus, and Ruminococcus, the predominant bacteria identified in the mucus layer and epithelial crypts of the small intestine are limited to Clostridium, Lactobacillus, Enterococcus, and Akkermansia[24].

GM FUNCTION

Numerous in-depth studies exist regarding GM and its function in maintaining balance, known as “eubiosis”, in both healthy and diseased conditions[25]. This harmonic state inhibits the proliferation of pathogenic microorganisms, thereby safeguarding overall health. Beneficial bacteria produce killing peptides, known as bacteriocins[26], that act as natural antibiotics, as well as plasmid-encoded protein antibiotics (colicins)[27], and short-chain fatty acids (SCFAs) such as butyrate, propionate, lactate, and acetate[28]. SCFAs are mainly derived from dietary fibers and are produced in the cecum and proximal colon. They provide a wide range of health benefits, including anti-inflammatory and immunoregulatory effects, and play crucial role in addressing constipation, obesity, diabetes, cancer prevention, cardiovascular health, liver protection, and neuroprotection[29,30]. More specifically, SFCAs contribute to leukocyte function and immune system response by inducing cytokines (IL-2, IL-6, IL-10, and TNF-α), and chemokines construction, protecting in this manner the balance between pro-inflammatory and anti-inflammatory mechanisms. Deficiency of SCFAs is a cause of gut inflammation and infiltration of pathogens[31,32].

GM IN CHILDREN

The traditional view held that the fetal environment in utero was sterile, with gut colonization starting at birth[33]. However, recent studies have challenged the "sterile womb" hypothesis by providing evidence of microbial presence in areas previously considered sterile, such as the placenta, amniotic fluid, and umbilical cord[34-36]. On the contrary, the presence of a well-established microbiota in healthy, term infants, even without any signs of inflammation, supports the idea that microbes not only colonize the fetus before birth but also contribute to its physiological development[37].

Studies on infancy and childhood have shown that these periods are crucial for the shaping and maturation of the GM, which finally will reach an adult-like composition of GM, at the age of 2-3 years[38]. Overall, gut maturation, including different microorganisms, occurs in four distinct stages: The neonatal period (0-4 weeks), the initial months of infancy (1-6 months), the transition period (6-12 months), and the later part of infancy to early childhood (12-24 months), extending into approximately 2-3 years, although that age has been recently under debate[39]. By the age of 2 to 3 years, the GM stabilizes and may resemble that of an adult, marked by a predominance of these same genera and family, indicating a similar microbial composition[39].

EFFECTS OF GM COLONIZATION AND INFECTION WITH BACTERIAL PATHOGENS

In healthy immunocompetent hosts, the protective mechanisms conferred by the GM plays a pivotal role including competitive microbial–microbial interactions and induction of host immune responses[40]. For instance, the GM competes with harmful microbes for essential nutrients, limiting their ability to thrive in the gut environment[41]. The integrity of the epithelial barrier is also reinforced by commensal bacteria, which promote mucus production and strengthen tight junctions between intestinal cells, reducing pathogen entry into the bloodstream[42]. Furthermore, the GM interacts with bacteriophages-viruses that selectively target and eliminate harmful bacteria-thereby controlling pathogenic populations[42]. Lastly, the GM plays a key role to immune system modulation by stimulating innate and adaptive responses, including the activation of regulatory T cells and the production of immunoglobulins that enhance pathogen resistance[43]. Through these synergistic mechanisms, the GM maintains intestinal homeostasis and provides a robust defense against infections.

GM as a source of MDR bacteria

The human GM serves as a significant source for MDR bacteria, facilitating their proliferation and the exchange of ARGs among diverse microbial species[44]. The mechanisms contributing to the gut as a source of MDR bacteria include various factors such as antibiotics[45], horizontal gene-transfer[46,47], and environmental influences[48]. For example, the misuse and overuse of antibiotics can lead to antimicrobial resistance, as bacteria adapt to these drugs, rendering treatments ineffective[44]. Furthermore, the GM contains a wide variety of bacteria, many of which harbor ARGs. These ARGs can be transferred horizontally between commensal and pathogenic bacteria through mechanisms such as conjugation, transformation, and transduction, facilitating the spread of resistance traits[45,46]. Last but not least, environmental factors such as MDR bacteria[48].

Colonization resistance

Colonization resistance is a critical function of the GM, providing protection against the establishment and overgrowth of harmful pathogens. This mechanism operates through various strategies, including: (1) Niche competition; (2) Nutrient competition; (3) Secretion of antimicrobial compounds; (4) Reinforcement of gut barrier integrity; and (5) Immune system modulation[41]. The GM can effectively inhibit pathogen colonization by outcompeting them for essential resources, as well as by producing metabolites that create an inhospitable environment for invaders[49]. However, factors such as antibiotic use, dietary changes, and diseases can disrupt microbial balance, leading to weakened colonization resistance and increased susceptibility to infections[50]. A recent study highlighted that colonization resistance is not only dependent on microbiota composition but also on specific metabolites, such as tryptophan derivatives, that modulate host responses and pathogen interactions. In an animal study, researchers found that dietary supplementation with L-tryptophan stimulates the production of specific microbial metabolites. These metabolites activate the dopamine receptor D2 (DRD2) in the intestinal epithelium, reducing pathogen adhesion to the gut lining. This discovery highlights the potential of dietary or pharmacological approaches targeting DRD2 to enhance gut health and prevent gastrointestinal infections[51].

Strategies to fight antimicrobial resistance

As antimicrobial resistance continues to pose a significant global health threat, a range of strategic approaches has been proposed to combat this challenge effectively. Key approaches include antibiotic stewardship programs, which promote the judicious use of antibiotics to reduce unnecessary prescriptions and slow resistance development[52]. Enhancing infection prevention through vaccination, improved hygiene, and hospital infection control measures can also limit the spread of resistant bacteria[53]. Additionally, research into alternative therapies, such as bacteriophage therapy and microbiome-based treatments, show promise in combating resistant infections[54]. The development of new antibiotics and antimicrobial agents, supported by global funding initiatives, is crucial to replenishing the diminishing arsenal of effective treatments[55]. Moreover, global collaboration, including surveillance programs and policy frameworks, is essential to monitor resistance patterns and implement coordinated responses[53]. Finally, in current clinical practice, the FMT is being used as a therapeutic option for recurrent infection with toxin producing Clostidrium difficile (C. difficile) in adults, with cure rates approaching 90%[56].

Protective role of GM against MDR bacteria

The increasing prevalence of AMR has made it crucial to explore how GM can serve as a protective mechanism against MDR infections. Several mechanisms, including nutrient competition, immune system modulation, metabolic interactions, and gut barrier integrity, contribute to preventing MDR colonization and subsequent infections[57]. In nutrient competition commensal bacteria consume vital nutrients required by pathogens, limiting their ability to proliferate[49]. Also, GM modulates the host immune response, promoting the secretion of protective cytokines and enhancing pathogen clearance[58]. Furthermore, microbial metabolites, such as SCFAs, regulate gut pH and inhibit pathogen growth[59], while commensals enhance the production of mucus and antimicrobial peptides, preventing pathogen adherence to the gut barrier integrity[41].

DECOLONIZATION OF MDR BACTERIA

The rise of MDR bacterial infections and their global impact on healthcare systems pose a significant public health challenge[10]. The limited availability of effective antibiotics can quickly lead to a therapeutic “dead end”, a scenario becoming increasingly common. Notably, AMR was estimated to have caused between 3.62 and 6.57 million deaths in 2019[60]. Furthermore, projections from the Review on Antimicrobial Resistance suggest that this number could double, reaching 10 million deaths annually by 2050[61].

WHO has identified a critical priority list of MDR bacteria, including Gram-negative pathogens such as extended-spectrum β-lactamase)-producing enterobacteruaceae (ESBL-E), carbapenemase-producing Enterobacterales (CPE), and vancomycin-resistant Enterococci (VRE). These organisms present a significant challenge due to the limited therapeutic options available to combat them[62]. However, challenges in the decolonization practices exist and include the limited time of MDR clearance after decolonization procedures[63], the increasing effects of the bacterial population during treatment with oral non-absorbable antibiotics and the “rebound effect” of select antibiotic-resistant organisms in the gut[64] after decontamination of the decolonization regimens. Herein, we present promising strategies that have been explored for potential clinical application, each with varying levels of supporting evidence.

Selective decontamination of the digestive tract

Zhang et al[65], in a recent meta-analysis of five randomized controlled trials (RCTs) and three non-RCT studies on patients with ESBL-E/CPE, reported a greater decolonization effect in the experimental group compared to the control group one month after treatment. Similarly, a study from Spain assessed the impact of selective decontamination of the digestive tract on reducing MDR infections in an intensive care unit setting[66]. The findings indicated a 30% reduction in overall antibiotic consumption, including carbapenems, as well as decreased colonization by CPE carriers. Additionally, Daneman et al[67], in a systematic review and meta-analysis, observed a greater reduction in intestinal colonization or infection with MDR bacteria in the intervention group compared to the control group. However, the European Society of Clinical Microbiology and Infectious Diseases-European Study Group of Nosocomial Infections[68] reported that selective decontamination of the digestive tract does not demonstrate clear efficacy in gastrointestinal decolonization. Based on the current limited evidence, they do not recommend routine decolonization for carriers of third-generation cephalosporin-resistant Enterobacteriaceae and CRE. This discrepancy highlights the need for well-designed clinical trials to assess the long-term effectiveness of decolonization strategies while closely monitoring the development of antibiotic resistance.

Probiotics

A substantial number of clinical studies in adults have been reported regarding the impact of probiotics on decolonization of MDR bacteria from the gut[69-71]. In the review of Newman et al[69], the authors reported mixed findings regarding the overall benefits of probiotics. These inconsistencies may be attributed to the variation in probiotic strains used across studies and the lack of standardization in dosage across different products. Among studies, the most promising results derived from that of Manley et al[70]. The authors examined the impact of Lactobacillus GG on elimination of VRE carriers. At the end of the study, all of those in the treatment group were VRE negative. It is worth to say, that the treatment group had increased rates of antibiotic usage which could affect further the GM. However, no follow-up assessed the sustainability of the effect. A recent meta-analysis[71] of 29 RCTs found pathogenic bacteria persisted in 22% of probiotic-treated cases vs 30.8% in the placebo group, with greater efficacy against enterobacteriaceae than VRE. A key limitation was the aggregation of diverse bacterial strains and pathogens, potentially enhancing probiotic efficacy. All in all, further evidence is needed to clarify how probiotics could help in the decolonization of MDR bacteria.

FMT

The efficacy of FMT decolonization against MDR bacteria has been explored in many case reports and case-series[72]. The method has shown positive outcomes in patients with C. difficile infections but not in ESBL-E/CPE carriers, enterobacteriaceae, VRE and MDR Pseudomonas aeruginosa[73,74]. Huttner et al[75] in an open label RCT evaluated whether oral colistin sulphate followed by FMT can eradicate intestinal carriage in ESBL-E/CPE patients. Although recipients exhibited a reduction in ESBL-E/CPE carriage compared to the control group, this difference did not reach statistical significance. Recently, Woodworth et al[76] conducted a RCT comparing bowel preparation plus FMT to bowel preparation alone in renal transplant recipients. FMT led to faster MDR decolonization and reduced recurrent infections. Notably, in some participants, ESBL-producing strains were replaced by non-ESBL strains, indicating that strain competition rather than eradication may occur post-FMT. These findings underscore the effectiveness of FMT in decolonizing MDR, elucidate its underlying mechanisms and pose the need for further well-designed studies.

Bacteriophages

Bacteriophages targeting specific bacterial strains have been proposed as a potential strategy to combat AMR[77]. Phage therapy offers several advantages over antibiotics, including high host specificity and minimal toxicity in humans[78]. Furthermore, its effectiveness against biofilms makes it a promising option for treating biofilm-associated infections, such as those caused by methicillin-resistance Staphylococcus aureus[79] and Pseudomonas aeruginosa[80]. While the safety profile of current phage therapy products under investigation is generally excellent, both phage therapy and enzyme-based treatments can trigger a rapid release of endotoxins due to rapid bacterial cell lysis, similar to bactericidal antibiotics[81]. However, currently no phage therapy products have been approved for human use in the United States or European Union[82].

Natural products

Natural products are gaining attention as alternative or complementary approaches for GM decolonization. These compounds, often derived from plants, fungi, or traditional medicines, can modulate GM composition, enhance colonization resistance, and reduce pathogenic bacterial load[83]. Recent research highlights several promising natural products for gut decolonization. For example, traditional Chinese medicine-derived compounds like ginseng, berberine, and curcumin have been shown to influence GM, altering microbial composition and enhancing host immunity[83]. Additionally, GM-mediated biotransformation of herbal medicines has been identified as a novel avenue for therapeutic interventions in metabolic and inflammatory diseases[84]. Furthermore, GM-associated natural products have been found to regulate physiological functions, with compounds from ethnomedicines playing a key role in maintaining microbial balance and reducing colonization by harmful bacteria[85]. While these natural approaches offer promising avenues for GM decolonization, further research is needed to optimize formulations, establish clinical efficacy, and ensure safety in long-term applications.

DECOLONIZATION OF MDR BACTERIA IN PEDIATRICS

Research on decolonization strategies for MDR bacteria in pediatric patients is limited, with FMT being the most studied approach for eliminating C. difficile infections. In addition, most studies are case reports or case series, and only one large-scale study has been conducted to date[86]. For example, Pierog et al[87] reported on six children with refractory C. difficile infection who were cured with FMT, while Kronman et al[88] described 10 consecutive children, including three immunocompromised with recurrent C. difficile infection, achieving a 90% cure rate with one relapse. Brumbaugh et al[89] in a retrospective study including 47 patients reported a success rate of 95% in previously healthy children, 75% in children with complex diseases and 54% in children with IBD. In the largest multi-center retrospective study on 372 patients aged 11 months to 23 years (including and IBD patients), Nicholson et al[86] reported an 81% success rate after a single FMT for C. difficile infection and 86.6% after one or more FMTs. These findings highlight the promising role of FMT in treating C. difficile infections, particularly in refractory and recurrent cases. The high success rates observed across different studies, in a variety of diseases, underscore its potential as a valuable therapeutic option. As research continues to expand, FMT may become an essential tool in managing difficult-to-treat infections, offering hope for improved patient outcomes.

CURRENT DECOLONIZATION THERAPIES IN INTESTINAL DISORDERS RELATED TO PEDIATRIC SURGERY

The summary of current decolonization therapies based on clinical studies and recommendations in children regarding IBD, NEC, HAEC and SBS, are shown in Table 1.

Table 1 Current decolonization therapies in pediatric surgical disorders.

Therapy	Description	Advantages	Pediatric surgical disorders	Ref.
Selective digestive decontamination	Administration of non-absorbable antibiotics to reduce harmful bacteria load in the gut before surgery	Prevents postoperative infections; Reduces translocation of harmful pathogens	IBD; SBS	[98,159]
Probiotics	Combination pf beneficial bacteria and nutrients that promote their growth	Enhance colonization resistance; Reduces MDR bacteria like Acinetobacter baumannii	IBD; NEC; HAEC; SBS	[105,119-122,139,155]
FMT	Transfer of fecal material from a healthy donor to restore fecal balance	Restores microbial diversity; Suppresses MDR bacteria. Effective for Clostridium dif. infections	IBD; NEC; SBS	[112,126,156,157]

IBD: Inflammatory bowel disease; SBS: Small bowel syndrome; NEC: Necrotizingenterocolitis; HAEC: Hirschsprung-associated enterocolitis; FMT: Fecal microbiota transplantation; MDR: Multi-drug resistance.

IBD

IBD, which includes Crohn’s disease (CD), ulcerative colitis (UC), and IBD-unclassified, is a complex condition characterized by a dysregulated immune response to environmental factors in genetically susceptible individuals[90]. All these factors alter the GM and lead to a harmful situation called dysbiosis[91].

Current therapies for IBD primarily aim to suppress the immune response using immunomodulators or immunosuppressants, including corticosteroids, methotrexate, thiopurines, and biologics[92]. In pediatric CD, however, exclusive enteral nutrition is recommended as the first-line treatment to induce remission[93]. Despite these treatments, challenges such as treatment failures and adverse side effects have prompted the exploration of approaches targeting GM modification and decolonization. These approaches are presented below.

Selective decontamination

Antibiotics can impact GM and potentially influence the course of IBD by reducing luminal bacteria, altering microbial composition to favor beneficial species, and limiting the invasion of pathogenic microorganisms[94]. Data from systematic reviews and meta-analyses in adults remain inconclusive, and no clear recommendations are established[95,96]. Townsend et al[95] in a meta-analysis investigating the impact of antibiotics on induction and remission in CD reported that no safe conclusions could be drawn regarding the safety and efficacy of antibiotics. Furthermore, Su et al[96] reported that the use of ciprofloxacin in patients with CD was efficient only in the subgroup with perianal fistula. In the pediatric population, a recent systematic review by Verburgt et al[97] highlighted the lack of evidence supporting antibiotic use in IBD. On the contrary, a case series by Lev-Tzion et al[98] reported that oral vancomycin and gentamicin may have significant therapeutic effects in children with very early-onset IBD who are refractory to other treatments.

Probiotics

Probiotics are highly used in both adult and pediatric patients with IBD based on the evidence of high safety profile[99]. In addition, probiotics are highly used as protective mean from chronic pouchitis, a common complication of adult patients undergoing colectomy for UC[100]. The most common strains currently available as probiotics and possessing beneficial effects are Enterococcus facium, Bifidobacterium, Bacillus, Saccharomyces boulardii, Lactobacillus strains and Pediococcus[101]. The most common investigated probiotic is VSL#3 which includes four strains of Lactobacilli, three strains of Bifidobacteria and Streptococcus salivarius subsp. thermophilu[99].

Several clinical studies performed in adults and children population have shown conflicting results. The meta-analysis of Ganji-Arjenaki et al[102] showed no significant clinical effect on adult patients with CD (P = 0.07), but significant effect in patients with UC in different conditions (P = 0.007). In a systematic review of Cochrane Database[103] in adult patients, the authors investigated the safety and efficacy of probiotics for induction in remission in CD. They reported that the available evidence was very uncertain due to the lack of well-designed RCTs. Another recent meta-analysis of Cochrane data-base including 594 participants, investigated the effectiveness of probiotics for induction of remission on adults and children with UC[104] compared to placebo or standard medical treatment including 5-aminosalicylates, sulphasalazine or corticosteroid. Twelve articles were referred to adult patients and two to children. The authors concluded that probiotics improve induction of clinical remission when compared to placebo, while there may be little evidence to suggest that probiotics plus 5-aminosalicylic acid (ASA) when compared to 5-ASA alone may offer a slightly better chance of induction on remission. It is worth to say that both systematic reviews included patients who were in remission from either CD or UC, suggesting that many physicians may be hesitant to use probiotics during the induction phase of remission.

Evidence-based studies for the use on probiotics in pediatric IBD are limited. Miele et al[105] found that VSL#3 strain induced remission in 92.8% of children with UC vs 36.4% with placebo (P < 0.001). Oliva et al[106] reported that Lactobacillus reuteri ATCC 55730 enema improved cytokine levels and clinical outcomes in mild-to-moderate UC. On the other hand, a Cochrane review[103] found no evidence supporting probiotics in pediatric CD patients. Due to insufficient data, the Europeans Society for Pediatric Hepatology and Nutrition Position Paper provides no recommendations for or against probiotic use in UC or CD in children[107].

FMT

FMT has demonstrated effectiveness in treating C.difficile. A systematic review reported that approximately 85% to 90% of patients with recurrent C.difficile achieved resolution of symptoms following FMT, either after single or repeated doses[108]. Regarding IBD, the first documented use of FMT for treating IBD occurred in 1989, in a patient with refractory UC with conventionaltreatment with sulfasalazine and steroids[109]. Since then, various pilot and RCTs studies have been performed for the treatment of IBD, but the majority of them are heterogeneous and appear to be patient- and donor-dependent[110]. Furthermore, a recent updated Cochrane systematic review indicates that FMT may increase clinical and endoscopic remission rates in individuals with active UC. However, the evidence regarding FMT's impact on serious adverse events, quality of life, and its efficacy in maintaining remission in UC or inducing and maintaining remission in CD remains very uncertain. Consequently, no definitive conclusions can be drawn in these areas[111]. Similar results are obtained for the impact of FMT on pediatric IBD, according to a recent systematic review[112]. The authors retrieved nine studies on UC and two on CD. The results showed that FMT is a promised and reliable treatment option for pediatric IBD, demonstrating at least moderate efficacy. Furthermore, it was well tolerated from the majority of patients and usually resulted in improvement of clinical response and endoscopic pictures. In addition, enrichment of GM diversity was detected with remission of the disease post-FMT. Most of the side-effects were self-limited. However, the lack of RCTs significantly hampers the strength of evidence supporting the use of FMT in treating pediatric IBD, posing the need for future well-organized studies.

NEC

NEC is a serious complication of prematurity and the leading cause of death of babies less than 29 weeks at birth[113]. Bacteria from the mother’s skin, vagina, and gut serve as the first colonizers of the newborn’s intestine[114], and play a crucial role in maintaining homeostasis and supporting immune development[115]. With respect to the GM composition, two major phyla are predominant, the Bacteroidetes (Gram negative bacteria) and Firmicutes (Gram positive bacteria). Other important phyla include Proteobacteria (pathogenic negative bacteria) and Actinobacteria[116]. However, factors such as low birth weight, chorioamnionitis, prematurity, multiple maternal infections, membrane rupture, and antibiotics to combat very early sepsis can disrupt the GM balance, increasing the risk of NEC and infections[117,118]. For example, in premature babies, the GM is characterized by high numbers of Firmicutes and Proteobacteria[117]. In addition, antibiotics increase the presence of Proteobacteria and decrease the numbers of Firmicutes[118]. This imbalance weakens intestinal barriers, contributing to NEC development. Five meta-analyses support the evidence that probiotic administration to premature babies is safe and decrease the risk of NEC, sepsis and death. Olsen et al[119] in a meta-analysis including 12 studies with equal ratio of recipient and control groups, showed that probiotics significantly decrease the incidence of NEC (RR = 0.72, 95%CI: 0.61-0.85; P < 0.0001). The authors highlighted the importance of further investigation of the optimal strain, the dose and timing. Sawh et al[120] in a systematic review and meta-analysis conducting to investigating the efficacy and safety of probiotics (given in any dose and any space or combination with prebiotics) to prevent NEC in preterm neonates, reported a reduced incidence of NEC and mortality. Furthermore, Aceti et al[121], evaluated the effect of probiotics for NEC prevention in preterm infants in a meta-analysis including 26 studies, either prospective, randomized, double-blinded or multi-centers. They reported that probiotics had an overall protective role in prevention NEC. In addition, Dermyshi et al[122] in a meta-analysis including both 44 RCTs and observational studies, support further the beneficial effect of probiotics in prevention NEC, late-onset sepsis and mortality. Finally, a recent network meta-analysis including 51 RCTs, studied 19 different probiotics regimens in the prevention of NEC. The authors found that L. acidophilus, B. lactis BB-12 or B94, L. reuteri DSM 17938/ATCC 55730, and multispecies probiotic formulations effectively reduced all stages of NEC[123]. The importance of special regimens in the construction of probiotics is underscored in the recommendations of Special Group Interest for GM and probiotics of the European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN)[107]. Regarding NEC, health professionals suggested that the combinations of any Lactobacillus spp. and any Bifidobacterium spp. in general seemed most effective and were graded as high certainty of evidence ESPGHAN. Although evidence supports the use of specific probiotics in certain clinical scenarios, further research is needed to refine their effects and determine the optimal type, dose, and timing. Since GM dysbiosis is a risk factor for NEC[124], FMT, a strategy commonly used to restore microorganism balance in patients with C. difficile infections[125], has been proposed as a potential alternative treatment for NEC[126]. However, up to date, FMT has been investigated only in experimental NEC models[127,128].

HAEC

HAEC is a critical and potentially fatal complication of Hirschsprung disease (HD) that can occur either before or after surgery[129]. HAEC is marked by inflammation of the intestinal crypts, accompanied by dilation and mucin accumulation within these crypts. Additionally, it involves the formation of abscesses and necrosis that extends through all layers of the intestinal wall in the affected area[130]. In up to 25% of infants, HAEC is the first sign of HD[131]. The incidence of HAEC ranges from 20% to 60%, with an overall mortality rate ranging from 1% to 10%, with the majority of deaths occurring in the neonatal period, before surgery[132,133]. Interestingly, a subset of patients is susceptible to recurrent HAEC in a range between 5.2% to 55%[132].

Several risk factors have been identified, including delayed diagnosis of HD, anastomotic stricture[134], male gender, a family history, the presence of trisomy 21 and other genetic syndromes[135].

Multiple pathophysiological hypotheses have been proposed to elucidate the pathogenesis of HAEC including intestinal dysmotility, impaired mucosal defense, intestinal barrier function, and enteric nervous system[129]. However, emerging evidence has established a critical role for GM dysbiosis of in the pathogenesis of HAEC, providing novel insights into disease development[136]. The authors by using DNA sequences showed that the bacteria and fungi of children with HEAC were different to those without HEAC. The study observed a slight decrease in Firmicutes and Verrucomicrobia and a corresponding slight increase in Bacteroidetes and Proteobacteria. Various types of Fungi were also found and an increase in Candida, while Malassezia and Saccharomyces were reduced. More recently, Arbizu et al[137] reported that the GM composition and diversity differ between patients with and without a history of postoperative HAEC, as determined by 16S rDNA sequencing of colon samples.

Although there is no universally accepted, evidence-based standard of care for the treatment of HAEC, current practices are guided by severity-based management protocols and include fluids, correction of electrolyte abnormalities, and antibiotics as initial management[138]. Additional strategies for managing HAEC may include dietary adjustments, rectal irrigations, and close monitoring in an intensive care unit setting. These interventions are tailored to address the severity of HAEC and support recovery by alleviating symptoms and preventing complications.

Probiotics have been explored as a potential treatment or preventive measure for HAEC, given their beneficial effects on gut health and microbiome balance. More specifically, probiotics can help regulate intestinal flora, and modulate immune response that is crucial in patients with HAEC[139]. However, the results of the current literature are conflictive. For example, in a prospective randomized trial conducted by El-Sawaf et al[139], the prophylactic administration of probiotics did not yield statistically significant differences in the incidence of enterocolitis compared to the control group[140]. Similar findings were reported in a meta-analysis by Nakamura et al[140] and a systematic review by Mei et al[141]. However, Wang et al’s prospective multicenter randomized trial showed contrasting results, indicating not only a reduction in the incidence of HAEC but also a decrease in its severity[142]. The current evidence suggests that there is insufficient data to conclusively assess the efficacy of probiotics in preventing HAEC.

SBS

Pediatric SBS is a severe condition that occurs in children due to a congenital or acquired shortening of the small intestine. NEC, malrotation with midgut volvulus, gastroschisis, congenital intestinal atresia, HD of the extensively aganglionosis type are the commonest causes[143]. This leads to excessive fluid loss, nutrient malabsorption, electrolyte imbalances, increased risk of infections, complications related to parenteral nutrition, and impaired weight gain and growth, a state called intestinal failure[144,145]. Factors that determine the severity and prognosis of intestinal failure include the presence of ileocecal valve, the length of remnant small bowel, the resection site of the bowel, and the presence of continuity of the bowel or stoma[146]. Research indicates that the small bowel microbiota significantly influences outcomes in patients with SBS[147]. Small bowel bacterial overgrowth, a key feature of gut dysbiosis, is a potential contributor to symptoms in IBS patients, and is associated with increased morbidity and mortality in affected children[147]. Small bowel bacterial overgrowth contributes to several harmful effects, including delayed intestinal adaptation, impaired weaning from parenteral nutrition[148], and an increased risk of bacterial translocation and bloodstream infections[149]. Although studies examining changes in the SBS microbiome in human subjects are limited[150], published series in pediatric patients have shown that the GM in patients with SBS is less diverse with an increased abundance on proteobacteria and a decreased in beneficial clostridia[151-153]. In addition, in pediatric patients with SBS and poor growth, Piper et al[154] identified deficiencies in six bacterial species, including two Lactobacillus species (L. johnsonii and L. rhamnosus). In a subsequent RCTs, the same author investigated the effects of probiotics containing these two species compared to a placebo. The results did not demonstrate a consistent alteration in fecal microbiota or improvements in growth relative to the placebo. Alternative treatments using synbiotics, a combination of prebiotics and probiotics, may provide additional benefits for patients with SBS. For instance, Uchida et al[155] reported positive effects on GM in four SBS patients who received a combination therapy featuring Bifidobacterium breve, Lactobacillus casei, and galactooligosaccharides. This approach suggests that synbiotics could play a promising role in supporting microbiome balance and gut health in SBS patients.

The use of FMT in the treatment of SBS has not been extensively investigated in children. However, two case-reports[156,157] described successful treatment with FMT in children aged 15 and 7 years respectively, who had lactic acidosis as a complication of an altered intestinal microbiome. Furthermore, in an experimental study of SBS, Hinchliffe et al[158] investigated the post-surgical efficacy and safety of FMT in neonatal piglets. The study showed no mortality or sepsis postoperatively for a transient time only.

Antibiotics are the cornerstone of small bowel bacterial overgrowth treatment, aiming to reduce bacterial burden rather than fully decolonize the small intestine. Erythromycin and amoxicillin have been used to modify GM[159], but patients often become dependent on cyclic regimens, increasing the risk of antibiotic resistance and fungal infections. Rifaximin, a non-absorbable broad-spectrum antibiotic that inhibits bacterial mRNA synthesis, has shown promise in adults[160]. However, clinical data in children are limited and inconsistent, with its use recommended only for those over eight years old[161].

CHALLENGES IN GM DECOLONIZATION THERAPIES

Decolonization therapies aimed at eliminating MDR bacteria from the gut in pediatric patients present multifaceted challenges, that require a comprehensive understanding of biological, clinical, and social factors that can complicate treatment efforts. Addressing these challenges will necessitate ongoing research into effective treatments tailored specifically for pediatric populations while considering the unique aspects of their developing microbiomes. The key challenges associated with pediatric decolonization therapies in children are discussed below.

Children, especially infants and neonates, have an immature immune system that may respond differently to decolonization therapies compared to adults. This variability can affect the efficacy and safety of treatments[7]. The GM of children is still developing and can be influenced by numerous factors, including mode of delivery, diet, and antibiotic exposure. This variability of GM makes it difficult to predict how individual children will respond to innovative decolonization strategies such as FMT[1]. Additionally, the presence of ARGs in the GM poses a significant challenge for decolonization efforts. These genes can be transferred between bacteria, while the co-location with mobile genetic elements makes difficult to eradicate resistant strains completely[3]. The "resistome" can complicate treatment by allowing resistant bacteria to persist despite therapeutic interventions[5]. Moreover, many decolonization strategies are still in experimental phases or lack regulatory approval for use in pediatric populations. For instance, while FMT shows promise, its application in pediatric patients lacks standardized protocols[16,17]. Similarly, bacteriophage therapy is still largely experimental and not widely available for clinical use[82]. Ensuring compliance with treatment protocols can be challenging in pediatric populations. Children may be reluctant or unable to adhere to prescribed regimens, particularly if they involve complex dosing schedules or unpleasant administration routes[162]. Finally, the safety of decolonization therapies in children is a major concern. For example, antibiotics can disrupt the GM balance and lead to adverse effects such as C. difficile infections or other gastrointestinal disturbances[127]. The long-term effects of therapies like FMT are still being studied, raising concerns about potential complications.

FUTURE OUTLOOK OF DECOLONIZATION STRATEGIES IN PEDIATRIC SURGICAL INTESTINAL DISORDERS

The GM plays a crucial role in maintaining intestinal health, particularly in pediatric patients undergoing surgery for intestinal disorders. Pathogen decolonization is essential to prevent postoperative complications, enhance recovery, and support long-term gastrointestinal function. Current strategies, including targeted antibiotic therapy, probiotics, FMT, and dietary interventions, have shown promise in modulating the GM and reducing pathogen colonization. However, future research should focus on optimizing these strategies by exploring the following options.

Personalized medicine approaches

Future decolonization strategies may increasingly focus on personalized medicine, where therapies are customized based on an individual child’s microbiota composition, genetic background, and specific health conditions. This approach could enhance the efficacy of treatments and reduce adverse effects[163,164].

Advancements in FMT

As FMT gains acceptance for treating recurrent C. difficile infections and other gut dysbiosis-related conditions, efforts will be made to standardize protocols and ensure the safety of FMT in pediatric populations. Ongoing research will help to clarify long-term outcomes and potential risks associated with FMT[16,17].

Innovative synbiotic formulations

The development of novel synbiotic formulations that combine specific probiotics with prebiotics tailored for pediatric patients may enhance gut health and resilience against MDR bacteria. Research into the mechanisms by which these formulations exert their effects will be crucial[165].

Bacteriophage therapy

Bacteriophage therapy represents a promising avenue for targeting specific MDR pathogens without disrupting the overall GM. As research progresses, clinical applications of phage therapy in children may expand, particularly for infections resistant to conventional antibiotics[18,19].

CRISPR-based technologies

The use of CRISPR-Cas systems to develop targeted antibacterial plasmids offers a novel method for selectively eliminating MDR bacteria from the gut. This technology holds promise for future applications in pediatric surgery, allowing for precise interventions while preserving beneficial microbes[20,21].

Antibiotic stewardship programs

Continued emphasis on antibiotic stewardship in pediatric settings will be vital to prevent the emergence of MDR strains. Educational initiatives aimed at healthcare providers and parents can promote responsible antibiotic use and enhance awareness of the implications of antibiotic exposure on gut health[82].

Integration of gut health into pediatric care

There is a growing recognition of the importance of gut health in overall pediatric care. Future strategies may involve integrating GM assessments into routine clinical practice, enabling early identification of dysbiosis and timely interventions[1].

Research on environmental influences

Ongoing research into how environmental factors, such as diet, lifestyle, and exposure to microbes-affect GM development in children will inform future decolonization strategies. Understanding these influences can help create preventive measures against dysbiosis and associated infections[166,167].

CONCLUSION

GM-targeted decolonization strategies have been successfully used for intestinal pediatric surgical disorders, including IBD, NEC, HAEC, and SBS. Decontamination of the digestive tract with antibiotics, the use of prebiotics and FMT, has introduced new options for clinical therapy. However, these therapies are still in their developmental phase and require further research. Future research should focus on personalized microbiota-based therapies to develop precise and effective interventions. Additionally, large-scale clinical trials are needed to establish standardized protocols and validate the efficacy of these therapies. A deeper understanding of host-microorganism interactions will pave the way for innovative strategies that promote microbiota resilience, ultimately improving surgical outcomes and long-term health in pediatric patients with these intestinal disorders.