Host Microbiome-Pathogen Interactions in Pediatric Infections

Abstract

Purpose of Review:

In this review, we discuss recent research that has furthered our understanding of microbiome development during childhood, the role of the microbiome in infections during this life stage, and emerging opportunities for microbiome-based therapies for infection prevention or treatment in children.

Recent Findings:

The microbiome is highly dynamic during childhood and shaped by a variety of host and environmental factors. In turn, the microbiome influences risk and severity of a broad range of infections during childhood, with recent studies highlighting potential roles in respiratory, gastrointestinal, and systemic infections. The microbiome exerts this influence through both direct interactions with potential pathogens and indirectly through modulation of host immune responses. The elucidation of some of these mechanisms by recent studies and the development of effective microbiome-based therapies for adults with recurrent Clostridioides difficile infection highlight the enormous promise that targeting the microbiome has for reducing the burden of infectious diseases during childhood.

Summary:

The microbiome has emerged as a key modifier of infection susceptibility and severity among children. Further research is needed to define the roles of microbes other than bacteria and to elucidate the mechanisms underlying microbiome-host and microbiome-pathogen interactions of importance to infectious diseases in children.

Introduction

Over the past two decades, the microbial communities that colonize our bodies (referred to as the “microbiome”) have been established as being critical for human growth, development, and health. These microbiomes undergo substantial shifts in composition during infancy and childhood that parallel development of the immune system and multiple organ systems. As ‘omic technologies have become more affordable and accessible, investigation of the pediatric microbiome has expanded substantially, increasing our understanding of intersections between the microbiome and childhood infectious diseases. This review highlights the most recent scientific literature from this field, including advances in our knowledge of the influences of the upper respiratory tract (URT) and gut microbiomes on the risk and severity of infections among children, the development of microbiome-targeted therapies, and emerging areas of research.

Early life factors shape microbiome development and infection susceptibility

Recent research has furthered our understanding of relationships between early life exposures, microbiome development, and immune maturation. De Koff and colleagues reported that vaginally delivered infants had higher gut microbiome abundances of Bifidobacterium and Escherichia coli in the first weeks of life and developed superior mucosal antibody responses to meningococcal and pneumococcal vaccination than infants born via Caesarean section (1). Several recent studies investigated the impact of breastfeeding on the infant gut and URT microbiomes and immune development (2-4). For instance, Rosas-Salazar et al. reported that exclusive breastfeeding was associated with higher gut and URT microbiome diversity (number of species), higher URT levels of several cytokines, and a lower risk of lower respiratory tract infection (LRTI) among 1495 healthy infants (2). On the other hand, undernutrition can be associated with disrupted microbiome maturation, with infants with growth failure having gut microbiomes that are more similar to younger infants than to age-matched controls (5,6). Data from animal models suggest that such an arrest of microbiome development could have profound consequences for immune development. Lubin and colleagues demonstrated that gnotobiotic mice colonized with a restricted gut microbiome during weaning had fewer peripheral regulatory T cells, lower immunoglobulin A levels, and were more susceptible to enteric Salmonella infection than mice colonized with a typical pre-weaning microbiome (7). Analogous disruptions of gut microbiome maturation have been shown to occur among several vulnerable infant populations, including infants with severe malnutrition and premature infants (8-11). Finally, de Steenhuijsen Piters et al. found that respiratory viral infections in the first few months of life were associated with a strong interferon response in the URT, an altered trajectory of URT microbiome development, and a higher risk of respiratory infections later in infancy (12). Taken together, these studies demonstrate that early life exposures have the potential to profoundly affect human microbiome development, with consequences for immune maturation and infection susceptibility.

The upper respiratory microbiome and childhood infections

Acute respiratory infections are the most frequent infections across the lifespan and the leading infectious cause of death among children globally. Increasingly, both the URT and gut microbiomes are recognized to influence respiratory tract infection susceptibility and severity. The URT is the primary entry point for most bacterial and viral respiratory pathogens, and microbes that inhabit the URT provide a barrier to colonization and infection by these pathogens. Several recent studies furthered our understanding of this colonization resistance within the URT. In a longitudinal study of infants in Botswana, Kelly et al. demonstrated that a higher URT abundance of Corynebacterium was associated with a lower incidence of Streptococcus pneumoniae colonization and that specific Corynebacterium strains secrete factors that inhibit pneumococcal growth in vitro (13). Potential respiratory pathogens have also developed mechanisms to overcome this colonization resistance and to avoid elimination by host responses. Yang and colleagues recently demonstrated that Staphylococcus aureus strains isolated from the nares of children express a phenol-soluble modulin transporter system that resists killing by host-secreted antimicrobial peptides (14). These findings illustrate that the complex and bidirectional interactions that exist between the URT microbiome, host immune system, and pathogens can modify infection susceptibility among children.

Multiple recent studies identified associations between URT microbiome composition and the outcomes of specific respiratory virus infections. A study of Zambian infants identified lower URT abundances of Gemella and Staphylococcus and a higher abundance of Moraxella among deceased infants with respiratory syncytial virus (RSV) relative to RSV-uninfected decedents, suggesting that these genera could influence RSV disease severity (15). Rosas-Salazar and colleagues profiled the URT microbiomes and immune responses of 357 RSV-infected infants and identified associations between microbiome diversity, local inflammatory and antiviral immune responses, and both short-term (illness severity) and long-term (subsequent wheezing episodes) outcomes (16). Similarly, a study of 244 infants hospitalized with bronchiolitis found that a S. pneumoniae/S. aureus URT microbiome profile was associated with downregulation of T cell activation pathways, upregulation of neutrophil pathways, and severe disease requiring positive pressure ventilation (17). Over the course of the COVID-19 pandemic, SARS-CoV-2 has emerged as a common pediatric pathogen, with over 15 million children in the United States having acquired the virus as of May 2023 (18). In a recent cross-sectional study of 285 children (age <21 years) with a known exposure to SARS-CoV-2, URT microbiome composition was associated both with SARS-CoV-2 infection and infection-associated respiratory symptoms (19). Most notably, SARS-CoV-2-infected participants with microbiomes dominated by Corynebacterium and Dolosigranulum were less likely to have respiratory symptoms than infected subjects with other microbiome profiles (19). Finally, Penela-Sánchez and colleagues found that critically ill children with rhinovirus/enterovirus LRTI had lower URT microbiome diversity, higher abundance of Haemophilus, and lower abundance of Dolosigranulum compared to healthy children or children with asymptomatic or mild infections (20). Additional studies investigating relationships between the URT microbiome, host immune responses, and respiratory virus infection outcomes have the potential to shed further light on microbiome-host interactions that influence the risk and severity of these infections in children.

The gut microbiome and childhood infections

The gut microbiome has extensive interactions with the host immune system and has been associated with risk or severity of both enteric infections and infections at other body sites (e.g., bloodstream infection, LRTI). These infections are particularly frequent among populations with frequent exposure to broad-spectrum antibiotics, immature or disrupted gut barrier function, or impaired immunity (8,21,22). Schwartz and colleagues reported that premature infants who developed a bloodstream infection often had gut colonization by this strain weeks prior to infection (22). Moreover, among 74 children undergoing allogeneic hematopoietic cell transplantation (HCT), Margolis et al. found that the gut microbiome prior to transplantation or at the time of neutrophil engraftment was associated with bacterial infections (including bloodstream infection) and viral enterocolitis in the year following transplantation (23). Finally, in a small clinical trial of pediatric allogeneic HCT recipients, Severyn and colleagues noted a trend toward fewer bloodstream infections among children receiving gut decontamination with oral vancomycin-polymyxin B and, as demonstrated by prior studies, identified the bloodstream infection-causing strain in fecal samples from children prior to infection onset (24). Taken together, these studies demonstrate the potential utility of serial profiling of the microbiome for the prediction of infections among high-risk groups of children.

The gut microbiome is also the primary reservoir for antibiotic-resistant organisms, with several recent studies using next-generation sequencing to study acquisition of antibiotic resistance genes among children. A longitudinal analysis of the gut microbiomes of premature infants in six Norwegian neonatal intensive care units found that both antibiotics and probiotics were associated with carriage of mobile genetic elements, with subsequent analyses suggesting that E. coli and Klebsiella sp. likely harbored the largest numbers of antibiotic resistance genes (8). Similarly, MacDonald and colleagues found that repeated or prolonged antibiotic courses were associated with increases in the abundances of Proteobacteria and multidrug resistance genes among 39 children with hematological malignancies (25). Finally, using metagenomic sequencing data from 693 fecal samples from 80 children undergoing HCT, Heston et al. found that exposure to antibiotics with an anaerobic spectrum of activity was associated with increases in the number and abundances of antibiotic resistance genes in the gut microbiome (26). These studies demonstrate the importance of antimicrobial stewardship efforts in these vulnerable groups of children and highlight the need for effective strategies to prevent acquisition and transmission of antibiotic-resistant organisms in these populations.

Despite its distance from the URT, a growing body of literature indicates that the gut microbiome modifies respiratory infection susceptibility and severity. This relationship is likely mediated both through the influence of the gut microbiome on systemic immunity and the gut-lung axis, which encompasses a variety of mechanisms underlying cross-talk between these two niches. Stevens and colleagues recently demonstrated that antibiotic pretreatment in a newborn macaque model of pneumococcal challenge resulted in more severe infection associated with gut microbiome alterations and pulmonary immune responses dominated by senescent and hyperinflammatory neutrophils (27). Notably, transfer of fecal contents from control newborn animals to antibiotic-treated animals reduced illness severity and partially corrected these abnormal pulmonary immune responses (27). Recent clinical studies have also identified associations between the gut microbiome and respiratory infections, including SARS-CoV-2 (28). Future studies delineating the mechanisms underlying this gut-lung axis have the potential to identify new therapeutic targets that could be leveraged to prevent or treat respiratory infections among children.

Development of microbiome-directed therapies

With our growing understanding of the role of the microbiome in infectious diseases, there has been an increase in efforts to develop microbiome-targeted therapies for childhood infections. Probiotic supplementation is perhaps the most established such strategy, and use has become increasingly common among premature infants because of data suggesting that these products may reduce the risks of necrotizing enterocolitis and sepsis. Recent studies reported that administration of probiotics containing Bifidobacterium or Lacticaseibacillus strains can accelerate gut microbiome maturation and reduce antibiotic resistance gene abundances among premature infants (29-31). Most notably, two of these studies demonstrated that infants who received probiotics often transitioned to microbiome profiles dominated by a probiotic strain that persisted after probiotic discontinuation (29,30). Probiotics are also being evaluated for treatment of common childhood gastrointestinal illnesses, as highlighted by a recent randomized controlled trial for acute gastroenteritis. Unfortunately, treatment of children with this diagnosis with a probiotic containing Lacticaseibacillus rhamnosus and Lactobacillus helveticus did not decrease illness severity compared to placebo, with subsequent analyses revealing only the transient presence of probiotic species in the guts of probiotic recipients and no changes in gut microbiome community structure compared to children receiving placebo (32,33). Finally, a recent meta-analysis of three trials of Limosilactobacillus fermentum CECT 5716 suggested that supplementation may be associated with an up to 73% decreased risk of gastrointestinal infections among term infants delivered by Cesarean section (34). These studies indicate that the infant gut microbiome is more malleable to probiotics than the gut microbiomes of older children and adults and that these products could play a growing role in preventing childhood infections.

Clostridioides difficile infection (CDI) is the prototypical infection resulting from reduced colonization resistance, most frequently as a result of losses of beneficial gut bacteria during antibiotic treatment. Over the past decade, fecal microbiota transplantation has increasingly been used as a therapy for recurrent CDI; however, use of this procedure in pediatric medicine has been limited in part because of a relative lack of safety and efficacy data (35-37). There are several new microbiome-targeted therapies that have been developed for use in adults with CDI (38-40). RBX2660 is an enema-administered fecal microbiota suspension consisting of a standardized consortium of human stool-derived microbes; it became the first United States Food and Drug Administration (FDA)-approved fecal microbiome product in November 2022 (41). SER-109, an orally-administered mixture of spore-forming Firmicutes, was approved by the FDA in 2023 on the basis of its efficacy in preventing recurrent CDI in a randomized controlled trial of 182 adults (39). Finally, a defined consortium of eight Clostridia strains, referred to as VE303, was recently shown to be safe and effective in preventing CDI recurrence among 79 high-risk adults (42). Although these products have not yet been studied in children, they may offer future alternatives to fecal microbiota transplantation for children with recurrent CDI and pave the way for licensing of other microbiome-based therapies.

Recent preclinical studies also highlight the potential of microbiome-based therapies to prevent childhood infections other than CDI. Using fecal samples from children, Osbelt and colleagues found that samples that were resistant to in vitro colonization by a carbapenem-resistant Klebsiella pneumoniae strain had higher abundances of Klebsiella oxytoca (43). They then cultured K. oxytoca strains from these protected samples and demonstrated that several strains prevented and eradicated gut colonization by the K. pneumoniae strain in antibiotic-treated and gnotobiotic mouse models (43). Stubbendieck and colleagues sought to identify microbes in the URT that prevent colonization by Moraxella catarrhalis, a common cause of acute otitis media among children (44). Nasal microbiome analyses identified Rothia species as being negatively associated with M. catarrhalis colonization among children, and the authors subsequently identified a novel peptidoglycan endopeptidase that some Rothia strains secrete and that inhibits M. catarrhalis growth in vitro (44). Finally, the microorganisms that colonize our bodies also produce metabolites through nutrient consumption that influence human health and have potential benefits when used as therapies (postbiotics). Short-chain fatty acids (SCFAs), the major byproducts of bacterial fermentation in the large intestine, were recently demonstrated to prevent bloodstream infection in a mouse model of pediatric acute lymphoblastic leukemia (45). Lower fecal abundances of SCFAs have previously been associated with severe illness among infants with RSV bronchiolitis; Antunes and colleagues recently demonstrated that treatment with the SCFA acetate reduced viral replication in RSV-infected human lung epithelial cells and improved recovery of RSV-infected mice (46). Use of such postbiotics may represent an alternative to live microbiome-based therapies that is particularly attractive for use in immunocompromised pediatric populations.

Future Directions

While most pediatric studies have focused on the gut and URT microbiomes, recent data suggest that microbial communities at other body sites, including the urinary tract, oral cavity, tonsils, and skin, may modify infection susceptibility and severity among children (47-52). Additionally, the overwhelming majority of studies conducted to date have focused on bacteria; however, other microbial kingdoms, including viruses and fungi, are increasingly recognized to play important roles in the pathogenesis of human infectious diseases (51,53). Our understanding of the role of the microbiome in shaping immune function is also advancing. Multiple recent studies identified associations between the microbiome and immune responses to childhood vaccines, suggesting that microbial adjuvants could be used to promote robust vaccine responses among children (54-58). Finally, next-generation sequencing holds substantial promise for the diagnosis of infectious diseases, as illustrated by recent studies that used this technology to identify potential causative pathogens among critically ill children with LRTI (59,60).

Conclusion

The studies described in this review highlight our growing understanding of the role of the microbiome in pediatric infections. While many of these studies reported associations between the microbiome and risk or severity of a variety of pediatric infections, future studies will need to evaluate the mechanisms that underly these associations, including both microbiome-host and microbiome-pathogen interactions. Such studies have the potential to inform development of microbiome-based therapies that could reduce the burden of infections among children.

Key Points.

• The developmental trajectory of the microbiome affects immune system maturation and infection susceptibility during childhood.

• The upper respiratory and gut microbiomes influence the risk or severity of multiple infections during childhood through direct interactions with potential pathogens and indirectly through modulation of the host immune system.

• Microbiome-based therapies, including live microbial products and postbiotics, present future opportunities for the prevention and treatment of pediatric infectious diseases.