Elizete Batista Neves Araujo

The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in gnotobiotic mice. Whereas single species alone had negligible effects, colonization resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explained these ecological patterns through the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Furthermore, we applied our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities.

Abstract Background Klebsiella pneumoniae (Kp) commonly colonizes mucosal surfaces, with high hospital-acquired colonization rates. Gastrointestinal colonization with antimicrobial resistant (AMR)-Kp increases patient risk of subsequent infection, via unclear mechanisms. We hypothesize that antibiotic treatment facilitates AMR-Kp expansion, leading to altered immune landscapes (colon and secondary sites), creating vulnerability to subsequent infections. Methods To investigate how AMR-Kp colonization influences the local immune response and native microbiome, germ-free (GF), Gnotobiotic Oligo-MM12 mice (representative minimal microbiome of 12 physiologically relevant bacteria, MM12), or specific pathogen free (SPF) mice were orally gavaged with AMR-Kp strain KP35. Gastrointestinal colonization was monitored through stool cfu. Results KP35 poorly colonizes SPF mice but does stably colonize MM12 and GF animals. This colonization does not result in overt histopathology or inflammation of the colon. Antibiotic treatment of MM12 and SPF mice results in KP35 expansion in the gastrointestinal tract, comparable to levels observed in GF mice. KP35 expansion is accompanied by increased colonic neutrophils and relevant recruitment markers (determined by flow cytometry and qPCR respectively) for the duration of antibiotic treatment. When antibiotic treatment is stopped, KP35 cfu drops back below detectable limits. KP35 expansion is also observed in the lung following antibiotics in both MM12 and SPF models, and preliminary studies suggest AMR-Kp colonization combined with antibiotic treatment can influence subsequent lung infection. Therefore, AMR-Kp gastrointestinal colonization is influenced by microbiome complexity, which is disrupted by antibiotic treatment, leading to an expansion of AMR-Kp and recruitment of neutrophils to the colon. AMR-Kp expansion within the gut may not be overtly pathogenic but may generate a more ‘primed’ environment and influence mucosal barrier integrity making the host more vulnerable to secondary infections. Conclusions Understanding microbe or host factors that may prevent or reduce AMR-Kp colonization and antibiotic-induced enteric blooms could provide new therapeutic avenues for opportunistic AMR infections.