Protein malnutrition facilitates intestinal colonization with highly resistant Klebsiella pneumoniae through disrupted intestinal microbial metabolism

ABSTRACT Pediatric infections with highly resistant Klebsiella pneumoniae (HR-Kp) disproportionately affect low-income countries where childhood malnutrition is prevalent. Malnutrition is an identified risk factor for infection with HR-Kp and other antimicrobial-resistant Enterobacterales, but the mechanistic underpinnings of this link and independence from other common exposures, like antibiotics, in children are unclear. Using a murine model of pediatric malnutrition, we found that mice fed a protein-deficient diet (PD) were more susceptible to colonization with HR-Kp at a 4-log lower challenge inoculum and developed a 3-log higher intestinal burden in comparison to adequately nourished mice. HR-Kp colonization in PD-fed mice persisted beyond 5 weeks, and colonization was transmitted to diet-matched cage mates. Antibiotic treatment resulted in similar HR-Kp colonization burdens regardless of diet, suggesting that nutrition-dependent colonization risk is driven by altered intestinal microbiota. Despite reduced dietary protein intake, intestinal amino acid content was maintained in PD-fed mice, supporting optimal HR-Kp growth. Furthermore, secondary bile acids, prototypic intestinal microbiota-derived molecules, were reduced in PD-fed mice, demonstrated an inverse correlation with HR-Kp burden in vivo , and partially inhibited the growth of HR-Kp in vitro . Collectively, these findings reveal a role for dietary protein intake in determining nutrition-dependent colonization resistance to HR-Kp. IMPORTANCE Antimicrobial-resistant Klebsiella pneumoniae are responsible for a growing mortality burden worldwide, with disproportionate rates of infection in low-income countries where childhood malnutrition is prevalent. Several publications have demonstrated high rates of intestinal colonization with antimicrobial-resistant K. pneumoniae in children admitted with severe malnutrition in sub-Saharan Africa. However, numerous confounding risk factors in malnourished children (antibiotic use, healthcare exposure, and immune dysfunction) make it difficult to assess the direct impact of nutrition on K. pneumoniae colonization. In this study, we utilized a novel mouse model of protein malnutrition to demonstrate that dietary protein deficiency renders mice susceptible to a higher burden of intestinal colonization at a lower inoculating dose of K. pneumoniae . Furthermore, reduced microbiota-derived bile acid metabolites correlate with increased burden of colonization in protein-deficient mice. These results are the first to establish a direct mechanistic link associating dietary protein deficiency, bile acid metabolism, and intestinal colonization with antimicrobial-resistant K. pneumoniae .