Enlisting commensal microbes to resist antibiotic-resistant pathogens

Abstract

The emergence of antibiotic-resistant bacterial pathogens is an all-too-common consequence of antibiotic use. Although antibiotic resistance among virulent bacterial pathogens is a growing concern, the highest levels of antibiotic resistance occur among less pathogenic but more common bacteria that are prevalent in healthcare settings. Patient-to-patient transmission of these antibiotic-resistant bacteria is a perpetual concern in hospitals. Many of these resistant microbes, such as vancomycin-resistant Enterococcus faecium and carbapenem-resistant Klebsiella pneumoniae, emerge from the intestinal lumen and invade the bloodstream of vulnerable patients, causing disseminated infection. These infections are associated with preceding antibiotic administration, which changes the intestinal microbiota and compromises resistance to colonization by antibiotic-resistant bacteria. Recent and ongoing studies are increasingly defining commensal bacterial species and the inhibitory mechanisms they use to prevent infection. The use of next-generation probiotics derived from the intestinal microbiota represents an alternative approach to prevention of infection by enriching colonization with protective commensal species, thereby reducing the density of antibiotic-resistant bacteria and also reducing patient-to-patient transmission of infection in healthcare settings.

Figure 1.

The microbiota plays an important role in intestinal homeostasis and prevention of opportunistic pathogen infection. A healthy microbiota is comprised predominantly of bacteria that are members of the Bacteroidetes (blue) and Firmicutes (yellow) phyla. These bacteria interact and cooperate to break down dietary fiber and host-derived mucus into a variety of carbohydrates that support the complex community. SCFAs are by-products of carbohydrate fermentation that promote differentiation of regulatory T cells (Treg). Bacteria-derived TLR ligands promote production of antimicrobial peptides such as RegIIIγ, helping prevent bacterial penetration into the inner mucus layer. Specific bacterial species can produce secondary and iso-bile acids, which contribute to colonization resistance against C. difficile. Bacteria such as B. fragilis maintain long-term colonization by using distinct polysaccharides so that similar strains that would otherwise use these same polysaccharides cannot engraft due to competitive exclusion. A healthy microbiota also allows for the maintenance of two distinct mucus layers: an ∼50-µm epithelium-associated inner mucus layer that is largely impenetrable by intestinal bacteria and a less dense outer layer that serves as a microbial habitat. (A) Dietary fiber is an important substrate of the healthy microbiota, but when dietary changes result in low fiber availability, bacteria resort to using the glycoprotein-rich mucus layer as an alternative energy source. As a result, dietary changes can lead to thinning of the mucus layer, permitting increased bacterial penetration of the mucus layer, which can lead to epithelial inflammation and increased pathogen susceptibility. (B) Antibiotic administration disrupts complex feedback loops that sustain the complex microbial community, causing loss of mucus due to the diminishment of microbiota-derived host factors that regulate the production and secretion of mucus. In addition, some antibiotics can cause colonization resistance to be lost, leaving the host vulnerable to opportunistic enteric pathogen (red) expansion.

Figure 2.

The microbiota drives defense against nosocomial bacterial pathogens. (A) Enterococcal infections can be deleterious to the antibiotic-treated host, as Enterococci can translocate into the bloodstream. Loss of colonization resistance is an important component in the manifestation of these infections, and colonization resistance is mediated through several mechanisms, including direct inhibition by commensal strains of E. faecalis and obligate anaerobes such as B. producta, Parabacteroides distasonis, Bacteroides sartorii, and C. bolteae. Bacteria-derived TLR ligands drive indirect inhibition by stimulating production of RegIIIγ. (B) C. difficile infection can cause severe colitis by inducing epithelial cell death, and this loss of epithelial integrity allows for residual bacteria remaining after antibiotic treatment to spill into the underlying tissue and bloodstream. Spores of C. difficile are ingested by the host and germinate into vegetative cells upon stimulation by primary bile acids. When the microbiota is unperturbed by antibiotics, bacteria such as C. scindens are present and can convert primary bile acids into secondary bile acids, which inhibit vegetative cell growth. Succinate is a metabolic by-product of commensal bacteria, and sialic acid is a host-derived carbohydrate that is cleaved from epithelial cells by commensals and released into the intestinal lumen. At steady state, succinate and sialic acid support sustained growth of various commensal species, but when antibiotics are administered, the commensal species that would benefit from these factors are eliminated, leaving them to be used by vegetative C. difficile to facilitate its own growth instead. (C) Enterobacteriaceae are a family of bacteria that are adept at exploiting the antibiotic treated intestine by inducing inflammation, a setting in which Enterobacteriaceae can exploit to facilitate their own expansion. Commensal bacteria produce butyrate as a by-product of carbohydrate fermentation, which in turn prevents inflammation and also directly kills Enterobacteriaceae in the presence of acidified pH. Loss of butyrate production reduces PPARγ signaling in epithelial cells, inducing inducible nitric oxide synthase (iNOS) expression that can be used as a substrate for nitrogen respiration in Enterobacteriaceae. This increased availability of iNOS is exploited by Enterobacteriaceae, creating a positive feedback loop that enables expansion of these opportunistic pathogens since the increased presence of Enterobacteriaceae can in turn lead to increased expression of iNOS.