The State of Microbiome Science at the Intersection of Infectious Diseases and Antimicrobial Resistance

Abstract

Along with the rise in modern chronic diseases, ranging from diabetes to asthma, there are challenges posed by increasing antibiotic resistance, which results in difficult-to-treat infections, as well as sepsis. An emerging and unifying theme in the pathogenesis of these diverse public health threats is changes in the microbial communities that inhabit multiple body sites. Although there is great promise in exploring the role of these microbial communities in chronic disease pathogenesis, the shorter timeframe of most infectious disease pathogenesis may allow early translation of our basic scientific understanding of microbial ecology and host-microbiota-pathogen interactions. Likely translation avenues include development of preventive strategies, diagnostics, and therapeutics. For example, as basic research related to microbial pathogenesis continues to progress, Clostridioides difficile infection is already being addressed clinically through at least 2 of these 3 avenues: targeted antibiotic stewardship and treatment of recurrent disease through fecal microbiota transplantation.

Keywords: Microbiota; antimicrobial resistance; host; infectious disease; pathogen.

Figure 1.

The complex interactions between pathogen, host, and indigenous microbiota. There are multiple bidirectional interactions that influence the outcome of infection and other host inflammatory or immune-related processes. The microbiota appears to play a central role in influencing both host and pathogen behavior thus necessitating a system-level approach that improves our understanding of disease pathogenesis.