Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome

Abstract

A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.

Comparison of the gut microflora of common kestrel (Falco tinnunculus) according to differences in sex, age, and physiological condition

“…5b). It is speculated that this may also be related to the transfer of ARGs among these pathogenic bacteria [52] or to the survival mechanism by which some pathogenic bacteria borrow certain protein and RNA components from other bacteria to enhance their own reproductive ability [53].…”

Characterization of the Composition Variation of Healthy Human Gut Microbiome in Correlation with Antibiotic Usage and Yogurt Consumption

“…However, we need to be careful when antimicrobial resistance is taken into consideration. It has been reported that antibiotic usage would assist AMR genes’ horizontal transfer in patients [ 10 ]. However, the mechanisms of antibiotic resistance transmission during microbiome modification remain unclear.…”

“…Antibiotic usage can disrupt the ability of gut micobiota to inhibit pathogen growth, due to the reduction of native bacterial species, therefore causing antibiotic diarrhea [ 9 ]. Antibiotic usage may also enhance horizontal AMR gene transfer from commensal bacteria to pathogens in gut microbiota, through which antibiotic resistant pathogens that are difficult to treat with common antibiotics are created [ 10 , 11 ]. Probiotics are microorganisms that are beneficial to health when supplemented as part of the human diet [ 12 ].…”

The role of the gut microbiota in health and cardiovascular diseases

“…There is evidence that antibiotics may play a role in CVDs, but the possible drug resistance caused by long-term use of antibiotics is also of concern, as long-term use of antibiotics may disrupt the dynamic balance of intestinal microorganisms [ 553 ]. Therefore, based on the current findings, we believe that more preclinical and clinical studies are needed to clarify the role of antibiotics in the gut microbiota and CVDs, and individualized use of antibiotics in patients with CVDs should also be considered.…”