Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance

Abstract

Background: The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities.Results: The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence-and phenotypebased analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. Conclusions:Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

“…Freshwater environments, including rivers, are considered reservoirs and dissemination routes for AMR 34 . Several studies have clearly depicted a larger increase in ARGs in human-impacted river sites than in the pristine river sites, indicating the effects of anthropogenic activities on the river resistome 35 – 37 . The river resistome is important for the potential reintroduction of AMR in humans because rivers are a major source of drinking water and irrigation water for agriculture 38 , 39 .…”

Antimicrobial Resistance in Escherichia coli

“…As anthropogenic activities largely shape the resistome of different environments, transmission of resistant genes between bacteria in a community can be influenced by its contamination with human and animal feces and its impact is largely driven not by the presence of resistant bacteria but rather from the presence of human-related mobile resistance genes [44]. If poor sanitation, manifested by fecal contamination, of a given community is the key to transmit and maintain resistant clones, the reduction of antibiotic consumption will not be sufficient to control antimicrobial resistance.…”

Host genetics affected the resistome and its expression patterns in the rumen of beef cattle raised without antibiotics used in humans

“…Plasmids are mobile genetic elements found in high abundance in the bacterial populations of bovine rumen [36], which play a major role in the spread of antimicrobial resistance through horizontal gene transfer [37]. Metagenomic approaches have been used to characterize plasmid encoded ARGs in several non-biological habitats such as activated sludge [38,39] as well as the human gut [40]. We found that aadA and tetW were the most abundant plasmid-associated ARG in the rumen of beef steers.…”