Country-specific antibiotic use practices impact the human gut resistome

Abstract

Despite increasing concerns over inappropriate use of antibiotics in medicine and food production, population-level resistance transfer into the human gut microbiota has not been demonstrated beyond individual case studies. To determine the ''antibiotic resistance potential'' for entire microbial communities, we employ metagenomic data and quantify the totality of known resistance genes in each community (its resistome) for 68 classes and subclasses of antibiotics. In 252 fecal metagenomes from three countries, we show that the most abundant resistance determinants are those for antibiotics also used in animals and for antibiotics that have been available longer. Resistance genes are also more abundant in samples from Spain, Italy, and France than from Denmark, the United States, or Japan. Where comparable country-level data on antibiotic use in both humans and animals are available, differences in these statistics match the observed resistance potential differences. The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year.

Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

“…Although recently also found in aerobic Sphingobacterium sp. (Ghosh et al, 2009b) and some Enterobacteriaceae and Pseudomonadaceae strains (Leski et al, 2013), the host diversity of tet(X) is relatively low (Chopra and Roberts, 2001), being mainly carried by Bacteroides (Guiney et al, 1984;Bartha et al, 2011;de Vries et al, 2011;Forslund et al, 2013). As described previously (Tian et al, 2015), Bacteroides was the dominant fermentative bacteria in mesophilic sludge, and experienced fast decline after temperature increase because all species of this genus are mesophilic (Garrity et al, 2004).…”

“…S3). aadE is reported to be harbored by Haloplasma (Forslund et al, 2013), whose only type species, Haloplasma contractile, is mesophilic (Antunes et al, 2008). It is possible that some unknown thermophilic species in Haloplasma might be responsible for the observed relevance between aadE and Haloplasma.…”

Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil

“…Only few of the ARGs hosts have been verified in previous studies, for instance, by using network analysis, Li et al found that Blautia was the host of tet32, tetM, tetQ and tetO and ermB, and Escherichia carry resistance genes of cfxA3, tetQ, acrA, mdtH, mdtL and mdtO (Li et al, 2015b). Forslund et al suggested that Blautia and Clostridium harbored tet32, tetO and ermB, whereas Escherichia was the host of acrA, mdtH, mdtL and mdtO (Forslund et al, 2013). Network analysis is a reasonable tool to provide us new insights into the ARGs and their possible hosts in complex environmental samples (Ju et al, 2016).…”

The effect of the administration of three different antimicrobial premix formulations via the liquid feeding system on the occurrence of Enterobacteriaceae resistant to tetracycline in the liquid feed for pigs

“…Antimicrobial resistant bacteria arise by mutations or by the acquisition of antimicrobial resistance determinants by HGT (Andersson and Hughes, 2011;Huddleston, 2014;van Schaik, 2015). It is well documented and widely accepted that the use of a given antimicrobial is the driving force behind the selection of bacteria resistant to the applied antimicrobial agent (Davies and Davies, 2010;Forslund et al, 2013;Modi et al 2014). Interestingly, resistance to an antimicrobial can also be selected by the use of a structurally related (cross-selection) or unrelated (co-selection) antimicrobial (Guardabassi and Kruse, 2008).…”