Genomic and metagenomic technologies to explore the antibiotic resistance mobilome

Abstract

Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health‐integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so‐called resistance mobilome. High‐throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.

Consumer Exposure to Antimicrobial Resistant Bacteria From Food at Swiss Retail Level

“…However, data on AMR genetics is still limited for public health relevant bacteria that are not as frequently isolated from food such as C. difficile . Furthermore, quantifiable data on AMR gene prevalence as well as the detailed elucidation of genetic linkages between AMR genes and mobile genetic elements such as plasmids, transposons or integrons is rarely reported (Lanza et al, 2015; Martínez et al, 2017). This unfortunately hinders better estimations on AMR gene prevalence and transferability.…”

Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for Five Bacillus Species Relevant for Use as Animal Feed Additives or for Plant Protection

“…Although antimicrobial resistance has dramatically increased in the postantibiotic era, the mechanisms responsible for resistance existed long before and are found in bacteria in all environments (2,6). Consequently, nonpathogenic bacteria may contain antimicrobial resistance genes and pose a risk for disseminating these to pathogenic bacteria, especially if the resistance mechanism is encoded on a mobile genetic element (e.g., a plasmid or a conjugative transposon) (7). For this reason, legislation exists that requires viable microorganisms used as active agents in feed additives to be free of antimicrobial resistance genes that potentially could be transferred to other bacteria (8,9).…”

Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance

“…Species located in very stable, reduced, highly specialized niches are less exposed to the gene-traffic circuit; thus, their pangenome is close to their core genome (Martínez et al, 2017;McInerney et al, 2017). Significant examples are Listeria monocytogenes, or Legionella pneumophila, able to exploit intracellular (stable, isolated) niches, which have larger core genomes ("closed genomes") than other members of their phylogenetic relatives, indicating less exposure to horizontal gene transfer (Gomez-Valero et al, 2011;Collins and Higgs, 2012).…”