Are Virulence and Antibiotic Resistance Genes Linked? A Comprehensive Analysis of Bacterial Chromosomes and Plasmids

Abstract

Although pathogenic bacteria are the targets of antibiotics, these drugs also affect hundreds of commensal or mutualistic species. Moreover, the use of antibiotics is not only restricted to the treatment of infections but is also largely applied in agriculture and in prophylaxis. During this work, we tested the hypothesis that there is a correlation between the number and the genomic location of antibiotic resistance (AR) genes and virulence factor (VF) genes. We performed a comprehensive study of 16,632 reference bacterial genomes in which we identified and counted all orthologues of AR and VF genes in each of the locations: chromosomes, plasmids, or in both locations of the same genome. We found that, on a global scale, no correlation emerges. However, some categories of AR and VF genes co-occur preferentially, and in the mobilome, which supports the hypothesis that some bacterial pathogens are under selective pressure to be resistant to specific antibiotics, a fact that can jeopardize antimicrobial therapy for some human-threatening diseases.

Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome

“…Resistance to disinfectants reveals a worrying effect of the increasing use of products on the adaptive and evolutionary response of microbial communities. This result agrees with our previous research on a dataset consisting of over 16,000 reference bacterial genomes that showed enrichment of the mobilome with genes encoding resistance to disinfectants [ 33 ]. These high levels of resistance genes and the fact that they tend to be encoded in the mobilome highlights, on the one hand, the selective pressure effect that bacteria and microbiomes are subjected to, but also the epidemic potential of these newly acquired traits.…”

“…Previous studies show that sediments are biomes that possess a great diversity of antibiotic-resistance genes [ 32 ]. A comprehensive study of bacterial genomes reveals that, at the genomic level, the most frequent resistance genes present are those conferring resistance to beta-lactams, sulfonamide, quinolones, and only then to macrolides and tetracycline, and that resistance to oxazolidinone is rare [ 33 ]. This profile at the genomic level is different from that found in the metagenomes of aquaculture sediments, thus revealing a specific profile of these metagenomes.…”

Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle

“…The similar burden of VFGs detected in CONT and TREAT cattle on days 3, 7, and 14 suggests that antibiotic treatment was unlikely to be a practice promoting VFGs dissemination through pathogen enrichment in the gastrointestinal tract of cattle. As the entire host’s microbiome is under antibiotics’ selective pressure, not only bacterial pathogens but also the association between ARGs and pathogenic VFGs weakens [ 62 ]. Moreover, the increase in the number of reads aligned to ARGs conferring resistance to tetracyclines observed after antibiotic administration in TREAT cattle did not correlate with an increase in VFGs, suggesting that those tetracycline-resistance genes were enriched in commensal bacteria that may act as a reservoir of ARGs [ 51 , 63 ].…”

Genomic Study of Chromosomally and Plasmid-Mediated Multidrug Resistance and Virulence Determinants in Klebsiella Pneumoniae Isolates Obtained from a Tertiary Hospital in Al-Kharj, KSA

“…ICEs are also known as conjugative transposons that are crucial for horizontal gene transfer between cells, and they can carry insertion sequences and/or transposons, integrases, and the relaxase enzyme, which is critical for conjugation. Antimicrobial resistance (AMR) is continuously evolving and the genes are transferred horizontally through plasmids [ 10 , 11 ].…”