Metagenomic Insights Into the Contribution of Phages to Antibiotic Resistance in Water Samples Related to Swine Feedlot Wastewater Treatment

Abstract

In this study, we examined the types of antibiotic resistance genes (ARGs) possessed by bacteria and bacteriophages in swine feedlot wastewater before and after treatment using a metagenomics approach. We found that the relative abundance of ARGs in bacterial DNA in all water samples was significantly higher than that in phages DNA (>10.6-fold), and wastewater treatment did not significantly change the relative abundance of bacterial- or phage-associated ARGs. We further detected the distribution and diversity of the different types of ARGs according to the class of antibiotics to which they confer resistance, the tetracycline resistance genes were the most abundant resistance genes and phages were more likely to harbor ATP-binding cassette transporter family and ribosomal protection genes. Moreover, the colistin resistance gene mcr-1 was also detected in the phage population. When assessing the contribution of phages in spreading different groups of ARGs, β-lactamase resistance genes had a relatively high spreading ability even though the abundance was low. These findings possibly indicated that phages not only could serve as important reservoir of ARG but also carry particular ARGs in swine feedlot wastewater, and this phenomenon is independent of the environment.

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

“…optrA was identified in prophages and ICEs only in Streptococcus suis [32,73,74], but the mobilization of optrA through phage-mediated transduction cannot be discarded also in enterococci. Wang et al [75] also recently demonstrated by a metagenomic approach in swine feedlot wastewater samples that phages were more likely to harbor ABC transporter family and ribosomal protection genes including optrA.…”

Comparative genomics of globaloptrA-carryingEnterococcus faecalisuncovers common genetic features and a chromosomal hotspot foroptrAacquisition

“…Moreover, Wang et al . [66] recently demonstrated by a metagenomic approach in swine feedlot wastewater samples that phages were more likely to harbor ABC transporter family and ribosomal protection genes including optrA . Adding to the fact that transfer frequency of Tn 554 via transduction is higher than most plasmids [61], we could expect a tremendously fast dissemination of optrA among different Gram-positive species and across different hosts and settings, as seems to be occurring more expressively in the animal production scenario.…”

Massive analysis of 64’628 bacterial genomes to decipher a water reservoir and origin of mobile colistin resistance (mcr) gene variants: is there another role for this family of enzymes?

“…Indeed, almost all MCR variants described so far have been reported from bacteria from water in different environments. MCR-1 was detected and identified directly from swine wastewater of purification facilities 35,36 , directly from water or from bacteria (e.g. E. coli and E. cloacae ) collected from urban surface water, rivers or lakes 37–39 .…”