High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria

Abstract

Background Our interconnected world and the ability of bacteria to quickly swap antibiotic resistance genes (ARGs) make it particularly important to establish the epidemiological links of multidrug resistance (MDR) transfer between wastewater treatment plant (WWTP)- and human/animal-associated bacteria, under the One Health framework. However, evidence of ARGs exchange and potential factors that contribute to this transfer remain limited. Results Here, by combining culture-based population genomics and genetic comparisons with publicly available datasets, we reconstructed the complete genomes of 82 multidrug-resistant isolates from WWTPs and found that most WWTP-associated isolates were genetically distinct from their closest human/animal-associated relatives currently available in the public database. Even in the minority of lineages that were closely related, WWTP-associated isolates were characterized by quite different plasmid compositions. We identified a high diversity of circular plasmids (264 in total, of which 141 were potentially novel), which served as the main source of resistance, and showed potential horizontal transfer of ARG-bearing plasmids between WWTP- and humans/animal-associated bacteria. Notably, the potentially transferred ARGs and virulence factors (VFs) with different genetic backgrounds were closely associated with flanking insertion sequences (ISs), suggesting the importance of synergy between plasmids and ISs in mediating a multilayered hierarchical transfer of MDR and potentiating the emergence of MDR-hypervirulent clones. Conclusion Our findings advance the current efforts to establish potential epidemiological links of MDR transmission between WWTP- and human/animal-associated bacteria. Plasmids play an important role in mediating the transfer of ARGs and the IS-associated ARGs that are carried by conjugative plasmids should be prioritized to tackle the spread of resistance.

The diversity in antimicrobial resistance of MDR Enterobacteriaceae among Chinese broiler and laying farms and two mcr-1 positive plasmids revealed their resistance-transmission risk

“…In particular, p20432-mcr, found in broiler MDRE, carries a novel integron In1866 and multiple drug resistance genes. The emergence of In1866 confirms that selection pressure is an important condition for the generation of new mobile components (Che et al, 2022). However, it remains to be studied how MGEs evolve through high-frequency HGT in a particular pattern of the family farms.…”

Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo

“…The complete sequence of each class 1 integron would provide novel insights into the mobile genetic element (MGE)-dependent HGT among bacteria in WWTP active sludge. 5 Furthermore, such short read sequencing (150-mer paired-end) is not an appropriate method for determining whether ARG is located on a plasmid or chromosome.…”

“…[2][3][4] Indeed, the high density of bacteria in WWTPs provides an optimum environment for horizontal gene transfer (HGT) between environmental bacteria and human pathogens. 5 Moreover, WWTP wastewater and active sludge act as reservoirs and environmental suppliers of AMR, which implies that WWTPs are hotspots for HGT under the selective pressure of antibiotics, disinfectants, and metals, even at low concentrations. Thus, WWTPs could facilitate the dissemination of antibiotic resistance genes among different bacterial species.…”

Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo

“…The prevalence of AMR bacteria (ARB) and AMR genes (ARGs) in rivers would increase downstream of WWTPs because of effluents [ 3 , 4 ]. Indeed, the high density of bacteria in WWTPs could provide an optimum environment for horizontal gene transfer (HGT) between human pathogens and environmental bacteria [ 5 ]. Moreover, such environmental bacteria persist in the environment and later they might transfer back such genes to clinically relevant pathogens [ 6 ].…”

“…Thus far, the potential correlation between the integron intI1 and anthropogenic pollution in WWTPs has been documented among the main hotspots of ARGs in the environment [ 8 ]. The importance of the synergy between plasmids and ARGs with flanking insertion sequences (ISs) has also been documented to potentiate the emergence of MDR-hypervirulent clones between WWTP- and human/animal-associated bacteria [ 5 ]. Ekanzala et al reported that hospital wastewater showed significantly higher environmental resistome risk scores than all other assessed matrices [ 9 , 10 ], suggesting that hospital wastewater, effluent, and sewage sludge should be subjected to stringent mitigation measures to minimize such dissemination.…”