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Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater

Abdulkadir, Nafi'u ; Saraiva, Joao Pedro ; Zhang, Junya ; Stolte, Stefan ; Gillor, Osnat ; Harms, Hauke ; Rocha, Ulisses Rosato, Adriana E.

Microbiology spectrum, 2024-03, Vol.12 (3), p.e0291823-e0291823 [Periódico revisado por pares]

United States: American Society for Microbiology

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  • Título:
    Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater
  • Autor: Abdulkadir, Nafi'u ; Saraiva, Joao Pedro ; Zhang, Junya ; Stolte, Stefan ; Gillor, Osnat ; Harms, Hauke ; Rocha, Ulisses
  • Rosato, Adriana E.
  • Assuntos: activated sludge ; Animals ; Anti-Bacterial Agents - pharmacology ; antimicrobial resistance genes ; Bacteria ; Computational Biology ; Drug Resistance, Bacterial - genetics ; Genes, Bacterial - genetics ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; metagenome-assembled genomes ; Microbiota ; mobile genetic elements ; pathogens ; Research Article ; Sewage - microbiology ; Wastewater
  • É parte de: Microbiology spectrum, 2024-03, Vol.12 (3), p.e0291823-e0291823
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    The authors declare no conflict of interest.
  • Descrição: Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species ( average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to , , , , , and . Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities. Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including , , , , , , and , which could have significant implications for AMR transmission. The abundance of , , and in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.
  • Editor: United States: American Society for Microbiology
  • Idioma: Inglês
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