Molecular characterization of carbapenem resistant E. coli of fish origin reveals the dissemination of NDM-5 in freshwater aquaculture environment by the high risk clone ST167 and ST361

Aquatic environment can act as reservoir and disseminator of antimicrobial resistance and resistant pathogens. Novel high-risk carbapenem resistant E. coli (CREC) are continuously emerging worldwide; however, the occurrence of CREC in freshwater aquaculture environment is largely unexplored. To fill this gap, large scale sampling of freshwater pond sites and retail fish markets was done between Oct 2020 and Oct 2021 to investigate the CREC contamination in fish. The frequency of CREC contamination in the freshwater fish was 6.99% (95% CI: 3.78-10.20%). All the isolates were MDR and harbored carbapenemase encoding gene, bla(NDM-5) along with other antimicrobial resistance genes (ARGs), bla(TEM) (64.7%), bla(CTX-M-15) (35.3%), bla(OXA-1) (5.9%), tet(A) (100%), sul1 (94.1%), qnrS (82.3%), cat1 (35.3%), and cat2 (23.5%). The isolates belonged to phylogroup C and showed low virulence gene profile. ERIC-PCR grouped the isolates into five clusters (I-V). The isolates of clusters I, II, and III were identified as ST167 (76.4%) and of cluster IV as ST361 (17.6%). This is the first report documenting the contamination of NDM-5 producing E. coli ST167 and ST361 of clinical/livestock lineage in freshwater fish from India. The bla(NDM-5) was significantly associated with ARGs, tet(A), and sul1; and plasmid replicons, IncF, IncI1, and IncP, signifying the presence of bla(NDM-5) and associated ARGs on these transferable plasmids. These findings were validated by the successful conjugal transfer of bla(NDM-5) and associated ARGs into non-CREC strain (J53). Our study highlights the ability of CREC to disseminate antimicrobial resistance which has health implications and environmental concerns.

Automated summary

The aquatic environment serves as a reservoir and disseminator of antimicrobial resistance and resistant pathogens. This study investigated the contamination of carbapenem resistant E. coli (CREC) in freshwater fish in India. The results showed a frequency of 6.99% CREC contamination in freshwater fish, with all isolates being multidrug-resistant and carrying the carbapenemase encoding gene bla(NDM-5), along with other antimicrobial resistance genes. The study highlights the ability of CREC to disseminate antimicrobial resistance and raises health and environmental concerns.