Abstract
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, blaNDM-5 along with other antimicrobial resistance genes (ARGs), blaTEM (64.7%), blaCTX-M-15 (35.3%), blaOXA-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 blaNDM-5 was significantly associated with ARGs, tet(A), and sul1; and plasmid replicons, IncF, IncI1, and IncP, signifying the presence of blaNDM-5 and associated ARGs on these transferable plasmids. These findings were validated by the successful conjugal transfer of blaNDM-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.
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Nucleotide sequences data generated in this study have been submitted to the NCBI database. The data generated in the study will be provided on request.
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Acknowledgements
The authors wish to express their sincere thanks to Dr. J.K. Jena, DDG (Fisheries Science), ICAR, New Delhi, and Dr. Kuldeep K Lal, Director, ICAR-NBFGR, Lucknow, India, for institutional funding and support to carry out the work. We are thankful to Dr. Sanath Kumar H, Principal Scientist, ICAR-Central Institute of Fisheries Education, Mumbai, for his support in the conjugation experiment. The first author is also thankful to Maharaja Agrasen University, Solan, for its support, as this work also forms part of the PhD thesis.
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This work was supported by the ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India, under the institute-funded project, code: FISHNBFGRCIL 201701200201.
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The manuscript was reviewed and approved for publication by all authors. Dr. Gaurav Rathore, Dr. Abhishek Awasthi, and Arti Dwivedi contributed to the conception and design of the study. Sampling was done by Dr. Chandra Bhushan Kumar, Anil Kumar, Mayank Soni, Dr. Vikash Sahu, and Arti Dwivedi. Draft manuscript preparation was performed by Arti Dwivedi. The statistical data analysis and manuscript editing was done by Dr. Gaurav Rathore and Dr. Chandra Bhushan Kumar.
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Dwivedi, A., Kumar, C.B., Kumar, A. et al. 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. Environ Sci Pollut Res 30, 49314–49326 (2023). https://doi.org/10.1007/s11356-023-25639-9
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DOI: https://doi.org/10.1007/s11356-023-25639-9