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Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India

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Abstract

Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g−1. Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54–0.77. The fish microflora showed high prevalence of AR genes like bla TEM, Class I integron, tetA, aph(3′)-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M, dfr1, tetA, bla TEM, and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.

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Funding

The present study was supported by the financial grant from the Department of Atomic Energy-Board of Research in Nuclear Sciences (DAE-BRNS), Sanction No. 2012/37B/50/BRNS.

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Authors and Affiliations

  1. Department of Biotechnology, University of Mumbai, Vidyanagari, Santacruz (East), Mumbai, 400098, India

    Onkar A. Naik & Archana Rath

  2. Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India

    Ravindranath Shashidhar & Jayant R. Bandekar

  3. Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India

    Devashish Rath

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  1. Onkar A. Naik
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  2. Ravindranath Shashidhar
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Correspondence to Archana Rath.

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Naik, O.A., Shashidhar, R., Rath, D. et al. Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India. Environ Sci Pollut Res 25, 6228–6239 (2018). https://doi.org/10.1007/s11356-017-0945-7

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