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Predicting Human Risk with Multidrug Resistant Enterobacter hormaechei MS2 having MCR 9 Gene Isolated from the Feces of Healthy Broiler Through Whole-Genome Sequence-Based Analysis

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Abstract

The zoonotic spread of antimicrobial resistance (AMR) and the associated infections are becoming a major threat to the human population worldwide. Strategies to identify the potential pathogen dissemination by seemingly healthy livestock are at a nascent stage and it is of significant importance to monitor environmental evolution of AMR. In this study, a multidrug resistant strain (MDR) of Enterobacter hormaechei MS2 isolated from the feces of healthy broiler chicken has been characterized by whole-genome sequencing-based method. Here, the isolate was primarily subjected to antimicrobial susceptibility testing followed genome sequencing and analysis. From the antimicrobial susceptibility testing result, the strain was found to be resistant to multiple classes of drugs including the colistin which is an important  last resort drug used to treat infectious diseases. The resistome prediction of genomic data further revealed the presence of 7 perfect and 26 strict hits including those for MCR-9 and FosA2. The pathogenicity prediction has also demonstrated the strain to have the potential to be a human pathogen with 0.72 probability. The phylogenetic analysis has also supported the zoonotic potential of the strain due to its clustering with isolates from both human and livestock-associated host groups. The results of the study suggest the need for a strong surveillance system to identify the opportunistic zoonotic pathogens to prevent a silent AMR menace mediated by them. Carriage of multi-drug resistant strains in the livestock gut microbiome is also a serious concern as it has high AMR transmissibility through contact and supply chain activities.

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Data availability

The datasets analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

Acknowledging the funding provided by The Department of Animal Husbandry, Government of Kerala, and the support form Kerala Antimicrobial Resistance Strategic Action Plan (KARSAP). Acknowledging the instrumentation facility provided by The Kerala State Council for Science, Technology and Environment (KSCSTE) SRS project.

Funding

The Department of Animal Husbandry, Government of Kerala.

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Authors and Affiliations

  1. School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, Kerala, 686 560, India

    Sreejith Sreekumaran, Manjusha Premnath, Jyothis Mathew & E. K. Radhakrishnan

  2. State Institute of Animal Diseases, Thiruvananthapuram, Kerala, 695 563, India

    P. R. Prathyush & Swapna Susan Abraham

  3. Department of Microbiology, Government Medical College, Kottayam, Kerala, 686 008, India

    Chitra C. Nath & Nimmy Paul

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  1. Sreejith Sreekumaran
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Contributions

SS: conceptualization, data analysis, writing; MP: Data analysis, writing; PRP: review and editing, CCN: data analysis, NP: review and editing; SSA: review and editing, JM: supervision and editing; EKRR: conceptualization, supervision and editing.

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Correspondence to E. K. Radhakrishnan.

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Sreekumaran, S., Premnath, M., Prathyush, P.R. et al. Predicting Human Risk with Multidrug Resistant Enterobacter hormaechei MS2 having MCR 9 Gene Isolated from the Feces of Healthy Broiler Through Whole-Genome Sequence-Based Analysis. Curr Microbiol 81, 8 (2024). https://doi.org/10.1007/s00284-023-03492-w

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