Predicting human risk with multidrug resistant Enterobacter hormaechei MS2 with MCR 9 gene isolated from the feces of healthy broiler through whole genome sequence based analysis.

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 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 candidate 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 FosA6. 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.