First report on the detection and whole genome sequencing analysis of virulent and multidrug resistant Enterobacter cloacae ST84 strain harboring qacE-like disinfectant resistance gene isolated from bovine mastitis

Enterobacter cloacae is infrequently reported in milk samples and bovine mastitis. Here we report for the first time, the detection and phylogenomic analysis of an Enterobacter cloacae strain isolated from a raw milk sample obtained from a clinical mastitis-infected cow in Bangladesh using whole genome sequence analyses. Enterobacter cloacae strain BRMHR107Ecl belonged to sequence type ST84, belonging to a rarely reported ST in the Enterobacter genus. Phylogenomic analyses revealed that the strain is closely related to a strain previously isolated in Bangladesh. The closest relative to BR-MHR107Ecl was a strain isolated in 2016 from a human rectal swab sample in Nigeria. The BR-MHR107Ecl strain co-harbored beta-lactamase genes including bla_DHA-1 and bla_CMH-3-like. Other antimicrobial resistance genes were detected and included aminoglycoside resistance genes (aph(3″)-Ib-like, aph(6)-Id), fluoroquinolone resistance gene (qnrB4) and sulphonamide resistance gene (sul1). The genome harbored an additional disinfectant resistance gene (qacE-like). Several plasmid replicons, including Col(pHAD28), IncFIA(HI1), IncFIB(K), IncR, and repB(R1701) were detected. Virulence genes encoding for heat-stable enterotoxin EAST-1 (astA) and lipoprotein NlpI precursor (nlpI) were detected. The multidrug resistance and virulence genes repertoire of BR-MHR107Ecl and its isolation from bovine mastitis milk render it a potentially significant public health concern, highlighting its emerging threat to dairy herds and underscoring the importance of genomic surveillance in food animals and non-clinical environment to detect emerging pathogens. This study will contribute to understanding the transmission of E. cloacae from farm-to-fork which requires collaborative and comprehensive One health approaches. The findings will help monitor the global dissemination of antimicrobial resistance in livestock-associated Enterobacter cloacae in the One Health context.