AUTHOR=Tartor Yasmine H. , Abd El-Aziz Norhan K. , Gharieb Rasha M. A. , El Damaty Hend M. , Enany Shymaa , Soliman Enas A. , Abdellatif Samah S. , Attia Amira S. A. , Bahnass Mosa M. , El-Shazly Yousry A. , Elbediwi Mohammed , Ramadan Hazem 

TITLE=Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr-10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.770813

DOI=10.3389/fmicb.2021.770813

ISSN=1664-302X

ABSTRACT=<p>Antimicrobial resistance is a major concern in the dairy industry. This study investigated the prevalence, antimicrobial resistance phenotypes, and genome sequencing of Gram-negative bacteria isolated from clinical (<italic>n</italic> = 350) and subclinical (<italic>n</italic> = 95) bovine mastitis, and raw unpasteurized milk (<italic>n</italic> = 125). <italic>Klebsiella pneumoniae</italic>, <italic>Aeromonas hydrophila</italic>, <italic>Enterobacter cloacae</italic> (100% each), <italic>Escherichia coli</italic> (87.78%), and <italic>Proteus mirabilis</italic> (69.7%) were the most prevalent multidrug-resistant (MDR) species. Extensive drug-resistance (XDR) phenotype was found in <italic>P. mirabilis</italic> (30.30%) and <italic>E. coli</italic> (3.33%) isolates. Ten isolates (four <italic>E. coli</italic>, three <italic>Klebsiella</italic> species and three <italic>P. mirabilis</italic>) that displayed the highest multiple antibiotic resistance (MAR) indices (0.54–0.83), were exposed to whole-genome sequencing (WGS). Two multilocus sequence types (MLST): ST2165 and ST7624 were identified among the sequenced <italic>E. coli</italic> isolates. Three <italic>E. coli</italic> isolates (two from clinical mastitis and one from raw milk) belonging to ST2165 showed similar profile of plasmid replicon types: IncFIA, IncFIB, IncFII, and IncQ1 with an exception to an isolate that contained IncR, whereas <italic>E. coli</italic> ST7624 showed a different plasmid profile including IncHI2, IncHI2A, IncI1α, and IncFII replicon types. ResFinder findings revealed the presence of plasmid-mediated colistin <italic>mcr</italic>-<italic>10</italic> and fosfomycin <italic>fosA</italic>5 resistance genes in a <italic>K. pneumoniae</italic> (K1) isolate from bovine milk. Sequence analysis of the reconstructed <italic>mcr-10</italic> plasmid from WGS of K1 isolate, showed that <italic>mcr-10</italic> gene was bracketed by <italic>xer</italic>C and insertion sequence IS26 on an IncFIB plasmid. Phylogenetic analysis revealed that K1 isolate existed in a clade including <italic>mcr-10</italic>-harboring isolates from human and environment with different STs and countries [United Kingdom (ST788), Australia (ST323), Malawi (ST2144), Myanmar (ST705), and Laos (ST2355)]. This study reports the first emergence of <italic>K. pneumoniae</italic> co-harboring <italic>mcr</italic>-<italic>10</italic> and <italic>fosA5</italic> genes from bovine milk in the Middle East, which constitutes a public health threat and heralds the penetration of the last-resort antibiotics. Hence, prudent use of antibiotics in both humans and animals and antimicrobial surveillance plans are urgently required.</p>