Genomic characterization of an extensively drug-resistant chicken-borne Salmonella Indiana isolate carrying an IncHI2-IncHI2A plasmid. (July 2021) - Zhang, Zengfeng
Abstract: The recent emergence of e xtensively d rug-r esistant (XDR) foodborne bacteria is posing a huge threat to food safety and public health. In this study, we reported the genome features of an XDR Salmonella Indiana isolate (SJTUF87912v2 ) recovered from a chicken carcass in 2012 in Guangdong, China. This isolate was resistant to 10 antimicrobial classes including penicillins, β-lactam combination agents, cephems, aminoglycosides, folate pathway antagonists, fosfomycins, macrolides, phenicols, quinolones, and tetracyclines, and thus, it should be considered as an XDR isolate. A prominent feature of its genome was that it possessed 28 g enomic i slands (GIs) encoding proteins for phage, type IV secretion, DNA repair, and biofilm formation, as well as 5 S almonella p athogenicity i slands (SPIs) including C63PI, SPI-2, SPI-3, SPI-4 and SPI-5. Type Ⅲ secretion system (TTSS) genes ( hil ACD, iac P, iag B, inv ABCEFGHIJ, org ABC, prg HIJK, sic AP, sip D, spa OPQRS and spr B) were located on SPI-1 and TTSS genes ( ssa CDEGHIJKLMNOPQRSTUV, ssc AB, sse ABCDE and ssr AB) were located on SPI-2. A variety of 27 acquired antimicrobial resistance genes (ARGs) was located on the IncHI2-IncHI2A-type plasmid p87912 with 236, 217 bp in size, including bla CTX-M-65, fos A3, mph A, qep A and rmt B interspersed with different insertion sequences and transposons (IS 26, IS 903, IS 6100, IS CR3 and ΔTn2). The co-transfer of bla CTX-M-65, fos A3, mph A, rmt B, and qep A genes and corresponding antibiotic resistance profiles driven by plasmid p87912 occurred. Taken together, these results revealed the genomic characterization of an XDR chicken isolates in S . Indiana, and that the co-existence of numbers of ARGs on plasmid played an important role in XDR profile in S . Indiana isolates. Highlights: An extensively drug-resistant Salmonella Indiana isolate was identified. Genomic islands and Salmonella pathogenicity islands were detected. A total of 27 antimicrobial resistance genes were located on the IncHI2-IncHI2A plasmid. Co-transfer of bla CTX-M-65, fos A3, mph A, rmt B and qep A genes occurred.