Genomic characterization of an extensively drug-resistant chicken-borne Salmonella Indiana isolate carrying an IncHI2-IncHI2A plasmid

The recent emergence of extensively drug-resistant (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 genomic islands (GIs) encoding proteins for phage, type IV secretion, DNA repair, and biofilm formation, as well as 5 Salmonella pathogenicity islands (SPIs) including C63PI, SPI-2, SPI-3, SPI-4 and SPI-5. Type Ⅲ secretion system (TTSS) genes (hilACD, iacP, iagB, invABCEFGHIJ, orgABC, prgHIJK, sicAP, sipD, spaOPQRS and sprB) were located on SPI-1 and TTSS genes (ssaCDEGHIJKLMNOPQRSTUV, sscAB, sseABCDE and ssrAB) 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 blaCTX-M-65, fosA3, mphA, qepA and rmtB interspersed with different insertion sequences and transposons (IS26, IS903, IS6100, ISCR3 and ΔTn2). The co-transfer of blaCTX-M-65, fosA3, mphA, rmtB, and qepA 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.