Genetic Characterization of Colistin-Resistant Salmonella enterica ST34 Co-Harbouring Plasmid-Borne mcr-1, bla(CTX-M-15) and bla(KPC-2) Recovered from a Paediatric Patient in Shenzhen, China

BACKGROUND: Since 2015, plasmid-borne mcr-1 has been reported in various bacterial strains in the clinical setting globally. However, the transmission mechanisms of this gene in Salmonella are not well defined. This study aimed to characterize the genomic features of a Salmonella enterica ST34 isolate, which carried a mcr-1, mapped to a carbapenemase and extended spectrum β-lactamase encoding gene located on the IncX4 plasmid. METHODS: Salmonella enterica was recovered from a diarrheal paediatric patient in Shenzhen, China. Antimicrobial susceptibility testing was performed by using the VITEK 2 system. Drug resistance genes were identified using targeted primers and Sanger sequencing. The transferability and genome location of mcr-1 was determined by performing conjugation, S1-PFGE and Southern blot hybridization analysis. WGS was performed by Illumina MiSeq sequencing and was assembled using the A5-Miseq pipeline, and gene annotation was performed using RAST 2.0. The database Centre for Genomic Epidemiology’s website was used to identify resistance genes and sequence types (STs). RESULTS: We found that the isolate was extensively drug resistant and belonging to ST34, carrying an IncX4 plasmid with mcr-1, bla(KPC-2) and bla(CTX-M-15.) We also noticed that genes bla(PAO), fosA, catB, the mutation in oprD and mexT (MexEF-OprN efflux regulator), and exotoxin-encoding genes (exoS, exoY and exoT) were associated with resistance and virulence in the genome. In addition, heavy metal resistance genes as silP and silE were determined. CONCLUSION: This study highlights the potential risk of ST34 of Salmonella enterica serotype Typhimurium carrying multiple drug resistance encoding genes in a single IncX4 plasmid.