First genome of a mcr-9-mediated colistin-resistant Salmonella Typhimurium from Brazilian livestock.

OBJECTIVE To investigate the genetic context of colistin resistance in a mcr-9-harboring Salmonella Typhimurium ST19 strain from swine in Brazil. METHODS Colistin-resistance was determined by minimum inhibitory concentration (MIC) by means of broth microdilution method. Whole genome sequencing was performed in Illumina MiSeq, followed by de novo genome assembly using SPAdes 1.13.1. The draft genome sequence was annotated in Prokka using KBase online server. Download analyses for resistome and plasmid detection were performed using tools available at the Center for Genomic Epidemiology (CGE). The strain was typed in silico using MLST 2.0. We also performed a phylogenetic analysis involving other 24 genomes of S. Typhimurium ST19 and mcr-9-harboring S. Typhimurium isolated from humans, livestock, and foodstuff in different regions. RESULTS The assembly of the draft genome resulted in 5,245 protein-coding sequences, 14 rRNAs, 83 tRNAs, and a GC content of 51.81 %. The strain was identified as S. Typhimuirium ST19 harboring a 265.5 kbp pN1566-2 plasmid carryingthe genes encoding for resistance against colistin (mcr-9.1), aminoglycoside (aadA1), tetracycline (tet(C)), and sulfonamide (sul1). Our findings indicate that the S. Typhimurium ST19 strain in this study showed low genetic variability as compared with S. Typhimurium ST19 isolated from swine and poultry in Brazil, and less related to those reported in other countries. CONCLUSION This is the first genome of a phenotypically colistin-resistant S. Typhimurium harboring the mcr-9 variant in Brazilian livestock. This genome will serve global investigations on epidemiological and evolutionary aspects of plasmid-mediated colistin resistance and the role of colistin-resistant S. Typhimurium ST19lineage as a zoonotic pathogen.