The draft genome of a macrolide resistant XDR Salmonella Paratyphi A strain using a shotgun sequencing approach

Abstract Objectives Salmonella Paratyphi A (S. Paratyphi A), the potent pathogen of enteric fever is a major public health concern affecting millions of people around the world. We conducted whole-genome sequencing and analysis of a novel macrolide resistant S. Paratyphi A in Pakistan. Method The genomic DNA of S. Paratyphi A was sequenced on MiSeq platform. The quality of output read were evaluated and assembled into contigs and scaffolds. The quality of contigs and scaffolds were evaluated and assembled contigs were annotated. Virulence genes, drug resistance genes, tRNA, rRNA, CDSs and clustered regularly interspaced short palindromic repeats (CRISPRs) were identified. Resistance genes identified were identified by Resfinder, Antimicrobial Resistance Identification By Assembly (ARIBA) and quinolone-resistance determining regions (QRDR). Known as well as unknow mutation were predicted in the quinolone-resistance determining regions (QRDR). Results The genome of S. Paratyphi A was calculated at 4529866 bp with 4381 genes and 1088 hypothetical proteins. Several putative genes that codes for multidrug efflux pumps were identified. In addition, genes mutations conferring resistance to nitrofurantoin (e.g., marA, mdsC, E. coli soxS, mdsC), Pulvomycin (e.g., h-ns, cpxA, E. coli EF-Tu) and fosfomycin (CRP, kdpE, E. coli GlpT) were also identified. Several antibiotic resistance genes along with mobile element transposon Tn10 were also identified. It is evident from the results that diverse redundant mechanism is involved in regulation of drug tolerance in this strain. Conclusions The current findings provide valuable data for understanding the multidrug resistance and pathogenic characteristics of Salmonella Paratyphi A in medicine.