Draft genome of a macrolide resistant XDR Salmonella enterica serovar Paratyphi A strain using a shotgun sequencing approach

A Khatoon; H M T Malik; M Aurongzeb; S A Raza; A Karim

doi:10.1016/j.jgar.2019.09.001

Draft genome of a macrolide resistant XDR Salmonella enterica serovar Paratyphi A strain using a shotgun sequencing approach

J Glob Antimicrob Resist. 2019 Dec:19:129-131. doi: 10.1016/j.jgar.2019.09.001. Epub 2019 Sep 7.

Authors

A Khatoon¹, H M T Malik¹, M Aurongzeb¹, S A Raza¹, A Karim²

Affiliations

¹ Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan.
² Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan; Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France. Electronic address: asad.karim.alvi@gmail.com.

PMID: 31505298
DOI: 10.1016/j.jgar.2019.09.001

Abstract

Objectives: Salmonella enterica serovar Paratyphi A, the causative 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 Salmonella Paratyphi A strain isolated from Karachi, Pakistan.

Methods: Genomic DNA of Salmonella Paratyphi A strain JRCGR-AK14 was sequenced on a MiSeq platform. Read quality was evaluated and paired-end reads were assembled into contigs and scaffolds. The quality of contigs and scaffolds was evaluated and assembled contigs were annotated. Virulence genes, antimicrobial resistance genes (ARGs), tRNAs, rRNAs, coding sequences and clustered regularly interspaced short palindromic repeats (CRISPRs) were identified. ARGs and mutations in quinolone-resistance determining regions (QRDRs) were identified by Antimicrobial Resistance Identification By Assembly (ARIBA) and ResFinder. Known and unknow mutations in the QRDRs were predicted.

Results: The genome of Salmonella Paratyphi A was calculated at 4529866 bp with 4381 genes and 1088 hypothetical proteins. Several putative genes coding for multidrug efflux pumps were identified. In addition, gene mutations conferring resistance to nitrofurantoin (e.g. marA, mdsC, Escherichia coli soxS), pulvomycin (e.g. H-NS, cpxA, E. coli EF-Tu) and fosfomycin (CRP, kdpE, E. coli glpT) were also identified. Several ARGs along with the mobile genetic element transposon Tn10 were also identified. It is evident from the results that diverse redundant mechanisms are involved in regulation of drug resistance in this strain.

Conclusion: The current findings provide valuable data for understanding the multidrug resistance and pathogenic characteristics of clinical Salmonella Paratyphi A isolates.

Keywords: Enteric fever; Macrolide resistance; Multidrug resistance; Salmonella Paratyphi A; Whole-genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adolescent
Clustered Regularly Interspaced Short Palindromic Repeats
Drug Resistance, Bacterial*
Female
Genome, Bacterial
Humans
Macrolides / pharmacology*
Microbial Sensitivity Tests
Mutation
Pakistan
Salmonella paratyphi A / drug effects
Salmonella paratyphi A / genetics*
Salmonella paratyphi A / isolation & purification
Virulence Factors / genetics
Whole Genome Sequencing / methods*

Substances

Macrolides
Virulence Factors