Draft genome of clinical isolate Salmonella enterica Typhimurium ms204 from Odisha, India, reveals multi drug resistance and decreased virulent gene expression

• Published in: Gene Vol. 863; p. 147248
• Main Authors: Kumar Panda, Rakesh, Darshana Patra, Saumya, Kumar Mohakud, Nirmal, Ranjan Sahu, Bikash, Ghosh, Mrinmoy, Misra, Namrata, Suar, Mrutyunjay
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 05-05-2023
• Subjects: Anti-Bacterial Agents; Antimicrobial Resistance Genes; Bacterial Proteins - genetics; Drug Resistance, Multiple; Drug Resistance, Multiple, Bacterial - genetics; Gastroenteritis; Gene Expression; Humans; Pathogenicity islands; Phylogeny; Resistance islands; RNA, Ribosomal, 16S; Salmonella enterica - genetics; Salmonella enterica Typhimurium; Salmonella typhimurium - genetics; ORF; TTD; Gastroenteritis; VFDB; Resistance islands; HQ; DAVID; TCDB; NTS; SPI; EASE; LPS; CARD; CDS; NCBI; KEGG; T3SS; MDR; PHASTER; BLAST; SIGI; Antimicrobial Resistance Genes; NDARO; tRNA; rRNA; SPAdes; AMR; GO; AAI; TSI; qRT; RGI; Pathogenicity islands; RAST; LB; PATRIC; REI; Salmonella enterica Typhimurium; PAI; STRING; ANI; XLT4
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2023.147248

•Genome length of MDR Salmonella Typhimurium was found as 5034110 bp size consisting of 37 contigs.•A total of 12 prophage regions was identified in the genome draft of MDR S. Typhimurium.•Genome analysis revealed identification of several virulent genes and genes encoding antimicrobial resistance.•Genes encoding SPI1 and SPI2 of the MDR bacteria were found to be highly conserved across other S. Typhimurium strains.•Study on virulent gene expression indicates a significant downregulation of SPI2 encoded genes.
Salmonellosis, a food-borne illnesses caused by enteropathogenic bacterium Salmonella spp., is a continuous concern in both developed and developing countries. This study was carried out to perform an in-depth examination of an MDR Salmonella strain isolated from gastroenteritis patients in Odisha, India, in order to understand the genomic architecture, distribution of pathogenic island regions, and virulence factor diversity. Fecal samples were obtained from individuals with acute gastroenteritis and further subjected to panel of biochemical tests. The IlluminaHiSeq X sequencer system was used to generate whole-genome sequencing. The draft genome was submitted to gene prediction and annotation using RAST annotation system. Pathogenicity Island database and bioinformatics pipeline were used to find Salmonella pathogenicity islands (SPI) from the built scaffold. The gene expression in SPI1 and SPI2 encoded regions was investigated using qRT-PCR. The taxonomic position of Salmonella enterica subsp. enterica serovar Typhimurium was validated by serotype analysis and 16S rRNA based phylogenetic analysis. The de-novo genome assembly showed total length of 5,034,110 bp and produced 37 contigs. There are nine prophage areas, comprising of 12 regions and scaffold 8 contained a single plasmid, IncFIB. The isolate contains six known SPI genes content which was shown to be largely conserved from SPI1 to SPI2. We identified the sit ABCD cluster regulatory cascade and acquired antibiotic resistance genes in S. enterica Typhimurium ms204. Further research may aid in the correct diagnosis and monitoring of MDR Salmonella strains with a variety of physiological activities.