Virulotyping of Salmonella enterica serovar Typhi isolates from Pakistan: Absence of complete SPI-10 in Vi negative isolates

PLoS Negl Trop Dis. 2018 Nov 30;12(11):e0006839. doi: 10.1371/journal.pntd.0006839. eCollection 2018 Nov.

Abstract

The pathogenesis of Salmonella enterica serovar Typhi (S. Typhi), the cause of typhoid fever in humans, is mainly attributed to the acquisition of horizontally acquired DNA elements. Salmonella pathogenicity islands (SPIs) are indubitably the most important form of horizontally acquired DNA with respect to pathogenesis of this bacterium. The insertion or deletion of any of these transferrable SPIs may have impact on the virulence potential of S. Typhi. In this study, the virulence potential and genetic relatedness of 35 S. Typhi isolates, collected from 2004 to 2013 was determined by identification of SPI and non-SPI virulence factors through a combination of techniques including virulotyping, Whole Genome Sequencing (WGS), and Variable Number of Tandem Repeats (VNTR) profiling. In order to determine the virulence potential of local S. Typhi isolates, 56 virulence related genes were studied by PCR. These genes are located in the core as well as accessory genome (SPIs and plasmid). Major variations among studied virulence determinants were found in case of SPI-7 and SPI-10 associated genes. On the basis of presence of virulence related genes, the studied S. Typhi isolates from Pakistan were clustered into two virulotypes Vi-positive and Vi-negative. Interestingly, SPI-7 and SPI-10 were collectively absent or present in Vi-negative and Vi-positive strains, respectively. Two Vi-negative and 11 Vi-positive S. Typhi strains were also analyzed by whole genome sequencing (WGS) and their results supported the PCR results. Genetic diversity was tested by VNTR-based molecular typing. All 35 isolates were clustered into five groups. Overall, all Vi-negative isolates were placed in a single group (T5) whereas Vi-positive isolates were grouped into four types. Vi-negative and Vi-positive isolates were mutually exclusive. This is the first report on the comparative distribution of SPI and non-SPI related virulence genes in Vi-negative and Vi-positive S. Typhi isolates with an important finding that SPI-10 is absent in all Vi-negative isolates.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Genome, Bacterial
  • Genomic Islands*
  • Humans
  • Minisatellite Repeats
  • Pakistan
  • Polysaccharides, Bacterial / genetics
  • Polysaccharides, Bacterial / metabolism*
  • Salmonella typhi / classification
  • Salmonella typhi / genetics
  • Salmonella typhi / isolation & purification*
  • Salmonella typhi / pathogenicity
  • Typhoid Fever / microbiology*
  • Virulence
  • Virulence Factors / genetics

Substances

  • Bacterial Proteins
  • Polysaccharides, Bacterial
  • Virulence Factors
  • capsular polysaccharide, Salmonella

Grants and funding

The Whole Genome Sequencing (WGS) was funded by the Consolider-Ingenio 2010 program of the Spanish Government (CDS 2009-00006), and Innuendo project co-funded by the European Food Safety Agency (EFSA) (GP/EFSA/AFSCO/2015/01/CT2).The rest of the research work was funded by Higher Education Commission of Pakistan (HEC) and Vital Foundation of Vitoria-Gastiez. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.