A novel broadly applicable PCR-RFLP method for rapid identification and subtyping of H58 Salmonella Typhi

J Microbiol Methods. 2016 Aug:127:219-223. doi: 10.1016/j.mimet.2016.06.018. Epub 2016 Jun 16.

Abstract

Salmonella Typhi (S. Typhi), the human-adapted agent of typhoid fever, is genetically monomorphic. SNPs accumulation divided the S. Typhi population in 85 haplotypes (H) of which one, H58, has undergone a clonal expansion. The surveillance of H58 S. Typhi is particularly important, especially in areas where typhoid fever is endemic. We developed a simple PCR and PCR-RFLP method to detect and subtype H58 S. Typhi based on the presence of genomic deletion and specific SNPs. The method was validated against 39 S. Typhi isolates of known haplotype, showing 100% of specificity and high sensitivity, and then used to screen a collection of 99 S. Typhi from Asia, demonstrating a high incidence of H58 S. Typhi in Jordan and India. Our method is designed to be applied in all laboratories with basic molecular biology equipment and few financial resources and allows the surveillance of H58 S. Typhi in resource poor settings.

Keywords: H58 identification; PCR-RFLP; Phylogenetic tree; S. Typhi; SNPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Typing Techniques / methods*
  • DNA, Bacterial / genetics
  • Genotype
  • Haplotypes
  • Humans
  • Polymerase Chain Reaction / methods*
  • Polymorphism, Restriction Fragment Length*
  • Polymorphism, Single Nucleotide*
  • Salmonella typhi / classification*
  • Salmonella typhi / genetics
  • Salmonella typhi / isolation & purification*
  • Sensitivity and Specificity
  • Typhoid Fever / microbiology

Substances

  • DNA, Bacterial