Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences

PLoS One. 2017 Aug 31;12(8):e0183925. doi: 10.1371/journal.pone.0183925. eCollection 2017.

Abstract

Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74) and non-pseudintermedius genomes (n = 138). Six sequences specific for S. pseudintermedius were identified (sequence length between 300-500 nt). One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54), and eight other staphylococcal species (n = 43). In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

MeSH terms

  • Animals
  • Base Sequence
  • Cat Diseases / diagnosis
  • Cat Diseases / microbiology
  • Cats
  • DNA Primers / chemical synthesis
  • DNA Primers / chemistry
  • Diagnosis, Differential
  • Dog Diseases / diagnosis
  • Dog Diseases / microbiology
  • Dogs
  • Genome, Bacterial*
  • Humans
  • Phylogeny*
  • Real-Time Polymerase Chain Reaction / methods*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Staphylococcal Infections / diagnosis
  • Staphylococcal Infections / microbiology
  • Staphylococcal Infections / veterinary*
  • Staphylococcus / classification
  • Staphylococcus / genetics*
  • Staphylococcus / isolation & purification
  • Staphylococcus aureus / classification
  • Staphylococcus aureus / genetics
  • Staphylococcus aureus / isolation & purification

Substances

  • DNA Primers

Grants and funding

The authors received no specific funding for this work.