1887

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Volume 67, Issue 2

Rapid discrimination of genotypes in a routine clinical microbiological laboratory using single nucleotide polymorphisms in housekeeping genes Free

Abstract

colonies often display several morphologies and antimicrobial susceptibility patterns when cultured from device-related infections, and may represent one or multiple genotypes. Genotyping may be helpful in the clinical interpretation, but is time consuming and expensive. We wanted to establish a method for rapid discrimination of genotypes for use in a routine microbiology laboratory.

A real-time PCR targeting eight discriminatory class I or II single-nucleotide polymorphisms (SNPs) in six of the seven housekeeping genes was constructed. Post PCR, high-resolution melt (HRM) analysis using EvaGreen as fluorophore discriminated amplicons based on their percentage GC content.

, 42 representative sequence types (STs), including all major MLST group and subgroup founders, were separated into 23 different cluster profiles with a Simpson’s index of diversity of 0.97. By HRM-PCR, 11 commonly encountered hospital and outbreak STs were separated into eight HRM patterns.

This method can rapidly establish whether strains belong to different genotypes. It can be used in patients with infections, as an aid in outbreak investigations and to select strains for investigation with more discriminatory methods, saving workload and costs. Results may be obtained the same day as culture results. Its strength lies mainly in indicating differences, as some STs may have the same melt profile. Changes in epidemiology may warrant alterations in the inclusion of SNPs. We believe this method can reduce the threshold for performing genotyping analysis on an increasingly important nosocomial pathogen.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): clinical routine , HRM-PCR , rapid genotyping , S. epidermidis , sequence types and single nucleotide polymorphisms
© 2018 The Authors
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2018-02-01
2024-04-24
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Rapid discrimination of Staphylococcus epidermidis genotypes in a routine clinical microbiological laboratory using single nucleotide polymorphisms in housekeeping genes
J. Med. Microbiol. 67, 169 (2018); https://doi.org/10.1099/jmm.0.000663
/content/journal/jmm/10.1099/jmm.0.000663
/content/journal/jmm/10.1099/jmm.0.000663
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