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Minim typing - a rapid and low cost MLST based typing tool for Klebsiella pneumoniae

Andersson, Patiyan, Tong, Steven Y. C., Bell, Jan M., Turnidge, John D. and Giffard, Philip M. (2012). Minim typing - a rapid and low cost MLST based typing tool for Klebsiella pneumoniae. PLoS One,7(3):e33530-1-e33530-7.

Document type: Journal Article
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IRMA ID cmartelxPUB12
Title Minim typing - a rapid and low cost MLST based typing tool for Klebsiella pneumoniae
Author Andersson, Patiyan
Tong, Steven Y. C.
Bell, Jan M.
Turnidge, John D.
Giffard, Philip M.
Journal Name PLoS One
Publication Date 2012
Volume Number 7
Issue Number 3
ISSN 1932-6203   (check CDU catalogue  open catalogue search in new window)
Scopus ID 2-s2.0-84858054024
Start Page e33530-1
End Page e33530-7
Total Pages 7
Place of Publication United States
Publisher Public Library of Science
HERDC Category C1 - Journal Article (DIISR)
Abstract Here we report a single nucleotide polymorphism (SNP) based genotyping method for Klebsiella pneumoniae utilising high-resolution melting (HRM) analysis of fragments within the multilocus sequence typing (MLST) loci. The approach is termed mini-MLST or Minim typing and it has previously been applied to Streptococcus pyogenes, Staphylococcus aureus and Enterococcus faecium. Six SNPs were derived from concatenated MLST sequences on the basis of maximisation of the Simpsons Index of Diversity (D). DNA fragments incorporating these SNPs and predicted to be suitable for HRM analysis were designed. Using the assumption that HRM alleles are defined by G+C content, Minim typing using six fragments was predicted to provide a D = 0.979 against known STs. The method was tested against 202 K. pneumoniae using a blinded approach in which the MLST analyses were performed after the HRM analyses. The HRM-based alleles were indeed in accordance with G+C content, and the Minim typing identified known STs and flagged new STs. The tonB MLST locus was determined to be very diverse, and the two Minim fragments located herein contribute greatly to the resolving power. However these fragments are refractory to amplification in a minority of isolates. Therefore, we assessed the performance of two additional formats: one using only the four fragments located outside the tonB gene (D = 0.929), and the other using HRM data from these four fragments in conjunction with sequencing of the tonB MLST fragment (D = 0.995). The HRM assays were developed on the Rotorgene 6000, and the method was shown to also be robust on the LightCycler 480, allowing a 384-well high through-put format. The assay provides rapid, robust and low-cost typing with fully portable results that can directly be related to current MLST data. Minim typing in combination with molecular screening for antibiotic resistance markers can be a powerful surveillance tool kit.

DOI http://dx.doi.org/10.1371/journal.pone.0033530   (check subscription with CDU E-Gateway service for CDU Staff and Students  check subscription with CDU E-Gateway in new window)


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