Novel single nucleotide polymorphism-based assay for genotyping Mycobacterium avium subsp. paratuberculosis

Leão, C., Goldstone, R. J., Bryant, J., McLuckie, J., Inácio, J., Smith, D. G.E. and Stevenson, K. (2016) Novel single nucleotide polymorphism-based assay for genotyping Mycobacterium avium subsp. paratuberculosis. Journal of Clinical Microbiology, 54(3), pp. 556-564. (doi: 10.1128/jcm.01958-15) (PMID:26677250)

Abstract

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates.

• Item Type: Articles
• Additional Information: Scottish Government Rural and Environmental Science and Analytical Services Division provided funding to Karen Stevenson. Fundação para a Ciência e a Tecnologia provided funding to Célia Leão under grant number SFRH/BD/62469/2009.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Smith, Professor David and Goldstone, Mr Robert
• Authors: Leão, C., Goldstone, R. J., Bryant, J., McLuckie, J., Inácio, J., Smith, D. G.E., and Stevenson, K.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Journal of Clinical Microbiology
• Publisher: American Society for Microbiology
• ISSN: 0095-1137
• ISSN (Online): 1098-660X
• Published Online: 16 December 2015
• Copyright Holders: Copyright © 2016 American Society for Microbiology
• First Published: First published in Journal of Clinical Microbiology 54(3): 556-564
• Publisher Policy: Reproduced in accordance with the publisher copyright policy