Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

Autor: Bryant JM; Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. j.bryant@ucl.ac.uk.; Division of Infection and Immunity, University College London, London, UK. j.bryant@ucl.ac.uk., Thibault VC; Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. virginie.c.thibault@gmail.com., Smith DG; Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. David.G.E.Smith@moredun.ac.uk.; Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8QQ, UK. David.G.E.Smith@moredun.ac.uk., McLuckie J; Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. joyce.mcluckie@moredun.ac.uk., Heron I; Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. ianheron23@hotmail.com., Sevilla IA; Neiker-tecnalia, Dpto. de Producción y Sanidad Animal, Berreaga 1, 48160, Derio, Bizkaia, Spain. isevilla@neiker.net., Biet F; INRA, UMR1282, Infectiologie Santé Publique (ISP-311), F-37380, Nouzilly, France. Franck.Biet@tours.inra.fr., Harris SR; Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. sh16@sanger.ac.uk., Maskell DJ; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. djm47@cam.ac.uk., Bentley SD; Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. sdb@sanger.ac.uk., Parkhill J; Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK. Parkhill@sanger.ac.uk., Stevenson K; Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK. karen.stevenson@moredun.ac.uk.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2016 Jan 26; Vol. 17, pp. 79. Date of Electronic Publication: 2016 Jan 26.
DOI: 10.1186/s12864-015-2234-5
Abstrakt: Background: Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne's disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods.
Results: Single nucleotide polymorphism (SNP) and phylogenetic analyses confirmed two major lineages concordant with the former Type S and Type C designations. The Type I and Type III strain groups are subtypes of Type S, and Type B strains are a subtype of Type C and not restricted to Bison species. We found that the genome-wide SNPs detected provided greater resolution between isolates than currently employed genotyping methods. Furthermore, the SNP used for IS1311 typing is not informative, as it is likely to have occurred after Type S and C strains diverged and does not assign all strains to the correct lineage. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) differentiates Type S from Type C but provides limited resolution between isolates within these lineages and the polymorphisms detected do not necessarily accurately reflect the phylogenetic relationships between strains. WGS of passaged strains and coalescent analysis of the collection revealed a very high level of genetic stability, with the substitution rate estimated to be less than 0.5 SNPs per genome per year.
Conclusions: This study clarifies the phylogenetic relationships between the previously described Map strain groups, and highlights the limitations of current genotyping techniques. Map isolates exhibit restricted genetic diversity and a substitution rate consistent with a monomorphic pathogen. WGS provides the ultimate level of resolution for differentiation between strains. However, WGS alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections.
Databáze: MEDLINE
Externí odkaz: