Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://doi.org/10.1128/JCM.01958-15 |
Resumo: | 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 wholegenome 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 largescale global typing of Mycobacterium avium subspecies paratuberculosis isolates. |
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Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. ParatuberculosisMicrobiology (medical)GeneticsInfectious DiseasesSDG 3 - Good Health and Well-beingTyping 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 wholegenome 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 largescale global typing of Mycobacterium avium subspecies paratuberculosis isolates.Instituto de Higiene e Medicina Tropical (IHMT)RUNLeão, CéliaGoldstone, Robert J.Bryant, JosephineMcLuckie, JoyceInácio, JoãoSmith, David G EStevenson, Karen2018-05-11T22:06:04Z2016-03-012016-03-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article9application/pdfhttps://doi.org/10.1128/JCM.01958-15eng0095-1137PURE: 2452260http://www.scopus.com/inward/record.url?scp=84959566952&partnerID=8YFLogxKhttps://doi.org/10.1128/JCM.01958-15info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:20:08Zoai:run.unl.pt:10362/36637Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:30:36.399880Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
title |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
spellingShingle |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis Leão, Célia Microbiology (medical) Genetics Infectious Diseases SDG 3 - Good Health and Well-being |
title_short |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
title_full |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
title_fullStr |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
title_full_unstemmed |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
title_sort |
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. Paratuberculosis |
author |
Leão, Célia |
author_facet |
Leão, Célia Goldstone, Robert J. Bryant, Josephine McLuckie, Joyce Inácio, João Smith, David G E Stevenson, Karen |
author_role |
author |
author2 |
Goldstone, Robert J. Bryant, Josephine McLuckie, Joyce Inácio, João Smith, David G E Stevenson, Karen |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Instituto de Higiene e Medicina Tropical (IHMT) RUN |
dc.contributor.author.fl_str_mv |
Leão, Célia Goldstone, Robert J. Bryant, Josephine McLuckie, Joyce Inácio, João Smith, David G E Stevenson, Karen |
dc.subject.por.fl_str_mv |
Microbiology (medical) Genetics Infectious Diseases SDG 3 - Good Health and Well-being |
topic |
Microbiology (medical) Genetics Infectious Diseases SDG 3 - Good Health and Well-being |
description |
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 wholegenome 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 largescale global typing of Mycobacterium avium subspecies paratuberculosis isolates. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-03-01 2016-03-01T00:00:00Z 2018-05-11T22:06:04Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.1128/JCM.01958-15 |
url |
https://doi.org/10.1128/JCM.01958-15 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
0095-1137 PURE: 2452260 http://www.scopus.com/inward/record.url?scp=84959566952&partnerID=8YFLogxK https://doi.org/10.1128/JCM.01958-15 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
9 application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799137929884336128 |