A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

被引：500

作者：

Coll, Francesc ^{[1
]}

McNerney, Ruth ^{[1
]}

Guerra-Assuncao, Jose Afonso ^{[2
]}

Glynn, Judith R. ^{[2
]}

Perdigao, Joao ^{[3
]}

Viveiros, Miguel ^{[4
]}

Portugal, Isabel ^{[3
]}

Pain, Arnab ^{[5
]}

Martin, Nigel ^{[6
]}

Clark, Taane G. ^{[1
,2
]}

机构：

[1] London Sch Hyg & Trop Med, Fac Infect & Trop Dis, London WC1E 7HT, England

[2] London Sch Hyg & Trop Med, Fac Epidemiol & Populat Hlth, London WC1E 7HT, England

[3] Univ Lisbon, Fac Farm, Ctr Patogenese Mol, P-1649003 Lisbon, Portugal

[4] Univ Nova Lisboa, Inst Higiene & Med Trop, Unidade Microbiol Med, Grp Micobacterias, P-1349008 Lisbon, Portugal

[5] King Abdullah Univ Sci & Technol, Biol & Environm Sci & Engn BESE Div, Thuwal 239556900, Saudi Arabia

[6] Birkbeck Coll, Sch Comp Sci & Informat Syst, London WC1E 7HX, England

来源：

NATURE COMMUNICATIONS | 2014年 / 5卷

基金：

英国惠康基金;

关键词：

DRUG-RESISTANT TUBERCULOSIS; MOLECULAR EPIDEMIOLOGY; POLYMORPHISMS; SPOLIGOTYPES; TRANSMISSION; EVOLUTION; PULMONARY; BACTERIA; ETHIOPIA; LINEAGE;

D O I：

10.1038/ncomms5812

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify similar to 92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the similar to 7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type.

引用

页数：5

共 35 条

[1]

Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method [J].

Abadia, Edgar ;

Zhang, Jian ;

dos Vultos, Tiago ;

Ritacco, Viviana ;

Kremer, Kristin ;

Aktas, Elif ;

Matsumoto, Tomoshige ;

Refregier, Guislaine ;

van Soolingen, Dick ;

Gicquel, Brigitte ;

Sola, Christophe .

INFECTION GENETICS AND EVOLUTION, 2010, 10 (07) :1066-1074

[2]

[Anonymous], 2005, PHYLIP (phylogeny inference package) version 3.6

[3]

The challenges of tuberculosis on antimicrobial resistance [J].

REVISTA DE SAUDE PUBLICA, 2011, 45 (05) :997-1000

[4]

BATES JH, 1969, AM REV RESPIR DIS, V100, P189

[5]

Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade [J].

Blouin, Yann ;

Hauck, Yolande ;

Soler, Charles ;

Fabre, Michel ;

Vong, Rithy ;

Dehan, Celine ;

Cazajous, Geraldine ;

Massoure, Pierre-Laurent ;

Kraemer, Philippe ;

Jenkins, Akinbowale ;

Garnotel, Eric ;

Pourcel, Christine ;

Vergnaud, Gilles .

PLOS ONE, 2012, 7 (12)

[6]

Evolution and transmission of drug-resistant tuberculosis in a Russian population [J].

Casali, Nicola ;

Nikolayevskyy, Vladyslav ;

Balabanova, Yanina ;

Harris, Simon R. ;

Ignatyeva, Olga ;

Kontsevaya, Irina ;

Corander, Jukka ;

Bryant, Josephine ;

Parkhill, Julian ;

Nejentsev, Sergey ;

Horstmann, Rolf D. ;

Brown, Timothy ;

Drobniewski, Francis .

NATURE GENETICS, 2014, 46 (03) :279-+

[7]

The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis [J].

Caws, Maxine ;

Thwaites, Guy ;

Dunstan, Sarah ;

Hawn, Thomas R. ;

Lan, Nguyen Thi Ngoc ;

Thuong, Nguyen Thuy Thuong ;

Stepniewska, Kasia ;

Huyen, Mai Nguyet Thu ;

Bang, Nguyen Duc ;

Loc, Tran Huu ;

Gagneux, Sebastien ;

van Soolingen, Dick ;

Kremer, Kristin ;

van der Sande, Marianne ;

Small, Peter ;

Anh, Phan Thi Hoang ;

Chinh, Nguyen Tran ;

Quy, Hoang Thi ;

Duyen, Nguyen Thi Hong ;

Tho, Dau Quang ;

Hieu, Nguyen T. ;

Torok, Estee ;

Hien, Tran Tinh ;

Dung, Nguyen Huy ;

Nhu, Nguyen Thi Quynh ;

Duy, Phan Minh ;

Chau, Nguyen van Vinh ;

Farrar, Jeremy .

PLOS PATHOGENS, 2008, 4 (03)

[8]

PolyTB: A genomic variation map for Mycobacterium tuberculosis [J].

Coll, Francesc ;

Preston, Mark ;

Guerra-Assuncao, Jose Afonso ;

Hill-Cawthorn, Grant ;

Harris, David ;

Perdigao, Joao ;

Viveiros, Miguel ;

Portugal, Isabel ;

Drobniewski, Francis ;

Gagneux, Sebastien ;

Glynn, Judith R. ;

Pain, Arnab ;

Parkhill, Julian ;

McNerney, Ruth ;

Martin, Nigel ;

Clark, Taane G. .

TUBERCULOSIS, 2014, 94 (03) :346-354

[9]

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences [J].

Coll, Francesc ;

Mallard, Kim ;

Preston, Mark D. ;

Bentley, Stephen ;

Parkhill, Julian ;

McNerney, Ruth ;

Martin, Nigel ;

Clark, Taane G. .

BIOINFORMATICS, 2012, 28 (22) :2991-2993

[10]

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies [J].

Comas, Inaki ;

Homolka, Susanne ;

Niemann, Stefan ;

Gagneux, Sebastien .

PLOS ONE, 2009, 4 (11)

← 1 2 3 4 →