TY - JOUR
T1 - SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil
AU - Lopes, João S.
AU - Marques, Isabel
AU - Soares, Patricia
AU - Nebenzahl-Guimaraes, Hanna
AU - Costa, Joao
AU - Miranda, Anabela
AU - Duarte, Raquel
AU - Alves, Adriana
AU - Macedo, Rita
AU - Duarte, Tonya A.
AU - Barbosa, Theolis
AU - Oliveira, Martha
AU - Nery, Joilda S.
AU - Boechat, Neio
AU - Pereira, Susan M.
AU - Barreto, Mauricio L.
AU - Pereira-Leal, José
AU - Gomes, Maria Gabriela Miranda
AU - Penha-Goncalves, Carlos
N1 - Funding Information:
We thank two anonymous reviewers and editor for thoughtful comments which raise the quality of the original manuscript. The work was funded by the Portuguese Foundation for Science and Technology (FCT) and by the European Commission [grant EC-ICT-231807 ]. Data collection in Brazil was supported by National Counsel of Technological and Scientific Development (CNPQ) [Project Number 410498/2006-8 ] and Coordination of Improvement of Higher Education Personnel (CAPES) [Project Number 23038.005107/2011-83 ].
Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013/8
Y1 - 2013/8
N2 - Human tuberculosis is an infectious disease caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Although spoligotyping and MIRU-VNTR are standard methodologies in MTBC genetic epidemiology, recent studies suggest that Single Nucleotide Polymorphisms (SNP) are advantageous in phylogenetics and strain group/lineages identification. In this work we use a set of 79 SNPs to characterize 1987 MTBC isolates from Portugal and 141 from Northeast Brazil. All Brazilian samples were further characterized using spolygotyping. Phylogenetic analysis against a reference set revealed that about 95% of the isolates in both populations are singly attributed to bacterial lineage 4. Within this lineage, the most frequent strain groups in both Portugal and Brazil are LAM, followed by Haarlem and X. Contrary to these groups, strain group T showed a very different prevalence between Portugal (10%) and Brazil (1.5%). Spoligotype identification shows about 10% of mis-matches compared to the use of SNPs and a little more than 1% of strains unidentifiability. The mis-matches are observed in the most represented groups of our sample set (i.e., LAM and Haarlem) in almost the same proportion. Besides being more accurate in identifying strain groups/lineages, SNP-typing can also provide phylogenetic relationships between strain groups/lineages and, thus, indicate cases showing phylogenetic incongruence.Overall, the use of SNP-typing revealed striking similarities between MTBC populations from Portugal and Brazil.
AB - Human tuberculosis is an infectious disease caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Although spoligotyping and MIRU-VNTR are standard methodologies in MTBC genetic epidemiology, recent studies suggest that Single Nucleotide Polymorphisms (SNP) are advantageous in phylogenetics and strain group/lineages identification. In this work we use a set of 79 SNPs to characterize 1987 MTBC isolates from Portugal and 141 from Northeast Brazil. All Brazilian samples were further characterized using spolygotyping. Phylogenetic analysis against a reference set revealed that about 95% of the isolates in both populations are singly attributed to bacterial lineage 4. Within this lineage, the most frequent strain groups in both Portugal and Brazil are LAM, followed by Haarlem and X. Contrary to these groups, strain group T showed a very different prevalence between Portugal (10%) and Brazil (1.5%). Spoligotype identification shows about 10% of mis-matches compared to the use of SNPs and a little more than 1% of strains unidentifiability. The mis-matches are observed in the most represented groups of our sample set (i.e., LAM and Haarlem) in almost the same proportion. Besides being more accurate in identifying strain groups/lineages, SNP-typing can also provide phylogenetic relationships between strain groups/lineages and, thus, indicate cases showing phylogenetic incongruence.Overall, the use of SNP-typing revealed striking similarities between MTBC populations from Portugal and Brazil.
KW - Brazil
KW - Mycobacterium tuberculosis complex
KW - Phylogeny
KW - Portugal
KW - SNP-typing
KW - Spoligotyping
UR - http://www.scopus.com/inward/record.url?scp=84879517694&partnerID=8YFLogxK
U2 - 10.1016/j.meegid.2013.04.028
DO - 10.1016/j.meegid.2013.04.028
M3 - Article
C2 - 23648425
AN - SCOPUS:84879517694
SN - 1567-1348
VL - 18
SP - 238
EP - 246
JO - Infection, Genetics and Evolution
JF - Infection, Genetics and Evolution
ER -