title: SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil.
abstract: 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.
authors: Instituto Gulbenkian de Ciencia, 2781-901 Oeiras, Portugal. sollari.lopes@gmail.com
authors: Joao S
authors: JS
authors: Lopes
authors: Isabel
authors: I
authors: Marques
authors: Patricia
authors: P
authors: Soares
authors: Hanna
authors: H
authors: Nebenzahl-Guimaraes
authors: Joao
authors: J
authors: Costa
authors: Anabela
authors: A
authors: Miranda
authors: Raquel
authors: R
authors: Duarte
authors: Adriana
authors: A
authors: Alves
authors: Rita
authors: R
authors: Macedo
authors: Tonya A
authors: TA
authors: Duarte
authors: Theolis
authors: T
authors: Barbosa
authors: Martha
authors: M
authors: Oliveira
authors: Joilda S
authors: JS
authors: Nery
authors: Neio
authors: N
authors: Boechat
authors: Susan M
authors: SM
authors: Pereira
authors: Mauricio L
authors: ML
authors: Barreto
authors: Jose
authors: J
authors: Pereira-Leal
authors: Maria Gabriela Miranda
authors: MG
authors: Gomes
authors: Carlos
authors: C
authors: Penha-Goncalves
mesh_terms: D001938:Brazil / Q000453:epidemiology; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D006801:Humans; D017720:Molecular Epidemiology; D058889:Molecular Typing; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011174:Portugal / Q000453:epidemiology; D014376:Tuberculosis / Q000453:epidemiology* / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic
keywords: Brazil; Mycobacterium tuberculosis complex; Phylogeny; Portugal; SNP-typing; Spoligotyping