SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil

Abstract

Abstract:Human tuberculosis is an infectious disease caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Although Spoligotyping and MIRU-VNTR are standard methodology in MTBC genetic epidemiology, recent studies suggest that Single Nucleotide Polymorphisms (SNP) are advantageous in phylogenetics and strain identification. In this work we use a set of 79 SNPs to characterize 1915 MTBC isolates from Portugal and 141 from Northeast Brazil. All Brazilian samples and a subset of 111 Portuguese isolates were further characterized using Spolygotyping. Phylogenetic analysis against a reference set revealed that about 95% of the isolates in both populations were singly attributed to bacterial lineage 4. Within this lineage, the most frequent strain groups in both Portugal and Brazil were LAM, followed by Haarlem and then X. Contrarily to these groups, strain group T showed a very different prevalence between Portugal and Brazil, with a frequency of 7% and less than 1.5%, respectively. Taking the classification by SNPs as the most accurate, we analyze the performance of Spoligotyping in strain identification. The former marker shows about 12% of miss-matches and less than 1% of unidentifiable strains. The miss-matches are observed in the most represented groups of our sample set (i.e., LAM, Haarlem and T) in almost the same proportion. Besides being more accurate in strain identification, SNPs typing can also provide phylogenetic relationships between the strain groups. Indeed, using this molecular markers we were able to observe possible signs of rare recombination events in Mtb.Overall, the use of SNP typing revealed striking similarities between MTBC populations from Portugal and Brazil. In addition this marker suggest that, albeit rare, recombination events in MTBC are likely to occur.

Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production

“…A large predominance of the MTBC L4 and of sublineage L4.3/LAM was revealed within the pathogen population ( Fig. 1e), in line with other reports focused in Europe 14,15 . The pathogen population structure was replicated across the different TB severity groups (Fig.…”

Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

“…tuberculosis isolates, a total of 17119 (80.8%) strains belonged to lineage 4 (Euro-American) according to spoligotyping [ 56 ] ( Table 1 ). This widely predominant lineage supports the hypothesis of a European dissemination from either early settlement or trade associations [ 8 – 10 ]. Among the lineage 4 strains, a total of 6386 (30.1%) belonged to the LAM lineage; 4843 (22.9%) belonged to the T lineage; 3699 (17.5%) belonged to the H (Haarlem) lineage; 1564 (7.4%) belonged to the X lineage; 1163 belonged to the EAI lineage; 1105 belonged to the Beijing lineage; 497 (2.3%) belonged to the S lineage; 162 (0.8%) belonged to the CAS lineage; 102 (0.5%) belonged to the MANU lineage; 94 (0.4%) belonged to the AFRI lineage; 67 (0.3%) belonged to the Cameroon lineage and 63 (0.3%) belonged to the URAL lineage.…”

“…The M . tuberculosis strains currently circulating in Americas were brought by Europeans with the Euro-American lineage 4 being the most predominant [ 8 ], highlighting past and present European colonial and cultural influence on the current TB situation [ 9 , 10 ]. Among the large and heterogeneous lineage 4, the Latin American Mediterranean (LAM) family was first suggested based on the phylogenetic analysis of a large spoligotyping dataset and its name reflects the strains’ origin [ 11 ].…”

Strain Classification of Mycobacterium tuberculosis Isolates in Brazil Based on Genotypes Obtained by Spoligotyping, Mycobacterial Interspersed Repetitive Unit Typing and the Presence of Large Sequence and Single Nucleotide Polymorphism

“…Indeed, several authors have suggested that SNPs are more suitable than spoligotyping and MIRU-VNTR settings for phylogenetic classification [16] , [38] , [53] , [54] , [55] , [56] . The fbpC 103 is described as a good marker for the LAM family [7] , [38] , [49] , [57] , [58] , [59] , and our original intention was to evaluate if strains RD Rio was still prevalent in Rio de Janeiro as seen previously by Lazzarini in clinical isolates collected between 2002 and 2003 [2] , for this purpose we believed only a marker that could differentiate LAM and non-LAM associated with the 24 MIRU-VNTR and Spoligotyping could be sufficient, however the scenario was observed more complex.…”