Contextualizing Mycobacterium tuberculosis Genetic Diversity in Portugal using MIRU-VNTR Data

Abstract

Tuberculosis (TB) is an ancient and highly contagious disease caused by a pathogenic bacterium called Mycobacterium tuberculosis (Mtb). Mtb causes pulmonary or extrapulmonary bacterial infections, which can lead to an excess mortality or morbidity. TB has high transmissibility, making it a Public Health priority worldwide. This study aimed to develop better understanding of transmission dynamics of Mtb based on genotypic data analysis using Mycobacterial Interspersed Repetitive Units - Variable Number Tandem Repeats (MIRU-VNTR). Published data from all over the world were collected to establish a database and new data from Portugal was also included. The initial data were screened to ensure the removal of any ambiguous data, followed by genotypic and phylogenetic analyses to understand transmission dynamics and genetic links of the Mtb isolates worldwide. Analysis of genetic diversity based on each one of 24 MIRU-VNTR showed that loci 4052, 2531, and 2996 had the most genetic diversity whereas loci 2687, 154, and 580 had the lowest genetic diversity, providing almost no discriminatory value in the phylogenetic reconstruction. A distance tree was generated which showed no geographic clustering of Mtb genotypes. In order to contextualize genetic and transmission diversity of Mtb genotypes in Portugal, median-joining phylogenetic and phylogeographic networks were used. Phylogenetic analysis showed large clusters of Latin American and Mediterranean (LAM), Haarlem and Beijing lineages in Portugal. Phylogeographic median-joining network analysis showed 10 major clusters exclusive to Portugal indicating that the majority of TB cases in Portugal were indigenous. A small number of clusters in Portugal were related with Europe, Americas, and Africa, however, their closer proximity on the network to the Portugal genotype indicated less genetic diversity among the Mtb strains. Presence of Mtb genotypes from regions such as Americas, Asia and Oceania indicated the role of migrants in Mtb transmission, however that was a small percentage of cases. Overall analysis showed 43% clustered cases in Portugal with a direct transmission rate of 33%. The genetic information used for the establishment and characterisation of transmission routes of infection, coupled with the epidemiological characterisation of the population affected by TB can prove essential to eliminate this disease.