Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

Abstract

BackgroundMultidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades.ResultsIn the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM).The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation.ConclusionsGlobally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-991) contains supplementary material, which is available to authorized users.

Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil

“…Because of the size of this insertion and its possible putative influence on the structure of the beta polymerase unit (unpublished data), we expected to observe compensatory mutations in either rpoA or rpoC, as described recently in M. tuberculosis strains (37,54,55). Surprisingly, we did not observe any non-synonymous mutations in the rpoA and rpoC regions covered by our sequencing approach, and this might mean that (i) the duplication does not interfere with the biological function of the polymerase, which seems unlikely due to the size of the duplication; (ii) unknown and undescribed compensatory mutations are present in other regions of the genome; or (iii) this is a recent evolutionary event for which no compensatory mutation has yet been acquired and is fixed in the population that contains the clinical isolate.…”

Tuberculose Multirresistente por Estirpes da Família Beijing, em Doentes de Lisboa, Portugal: Estudo Preliminar

“…Tal como já anteriormente demonstrado 36,40,41 no presente estudo, a maioria de estirpes de M. tuberculosis em doentes com TB MR e TB ER da área de Lisboa pertence à família Lisboa (71,2% de 104 estirpes). Apenas 4,8% (n = 5) foram identificadas como pertencendo à família Beijing, apenas depois de 2009.…”

“…Apenas 4,8% (n = 5) foram identificadas como pertencendo à família Beijing, apenas depois de 2009. Embora o objectivo do estudo não fosse o de avaliar a prevalência desta família, entre a população da região de Lisboa com TB MR e TB ER, é certo que a sua importância real na epidemia é maior, se tivermos em linha de conta a sua identificação nesta região, desde 1999, e as prevalências já referidas em algumas publicações [41][42][43] e o facto da técnica de spoligotyping só ter sido utilizada no nosso estudo, de forma sustentada, a partir de 2009. O método de spoligotyping, introduzido em 1997, se bem que com menor capacidade discriminativa quando comparado com o RFLP-IS6110 e com a tipagem por MIRU-VNTR, é particularmente útil para a identificação das famílias Beijing, LAM, Haarlem, CAS e de outras estirpes e linhagens de M. tuberculosis, tendo emergido, como um método alternativo, rápido, sensível e custo-eficaz, que pode ser usado directamente na amostra, sem necessitar de cultura.…”

“…[36][37][38][39] Um estudo de 2010, por exemplo, apontava para que mais de 50% das estirpes ER, a circular em Lisboa, pertencesse a esta família e, ainda, num outro estudo mais recente, demonstrou-se que a família Lisboa continua a ser dominante, propagando-se há mais de 20 anos. 40,41 Em paralelo, alguns estudos referem a identificação de estirpes da família Beijing, entre os casos de TB MR e de TB ER de Lisboa, com prevalências inferiores a 2,5%, mas, até à data, nenhum caracterizou os doentes infectados por esta família, no que diz respeito à epidemiologia, à clínica e à evolução.…”

A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics

“…Sequencing of 56 TB genomes from Lisbon, Portugal, a city with high MDR rates, demonstrated the potential of genomics for identifying MTBC lineages responsible for local trends in drug-resistant TB (94). WGS-based insights into the emergence of drug resistance and the order in which mutations arise might provide a barometer for evaluating a region's resistance trends.…”