Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

Authors: Clark T, Coll F, Couto I, Hill-Cawthorne GA, Jordao L, Macedo R, Machado D, Mallard K, Maltez F, McNerney R, Pain A, Perdigão J, Portugal I, Silva C, Silva H, Viveiros M
Publication Year: 2015
Journal: International Journal of Mycobacteriology
Link: https://www.sciencedirect.com/science/article/pii/S2212553115000254

Multidrug- (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidence rate and unusual and successful XDR-TB strains that have been found in circulation for almost two decades. For the last 20 years, a continued circulation of two phylogenetic clades, Lisboa3 and […]
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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

Authors: Clark TG, da Silva PA, Dalla Costa ER, Esteves LS, Gomes HM, Gomes LL, McNerney R, Pain A, Perdigão J, Portugal I, Rastogi N, Rossetti ML, Suffys PN, Unis G, Vasconcelos SE, Viveiros M
Publication Year: 2015
Link: http://jcm.asm.org/content/53/12/3805.full%20

We recently detected the spoligotype patterns of strains of Mycobacterium pinnipedii, a species of the Mycobacterium tuberculosis complex, in sputum samples from nine cases with pulmonary tuberculosis residing in Porto Alegre, South Brazil. Because this species is rarely encountered in humans, we further characterized these nine isolates by additional genotyping techniques, including 24-locus mycobacterial interspersed […]
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Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

Authors: Alves A, Anthony RM, Bergval I, Bessa TB, Campino S, Clark TG, Coll F, Crampin AC, de Oliveira Sousa E, Dheda K, Gey van Pittius NC, Glynn JR, Grandjean L, Hasan R, Hasan Z, Hibberd ML, McNerney R, Miranda A, Moore D, Pain A, Panaiotov S, Perdigão J, Phelan JE, Portugal I, Sampson SL, Sheen P, Streicher EM, van Helden PD, Viveiros M, Warren R
Publication Year: 2016
Journal: BMC Genomics
Link: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2467-y

Background Approximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised […]
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The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

Authors: Campino S, Clark TG, Dheda K, Huggett JF, Machado D, McNerney R, O'Grady J, O'Sullivan DM, Phelan J, Ramos J, Viveiros M, Whale AS
Publication Year: 2016
Journal: Genome Medicine
Link: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0385-x

The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resistance in Mycobacterium tuberculosis to aid treatment decisions. However, there are few little data regarding the precision of such sequencing for assigning resistance profiles.
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A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Authors: Clark TG, Coll F, Glynn JR, Guerra-Assunção JA, Martin N, McNerney R, Pain A, Perdigão J, Portugal I, Viveiros M
Publication Year: 2014
Journal: Nature Communications
Link: http://www.nature.com/ncomms/2014/140901/ncomms5812/full/ncomms5812.html

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes.
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Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

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

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

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