Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

Authors: Phelan JE, O’Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino L, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG
Publication Year: 2019
Journal: Genome Medicine
Link: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0650-x

Background Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis settings. To support this informatically, previous work led to the development of the widely used TBProfiler webtool, which predicts resistance to 14 drugs from WGS data. However, for […]
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Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Authors: Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG
Publication Year: 2018
Journal: BMC Genomics
Link: https://www.ncbi.nlm.nih.gov/pubmed/30107785

Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and […]
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Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Authors: Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG
Publication Year: 2018
Journal: Nature Genetics
Link: https://www.nature.com/articles/s41588-017-0029-0%20

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, […]
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Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally

Authors: Phelan J, De Sessions PF, Tientcheu L, Perdigão J, Machado D, Hasan R, Hasan Z, Bergval I, Anthony R, McNerney R, Antonio M, Portugal I, Viveiros M, Campino S, Hibberd ML, Clark TG
Publication Year: 2018
Journal: Scientific Reports
Link: https://www.nature.com/articles/s41598-017-18188-y%20

DNA methylation is an epigenetic modification of the genome involved in regulating crucial cellular processes, including transcription and chromosome stability. Advances in PacBio sequencing technologies can be used to robustly reveal methylation sites. The methylome of the Mycobacterium tuberculosis complex is poorly understood but may be involved in virulence, hypoxic survival and the emergence of […]
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Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries

Authors: Perdigão J, Silva C, Diniz J, Pereira C, Machado D, Ramos J, Silva H, Abilleira F, Brum C, Reis AJ, Macedo M, Scaini JL, Silva AB, Esteves L, Macedo R, Maltez F, Clemente S, Coelho E, Viegas S, Rabna P, Rodrigues A, Taveira N, Jordao L, Kritski A, Lapa e Silva JR, Mokrousov I, Couvin D, Rastogi N, Couto I, Pain A, McNerney R, Clark TG, von Groll A, Dalla Costa ER, Rossetti ML, Silva PEA, Viveiros M, Portugal I
Publication Year: 2019
Journal: Infection Genetics and Evolution
Link: https://www.sciencedirect.com/science/article/pii/S1567134818301023?via%3Dihub%20

Tuberculosis (TB) remains a major health problem within the Community of Portuguese Language Speaking Countries (CPLP). Despite the marked variation in TB incidence across its member-states and continued human migratory flux between countries, a considerable gap in the knowledge on the Mycobacterium tuberculosis population structure and strain circulation between the countries still exists. To address […]
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Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries

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