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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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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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

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

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