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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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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Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Authors: Alves A, Coll F, Guerra-Assunção JA, Hill-Cawthorne G, Mallard K, McNerney R, Miranda A, Nair M, Preston MD, Viveiros M, Warry A
Publication Year: 2015
Journal: Genome Medicine
Link: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0164-0

Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using […]
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Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

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