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

Authors: Clark TG, 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: 2014
Journal: BMC Genomics
Link: http://www.biomedcentral.com/1471-2164/15/991

Multidrug- (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.
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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

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

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