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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Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

Authors: Beraldi D, Blaxter M, Borges S, Cravo P, Creasey A, Fawcett R, Hunt P, Kumar S, Loewe L, Martinelli A, Modrzynska K, Otto TD, Pain A, Rodrigues L, Thomson M, Trivedi U
Journal: BMC Genomics
Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Experimental+evolution%2C+genetic+analysis+and+genome+re-sequencing+reveal+the+mutation+conferring+artemisinin+resistance+in+an+isogenic+lineage+of+malaria+parasites

BACKGROUND: Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic […]
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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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A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

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

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