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This Week in PLOS: Feb 18, 2013

Whole-genome sequencing provides refined resolution for tuberculosis tracking compared with conventional methods based on strain typing, according to a PLOS Medicine study. Researchers from Germany and France did whole-genome sequencing on 86 Mycobacterium tuberculosis isolates from a German TB outbreak, which occurred in the midst of a prospective epidemiological survey spanning more than a decade. With the genome sequence data, they tracked down 85 SNPs that proved useful for finding clusters of isolates and following the course of the outbreak, which started with the emergence a so-called Hamburg clone in the early- to mid-1990s, followed by its expansion in 1998, and subsequently spread to a nearby state called Schleswig-Holstein. "Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997," authors of the study conclude, "shortly before the discovery of the outbreak through epidemiological surveillance."

Our sister publication, GenomeWeb Daily News, has more on the study here.

A new PLOS Pathogens study by French researchers suggests that an enzyme in the pneumonia-causing pathogenic bacterial species called Streptococcus pneumoniae allows for the effective exchange of pathogenicity islands by protecting newly acquired foreign DNA from degradation. Through a series of transformation, gene replacements, and other experiments in S. pneumoniae, the group found that this methylating enzyme — known as DpnA — contributes to pathogenicity island exchange by guarding internalized transforming single-stranded DNA, saving such sequences from degradation via S. pneumoniae restriction-modification systems that defend the bugs from possible bacteriophages. "This finding is the first evidence for a mechanism that actively promotes genetic diversity of S. pneumoniae through programmed protection and integration of foreign DNA," the team explains.

Members of the Genographic Consortium present evidence for prehistoric gene flow from Siberia into populations in Europe's North East in PLOS Genetics. Clio Der Sarkissian, with the University of Adelaide's Australian Centre for Ancient DNA, and colleagues from Australia, Russia, and Germany determined the mitochondrial genotypes for 34 ancient individuals from 3,500-to-7,500 year old archeological sites in northwest Russia. Based on their analyses of mitochondrial sequence profiles in these samples and in present-day populations, the researchers identified a shift in mitochondrial lineages present in Northeastern Europe. Whereas hunter-gatherer-like mitochondrial lineages were predominant into the Mesolithic period, they reported, there seems to have been a rise in mitochondrial sequences from populations in central or eastern Siberia during the Early Metal Age, followed by the introduction of additional sequences from Western Europe.