In PLOS One, researchers from The Netherlands and the United Arab Emirates describe the mixed-genome microarray method they used to characterize more than 200 strains of Legionella pneumophila, the bacterial species behind Legionnaires' disease. Using mixed-genome arrays targeting a few thousand L. pneumophila genome fragments, the group interrogated 222 environmental and clinical L. pneumophila strains collected in The Netherlands. They then used an algorithm to narrow in on four genetic markers that appear to show promise for distinguishing between clinical and environmental L. pneumophila strains. "The identification of these predictive genetic markers could offer the possibility to identify virulence factors within the Legionella genome," the study's authors say, "which in the future may be implemented in the daily practice of controlling Legionella in the public health environment."
Systems approaches that bring together genetic and metabolic data have the potential to identify unknown metabolites, according to a study by researchers based in Germany, Qatar, and the US. As they report in PLOS Genetics, the investigators came up with a systems approach to predict metabolite identities that relies on information from genome-wide association studies, metabolomics analyses, and a method called Gaussian graphical modeling. Using metabolic information and genotyping data from nearly 1,800 human blood samples, for instance, the team found new genotype-metabotype ties involving half a dozen genetic loci. And from the wider association, metabolic pathway, and network patterns, they say, it was possible to predict biochemical features for 106 previously unknown metabolites — nine of which were subsequently verified using experimental methods.
A team from the UK and Tanzania takes a look at the types of trypanosomes circulating in wildlife from two African ecosystems — and the genetic diversity of these parasites—in PLOS Neglected Tropical Diseases. The University of Edinburgh's Susan Welburn and her colleagues collected blood samples from a variety of wildlife species in Serengeti National Park in Tanzania and in Zambia's Luangwa Valley over the course of several years. Through ribosomal gene sequence assessments and phylogenetic analyses, they tracked down representatives from around half a dozen Trypanosoma species, including three forms of T. vivax. In particular, their search unearthed T. vivax sequences in samples from a giraffe and a waterbuck sampled in the Serengeti that contained variants not described in the parasite in the past.