In PLOS Genetics, a team led by University of Melbourne investigators considers population structure for malaria-causing Plasmodium falciparum parasites from almost two-dozen sites in 10 countries in Africa, South America, Asia, and Oceania, focusing on genes coding for variant surface antigens (VSA) such as PfEMP1. Using a bioinformatic method for analyzing genes that code for PfEMP1 and other members of the same gene family, the researchers not only got a look at Plasmodium evolution, but also demonstrated the possibility of teasing out P. falciparum parasite population structure within Africa and beyond. "The important outcome of our work was the ability to identify geographic signatures specific to countries and continents that were consistent with the 'out of Africa' origin of P. falciparum," they report, noting that "[w]e can now identify malaria parasites from countries within Africa, South America, and Asia/Oceania using a diverse region of VS genes without having to sequence and assemble whole parasite genomes."
For a paper appearing in PLOS Neglected Tropical Diseases, researchers at QIMR Berghofer Medical Research Institute and elsewhere propose a non-invasive qPCR assay for diagnosing scabies, a parasitic skin infection caused by the Sarcoptes scabiei itch mite. Starting with the S. scabiei draft genome, the team came up with PCR-based assays targeting two distinct repetitive DNA elements in the parasite genome. After assessing the sensitivity and specificity of the qPCR assay approach using swab samples or DNA from an individual mite, the authors applied the approach to skin scrape or swab samples from 12 individuals with scabies or 19 patients with unrelated skin infections. "Targeting [repetitive DNA] elements by PCR improved the detection of scabies DNA," they report, noting that the strategy showed favorable sensitivity compared to microscopy-based mite detection and to another PCR assay reported in the past.
A University of Wisconsin at Madison-led team takes a genomics- and metabolomics-based look at contributors to lower urinary tract symptoms in aging men for a paper in PLOS One. Using metagenomic sequencing, liquid chromatography-tandem mass spectrometry, and other approaches, the researchers did microbiome profiling, viral searches, and metabolomic profiling on urine samples from 29 men with lower urinary tract symptoms and nine unaffected controls, identifying a human polyomavirus known as JC virus (JCV) that appeared to be over-represented in samples from the affected individuals. While the JCV association did not hold up in follow-up experiments done using more sensitive PCR-based testing on dozens more individuals, the authors saw hints that the presence of the virus may coincide with altered microbial communities and metabolite profiles in the urine, suggesting that it may "merit further investigation" in lower urinary tract cases or other conditions.