In PLOS Genetics, researchers from Italy, Spain, and California share exome sequence data from a preconception carrier screening program involving infertile patients or gamete donors. The team focused on 8,280 infertile individuals with no known family history of infertility from couples undergoing in vitro fertilization, along with 5,845 sperm or egg donors. Along with insights into IVF couples who may be at increased risk of conditions with reproductive risks, the authors analyzed genes with ties to high penetrance childhood-onset conditions, uncovering risky fetal variants in roughly one in every 300 pregnancies. Based on these and other findings, they argued that "the use of exome sequencing and parallel gene testing is clinically effective and feasible for preconception carrier screening after proper validation and translational research has been carried out."
For a paper appearing in PLOS One, Michigan State University-led team presents findings from its comparative genomics-based analyses of Elizabethkingia meningoseptica, a normally harmless environmental bacterial species that can cause pneumonia, meningitis, and other infections in immune-compromised individuals. Using whole-genome sequencing, the researchers assessed three clinical isolates of E. meningoseptica from patients at a Michigan hospital, comparing them to one another and to sequences from other strains or Elizabethkingia species sequenced in the past. The analyses, along with antibiotic screening results, highlighted dozens of genes involved in everything from E. meningoseptica virulence and antibiotic resistance to adaptation and biofilm formation, they report.
A team from Denmark, Kenya, and the US describes results from a metagenomics-centered pathogen surveillance program in Nairobi, Kenya, for another PLOS One study. The researchers did metagenomic DNA and RNA sequencing on sewage samples collected over time from drainage ditches in an informal urban settlement called Kibera, searching for sequence reads that might signal the presence of pathogenic bacteria, viruses, or parasites, particularly those carrying antimicrobial resistance genes. In the process, they saw shifts in the presence of pathogenic microbes and parasites such as Giardia, Plasmodium, and Ascaris species over time, which were considered alongside resistance gene reads and the diarrhea, fever, or other symptoms reported at local clinics. "This work represents a proof of concept study and suggests that metagenomics have a high surveillance sensitivity," the authors conclude, "and may as such become a valuable supplement for clinical and syndromic surveillance of large, urban populations."