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PLOS Papers on Methylation, Cystic Fibrosis Pathogen, Salmonella Surveillance Sequencing Cost

In PLOS Genetics, investigators from the University of Exeter Medical School, the University of Queensland, and elsewhere present findings from a DNA methylation analysis focused on several blood cell types and epithelial cell samples. The team performed array-based profiling on DNA methylation (DNAm) profiling on buccal epithelial swab, nasal swab, and whole blood samples from 30 individuals from identical or non-identical twin pairs from the Environmental Risk Longitudinal Twin Study, along with cell-sorted monocyte, granulocyte, CD4+ T cell, CD8+ T cell, or B cell types from the participants' blood samples. "Our results enabled us to assess the extent to which variable DNAm in each individual blood cell type relates to variation measured in whole blood," the authors report. "We found that although individual blood cell types predict more of the variation in DNAm in whole blood compared to buccal and nasal epithelial cells, the actual proportion of variance explained is relatively small, except for at sites where DNAm is under genetic control."

A Belgian-led team shares results from a genomic analysis of Burkholderia multivorans isolates for a paper in PLOS Pathogens. With short- and long-read sequence reads, antibiotic resistance profiles, and other data, the investigators focused on 13 isolates from an endemic environmental strain found in four individuals treated at pediatric cystic fibrosis centers in Belgium over a decade. Their results hinted at relatively low within-patient adaptive evolution, despite genetic differences in isolates from one patient to the next. "Our study shows limited within-patient B. multivorans evolution and high between-patient strain diversity, indicating that an environmental micro-diverse reservoir must be present for this endemic strain, in which active diversification is taking place," they write, noting that "the specific genomic background of a given strain may dictate the route of adaptation within the cystic fibrosis lung."

For a paper in PLOS One, researchers at the Australian National University and other centers explore cost-effectiveness of whole-genome sequencing (WGS), as compared to pulse field gel electrophoresis-based serotyping, multi-locus variable-number tandem repeat analysis (MLVA), or PCR testing, for foodborne disease surveillance involving non-typhoidal Salmonella enterica. Using test cost, culturing, clinical, and other data for Salmonella cases caught or prevented in Australia in 2018, the team found that serotyping was cheaper per isolate than MLVA or sequencing, though WGS appears cost-effective when it catches enough non-Typhimurium Salmonella infections annually. "WGS data needs to prevent approximately 2 percent of all notifications currently serotyped, or approximately 10 percent of all notifications if they were only tested through PCR to be cost-equal to current testing and typing methods and PCR, respectively," the authors write, noting that WGS "could also significantly reduce costs in prolonged outbreaks where the data helps public health officials to implement interventions earlier."

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