Posted: Nov 11, 2023
Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.
Jody E Phelan et al. Genome Med 2023 11 (1) 96
From the abstract: "Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data. "
Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.
Madikay Senghore et al. Nat Commun 2023 11 (1) 6397
From the abstract: "In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. "
A machine learning classifier using 33 host immune response mRNAs accurately distinguishes viral and non-viral acute respiratory illnesses in nasal swab samples.
Rushika Pandya et al. Genome Med 2023 8 (1) 64
From the abstract: "Viral acute respiratory illnesses (viral ARIs) contribute significantly to human morbidity and mortality worldwide, but their successful treatment requires timely diagnosis of viral etiology, which is complicated by overlap in clinical presentation with the non-viral ARIs. Multiple pandemics in the twenty-first century to date have further highlighted the unmet need for effective monitoring of clinically relevant emerging viruses. Recent studies have identified conserved host response to viral infections in the blood."
AMD Days 2023
From the website: "CDC OAMD and APHL have co-sponsored AMD day, AMD 2-day, Virtual AMD-days, and now AMD days since 2016. This symposium began as an opportunity for OAMD funded CDC projects to be shared and presented. It has evolved to be an opportunity for state and local public health laboratories, CDC laboratories to present their work, network, and hear from leaders in the field. We are excited to bring back AMD-days! This event will be held September 12-14, 2023 at the CDC Roybal Campus in Atlanta, GA."