Whole-genome sequencing – lessons for public health surveillance

Genomic sequencing has proven vital in detecting the source and variants of COVID-19, improving contact tracing, reducing disease transmission and ensuring health security for Australia. But genomic sequencing isn’t new and researchers from the NHMRC Centre of Digital Health (CRE) have been investigating it’s use in cases from public surveillance of Salmonella Typhimurium, predicting antibiotic

Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, Shamout F; CRyPTIC Consortium, Zhu T, Clifton DA. DeepAMR for predicting co-occurent resistance of Mycobacterium tuberculosis. Bioinformatics 2019;35(18):3240-3249.

Motivation: Resistance co-occurrence within first-line anti-tuberculosis (TB) drugs is a common phenomenon. Existing methods based on genetic data analysis of Mycobacterium tuberculosis (MTB) have been able to predict resistance of MTB to individual drugs, but have not considered the resistance co-occurrence and cannot capture latent structure of genomic data that corresponds to lineages. Results: We