Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction
Kayzad Nilgiriwala, Marie Sylvianne Rabodoarivelo, Michael B. Hall, Grishma Patel, Ayan Mandal, Shefali Mishra, Fanantenana Randria Andrianomanana, Kate E. Dingle, Gillian Rodger, Sophie George, Derrick W. Crook, Sarah Hoosdally, Nerges Mistry, Niaina Rakotosamimanana, Zamin Iqbal, Simon Grandjean Lapierre, A Sarah Walker
Abstract
0.01). No significant differences in sensitivity and specificity of drug susceptibility predictions were seen across sequencing modalities or within each technology when stratified by smear grade. Illumina sequencing from sputum accurately identified 1/8 (rifampin) and 6/12 (isoniazid) resistant samples, compared to 2/3 (rifampin) and 3/6 (isoniazid) accurately identified with Nanopore monoplex. Lineage agreement levels between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina), and 100% (MinION-multiplex). M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.