Comparing WGS MTB samples from Thailand with separate technologies to discover whether ONT is comparable to Illumina data

Whole genome sequencing of Mycobacterium tuberculosis can provide insights into the control of tuberculosis (TB), including through informing surveillance activities, transmission investigations, and clinical and treatment decision making in the presence of drug resistance. High throughput Illumina and portable Oxford Nanopore Technology (ONT) sequencing platforms are being rolled out in Southeast Asia for such applications, but the latter is known to have a higher error rate and is less established for genomics-based investigations. Methods: DNA from 59 clinical isolates from highly endemic TB regions of Thailand were sequenced on both long-read ONT and short-read Illumina platforms. The sequence data were used to profile the M. tuberculosis for their strain-type, drug resistance and presence in transmission chains, and compared to publicly available whole genome sequences from Thailand (n=1,456). Findings: Both Illumina and ONT platforms led to replicates with identical drug resistance profiles (6 multidrug resistant), which were positioned together on a phylogenetic tree, but the lengths of branches for ONT data are longer, indicative of a higher error rate. A combined analysis with 1,456 Thailand isolates revealed that fifteen of the study samples were part of six potential transmission clusters (based on <= 20 mutations difference), including a large clade consisting of 41 multi-drug resistant isolates. Further, the longer ONT sequences revealed strain-specific structural variants, including in highly variable pe/ppe genes (e.g., ppe50), which are potential TB vaccine candidates. Interpretation: ONT sequencing is a highly promising tool for TB genomic investigations in Southeast Asia, particularly for precision medicine, and can inform clinical and surveillance decision making in high burden settings with less well-established laboratory infrastructure.