Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications

Abstract Whole genome sequencing of Mycobacterium tuberculosis offers valuable insights for tuberculosis (TB) control. High throughput platforms like Illumina and Oxford Nanopore Technology (ONT) are increasingly used globally, although ONT is known for higher error rates and is less established for genomic studies. Here we present a study comparing the sequencing outputs of both Illumina and ONT platforms, analysing DNA from 59 clinical isolates in highly endemic tuberculosis regions of Thailand. The resulting 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). Our results revealed predominantly lineages 1 and 2 strain-types, with consistent drug resistance profiles, including six multidrug-resistant strains, however, ONT showed longer phylogenetic branches, emphasising its higher error rate. Analysis incorporating the larger dataset identified fifteen of our samples within six potential transmission clusters, including a significant clade of 41 multi-drug resistant isolates. ONT's extended sequences also revealed strain-specific structural variants in pe/ppe genes ( e.g. ppe50 ), candidates for vaccine development. Despite limitations, ONT sequencing is promising for tuberculosis genomic research, supporting precision medicine and decision-making in areas with less developed infrastructure, crucial for tackling the disease’s significant regional burden.