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

Whole genome sequencing (WGS) 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 TB regions of Thailand. The resulting sequence data were used to profile the M. tuberculosis pairs for their lineage, drug resistance and presence in transmission chains, and were compared to publicly available WGS data from Thailand (n = 1456). Our results revealed isolates that are predominantly from lineages 1 and 2, with consistent drug resistance profiles, including six multidrug-resistant strains; however, analysis of ONT data showed longer phylogenetic branches, emphasising the technologies higher error rate. An 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), which are candidate loci for vaccine development. Despite some limitations, our results show that ONT sequencing is a promising approach for TB genomic research, supporting precision medicine and decision-making in areas with less developed infrastructure, which is crucial for tackling the disease's significant regional burden.

A rapidly fatal case of Panton-valentine leukocidin positive Staphylococcus aureus necrotizing pneumonia in an HIV-infected patient

This article reports a rare case of necrotizing pneumonia caused by Panton-Valentine leukocidin (PVL) positive Staphylococcus aureus in an HIV-infected patient presenting with severe back pain and rash. The back pain progressed to excruciating abdominal pain which was misleading, resulting in an investigation on intraabdominal conditions. He developed massive hemoptysis and died within 2 days of the first clinical symptoms. Recognizing the emergence of PVL-producing S. aureus is important in both immunocompetent and immunocompromised patients. This organism was transmitted from his wife.