TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data

TL;DR

This paper introduces TBpore, a new bioinformatics pipeline for studying tuberculosis transmission using nanopore sequencing data, and compares it with traditional methods.

Contribution

TBpore is a novel pipeline validated for clustering TB isolates using nanopore sequencing data, showing potential increased sensitivity over existing methods.

Findings

TBpore and Illumina sequencing showed high concordance in clustering TB isolates from two outbreaks.

Nanopore sequencing produced lower pairwise SNP distances within outbreaks compared to Illumina.

All isolates from the M. africanum outbreak clustered within defined thresholds, consistent with MIRU-VNTR and epidemiological data.

Abstract

Molecular typing of Mycobacterium tuberculosis complex isolates enhances understanding of tuberculosis (TB) transmission dynamics, supporting public health efforts in outbreak investigations. This study aims to validate TBpore, a novel bioinformatic pipeline for clustering TB transmission isolates using Oxford Nanopore Technology (ONT) data and comparing it against conventional Mycobacterial Interspersed Repetitive-Unit Variable Number (MIRU-VNTR) typing and Illumina sequencing.

This retrospective case-control study included 58 clinical isolates from two TB outbreaks in Canada, previously characterized by public health investigations and MIRU-VNTR typing. DNA extraction and sequencing were performed on both Illumina and ONT platforms. Illumina data were processed using Clockwork and psdm, while Nanopore data were analyzed with TBpore. SNP distances were used to compare clustering results across methods, with clusters defined by SNP distance thresholds of ≤5 and ≤12. Both sequencing methods showed a high degree of concordance in clustering results. All isolates from the M. africanum outbreak clustered within the defined SNP thresholds, consistent with MIRU-VNTR and epidemiological data. In the M. tuberculosis outbreak, 20 out of 21 isolates clustered similarly across methods, with one exception. Within outbreak pairwise SNP distances were lower with Nanopore.

ONT sequencing and the TBpore pipeline offer an accurate alternative to Illumina technology for TB molecular epidemiology. This study suggests potential increased clustering sensitivity with Nanopore technology, warranting further validation on larger datasets with robust epidemiological metadata.

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