Phylodynamic assessment of SNP distances from whole genome sequencing for determining Mycobacterium tuberculosis transmission.

ABSTRACT: The global tuberculosis (TB) epidemic is driven by primary transmission. Pathogen genome sequencing is increasingly used in molecular epidemiology and outbreak investigations. Based on contact tracing and epidemiological links, Single Nucleotide Polymorphism (SNP) cut-offs, ranging from 3 to 12 SNPs, identify probable transmission clusters or exclude direct transmission. However, contact tracing can be limited by recall bias and inconsistent methodologies across TB settings. We propose phylodynamic models, i.e. methods to infer transmission processes from pathogen genomes and associated epidemiological data, as an alternative reference to infer transmission events. We analyzed 2,008 whole-genome sequences from Dutch TB patients collected from 2015 to 2019. Genetic clusters were defined wit

SUBMITTER: Van der Roest BR 

PROVIDER: S-EPMC11953417 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature