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 within a 20-SNP range, and the phylodynamic model phybreak was employed to infer transmission. Probable transmission SNP cut-offs were assessed by the proportion of inferred transmission events with a SNP distance below these cut-offs. A total of 79 clusters were identified, with a median size of 4 isolates (IQR = 3-8). A SNP cut-off of 4 captured 98% of inferred transmission events while reducing pairs without transmission links. A cut-off beyond 12 SNPs effectively excluded transmission. Phylodynamic approaches provide a valuable alternative to contact tracing for defining SNP cut-offs, allowing for a more precise assessment of transmission events.