RT Journal Article SR Electronic T1 The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology JF bioRxiv FD Cold Spring Harbor Laboratory SP 302232 DO 10.1101/302232 A1 Conor J Meehan A1 Pieter Moris A1 Thomas A. Kohl A1 Jūlija Pečerska A1 Suriya Akter A1 Matthias Merker A1 Christian Utpatel A1 Patrick Beckert A1 Florian Gehre A1 Pauline Lempens A1 Tanja Stadler A1 Michel K. Kaswa A1 Denise Kühnert A1 Stefan Niemann A1 Bouke C de Jong YR 2018 UL http://biorxiv.org/content/early/2018/04/16/302232.abstract AB Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple approaches exist for detecting recent transmission chains, usually by clustering strains based on the similarity of their genotyping results. However, each method gives varying estimates of transmission cluster sizes and inferring when transmission events within these clusters occurred is almost impossible. This study combines whole genome sequence (WGS) data derived from a high endemic setting with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Our results suggest that clusters based on spoligotyping could encompass transmission events that occurred hundreds of years prior to sampling while 24-loci-MIRU-VNTR often represented decades of transmission. Instead, WGS based genotyping applying a low SNP thresholds allows for estimation of recent transmission events. These findings can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period.