Journal article | How was threshold defined? | Cut-off | Sampling fraction | Lineages |
---|---|---|---|---|
Bryant et al. [30] | Own data | ≤6 SNPs relapse (same strain); >1,306 re-infection (different) | 47 sequenced out of 50 chosen | Four major lineages |
Clark et al. [23] | Unknown | <50 SNPs defined a cluster | Â | CAS, LAM, EAI, T1, T2, Beijing, X1 |
Guerra-Assunção et al. [29] | Own data | ≤10 SNPs relapse; >100 re-infection | 60 out of 139 WGS confirmed recurrences | Four major lineages |
Guerra-Assunção et al. [18] | Own data (transmission); Guerra-Assunção et al. [29] (relapse) | ≤10 SNPs confirmed transmission; ≤10 SNPs defined a relapse | 1,687 out of 2,332 had WGS | Four major lineages |
Kato-Maeda et al. [26] | Own data | 0–2 SNPs per transmission event |  |  |
Lee et al. [17] | Own data | 0–1 SNPs confirmed transmission | 631 ‘improbable’ transmission pairs—between outbreak cases and cases in other villages | Outbreak isolates were Euro-American lineage |
Luo et al. [16] | Walker et al. [21] | Â | Â | Â |
Roetzer et al. [14] | Own data | 3 SNPs confirmed transmission | 31 out of 2,301 (for the threshold). Equivalent to eight transmission chains of 2–7 patients | Haarlem lineage |
Walker et al. [21] | Own data | ≤5 SNPs cluster; >12 SNPs no transmission | 303 out of 609 (for the threshold) | All five major lineages |
Walker et al. [22] | Own data | 475, 1,032 and 1,096 SNPs suggested that patients had been secondarily infected with a different strain rather than within-host evolution | Pulmonary vs extra pulmonary pairs from 49 patients and 110 longitudinal isolates from 30 patients | All five major lineages |
Witney et al. [19] | Walker et al. [21] | Â | Â | Â |