Table 1 Studies using SNP thresholds to confirm recent transmission, relapse versus re-infection or microevolution versus mixed infection

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

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]

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]