TABLE 2.

Use of whole-genome sequencing in TB outbreak investigations and to understand microevolution of M. tuberculosis

Study focus and period	Location	No. of WGS isolates	Genome coverage (%)	No. of SNVsa	Sequencerb	Major finding(s)	Reference
Studies on transmission of TB
2001–2004	Uzbekistan	2	95.9	1,209c	Illumina	Showed that isolates with identical IS6110 patterns differed by 130 SNVs	69
1992–2008	Netherlands	3	95.4	8c	Roche/454	Discovered that SNVs can be used to identify transmission chains in RFLP clusters	70
2006–2009	Canada	36	99.2	204	Illumina	Integration of WGS with a social network questionnaire generated a more accurate transmission network; used WGS to identify “superspreader” cases	62
2010	UK	2	95	0	Illumina	Outbreak identification with WGS; showed the utility of WGS to identify drug resistance markers	78
1994–2011	UK	390	88.5	1,096	Illumina	Rate of genetic changes was 0.5 SNV/genome/year; used WGS to identify “superspreader” cases	63
1997–2010	Germany	86	96.4	85	Roche/454	WGS was proven to be more effective at generating clustering patterns than classical genotyping methods; used WGS to estimate a rate of genetic change of 0.4 SNV/genome/year	71
22 mo	USA	9	95.7	7c	Illumina	WGS allowed the identification of new epidemiological links in the transmission chain; used WGS to characterize a mutation rate of 0–2 SNVs/transmission event resulting in a secondary case	72
2007–2012	UK	256	92.6	1,715	Illumina	Patients born in low-incidence countries are more likely to have pulmonary disease and social risk factors, causing secondary cases in the UK	79
1992–2008	Netherlands	199	95.6	11,879	Roche/454	Estimated an average mutation rate of 0.3 SNV/genome/year, with a large degree of variation, i.e., 0.4–17 SNVs/genome/year	88
2009–2010	China	32	ND	1,790	Illumina	Evaluated the usefulness of WGS in a high-incidence country	73
1991–2011	Switzerland	69	98.3	133	Illumina	WGS suggested a single origin for an outbreak involving 68 patients over 21 years that could be divided into 3 subclusters with epidemiological links differing by 0–11 SNVs	76
2008–2011	Canada	33	ND	21	Illumina	WGS revealed within-host diversity in an index case; a computational method was developed to infer transmission from phylogenetic data, accounting for within-host diversity	80
Not specified	Canada	36	ND	3,523	Illumina	WGS of M. tuberculosis strains belonging to the Manila sublineage showed better resolution than that of MIRU-VNTR assay and decreased the frequency of clustered cases	74
1997–2013	Canada	61	ND	722	Illumina	WGS revealed 6 subclusters of the 17-year outbreak showing unique patterns of evolution	75
Studies on microevolution of M. tuberculosis
1994–2011	UK	390	88.5	1,096	Illumina	Defined epidemiologically linked transmission events by using SNV cutoffs of <5 SNVs for transmission and >12 SNVs for no evidence of transmission; intrapatient variation was limited to <5 SNVs; rate of genetic changes was 0.5 SNV/genome/year	63
2003–2010	Spain	36	98	28	Illumina	Examined inter- and intrapatient variations and determined them to be equivalent	89
2008	Malaysia, South Africa, Thailand	96	ND	1,419	Illumina	Showed that WGS can be used to discriminate between relapse and reinfection	86
1990–2010	New Zealand	10	98	747	SOLiD	Used WGS to show that mutation rates during latent infection in humans are substantially lower than those during active disease	93

^aND, not defined in the report.

^bThe Illumina, Roche/454, and SOLiD platforms all represent short-read sequencing-by-synthesis platforms and are reviewed in reference 18. Newer technologies, such as nanopore-based sequencing or the PacBio platform, have also been applied to microbial genomics but have yet to be used in a TB study.

^cSNVs were verified by secondary Sanger sequencing.