Utilizing whole genome sequencing to delineate relapse and reinfection tuberculosis on the Canadian prairies

Figures & data

Figure 1. Phylogenetic tree scale.

Unrooted tree scale that measures genetic distance between 50 genomes comprised of 22 pairs and two triplets. Genomes are listed by CaseNo., episode and lineage. The horizontal axis shows the scale representing the number of single nucleotide polymorphism (SNP)s divided by the sequence length; 0.100 is equivalent to 10%. CaseNo. 1, 9, 11, 14, 20, 24 (all episode 2) and 11 (episode 3) had SNPs >160 whose final tree scale positions were different from Episode 1 and 2. They were all lineage 4. The horizontal final position can also be obtained from Online Supplementary Table S1.

Figure 2. Distribution of reported tuberculosis (TB) cases 1989–2018.

Shows the distribution for all reported TB cases 1989 to 2018 by step to the number of sequenced cases. A total of 67 culture positive recurrent pairs were not sequenced because they could not be found or could not be reconstituted, 26 pairs were sequenced and 67 pairs were not sequenced.

Table 1. Paired SNP matrix for 26 recurrent TB cases.

	Case	1	2	3	4	4	5	6	7	8	9	10	11	11	12	13	14	15	16	17	18	19	20	21	22	23	24
Case	Epis	1	1	1	1	2	1	1	1	1	1	1	1	2	1	1	1	1	1	1	1	1	1	1	1	1	1
1	2	1116
2	2		4
3	2			2
4	2				1
4	3				8	9
5	2						4
6	2							0
7	2								0
8	2									2
9	2										612
10	2											1
11	2												603
11	3												44	607
12	2														0
13	2															5
14	2																161
15	2																	1
16	2																		24
17	2																			0
18	2																				25
19	2																					6
20	2																						570
21	2																							1
22	2																								2
23	2																									2
24	2																										695

Abbreviations: SNP, single nucleotide polymorphism. CaseNo. episodes 2 and 3 are listed on the vertical axis and episodes 1 and 2 are listed on the horizontal axis. SNP is obtained at the intersection of CaseNo. episode 1 on the horizontal axis and episode 2 on the vertical axis. The bold CaseNo. are for SNPs >160. Seven cases were classified reinfection.

Table 2. Paired phylogenetic TIP difference matrix for 26 recurrent TB cases.

	Case	1	2	3	4	4	5	6	7	8	9	10	11	11	12	13	14	15	16	17	18	19	20	21	22	23	24
Case	Epis	1	1	1	1	2	1	1	1	1	1	1	1	2	1	1	1	1	1	1	1	1	1	1	1	1	1
1	2	.007
2	2		.000
3	2			.000
4	2				.000
4	3				.001	.001
5	2						.001
6	2							.000
7	2								.000
8	2									.000
9	2										.004
10	2											.000
11	2												.003
11	3												.001	.002
12	2														.000
13	2															.001
14	2																.004
15	2																	.000
16	2																		.000
17	2																			.000
18	2																				.000
19	2																					.001
20	2																						.006
21	2																							.000
22	2																								.000
23	2																									.001
24	2																										.003

Abbreviations: TIP, phylogenetic tree scale differences; TB, tuberculosis. CaseNo. episodes 2 and 3 are listed on the vertical axis and episodes 1 and 2 are listed on the horizontal axis. TIP difference is obtained at the intersection of CaseNo. episode 1 on the horizontal axis and episode 2 on the vertical axis. The bold CaseNo. are for TIPs > .001. Seven cases were classified reinfection.

Table 3. Determining relapse and reinfection combining SNPs and TIPs.

Table 4. Reinfection risk score.

Table 5. Epidemiological and clinical comparison of relapse and reinfection cases.

Parameter	Relapse	Reinfection	p value	Test
Number	19	7
Age Mean (SD)	53.2 (19.9)	38.6 (14.8)	.107	Mann-Whitney
Sex
Female	9	4	1.000	Fisher’s Exact
Male	10	3
Pop Group
Foreign-born	12	1	<.05	Fisher’s Exact
Indigenous	6	6
Non-Indigenous	1	0
Diagnosis Year
1989–2003	5	1	1.000	Fisher’s Exact
2004–2018	14	6
Comm TB Rate
High	3	5	<.05	Fisher’s Exact
Low	16	2
Lineage
1–3	8	0	<.05	Fisher’s Exact
4	11	7
Contacts
Yes	2	4	<.05	Fisher’s Exact
No	16	3
Unknown	1	0
Episode Interval
Mean (SD)	5.1 (5.1)	9.12 (8.2)	.094	Mann-Whitney
Site
EPTB	3	0	.540	Fisher’s Exact
PTB	16	7
Reinfect Score
≤1	15	2	<.05	Fisher’s Exact
>1	4	5

Abbreviations: SD, standard deviation; TB, tuberculosis; EPTB, extrapulmonary TB; PTB, pulmonary TB; SNP, single nucleotide polymorphism; TIP, phylogenetic tree scale differences. The table compares epidemiological and clinical parameters by SNP and TIP delineation using the Fisher’s exact and Mann-Whitney tests. SNPs ≤ 25 and TIPs ≤ .001 were considered relapse and SNPs > 160 and TIP > .001 were considered reinfection. Relapse and reinfection numbers were obtained from episode 2 and 3 for 26 sequenced pairs. Reinfection parameters that were significant for reinfection were Indigenous persons, living in high TB incidence community, lineage 4, history of TB contact, and clinical reinfection risk score >1.