Whole-Genome Sequencing and Epidemiological Investigation of Tuberculosis Outbreaks in High Schools in Hunan, China

Figures & data

Table 1 The Status of Contact Survey of Tuberculosis Outbreaks in Three Schools

	Index Case						No. of First Round Screening in Class and Dormitory of the Index Case	Putative Attack Rate in the Class* n (%)	No. of Expanding Screening in the Same Floor^#	Putative Attack Rate of Expanding Screening n (%)	P value (Putative Attack Rate in the Class VS in the School)
	Sputum Smear	Sputum Culture	Cavity	First Symptom	Time Interval from First Symptom to Definitive Diagnosis (d)	Reason for Finding Delay
School A	Negative	Positive	No	Cough, Expectoration	46	Conceal the disease	57	8 (13.8)	361	1 (0.3)	P< 0.01
School B	Negative	Positive	Yes	Cough, Expectoration, Hemoptysis	37	Delay in seeking medical treatment	65	5 (7.6)	3955	9 (0.2)	P< 0.01
School C	Negative	Negative	Yes	Cough, Expectoration, Hemoptysis	247	Delay in seeking medical treatment	51	21 (40.4)	2080	5 (0.2)	P< 0.01

Notes: *Putative attack rate in the class = No. of cases in class and dormitory of the index cases (including the index case) /No. of students in the class and dormitory of the index case. ^#The expanding screening on the same floor was conducted for the persons except in the first round.

Table 2 Demographics and Clinical Characteristics of the TB Cases (N = 49)

Characteristics	School A n (%)	School B n (%)	School C n (%)	Total n (%)	P value
Gender
Male	9(100.0)	8(57.1)	19(73.1)	36(73.5)	0.07
Female	0(0.0)	6(42.9)	7(26.9)	13(26.5)
Age
16	0(0.0)	7(50.0)	1(3.8)	8(16.3)	< 0.01
17	4(44.4)	7(50.0)	12(46.2)	23(46.9)
18	5(55.6)	0(0.0)	12(46.2)	17(34.7)
31	0(0.0)	0(0.0)	1(3.8)	1(2.0)
Occupation
Student	9(100.0)	14(100.0)	25(96.2)	48(98.0)	1.00
Teacher	0(0.0)	0(0.0)	1(3.8)	1(2.0)
Grade
10th	0(0.0)	0(0.0)	1(3.8)	1(2.0)	< 0.01
11th	0(0.0)	13(92.9)	1(3.8)	14(28.6)
12th	9(100.0)	1(7.1)	24(92.3)	34(69.4)
The same class or dormitory with the index cases
Yes	8(88.9)	5(35.7)	21(80.8)	34(69.4)	0.009
No	1(11.1)	9(64.3)	5(19.2)	15(30.6)
Living in dormitory
Yes	1(11.1)	3(21.4)	3(11.5)	7(14.3)	0.857
No	8(88.9)	11(78.6)	23(88.5)	42(85.7)
Contact history
Yes	1(11.1)	0(0.0)	1(3.8)	2(4.1)	0.414
No	8(88.9)	14(100.0)	25(96.2)	47(95.9)
TST
≥ 10mm	4(44.4)	3(21.4)	17(65.4)	24(49.0)	0.031
< 10mm	5(55.6)	11(78.6)	9(34.6)	25(51.0)
Cavity
Yes	3(33.3)	5(35.7)	2(7.7)	10(20.4)	0.05
No	6(66.7)	9(64.3)	24(92.3)	39(79.6)
Pathogen positive for AFB logy
Yes	7(77.8)	7(50.0)	6(23.1)	20(40.8)	0.012
No	2(22.2)	7(50.0)	20(76.9)	29(59.2)
RIF-resistant
Yes	5(55.6)	0(0.0)	0(0.0)	5(10.2)	< 0.01
No	3(33.3)	7(50.0)	5(19.2)	15(30.6)
Not detected	1(11.1)	7(50.0)	21(80.8)	29(59.2)

Figure 1 Diagram of the close contact survey process. Laboratory test: sputum smear and culture for suspects, DST also conducted if culture positive.

Figure 2 The first symptom proportion of the patients.

Figure 3 Maximum-likelihood tree of 15 strains annotated with epidemiological characteristics related to drug resistance. Branches are colored by different schools. MDR, rifampicin and isoniazid resistant. INH-mono, rifampicin susceptible and isoniazid resistant. Pan-susceptible, rifampicin and isoniazid susceptible. Patients A0 and B0 were index cases.

Table 3 The Pairwise SNP Distance Matrix of the 15 School TB Isolates and Reference Strain

	H37Rv	School-C1	School-C2	School-C3	School-C4	School-C5	School-A0	School-A1	School-A2	School-A3	School-B0	School-B1	School-B2	School-B3	School-B4	School-B5
H37Rv	0
School-C1	1135	0
School-C2	1140	5	0
School-C3	1136	3	4	0
School-C4	1136	5	4	2	0
School-C5	1120	19	20	18	18	0
School-A0	1205	370	373	373	373	387	0
School-A1	1206	373	374	376	374	388	3	0
School-A2	656	1030	1035	1031	1031	1025	1098	1099	0
School-A3	1204	369	372	372	372	386	7	10	1097	0
School-B0	1134	351	352	352	350	364	413	414	1025	410	0
School-B1	1137	350	349	351	351	365	412	413	1028	409	3	0
School-B2	1136	351	350	352	352	366	413	414	1027	412	4	3	0
School-B3	1128	357	356	356	356	372	419	420	1023	418	12	9	10	0
School-B4	1133	354	353	353	351	367	416	415	1026	413	5	4	7	7	0
School-B5	1134	351	350	350	350	366	413	414	1025	412	6	3	4	6	3	0

Note: The red-white-blue color scale represents the pairwise SNP distance from small to large.