Genomic analysis of Mycobacterium tuberculosis in border and non-border areas of Guangxi Zhuang Autonomous Region

doi:10.3969/j.issn.1672-2302.2023.02.005

Abstract

Abstract:

Objective To analyze the distribution of genotype characteristics and drug resistance-related genes of Mycobacterium tuberculosis (MTB) in border and non-border areas of Guangxi. Methods Sputum samples were collected from tuberculosis patients in designated medical institutions in five regions of Guangxi from 2015 to 2017, and MTB isolates from border and non-border cities were compared. The next-generation whole genome with high-throughput sequencing technology was used to genotype the strains，identify the MTB lineage and collect information on changes in MTB resistance genes. Results A total of 646 strains were included in the study, including 199 strains in the border group. Among them, 8 strains were found in Lineage 1 (4.02%), 126 strains in Lineage 2 (63.32%), 1 strain in Lineage 3 (0.01%), and 64 strains in Lineage 4 (32.16%). 447 strains were identified in the non-border group, including 4 strains in Lineage 1 (0.89%), 299 strains in Lineage 2 (66.89%), and 144 strains in Lineage 4 (32.21%). Lineage 3 was absent in this group. There was significant difference in the distribution of genotype composition between border and non-border group (χ2=9.754, P< 0.05). The difference was significant in the distribution of Lineage 1 and Lineage 4.2 genotypes between border and non-border group (χ2=5.763, 4.833, all P<0.05). Mutations occurred in 196 MTB isolates with drug-resistance related gene, in which the mutation rate in border group was 40.70% (81/199), higher than 25.73% (115/447) in non-border group (χ2=14.613, P<0.05). The top 5 drug resistance genes with mutation rate from high to low were katG (15.94%, 103/646), ropB (11.30%,73/646), embB (6.04%, 39/646), rpsL (5.88%, 38/646) and rrsL (3.72%, 24/646). The mutation rate of katG, ropB and rpsL genes was higher in border group than in non-border group (χ2=5.716, 9.603, 6.979, all P<0.05). The distribution of corresponding katG315, rpoB450 and rpsL43 gene loci in border and non-border group was also significant different (χ2=5.153, 12.893, 11.693, all P<0.05). Conclusion The emergence of Lineage 1 and Lineage 3 in Guangxi suggests that these strains may have been spread from neighboring countries, which requires further empirical research. In addition, the distribution of drug resistance related gene site mutations in Guangxi is related to the composition of MTB genotype.

Key words: Mycobacterium tuberculosis, Whole genome sequencing, Genotyping, Lineage, Drug resistance gene mutation, Guangxi Zhuang Autonomous Region

CLC Number:

YE Jing, ZHOU Chong-xing, LIN Mei, XIAN Xiao-min, LIANG Xiao-yan, ZHANG Ying-kun, LAN Ru-shu, CUI Zhe-zhe. Genomic analysis of Mycobacterium tuberculosis in border and non-border areas of Guangxi Zhuang Autonomous Region[J]. Journal of Tropical Diseases and Parasitology, 2023, 21(2): 82-87.

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年份	L1	L2	L3	L4
2015	6（2.79）	146（67.91）	0（0）	63（29.30）
2016	1（0.47）	147（68.37）	0（0）	67（31.16）
2017	5（2.33）	132（61.40）	1（0.47）	78（36.28）

谱系	边境组	非边境组	χ²值	P值
L1	8（4.02）	4（0.89）	5.763	<0.05
L2	126（63.32）	299（66.59）	0.781	>0.05
L2.1	11（5.53）	29（6.49）	0.219	>0.05
L2.2	43（21.61）	107（23.94）	0.419	>0.05
L2.3	72（36.18）	163（36.47）	0.005	>0.05
L3	1（0.50）	0（0）		>0.05*
L4	64（32.16）	144（32.21）	0.000	>0.05
L4.1.2	0（0）	1（0.22）		>0.05*
L4.2	9（4.52）	43（9.62）	4.833	<0.05
L4.3	0（0）	1（0.22）		>0.05*
L4.4	37（18.59）	57（12.75）	3.779	>0.05
L4.5	15（7.54）	32（7.16）	0.029	>0.05
L4.7	1（0.50）	2（0.45）		>0.05*
L4.9	2（1.00）	8（1.79）	0.161	>0.05

药物	耐药基因	总菌株数	组别		χ²值	P值
药物	耐药基因	总菌株数	边境组	非边境组	χ²值	P值
异烟肼	katG	103（15.94）	42（21.11）	61（13.65）	5.716	<0.05
	fabG1	11（1.70）	5（2.51）	6（1.34）	0.536	>0.05
	ahpC	7（1.08）	2（1.01）	5（1.12）	<0.001	>0.05
	inhA	3（0.46）	1（0.50）	2（0.45）		>0.05*
利福平	rpoB	73（11.30）	34（17.09）	39（8.72）	9.603	<0.01
乙胺丁醇	embB	39（6.04）	15（7.54）	24（5.37）	1.142	>0.05
	embC	14（2.17）	8（4.02）	6（1.34）	3.480	>0.05
链霉素	rpsL	38（5.88）	19（9.55）	19（4.25）	6.979	<0.01
	rrsL	24（3.72）	4（2.01）	20（4.47）	2.337	>0.05
吡嗪酰胺	pncA	20（3.10）	9（4.52）	11（2.46）	1.951	>0.05

基因	位点	碱基的改变	氨基酸的改变	组别		χ²值	P值
基因	位点	碱基的改变	氨基酸的改变	边境组[n（%）]	非边境组[n（%）]	χ²值	P值
katG	315	AGC→ACC	丝氨酸→苏氨酸	38（19.10）	55（12.30）	5.153	<0.05
rpoB	450	TCG→TTG	丝氨酸→亮氨酸	19（9.55）	13（2.91）	12.893	<0.01
rpoB	445	CAC→CCC	组氨酸→脯氨酸	7（3.52）	12（2.68）	0.335	>0.05
		CAC→TAC	组氨酸→酪氨酸
		CAC→GAC	组氨酸→天门冬氨酸
		CAC→AAC	组氨酸→天门冬氨酸
		CAC→CGC	组氨酸→精氨酸
embB	306	ATG→GTG	甲硫氨酸→缬氨酸	10（5.03）	15（3.36）	1.032	>0.05
		ATG→ATT	甲硫氨酸→异亮氨酸
		ATG→ATC	甲硫氨酸→异亮氨酸
		ATG→ATA	甲硫氨酸→异亮氨酸
rpsL	43	AAG→AGG	赖氨酸→精氨酸	19（9.55）	14（3.13）	11.693	<0.01