Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Sites
2.2. Study Design
2.3. Participants
2.4. TB Culture Testing
2.5. Extraction of Genomic DNA
2.6. Sequencing at University of Otago
2.7. Data Analysis Steps
2.7.1. Genomic Characterization
2.7.2. Phylogenetic Analysis
2.7.3. Identification of Genetic Clusters
2.7.4. Biodiversity
2.7.5. Drug Resistance
2.7.6. Merging with Kayin State Data
2.8. Statistical Analysis
3. Results
3.1. Participant Characteristics
3.2. Phylogenetic Analysis
3.3. Identification of Genetic Clusters
3.4. Distribution of Sublineages and Biodiversity in Mandalay Region and Kayin State
3.5. Distribution of Drug-Resistance Mutation and Sublineages in Mandalay Region
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Lineage 1 N = 55 (%) | Lineage 2 N = 65 (%) | Lineage 3 N = 9 (%) | Lineage 4 N = 22 (%) | p Value * | |
---|---|---|---|---|---|
Age in year | 0.903 | ||||
<20 | 4 (7.3) | 4 (6.2) | 0 (0.0) | 1 (4.5) | |
20–30 | 8 (14.5) | 15 (23.1) | 0 (0.0) | 5 (22.7) | |
31–40 | 15 (27.3) | 13 (20.0) | 2 (22.2) | 4 (18.2) | |
41–50 | 12 (21.8) | 16 (24.6) | 3 (33.3) | 5 (22.7) | |
51–60 | 7 (12.7) | 10 (15.4) | 3 (33.3) | 3 (13.6) | |
>60 | 9 (16.4) | 7 (10.8) | 1 (11.1) | 4 (18.2) | |
Gender | 0.066 | ||||
Male | 34 (61.8) | 44 (67.7) | 9 (100) | 18 (81.8) | |
Female | 21 (38.2) | 21 (32.3) | 0 (0) | 4 (18.2) | |
Township | 0.304 | ||||
Chanmyathazi | 8 (14.5) | 11 (16.9) | 1 (11.1) | 4 (18.1) | |
Kyaukpadaung | 8 (14.5) | 13 (20.0) | 5 (55.6) | 5 (22.8) | |
Meiktila | 14 (25.5) | 12 (18.5) | 1 (11.1) | 2 (9.1) | |
Singaing | 7 (12.7) | 6 (9.2) | 0 (0.0) | 2 (9.1) | |
Singu | 18 (32.8) | 23 (35.4) | 2 (22.2) | 9 (40.9) |
Sublineages | Mandalay Region (n) | Kayin State (n) |
---|---|---|
L1.1.1 | 0 | 8 |
L1.1.1.2 | 0 | 1 |
L1.1.1.3 | 1 | 0 |
L1.1.1.5 | 2 | 2 |
L1.1.1.7 | 0 | 1 |
L1.1.1.8 | 1 | 3 |
L1.1.2.1 | 0 | 1 |
L1.1.2.2 (EAI3_IND) | 2 | 10 |
L1.1.3 | 0 | 3 |
L1.1.3.1 (EAI6_BGD) | 31 | 17 |
L1.1.3.3 (EAI6_BGD) | 3 | 0 |
L1.2.2 | 0 | 1 |
L1.2.2.1 | 0 | 2 |
L1.2.2.2 | 0 | 6 |
L1.2.2.3 | 0 | 1 |
L1.3 | 0 | 17 |
L1.2.2.2 (EAI2_NTB) | 8 | 0 |
L1.2.2.3 | 1 | 0 |
L1.3.2 | 6 | 0 |
L2.1 (ProtoBeijing) | 2 | 0 |
L2.2 (Unclassified Ancestral) | 3 | 0 |
L2.2.AA.1 | 9 | 1 |
L2.2.AA.2 | 8 | 1 |
L2.2.AA.3 | 0 | 1 |
L2.2.AA3.1 | 1 | 0 |
L2.2.AA3.2 | 17 | 0 |
L2.2.AA4 | 3 | 3 |
L2.2.M1.1 (Pacific RD150) | 6 | 2 |
L2.2.M1.2 | 1 | 0 |
L2.2.M2 | 0 | 8 |
L2.2.M2.1 (Asian African 2) | 2 | 0 |
L2.2.M2.2 (Asian African 2) | 2 | 0 |
L2.2.M2.3 | 2 | 0 |
L2.2.M3 (Asian African 3) | 3 | 1 |
L2.2.M4 | 2 | 0 |
L2.2.M4.1 (Bmyc22+) | 0 | 1 |
L2.2.1(Modern) | 0 | 8 |
L2.2.M4.4 | 1 | 0 |
L2.2.M6.1 | 1 | 0 |
L2.2.M6.2 (Asian African 1) | 2 | 0 |
L3 | 8 | 2 |
L3.1.2 | 0 | 1 |
L3.1.2.1 | 1 | 1 |
L4.1.1.1 | 5 | 0 |
L4.1.2 | 0 | 1 |
L4.1.2.1 | 2 | 0 |
L4.3 | 0 | 1 |
L4.3.3 | 2 | 0 |
L4.3.4.2 | 2 | 0 |
L4.4 | 0 | 1 |
L4.4.2 | 5 | 0 |
L4.5 | 0 | 1 |
L4.5.2 | 5 | 0 |
L4.5.3 | 0 | 1 |
L4.8 | 1 | 1 |
Biodiversity Index (D) | 0.0709 | 0.072885 |
Drug-Resistance Mutation | N = 151 | Sub-Lineage |
---|---|---|
Isoniazid | ||
InhA_C15T | 2 | L2.2.AA2, L4.3.3 |
katG_S315T | 7 | L2.2.AA1 (1), L1.1.3.1 (3), L2.2.AA3.2 (2), L1.2.2.2 (1) |
inhA_p.Ile21Val | 1 | L2.2.M2.1 |
Rifampicin | ||
rpoB_S450L | 2 | L1.1.3.1 |
rpoB_S450L | 1 | L2.2.AA3.2 |
Pyrazinamide | ||
ncA_408_ins_1_a_at | 1 | L1.1.3.1 |
Ethambutol | ||
embB_M306V | 1 | L1.1.3.1 |
embC_c-516t | 1 | L1.2.2.2 |
Streptomycin | ||
rpsL_K43R | 8 | L2.2.AA1 (1), L4.4.2 (1), L4.5.3 (1), L1.1.3.1 (2), L2.2.AA3.2 (2), L2.2.M2.1 (1) |
rpsL_K88R | 1 | L1.1.3.1 |
gidB_A138V | 1 | L1.1.3.1 |
Other (rpsL_p.Lys43Arg) | 1 | L2.2.AA3.2 |
Levofloxacin | ||
gyrA_D94G | 1 | L1.1.3.1 |
gyrA_A90V | 2 | L1.1.3.1 (2), L2.2.AA3.2 (1) |
Ethionamide | ||
inhA_C15T | 1 | L4.3.3 |
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Phyu, A.N.; Aung, S.T.; Palittapongarnpim, P.; Htet, K.K.K.; Mahasirimongkol, S.; Ruangchai, W.; Jaemsai, B.; Aung, H.L.; Maung, H.M.W.; Chaiprasert, A.; et al. Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar. Trop. Med. Infect. Dis. 2023, 8, 239. https://doi.org/10.3390/tropicalmed8040239
Phyu AN, Aung ST, Palittapongarnpim P, Htet KKK, Mahasirimongkol S, Ruangchai W, Jaemsai B, Aung HL, Maung HMW, Chaiprasert A, et al. Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar. Tropical Medicine and Infectious Disease. 2023; 8(4):239. https://doi.org/10.3390/tropicalmed8040239
Chicago/Turabian StylePhyu, Aye Nyein, Si Thu Aung, Prasit Palittapongarnpim, Kyaw Ko Ko Htet, Surakameth Mahasirimongkol, Wuthiwat Ruangchai, Bharkbhoom Jaemsai, Htin Lin Aung, Htet Myat Win Maung, Angkana Chaiprasert, and et al. 2023. "Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar" Tropical Medicine and Infectious Disease 8, no. 4: 239. https://doi.org/10.3390/tropicalmed8040239