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Li YF, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Yu CB, Li HC, Liu Y. Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China. Emerg Microbes Infect 2024; 13:2294858. [PMID: 38126135 PMCID: PMC10866052 DOI: 10.1080/22221751.2023.2294858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVES We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. METHODS We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. RESULT The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. CONCLUSION MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
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Affiliation(s)
- Yi-fan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University, Jinan, People’s Republic of China
| | - Xiang-long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, People’s Republic of China
| | - Wan-mei Song
- Department of Respiratory Medicine, Ruijin Hospital Affiliated to Shanghai Jiaotong University, Shanghai, People’s Republic of China
| | - Ya-meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Wei-wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Jie-yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, People’s Republic of China
| | - Huai-chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
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Liu Z, Li X, Xiong H, Zhou Q, Yi H, Wu K, Zhou Z, Lu Y, Zhu Y, Zhou L, Zhang M, Gao J, Gao J, Chen S, Wang X, Wang W. Genomic and spatial analysis reveal the transmission dynamics of tuberculosis in areas with high incidence of Zhejiang, China: A prospective cohort study. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 121:105603. [PMID: 38723983 DOI: 10.1016/j.meegid.2024.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/28/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
In the mountainous, rural regions of eastern China, tuberculosis (TB) remains a formidable challenge; however, the long-term molecular epidemiological surveillance in these regions is limited. This study aimed to investigate molecular and spatial epidemiology of TB in two mountainous, rural counties of Zhejiang Province, China, from 2015 to 2021, to elucidate the recent transmission and drug-resistance profiles. The predominant Lineage 2 (L2) Beijing family accounted for 80.1% of total 532 sequenced Mycobacterium tuberculosis (Mtb) strains, showing consistent prevalence over seven years. Gene mutations associated with drug resistance were identified in 19.4% (103/532) of strains, including 47 rifampicin or isoniazid-resistant strains, eight multi-drug-resistant (MDR) strains, and five pre-extensively drug-resistant (pre-XDR) strains. Genomic clustering revealed 53 distinct clusters with an overall transmission clustering rate of 23.9% (127/532). Patients with a history of retreatment and those infected with L2 strains had a higher risk of recent transmission. Spatial and epidemiological analysis unveiled significant transmission hotspots, especially in densely populated urban areas, involving various public places such as medical institutions, farmlands, markets, and cardrooms. The study emphasizes the pivotal role of Beijing strains and urban-based TB transmission in the western mountainous regions in Zhejiang, highlighting the urgent requirement for specific interventions to mitigate the impact of TB in these unique communities.
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Affiliation(s)
- Zhengwei Liu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China
| | - Haiyan Xiong
- School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Qingrong Zhou
- Center for Disease Control and Prevention of Jiangshan City, Zhejiang 324100, China
| | - Huaiming Yi
- Center for Disease Control and Prevention of Changshan County, Zhejiang 324200, China
| | - Kunyang Wu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Zonglei Zhou
- School of Public Health, Fudan University, Shanghai 200032, China
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China
| | - Yelei Zhu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Lin Zhou
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Mingwu Zhang
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Junshun Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China
| | - Junli Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China
| | - Songhua Chen
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
| | - Xiaomeng Wang
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
| | - Weibing Wang
- School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai 200032, China.
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Zhao B, Zheng H, Timm J, Song Z, Pei S, Xing R, Guo Y, Ma L, Li F, Li Q, Li Y, Huang L, Teng C, Wang N, Gupta A, Juneja S, Huang F, Zhao Y, Ou X. Prevalence and genetic basis of Mycobacterium tuberculosis resistance to pretomanid in China. Ann Clin Microbiol Antimicrob 2024; 23:40. [PMID: 38702782 PMCID: PMC11069242 DOI: 10.1186/s12941-024-00697-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/20/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Pretomanid is a key component of new regimens for the treatment of drug-resistant tuberculosis (TB) which are being rolled out globally. However, there is limited information on the prevalence of pre-existing resistance to the drug. METHODS To investigate pretomanid resistance rates in China and its underlying genetic basis, as well as to generate additional minimum inhibitory concentration (MIC) data for epidemiological cutoff (ECOFF)/breakpoint setting, we performed MIC determinations in the Mycobacterial Growth Indicator Tube™ (MGIT) system, followed by WGS analysis, on 475 Mycobacterium tuberculosis (MTB) isolated from Chinese TB patients between 2013 and 2020. RESULTS We observed a pretomanid MIC distribution with a 99% ECOFF equal to 0.5 mg/L. Of the 15 isolates with MIC values > 0.5 mg/L, one (MIC = 1 mg/L) was identified as MTB lineage 1 (L1), a genotype previously reported to be intrinsically less susceptible to pretomanid, two were borderline resistant (MIC = 2-4 mg/L) and the remaining 12 isolates were highly resistant (MIC ≥ 16 mg/L) to the drug. Five resistant isolates did not harbor mutations in the known pretomanid resistant genes. CONCLUSIONS Our results further support a breakpoint of 0.5 mg/L for a non-L1 MTB population, which is characteristic of China. Further, our data point to an unexpected high (14/475, 3%) pre-existing pretomanid resistance rate in the country, as well as to the existence of yet-to-be-discovered pretomanid resistance genes.
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Affiliation(s)
- Bing Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children's Hospital, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | | | - Zexuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, 100191, China
| | - Ruida Xing
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yajie Guo
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children's Hospital, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Ling Ma
- Institute of Tuberculosis Prevention and Control, Gansu Provincial Center for Disease Control and Prevention, Lanzhou, 730020, China
| | - Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children's Hospital, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Qing Li
- Institute of Tuberculosis Prevention and Control, Gansu Provincial Center for Disease Control and Prevention, Lanzhou, 730020, China
| | - Yan Li
- Department of Tuberculosis Control, Chengde Center of Disease Prevention and Control, Chengde, 067000, China
| | - Lin Huang
- Department of Tuberculosis Control, Chengde Center of Disease Prevention and Control, Chengde, 067000, China
| | - Chong Teng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ni Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | | | | | - Fei Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Yanlin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Xichao Ou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Li Y, Li Y, Liu Y, Kong X, Tao N, Hou Y, Wang T, Han Q, Zhang Y, Long F, Li H. Iron-related gene mutations driving global Mycobacterium tuberculosis transmission revealed by whole-genome sequencing. BMC Genomics 2024; 25:249. [PMID: 38448842 PMCID: PMC10916221 DOI: 10.1186/s12864-024-10152-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Iron plays a crucial role in the growth of Mycobacterium tuberculosis (M. tuberculosis). However, the precise regulatory mechanism governing this system requires further elucidation. Additionally, limited studies have examined the impact of gene mutations related to iron on the transmission of M. tuberculosis globally. This research aims to investigate the correlation between mutations in iron-related genes and the worldwide transmission of M. tuberculosis. RESULTS A total of 13,532 isolates of M. tuberculosis were included in this study. Among them, 6,104 (45.11%) were identified as genomic clustered isolates, while 8,395 (62.04%) were classified as genomic clade isolates. Our results showed that a total of 12 single nucleotide polymorphisms (SNPs) showed a positive correlation with clustering, such as Rv1469 (ctpD, C758T), Rv3703c (etgB, G1122T), and Rv3743c (ctpJ, G676C). Additionally, seven SNPs, including Rv0104 (T167G, T478G), Rv0211 (pckA, A302C), Rv0283 (eccB3, C423T), Rv1436 (gap, G654T), ctpD C758T, and etgB C578A, demonstrated a positive correlation with transmission clades across different countries. Notably, our findings highlighted the positive association of Rv0104 T167G, pckA A302C, eccB3 C423T, ctpD C758T, and etgB C578A with transmission clades across diverse regions. Furthermore, our analysis identified 78 SNPs that exhibited significant associations with clade size. CONCLUSIONS Our study reveals the link between iron-related gene SNPs and M. tuberculosis transmission, offering insights into crucial factors influencing the pathogenicity of the disease. This research holds promise for targeted strategies in prevention and treatment, advancing research and interventions in this field.
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Affiliation(s)
- Yameng Li
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China
| | - Yifan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), 250031, Jinan, Shandong, People's Republic of China
| | - Yao Liu
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), 250011, Jinan, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China
| | - Yawei Hou
- Institute of Chinese Medical Literature and Culture of Shandong University of Traditional Chinese Medicine, 250355, Jinan, Shandong, People's Republic of China
| | - Tingting Wang
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, People's Republic of China
| | - Yuzhen Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, People's Republic of China
| | - Fei Long
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), 250031, Jinan, Shandong, People's Republic of China.
| | - Huaichen Li
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China.
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China.
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Li YF, Yang Y, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Men D, Yu CB, Yang GR, Han WG, Liu WY, Yan K, Li HC, Liu Y. Transmission dynamics and phylogeography of Mycobacterium tuberculosis in China based on whole-genome phylogenetic analysis. Int J Infect Dis 2024; 140:124-131. [PMID: 37863309 DOI: 10.1016/j.ijid.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/30/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
OBJECTIVES This study aimed to describe the lineage-specific transmissibility and epidemiological migration of Mycobacterium tuberculosis in China. METHODS We curated a large set of whole-genome sequences from 3204 M. tuberculosis isolates, including thousands of newly sequenced genomes, and applied a series of metrics to compare the transmissibility of M. tuberculosis strains between lineages and sublineages. The countrywide transmission patterns of major lineages were explored. RESULTS We found that lineage 2 (L2) was the most prevalent lineage in China (85.7%), with the major sublineage 2.2.1 (80.9%), followed by lineage 4 (L4) (13.8%), which comprises major sublineages 4.2 (1.5%), 4.4 (6.2%) and 4.5 (5.8%). We showed evidence for frequent cross-regional spread and large cluster formation of L2.2.1 strains, whereas L4 strains were relatively geographically restricted in China. Next, we applied a series of genomic indices to evaluate M. tuberculosis strain transmissibility and uncovered higher transmissibility of L2.2.1 compared with the L2.2.2 and L4 sublineages. Phylogeographic analysis showed that southern, eastern, and northern China were highly connected regions for countrywide L2.2.1 strain spread. CONCLUSIONS The present study provides insights into the different transmission and migration patterns of the major M. tuberculosis lineages in China and highlights that transmissible L2.2.1 is a threat to tuberculosis control.
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Affiliation(s)
- Yi-Fan Li
- Department of Respiratory and Critical Care Medicine, the Third Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, PR China
| | - Yang Yang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao, PR China
| | - Xiang-Long Kong
- Xiang-long Kong, Shandong Artificial Intelligence Institute Qilu University of Technology & Shandong Academy of Sciences, Jinan, Shandong, PR China
| | - Wan-Mei Song
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Ya-Meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China; Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China; Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Wei-Wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Jie-Yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Dan Men
- College of Geography and Environmental Science, Northwest Normal University, No. 967 Anning East Road, Lanzhou, Gansu Province, China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, Shandong, PR China
| | - Guo-Ru Yang
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Wen-Ge Han
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Wen-Yu Liu
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Kun Yan
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Huai-Chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China.
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Quan Z, Li M, Chen Y, Liang J, Takiff H, Gao Q. Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection. Eur J Clin Microbiol Infect Dis 2024; 43:297-304. [PMID: 38041721 DOI: 10.1007/s10096-023-04720-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate. METHODS We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering. RESULTS The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.
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Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Yiwang Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Jialei Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
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7
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Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. PLoS Pathog 2024; 20:e1012050. [PMID: 38422159 DOI: 10.1371/journal.ppat.1012050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/12/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2, which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulate Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage-defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2, label preferentially accumulates in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accrued lactate toxicity via the deleterious buildup of sugar phosphates. The evolved lldD2 variants increase lactate incorporation to pyruvate while altering triose phosphate flux, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX- 1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provides context for the selective advantage of lldD2 mutations in adapting to host stress.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Xin Wang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Young Yon Kwon
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Abigail M Frey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Andrew J Vickers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sheng Hui
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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8
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Song Z, He W, Cao X, Ma A, He P, Zhao B, Wang S, Liu C, Zhao Y. The Recent Transmission and Associated Risk Factor of Mycobacterium tuberculosis in Golmud City, China. Infect Drug Resist 2024; 17:417-425. [PMID: 38318210 PMCID: PMC10840525 DOI: 10.2147/idr.s437026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/05/2023] [Indexed: 02/07/2024] Open
Abstract
Background Tuberculosis (TB) remains a severe public health problem globally, and it is essential to comprehend the transmission pattern to control tuberculosis. Herein, we evaluated the drug-resistant characteristics, recent transmission, and associated risk factors of TB in Golmud, Qinghai, China. Methods In this study, we performed a population-based study of patients diagnosed with TB in Golmud from 2013 to 2018. Drug-susceptibility testing and whole-genome sequencing were performed on 133 Mycobacterium tuberculosis strains. The genomic clustering rate was calculated to evaluate the level of recent transmission. Risk factors were identified by logistic regression analysis. Results Our results showed that 46.97% (62/132) of strains were phylogenetically clustered and formed into 23 transmission clusters, suggesting a high recent transmission of TB in the area. 12.78% (17/133) strains were multidrug-resistant/rifampicin tuberculosis (MDR/RR-TB), with a high drug-resistant burden. Based on drug resistance gene analysis, we found 23 strains belonging to genotype MDR/RR-TB, where some strains may have borderline mutations. Among these strains, 65.2% (15/23) were found within putative transmission clusters. Additionally, risk factor analysis showed that recent transmission of TB happened more in patients with Tibetan nationality or older age. Conclusion Overall our study indicates that the recent transmissions of MTB strains, especially genotypic MDR/RR strains, drive the tuberculosis epidemic in Golmud, which could contribute to developing effective TB prevention and control strategies.
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Affiliation(s)
- Zexuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Wencong He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Xiaolong Cao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Aijing Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Ping He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Bing Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Shengfen Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Chunfa Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
- Animal Science and Technology College, Beijing University of Agriculture, Huilongguan, Changping, Beijing, 102206, People’s Republic of China
| | - Yanlin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
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Wang TT, Hu YL, Li YF, Kong XL, Li YM, Sun PY, Wang DX, Li YY, Zhang YZ, Han QL, Zhu XH, An QQ, Liu LL, Liu Y, Li HC. Polyketide synthases mutation in tuberculosis transmission revealed by whole genomic sequence, China, 2011-2019. Front Genet 2024; 14:1217255. [PMID: 38259610 PMCID: PMC10800454 DOI: 10.3389/fgene.2023.1217255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis (Mtb). Previous studies have primarily focused on the transmissibility of multidrug-resistant (MDR) or extensively drug-resistant (XDR) Mtb. However, variations in virulence across Mtb lineages may also account for differences in transmissibility. In Mtb, polyketide synthase (PKS) genes encode large multifunctional proteins which have been shown to be major mycobacterial virulence factors. Therefore, this study aimed to identify the role of PKS mutations in TB transmission and assess its risk and characteristics. Methods: Whole genome sequences (WGSs) data from 3,204 Mtb isolates was collected from 2011 to 2019 in China. Whole genome single nucleotide polymorphism (SNP) profiles were used for phylogenetic tree analysis. Putative transmission clusters (≤10 SNPs) were identified. To identify the role of PKS mutations in TB transmission, we compared SNPs in the PKS gene region between "clustered isolates" and "non-clustered isolates" in different lineages. Results: Cluster-associated mutations in ppsA, pks12, and pks13 were identified among different lineage isolates. They were statistically significant among clustered strains, indicating that they may enhance the transmissibility of Mtb. Conclusion: Overall, this study provides new insights into the function of PKS and its localization in M. tuberculosis. The study found that ppsA, pks12, and pks13 may contribute to disease progression and higher transmission of certain strains. We also discussed the prospective use of mutant ppsA, pks12, and pks13 genes as drug targets.
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Affiliation(s)
- Ting-Ting Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuan-Long Hu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi-Fan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ya-Meng Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | | | - Da-Xing Wang
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Ying-Ying Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yu-Zhen Zhang
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Lin Han
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xue-Han Zhu
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Qi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Li-Li Liu
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huai-Chen Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Dorji T, Horan K, Sherry NL, Tay EL, Globan M, Viberg L, Bond K, Denholm JT, Howden BP, Andersson P. Whole genome sequencing of drug-resistant Mycobacterium tuberculosis isolates in Victoria, Australia. Int J Infect Dis 2024; 138:46-53. [PMID: 37967715 DOI: 10.1016/j.ijid.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
OBJECTIVES Whole genome sequencing (WGS) can identify clusters, transmission patterns, and drug resistance mutations. This is important in low-burden settings such as Australia, as it can assist in efficient contact tracing and surveillance. METHODS We conducted a retrospective cohort study using WGS from 155 genomically defined drug-resistant Mycobacterium tuberculosis (DR-TB) isolates collected between 2018-2021 in Victoria, Australia. Bioinformatic analysis was performed to identify resistance-conferring mutations, lineages, clusters and understand how local sequences compared with international context. RESULTS Of the 155 sequences, 42% were identified as lineage 2 and 35% as lineage 1; 65.8% (102/155) were isoniazid mono-resistant, 8.4% were multi-drug resistant TB and 5.8% were pre-extensively drug-resistant / extensively drug-resistant TB. The most common mutations were observed in katG and fabG1 genes, especially at Ser315Thr and fabG1 -15 C>T for first-line drugs. Ser450Leu was the most frequent mutation in rpoB gene. Phylogenetic analysis confirmed that Victorian DR-TB were associated with importation events. There was little evidence of local transmission with only five isolate pairs. CONCLUSION Isoniazid-resistant TB is the commonest DR-TB in Victoria, and the mutation profile is similar to global circulating DR-TB. Most cases are diagnosed among migrants with limited transmission. This study highlights the value of WGS in identification of clusters and resistance-conferring mutations. This information is crucial in supporting disease mitigation and treatment strategies.
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Affiliation(s)
- Thinley Dorji
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Melbourne, Australia
| | - Maria Globan
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Linda Viberg
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Katherine Bond
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Royal Melbourne Hospital, Melbourne, Australia
| | - Justin T Denholm
- Royal Melbourne Hospital, Melbourne, Australia; Victorian Tuberculosis Program. Melbourne Health at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Department of Infectious Diseases at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Centre for Pathogen Genomics, University of Melbourne, Australia.
| | - Patiyan Andersson
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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11
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Song Z, He W, Pei S, Zhao B, Cao X, Wang Y, He P, Liu D, Ma A, Ou X, Xia H, Wang S, Liu C, Zhao Y. Association of lineage 4.2.2 of Mycobacterium tuberculosis with the 63-bp deletion variant of the mpt64 gene. Microbiol Spectr 2023; 11:e0184223. [PMID: 37947405 PMCID: PMC10714870 DOI: 10.1128/spectrum.01842-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/03/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE To date, rapid diagnostic methods based on the MPT64 antigen assay are increasingly utilized to differentiate between non-tuberculous mycobacteria and TB disease in clinical settings. Furthermore, numerous novel techniques based on the MPT64 release assay are continuously being developed and applied for the identification of both pulmonary and extrapulmonary TB. However, the diagnostic accuracy of the MPT64 antigen assay is influenced by the presence of 63 bp deletion variants within the mpt64 gene. To our knowledge, this is the first report on the association between the 63 bp deletion variant in mpt64 and Mycobacterium tuberculosis L4.2.2 globally, which highlights the need for the cautious utilization of MPT64-based testing in regions where L4.2.2 isolates are prevalent, such as China and Vietnam, and MPT64 negative results should be confirmed with another assay. In addition, further studies on vaccine development and immunology based on MPT64 should consider these isolates with 63 bp deletion variant.
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Affiliation(s)
- Zexuan Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wencong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaolong Cao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongxin Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aijing Ma
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
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12
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Li Y, Kong X, Li Y, Tao N, Wang T, Li Y, Hou Y, Zhu X, Han Q, Zhang Y, An Q, Liu Y, Li H. Association between fatty acid metabolism gene mutations and Mycobacterium tuberculosis transmission revealed by whole genome sequencing. BMC Microbiol 2023; 23:379. [PMID: 38041005 PMCID: PMC10691062 DOI: 10.1186/s12866-023-03072-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Fatty acid metabolism greatly promotes the virulence and pathogenicity of Mycobacterium tuberculosis (M.tb). However, the regulatory mechanism of fatty acid metabolism in M.tb remains to be elucidated, and limited evidence about the effects of gene mutations in fatty acid metabolism on the transmission of M.tb was reported. RESULTS Overall, a total of 3193 M.tb isolates were included in the study, of which 1596 (50%) were genomic clustered isolates. Most of the tuberculosis isolates belonged to lineage2(n = 2744,85.93%), followed by lineage4(n = 439,13.75%) and lineage3(n = 10,0.31%).Regression results showed that the mutations of gca (136,605, 317G > C, Arg106Pro; OR, 22.144; 95% CI, 2.591-189.272), ogt(1,477,346, 286G > C ,Gly96Arg; OR, 3.893; 95%CI, 1.432-10.583), and rpsA (1,834,776, 1235 C > T, Ala412Val; OR, 3.674; 95% CI, 1.217-11.091) were significantly associated with clustering; mutations in gca and rpsA were also significantly associated with clustering of lineage2. Mutation in arsA(3,001,498, 885 C > G, Thr295Thr; OR, 6.278; 95% CI, 2.508-15.711) was significantly associated with cross-regional clusters. We also found that 20 mutation sites were positively correlated with cluster size, while 11 fatty acid mutation sites were negatively correlated with cluster size. CONCLUSION Our research results suggested that mutations in genes related to fatty acid metabolism were related to the transmission of M.tb. This research could help in the future control of the transmission of M.tb.
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Affiliation(s)
- Yameng Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250011, Shandong, People's Republic of China
| | - Yifan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, 250031, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China
| | - Tingting Wang
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Yingying Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Yawei Hou
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Xuehan Zhu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Yuzhen Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Qiqi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China.
| | - Huaichen Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China.
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China.
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13
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Li Y, Kong X, Li Y, Tao N, Hou Y, Wang T, Li Y, Han Q, Liu Y, Li H. Association between two-component systems gene mutation and Mycobacterium tuberculosis transmission revealed by whole genome sequencing. BMC Genomics 2023; 24:718. [PMID: 38017383 PMCID: PMC10683263 DOI: 10.1186/s12864-023-09788-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Two-component systems (TCSs) assume a pivotal function in Mycobacterium tuberculosis (M.tuberculosis) growth. However, the exact regulatory mechanism of this system needs to be elucidated, and only a few studies have investigated the effect of gene mutations within TCSs on M.tuberculosis transmission. This research explored the relationship between TCSs gene mutation and the global transmission of (M.tuberculosis). RESULTS A total of 13531 M.tuberculosis strains were enrolled in the study. Most of the M.tuberculosis strains belonged to lineage4 (n=6497,48.0%), followed by lineage2 (n=5136,38.0%). Our results showed that a total of 36 single nucleotide polymorphisms (SNPs) were positively correlated with clustering of lineage2, such as Rv0758 (phoR, C820G), Rv1747(T1102C), and Rv1057(C1168T). A total of 30 SNPs showed positive correlation with clustering of lineage4, such as phoR(C182A, C1184G, C662T, T758G), Rv3764c (tcrY, G1151T), and Rv1747 C20T. A total of 19 SNPs were positively correlated with cross-country transmission of lineage2, such as phoR A575C, Rv1028c (kdpD, G383T, G1246C), and Rv1057 G817T. A total of 41 SNPs were positively correlated with cross-country transmission of lineage4, such as phoR(T758G, T327G, C284G), kdpD(G1755A, G625C), Rv1057 C980T, and Rv1747 T373G. CONCLUSIONS Our study identified that SNPs in genes of two-component systems were related to the transmission of M. tuberculosis. This finding adds another layer of complexity to M. tuberculosis virulence and provides insight into future research that will help to elucidate a novel mechanism of M. tuberculosis pathogenicity.
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Affiliation(s)
- Yameng Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250011, People's Republic of China
| | - Yifan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, Shandong, 250031, People's Republic of China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, Shandong, 250021, People's Republic of China
| | - Yawei Hou
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, People's Republic of China
| | - Tingting Wang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, People's Republic of China
| | - Yingying Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, People's Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, Shandong, 250021, People's Republic of China.
| | - Huaichen Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, People's Republic of China.
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, Shandong, 250021, People's Republic of China.
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14
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Ocampo JC, Alzate JF, Barrera LF, Baena A. Tuberculosis Severity Predictive Model Using Mtb Variants and Serum Biomarkers in a Colombian Cohort of APTB Patients. Biomedicines 2023; 11:3110. [PMID: 38137331 PMCID: PMC10740695 DOI: 10.3390/biomedicines11123110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, tuberculosis (TB) is a bacterial infection caused by Mycobacterium tuberculosis (Mtb) that primarily affects the lungs. The severity of active pulmonary TB (APTB) is an important determinant of transmission, morbidity, mortality, disease experience, and treatment outcomes. Several publications have shown a high prevalence of disabling complications in individuals who have had severe APTB. Furthermore, certain strains of Mtb were associated with more severe disease outcomes. The use of biomarkers to predict severe APTB patients who are candidates for host-directed therapies, due to the high risk of developing post-tuberculous lung disease (PTLD), has not yet been implemented in the management of TB patients. We followed 108 individuals with APTB for 6 months using clinical tools, flow cytometry, and whole-genome sequencing (WGS). The median age of the study population was 26.5 years, and the frequency of women was 53.7%. In this study, we aimed to identify biomarkers that could help us to recognize individuals with APTB and improve our understanding of the immunopathology in these individuals. In this study, we conducted a follow-up on the treatment progress of 121 cases of APTB. The follow-up process commenced at the time of diagnosis (T0), continued with a control visit at 2 months (T2), and culminated in an exit appointment at 6 months following the completion of medical treatment (T6). People classified with severe APTB showed significantly higher levels of IL-6 (14.7 pg/mL; p < 0.05) compared to those with mild APTB (7.7 pg/mL) at T0. The AUCs for the ROC curves and the Matthews correlation coefficient values (MCC) demonstrate correlations ranging from moderate to very strong. We conducted WGS on 88 clinical isolates of Mtb, and our analysis revealed a total of 325 genes with insertions and deletions (Indels) within their coding regions when compared to the Mtb H37Rv reference genome. The pattern of association was found between serum levels of CHIT1 and the presence of Indels in Mtb isolates from patients with severe APTB. A key finding in our study was the high levels of CHIT1 in severe APTB patients. We identified a biomarker profile (IL-6, IFN-γ, IL-33, and CHIT1) that allows us to identify individuals with severe APTB, as well as the identification of a panel of polymorphisms (125) in clinical isolates of Mtb from individuals with severe APTB. Integrating these findings into a predictive model of severity would show promise for the management of APTB patients in the future, to guide host-directed therapy and reduce the prevalence of PTLD.
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Affiliation(s)
- Juan C. Ocampo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
- Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Instituto de Investigaciones Médicas, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
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15
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Deng MZ, Liu Q, Cui SJ, Fu H, Gan M, Xu YY, Cai X, Sha W, Zhao GP, Fortune SM, Lyu LD. Mycobacterial DnaQ is an Alternative Proofreader Ensuring DNA Replication Fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563508. [PMID: 37961690 PMCID: PMC10634781 DOI: 10.1101/2023.10.24.563508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Remove of mis-incorporated nucleotides ensures replicative fidelity. Although the ε-exonuclease DnaQ is a well-established proofreader in the model organism Escherichia coli, proofreading in mycobacteria relies on the polymerase and histidinol phosphatase (PHP) domain of replicative polymerase despite the presence of an alternative DnaQ homolog. Here, we show that depletion of DnaQ in Mycolicibacterium smegmatis results in increased mutation rate, leading to AT-biased mutagenesis and elevated insertions/deletions in homopolymer tract. We demonstrated that mycobacterial DnaQ binds to the b-clamp and functions synergistically with the PHP domain to correct replication errors. Further, we found that the mycobacterial DnaQ sustains replicative fidelity upon chromosome topological stress. Intriguingly, we showed that a naturally evolved DnaQ variant prevalent in clinical Mycobacterium tuberculosis isolates enables hypermutability and is associated with extensive drug resistance. These results collectively establish that the alternative DnaQ functions in proofreading, and thus reveal that mycobacteria deploy two proofreaders to maintain replicative fidelity.
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Affiliation(s)
- Ming-Zhi Deng
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- These authors contributed equally
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- These authors contributed equally
| | - Shu-Jun Cui
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Mingyu Gan
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102, P.R.China
| | - Yuan-Yuan Xu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Wei Sha
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
| | - Guo-Ping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
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Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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17
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Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561592. [PMID: 37873410 PMCID: PMC10592758 DOI: 10.1101/2023.10.09.561592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2 , which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulates Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13 C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2 , label preferentially accumulates in methylglyoxal precursors dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accumulated lactate toxicity via a methylglyoxal pathway that has been proposed previously. The evolved lldD2 variants increase lactate incorporation to pyruvate but also alter flux in the methylglyoxal pathway, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX-1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provide context for the selective advantage of lldD2 mutations in adapting to host stress.
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18
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Berry SB, Espich S, Thuong NTT, Chang X, Dorajoo R, Khor CC, Heng CK, Yuan JM, Fox D, Anaya-Sanchez A, Tenney L, Chang CJ, Kotov DI, Vance RE, Dunstan SJ, Darwin KH, Stanley SA. Disruption of Aldehyde Dehydrogenase 2 protects against bacterial infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554661. [PMID: 37662190 PMCID: PMC10473740 DOI: 10.1101/2023.08.24.554661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ALDH2*2 (rs671) allele is one of the most common genetic mutations in humans, yet the positive evolutionary selective pressure to maintain this mutation is unknown, despite its association with adverse health outcomes. ALDH2 is responsible for the detoxification of metabolically produced aldehydes, including lipid-peroxidation end products derived from inflammation. Here, we demonstrate that host-derived aldehydes 4-hydroxynonenal (4HNE), malondialdehyde (MDA), and formaldehyde (FA), all of which are metabolized by ALDH2, are directly toxic to the bacterial pathogens Mycobacterium tuberculosis and Francisella tularensis at physiological levels. We find that Aldh2 expression in macrophages is decreased upon immune stimulation, and that bone marrow-derived macrophages from Aldh2 -/- mice contain elevated aldehydes relative to wild-type mice. Macrophages deficient for Aldh2 exhibited enhanced control of Francisella infection. Finally , mice lacking Aldh2 demonstrated increased resistance to pulmonary infection by M. tuberculosis , including in a hypersusceptible model of tuberculosis, and were also resistant to Francisella infection. We hypothesize that the absence of ALDH2 contributes to the host's ability to control infection by pathogens such as M. tuberculosis and F. tularensis , and that host-derived aldehydes act as antimicrobial factors during intracellular bacterial infections. One sentence summary Aldehydes produced by host cells contribute to the control of bacterial infections.
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19
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Zhu C, Yang T, Yin J, Jiang H, Takiff HE, Gao Q, Liu Q, Li W. The Global Success of Mycobacterium tuberculosis Modern Beijing Family Is Driven by a Few Recently Emerged Strains. Microbiol Spectr 2023; 11:e0333922. [PMID: 37272796 PMCID: PMC10434187 DOI: 10.1128/spectrum.03339-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/23/2023] [Indexed: 06/06/2023] Open
Abstract
Strains of the Mycobacterium tuberculosis complex (MTBC) Beijing family aroused concern because they were often found in clusters and appeared to be exceptionally transmissible. However, it was later found that strains of the Beijing family were heterogeneous, and the transmission advantage was restricted to sublineage L2.3 or modern Beijing. In this study, we analyzed the previously published genome sequences of 7,896 L2.3 strains from 51 different countries. Using BEAST software to approximate the temporal emergence of L2.3, our calculations suggest that L2.3 initially emerged in northern East Asia during the early 15th century and subsequently diverged into six phylogenetic clades, identified as L2.3.1 through L2.3.6. Using terminal branch length and genomic clustering as proxies for transmissibility, we found that the six clades displayed distinct population dynamics, with the three recently emerged clades (L2.3.4 to L2.3.6) exhibiting significantly higher transmissibility than the older three clades (L2.3.1 to L2.3.3). Of the Beijing family strains isolated outside East Asia, 83.1% belonged to the clades L2.3.4 to L2.3.6, which were also associated with more cross-border transmission. This work reveals the heterogeneity in sublineage L2.3 and demonstrates that the global success of Beijing family strains is driven by the three recently emerged L2.3 clades. IMPORTANCE The recent population dynamics of the global tuberculosis epidemic are heavily shaped by Mycobacterium tuberculosis complex (MTBC) strains with enhanced transmissibility. The infamous Beijing family strain stands out because it has rapidly spread throughout the world. Identifying the strains responsible for the global expansion and tracing their evolution should help to understand the nature of high transmissibility and develop effective strategies to control transmission. In this study, we found that the L2.3 sublineage diversified into six phylogenetic clades (L2.3.1 to L2.3.6) with various transmission characteristics. Clades L2.3.4 to L2.3.6 exhibited significantly higher transmissibility than clades L2.3.1 to L2.3.3, which helps explain why more than 80% of Beijing family strains collected outside East Asia belong to these three clades. We conclude that the global success of L2.3 was not caused by the entire L2.3 sublineage but rather was due to the rapid expansion of L2.3.4 to L2.3.6. Tracking the transmission of L2.3.4 to L2.3.6 strains can help to formulate targeted TB prevention and control.
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Affiliation(s)
- Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | | | - Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Howard E. Takiff
- Instituto Venezolano de Investigaciones Científicas, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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20
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Liang D, Song Z, Liang X, Qin H, Huang L, Ye J, Lan R, Luo D, Zhao Y, Lin M. Whole Genomic Analysis Revealed High Genetic Diversity and Drug-Resistant Characteristics of Mycobacterium tuberculosis in Guangxi, China. Infect Drug Resist 2023; 16:5021-5031. [PMID: 37554542 PMCID: PMC10405913 DOI: 10.2147/idr.s410828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 08/10/2023] Open
Abstract
Background Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a major public health issue in China. Nevertheless, the prevalence and drug resistance characteristics of isolates vary in different regions and provinces. In this study, we investigated the population structure, transmission dynamics and drug-resistant profiles of Mtb in Guangxi, located on the border of China. Methods From February 2016 to April 2017, 462 clinical M. tuberculosis isolates were selected from 5 locations in Guangxi. Drug-susceptibility testing was performed using 6 common anti-tuberculosis drugs. The genotypic drug resistance and transmission dynamics were analyzed by the whole genome sequence. Results Our data showed that the Mtb in Guangxi has high genetic diversity including Lineage 1 to Lineage 4, and mostly belong to Lineage 2 and Lineage 4. Novelty, 9.6% of Lineage 2 isolates were proto-Beijing genotype (L2.1), which is rare in China. About 12.6% of isolates were phylogenetically clustered and formed into 28 transmission clusters. We observed that the isolates with the high resistant rate of isoniazid (INH, 21.2%), followed by rifampicin (RIF, 13.2%), and 6.7%, 12.1%, 6.7% and 1.9% isolates were resistant to ethambutol (EMB), streptomycin (SM), ofloxacin (OFL) and kanamycin (KAN), respectively. Among these, 6.5% and 3.3% of isolates belong to MDR-TB and Pre-XDR, respectively, with a high drug-resistant burden. Genetic analysis identified the most frequently encountered mutations of INH, RIF, EMB, SM, OFL and KAN were katG_Ser315Thr (62.2%), rpoB_Ser450Leu (42.6%), embB_Met306Vol (45.2%), rpsL_Lys43Arg (53.6%), gyrA_Asp94Gly (29.0%) and rrs_A1401G (66.7%), respectively. Additionally, we discovered that isolates from border cities are more likely to be drug-resistant than isolates from non-border cities. Conclusion Our findings provide a deep analysis of the genomic population characteristics and drug-resistant of M. tuberculosis in Guangxi, which could contribute to developing effective TB prevention and control strategies.
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Affiliation(s)
- Dabin Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Zexuan Song
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiaoyan Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Huifang Qin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Liwen Huang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Jing Ye
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Rushu Lan
- Department of Clinical Laboratory, Jiangbin Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, People’s Republic of China
| | - Dan Luo
- School of Public Health and Management, Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Mei Lin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
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21
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Lin Y, Du Y, Shen H, Guo Y, Wang T, Lai K, Zhang D, Zheng G, Wu G, Lei Y, Liu J. Transmission of Mycobacterium tuberculosis in schools: a molecular epidemiological study using whole-genome sequencing in Guangzhou, China. Front Public Health 2023; 11:1156930. [PMID: 37250072 PMCID: PMC10219607 DOI: 10.3389/fpubh.2023.1156930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Background China is a country with a high burden of tuberculosis (TB). TB outbreaks are frequent in schools. Thus, understanding the transmission patterns is crucial for controlling TB. Method In this genomic epidemiological study, the conventional epidemiological survey data combined with whole-genome sequencing was used to assess the genotypic distribution and transmission characteristics of Mycobacterium tuberculosis strains isolated from patients with TB attending schools during 2015 to 2019 in Guangzhou, China. Result The TB incidence was mainly concentrated in regular secondary schools and technical and vocational schools. The incidence of drug resistance among the students was 16.30% (22/135). The phylogenetic tree showed that 79.26% (107/135) and 20.74% (28/135) of the strains belonged to lineage 2 (Beijing genotype) and lineage 4 (Euro-American genotype), respectively. Among the 135 isolates, five clusters with genomic distance within 12 single nucleotide polymorphisms were identified; these clusters included 10 strains, accounting for an overall clustering rate of 7.4% (10/135), which showed a much lower transmission index. The distance between the home or school address and the interval time of symptom onset or diagnosis indicated that campus dissemination and community dissemination may be existed both, and community dissemination is the main. Conclusion and recommendation TB cases in Guangzhou schools were mainly disseminated and predominantly originated from community transmission. Accordingly, surveillance needs to be strengthened to stop the spread of TB in schools.
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Affiliation(s)
- Ying Lin
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Yuhua Du
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Hongcheng Shen
- Department of Preventive Health Care, Guangzhou Chest Hospital, Guangzhou, China
| | - Yangfeng Guo
- Guangzhou Primary and Secondary School Health and Health Promotion Center, Guangzhou, China
| | - Ting Wang
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Keng Lai
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Danni Zhang
- Academy of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Guangmin Zheng
- Academy of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Guifeng Wu
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Yu Lei
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Jianxiong Liu
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou, China
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22
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Phyu AN, Aung ST, Palittapongarnpim P, Htet KKK, Mahasirimongkol S, Ruangchai W, Jaemsai B, Aung HL, Maung HMW, Chaiprasert A, Pungrassami P, Chongsuvivatwong V. Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar. Trop Med Infect Dis 2023; 8:239. [PMID: 37104364 PMCID: PMC10141229 DOI: 10.3390/tropicalmed8040239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
This study aimed to characterize whole-genome sequencing (WGS) information of Mycobacterium tuberculosis (Mtb) in the Mandalay region of Myanmar. It was a cross-sectional study conducted with 151 Mtb isolates obtained from the fourth nationwide anti-tuberculosis (TB) drug-resistance survey. Frequency of lineages 1, 2, 3, and 4 were 55, 65, 9, and 22, respectively. The most common sublineage was L1.1.3.1 (n = 31). Respective multi-drug resistant tuberculosis (MDR-TB) frequencies were 1, 1, 0, and 0. Four clusters of 3 (L2), 2 (L4), 2 (L1), and 2 (L2) isolates defined by a 20-single-nucleotide variant (SNV) cutoff were detected. Simpson's index for sublineages was 0.0709. Such high diversity suggests that the area probably had imported Mtb from many geographical sources. Relatively few genetic clusters and MDR-TB suggest there is a chance the future control will succeed if it is carried out properly.
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Affiliation(s)
- Aye Nyein Phyu
- National Tuberculosis Programme, Department of Public Health, Ministry of Health, Mandalay 05071, Myanmar
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Si Thu Aung
- Department of Public Health, Ministry of Health, Keng Tung 06231, Myanmar
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Kyaw Ko Ko Htet
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Surakameth Mahasirimongkol
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Bharkbhoom Jaemsai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Htin Lin Aung
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Htet Myat Win Maung
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Angkana Chaiprasert
- Office of Research and Innovation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Petchawan Pungrassami
- Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand
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23
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López MG, Campos-Herrero MI, Torres-Puente M, Cañas F, Comín J, Copado R, Wintringer P, Iqbal Z, Lagarejos E, Moreno-Molina M, Pérez-Lago L, Pino B, Sante L, García de Viedma D, Samper S, Comas I. Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants. Microbiol Spectr 2023; 11:e0282622. [PMID: 36786614 PMCID: PMC10100973 DOI: 10.1128/spectrum.02826-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Outbreak strains of Mycobacterium tuberculosis are promising candidates as targets in the search for intrinsic determinants of transmissibility, as they are responsible for many cases with sustained transmission; however, the use of low-resolution typing methods and restricted geographical investigations represent flaws in assessing the success of long-lived outbreak strains. We can now address the nature of outbreak strains by combining large genomic data sets and phylodynamic approaches. We retrospectively sequenced the whole genome of representative samples assigned to an outbreak circulating in the Canary Islands (the GC strain) since 1993, which accounts for ~20% of local tuberculosis cases. We selected a panel of specific single nucleotide polymorphism (SNP) markers for an in-silico search for additional outbreak-related sequences within publicly available tuberculosis genomic data. Using this information, we inferred the origin, spread, and epidemiological parameters of the GC strain. Our approach allowed us to accurately trace the historical and more recent dispersion of the GC strain. We provide evidence of a highly successful nature within the Canarian archipelago but limited expansion abroad. Estimation of epidemiological parameters from genomic data disagree with a distinctive biology of the GC strain. With the increasing availability of genomic data allowing for the accurate inference of strain spread and critical epidemiological parameters, we can now revisit the link between Mycobacterium tuberculosis genotypes and transmission, as is routinely carried out for SARS-CoV-2 variants of concern. We demonstrate that social determinants rather than intrinsically higher bacterial transmissibility better explain the success of the GC strain. Importantly, our approach can be used to trace and characterize strains of interest worldwide. IMPORTANCE Infectious disease outbreaks represent a significant problem for public health. Tracing outbreak expansion and understanding the main factors behind emergence and persistence remain critical to effective disease control. Our study allows researchers and public health authorities to use Whole-Genome Sequencing-based methods to trace outbreaks, and shows how available epidemiological information helps to evaluate the factors underpinning outbreak persistence. Taking advantage of all the freely available information placed in public repositories, researchers can accurately establish the expansion of an outbreak beyond original boundaries, and determine the potential risk of a strain to inform health authorities which, in turn, can define target strategies to mitigate expansion and persistence. Finally, we show the need to evaluate strain transmissibility in different geographic contexts to unequivocally associate spread to local or pathogenic factors, an important lesson taken from genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Mariana G. López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Ma Isolina Campos-Herrero
- Servicio de Microbiología, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Fernando Cañas
- Hospital Universitario Insular de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Jessica Comín
- Instituto Aragonés de Ciencias de la Salud, Fundación IIS Aragón, Zaragoza, Spain
| | - Rodolfo Copado
- Hospital José Molina Orosa, Las Palmas de Gran Canaria, Spain
| | - Penelope Wintringer
- European Molecular Biology Laboratory – European Bioinformatics Institute, Hinxton, UK
| | - Zamin Iqbal
- European Molecular Biology Laboratory – European Bioinformatics Institute, Hinxton, UK
| | - Eduardo Lagarejos
- Servicio de Microbiología, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Miguel Moreno-Molina
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Laura Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Berta Pino
- Hospital Nuestra Señora de la Candelaria, Santa Cruz de Tenerife, Spain
| | - Laura Sante
- Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - Darío García de Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, Fundación IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
- CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
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24
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Ashton PM, Cha J, Anscombe C, Thuong NTT, Thwaites GE, Walker TM. Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia. Microb Genom 2023; 9:mgen000955. [PMID: 36729036 PMCID: PMC9997747 DOI: 10.1099/mgen.0.000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Molecular and genomic studies have revealed that Mycobacterium tuberculosis Lineage 4 (L4, Euro-American lineage) emerged in Europe before becoming distributed around the globe by trade routes, colonial migration and other historical connections. Although L4 accounts for tens or hundreds of thousands of tuberculosis (TB) cases in multiple Southeast Asian countries, phylogeographical studies have either focused on a single country or just included Southeast Asia as part of a global analysis. Therefore, we interrogated public genomic data to investigate the historical patterns underlying the distribution of L4 in Southeast Asia and surrounding countries. We downloaded 6037 genomes associated with 29 published studies, focusing on global analyses of L4 and Asian studies of M. tuberculosis. We identified 2256 L4 genomes including 968 from Asia. We show that 81 % of L4 in Thailand, 51 % of L4 in Vietnam and 9 % of L4 in Indonesia belong to sub-lineages of L4 that are rarely seen outside East and Southeast Asia (L4.2.2, L4.4.2 and L4.5). These sub-lineages have spread between East and Southeast Asian countries, with no recent European ancestor. Although there is considerable uncertainty about the exact direction and order of intra-Asian M. tuberculosis dispersal, due to differing sampling frames between countries, our analysis suggests that China may be the intermediate location between Europe and Southeast Asia for two of the three predominantly East and Southeast Asian L4 sub-lineages (L4.2.2 and L4.5). This new perspective on L4 in Southeast Asia raises the possibility of investigating host population-specific evolution and highlights the need for more structured sampling from Southeast Asian countries to provide more certainty of the historical and current routes of dispersal.
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Affiliation(s)
- Philip M. Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jaeyoon Cha
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Catherine Anscombe
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nguyen T. T. Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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25
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Liu Q, Zhu J, Dulberger CL, Stanley S, Wilson S, Chung ES, Wang X, Culviner P, Liu YJ, Hicks ND, Babunovic GH, Giffen SR, Aldridge BB, Garner EC, Rubin EJ, Chao MC, Fortune SM. Tuberculosis treatment failure associated with evolution of antibiotic resilience. Science 2022; 378:1111-1118. [PMID: 36480634 PMCID: PMC9968493 DOI: 10.1126/science.abq2787] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The widespread use of antibiotics has placed bacterial pathogens under intense pressure to evolve new survival mechanisms. Genomic analysis of 51,229 Mycobacterium tuberculosis (Mtb)clinical isolates has identified an essential transcriptional regulator, Rv1830, herein called resR for resilience regulator, as a frequent target of positive (adaptive) selection. resR mutants do not show canonical drug resistance or drug tolerance but instead shorten the post-antibiotic effect, meaning that they enable Mtb to resume growth after drug exposure substantially faster than wild-type strains. We refer to this phenotype as antibiotic resilience. ResR acts in a regulatory cascade with other transcription factors controlling cell growth and division, which are also under positive selection in clinical isolates of Mtb. Mutations of these genes are associated with treatment failure and the acquisition of canonical drug resistance.
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Affiliation(s)
- Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA,Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Eun Seon Chung
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA 02115, USA
| | - Xin Wang
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter Culviner
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yue J. Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nathan D. Hicks
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Gregory H. Babunovic
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Samantha R. Giffen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA 02115, USA
| | - Ethan C. Garner
- Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michael C. Chao
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Corresponding author.
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26
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Saelens JW, Sweeney MI, Viswanathan G, Xet-Mull AM, Jurcic Smith KL, Sisk DM, Hu DD, Cronin RM, Hughes EJ, Brewer WJ, Coers J, Champion MM, Champion PA, Lowe CB, Smith CM, Lee S, Stout JE, Tobin DM. An ancestral mycobacterial effector promotes dissemination of infection. Cell 2022; 185:4507-4525.e18. [PMID: 36356582 PMCID: PMC9691622 DOI: 10.1016/j.cell.2022.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/27/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
The human pathogen Mycobacterium tuberculosis typically causes lung disease but can also disseminate to other tissues. We identified a M. tuberculosis (Mtb) outbreak presenting with unusually high rates of extrapulmonary dissemination and bone disease. We found that the causal strain carried an ancestral full-length version of the type VII-secreted effector EsxM rather than the truncated version present in other modern Mtb lineages. The ancestral EsxM variant exacerbated dissemination through enhancement of macrophage motility, increased egress of macrophages from established granulomas, and alterations in macrophage actin dynamics. Reconstitution of the ancestral version of EsxM in an attenuated modern strain of Mtb altered the migratory mode of infected macrophages, enhancing their motility. In a zebrafish model, full-length EsxM promoted bone disease. The presence of a derived nonsense variant in EsxM throughout the major Mtb lineages 2, 3, and 4 is consistent with a role for EsxM in regulating the extent of dissemination.
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Affiliation(s)
- Joseph W Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mollie I Sweeney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ana María Xet-Mull
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kristen L Jurcic Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dana M Sisk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel D Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rachel M Cronin
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erika J Hughes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patricia A Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sunhee Lee
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jason E Stout
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA.
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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27
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Need for speed: Key driver of host cell migration varies among mycobacteria. Cell 2022; 185:4467-4469. [PMID: 36423577 DOI: 10.1016/j.cell.2022.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
In this issue of Cell, Saelens et al. describe a new function for mycobacterial Type VII secretion systems: manipulation of host cell migration. They find that a substantial proportion of global TB cases arise from bacteria lacking this function, raising questions about its role in pathoadaptation of Mycobacterium tuberculosis.
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28
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Drug Degradation Caused by mce3R Mutations Confers Contezolid (MRX-I) Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2022; 66:e0103422. [PMID: 36190243 PMCID: PMC9578412 DOI: 10.1128/aac.01034-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Contezolid (MRX-I), a safer antibiotic of the oxazolidinone class, is a promising new antibiotic with potent activity against Mycobacterium tuberculosis (MTB) both in vitro and in vivo. To identify resistance mechanisms of contezolid in MTB, we isolated several in vitro spontaneous contezolid-resistant MTB mutants, which exhibited 16-fold increases in the MIC of contezolid compared with the parent strain but were still unexpectedly susceptible to linezolid. Whole-genome sequencing revealed that most of the contezolid-resistant mutants bore mutations in the mce3R gene, which encodes a transcriptional repressor. The mutations in mce3R led to markedly increased expression of a monooxygenase encoding gene Rv1936. We then characterized Rv1936 as a putative flavin-dependent monooxygenase that catalyzes the degradation of contezolid into its inactive 2,3-dihydropyridin-4-one (DHPO) ring-opened metabolites, thereby conferring drug resistance. While contezolid is an attractive drug candidate with potent antimycobacterial activity and low toxicity, the occurrence of mutations in Mce3R should be considered when designing combination therapy using contezolid for treating tuberculosis.
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29
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Li M, Guo M, Peng Y, Jiang Q, Xia L, Zhong S, Qiu Y, Su X, Zhang S, Yang C, Mijiti P, Mao Q, Takiff H, Li F, Chen C, Gao Q. High proportion of tuberculosis transmission among social contacts in rural China: a 12-year prospective population-based genomic epidemiological study. Emerg Microbes Infect 2022; 11:2102-2111. [PMID: 35950916 PMCID: PMC9448380 DOI: 10.1080/22221751.2022.2112912] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is more prevalent in rural than urban areas in China, and delineating TB transmission patterns in rural populations could improve TB control. We conducted a prospective population-based study of culture-positive pulmonary TB patients diagnosed between July 1, 2009 and December 31, 2020 in two rural counties in China. Genomic clusters were defined with a threshold distance of 12-single-nucleotide-polymorphisms, based on whole-genome sequencing. Risk factors for clustering were identified by logistic regression. Transmission links were sought through epidemiological investigation of genomic-clustered patients. Of 1517 and 751 culture-positive pulmonary TB patients in Wusheng and Wuchang counties, respectively, 1289 and 699 strains were sequenced. Overall, 624 (31.4%, 624/1988) patients were grouped into 225 genomic clusters. Epidemiological links were confirmed in 41.8% (196/469) of clustered isolates, including family (32.7%, 64/196) and social contacts (67.3%, 132/196). Social contacts were generally with relatives, within the community or in shared aggregated settings outside the community, but the proportion of clustered contacts in each category differed between the two sites. The time interval between diagnosis of student cases and contacts was significantly shorter than family and social contacts, probably due to enhanced student contact screening. Transmission of multidrug-resistant (MDR) strains was likely responsible for 81.4% (83/102) of MDR-TB cases, with minimal acquisition of additional resistance mutations. A large proportion of TB transmission in rural China occurred among social contacts, suggesting that active screening and aggressive contact tracing could benefit TB control, but contact screening should be tailored to local patterns of social interactions.
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Affiliation(s)
- Meng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China
| | - Mingcheng Guo
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Ying Peng
- Heilongjiang Provincial Center for Tuberculosis Prevention and Control, Harbin, China
| | - Qi Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,School of Public Health, Wuhan University, Wuhan, China
| | - Lan Xia
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Sheng Zhong
- Wuchang City Center for Tuberculosis Control and Prevention, Harbin, China
| | - Yong Qiu
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Xin Su
- Wuchang City Center for Tuberculosis Control and Prevention, Harbin, China
| | - Shu Zhang
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Peierdun Mijiti
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qizhi Mao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Fabin Li
- Heilongjiang Provincial Center for Tuberculosis Prevention and Control, Harbin, China
| | - Chuang Chen
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China
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30
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Smith TM, Youngblom MA, Kernien JF, Mohamed MA, Fry SS, Bohr LL, Mortimer TD, O'Neill MB, Pepperell CS. Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. eLife 2022; 11:e78454. [PMID: 35726854 PMCID: PMC9213004 DOI: 10.7554/elife.78454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/15/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.
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Affiliation(s)
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - John F Kernien
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Mohamed A Mohamed
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Sydney S Fry
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Mary B O'Neill
- Laboratoire de Biochimie (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL UniversitéParisFrance
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
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31
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Liu Q, Qiu B, Li G, Yang T, Tao B, Martinez L, Zhu L, Wang J, Mao X, Lu W. Tuberculosis reinfection and relapse in eastern China: A prospective study using whole-genome sequencing. Clin Microbiol Infect 2022; 28:1458-1464. [PMID: 35700940 DOI: 10.1016/j.cmi.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Tuberculosis recurrence after an initial successful treatment episode can occur from either reinfection or relapse. In a population-based sample and whole genome sequencing (WGS) in eastern China, we aimed to evaluate risk factors for tuberculosis recurrence, and assess the proportion of recurrence due to either reinfection or relapse. METHODS Successfully treated pulmonary tuberculosis patients with sputum culture positive results were recruited from five cities in Jiangsu Province from 2013-2015 and followed for two years for tuberculosis recurrence. Among patients developing a second tuberculosis episode, WGS was performed to distinguish relapse or reinfection through a distance threshold of 6-single-nucleotide polymorphisms (SNP). We analyzed risk factors for recurrence and epidemiological characteristics of different types of recurrent patients. RESULTS Of 1,897 successful treated tuberculosis patients, 7.4% (141/1879) developed recurrent tuberculosis. Compared with non-recurrent tuberculosis, patients were at higher risk of recurrence in older age (Adjusted Odds Ratio [AOR], 1.02 for each additional year; 95% CI, 1.01-1.03, P=0.003), patients previously treated for tuberculosis (AOR=2.22; 95% CI, 1.52-3.26, P<0.001), or with bilateral cavities (AOR, 1.56; 95% CI, 1.05-2.32, P=0.029). Among 27.0% (38/141) recurrent tuberculosis patients with successfully sequenced pairs, relapse was substantially more common than reinfection (71.1% versus 28.9%, P=0.014). CONCLUSIONS Endogenous relapse was significantly more common than exogenous reinfection in the first two years after treatment in eastern China. Prioritization of high-risk groups for recurrence, such as the elderly, with a previous tuberculosis diagnosis, or with bilateral cavities, may provide opportunities to reduce post-tuberculosis morbidity.
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Affiliation(s)
- Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Guoli Li
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Tingting Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, PR China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, Massachusetts, United States
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Xuhua Mao
- Department of Clinical Laboratory, Affiliated Yixing People's Hospital, Jiangsu University, Wuxi, China.
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China.
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32
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Prediction of drug resistance profile of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) isolates from newly diagnosed case by whole genome sequencing (WGS): a study from a high tuberculosis burden country. BMC Infect Dis 2022; 22:499. [PMID: 35624432 PMCID: PMC9137048 DOI: 10.1186/s12879-022-07482-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Our aim was to assess the ability of the Whole-genome sequencing (WGS) in predicting drug resistance profile of multidrug-resistant mycobacterium tuberculosis (MDR-MTB) from newly diagnosed cases in China. METHODS We validated the Phenotypic drug Sensitivity Test (pDST) for 12 anti-tuberculosis drugs using the Bactec MGIT 960 system. We described the characteristics of the isolates enrolled and compared the pDST results with resistance profiles predicted by WGS. RESULTS The pDST showed that of the 43 isolates enrolled, 25.6% were sensitive to rifabutin (RFB); 97.7%、97.7%、93.0% and 93.0% were sensitive to cycloserine (Cs), amikacin/kanamycin (Ak/Km), para-aminosalicylic acid (Pas) and ethionamide Eto), respectively; 18.6% were resistant to fluoroquinolones (FQs) or second-line injections. Genotype DST determined by WGS of Ak/Km、Eto and RFP reached high consistency to 97.7% compared with pDST, followed by moxifloxacin (Mfx) 95.3%, levofloxaci (Lfx) and Pas 93%, streptomycin (Sm) 90.3%. The genotype DST of RFB and EMB showed low consistency with the pDST of 67.2 and 79.1%. WGS also detected 27.9% isolates of pyrazinamide(PZA)-related drug-resistant mutation. No mutations associated with linezolid (Lzd), bedaquiline (Bdq) and clofazimine (Cfz) were detectd. CONCLUSIONS WGS has the potential to infer resistance profiles without time-consuming phenotypic methods, which could be provide a basis to formulate reasonable treatment in high TB burden areas.
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Abstract
There are many reactive intermediates found in metabolic pathways. Could these potentially toxic molecules be exploited for an organism's benefit? We propose that during certain microbial infections, the production of inherently reactive aldehydes by an infected host is a previously unappreciated innate immune defence mechanism. While there has been a significant focus on the effects of aldehydes on mammalian physiology, the idea that they might be exploited or purposefully induced to kill pathogens is new. Given that aldehydes are made as parts of metabolic programmes that accompany immune cell activation by the cytokine interferon-gamma (IFN-γ) during infections, we hypothesize that aldehydes are among the arsenal of IFN-γ-inducible effectors needed for pathogen control.
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Affiliation(s)
- K. Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA,Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
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Xu AM, He CJ, Cheng X, Abuduaini A, Tuerxun Z, Sha YZ, Kaisaier A, Peng HM, Zhen YH, Zhang SJ, Xu JR, Li L, Zou XG. Distribution and identification of Mycobacterium tuberculosis lineage in Kashgar prefecture. BMC Infect Dis 2022; 22:312. [PMID: 35354436 PMCID: PMC8966310 DOI: 10.1186/s12879-022-07307-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
Objectives Kashgar prefecture is an important transportation and trade hub with a high incidence of tuberculosis. The following study analyzed the composition and differences in Mycobacterium tuberculosis (M.tb) lineage and specific tags to distinguish the lineage of the M.tb in Kashgar prefecture, thus providing a basis for the classification and diagnosis of tuberculosis in this area. Methods Whole-genome sequencing (WGS) of 161 M.tb clinical strains was performed. The phylogenetic tree was constructed using Maximum Likelihood (ML) based on single nucleotide polymorphisms (SNPs) and verified through principal component analysis (PCA). The composition structure of M.tb in different regions was analyzed by combining geographic information. Results M.tb clinical strains were composed of lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%) and lineage 4 (36/161, 22.36%). Moreover, the 3 lineages were subdivided into 11 sublineages, among which lineage 2 included lineage 2.2.2/Asia Ancestral 1 (9/73, 12.33%), lineage 2.2.1-Asia Ancestral 2 (9/73, 12.33%), lineage 2.2.1-Asia Ancestral 3 (18/73, 24.66%), and lineage 2.2.1-Modern Beijing (39/73, 53.42%). Lineage 3 included lineage 3.2 (14/52, 26.92%) and lineage 3.3 (38/52, 73.08%), while lineage 4 included lineage 4.1 (3/36, 8.33%), lineage 4.2 (2/36, 5.66%), lineage 4.4.2 (1/36, 2.78%), lineage 4.5 (28/36, 77.78%) and lineage 4.8 (2/36, 5.66%), all of which were consistent with the PCA results. One hundred thirty-six markers were proposed for discriminating known circulating strains. Reconstruction of a phylogenetic tree using the 136 SNPs resulted in a tree with the same number of delineated clades. Based on geographical location analysis, the composition of Lineage 2 in Kashgar prefecture (45.34%) was lower compared to other regions in China (54.35%-90.27%), while the composition of Lineage 3 (32.30%) was much higher than in other regions of China (0.92%-2.01%), but lower compared to the bordering Pakistan (70.40%). Conclusion Three lineages were identified in M.tb clinical strains from Kashgar prefecture, with 136 branch-specific SNP. Kashgar borders with countries that have a high incidence of tuberculosis, such as Pakistan and India, which results in a large difference between the M.tb lineage and sublineage distribution in this region and other provinces of China. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07307-4.
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Affiliation(s)
- Ai-Min Xu
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Chuan-Jiang He
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Xiang Cheng
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - AniKiz Abuduaini
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Zureguli Tuerxun
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Yin-Zhong Sha
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Aihemaitijiang Kaisaier
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Hong-Mei Peng
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Ya-Hui Zhen
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Su-Jie Zhang
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Jing-Ran Xu
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China
| | - Li Li
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China.
| | - Xiao-Guang Zou
- The First People's Hospital of Kashgar, No.66, Yingbin Avenue, Xinjiang, Kashgar, 844000, Kashgar City, China.
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Wang M, Zhang Y, Huang C, Li J, Shen X, Zhao G, Jiang Y, Pan Q. A Whole-Genome Sequencing-Based Study to Delineate the Risk and Characteristics of Tuberculosis Transmission in an Insular Population Over 10 Years in Shanghai. Front Microbiol 2022; 12:768659. [PMID: 35250898 PMCID: PMC8888905 DOI: 10.3389/fmicb.2021.768659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background Tuberculosis (TB) has remained a tough problem in China. This study aims to identify the risk of tuberculosis transmission and to assess its characteristics. Methods We performed a molecular epidemiological study for patients with culture-positive Mycobacterium tuberculosis (M. tuberculosis) in Shanghai, from 2009 to 2018. Demographic information was obtained from the Tuberculosis Information Management System. Whole-genome sequencing (WGS) was conducted with a threshold of 12 single-nucleotide polymorphisms (SNPs) to distinguish the genomic cluster. To analyze the characteristics of TB transmission, the contact investigation for clustered cases was performed. Results In total, 94 (27.25%) of the 345 enrolled patients were grouped into 42 genomic clusters, indicating local transmission of M. tuberculosis strains. Compared to a health system delay <14 days, patients with a health system delay ≥14 days [adjusted odds ratios (AOR) = 2.57, 95% confidence interval (CI): 1.34–4.95] were more likely to be clustered. Patients under 65 years old (AOR = 3.11, 95% CI: 1.76–5.49), residents (AOR = 2.43, 95% CI: 1.18–4.99), and Beijing genotype strains (AOR = 3.35, 95% CI: 1.32–8.53) were associated with increased risk of clustering. Interestingly, patients with resistance to isoniazid (AOR = 2.36, 95% CI: 1.15–4.88) had a higher risk of transmission. Sixteen confirmed/probable epidemiological links were identified. Local transmission of imported cases and household transmission were prominent. Conclusion Health system delay is a crucial factor for TB transmission. Patients with resistance to isoniazid should be priority targets for contact investigation to reduce transmission.
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Affiliation(s)
- Min Wang
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.,Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Yangyi Zhang
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.,Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Cheng Huang
- Department of Tuberculosis Control, Chongming District Center for Disease Control and Prevention, Shanghai, China
| | - Jing Li
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xin Shen
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Genming Zhao
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Yuan Jiang
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qichao Pan
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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Abstract
Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP) was 79.71%, 86.30%, 76.47%, 88.37%, 83.33%, 70.00% and 70.00%, respectively. The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17% (0.8615, 0.9646), and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86% (0.8158, 0.9796). The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
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Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, Cui Z, Chongsuvivatwong V, Palittapongarnpim P. Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2. Microb Genom 2021; 7. [PMID: 34787541 PMCID: PMC8743535 DOI: 10.1099/mgen.0.000697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) lineage 2 (L2) strains are present globally, contributing to a widespread tuberculosis (TB) burden, particularly in Asia where both prevalence of TB and numbers of drug resistant TB are highest. The increasing availability of whole-genome sequencing (WGS) data worldwide provides an opportunity to improve our understanding of the global genetic diversity of Mtb L2 and its association with the disease epidemiology and pathogenesis. However, existing L2 sublineage classification schemes leave >20 % of the Modern Beijing isolates unclassified. Here, we present a revised SNP-based classification scheme of L2 in a genomic framework based on phylogenetic analysis of >4000 L2 isolates from 34 countries in Asia, Eastern Europe, Oceania and Africa. Our scheme consists of over 30 genotypes, many of which have not been described before. In particular, we propose six main genotypes of Modern Beijing strains, denoted L2.2.M1–L2.2.M6. We also provide SNP markers for genotyping L2 strains from WGS data. This fine-scale genotyping scheme, which can classify >98 % of the studied isolates, serves as a basis for more effective monitoring and reporting of transmission and outbreaks, as well as improving genotype-phenotype associations such as disease severity and drug resistance. This article contains data hosted by Microreact.
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Affiliation(s)
- Yuttapong Thawornwattana
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose 204-8533, Japan
| | - Htet Myat Win Maung
- National TB Control Programme, Department of Public Health, Ministry of Health and Sports, Naypyitaw 15011, Myanmar.,Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Had Yai 90110, Thailand
| | - Zhezhe Cui
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Had Yai 90110, Thailand.,Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, 530028, PR China
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,National Science and Technology Development Agency, Pathumthani 12120, Thailand
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Li H, Liu C, Liang M, Liu D, Zhao B, Shi J, Zhao Y, Ou X, Zhang G. Tuberculosis Outbreak in an Educational Institution in Henan Province, China. Front Public Health 2021; 9:737488. [PMID: 34712640 PMCID: PMC8545879 DOI: 10.3389/fpubh.2021.737488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
On June 17, 2018, a case of pulmonary tuberculosis (TB) was reported among students at a senior high school in Luoning, China. The outbreak encompassed a total of 23 cases along with TB screening in the whole school by means of PPD and chest X-ray. By the end of September 2018, the entire 9 cases cultured positive had epidemiological association. All of the 9 Mycobacterium tuberculosis (Mtb) isolates available were sensitive to all drugs tested and had similar spoligotyping and 15 loci mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) profile. Whole-genome sequencing (WGS) of the Mtb isolates revealed 20 variable nucleotide positions within 8 cases, indicating a clonal outbreak. The index case, which was first identified and diagnosed, is separated from the cluster by a minimum number of 95 distinct SNPs. Minimum distance spanning tree (MST) indicted that the 8 cases were indeed part of a single transmission chain. It was concluded that this is an epidemic situation of TB outbreak exposed by the aggrieved index case at school, which was caused by the veiled infectious case wherein a student was suffering from TB and attending school simultaneously.
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Affiliation(s)
- Hui Li
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Chunfa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Liang
- Luoyang Center for Disease Control and Prevention, Luoyang, China
| | - Dongxin Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Shi
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guolong Zhang
- Henan Center for Disease Control and Prevention, Zhengzhou, China
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Wu B, Zhu W, Wang Y, Wang Q, Zhou L, Liu Z, Bi L, Barun M, Kreiswirth BN, Chen L, Chen S, Wang X, Wang W. Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations. Cell Biosci 2021; 11:162. [PMID: 34419157 PMCID: PMC8379736 DOI: 10.1186/s13578-021-00673-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Background There are seven human-adaptation lineages of Mycobacterium tuberculosis (Mtb). Tuberculosis (TB) dissemination is strongly influenced by human movements and host genetics. The detailed lineage distribution evolution of Mtb in Zhejiang Province is unknown. We aim to determine how different sub-lineages are transmitted and distributed within China and Zhejiang Province. Methods We analysed whole-genome sequencing data for a worldwide collection of 1154 isolates and a provincial collection of 1296 isolates, constructed the best-scoring maximum likelihood phylogenetic tree. Bayesian evolutionary analysis was used to calculate the latest common ancestor of lineages 2 and 4. The antigenic diversity of human T cell epitopes was evaluated by calculating the pairwise dN/dS ratios. Results Of the Zhejiang isolates, 964 (74.38%) belonged to lineage 2 and 332 (25.62%) belonged to lineage 4. The distributions of the sub-lineages varied across the geographic regions of Zhejiang Province. L2.2 is the most ancient sub-lineage in Zhejiang, first appearing approximately 6897 years ago (95% highest posterior density interval (HDI): 6513–7298). L4.4 is the most modern sub-lineage, first appearing approximately 2217 years ago (95% HDI: 1864–2581). The dN/dS ratios showed that the epitope and non-epitope regions of lineage 2 strains were significantly (P < 0.001) more conserved than those of lineage 4. Conclusions An increase in the frequency of lineage 4 may reflect its successful transmission over the last 20 years. The recent common ancestors of the sub-lineages and their transmission routes are relevant to the entry of humans into China and Zhejiang Province. Diversity in T cell epitopes may prevent Mycobacterium tuberculosis from being recognized by the immune system. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00673-7.
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Affiliation(s)
- Beibei Wu
- Zhejiang Center for Disease Control and Prevention, Institute of Tuberculosis Control, 3399 Binsheng Road, Binjiang District, Hangzhou, 310051, Zhejiang, China
| | - Wenlong Zhu
- Department of Epidemiology, School of Public Health, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Yue Wang
- Department of Epidemiology, School of Public Health, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Qi Wang
- Department of Epidemiology, School of Public Health, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Lin Zhou
- Zhejiang Center for Disease Control and Prevention, Institute of Tuberculosis Control, 3399 Binsheng Road, Binjiang District, Hangzhou, 310051, Zhejiang, China
| | - Zhengwei Liu
- Zhejiang Center for Disease Control and Prevention, Institute of Tuberculosis Control, 3399 Binsheng Road, Binjiang District, Hangzhou, 310051, Zhejiang, China
| | - Lijun Bi
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mathema Barun
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Barry N Kreiswirth
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Liang Chen
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Songhua Chen
- Zhejiang Center for Disease Control and Prevention, Institute of Tuberculosis Control, 3399 Binsheng Road, Binjiang District, Hangzhou, 310051, Zhejiang, China
| | - Xiaomeng Wang
- Zhejiang Center for Disease Control and Prevention, Institute of Tuberculosis Control, 3399 Binsheng Road, Binjiang District, Hangzhou, 310051, Zhejiang, China.
| | - Weibing Wang
- Department of Epidemiology, School of Public Health, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China. .,Department of Epidemiology, Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China.
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Lin D, Wang J, Cui Z, Ou J, Huang L, Wang Y. A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China. BMC Infect Dis 2021; 21:840. [PMID: 34412585 PMCID: PMC8377953 DOI: 10.1186/s12879-021-06385-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is caused by a bacterium called Mycobacterium tuberculosis (Mtb). China is the third in top 8 high TB burden countries and Guangxi is one of the high incidence areas in South China. Determine bacterial factors that affected TB incidence rate is a step toward Ending the TB epidemic. RESULTS Genomes of M. tuberculosis cultures from a relatively high and low incidence region in Guangxi have been sequenced. 347 of 358(96.9%) were identified as M. tuberculosis. All the strains belong to Lineage 2 and Lineage 4, except for one in Lineage 1. We found that the genetic structure of the M. tuberculosis population in each county varies enormously. Low incidence rate regions have a lower prevalence of Beijing genotypes than other regions. Four isolates which harbored mutT4-48 also had mutT2-58 mutations. It is suggested that strains from the ancestors of modern Beijing lineage is circulating in Guangxi. Strains of modern Beijing lineage (OR=2.04) were more likely to acquire drug resistances than Lineage 4. Most of the lineage differentiation SNPs are related to cell wall biosynthetic pathways. CONCLUSIONS These results provided a higher resolution to better understand the history of transmission of M. tuberculosis from/to South China. And the incidence rate of tuberculosis might be affected by bacterial population structure shaped by demographic history. Our findings also support the hypothesis that Modern Beijing lineage originated in South China.
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Affiliation(s)
- Dingwen Lin
- Department of Nutrition and School Health, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, China
| | - Junning Wang
- Zeta Biosciences(Shanghai) Co.,Ltd., Shanghai, China
| | - Zhezhe Cui
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, China
| | - Jing Ou
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, China
| | - Liwen Huang
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, China
| | - Ya Wang
- Zeta Biosciences(Shanghai) Co.,Ltd., Shanghai, China
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Liu M, Xu P, Liao X, Li Q, Chen W, Gao Q, Li N, Luo T, Chen L. Molecular epidemiology and drug-resistance of tuberculosis in Luodian revealed by whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2021; 93:104979. [PMID: 34175481 DOI: 10.1016/j.meegid.2021.104979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
In this study, we aimed to investigate the molecular epidemiology and drug-resistance profiles of tuberculosis (TB) in Luodian, an area with highest TB incidence and limited healthcare resources in Guizhou, China. The passive case finding strategy was used to identify suspected pulmonary TB with symptoms, and individuals with positive Mycobacterium tuberculosis (MTB) culture were enrolled from May 22, 2018 to April 21, 2019. All the 107 cases except three came from nine towns, including 55.1% from Longping and Bianyang. The phylogeny tree showed that 53.3% of strains were Lineage 2 (Beijing genotype), while 46.7% were Lineage 4 (Euro-American genotype). Among Lineage 2 strains, 66.7% were of "modern" Beijing type. Seven clusters with genomic distance within 12 SNPs were identified. The clusters included 14 strains, accounting for a clustering rate of 13.1%. The distance separating the clustered cases was between 2.1 and 71.0 km (Km), with an average paired distance of 21.8 Km (interquartile range, 2.8-38.0 Km). Based on the gene mutations associated with drug-resistance, we predicted that 4.8% of strains were resistant to isoniazid, 3.7% to rifampicin, and 3.7% to streptomycin; only one strain (0.9%) had multidrug resistance (MDR). This study found low drug-resistance rates in Luodian, and the sub-lineage of the "modern" Beijing branch has recent expansion in Luodian. This work may also serve as a genomic baseline to assess the evolution and spread of MTB in Guizhou.
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Affiliation(s)
- Mei Liu
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Dongan Road No.131, Shanghai 200032, China
| | - Peng Xu
- Key Laboratory of Infectious Disease & Biosafety, Institute of life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province 563000, China
| | - Xingwei Liao
- Department of Infectious Diseases, Hospital of Luodian County, No.96 Jiefang East Road, Luodian 550100, Guizhou, China
| | - Qing Li
- Department of Respiratory Medicine, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi 563000, Guizhou, China
| | - Wei Chen
- Department of TB Control, Center of Disease Control and Prevention, Guiyang 550004, Guizhou, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Dongan Road No.131, Shanghai 200032, China
| | - Nana Li
- Department of Respiratory Medicine, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi 563000, Guizhou, China
| | - Tao Luo
- Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, No.17 People's South Road, Chengdu 610041, China.
| | - Ling Chen
- Department of Respiratory Medicine, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi 563000, Guizhou, China.
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Menardo F, Gagneux S, Freund F. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis. Mol Biol Evol 2021; 38:290-306. [PMID: 32667991 PMCID: PMC8480183 DOI: 10.1093/molbev/msaa179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Freund
- Department of Plant Biodiversity and Breeding Informatics, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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44
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Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A 2021; 118:2017831118. [PMID: 33879609 DOI: 10.1073/pnas.2017831118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host-pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.
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45
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A population-based genomic epidemiological study of the source of tuberculosis infections in an emerging city: Shenzhen, China. LANCET REGIONAL HEALTH-WESTERN PACIFIC 2021; 8:100106. [PMID: 34327429 PMCID: PMC8315418 DOI: 10.1016/j.lanwpc.2021.100106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/13/2021] [Accepted: 01/27/2021] [Indexed: 11/28/2022]
Abstract
Background Tuberculosis (TB) in emerging cities is often a disease of recent immigrants, and understanding this epidemiology is crucial for designing effective control and prevention strategies. Methods We conducted a retrospective population-based genomic epidemiological study of culture-positive pulmonary TB patients diagnosed between June 2014 and November 2017 in the Bao'an District of Shenzhen, a Chinese city with dramatic recent growth. After whole genome sequencing, transmission clusters were defined as strains differing by no more than 12 SNPs. Findings Of 1696 culture-positive TB patients, 93•8% (1591/1696) were migrants, with 51•6% (821/1591) employed in housekeeping or unemployed. Of the 1460 migrants with known residence time, 47•7% (697/1460) developed TB within two years after arriving in Bao'an. Only 12•2% (207/1696) of Bao'an isolates were in genomic clusters, indicating that recent transmission was not the primary cause of TB in Bao'an. The isolates’ median terminal branch length was 56 SNPs, more than could have accumulated since the arrival of the migrants in Bao'an. The migrants’ isolates had genotypic distributions similar to those in their home provinces. One strain isolated in Bao'an belonged to a clade circulating in the patient's home province, providing further evidence that the strains were brought to Bao'an with the migrants. Interpretation TB in the Bao'an District is principally caused by reactivation of infections acquired by migrants in their home provinces. Nearly half developed TB within two years after arriving in Bao'an, suggesting a need for increased TB screening of migrants, especially housekeeping workers and the unemployed. Funding Sanming Project of Medicine in Shenzhen; National Science and Technology Major Project of China; Natural Science Foundation of China.
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Srilohasin P, Prammananan T, Faksri K, Phelan JE, Suriyaphol P, Kamolwat P, Smithtikarn S, Disratthakit A, Regmi SM, Leechawengwongs M, Twee-Hee Ong R, Teo YY, Tongsima S, Clark TG, Chaiprasert A. Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto -Beijing genotype. Emerg Microbes Infect 2020; 9:2632-2641. [PMID: 33205698 PMCID: PMC7738298 DOI: 10.1080/22221751.2020.1852891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/15/2020] [Indexed: 01/21/2023]
Abstract
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With ≤ 12 pairwise SNP distances, 43.2% of L2.1 patients belong to MDR-TB or XDR-TB transmission clusters suggesting a high level of clonal expansion across four Thai provinces. All XDR-TB (100%) were likely due to transmission rather than inadequate treatment. We found a 47 mutation signature and a partial deletion of the fadD14 gene in the circulating XDR-TB cluster, which can be used for surveillance of this rare and resilient M. tuberculosis strain-type that is causing increasing health burden. We also detected three novel deletion positions, a deletion of 1285 bp within desA3 (Rv3230c), large deletions in the plcB, plcA, and ppe38 gene which may play a role in the virulence, pathogenesis or evolution of the L2.1 strain-type.
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Affiliation(s)
- Prapaporn Srilohasin
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
| | - Therdsak Prammananan
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Phalin Kamolwat
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Saijai Smithtikarn
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Areeya Disratthakit
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Sanjib Mani Regmi
- Department of Microbiology, Gandaki Medical College Teaching Hospital, Pokhara, Nepal
| | - Manoon Leechawengwongs
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
- Vichaiyut Hospital, Bangkok, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
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47
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Hicks ND, Giffen SR, Culviner PH, Chao MC, Dulberger CL, Liu Q, Stanley S, Brown J, Sixsmith J, Wolf ID, Fortune SM. Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis. PLoS Pathog 2020; 16:e1009063. [PMID: 33253310 PMCID: PMC7738170 DOI: 10.1371/journal.ppat.1009063] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/15/2020] [Accepted: 10/09/2020] [Indexed: 01/26/2023] Open
Abstract
Genomic dissection of antibiotic resistance in bacterial pathogens has largely focused on genetic changes conferring growth above a single critical concentration of drug. However, reduced susceptibility to antibiotics-even below this breakpoint-is associated with poor treatment outcomes in the clinic, including in tuberculosis. Clinical strains of Mycobacterium tuberculosis exhibit extensive quantitative variation in antibiotic susceptibility but the genetic basis behind this spectrum of drug susceptibility remains ill-defined. Through a genome wide association study, we show that non-synonymous mutations in dnaA, which encodes an essential and highly conserved regulator of DNA replication, are associated with drug resistance in clinical M. tuberculosis strains. We demonstrate that these dnaA mutations specifically enhance M. tuberculosis survival during isoniazid treatment via reduced expression of katG, the activator of isoniazid. To identify DnaA interactors relevant to this phenotype, we perform the first genome-wide biochemical mapping of DnaA binding sites in mycobacteria which reveals a DnaA interaction site that is the target of recurrent mutation in clinical strains. Reconstructing clinically prevalent mutations in this DnaA interaction site reproduces the phenotypes of dnaA mutants, suggesting that clinical strains of M. tuberculosis have evolved mutations in a previously uncharacterized DnaA pathway that quantitatively increases resistance to the key first-line antibiotic isoniazid. Discovering genetic mechanisms that reduce drug susceptibility and support the evolution of high-level drug resistance will guide development of biomarkers capable of prospectively identifying patients at risk of treatment failure in the clinic.
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Affiliation(s)
- Nathan D. Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Samantha R. Giffen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Peter H. Culviner
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Michael C. Chao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jessica Brown
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jaimie Sixsmith
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ian D. Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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48
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Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity (Edinb) 2020; 126:1-9. [PMID: 33060846 DOI: 10.1038/s41437-020-00377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/09/2022] Open
Abstract
Recent progress in genomic sequencing from patient samples has allowed for the first detailed insight into the within-host genetic diversity of Mycobacterium tuberculosis (M.TB), revealing remarkably low levels of variation. While this has often been attributed to low mutation rates, other factors have been described, including resistance evolution (i.e., selective sweeps), widespread purifying and background selection, and, more recently, progeny skew. Here we review recent findings pertaining to the processes governing the evolutionary dynamics of M.TB, discuss their implications for improving our understanding of this important human pathogen, and make recommendations for future work. Significantly, this emerging evolutionary framework involving the joint estimation of demographic, selective, and reproductive processes is forming a new paradigm for the study of within-host pathogen evolution that will be widely applicable across organisms.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
| | - Susanna J Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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49
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Godfroid M, Dagan T, Merker M, Kohl TA, Diel R, Maurer FP, Niemann S, Kupczok A. Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak. PLoS Pathog 2020; 16:e1008357. [PMID: 32997707 PMCID: PMC7549793 DOI: 10.1371/journal.ppat.1008357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/12/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
In genome evolution, genetic variants are the source of diversity, which natural selection acts upon. Treatment of human tuberculosis (TB) induces a strong selection pressure for the emergence of antibiotic resistance-conferring variants in the infecting Mycobacterium tuberculosis (MTB) strains. MTB evolution in response to treatment has been intensively studied and mainly attributed to point substitutions. However, the frequency and contribution of insertions and deletions (indels) to MTB genome evolution remains poorly understood. Here, we analyzed a multi-drug resistant MTB outbreak for the presence of high-quality indels and substitutions. We find that indels are significantly enriched in genes conferring antibiotic resistance. Furthermore, we show that indels are inherited during the outbreak and follow a molecular clock with an evolutionary rate of 5.37e-9 indels/site/year, which is 23 times lower than the substitution rate. Inherited indels may co-occur with substitutions in genes along related biological pathways; examples are iron storage and resistance to second-line antibiotics. This suggests that epistatic interactions between indels and substitutions affect antibiotic resistance and compensatory evolution in MTB.
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Affiliation(s)
- Maxime Godfroid
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Roland Diel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany
- Lungenclinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Florian P. Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Anne Kupczok
- Institute of General Microbiology, Kiel University, Kiel, Germany
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50
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Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microb Genom 2020; 6:mgen000418. [PMID: 32735210 PMCID: PMC7641424 DOI: 10.1099/mgen.0.000418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach on transmission inferences for Mycobacterium tuberculosis, we conducted an experiment in which five genomic epidemiology groups applied variant-identification pipelines to the same outbreak sequence data. We compared the variants identified by each group in addition to transmission and phylogenetic inferences made with each variant set. To measure the performance of commonly used variant-identification tools, we simulated an outbreak. We compared the performance of three mapping algorithms, five variant callers and two variant filters in recovering true outbreak variants. Finally, we investigated the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant-calling approaches used by different groups do not recover consistent sets of variants, which can lead to conflicting transmission inferences. Further, performance in recovering true variation varied widely across approaches. While no single variant-identification approach outperforms others in both recovering true genome-wide and outbreak-level variation, variant-identification algorithms calibrated upon real sequence data or that incorporate local reassembly outperform others in recovering true pairwise differences between isolates. The choice of variant filters contributed to extensive differences across pipelines, and applying increasingly stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. Commonly used approaches to identify M. tuberculosis genomic variation have variable performance, particularly when predicting potential transmission links from pairwise genetic distances. Phylogenetic reconstruction may be improved by less stringent variant filtering. Approaches that improve variant identification in repetitive, hypervariable regions, such as long-read assemblies, may improve transmission inference.
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Affiliation(s)
- Katharine S. Walter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Qingyun Liu
- School of Basic Medical Science of Fudan University, Shanghai, PR China
| | - Jolene Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
- Oswaldo Cruz Foundation, Campo Grande, Brazil
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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