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Che Y, Li X, Chen T, Lu Y, Sang G, Gao J, Gao J, Liu Z, He T, Chen Y. Transmission dynamics of drug-resistant tuberculosis in Ningbo, China: an epidemiological and genomic analysis. Front Cell Infect Microbiol 2024; 14:1327477. [PMID: 38384306 PMCID: PMC10879548 DOI: 10.3389/fcimb.2024.1327477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Background Tuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a significant public health concern in Ningbo, China. Understanding its molecular epidemiology and spatial distribution is paramount for effective control. Methods From December 24, 2020, to March 12, 2023, we collected clinical Mycobacterium tuberculosis (MTB) strains in Ningbo, with whole-genome sequencing performed on 130 MTB strains. We analyzed DR-related gene mutations, conducted phylogenetic and phylodynamic analyses, identified recent transmission clusters, and assessed spatial distribution. Results Among 130 DR-TB cases, 41% were MDR-TB, 36% pre-XDR-TB, 19% RR-TB, and 3% HR-TB. The phylogenetic tree showed that 90% of strains were Lineage 2 (Beijing genotype), while remaining 10% were Lineage 4 (Euro-American genotype). The spatial analysis identified hotspots of DR-TB in Ningbo's northern region, particularly in traditional urban centers. 31 (24%) of the DR-TB cases were grouped into 7 recent transmission clusters with a large outbreak cluster containing 15 pre-XDR-TB patients. Epidemiological analyses suggested a higher risk of recent DR-TB transmission among young adult patients who frequently visited Internet cafes, game rooms, and factories. Conclusion Our study provides comprehensive insights into the epidemiology and genetics of DR-TB in Ningbo. The presence of genomic clusters highlights recent transmission events, indicating the need for targeted interventions. These findings are vital for informing TB control strategies in Ningbo and similar settings.
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Affiliation(s)
- Yang Che
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Tong Chen
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Guoxin Sang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Junli Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Junshun Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhengwei Liu
- The Institute of Tuberculosis (TB) Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Tianfeng He
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Yi Chen
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
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2
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Bermúdez-Hernández GA, Pérez-Martínez D, Ortiz-León MC, Muñiz-Salazar R, Licona-Cassani C, Zenteno-Cuevas R. Mutational Dynamics Related to Antibiotic Resistance in M. tuberculosis Isolates from Serial Samples of Patients with Tuberculosis and Type 2 Diabetes Mellitus. Microorganisms 2024; 12:324. [PMID: 38399727 PMCID: PMC10892438 DOI: 10.3390/microorganisms12020324] [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: 12/14/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic variation in tuberculosis is influenced by the host environment, patients with comorbidity, and tuberculosis-type 2 diabetes mellitus (TB-T2DM) and implies a higher risk of treatment failure and development of drug resistance. Considering the above, this study aimed to evaluate the influence of T2DM on the dynamic of polymorphisms related to antibiotic resistance in TB. Fifty individuals with TB-T2DM and TB were initially characterized, and serial isolates of 29 of these individuals were recovered on day 0 (diagnosis), 30, and 60. Genomes were sequenced, variants related to phylogeny and drug resistance analyzed, and mutation rates calculated and compared between groups. Lineage X was predominant. At day 0 (collection), almost all isolates from the TB group were sensitive, apart from four isolates from the TB-T2DM group showing the mutation katG S315T, from which one isolate had the mutations rpoB S450L, gyrA A90G, and gyrA D94G. This pattern was observed in a second isolate at day 30. The results provide a first overview of the dynamics of mutations in resistance genes from individuals with TB-T2DM, describing an early development of resistance to isoniazid and a rapid evolution of resistance to other drugs. Although preliminary, these results help to explain the increased risk of drug resistance in individuals with TB and T2DM.
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Affiliation(s)
- Gustavo A. Bermúdez-Hernández
- Biomedical Sciences Doctoral Program, Institute of Health Sciences, University of Veracruz, Xalapa 91190, Veracruz, Mexico;
| | - Damián Pérez-Martínez
- Institute of Public Health, University of Veracruz, Xalapa 91190, Veracruz, Mexico; (D.P.-M.); (M.C.O.-L.)
| | - Maria Cristina Ortiz-León
- Institute of Public Health, University of Veracruz, Xalapa 91190, Veracruz, Mexico; (D.P.-M.); (M.C.O.-L.)
| | - Raquel Muñiz-Salazar
- School of Health Sciences, Autonomous University of Baja California, Ensenada 22860, Baja California, Mexico;
| | - Cuauhtemoc Licona-Cassani
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Nuevo León, Mexico;
| | - Roberto Zenteno-Cuevas
- Institute of Public Health, University of Veracruz, Xalapa 91190, Veracruz, Mexico; (D.P.-M.); (M.C.O.-L.)
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3
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He W, Tan Y, Song Z, Liu B, Wang Y, He P, Xia H, Huang F, Liu C, Zheng H, Pei S, Liu D, Ma A, Cao X, Zhao B, Ou X, Wang S, Zhao Y. Endogenous relapse and exogenous reinfection in recurrent pulmonary tuberculosis: A retrospective study revealed by whole genome sequencing. Front Microbiol 2023; 14:1115295. [PMID: 36876077 PMCID: PMC9981662 DOI: 10.3389/fmicb.2023.1115295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Background Tuberculosis may reoccur due to reinfection or relapse after initially successful treatment. Distinguishing the cause of TB recurrence is crucial to guide TB control and treatment. This study aimed to investigate the source of TB recurrence and risk factors related to relapse in Hunan province, a high TB burden region in southern China. Methods A population-based retrospective study was conducted on all culture-positive TB cases in Hunan province, China from 2013 to 2020. Phenotypic drug susceptibility testing and whole-genome sequencing were used to detect drug resistance and distinguish between relapse and reinfection. Pearson chi-square test and Fisher exact test were applied to compare differences in categorical variables between relapse and reinfection. The Kaplan-Meier curve was generated in R studio (4.0.4) to describe and compare the time to recurrence between different groups. p < 0.05 was considered statistically significant. Results Of 36 recurrent events, 27 (75.0%, 27/36) paired isolates were caused by relapse, and reinfection accounted for 25.0% (9/36) of recurrent cases. No significant difference in characteristics was observed between relapse and reinfection (all p > 0.05). In addition, TB relapse occurs earlier in patients of Tu ethnicity compared to patients of Han ethnicity (p < 0.0001), whereas no significant differences in the time interval to relapse were noted in other groups. Moreover, 83.3% (30/36) of TB recurrence occurred within 3 years. Overall, these recurrent TB isolates were predominantly pan-susceptible strains (71.0%, 49/69), followed by DR-TB (17.4%, 12/69) and MDR-TB (11.6%, 8/69), with mutations mainly in codon 450 of the rpoB gene and codon 315 of the katG gene. 11.1% (3/27) of relapse cases had acquired new resistance during treatment, with fluoroquinolone resistance occurring most frequently (7.4%, 2/27), both with mutations in codon 94 of gyrA. Conclusion Endogenous relapse is the main mechanism leading to TB recurrences in Hunan province. Given that TB recurrences can occur more than 4 years after treatment completion, it is necessary to extend the post-treatment follow-up period to achieve better management of TB patients. Moreover, the relatively high frequency of fluoroquinolone resistance in the second episode of relapse suggests that fluoroquinolones should be used with caution when treating TB cases with relapse, preferably guided by DST results.
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Affiliation(s)
- Wencong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yunhong Tan
- Hunan Provincial Chest Hospital, Tuberculosis Control Institution of Hunan Province, Changsha, Hunan, China
| | - Zexuan Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Binbin Liu
- Hunan Provincial Chest Hospital, Tuberculosis Control Institution of Hunan Province, Changsha, Hunan, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, 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
| | - Hui Xia
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fei Huang
- 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
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, China
| | - Dongxin Liu
- Shenzhen Third People's Hospital, Shenzhen, China
| | - Aijing Ma
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaolong Cao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- 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
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
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4
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Thakur M, Muniyappa K. Macrophage activation highlight an important role for NER proteins in the survival, latency and multiplication of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2023; 138:102284. [PMID: 36459831 DOI: 10.1016/j.tube.2022.102284] [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: 08/15/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Nucleotide excision repair (NER) is one of the most extensively studied DNA repair processes in both prokaryotes and eukaryotes. The NER pathway is a highly conserved, ATP-dependent multi-step process involving several proteins/enzymes that function in a concerted manner to recognize and excise a wide spectrum of helix-distorting DNA lesions and bulky adducts by nuclease cleavage on either side of the damaged bases. As such, the NER pathway of Mycobacterium tuberculosis (Mtb) is essential for its survival within the hostile environment of macrophages and disease progression. This review focuses on present published knowledge about the crucial roles of Mtb NER proteins in the survival and multiplication of the pathogen within the macrophages and as potential targets for drug discovery.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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5
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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: 29] [Impact Index Per Article: 14.5] [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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6
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Jones RM, Adams KN, Eldesouky HE, Sherman DR. The evolving biology of Mycobacterium tuberculosis drug resistance. Front Cell Infect Microbiol 2022; 12:1027394. [PMID: 36275024 PMCID: PMC9579286 DOI: 10.3389/fcimb.2022.1027394] [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: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/13/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.
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Affiliation(s)
| | | | | | - David R. Sherman
- Department of Microbiology, University of Washington, Seattle, WA, United States
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7
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Mave V, Chen L, Ranganathan UD, Kadam D, Vishwanathan V, Lokhande R, S SK, Kagal A, Pradhan N, Shivakumar SVBY, Paradkar MS, Deshmukh S, Tornheim JA, Kornfeld H, Farhat M, Gupta A, Padmapriyadarsini C, Gupte N, Golub JE, Mathema B, Kreiswirth BN. Whole Genome Sequencing Assessing Impact of Diabetes Mellitus on Tuberculosis Mutations and Type of Recurrence in India. Clin Infect Dis 2022; 75:768-776. [PMID: 34984435 PMCID: PMC9477453 DOI: 10.1093/cid/ciab1067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evidence describing the impact of diabetes mellitus (DM) on the recurrence and mutation rate of Mycobacterium tuberculosis (Mtb) is limited. METHODS This study was nested in 3 cohort studies of tuberculosis (TB) patients with and without DM in India. Paired Mtb isolates recovered at baseline and treatment failure/recurrence underwent whole genome sequencing. We compared acquisition of single-nucleotide polymorphisms (SNPs), TB drug resistance mutations, and type of recurrence (endogenous reactivation [<8 SNPs] or exogenous reinfection [≥8 SNPs]) by DM status. RESULTS Of 1633 enrolled in the 3 parent cohorts, 236 (14.5%) had microbiologically confirmed TB treatment failure/recurrence; 76 Mtb isolate pairs were available for sequencing (22 in TB-DM and 54 in TB-only). The SNP acquisition rate was overall was 0.43 (95% confidence interval [CI], .25-.64) per 1 person-year (PY); 0.77 (95% CI, .40-1.35) per 1 PY, and 0.44 (95% CI, .19-.86) per 1 PY at treatment failure and recurrence, respectively. Significant difference in SNP rates by DM status was seen at recurrence (0.21 [95% CI, .04-.61]) per 1 PY for TB-only vs 1.28 (95% CI, .41-2.98) per 1 PY for TB-DM; P = .02). No significant difference in SNP rates by DM status was observed at treatment failure. Acquired TB drug resistance was seen in 4 of 18 (22%) in TB-DM vs 4 of 45 (9%) in TB-only (P = .21). Thirteen (17%) participants had exogenous reinfection; the reinfection rate at recurrence was 25% (3/12) for TB-DM vs 17% (4/24) in TB-only (P = .66). CONCLUSIONS Considerable intrahost Mtb mutation rates were present at recurrence among patients with DM in India. One-fourth of patients with DM had exogenous reinfection at recurrence.
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Affiliation(s)
- Vidya Mave
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins India, Pune, India
| | - Liang Chen
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, New Jersey, USA
| | | | - Dileep Kadam
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | | | - Rahul Lokhande
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | - Siva Kumar S
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Anju Kagal
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | - Neeta N Pradhan
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins India, Pune, India
| | | | - Mandar S Paradkar
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins India, Pune, India
| | - Sona Deshmukh
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins India, Pune, India
| | | | | | - Maha Farhat
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amita Gupta
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Nikhil Gupte
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins India, Pune, India
| | - Jonathan E Golub
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Barry N Kreiswirth
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, New Jersey, USA
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8
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Jiang H, Zhu C, Qin L, Wu X, Yin J, Guo Y, Ma H, Jia J, Huo F, Xue Y, Gao M, Li W. Case report: A 9-year systematic treatment failure of a pulmonary tuberculosis patient. Front Public Health 2022; 10:966891. [PMID: 36148360 PMCID: PMC9487995 DOI: 10.3389/fpubh.2022.966891] [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: 06/11/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Objective To explore the reasons of failure in a case of pulmonary tuberculosis (PTB) after 9 years systematic treatment. Methods We extracted the patients' treatment history, drug susceptibility testing (DST), Computed tomography (CT) images, and sequenced the isolated strains by whole gene sequencing (WGS). Results Although most results of the phenotypical DSTs were consistent with the genotype DST, the occurrence of gene resistance to amikacin (AMK), capreomycin (CAP), moxifloxacin (MFX) was earlier than the phenotypical DST. Based on the continuously reversed results of phenotypical DSTs, CT images in different stages and WGS, it can be confirmed that the patient was infected with two different strains of Mycobacterium tuberculosis (M.TB). Moreover, severe cavities may be another factor leading to treatment failure. Conclusion Given the suggestive effect of genotype DST is earlier than the phenotypical DST, so genotype DST can play a better guiding role in patients with MDR-TB. Additionally, for patients who have not been cured for a long time, medication should be more cautious and the role of WGS in drug resistance surveillance should be fully utilized.
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Affiliation(s)
- Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China,Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Liyi Qin
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Xiaoguang Wu
- Beijing Chest Hospital, Capital Medical University, Beijing, China,Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Yijia Guo
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Huan Ma
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Junnan Jia
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Fengmin Huo
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Yi Xue
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Mengqiu Gao
- Beijing Chest Hospital, Capital Medical University, Beijing, China,Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China,*Correspondence: Weimin Li
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9
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Tomasi FG, Hall AMJ, Schweber JTP, Dulberger CL, McGowen K, Liu Q, Fortune SM, Helaine S, Rubin EJ. A tRNA-Acetylating Toxin and Detoxifying Enzyme in Mycobacterium tuberculosis. Microbiol Spectr 2022; 10:e0058022. [PMID: 35638832 PMCID: PMC9241777 DOI: 10.1128/spectrum.00580-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems allow bacteria to adapt to changing environments without altering gene expression. Despite being overrepresented in Mycobacterium tuberculosis, their physiological roles remain elusive. We describe a TA system in M. tuberculosis which we named TacAT due to its homology to previously discovered systems in Salmonella. The toxin, TacT, blocks growth by acetylating glycyl-tRNAs and inhibiting translation. Its effects are reversed by the enzyme peptidyl tRNA hydrolase (Pth), which also cleaves peptidyl tRNAs that are prematurely released from stalled ribosomes. Pth is essential in most bacteria and thereby has been proposed as a promising drug target for complex pathogens like M. tuberculosis. Transposon sequencing data suggest that the tacAT operon is nonessential for M. tuberculosis growth in vitro, and premature stop mutations in this TA system present in some clinical isolates suggest that it is also dispensable in vivo. We assessed whether TacT modulates pth essentiality in M. tuberculosis because drugs targeting Pth might prompt resistance if TacAT is disrupted. We show that pth essentiality is unaffected by the absence of tacAT. These results highlight a fundamental aspect of mycobacterial biology and indicate that Pth's essential role hinges on its peptidyl-tRNA hydrolase activity. Our work underscores Pth's potential as a viable target for new antibiotics. IMPORTANCE The global rise in antibiotic-resistant tuberculosis has prompted an urgent search for new drugs. Toxin-antitoxin (TA) systems allow bacteria to adapt rapidly to environmental changes, and Mycobacterium tuberculosis encodes more TA systems than any known pathogen. We have characterized a new TA system in M. tuberculosis: the toxin, TacT, acetylates charged tRNA to block protein synthesis. TacT's effects are reversed by the essential bacterial enzyme peptidyl tRNA hydrolase (Pth), which is currently being explored as an antibiotic target. Pth also cleaves peptidyl tRNAs that are prematurely released from stalled ribosomes. We assessed whether TacT modulates pth essentiality in M. tuberculosis because drugs targeting Pth might prompt resistance if TacT is disrupted. We show that pth essentiality is unaffected by the absence of this TA system, indicating that Pth's essential role hinges on its peptidyl-tRNA hydrolase activity. Our work underscores Pth's potential as a viable target for new antibiotics.
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Affiliation(s)
- Francesca G. Tomasi
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Jessica T. P. Schweber
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kerry McGowen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sophie Helaine
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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10
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Pérez-Martínez DE, Bermúdez-Hernández GA, Madrazo-Moya CF, Cancino-Muñoz I, Montero H, Licona-Cassani C, Muñiz-Salazar R, Comas I, Zenteno-Cuevas R. SNPs in Genes Related to DNA Damage Repair in Mycobacterium Tuberculosis: Their Association with Type 2 Diabetes Mellitus and Drug Resistance. Genes (Basel) 2022; 13:genes13040609. [PMID: 35456415 PMCID: PMC9029044 DOI: 10.3390/genes13040609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
Genes related to DNA damage repair in Mycobacterium tuberculosis are critical for survival and genomic diversification. The aim of this study is to compare the presence of SNPs in genes related to DNA damage repair in sensitive and drug-resistant M. tuberculosis genomes isolated from patients with and without type 2 diabetes mellitus (T2DM). We collected 399 M. tuberculosis L4 genomes from several public repositories; 224 genomes belonging to hosts without T2DM, of which 123 (54.9%) had drug sensitive tuberculosis (TB) and 101 (45.1%) had drug resistance (DR)-TB; and 175 genomes from individuals with T2DM, of which 100 (57.1%) had drug sensitive TB and 75 (42.9%) had DR-TB. The presence of SNPs in the coding regions of 65 genes related to DNA damage repair was analyzed and compared with the resistance profile and the presence/absence of T2DM in the host. The results show the phylogenetic relationships of some SNPS and L4 sub-lineages, as well as differences in the distribution of SNPs present in DNA damage repair-related genes related to the resistance profile of the infecting strain and the presence of T2DM in the host. Given these differences, it was possible to generate two discriminant functions to distinguish between drug sensitive and drug resistant genomes, as well as patients with or without T2DM.
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Affiliation(s)
- Damián E. Pérez-Martínez
- Programa de Doctorado en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Av. Luis, Dr. Castelazo Ayala s/n, Col. Industrial Animas, Xalapa 91190, Mexico; (D.E.P.-M.); (G.A.B.-H.)
| | - Gustavo A. Bermúdez-Hernández
- Programa de Doctorado en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Av. Luis, Dr. Castelazo Ayala s/n, Col. Industrial Animas, Xalapa 91190, Mexico; (D.E.P.-M.); (G.A.B.-H.)
| | - Carlos F. Madrazo-Moya
- Biomedical Institute of Valencia IBV-CSIC, C. de Jaume Roig, 11, 46010 Valencia, Spain; (C.F.M.-M.); (I.C.-M.); (I.C.)
| | - Irving Cancino-Muñoz
- Biomedical Institute of Valencia IBV-CSIC, C. de Jaume Roig, 11, 46010 Valencia, Spain; (C.F.M.-M.); (I.C.-M.); (I.C.)
- CIBER of Epidemiology and Public Health, 08908 Madrid, Spain
| | - Hilda Montero
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala s/n, A.P. 57, Col. Industrial Animas, Xalapa 91190, Mexico;
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501 Sur, Monterrey 64849, Mexico;
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City 14080, Mexico;
- Division of Integrative Biology, The Institute for Obesity Research, Tecnológico de Monterrey, Monterrey 64849, Mexico
| | - Raquel Muñiz-Salazar
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City 14080, Mexico;
- Laboratorio de Epidemiología y Ecología Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada 22890, Mexico
| | - Iñaki Comas
- Biomedical Institute of Valencia IBV-CSIC, C. de Jaume Roig, 11, 46010 Valencia, Spain; (C.F.M.-M.); (I.C.-M.); (I.C.)
- CIBER of Epidemiology and Public Health, 08908 Madrid, Spain
| | - Roberto Zenteno-Cuevas
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala s/n, A.P. 57, Col. Industrial Animas, Xalapa 91190, Mexico;
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City 14080, Mexico;
- Correspondence:
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11
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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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12
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Jia H, Chu H, Dai G, Cao T, Sun Z. Rv1258c acts as a drug efflux pump and growth controlling factor in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2022; 133:102172. [PMID: 35158297 DOI: 10.1016/j.tube.2022.102172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 11/27/2022]
Abstract
The possible role of efflux pump as a survival mechanism in Mycobacterium tuberculosis (M. tb) is gaining an increasing attention. Previously, Rv1258c (Tap) and its certain mutations confer the clinically relevant drug resistance. In this study, we found new mutations of Rv1258c in G195C, T297P and I328T. Effect of modulating T297P and I328T on the drug resistance by knockout and complement in M. tb H37Rv showed that M. tb ΔRv1258c showed a slightly lower MIC for rifampin, ethambutol, ofloxacin, amikacin, capreomycin and streptomycin than M. tb H37Rv WT and the complement. Rv1258c T297P and Rv1258c I328T showed an increased drug resistance to ethambutol and capreomycin than the complement of Rv1258c WT. Most importantly, M. tb ΔRv1258c exhibited a slow growth in the normal culture medium. TMT-based quantitative proteomics analysis of M. tb ΔRv1258c and WT showed that the knockout of Rv1258c greatly down-regulated the expression of the ribosome system and one of the special five type VII secretion systems, ESX-3, which impaired the bacterial growth. These results indicate that the newly found T297P and I328T mutations of Rv1258c contributed to an increased resistance to ethambutol and capreomycin, and Rv1258c as growth controlling factor influencing the growth of M. tb.
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Affiliation(s)
- Hongbing Jia
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Hongqian Chu
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Guangming Dai
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Tingming Cao
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
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13
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Liu M, Wang Q, Liu H, Yin C, Mijiti X, Anwaierjiang A, Wan K, Xu M, Li M, Nong S, Li G, Xiao H. Association of Mannose-Binding Lectin 2 Gene Polymorphism with Tuberculosis Based on Mycobacterium tuberculosis Lineages. Infect Drug Resist 2022; 15:1225-1234. [PMID: 35355619 PMCID: PMC8959721 DOI: 10.2147/idr.s344935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Polymorphisms in MBL2 may contribute to the susceptibility to tuberculosis. The aim of the present study was to determine the associations of the polymorphisms of five loci (rs1800450, rs1800451, rs7096206, rs7095891, and rs11003125) in the MBL2 gene with susceptibility to tuberculosis and specific lineages of Mycobacterium tuberculosis causing tuberculosis in the Uyghur population of Xinjiang, China. Methods From January 2019 to January 2020, we enrolled 170 Uyghur tuberculosis patients as the case group and 147 Uyghur staff with no clinical symptoms as the control group from four designated tuberculosis hospitals in southern Xinjiang, China. The polymorphisms of five loci in MBL2 of human were detected by sequencing. Whole-genome sequencing was applied in 68 M. tuberculosis isolates from the case group and the data were used to perform genealogy analysis. Results The distributions of allele and genotype frequencies of five loci in MBL2 varied little between the case and control groups and varied little among the groups, including those infected with different lineages of M. tuberculosis and the control (except those of rs11003125), the P values were all >0.05. The distribution of alleles of rs11003125 was statistically different between patients infected with lineages 3 and 4 M. tuberculosis (χ2=7.037, P=0.008). The C allele and CC genotype of rs11003125 were found to be protective factors against lineage 4 infection when compared to lineage 3 (ORs were 0.190 and 0.158, respectively; 95% confidence intervals were 0.053~0.690 and 0.025~0.999, respectively). Conclusion Our results suggested that human’s susceptibility to tuberculosis is affected both by the host genetic polymorphisms and the lineage of the M. tuberculosis that people were exposed to. However, due to the limitation of the sample size in the present study, larger sample size and more rigorous design should be guaranteed in future studies.
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Affiliation(s)
- Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Aiketaguli Anwaierjiang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Siqin Nong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Correspondence: Guilian Li; Hui Xiao, Email ;
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
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Multiple genetic paths including massive gene amplification allow Mycobacterium tuberculosis to overcome loss of ESX-3 secretion system substrates. Proc Natl Acad Sci U S A 2022; 119:2112608119. [PMID: 35193958 PMCID: PMC8872769 DOI: 10.1073/pnas.2112608119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2021] [Indexed: 01/18/2023] Open
Abstract
The Mycobacterium tuberculosis (Mtb) ESX-3 type VII secretion system plays a critical role in iron acquisition. Infection of mice with highly attenuated Mtb deletion mutants lacking esxG or esxH, genes encoding key ESX-3 substrates, unexpectedly yielded suppressor mutants with restored capacity to grow in vivo and in vitro in the absence of iron supplementation. Whole-genome sequencing identified two mechanisms of suppression, the disruption of a transcriptional repressor that regulates expression of an ESX-3 paralogous region encoding EsxR and EsxS, and a massive 38- to 60-fold gene amplification of this same region. These data are significant because they reveal a previously unrecognized iron acquisition regulon and inform mechanisms of Mtb chromosome evolution. Mycobacterium tuberculosis (Mtb) possesses five type VII secretion systems (T7SS), virulence determinants that include the secretion apparatus and associated secretion substrates. Mtb strains deleted for the genes encoding substrates of the ESX-3 T7SS, esxG or esxH, require iron supplementation for in vitro growth and are highly attenuated in vivo. In a subset of infected mice, suppressor mutants of esxG or esxH deletions were isolated, which enabled growth to high titers or restored virulence. Suppression was conferred by mechanisms that cause overexpression of an ESX-3 paralogous region that lacks genes for the secretion apparatus but encodes EsxR and EsxS, apparent ESX-3 orphan substrates that functionally compensate for the lack of EsxG or EsxH. The mechanisms include the disruption of a transcriptional repressor and a massive 38- to 60-fold gene amplification. These data identify an iron acquisition regulon, provide insight into T7SS, and reveal a mechanism of Mtb chromosome evolution involving “accordion-type” amplification.
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15
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Investigation on the cause of recurrent tuberculosis in a rural area in China using whole-genome sequencing: A retrospective cohort study. Tuberculosis (Edinb) 2022; 133:102174. [DOI: 10.1016/j.tube.2022.102174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/17/2022]
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16
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Antimycobacterial and anti-inflammatory activities of thiourea derivatives focusing on treatment approaches for severe pulmonary tuberculosis. Bioorg Med Chem 2022; 53:116506. [PMID: 34890996 DOI: 10.1016/j.bmc.2021.116506] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) remains a serious public health problem and one of the main concern is the emergence of multidrug-resistant and extensively resistant TB. Hyper-reactive patients develop inflammatory necrotic lung lesions that aggravate the pathology and facilitate transmission of mycobacteria. Treatment of severe TB is a major clinical challenge that has few effective solutions and patients face a poor prognosis, years of treatment and different adverse drug reactions. In this work, fifteen novel and thirty-one unusual thiourea derivatives were synthesized and evaluated in vitro for their antimycobacterial and anti-inflammatory potential and, in silico for ADMET parameters and for structure-activity relationship (SAR). Thioureas derivatives 10, 15, 16, 28 and 29 that had shown low cytotoxicity and high activities were selected for further investigation, after SAR study. These five thioureas derivatives inhibited Mtb H37Rv growth in bacterial culture and in infected macrophages, highlighting thiourea derivative 28 (MIC50 2.0 ± 1.1 and 2.3 ± 1.1 µM, respectively). Moreover, these compounds were active against the hypervirulent clinical Mtb strain M299, in bacterial culture, especially 16, 28 and 29, and in extracellular clumps, highlighting 29, with MIC50 5.6 ± 1.2 µM. Regarding inflammation, they inhibited NO through the suppression of iNOS expression, and also inhibited the production of TNF-α and IL-1β. In silico studies were carried out suggesting that these five compounds could be administered by oral route and have low toxicological effects when compared to rifampicin. In conclusion, our data show that, at least, thiourea derivatives 16, 28 and 29 are promising antimycobacterial and anti-inflammatory agents, and candidates for further prospective studies aiming new anti-TB drugs, that can be used on a dual approach for the treatment of severe TB cases associated with exacerbated inflammation.
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17
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Du J, Li Q, Liu M, Wang Y, Xue Z, Huo F, Zhang X, Shang Y, Li S, Huang H, Pang Y. Distinguishing Relapse From Reinfection With Whole-Genome Sequencing in Recurrent Pulmonary Tuberculosis: A Retrospective Cohort Study in Beijing, China. Front Microbiol 2021; 12:754352. [PMID: 34956119 PMCID: PMC8693897 DOI: 10.3389/fmicb.2021.754352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Tuberculosis recurrence is still a major problem for the control of tuberculosis, and the cause of the recurrence is still unclear. Methods: We retrospectively recruited 68 pairs of samples of Mycobacterium tuberculosis (MTB) from recurrent TB cases in Beijing Chest Hospital between January 2008 and December 2019. The whole-genome sequencing was conducted to analyze single-nucleotide polymorphism (SNP) and to identify whether recurrent disease was due to relapse or reinfection. The BACTEC MGIT was performed to compare differences in drug susceptibility profiles between two episodes. Results: 62 (91.2%) out of 68 confirmed recurrence were due to relapse, whereas the remaining six (8.8%) were due to reinfection. And there was a strong association between earlier relapse and underlying chronic diseases. In addition, the MTB isolates from non-diabetic patients had a higher mutation rate than those from diabetic patients. A community transmission was also identified in our cohort. Levofloxacin resistance was the most frequently observed drug resistance for 12.9% relapse cases. Conclusion: The relapse of a previous episode in Beijing. The underlying chronic diseases are associated with an earlier TB relapse. MTB isolates were more prone to develop levofloxacin resistance than moxifloxacin resistance after FQ exposure. The patients at high-risk for relapses deserve more careful investigation.
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Affiliation(s)
- Jian Du
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qing Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Min Liu
- Provincial Center for Tuberculosis Control and Prevention, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Yufeng Wang
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Zhongtan Xue
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems 2021; 6:e0119421. [PMID: 34665012 PMCID: PMC8525567 DOI: 10.1128/msystems.01194-21] [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] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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20
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Moreno-Molina M, Shubladze N, Khurtsilava I, Avaliani Z, Bablishvili N, Torres-Puente M, Villamayor L, Gabrielian A, Rosenthal A, Vilaplana C, Gagneux S, Kempker RR, Vashakidze S, Comas I. Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections. Nat Commun 2021; 12:2716. [PMID: 33976135 PMCID: PMC8113332 DOI: 10.1038/s41467-021-22705-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/22/2021] [Indexed: 01/15/2023] Open
Abstract
Polyclonal infections occur when at least two unrelated strains of the same pathogen are detected in an individual. This has been linked to worse clinical outcomes in tuberculosis, as undetected strains with different antibiotic resistance profiles can lead to treatment failure. Here, we examine the amount of polyclonal infections in sputum and surgical resections from patients with tuberculosis in the country of Georgia. For this purpose, we sequence and analyse the genomes of Mycobacterium tuberculosis isolated from the samples, acquired through an observational clinical study (NCT02715271). Access to the lung enhanced the detection of multiple strains (40% of surgery cases) as opposed to just using a sputum sample (0-5% in the general population). We show that polyclonal infections often involve genetically distant strains and can be associated with reversion of the patient's drug susceptibility profile over time. In addition, we find different patterns of genetic diversity within lesions and across patients, including mutational signatures known to be associated with oxidative damage; this suggests that reactive oxygen species may be acting as a selective pressure in the granuloma environment. Our results support the idea that the magnitude of polyclonal infections in high-burden tuberculosis settings is underestimated when only testing sputum samples.
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MESH Headings
- Antitubercular Agents/therapeutic use
- Biopsy
- Clone Cells
- Cohort Studies
- Drug Resistance, Multiple, Bacterial/genetics
- Genetic Variation
- Genome, Bacterial
- Georgia (Republic)
- Granuloma/drug therapy
- Granuloma/microbiology
- Granuloma/pathology
- Granuloma/surgery
- Humans
- Lung/microbiology
- Lung/pathology
- Lung/surgery
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/pathogenicity
- Reactive Oxygen Species/metabolism
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Multidrug-Resistant/pathology
- Tuberculosis, Multidrug-Resistant/surgery
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/pathology
- Tuberculosis, Pulmonary/surgery
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Affiliation(s)
| | - Natalia Shubladze
- National Center for Tuberculosis and Lung Diseases of Georgia, Tbilisi, Georgia
| | - Iza Khurtsilava
- National Center for Tuberculosis and Lung Diseases of Georgia, Tbilisi, Georgia
| | - Zaza Avaliani
- National Center for Tuberculosis and Lung Diseases of Georgia, Tbilisi, Georgia
| | - Nino Bablishvili
- National Center for Tuberculosis and Lung Diseases of Georgia, Tbilisi, Georgia
| | | | | | - Andrei Gabrielian
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Maryland, USA
| | - Alex Rosenthal
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Maryland, USA
| | - Cristina Vilaplana
- Fundació Institut Germans Trias i Pujol (IGTP), Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- CIBER of Respiratory Diseases, Madrid, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Russell R Kempker
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, USA
| | - Sergo Vashakidze
- National Center for Tuberculosis and Lung Diseases of Georgia, Tbilisi, Georgia
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain.
- CIBER in Epidemiology and Public Health, Madrid, Spain.
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21
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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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22
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Guevara Salazar JA, Morán Díaz JR, Ramírez Segura E, Trujillo Ferrara JG. What are the origins of growing microbial resistance? Both Lamarck and Darwin were right. Expert Rev Anti Infect Ther 2020; 19:563-569. [PMID: 33073640 DOI: 10.1080/14787210.2021.1839418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Microorganisms of clinical importance frequently develop resistance to drug therapy, now a growing problem. The experience with Mycobacterium tuberculosis is a representative example of increasing multi-drug resistance. To avoid reaching a crisis in which patients could be left without adequate treatment, a new strategy is needed. Anti-microbial therapy has historically targeted the mechanisms rather than origin of drug resistance, thus allowing microorganisms to adapt and survive. AREAS COVERED This contribution analyses the historical development (1943-2020) of the evolution of multi-drug resistance by M. tuberculosis strains in light of Darwin's and Lamarck's theories of evolution. EXPERT OPINION Regarding the molecular origin of microbial drug resistance, genetic mutations and epigenetic modifications are known to participate. The analysis of the history of drug resistance by M. tuberculosis evidences a gradual development of resistance to some antibiotics, undoubtedly due to random mutations together with natural selection based on environmental pressures (e.g., antibiotics), representing Darwin's idea. More rapid adaptation of M. tuberculosis to new antibiotic treatments has also occurred, probably because of heritable acquired characteristics, evidencing Lamarck's proposal. Therefore, microbial infections should be treated with an antibiotic producing null or low mutagenic activity along with a resistance inhibitor, preferably in a single medication.
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Affiliation(s)
- Juan Alberto Guevara Salazar
- Departamento De Farmacología, Escuela Superior De Medicina, Instituto Politécnico Nacional, Ciudad De México, CDMX, Mexico
| | - Jessica Rubí Morán Díaz
- Departamento De Farmacología, Escuela Superior De Medicina, Instituto Politécnico Nacional, Ciudad De México, CDMX, Mexico
| | - Enrique Ramírez Segura
- Laboratorio De Bioquímica Médica, Escuela Superior De Medicina, Instituto Politécnico Nacional, Ciudad De México, CDMX, Mexico
| | - José Guadalupe Trujillo Ferrara
- Laboratorio De Bioquímica Médica, Escuela Superior De Medicina, Instituto Politécnico Nacional, Ciudad De México, CDMX, Mexico
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