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Fuchs I, Losev Y, Mor Z, Rubinstein M, Polyakov M, Wagner T, Gobay T, Bayene E, Mula G, Kaidar-Shwartz H, Dveyrin Z, Rorman E, Kaliner E, Perl SH. Multidisciplinary Effort Leading to Effective Tuberculosis Community Outbreak Containment in Israel. Microorganisms 2024; 12:1592. [PMID: 39203435 PMCID: PMC11356750 DOI: 10.3390/microorganisms12081592] [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: 07/17/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/03/2024] Open
Abstract
Tuberculosis (TB) is the second-most prevalent cause of mortality resulting from infectious diseases worldwide. It is caused by bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). In Israel, TB incidence is low, acknowledged by the WHO as being in a pre-elimination phase. Most cases occur among immigrants from high TB incidence regions like the Horn of Africa and the former Soviet Union (FSU), with occasional outbreaks. The outbreak described in this report occurred between 2018 and 2024, increasing the incidence rate of TB in the region. Control of this outbreak posed challenges due to factors including a diverse population (including Ethiopian immigrants, Israeli-born citizens, and immigrants from other countries), economic and social barriers, and hesitancy to disclose information. The unique multidisciplinary team formed to address these challenges, involving the local TB clinic, district health ministry, health maintenance organization (HMO) infectious disease consultant, neighborhood clinic, and National Mycobacterium Reference Laboratory (NMRL), achieved effective treatment and containment. Whole genome sequencing (WGS) proved pivotal in unraveling patient connections during the outbreak. It pinpointed those patients overlooked in initial field investigations, established connections between patients across different health departments, and uncovered the existence of two distinct clusters with separate transmission chains within the same neighborhood. This study underscores collaborative efforts across sectors that successfully contained a challenging outbreak.
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Affiliation(s)
- Inbal Fuchs
- Clalit Health Services, Central District, Rishon LeTsiyon 7528809, Israel; (I.F.); (E.B.); (G.M.)
| | - Yelena Losev
- National Mycobacterium Reference Center, Ministry of Health, Tel Aviv 6810416, Israel; (Y.L.); (H.K.-S.)
| | - Zohar Mor
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem 9438317, Israel; (Z.M.); (T.W.)
| | - Mor Rubinstein
- National Public Health Laboratories, Ministry of Health, Tel Aviv 6810416, Israel; (M.R.); (Z.D.)
| | - Marina Polyakov
- Central District Department of Health, Ministry of Health, Ramla 7243003, Israel; (M.P.); (T.G.); (E.K.)
| | - Tali Wagner
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem 9438317, Israel; (Z.M.); (T.W.)
| | - Tamar Gobay
- Central District Department of Health, Ministry of Health, Ramla 7243003, Israel; (M.P.); (T.G.); (E.K.)
| | - Ester Bayene
- Clalit Health Services, Central District, Rishon LeTsiyon 7528809, Israel; (I.F.); (E.B.); (G.M.)
| | - Gila Mula
- Clalit Health Services, Central District, Rishon LeTsiyon 7528809, Israel; (I.F.); (E.B.); (G.M.)
| | - Hasia Kaidar-Shwartz
- National Mycobacterium Reference Center, Ministry of Health, Tel Aviv 6810416, Israel; (Y.L.); (H.K.-S.)
| | - Zeev Dveyrin
- National Public Health Laboratories, Ministry of Health, Tel Aviv 6810416, Israel; (M.R.); (Z.D.)
| | - Efrat Rorman
- Ministry of Health Laboratories Department, Ministry of Health, Jerusalem 9134302, Israel;
| | - Ehud Kaliner
- Central District Department of Health, Ministry of Health, Ramla 7243003, Israel; (M.P.); (T.G.); (E.K.)
| | - Sivan Haia Perl
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem 9438317, Israel; (Z.M.); (T.W.)
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Rudeeaneksin J, Bunchoo S, Phetsuksiri B, Srisungngam S, Khummin R, Thapa J, Nakajima C, Suzuki Y. The first insight into Mycobacterium tuberculosis complex isolates in the lower northern region in Thailand. Trans R Soc Trop Med Hyg 2024; 118:527-536. [PMID: 38554067 DOI: 10.1093/trstmh/trae014] [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: 11/19/2023] [Revised: 01/21/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) remains an important infectious disease and different genotypes have been reported. This study aimed to investigate the genetic diversity and molecular epidemiology of TB in the lower northern region of Thailand, where genotyping data are limited. METHODS A total of 159 Mycobacterium tuberculosis complex (MTBC) isolates from this region were genotyped by spoligotyping and the major spoligotypes were further subdivided by the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method. RESULTS Spoligotyping identified 34 types and classified them into 14 clusters. East African-Indian (EAI) groups were the most frequent (44.7%), followed by Beijing (36.5%), with a higher prevalence of drug resistance. By 15-loci MIRU-VNTR typing, the major groups of the Beijing and EAI2_NTB were further differentiated into 44 and 21 subtypes forming 9 and 5 subclusters with cluster rates of 0.26 and 0.44, respectively. The Hunter-Gaston Discriminatory Index among the Beijing and EAI2_NTB groups were 0.987 and 0.931, respectively, indicating high diversity. CONCLUSIONS This is the first look at the MTBC genotypes in the lower northern region of Thailand, which could aid in understanding the distribution and potential spread of MTBC and Mycobacterium bovis in the target region to support TB control in Thailand.
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Affiliation(s)
- Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
- Medical Sciences Technical Office, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Ratchaneeporn Khummin
- Office of Disease Prevention and Control Region 2 Phitsanulok, Department of Disease Control, Ministry of Public Health, Phitsanulok 65000, Thailand
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
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Losev Y, Rubinstein M, Nissan I, Haviv P, Barsky Y, Volinsky M, Bar-Giora G, Zouher T, Hamawi M, Valenci GZ, Kutikov I, Shwartz HK, Dveyrin Z, Chemtob D, Rorman E. Genomic, phenotypic and demographic characterization of Mycobacterium tuberculosis in Israel in 2021. Front Cell Infect Microbiol 2023; 13:1196904. [PMID: 37928179 PMCID: PMC10622789 DOI: 10.3389/fcimb.2023.1196904] [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: 03/30/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
According to World Health Organization WHO, Tuberculosis (TB) is the second cause of death from infectious disease worldwide. During 2021, 10.6 million people were infected with TB, and 1.6 million people died. TB is caused by pathogens belonging to the Mycobacterium tuberculosis complex (MTBC), mainly by Mycobacterium tuberculosis (M.tb). Members of this complex are acid-fast bacilli, which can cause intrapulmonary and extra pulmonary TB, and can be divided into various lineages, based on genomic markers. The main public health threat comes from drug resistant M.tb strains, which are responsible for about 25% of TB death and treatment failure worldwide. Treating drug resistant TB patients significantly raises the costs of TB treatment. This study provides an overview of the demographic and drug susceptibility characteristics of newly diagnosed TB patients in Israel in 2021. The State of Israel has a very low level of TB endemicity and is at a pre-elimination phase. Notably, only 11.7% of the newly diagnosed TB patients were born in Israel. In this report, of the 154 new laboratory-confirmed TB patients, 66.7% had pulmonary TB, while 16% had extrapulmonary TB. Males accounted for 52% of the patients, with the most prevalent age group being 21-40. Most patients were citizens of Israel (53.9%), while 37.7% had no Israeli citizenship. Among non-citizens, there was a predominance of males and patients aged 21-40. The susceptibility profile showed a high resistance rate to streptomycin (18.2%) and to a lower extent to isoniazid (13.6%), pyrazinamide (8.4%), rifampicin (7.8%), and ethambutol (3.2%). Only 2 cases of XDR-TB and 10 MDR-TB strains were detected in Israel in 2021, with both XDR strains and 5 out of 10 MDR strains belonging to the Beijing lineage. Most of Beijing isolates were resistant to at least one tested drug. Genomic sequencing of 134 out of 156 strains and bioinformatics analysis using the MTBseq program and WHO mutation catalogue shows a good match with only 9 discrepancies between phenotypic and genotypic susceptibility profiles in first line drugs. The most common lineage is Delhi-Cas (23%) followed by the Beijing lineage (17%). Most patients from the Delhi-Cas lineage were born in Africa, while patients with Beijing isolates were born in different countries. Minimum spanning tree analysis identified 15 clusters. The study highlights the need for ongoing surveillance of TB using molecular and phenotypic tools to further decreasing the spreading level of the disease and develop effective treatment strategies.
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Affiliation(s)
- Yelena Losev
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Mor Rubinstein
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Paz Haviv
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yohi Barsky
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Martha Volinsky
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gefen Bar-Giora
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Tamara Zouher
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Mazal Hamawi
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Ina Kutikov
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Hasia Kaidar Shwartz
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Daniel Chemtob
- Department of Tuberculosis (TB) and AIDS and National TB Program Manager, Ministry of Health, Jerusalem, Israel
- Hebrew University-Hadassah Faculty of Medicine, School of Public Health and Community Medicine, Jerusalem, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
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BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain. Sci Rep 2023; 13:1663. [PMID: 36717601 PMCID: PMC9886903 DOI: 10.1038/s41598-023-28983-5] [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: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Autophagy induction by starvation has been shown to enhance lysosomal delivery to mycobacterial phagosomes, resulting in the restriction of the Mycobacterium tuberculosis reference strain H37Rv. In contrast to H37Rv, our previous study showed that strains belonging to the notorious M. tuberculosis Beijing genotype could evade autophagic elimination. Our recent RNA-Seq analysis also discovered that the autophagy-resistant M. tuberculosis Beijing strain (BJN) evaded autophagic control by upregulating the expression of Kxd1, a BORC complex component, and Plekhm2, both of which function in lysosome positioning towards the cell periphery in host macrophages, thereby suppressing enhanced lysosomal delivery to its phagosome and sparing the BJN from elimination as a result. In this work, we further characterised the other specific components of the BORC complex, BORC5-8, and Kinesin proteins in autophagy resistance by the BJN. Depletion of BORCS5-8 and Kinesin-1, but not Kinesin-3, reverted autophagy avoidance by the BJN, resulting in increased lysosomal delivery to the BJN phagosomes. In addition, the augmented lysosome relocation towards the perinuclear region could now be observed in the BJN-infected host cells depleted in BORCS5-8 and Kinesin-1 expressions. Taken together, the data uncovered new roles for BORCS5-8 and Kinesin-1 in autophagy evasion by the BJN.
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Kim N, Seok KH, Shin S, Kim B, Park H, Roh EY, Yoon JH, Shin S. Evaluation of Five User-Friendly Whole Genome Sequencing Software for Mycobacterium tuberculosis in Clinical Application. J Korean Med Sci 2022; 37:e328. [PMID: 36631026 PMCID: PMC9705210 DOI: 10.3346/jkms.2022.37.e328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/15/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is an increasingly useful tool for tuberculosis (TB) diagnosis and disease management. In this study, we evaluated the utility of user-friendly WGS tools in reporting resistance profiles and identifying lineages of clinical TB isolates from South Korea. METHODS Forty clinical samples from TB patients showing discrepancies between their rapid molecular and conventional drug susceptibility tests were used in this study. Among these clinical isolates, 37 strains were successfully evaluated via WGS software, using the GenTB, TB Profiler, PhyResSE, CASTB, and Mykrobe. RESULTS More accurate and faster susceptibility results could be obtained with isoniazid than with rifampin. Using the phenotypic test as the gold standard, the isoniazid concordance rate between phenotypic drug susceptibility test (DST) and WGS (GenTB: 45.9%, TB profiler: 40.5%, PhyResSE: 40.5%, CASTB: 48.6%, and Mykrobe: 43.2%) was much higher than between phenotypic DST and rapid molecular genotypic DST (18.9%) among the 37 strains. In contrast, the rifampin concordance rate between phenotypic DST and WGS and that between phenotypic DST and rapid molecular genotypic DST was similar (81.1-89.2%). We also found novel mutations associated with INH in katG and ahpC gene region, not covered by the line probe assay. In addition, lineage analysis identified 81.1% of these samples as L2 East Asian lineage strains, and 18.9% as L4 Euro-American lineage strains. CONCLUSION WGS may play a pivotal role in TB diagnosis and the detection of drug resistance, genetic diversity, and transmission dynamics in the near future because of its accuracy, speed, and extensibility.
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Affiliation(s)
- Namhee Kim
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kwang Hyuk Seok
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Cheongju, Korea
| | - Soyoun Shin
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Cheongju, Korea
- Seegene Medical Foundation, Daejeon, Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.
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Lin S, Wei S, Zhao Y, Dai Z, Lin J, Pang Y. The Emergence of Novel Spoligotypes of Highly Drug-Resistant Mycobacterium tuberculosis Isolates in Fujian, China. Infect Drug Resist 2022; 15:5781-5793. [PMID: 36213768 PMCID: PMC9533782 DOI: 10.2147/idr.s380950] [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: 07/02/2022] [Accepted: 09/11/2022] [Indexed: 11/23/2022] Open
Abstract
Background Here, we aimed to determine the population structure of Mycobacterium tuberculosis (MTB) genotypes in Fujian and explore risk factors associated with infection with the Beijing genotype. We also explored the association between Beijing genotype and drug resistance. Methods Representative MTB isolates obtained during provincial-level routine anti-tuberculosis drug resistance surveillance conducted since 2013 in 11 Fujian counties were analyzed using McSpoligotyping. In vitro drug susceptibilities to anti-tuberculosis drugs were determined using the standard Löwenstein–Jensen proportion method. Results Overall, 477 MTB isolates were included in the study, of which 245 isolates belonged to the Beijing genotype family and 232 possessed non-Beijing genotypes. Ultimately, a total of 204 spoligotypes were identified that included 58 spoligotype international types (SITs) from the SITVITWEB database and 146 novel spoligotypes. As compared to patients <25 years of age (control group), elderly patients (≥65 years of age) were more likely to be infected with non-Beijing genotypes [aOR 18.69, 95% CI (5.80–60.26)], with risk of infection with non-Beijing genotypes increasing with age [aOR 3.73, 95% CI (1.67–8.30) for patients 45–64 years of age]. Additionally, as compared to isolates with Beijing and other non-Beijing genotypes, significantly greater proportions of isolates with novel spoligotypes exhibited PTO- and PAS-resistance. Moreover, a markedly higher proportion of isolates with novel spoligotypes exhibited OFX-resistance as compared to isolates with other non-Beijing genotypes. Conclusion Our data demonstrated that the Beijing genotype is the predominant MTB sublineage in Fujian and that the prevalence rate of infection with this MTB genotype decreases with advancing patient age. Notably, the prevalence rate of this genotype in Fujian TB patients is relatively lower than in other regions of China. In addition, the emergence of novel spoligotypes of highly drug-resistant MTB isolates highlights the urgent need for ongoing molecular genotyping surveillance in Fujian.
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Affiliation(s)
- Shufang Lin
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People’s Republic of China
| | - Shuzhen Wei
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People’s Republic of China
- Correspondence: Shuzhen Wei, Fujian Center for Disease Control and Prevention, No. 386, Chong’an Road, Jin’an District, Fuzhou, Fujian, 350012, People’s Republic of China, Tel/Fax +86 591 8343 1464, Email
| | - Yong Zhao
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People’s Republic of China
| | - Zhisong Dai
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People’s Republic of China
| | - Jian Lin
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People’s Republic of China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People’s Republic of China
- Yu Pang, Beijing Chest Hospital, Capital Medical University, No. 97, Machang, Tongzhou District, Beijing, 101149, People’s Republic of China, Tel/Fax +86 10 8950 9359, Email
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Soler-Camargo NC, Silva-Pereira TT, Zimpel CK, Camacho MF, Zelanis A, Aono AH, Patané JS, Dos Santos AP, Guimarães AMS. The rate and role of pseudogenes of the Mycobacterium tuberculosis complex. Microb Genom 2022; 8. [PMID: 36250787 DOI: 10.1099/mgen.0.000876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI's PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC's evolution and genetic diversity.
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Affiliation(s)
- Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Maurício F Camacho
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Alexandre H Aono
- Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil.,Institute of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | | | | | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University
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Multidrug-Resistant Tuberculosis—Diagnostic Procedures and Treatment of Two Beijing-like TB Cases. Diagnostics (Basel) 2022; 12:diagnostics12071699. [PMID: 35885603 PMCID: PMC9318939 DOI: 10.3390/diagnostics12071699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
The Beijing/W genotype is one of the major molecular families of Mycobacterium tuberculosis complex (MTBC), responsible for approximately 50% of tuberculosis (TB) cases in Far East Asia and at least 25% of TB cases globally. Studies have revealed that the Beijing genotype family is associated with a more severe clinical course of TB, increased ability to spread compared to other genotypes, and an unpredictable response to treatment. Based on the profile of spacers 35–43 in the Direct Repeat (DR) locus of the MTBC genome determined by spoligotyping, classical (typical) and modern (Beijing-like) clones can be identified within the Beijing family. While the modern and ancient Beijing strains appear to be closely related at the genetic level, there are marked differences in their drug resistance, as well as their ability to spread and cause disease. This paper presents two cases of drug-resistant tuberculosis caused by rare mycobacteria from the Beijing family: the Beijing 265 and Beijing 541 subtypes. The genotypes of isolated strains were linked with the clinical course of TB, and an attempt was made to initially assess whether the Beijing subtype can determine treatment outcomes in patients.
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9
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Shanmugam SK, Kumar N, Sembulingam T, Ramalingam SB, Selvaraj A, Rajendhiran U, Solaiyappan S, Tripathy SP, Natrajan M, Chandrasekaran P, Swaminathan S, Parkhill J, Peacock SJ, Ranganathan UDK. Mycobacterium tuberculosis Lineages Associated with Mutations and Drug Resistance in Isolates from India. Microbiol Spectr 2022; 10:e0159421. [PMID: 35442078 PMCID: PMC9241780 DOI: 10.1128/spectrum.01594-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Current knowledge on resistance-conferring determinants in Mycobacterium tuberculosis is biased toward globally dominant lineages 2 and 4. In contrast, lineages 1 and 3 are predominant in India. In this study, we performed whole-genome sequencing of 498 MDR M. tuberculosis isolates from India to determine the prevalence of drug resistance mutations and to understand the genomic diversity. A retrospective collection of 498 M. tuberculosis isolates submitted to the National Institute for Research in Tuberculosis for phenotypic susceptibility testing between 2014 to 2016 were sequenced. Genotypic resistance prediction was performed using known resistance-conferring determinants. Genotypic and phenotypic results for 12 antituberculosis drugs were compared, and sequence data were explored to characterize lineages and their association with drug resistance. Four lineages were identified although lineage 1 predominated (43%). The sensitivity of prediction for isoniazid and rifampicin was 92% and 98%, respectively. We observed lineage-specific variations in the proportion of isolates with resistance-conferring mutations, with drug resistance more common in lineages 2 and 3. Disputed mutations (codons 430, 435, 445, and 452) in the rpoB gene were more common in isolates other than lineage 2. Phylogenetic analysis and pairwise SNP difference revealed high genetic relatedness of lineage 2 isolates. WGS based resistance prediction has huge potential, but knowledge of regional and national diversity is essential to achieve high accuracy for resistance prediction. IMPORTANCE Current knowledge on resistance-conferring determinants in Mycobacterium tuberculosis is biased toward globally dominant lineages 2 and 4. In contrast, lineages 1 and 3 are predominant in India. We performed whole-genome sequencing of 498 MDR M. tuberculosis isolates from India to determine the prevalence of drug resistance mutations and to understand genomic diversity. Four lineages were identified although lineage 1 predominated (43%). The sensitivity of prediction for isoniazid and rifampicin was 92% and 98%, respectively. We observed lineage-specific variations in the proportion of isolates with resistance-conferring mutations, with drug resistance more common in lineages 2 and 3. Disputed mutations (codons 430, 435, 445, and 452) in the rpoB gene were more common in isolates other than lineage 2. Phylogenetic analysis and pairwise SNP difference revealed high genetic relatedness of lineage 2 isolates. WGS based resistance prediction has huge potential, but knowledge of regional and national diversity is essential to achieve high accuracy for resistance prediction.
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Affiliation(s)
- Siva Kumar Shanmugam
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Narender Kumar
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Tamilzhalagan Sembulingam
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Suresh Babu Ramalingam
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Ashok Selvaraj
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Udhayakumar Rajendhiran
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Sudha Solaiyappan
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Srikanth P. Tripathy
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Mohan Natrajan
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | | | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Uma Devi K. Ranganathan
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
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10
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Oostvogels S, Ley SD, Heupink TH, Dippenaar A, Streicher EM, De Vos E, Meehan CJ, Dheda K, Warren R, Van Rie A. Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa. Microb Genom 2022; 8. [PMID: 35471145 PMCID: PMC9453078 DOI: 10.1099/mgen.0.000815] [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] [Indexed: 11/25/2022] Open
Abstract
Extensively drug-resistant tuberculosis (XDR-TB), defined as resistance to at least isoniazid (INH), rifampicin (RIF), a fluoroquinolone (FQ) and a second-line injectable drug (SLID), is difficult to treat and poses a major threat to TB control. The transmission dynamics and distribution of XDR Mycobacterium tuberculosis (Mtb) strains have not been thoroughly investigated. Using whole genome sequencing data on 461 XDR-Mtb strains, we aimed to investigate the geographical distribution of XDR-Mtb strains in the Western Cape Province of South Africa over a 10 year period (2006–2017) and assess the association between Mtb sub-lineage, age, gender, geographical patient location and membership or size of XDR-TB clusters. First, we identified transmission clusters by excluding drug resistance-conferring mutations and using the 5 SNP cutoff, followed by merging clusters based on their most recent common ancestor. We then consecutively included variants conferring resistance to INH, RIF, ethambutol (EMB), pyrazinamide (PZA), SLIDs and FQs in the cluster definition. Cluster sizes were classified as small (2–4 isolates), medium (5–20 isolates), large (21–100 isolates) or very large (>100 isolates) to reflect the success of individual strains. We found that most XDR-TB strains were clustered and that including variants conferring resistance to INH, RIF, EMB, PZA and SLIDs in the cluster definition did not significantly reduce the proportion of clustered isolates (85.5–82.2 %) but increased the number of patients belonging to small clusters (4.3–12.4 %, P=0.56). Inclusion of FQ resistance-conferring variants had the greatest effect, with 11 clustered isolates reclassified as unique while the number of clusters increased from 17 to 37. Lineage 2 strains (lineage 2.2.1 typical Beijing or lineage 2.2.2 atypical Beijing) showed the large clusters which were spread across all health districts of the Western Cape Province. We identified a significant association between residence in the Cape Town metropole and cluster membership (P=0.016) but no association between gender, age and cluster membership or cluster size (P=0.39). Our data suggest that the XDR-TB epidemic in South Africa probably has its origin in the endemic spread of MDR Mtb and pre-XDR Mtb strains followed by acquisition of FQ resistance, with more limited transmission of XDR Mtb strains. This only became apparent with the inclusion of drug resistance-conferring variants in the definition of a cluster. In addition to the prevention of amplification of resistance, rapid diagnosis of MDR, pre-XDR and XDR-TB and timely initiation of appropriate treatment is needed to reduce transmission of difficult-to-treat TB.
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Affiliation(s)
- Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- *Correspondence: Selien Oostvogels,
| | - Serej D. Ley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Present address: Sefunda AG, Muttenz, Switzerland
| | - Tim H. Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Elizabeth M. Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Elise De Vos
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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11
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Siregar TAP, Prombutara P, Kanjanasirirat P, Kunkaew N, Tubsuwan A, Boonmee A, Palaga T, Khumpanied T, Borwornpinyo S, Chaiprasert A, Utaisincharoen P, Ponpuak M. The autophagy-resistant Mycobacterium tuberculosis Beijing strain upregulates KatG to evade starvation-induced autophagic restriction. Pathog Dis 2022; 80:6509485. [PMID: 35038342 PMCID: PMC8829027 DOI: 10.1093/femspd/ftac004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/28/2021] [Accepted: 01/13/2022] [Indexed: 11/12/2022] Open
Abstract
Mycobacterium tuberculosis utilizes several mechanisms to block phagosome–lysosome fusion to evade host cell restriction. However, induction of host cell autophagy by starvation was shown to overcome this block, resulting in enhanced lysosomal delivery to mycobacterial phagosomes and the killing of the M. tuberculosis reference strain H37Rv. Nevertheless, our previous studies found that strains belonging to the M. tuberculosis Beijing genotype can resist starvation-induced autophagic elimination, though the mycobacterial factors involved remain unclear. In this study, we showed that KatG expression is upregulated in the autophagy-resistant M. tuberculosis Beijing strain (BJN) during autophagy induction by the starvation of host macrophages, while such increase was not observed in the H37Rv. KatG depletion using the CRISPR-dCas9 interference system in the BJN resulted in increased lysosomal delivery to its phagosome and decreased its survival upon autophagy induction by starvation. As KatG functions by catabolizing ROS, we determined the source of ROS contributing to the starvation-induced autophagic elimination of mycobacteria. Using siRNA-mediated knockdown, we found that Superoxide dismutase 2, which generates mitochondrial ROS but not NADPH oxidase 2, is important for the starvation-induced lysosomal delivery to mycobacterial phagosomes. Taken together, these findings showed that KatG is vital for the BJN to evade starvation-induced autophagic restriction.
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Affiliation(s)
- Tegar Adriansyah Putra Siregar
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Microbiology, Faculty of Medicine, University of Muhammadiyah Sumatera Utara, Medan, Indonesia
| | - Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Nawapol Kunkaew
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Alisa Tubsuwan
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Atsadang Boonmee
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Tanawadee Khumpanied
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Suparerk Borwornpinyo
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Angkana Chaiprasert
- Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Marisa Ponpuak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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12
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María Irene CC, Juan Germán RC, Gamaliel LL, Dulce Adriana ME, Estela Isabel B, Brenda Nohemí M, Payan Jorge B, Zyanya Lucía ZB, Myriam BDV, Fernanda CG, Adrian OL, Martha Isabel M, Rogelio HP. Profiling the immune response to Mycobacterium tuberculosis Beijing family infection: a perspective from the transcriptome. Virulence 2021; 12:1689-1704. [PMID: 34228582 PMCID: PMC8265813 DOI: 10.1080/21505594.2021.1936432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 01/15/2023] Open
Abstract
Tuberculosis continues to be an important public health problem. Particularly considering Beijing-family strains of Mycobacterium tuberculosis, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day 14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Conversely, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-suppression, including Nkiras, Dleu2, and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis.
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Affiliation(s)
- Cerezo-Cortés María Irene
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | | | - López-Leal Gamaliel
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mata-Espinosa Dulce Adriana
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bini Estela Isabel
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Marquina–Casitllo Brenda Nohemí
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Barrios Payan Jorge
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Zatarain-Barrón Zyanya Lucía
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bobadilla del Valle Myriam
- Departamento De Microbiología Clínica, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán Ciudad De México, México
| | - Cornejo-Granados Fernanda
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Ochoa-Leyva Adrian
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Murcia Martha Isabel
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | - Hernández-Pando Rogelio
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
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13
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Huang CC, Chu AL, Becerra MC, Galea JT, Calderón R, Contreras C, Yataco R, Zhang Z, Lecca L, Murray MB. Mycobacterium tuberculosis Beijing Lineage and Risk for Tuberculosis in Child Household Contacts, Peru. Emerg Infect Dis 2021; 26:568-578. [PMID: 32091363 PMCID: PMC7045848 DOI: 10.3201/eid2603.191314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Few studies have prospectively compared the relative transmissibility and propensity to cause disease of Mycobacterium tuberculosis Beijing strains with other human-adapted strains of the M. tuberculosis complex. We assessed the effect of Beijing strains on the risk for M. tuberculosis infection and disease progression in 9,151 household contacts of 2,223 culture-positive pulmonary tuberculosis (TB) patients in Lima, Peru. Child contacts exposed to Beijing strains were more likely than child contacts exposed to non-Beijing strains to be infected at baseline, by 12 months of follow-up, and during follow-up. We noted an increased but nonsignificant tendency for child contacts to develop TB. Beijing strains were not associated with TB in adult contacts. These findings suggest that Beijing strains are more transmissible in children than are non-Beijing strains.
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14
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Laopanupong T, Prombutara P, Kanjanasirirat P, Benjaskulluecha S, Boonmee A, Palaga T, Méresse S, Paha J, Siregar TAP, Khumpanied T, Borwornpinyo S, Chaiprasert A, Utaisincharoen P, Ponpuak M. Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberculosis Beijing strain. Sci Rep 2021; 11:4342. [PMID: 33619301 PMCID: PMC7900199 DOI: 10.1038/s41598-021-83835-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/09/2021] [Indexed: 01/04/2023] Open
Abstract
Induction of host cell autophagy by starvation was shown to enhance lysosomal delivery to mycobacterial phagosomes, resulting in the restriction of Mycobacterium tuberculosis reference strain H37Rv. Our previous study showed that strains belonging to M. tuberculosis Beijing genotype resisted starvation-induced autophagic elimination but the factors involved remained unclear. Here, we conducted RNA-Seq of macrophages infected with the autophagy-resistant Beijing strain (BJN) compared to macrophages infected with H37Rv upon autophagy induction by starvation. Results identified several genes uniquely upregulated in BJN-infected macrophages but not in H37Rv-infected cells, including those encoding Kxd1 and Plekhm2, which function in lysosome positioning towards the cell periphery. Unlike H37Rv, BJN suppressed enhanced lysosome positioning towards the perinuclear region and lysosomal delivery to its phagosome upon autophagy induction by starvation, while depletion of Kxd1 and Plekhm2 reverted such effects, resulting in restriction of BJN intracellular survival upon autophagy induction by starvation. Taken together, these data indicated that Kxd1 and Plekhm2 are important for the BJN strain to suppress lysosome positioning towards the perinuclear region and lysosomal delivery into its phagosome during autophagy induction by starvation to evade starvation-induced autophagic restriction.
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Affiliation(s)
- Thanida Laopanupong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Salisa Benjaskulluecha
- Inter-Disciplinary Graduate Program in Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Atsadang Boonmee
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Tanapat Palaga
- Inter-Disciplinary Graduate Program in Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand.,Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | | | - Jiraporn Paha
- Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | | | - Tanawadee Khumpanied
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Suparerk Borwornpinyo
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Angkana Chaiprasert
- Drug-Resistance Tuberculosis Research Fund, Siriraj Foundation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pongsak Utaisincharoen
- Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Marisa Ponpuak
- Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand. .,Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
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15
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Spoligotype Variation of Mycobacterium tuberculosis Strains Prevailing in Korea. ACTA ACUST UNITED AC 2021; 2020:8874309. [PMID: 33488887 PMCID: PMC7790563 DOI: 10.1155/2020/8874309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/30/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022]
Abstract
Tuberculosis (TB) is an ongoing global health problem, including in South Korea. To manage TB efficiently, it is necessary to understand the epidemiology, transmission route, and characteristics of prevailing Mycobacterium tuberculosis strains. In this study, we investigated microevolutions over time in the spoligotype patterns of M. tuberculosis isolated from TB patients in Korea. We collected 1,055 clinical M. tuberculosis isolates from 16 provinces in Korea from 1994 to 2006 and analyzed them by spoligotyping. We observed 26 subfamilies, including two large predominant families: a Beijing family (72.7%) and the T family (19.1%). Specifically, the abundance of spoligotype SIT269 from the Beijing-like subfamily significantly increased in the 2000s relative to the 1990s in Korea. This study provides an overview of the M. tuberculosis genotype trends over time in Korea. These data also indicate that we should consider the influence of the newly growing SIT269 subtype identified in the Beijing family.
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16
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Li Y, Pang Y, Zhang T, Xian X, Yang J, Wang R, Wang P, Zhang M, Chen W. Genotypes of Mycobacterium tuberculosis isolates circulating in Shaanxi Province, China. PLoS One 2020; 15:e0242971. [PMID: 33270700 PMCID: PMC7714122 DOI: 10.1371/journal.pone.0242971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
Objectives The prevalence of drug-resistant TB in Shaanxi Province is higher than other areas. This study was aimed to investigate the genetic diversity and epidemiology of Mycobacterium tuberculosis clinical strains in Shaanxi Province, China. Methods From January to December 2016, a total of 298 Mycobacterium tuberculosis clinical isolates from smear-positive pulmonary tuberculosis patients were genotyped by Mcspoligotyping and 15-locus VNTR. Results We found that the Beijing family strains was the most prominent family(81.54%, 243/298). Other family strains included T family(9.06%, 27/298), U family(0.67%, 2/298), LAM9 family(0.34%, 1/298) and Manu family(0.34%, 1/298). The rates of multidrug-resistant (MDR) M.Tuberculosis, age, type of case and education between Beijing and non-Beijing family strains were not statistically different, while the distribution in the three different regions among these was statistically significant. VNTR results showed that strains were classified into 280 genotypes, and 33 (11.07%) strains could be grouped into 14 clusters. 11 of the 15-VNTR loci were highly or moderately discriminative according to the Hunter-Gaston discriminatory index. Conclusions We concluded that the Beijing family genotype was the most prevalent genotype and 15-locus VNTR typing might be suitable for genotyping of M. tuberculosis in Shaanxi Province. There was less association between Beijing family genotypes and drug resistance in our study area.
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Affiliation(s)
- Yan Li
- Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, China
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Tianhua Zhang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Xiaoping Xian
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Jian Yang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Rui Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Panting Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Meng Zhang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, China
- * E-mail:
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17
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Kousha A, Farajnia S, Ansarin K, Khalili M, Shariat M, Sahebi L. Does the BCG vaccine have different effects on strains of tuberculosis? Clin Exp Immunol 2020; 203:281-285. [PMID: 33188532 DOI: 10.1111/cei.13549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
Several explanations have been suggested concerning the variety in bacille Calmette-Guerin (BCG) vaccine efficacy on strains of Mycobacterium tuberculosis (Mtb). This study aimed to compare the effect of BCG vaccination history in the prevention of the occurrence of Mtb-Beijing and non-Beijing strains. In this cross-sectional study, 64 patients with pulmonary tuberculosis (TB) were recruited from the Iranian border provinces (North West and West). Isolates were subjected to restriction fragment length polymorphism (RFLP) analysis, using the insertion sequence IS6110 as a probe (IS6110 RFLP) and drug susceptibility testing using the proportion method. Samples were analyzed with Gel Compare II 6.6 and spss version 18. The mean age [standard deviation (SD)] of the patients was 54·4 (SD = 17·0). Overall, 49 cases (76·56%) had no BCG vaccination scar. The prevalence of Beijing strains was 9·38% and drug resistance proportion among the isolates was 14·1% (nine cases). There was a significant relationship between Beijing strains and tuberculosis (TB)-drug resistance in isolates (χ2 = 26·29, P < 0·001). There was also a strong association between vaccination history and Beijing strains (χ2 = 13·23, P = 0·002). Also, a statistical relationship was observed between Beijing strains and drug-resistant TB among patients with a history of vaccination (χ2 = 7·47, P = 0·002). This association was not maintained in the unvaccinated group (P = 0·102). These findings confirm the claim that the vaccine has different effects on different subspecies of tuberculosis. The cause of the high probability of drug resistance in patients with Beijing-TB and vaccination history requires further investigation with a higher sample size.
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Affiliation(s)
- A Kousha
- Health Education and Promotion Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | - S Farajnia
- Doctoral of biotechnology, Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - K Ansarin
- Department of Medicine, Tuberculosis, and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - M Khalili
- Doctoral of History of Iranian Traditional Medicine, Department of Basic Science, University of Medical Sciences Maragheh, Maragheh, Iran
| | - M Shariat
- Family Health Research Institute, Maternal-Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - L Sahebi
- Family Health Research Institute, Maternal-Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Doctoral of Molecular Epidemiology, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Gupta A, Sinha P, Nema V, Gupta PK, Chakraborty P, Kulkarni S, Rastogi N, Anupurba S. Detection of Beijing strains of MDR M. tuberculosis and their association with drug resistance mutations in katG, rpoB, and embB genes. BMC Infect Dis 2020; 20:752. [PMID: 33054726 PMCID: PMC7557036 DOI: 10.1186/s12879-020-05479-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/05/2020] [Indexed: 11/29/2022] Open
Abstract
Background Molecular epidemiological studies of Mycobacterium tuberculosis (MTB) are the core of current research to find out the association of the M. tuberculosis genotypes with its outbreak and transmission. The high prevalence of the Beijing genotype strain among multidrug resistance (MDR) TB has already been reported in various studies around India. The overall objective of this study was to detect the prevalence of Beijing genotype strains of MDR M. tuberculosis and their association with the clinical characteristics of TB patients. Methods In this study 381 M. tuberculosis clinical isolates were obtained from sputum samples from 2008 to 2014. The multiplex-PCR and Spoligotyping (n = 131) methods were used to investigate the prevalence of the Beijing genotype strain by targeting the Rv2820 gene and their association with drug resistance and clinical characteristics of TB patients. The drug susceptibility testing of first-line anti-TB drugs was performed by using the proportion method and MGIT960. A collection of isolates having Beijing and non-Beijing strains were also characterized to see if Beijing genotype strains had a higher rate of mutations at codons 516, 526 and 531 of the 81-bp region of the rpoB gene, codon 315 of the katG gene, and codon 306 of the embB gene. Results The sensitivities and specificities of multiplex-PCR assay compared to that of standard Spoligotyping was detected to be 100%. Further, we observe that the multi drug-resistance was significantly associated with Beijing genotype strains (p = 0.03) and a strong correlation between Beijing genotype strains and specific resistance mutations at the katG315, rpoB531, and embB306 codons (p = < 0.0001, < 0.0001 & 0.0014 respectively) was also found. Conclusions This rapid, simple, and cost-effective multiplex PCR assay can effectively be used for monitoring the prevalence of Beijing genotype strains in low resource settings. Findings of this study may provide a scientific basis for the development of new diagnostic tools for detection and effective management of DR-TB in countries with a higher incidence rate of Beijing genotype strains.
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Affiliation(s)
- Anamika Gupta
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.,Division of Molecular Biology, National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411026, India
| | - Pallavi Sinha
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Vijay Nema
- Division of Molecular Biology, National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411026, India
| | - Pramod K Gupta
- Laboratory Nuclear Medicine Section, Isotope Group, Bhabha Atomic Research Centre C/o T.M.H. Annexe, Parel, Mumbai, 400012, India
| | - Pampi Chakraborty
- Laboratory Nuclear Medicine Section, Isotope Group, Bhabha Atomic Research Centre C/o T.M.H. Annexe, Parel, Mumbai, 400012, India
| | - Savita Kulkarni
- Laboratory Nuclear Medicine Section, Isotope Group, Bhabha Atomic Research Centre C/o T.M.H. Annexe, Parel, Mumbai, 400012, India
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, TB & Mycobacteria Unit, Institute Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.
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19
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Is International Travel an Emerging Issue on Transmission of Beijing Lineage Mycobacterium tuberculosis? J Trop Med 2020; 2020:9357426. [PMID: 32908549 PMCID: PMC7474789 DOI: 10.1155/2020/9357426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/19/2020] [Indexed: 01/29/2023] Open
Abstract
Mycobacterium tuberculosis belonging to Beijing sublineage (BL) is associated with high tuberculosis (TB) transmission, multidrug resistance, and adverse treatment outcomes. Sri Lanka experiences an increase in the number of travellers/workers to and from high TB-burden countries, and there is risk of getting BL strains imported into the country. In this context, a cohort study was conducted to assess the prevalence of BL strains among pulmonary tuberculosis (PTB) patients in the Kandy district of Sri Lanka (a popular tourist destination) and its association with patients' sociodemographic and clinical characteristics. The study population included sputum smear-positive PTB patients diagnosed from February 2018-July 2019. Fresh sputum samples were collected for culturing and conducted polymerase chain reaction using BL-specific primers. Among the 101 patients recruited, presence of BL strains could be ascertained in 94 patients of which 24 (26%; 95% CI: 18%-35%) had BL strains. Prevalence of BL strains was higher among those with high sputum smear grades (2+ and 3+) (P < 0.05) and those who had travelled abroad (P < 0.05). The prevalence was also higher among young people (aged <35 years). Treatment success rates were similar in patients with (83%) and without BL strains (83% vs. 81%; P value = 0.8375). The prevalence of BL strains in Kandy, Sri Lanka, was high compared to previously reported figures in Sri Lanka, and the percentage drives closer to the countries in South East Asia. International travel raises itself as an emerging issue in BL transmission urging the need of policies and practices in immigration/emigration strategies. The study findings have the potential to alter the TB epidemiology in the country and might represent the situation in other underexplored countries as well. Therefore, it is important to monitor the trends and factors related to the prevalence of Beijing strains globally and make decisions as a whole.
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20
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Nieto Ramirez LM, Ferro BE, Diaz G, Anthony RM, de Beer J, van Soolingen D. Genetic profiling of Mycobacterium tuberculosis revealed "modern" Beijing strains linked to MDR-TB from Southwestern Colombia. PLoS One 2020; 15:e0224908. [PMID: 32330146 PMCID: PMC7182180 DOI: 10.1371/journal.pone.0224908] [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: 10/22/2019] [Accepted: 04/06/2020] [Indexed: 01/01/2023] Open
Abstract
Beijing strains of Mycobacterium tuberculosis (lineage 2) have been associated with drug-resistance and transmission of tuberculosis worldwide. Most of the Beijing strains identified in the Colombian Pacific coast have exhibited a multidrug resistant (MDR) phenotype. We sought to evaluate the clonality and sublineage of Beijing strains circulating in Southwestern Colombia. Thirty-seven Beijing strains were identified through spoligotyping out of 311 clinical isolates collected in 9 years from 2002-2010. Further analysis by MIRU-VNTR 24 loci was conducted for the Beijing strains. For sublineage classification, deletions of RD105, RD207, and RD131 and point mutations at fbpB, mutT2, and acs were evaluated. Drug-resistance associated mutations to first- and second-line anti-TB drugs were also evaluated. Additionally, two Beijing strains were Illumina-whole genome sequenced (one MDR and one drug-susceptible). Among the 37 Beijing strains characterized, 36 belonged to the SIT190 type from which 28 were MDR, four pre-extensively drug resistant (XDR) TB, and four XDR-TB. The remaining strain was SIT1 and drug susceptible. MIRU-VNTR analysis allowed the identification of three Beijing clusters and two unique strains. Beijing strains were confirmed as "modern" sublineage. The mutations rpoB S531L and katG S315T were the most common among MDR strains. Moreover, the two strains evaluated by whole genome sequencing (WGS) shared most of the genetic features with the sublineage 2.2.1 "modern" Beijing previously characterized from Asian strains. WGS analysis of the MDR strain revealed the presence of eight SNPs previously reported in other MDR "Beijing-like" strains from Colombia. The presence of "modern" Beijing strains in Southwestern Colombia, most of them with MDR phenotype, suggests a different origin of this M. tuberculosis sublineage compared to other Beijing strains found in neighboring South American countries. This work may serve as a genetic baseline to study the evolution and spread of M. tuberculosis Beijing strains in Colombia, which play an important role in the propagation of MDR-TB.
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Affiliation(s)
| | - Beatriz E. Ferro
- Departamento de Salud Pública y Medicina Comunitaria, Universidad Icesi, Cali, Colombia
| | - Gustavo Diaz
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad Icesi, Cali, Colombia
| | - Richard M. Anthony
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jessica de Beer
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dick van Soolingen
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
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21
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Senghore M, Diarra B, Gehre F, Otu J, Worwui A, Muhammad AK, Kwambana-Adams B, Kay GL, Sanogo M, Baya B, Orsega S, Doumbia S, Diallo S, de Jong BC, Pallen MJ, Antonio M. Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali. Sci Rep 2020; 10:327. [PMID: 31941887 PMCID: PMC6962199 DOI: 10.1038/s41598-019-56001-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Whole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. Among the 76 patients, 61(80.3%) new cases and 15(19.7%) retreatment cases, 12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n = 20, 26%), followed by the Ghana genotype (n = 16, 21%). A sub-clade of the Cameroon genotype, which emerged ~22 years ago was likely to be involved in community transmission. A sub-clade of the Ghana genotype that arose approximately 30 years ago was an important cause of MDR-TB in Bamako. The Ghana genotype isolates appeared more likely to be MDR than other genotypes after controlling for treatment history. We identified a clade of four related Beijing isolates that included one MDR-TB isolate. It is a major concern to find the Cameroon and Ghana genotypes involved in community transmission and MDR-TB respectively. The presence of the Beijing genotype in Bamako remains worrying, given its high transmissibility and virulence.
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Affiliation(s)
- Madikay Senghore
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Florian Gehre
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Jacob Otu
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Abdul Khalie Muhammad
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Gemma L Kay
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Moumine Sanogo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Susan Orsega
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Mark J Pallen
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia.
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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22
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2019; 113:336-351. [PMID: 31903874 PMCID: PMC7006823 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- MI Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - JG Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - MI Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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23
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Guernier-Cambert V, Diefenbach-Elstob T, Klotoe BJ, Burgess G, Pelowa D, Dowi R, Gula B, McBryde ES, Refrégier G, Rush C, Sola C, Warner J. Diversity of Mycobacterium tuberculosis in the Middle Fly District of Western Province, Papua New Guinea: microbead-based spoligotyping using DNA from Ziehl-Neelsen-stained microscopy preparations. Sci Rep 2019; 9:15549. [PMID: 31664101 PMCID: PMC6820861 DOI: 10.1038/s41598-019-51892-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022] Open
Abstract
Tuberculosis remains the world's leading cause of death from an infectious agent, and is a serious health problem in Papua New Guinea (PNG) with an estimated 36,000 new cases each year. This study describes the genetic diversity of Mycobacterium tuberculosis among tuberculosis patients in the Balimo/Bamu region in the Middle Fly District of Western Province in PNG, and investigates rifampicin resistance-associated mutations. Archived Ziehl-Neelsen-stained sputum smears were used to conduct microbead-based spoligotyping and assess genotypic resistance. Among the 162 samples included, 80 (49.4%) generated spoligotyping patterns (n = 23), belonging predominantly to the L2 Lineage (44%) and the L4 Lineage (30%). This is consistent with what has been found in other PNG regions geographically distant from Middle Fly District of Western Province, but is different from neighbouring South-East Asian countries. Rifampicin resistance was identified in 7.8% of the successfully sequenced samples, with all resistant samples belonging to the L2/Beijing Lineage. A high prevalence of mixed L2/L4 profiles was suggestive of polyclonal infection in the region, although this would need to be confirmed. The method described here could be a game-changer in resource-limited countries where large numbers of archived smear slides could be used for retrospective (and prospective) studies of M. tuberculosis genetic epidemiology.
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Affiliation(s)
- Vanina Guernier-Cambert
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia.
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, 50010, IA, USA.
| | - Tanya Diefenbach-Elstob
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Bernice J Klotoe
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Graham Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Daniel Pelowa
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Robert Dowi
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Bisato Gula
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Guislaine Refrégier
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Catherine Rush
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Christophe Sola
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Jeffrey Warner
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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24
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Karmakar M, Trauer JM, Ascher DB, Denholm JT. Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and meta-analysis. J Infect 2019; 79:572-581. [PMID: 31585190 DOI: 10.1016/j.jinf.2019.09.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/30/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The globally distributed "Beijing" lineage of Mycobacterium tuberculosis has been associated with outbreaks worldwide. Laboratory based studies have suggested that Beijing lineage may have increased fitness; however, it has not been established whether these differences are of epidemiological significance with regards to transmission. Therefore, we undertook a systematic review of epidemiological studies of tuberculosis clustering to compare the transmission dynamics of Beijing lineages versus the non-Beijing lineages. METHODS We systematically searched Embase and MEDLINE before 31st December 2018, for studies which provided information on the transmission dynamics of the different M. tuberculosis lineages. We included articles that conducted population-based cross-sectional or longitudinal molecular epidemiological studies reporting information about extent of transmission of different lineages. The protocol for this systematic review was prospectively registered with PROSPERO (CDR42018088579). RESULTS Of 2855 records identified by the search, 46 were included in the review, containing 42,700 patients from 27 countries. Beijing lineage was the most prevalent and highly clustered strain in 72.4% of the studies and had a higher likelihood of transmission than non-Beijing lineages (OR 1·81 [95% 1·28-2·57], I2 = 94·0%, τ2 = 0·59, p < 0·01). CONCLUSIONS Despite considerable heterogeneity across epidemiological contexts, Beijing lineage appears to be more transmissible than other lineages.
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Affiliation(s)
- Malancha Karmakar
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - James M Trauer
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Biochemistry, University of Cambridge, CB2 1GA, UK
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
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25
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Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, Miyahara R, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Plitphonganphim S, Tantivitayakul P, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruangchai W, Palittapongarnpim P, Juthayothin T, Thawornwattana Y, Viratyosin W, Tongsima S, Mahasirimongkol S, Tokunaga K, Palittapongarnpim P. A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. Sci Rep 2019; 9:13718. [PMID: 31548561 PMCID: PMC6757101 DOI: 10.1038/s41598-019-50078-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/27/2019] [Indexed: 11/08/2022] Open
Abstract
Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolates together with their patient profiles. Our samples belonged to Lineage 1-4 (L1-L4) with those of L1 and L2 being equally dominant. Phylogenetic analysis revealed several new or rare sublineages. Differential associations between sublineages of M. tuberculosis and patient profiles, including ages, ethnicity, HIV (human immunodeficiency virus) infection and drug resistance were demonstrated. The Ancestral Beijing strains and some sublineages of L4 were associated with ethnic minorities while L1 was more common in Thais. L2.2.1.Ancestral 4 surprisingly had a mutation that is typical of the Modern Beijing sublineages and was common in Akha and Lahu tribes who have migrated from Southern China in the last century. This may indicate that the evolutionary transition from the Ancestral to Modern Beijing sublineages might be gradual and occur in Southern China, where the presence of multiple ethnic groups might have allowed for the circulations of various co-evolving sublineages which ultimately lead to the emergence of the Modern Beijing strains.
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Affiliation(s)
- Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Kiyose, Japan
| | - Nat Smittipat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Areeya Disratthakit
- Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Nonthaburi, Thailand
| | - Norio Yamada
- Research Institute of Tuberculosis, JATA, Kiyose, Japan
| | - Reiko Miyahara
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Worarat Imasanguan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Pacharee Kantipong
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | | | | | - Supada Plitphonganphim
- Department of Biostatistics, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pornpen Tantivitayakul
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Wuthiwat Ruangchai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | | | - Tada Juthayothin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Yuttapong Thawornwattana
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Wasna Viratyosin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | | | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand.
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26
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Ei PW, Lee JS, Aung WW, Yeun K, Korma W, Nyunt WW, Swe TL, Htwe MM, Win SM, Aung ST, Chang CL, Lee H. Genotypes and genetic characters of Mycobacterium tuberculosis from Myanmar using three typing methods. INFECTION GENETICS AND EVOLUTION 2019; 75:104005. [PMID: 31437559 DOI: 10.1016/j.meegid.2019.104005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/10/2019] [Accepted: 08/12/2019] [Indexed: 11/25/2022]
Abstract
Knowledge on basic characteristics of Mycobacterium tuberculosis (MTB) is helpful to understand the disease epidemiology and support the prediction of clinical outcome of the disease. The aim of this study was to detect the genotypes and genotypic characters of clinical Mycobacterium tuberculosis (MTB) isolates from new and retreatment rifampicin-resistant patients using three different genotyping methods. Mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) typing was used to determine the diversity of 222 clinical isolates. Spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) typing were also used to investigate the genetic characters of 105 MTB strains. Among the 15 genotypes detected by MIRU-VNTR, Beijing strains were the most prevalent of all strains (54.8%); new cases (40.5%) and retreatment cases (69.4%), followed by EAI strain. Spoligotyping categorized the strains into 11 lineages and 13 orphans whereas 96 different IS6110 patterns were identified using RFLP method. The mode number of IS6110 was 18 and 20. Higher band numbers were found in Beijing genotype (p < 0.001). Clustering rates by spoligotyping, MIRU-VNTR and IS6110-RFLP typing were 0.714, 0.004 and 0.085, respectively. Discriminatory powers of spoligotyping, MIRU-VNTR typing and IS6110-RFLP typing were 0.637, 1.000 and 0.997, respectively. Dominant Beijing genotype in both new and retreatment cases denoting that prevailing tuberculosis in Myanmar changed from EAI to Beijing lineage.
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Affiliation(s)
- Phyu Win Ei
- Advanced Molecular Research Centre, Department of Medical Research, 5, Ziwaka Road, Dagon Township, 11191 Yangon, Myanmar; Department of Biomedical Laboratory Science, Collage of Health Sciences, Yonsei University, Wonju Campus, 26493, Republic of Korea
| | - Jong Seok Lee
- Section of Microbiology, International Tuberculosis Research Center, 234 Gaposunhwan-ro, Masanhappo-gu, Changwon-si, Gyeongsangnam-do 51755, Republic of Korea
| | - Wah Wah Aung
- Advanced Molecular Research Centre, Department of Medical Research, 5, Ziwaka Road, Dagon Township, 11191 Yangon, Myanmar
| | - Kim Yeun
- Department of Biomedical Laboratory Science, Collage of Health Sciences, Yonsei University, Wonju Campus, 26493, Republic of Korea
| | - Workneh Korma
- Department of Biomedical Laboratory Science, Collage of Health Sciences, Yonsei University, Wonju Campus, 26493, Republic of Korea; Insititue of Biotechnology, Addis Ababa University, Ethiopia
| | - Wint Wint Nyunt
- National Tuberculosis Program, Department of Public Health, 15011, Myanmar
| | - Thyn Lei Swe
- National Tuberculosis Program, Department of Public Health, 15011, Myanmar
| | - Mi Mi Htwe
- Advanced Molecular Research Centre, Department of Medical Research, 5, Ziwaka Road, Dagon Township, 11191 Yangon, Myanmar
| | - Su Mon Win
- Advanced Molecular Research Centre, Department of Medical Research, 5, Ziwaka Road, Dagon Township, 11191 Yangon, Myanmar
| | - Si Thu Aung
- National Tuberculosis Program, Department of Public Health, 15011, Myanmar
| | - Chulhun L Chang
- Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea.
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, Collage of Health Sciences, Yonsei University, Wonju Campus, 26493, Republic of Korea.
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Beijing genotype of Mycobacterium tuberculosis is less associated with drug resistance in south China. Int J Antimicrob Agents 2019; 54:766-770. [PMID: 31398482 DOI: 10.1016/j.ijantimicag.2019.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/24/2022]
Abstract
Mycobacterium tuberculosis Beijing genotype strains are widespread globally. However, there has been no systematic study on the association between Beijing genotype and the characteristics of drug resistance. In this study, 359 M. tuberculosis isolates from south China were collected and their background information, genotype diversity and drug resistance was investigated. The results revealed that 66.0% of strains (237/359) were categorised as Beijing genotype. There was no statistical difference between Beijing and non-Beijing genotype strains in terms of patient sex, age, place of residence and treatment history. Drug resistance testing showed that 34.8% (125/359) of isolates were resistant to at least one of the seven drugs tested. The proportions of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis were 17.0% and 1.4%, respectively. Previously treated patients presented a significantly higher risk of developing drug resistance than new cases. Although the prevalence of drug resistance was higher in Beijing genotype than in non-Beijing genotype strains, there was no significant difference between these two genotypes in the multivariate analysis. Even in re-treated patients, the association of Beijing genotype with drug resistance was not significant. This study provides an insight into genotype diversity and demonstrates the characteristics of drug resistance in Beijing genotype strains, which will be useful in generating efficient tuberculosis prevention and control strategies in China.
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Liu Q, Wang D, Martinez L, Lu P, Zhu L, Lu W, Wang J. Mycobacterium tuberculosis Beijing genotype strains and unfavourable treatment outcomes: a systematic review and meta-analysis. Clin Microbiol Infect 2019; 26:180-188. [PMID: 31336202 DOI: 10.1016/j.cmi.2019.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/09/2019] [Accepted: 07/13/2019] [Indexed: 01/29/2023]
Abstract
OBJECTIVES The Mycobacterium tuberculosis Beijing genotype was first described in 1995 and is now the predominant strain among patients with tuberculosis in many Asian countries. The rapid global spread of the Beijing genotype is receiving increasing attention because it can cause a higher risk of treatment failures. Our objective was to assess the association between the Beijing genotype and unfavourable treatment outcomes of tuberculosis. METHODS We searched for eligible studies through PubMed, Web of Science, Chinese National Knowledge Infrastructure and Wanfang Data. We included cohort studies that evaluated treatment outcomes and Beijing genotype strains. Participants were individuals with active pulmonary tuberculosis. The association between Beijing genotype and the risk of unfavourable treatment outcomes was assessed using the pooled odds ratios (ORs) with corresponding confidence intervals (CIs). RESULTS In total, 7489 tuberculosis patients were involved in the analysis. Patients infected with the Beijing genotype were more likely to have unfavourable treatment outcomes, with the OR of 2.04 (95% CI 1.52-2.75). The pooled OR was 2.33 (95% CI 1.71-3.16) for recurrence, 2.36 (95% CI 1.69-3.30) for relapse and 2.62 (95% CI 1.90-3.61) for treatment failure, respectively. Subgroup analysis revealed that Beijing genotype was a significant risk factor for unfavourable treatment outcomes in Asians (OR 2.28, 95% CI 1.82-2.86) or in drug-susceptible TB patients (OR 2.11, 95% CI 1.31-3.39). No significant association was observed among non-Asian populations (OR 1.17, 95% CI 0.73-1.86) or patients with multidrug-resistant (MDR) tuberculosis (OR 0.97, 95% CI 0.48-1.94). CONCLUSIONS Our results suggest that Mycobacterium tuberculosis Beijing genotype is associated with an increased risk of unfavourable treatment outcomes, including treatment failure and relapse.
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Affiliation(s)
- Q Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China; Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - D Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing, PR China
| | - L Martinez
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - P Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - L Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - W Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - J Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China.
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Konstantynovska O, Rekrotchuk M, Hrek I, Rohozhyn A, Rudova N, Poteiko P, Gerilovych A, Bortz E, Solodiankin O. Severe Clinical Outcomes of Tuberculosis in Kharkiv Region, Ukraine, Are Associated with Beijing Strains of Mycobacterium tuberculosis. Pathogens 2019; 8:pathogens8020075. [PMID: 31185670 PMCID: PMC6631893 DOI: 10.3390/pathogens8020075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Genotypic variation in Beijing lineages of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has been associated with hyper virulence and the spread of extensively and multiple drug (X/MDR) resistant MTB strains in Eastern Europe, Central Asia, and East Asia. The clinical outcomes of 215 new cases of TB among the population of the Kharkiv region of Eastern Ukraine were analyzed to uncover factors associated with severe infection. Infecting MTB strains were profiled by 5 locus exact tandem repeats (ETRs) and 15 locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping. Among diverse MTB genotypes discovered in Ukraine, the Beijing genotype (MIRU-VNTR 42425) was significantly associated with risk factors for severe outcomes of disease in the study population, including TB/HIV co-infection and treatment failure. Strain replacement (superinfection) was observed in 10 patients, suggesting repeated exposure to novel MTB strains in hospital or community settings. Inclusion of MTB genotyping data may identify at-risk patients and improve treatment adherence to prevent X/MDR development for effective public health response against tuberculosis in Ukraine.
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Affiliation(s)
| | - Mariia Rekrotchuk
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Ivan Hrek
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Rohozhyn
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Nataliia Rudova
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Petro Poteiko
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Gerilovych
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Oleksii Solodiankin
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
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Genetic diversity and drug susceptibility patterns of the Mycobacterium tuberculosis complex in Yunnan, China. Biosci Rep 2019; 39:BSR20181746. [PMID: 30988070 PMCID: PMC6542976 DOI: 10.1042/bsr20181746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) which has been threatening global public health for many years. High genetic diversity is dominant feature of Mtb. Increasing cases of multidrug-resistant (MDR) tuberculosis (MDR-TB) is a serious public health problem to TB control in China. Spontaneous mutations in the Mtb genome can alter proteins which are the target of drugs, making the bacteria drug resistant. The purpose of the present study was to analyze the genotype of Mtb isolates from some areas in Yunnan, China and explore the association between genotypes and MDR-TB. Using spoligotyping, we identified Beijing genotypes, six non-Beijing genotypes and a number of orphan genotypes from 270 Mtb isolates from patients in Yunnan Province during 2014–2016. Of 270 Mtb isolates, 102 clinical Mtb strains were identified as drug-resistant (DR) by drug susceptibility testing (DST), among them, 52 MDR strains. Beijing genotypes occupied the highest MDR proportion (78.85%) followed by the orphan genotypes (15.38%). The characteristics of MDR strains showed high genetic diversity. The results will help to efficiently improve diagnosis and treatment and provide valuable information for Mtb molecular epidemiology.
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31
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Li D, Song Y, Yang P, Li X, Zhang AM, Xia X. Genetic diversity and drug resistance of Mycobacterium tuberculosis in Yunnan, China. J Clin Lab Anal 2019; 33:e22884. [PMID: 30896073 PMCID: PMC6595362 DOI: 10.1002/jcla.22884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 12/03/2022] Open
Abstract
Background China is a country with high burden of tuberculosis (TB), especially drug‐resistant TB (DR‐TB), which is still a serious health problem in Yunnan Province. Mycobacterium tuberculosis (MTB) is the pathogenic microorganism of TB. The epidemiological characteristics of MTB strains in local areas need to be described. Methods A total of 430 clinical MTB isolates were collected from Yunnan Province and genotyped through the method of 24‐locus mycobacterial interspersed repetitive unit‐variable number tandem DNA repeats (MIRU‐VNTR). Results The genotypes of the 24 loci showed abundantly genetic diversity, and allelic diversity index (h) of these loci varied from 0.012 to 0.817. Among the 430 strains, 30 clusters and 370 unique genotypes were identified. Beijing family was the predominant lineage (70.47%) in Yunnan MTB strains, and the other lineages contained T family (5.81%), MANU2 (0.70%), LAM (3.26%), CAS (0.23%), New‐1 (8.37%), and some unknown clades (11.16%). A total of 74 TB strains were identified as drug resistance through drug susceptibility testing (DST), including 38 multidrug‐resistant TB (MDR‐TB) and 36 single‐drug‐resistant TB (SDR‐TB). The frequency of MDR‐TB strains was significantly higher in Beijing family (10.89%) than that in non‐Beijing family (3.94%, P = 0.032). Conclusions Although MTB strains showed high genetic diversity in Yunnan, China, the Beijing family was still the dominant strain. A high frequency of MDR‐TB strains was recorded in the Beijing family.
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Affiliation(s)
- Daoqun Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Pengpeng Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiaofei Li
- Department of Clinical Laboratory, The Third People's Hospital of Kunming City, Kunming, China
| | - A-Mei Zhang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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32
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Verma S, Bhatt K, Lovey A, Ribeiro-Rodrigues R, Durbin J, Jones-López EC, Palaci M, Vinhas SA, Alland D, Dietze R, Ellner JJ, Salgame P. Transmission phenotype of Mycobacterium tuberculosis strains is mechanistically linked to induction of distinct pulmonary pathology. PLoS Pathog 2019; 15:e1007613. [PMID: 30840702 PMCID: PMC6422314 DOI: 10.1371/journal.ppat.1007613] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 03/18/2019] [Accepted: 02/02/2019] [Indexed: 12/19/2022] Open
Abstract
In a study of household contacts (HHC), households were categorized into High (HT) and Low (LT) transmission groups based on the proportion of HHC with a positive tuberculin skin test. The Mycobacterium tuberculosis (Mtb) strains from HT and LT index cases of the households were designated Mtb-HT and Mtb-LT, respectively. We found that C3HeB/FeJ mice infected with Mtb-LT strains exhibited significantly higher bacterial burden compared to Mtb-HT strains and also developed diffused inflammatory lung pathology. In stark contrast, a significant number of mice infected with Mtb-HT strains developed caseating granulomas, a lesion type with high potential to cavitate. None of the Mtb-HT infected animals developed diffused inflammatory lung pathology. A link was observed between increased in vitro replication of Mtb-LT strains and their ability to induce significantly high lipid droplet formation in macrophages. These results support that distinct early interactions of Mtb-HT and Mtb-LT strains with macrophages and subsequent differential trajectories in pathological disease may be the mechanism underlying their transmission potential.
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Affiliation(s)
- Sheetal Verma
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Kamlesh Bhatt
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Arianne Lovey
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Rodrigo Ribeiro-Rodrigues
- Cellular and Molecular Immunology Laboratory, Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Joan Durbin
- Rutgers University-New Jersey Medical School, Department of Pathology, Newark, New Jersey, United States of America
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Moises Palaci
- Mycobacteriology Laboratory, Núcleo de Doenças de Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Solange A. Vinhas
- Mycobacteriology Laboratory, Núcleo de Doenças de Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - David Alland
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Jerrold J. Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Padmini Salgame
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
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Qin L, Wang J, Lu J, Yang H, Zheng R, Liu Z, Huang X, Feng Y, Hu Z, Ge B. A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis. BMC Biol 2019; 17:7. [PMID: 30683096 PMCID: PMC6347829 DOI: 10.1186/s12915-019-0628-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), especially those that are multidrug resistant poses a serious threat to global tuberculosis control. However, the mechanism underlying the occurrence of drug resistance against more than one drug is poorly understood. Given that the Beijing/W strains are associated with outbreaks and multidrug resistance, they may harbor a genetic advantage and provide useful insight into the disease. One marker found in all Beijing/W Mtb strains is a deletion of RD105 region that results in a gene fusion, Rv0071/74, with a variable number (3-9 m) of VDP (V: Val, D: Asp; P: Pro) repeats (coded by gtggacccg repeat sequences) at the N-terminal. Here, we report that this variable number of VDP repeats in Rv0071/74 regulates the development of multidrug resistance. RESULTS We collected and analyzed 1255 Beijing/W clinical strains. The results showed that the number of VDP repeats in Rv0071/74 was related to the development of multidrug resistance, and the deletion of Rv0071/74-9 m from Beijing/W clinical strain restored drug susceptibility. Rv0071/74-9 m also increased resistance to multiple drugs when transferred to different mycobacterial strains. Cell-free assays indicate that the domain carrying 4-9 VDP repeats (4-9 m) showed a variable binding affinity with peptidoglycan and Rv0071/74 cleaves peptidoglycan. Furthermore, Rv0071/74-9 m increased cell wall thickness and reduced the intracellular concentration of antibiotics. CONCLUSIONS These findings not only identify Rv0071/74 with VDP repeats as a newly identified multidrug resistance gene but also provide a new model for the development of multiple drug resistance.
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Affiliation(s)
- Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Junmei Lu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yonghong Feng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Zhongyi Hu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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Woodman M, Haeusler IL, Grandjean L. Tuberculosis Genetic Epidemiology: A Latin American Perspective. Genes (Basel) 2019; 10:genes10010053. [PMID: 30654542 PMCID: PMC6356704 DOI: 10.3390/genes10010053] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
There are an estimated 10 million new cases of tuberculosis worldwide annually, with 282,000 new or relapsed cases each year reported from the Americas. With improvements in genome sequencing technology, it is now possible to study the genetic diversity of tuberculosis with much greater resolution. Although tuberculosis bacteria do not engage in horizontal gene transfer, the genome is far more variable than previously thought. The study of genome-wide variation in tuberculosis has improved our understanding of the evolutionary origins of tuberculosis, the arrival of tuberculosis in Latin America, the genetic determinants of drug resistance, and lineage-specific associations with important clinical phenotypes. This article reviews what is known about the arrival of tuberculosis in Latin America, the genetic diversity of tuberculosis in Latin America, and the genotypic determinants of clinical phenotypes.
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Affiliation(s)
- Marc Woodman
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Ilsa L Haeusler
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Louis Grandjean
- Institute of Child Health, University College London, London WC1N 3JH, UK.
- Department of Medicine, Imperial College London, London W2 1NY, UK.
- Great Ormond Street Hospital, Institute of Child Health, University College London, London WC1N 3JH, UK.
- Laboratorio de Investigacion y Desarollo, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martin de Porres 15102, Lima, Peru.
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Characterization of Mycobacterium tuberculosis strains in Beijing, China: drug susceptibility phenotypes and Beijing genotype family transmission. BMC Infect Dis 2018; 18:658. [PMID: 30547765 PMCID: PMC6295058 DOI: 10.1186/s12879-018-3578-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/03/2018] [Indexed: 11/16/2022] Open
Abstract
Background The most prevalent strains of Mycobacterium tuberculosis (M.tb) in Beijing belong to the Beijing genotype family. The influence of Beijing genotype prevalence on the development of drug resistance, and the association of infection with Beijing genotype M.tb with population characteristics, in Beijing, however, are still unclear. Methods In this retrospective study, 1189 isolates were subjected to drug susceptibility testing (DST) and molecular epidemiological analysis, and differences in the percentage of drug resistance between Beijing and non-Beijing genotype strains were compared. The association between the occurrence of drug resistance and the prevalence of Beijing genotype M.tb was analyzed using statistical methods. Results The Beijing genotype family was the dominant genotype (83.3%) among the 1189 M.tb isolates. Beijing genotype M.tb strains were more likely to spread among males [p = 0.018, OR (95% CI):1.127(1.004–1.264)] and people in the 45–64 age group [p = 0.016, OR (95% CI): 1.438 (1.027–2.015)]. On the contrary, non-Beijing genotype M.tb strains were more probably disseminated among the over 65 [p = 0.005, OR (95% CI):0.653 (0.474–0.9)] and non-resident population [p = 0.035, OR (95% CI):1.185(0.985–1.427)]. DST results showed that 849 (71.4%) strains were fully sensitive to first-line drugs, while 340 (28.6%) strains were resistant to at least one drug, and 9% (107/1189) were MDR-TB. The frequency of INH-resistance among Beijing genotype strains was significantly lower than that among non-Beijing genotype strains (p = 0.032). In addition, the Beijing genotype family readily formed clusters. Conclusions Our findings indicate that male and middle-aged people were more probably be infected by Beijing genotype M.tb, older people and non-residents were more probably be infected by non-Beijing genotype M.tb. The high percentage of resistance to INH occurring in non-Beijing genotype strains suggested that non-Beijing genotype strains should be given much more interest in Beijing. Electronic supplementary material The online version of this article (10.1186/s12879-018-3578-7) contains supplementary material, which is available to authorized users.
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Yamamoto K, Takeuchi S, Seto J, Shimouchi A, Komukai J, Hase A, Nakamura H, Umeda K, Hirai Y, Matsumoto K, Ogasawara J, Wada T, Yamamoto T. Longitudinal genotyping surveillance of Mycobacterium tuberculosis in an area with high tuberculosis incidence shows high transmission rate of the modern Beijing subfamily in Japan. INFECTION GENETICS AND EVOLUTION 2018; 72:25-30. [PMID: 30261265 DOI: 10.1016/j.meegid.2018.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 11/26/2022]
Abstract
Tuberculosis (TB) is a severe and wide-spread infectious disease worldwide. The modern Beijing subfamily, one lineage of M. tuberculosis, reportedly has high pathogenicity and transmissibility. This study used a molecular epidemiological approach to investigate the transmissibility of the modern Beijing subfamily in the Airin area of Osaka City, Japan. During 2006-2016, we collected 596 M. tuberculosis clinical isolates in the Airin area, Osaka city, Japan. We analyzed the 24-locus variable number of tandem repeats typing optimized for the Beijing family of isolates, M. tuberculosis lineage, and patient epidemiological data. The proportion of the modern Beijing subfamily was significantly higher not only than previously obtained data for the Airin area: it was also higher than the nationwide in Japan. The rate of recent clusters, defined as a variable number of tandem repeats profile identified within two years, of the modern Beijing subfamily was significantly higher than that the rate of recent clusters of the ancient Beijing subfamily. Results suggest that TB control measures formulated with attention to the modern Beijing subfamily might be an important benchmark to understanding recent TB transmission in the area.
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Affiliation(s)
- Kaori Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Shouhei Takeuchi
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, 1-1-1 Manabino, Nagayo, Nishisonogi, Nagasaki 851-2195, Japan
| | - Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Akira Shimouchi
- Nishinari Ward Office, 1-15-17 Taishi-cho, Nishinari-ku, Osaka 557-0002, Japan
| | - Jun Komukai
- Osaka City Public Health Center, 1-27-1000 Asahimachi, Abeno-ku, Osaka 545-0051, Japan
| | - Atsushi Hase
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Hiromi Nakamura
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Kaoru Umeda
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Yuki Hirai
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Kenji Matsumoto
- Osaka City Public Health Center, 1-27-1000 Asahimachi, Abeno-ku, Osaka 545-0051, Japan
| | - Jun Ogasawara
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Takayuki Wada
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
| | - Taro Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
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Erie H, Kaboosi H, Javid N, Shirzad-Aski H, Taziki M, Kuchaksaraee MB, Ghaemi EA. The high prevalence of Mycobacterium tuberculosis Beijing strain at an early age and extra-pulmonary tuberculosis cases. IRANIAN JOURNAL OF MICROBIOLOGY 2017; 9:312-317. [PMID: 29487728 PMCID: PMC5825930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Tuberculosis (TB) is still responsible for a wide range of deaths worldwide. Beijing genotype is one of the most important and virulent strains in Mycobacterium tuberculosis. This study was designed for determination Beijing genotypes of M. tuberculosis in Golestan province, north of Iran. MATERIALS AND METHODS In the current descriptive study, 238 clinical MTB isolates, obtained from patients with pulmonary and extra-pulmonary TB in north of Iran, were evaluated. Oligonucleotide primers for the Beijing and non-Beijing genotypes and specific probes for their detection by a real-time PCR method were employed. In addition, an association between the Beijing genotype and possible clinical and demographic factors was evaluated. RESULTS The method revealed that 33 cases (13.9%) were the Beijing lineage and 205 (86.1%) the non-Beijing genotype. The mean age of patients infected with the Beijing and non-Beijing strains was 37.27 ± 18.3 and 51 ± 21.2 years, respectively; the difference was statistically significant (P = 0.001). In addition, the prevalence of the Beijing strain decreased with age. Patients with a TB infection caused by the Beijing genotype were also more vulnerable to treatment failure. Based on the origin of the samples, the Beijing genotype was more often observed in extra-pulmonary samples compared with Pulmonary ones (P = 0.001). CONCLUSION The Beijing genotype of MTB is prevalent in our region especially among young people which could indicate the risk of further expansion in the future.
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Affiliation(s)
- Hanifeh Erie
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Hami Kaboosi
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Naeme Javid
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Masoumeh Taziki
- Tuberculosis Laboratory Center, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Ezzat Allah Ghaemi
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran,Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran,Corresponding author: Ezzat Allah Ghaemi, PhD, Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran; Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran. Tel: +981732440225, Fax: 01732235452,
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The study on the association between Beijing genotype family and drug susceptibility phenotypes of Mycobacterium tuberculosis in Beijing. Sci Rep 2017; 7:15076. [PMID: 29118425 PMCID: PMC5678160 DOI: 10.1038/s41598-017-14119-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/02/2017] [Indexed: 12/29/2022] Open
Abstract
The predominant prevalent Mycobacterium tuberculosis (M. tb) lineage was the Beijing genotype family in Beijing. There has been no systematic study on the association between drug resistance and Beijing genotype. Here we collected 268 M. tb strains, analyzed the background information and the bacteriological characteristics. The mean age of the cases was 40.12 years; male patients were almost three times than female patients. After genotyping analyzation, 81.7% (219/268) strains were categorized as Beijing genotype; no significant difference was observed between Beijing and non-Beijing genotype in gender, age and treatment history. Drug susceptibility testing (DST) analyzation demonstrated that 172 (64.2%) strains were fully sensitive to all drugs (Isoniazid, Rifampin, Streptomycin, and Ethambutol), while 96 (35.8%) strains were resistant to at least one of the drugs. Beijing genotype strains exhibited a significantly higher clustering rate. However, no significant association relationship was observed between drug resistance and Beijing genotype family. The study provided insights into the genotype diversity and revealed that the frequencies of drug-resistance of Beijing genotype strains.It would be helpful for the establishment of the efficient tuberculosis (TB) prevention and control strategy in Beijing.
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Mathema B, Andrews JR, Cohen T, Borgdorff MW, Behr M, Glynn JR, Rustomjee R, Silk BJ, Wood R. Drivers of Tuberculosis Transmission. J Infect Dis 2017; 216:S644-S653. [PMID: 29112745 PMCID: PMC5853844 DOI: 10.1093/infdis/jix354] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Measuring tuberculosis transmission is exceedingly difficult, given the remarkable variability in the timing of clinical disease after Mycobacterium tuberculosis infection; incident disease can result from either a recent (ie, weeks to months) or a remote (ie, several years to decades) infection event. Although we cannot identify with certainty the timing and location of tuberculosis transmission for individuals, approaches for estimating the individual probability of recent transmission and for estimating the fraction of tuberculosis cases due to recent transmission in populations have been developed. Data used to estimate the probable burden of recent transmission include tuberculosis case notifications in young children and trends in tuberculin skin test and interferon γ-release assays. More recently, M. tuberculosis whole-genome sequencing has been used to estimate population levels of recent transmission, identify the distribution of specific strains within communities, and decipher chains of transmission among culture-positive tuberculosis cases. The factors that drive the transmission of tuberculosis in communities depend on the burden of prevalent tuberculosis; the ways in which individuals live, work, and interact (eg, congregate settings); and the capacity of healthcare and public health systems to identify and effectively treat individuals with infectious forms of tuberculosis. Here we provide an overview of these factors, describe tools for measurement of ongoing transmission, and highlight knowledge gaps that must be addressed.
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Affiliation(s)
- Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, California
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Martien W Borgdorff
- Centers for Disease Control and Prevention, Kisumu, Kenya
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Marcel Behr
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montreal,Canada
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Roxana Rustomjee
- Tuberculosis Clinical Research Branch, Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Robin Wood
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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Hoffner S, Sahebi L, Ansarin K, Sabour S, Mohajeri P. Mycobacterium tuberculosis of the Beijing Genotype in Iran and the World Health Organization Eastern Mediterranean Region: A Meta-Analysis. Microb Drug Resist 2017; 24:693-698. [PMID: 29058526 DOI: 10.1089/mdr.2017.0160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE The Beijing genotype is a distinct genetic lineage of Mycobacterium tuberculosis, which is distributed worldwide, and may cause large outbreaks of multidrug resistance-tuberculosis (MDR-TB). The distribution of such strains in the Eastern Mediterranean region (EMR) is unclear, and clarifying the data is our purpose apart from the presence of Beijing TB in Iran. METHODS We searched Published literature from CINAHL Cochrane Library, Current Contents, Database of Abstracts of Reviews of Effects (DARE), ProQuest Google Scholar PubMed, PsycINFO, Thomson Reuters, (SID), and Medical Library (MedLib) to detect relevant studies from the year 2000 to July 2015 with the following keywords: M. tuberculosis, Beijing genotype, EMR, and drug resistance. Random-effect models were used to estimate the proportion of Beijing strains in STATA 14. Heterogeneity was investigated by subgroup analysis and meta-regression. RESULTS AND CONCLUSION The meta-prevalence of Beijing strains was 4% (CI 95% = 3-5). The prevalence was different based on types of detection techniques (spoligotyping = 4% vs. other techniques = 6%; p = 0.003) and years of study (before the year 2000 = 2% vs. after year 2000 = 4%, p = 0.004). The Beijing family was most prevalent in Iran and Pakistan. A strong relationship with drug resistance was reported in Pakistan and Iran, and an increasing trend was seen in Pakistan. Additional studies of drug-resistant TB distribution among Beijing strains in EMR countries are needed as well as a time-trend analysis of the Beijing strain infection in the region.
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Affiliation(s)
- Sven Hoffner
- 1 Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet , Stockholm, Sweden
| | - Leyla Sahebi
- 2 Maternal/Fetal and Neonatal Research Center, Tehran University of Medical Sciences , Tehran, Iran .,3 Department of Epidemiology, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Science , Tabriz, Iran
| | - Khalil Ansarin
- 4 Department of Medicine, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Siamak Sabour
- 5 Department of Clinical Epidemiology, Safety Promotion and Injury Prevention Research Center, School of Health, Shahid Beheshti University of Medical Sciences , Tehran, Iran
| | - Parviz Mohajeri
- 6 Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
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Klemm E, Dougan G. Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics. Cell Host Microbe 2017; 19:599-610. [PMID: 27173928 DOI: 10.1016/j.chom.2016.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 01/07/2023]
Abstract
The development of next-generation sequencing as a cost-effective technology has facilitated the analysis of bacterial population structure at a whole-genome level and at scale. From these data, phylogenic trees have been constructed that define population structures at a local, national, and global level, providing a framework for genetic analysis. Although still at an early stage, these approaches have yielded progress in several areas, including pathogen transmission mapping, the genetics of niche colonization and host adaptation, as well as gene-to-phenotype association studies. Antibiotic resistance has proven to be a major challenge in the early 21(st) century, and phylogenetic analyses have uncovered the dramatic effect that the use of antibiotics has had on shaping bacterial population structures. An update on insights into bacterial evolution from comparative genomics is provided in this review.
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Affiliation(s)
- Elizabeth Klemm
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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Lavrova AI, Postnikov EB, Manicheva OA, Vishnevsky BI. Bi-logistic model for disease dynamics caused by Mycobacterium tuberculosis in Russia. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171033. [PMID: 28989789 PMCID: PMC5627129 DOI: 10.1098/rsos.171033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/10/2017] [Indexed: 05/04/2023]
Abstract
In this work, we explore epidemiological dynamics by the example of tuberculosis in Russian Federation. It has been shown that the epidemiological dynamics correlates linearly with the virulence of Mycobacterium tuberculosis during the period 1987-2012. To construct an appropriate model, we have analysed (using LogLet decomposition method) epidemiological World Health Organization (WHO) data (period 1980-2014) and obtained, as result of their integration, a curve approximated by a bi-logistic function. This fact allows a subdivision of the whole population into parts, each of them satisfies the Verhulst-like models with different constant virulences introduced into each subsystem separately. Such a subdivision could be interconnected with the heterogeneous structure of mycobacterial population that has a high ability of adaptation to the host and strong mutability.
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Affiliation(s)
- Anastasia I. Lavrova
- Saint-Petersburg State University, Medical Faculty, Universitetskaya emb., 7/9, Saint-Petersburg, Russia
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky avenue 2-4, Saint-Petersburg, Russia
- Author for correspondence: Anastasia I. Lavrova e-mail:
| | - Eugene B. Postnikov
- Department of Theoretical Physics, Kursk State University, Radishcheva street 33, Kursk, Russia
| | - Olga A. Manicheva
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky avenue 2-4, Saint-Petersburg, Russia
| | - Boris I. Vishnevsky
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky avenue 2-4, Saint-Petersburg, Russia
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Complete Genome Sequences of Three Representative Mycobacterium tuberculosis Beijing Family Strains Belonging to Distinct Genotype Clusters in Hanoi, Vietnam, during 2007 to 2009. GENOME ANNOUNCEMENTS 2017; 5:5/27/e00510-17. [PMID: 28684565 PMCID: PMC5502846 DOI: 10.1128/genomea.00510-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present here three complete genome sequences of Mycobacterium tuberculosis Beijing family strains isolated in Hanoi, Vietnam. These three strains were selected from major genotypic clusters (15-MIRU-VNTR) identified in a previous population-based study. We emphasize their importance and potential as reference strains in this Asian region.
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Complete Genome Sequence of a Mycobacterium tuberculosis Strain Belonging to the East African-Indian Family in the Indo-Oceanic Lineage, Isolated in Hanoi, Vietnam. GENOME ANNOUNCEMENTS 2017; 5:5/24/e00509-17. [PMID: 28619797 PMCID: PMC5473266 DOI: 10.1128/genomea.00509-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The East African-Indian (EAI) family of Mycobacterium tuberculosis is an endemic group mainly observed in Southeast Asia. Here, we report the complete genome sequence of an M. tuberculosis strain isolated as a member of the EAI family in Hanoi, Vietnam, a country with a high incidence of tuberculosis.
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Biological and Epidemiological Consequences of MTBC Diversity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:95-116. [PMID: 29116631 DOI: 10.1007/978-3-319-64371-7_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis is caused by different groups of bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). The combined action of human factors, environmental conditions and bacterial virulence determine the extent and form of human disease. MTBC virulence is a composite of different clinical phenotypes such as transmission rate and disease severity among others. Clinical phenotypes are also influenced by cellular and immunological phenotypes. MTBC phenotypes are determined by the genotype, therefore finding genotypes responsible for clinical phenotypes would allow discovering MTBC virulence factors. Different MTBC strains display different cellular and clinical phenotypes. Strains from Lineage 5 and Lineage 6 are metabolically different, grow slower, and are less virulent. Also, at least certain groups of Lineage 2 and Lineage 4 strains are more virulent in terms of disease severity and human-to-human transmission. Because phenotypic differences are ultimately caused by genotypic differences, different genomic loci have been related to various cellular and clinical phenotypes. However, defining the impact of specific bacterial genomic loci on virulence when other bacterial determinants, human and environmental factors are also impacting the phenotype would contribute to a better knowledge of tuberculosis virulence and ultimately benefit tuberculosis control.
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Unique Regulation of the DosR Regulon in the Beijing Lineage of Mycobacterium tuberculosis. J Bacteriol 2016; 199:JB.00696-16. [PMID: 27799329 DOI: 10.1128/jb.00696-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022] Open
Abstract
The DosR regulon, a set of 48 genes normally expressed in Mycobacterium tuberculosis under conditions that inhibit aerobic respiration, is controlled via the DosR-DosS/DosT two-component system. While the regulon requires induction in most M. tuberculosis isolates, for members of the Beijing lineage, its expression is uncoupled from the need for signaling. In our attempts to understand the mechanistic basis for this uncoupling in the Beijing background, we previously reported the identification of two synonymous single-nucleotide polymorphisms (SNPs) within the adjacent Rv3134c gene. In the present study, we have interrogated the impact of these SNPs on dosR expression in wild-type strains, as well as a range of dosR-dosS-dosT mutants, for both Beijing and non-Beijing M. tuberculosis backgrounds. In this manner, we have unequivocally determined that the C601T dosR promoter SNP is the sole requirement for the dramatic shift in the pattern of DosR regulon expression seen in this globally important lineage. Interestingly, we also show that DosT is completely nonfunctional within these strains. Thus, a complex series of evolutionary steps has led to the present-day Beijing DosR phenotype that, in turn, potentially confers a fitness advantage in the face of some form of host-associated selective pressure. IMPORTANCE Mycobacterium tuberculosis strains of the Beijing lineage have been described as being of enhanced virulence compared to other lineages, and in certain regions, they are associated with the dramatic spread of multidrug-resistant tuberculosis (TB). In terms of trying to understand the functional basis for these broad epidemiological phenomena, it is interesting that, in contrast to the other major lineages, the Beijing strains all constitutively overexpress members of the DosR regulon. Here, we identify the mutational events that led to the evolution of this unique phenotype. In addition, our work highlights the fact that important phenotypic differences exist between distinct M. tuberculosis lineages, with the potential to impact the efficacy of diagnosis, vaccination, and treatment programs.
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Mohajeri P, Moradi S, Atashi S, Farahani A. Mycobacterium tuberculosis Beijing Genotype in Western Iran: Distribution and Drug Resistance. J Clin Diagn Res 2016; 10:DC05-DC07. [PMID: 27891336 DOI: 10.7860/jcdr/2016/20893.8689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/24/2016] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Mycobacterium tuberculosis Beijing genotype is gaining importance all over the world because this genotype is highly prevalent in several areas and is also frequently associated with drug resistance. AIM To identify and determine the frequency of Beijing genotype and mix infection with Beijing and non-Beijing in west of Iran and analyse the association between Beijing genotype and drug resistance. MATERIALS AND METHODS This cross-sectional study was conducted on 146 Tuberculosis (TB) samples collected at the TB reference laboratory in Kermanshah west of Iran from January 2014 to February 2015, Mycobacterium tuberculosis isolates from sputum samples, detected by microcopy, biochemical tests and solid culture were included and then the confirmed samples with Cepheid Xpert MTB/RIF assay were subjected to drug susceptibility tests for rifampicin, isoniazid, ethambutol using proportional method. The prevalence rate of Beijing and non-Beijing genotype was determined by Multiplex- Polymerase Chain Reaction (PCR). RESULT A total of 15/146 (10%) isolates were diagnosed as Beijing genotypes and the remaining 131/146(90%) isolates were non-Beijing genotypes by Multiplex PCR method. Among the 15 Beijing cases, 14 samples have shown mix infection indicating the presence of both Beijing and non-Beijing strains in samples. Three isolates from all cases were drug resistant. Interestingly all drug resistance isolates were from Beijing genotype which shows strong association between drug resistance and Beijing genotype. Also this genotype was more prevalent in younger age-group people (p=0.035). CONCLUSION Frequency of Beijing genotype in west of Iran is more than other sites of Iran but less than Asia. According to our result, mix infections with Beijing and non-Beijing, had the most prevalence therefore we should be concerned more about mix infections. Multiplex-PCR method is feasible, trustworthy and can distinguish mix infections. It is suggested to perform spoligotyping in addition to multiplex PCR method to discriminate mix infections.
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Affiliation(s)
- Parviz Mohajeri
- Associate Professor of Medical Bacteriology, Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Sakineh Moradi
- Research Assistant of Medical Bacteriology, Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Sara Atashi
- Research Assistant of Medical Bacteriology, West Tuberculosis Center, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Abbas Farahani
- Ph.D student of Medical Bacteriology, Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, IR Iran. Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
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Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2016; 113:13881-13886. [PMID: 27872285 DOI: 10.1073/pnas.1611283113] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The "Beijing" Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that recent historical events have contributed to the evolution and dispersal of the CAC. Our timing estimates indicate that the clade was likely introduced to Afghanistan during the 1979-1989 Soviet-Afghan war and spread further after population displacement in the wake of the American invasion in 2001. We also find that drug resistance mutations accumulated on a massive scale in Mtb isolates from former Soviet republics after the fall of the Soviet Union, a pattern that was not observed in CAC isolates from Afghanistan. Our results underscore the detrimental effects of political instability and population displacement on tuberculosis control and demonstrate the power of phylodynamic methods in exploring bacterial evolution in space and time.
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Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS 6110 Insertions and Tandem Repeat Analysis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5216530. [PMID: 27812529 PMCID: PMC5080463 DOI: 10.1155/2016/5216530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/22/2016] [Indexed: 11/17/2022]
Abstract
QUB11a is used as a locus for variable number of tandem repeats (VNTR) analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp) that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp) investigated contained IS6110 insertions and varied in the number of repeats (18 patterns) and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.
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de Keijzer J, Mulder A, de Ru AH, van Soolingen D, van Veelen PA. Parallel reaction monitoring of clinical Mycobacterium tuberculosis lineages reveals pre-existent markers of rifampicin tolerance in the emerging Beijing lineage. J Proteomics 2016; 150:9-17. [PMID: 27576137 DOI: 10.1016/j.jprot.2016.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/05/2016] [Accepted: 08/25/2016] [Indexed: 11/30/2022]
Abstract
The spread of multidrug resistant Mycobacterium tuberculosis is one of the major challenges in tuberculosis control. In Eurasia, the spread of multidrug resistant tuberculosis is driven by the M. tuberculosis Beijing genotype. In this study, we examined whether selective advantages are present in the proteome of Beijing isolates that contribute to the emergence of this genotype. To this end, we compared the proteome of M. tuberculosis Beijing to that of M. tuberculosis H37Rv, both in the presence and absence of the first-line antibiotic rifampicin. During rifampicin exposure, both M. tuberculosis genotypes express proteins belonging to the DosR dormancy regulon, which induces a metabolically hypoactive-, drug tolerant phenotype. However, these markers of rifampicin tolerance were already more abundant in the M. tuberculosis Beijing isolate prior to drug exposure. To determine whether the a priori high abundance of specific proteins contribute to the formation of antibiotic resistance in M. tuberculosis Beijing, we quantified the abundance of 33 selected proteins in 27 clinical isolates from the five most common M. tuberculosis lineages using parallel reaction monitoring. The observed pre-existing high abundance of dormancy proteins in Beijing strains provides an evolutionary advantage that allows these strains to persist for prolonged periods during rifampicin treatment. SIGNIFICANCE M. tuberculosis is the leading cause of death by a bacterial infection worldwide. Treatment-regimen to eradicate this pathogen make use of the first-line antibiotic rifampicin, which is considered to be the cornerstone of modern day anti-tuberculosis treatment. Despite the potency of rifampicin, there is an increasing occurrence of rifampicin resistant mutants in a specific cluster of M. tuberculosis, the Beijing genotype. Using both a data dependent acquisition and a targeted proteomic approach we identified markers of rifampicin tolerance to be high abundant in members of the M. tuberculosis Beijing genotype, already prior drug exposure. The identification of this M. tuberculosis Beijing specific trait will contribute to improved diagnostics and treatment of M. tuberculosis.
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Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands.
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, BA, The Netherlands; Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500, HB, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands
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