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Indriarini D, Rukmana A, Yasmon A. CLONING AND EXPRESSION OF MCE1A GENE FROM MYCOBACTERIUM TUBERCULOSIS BEIJING AND H37RV STRAIN FOR VACCINE CANDIDATE DEVELOPMENT. Afr J Infect Dis 2018; 12:127-132. [PMID: 29619443 PMCID: PMC5876784 DOI: 10.2101/ajid.12v1s.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Tuberculosis remains the leading cause of death in the world, especially wherever poverty, malnutrition and poor housing prevail. Mycobacterium tuberculosis Beijing strain is the most common strain that causes tuberculosis in Indonesia. The wide spread of tuberculosis has been further aggravated by HIV-AIDS and drug resistance. Unfortunately, Bacille Calmette-Guerin (BCG) as the current vaccine has different protection function and efficacy. According to function analysis, mce1A gene was predicted to have a role in host invasion and survival of Mycobacterium tuberculosis in human macrophages. MATERIALS AND METHODS We performed cloning and protein expression of Mce1A gene of Mycobacterium tuberculosis Beijing strain as local isolate and standard strain H37Rv as a comparison on the expression system Escherichia coli BL21(DE3). Mce1A gene from the strains were amplified by PCR and inserted into the vector pET28a. Each resulting recombinant plasmid was subsequently transformed into E. coli BL21(DE3) and Mce1A protein was expressed with IPTG induction. RESULTS E. coli BL21(DE3) was succesfully transformed with a recombinant plasmid that contains the Mce1A gene insert with correct orientation and reading frame. There was no mutation found in the amino acids sequence for B and T cell epitope. Mce1A expression in E. coli BL21(DE3) showed a protein band that was higher than expected. The protein was confirmed with Western blotting using anti-His detector. CONCLUSION We assumed that Mce1A recombinant protein that has been expressed in E. coli BL21(DE3) is in their dimeric form or alternatively formed aggregates of different sizes.
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Affiliation(s)
- Desi Indriarini
- Department of Microbiology, Faculty of Medicine, University of Nusa Cendana, Kupang, Indonesia
| | - Andriansjah Rukmana
- Department of Microbiology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Andi Yasmon
- Department of Microbiology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
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Chen YY, Chang JR, Wu CD, Yeh YP, Yang SJ, Hsu CH, Lin MC, Tsai CF, Lin MS, Su IJ, Dou HY. Combining molecular typing and spatial pattern analysis to identify areas of high tuberculosis transmission in a moderate-incidence county in Taiwan. Sci Rep 2017; 7:5394. [PMID: 28710410 PMCID: PMC5511213 DOI: 10.1038/s41598-017-05674-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/01/2017] [Indexed: 11/08/2022] Open
Abstract
In total, 303 randomly selected clinical Mycobacterium tuberculosis (MTB) isolates from 303 patients (collected January to December 2012) in central Taiwan were examined. The major lineages found were Beijing (N = 114, 37.62%), Haarlem (N = 76, 25.08%) and East African-Indian (EAI) (N = 42, 13.86%). Notably, younger persons (≤30 years old) were 6.58 times more likely to be infected with a Beijing genotype compared to older persons (>70 years) (p < 0.05). Combining molecular typing methods and geographical information system (GIS) analysis, we uncovered a twofold higher incidence of Beijing strains in a hotspot area (33%) compared to non-hotspot areas (17%). By 24 MIRU-VNTR typing, persons in clustered groups were 1.96 times more likely to be infected with a Beijing strain compared with non-clustered persons, suggesting recent spread and emergence of MTB. Finally, we observed a trend in which TB incidence increased as the density/concentration of analyzed environmental factors increased, suggesting that environmental factors are associated with TB transmission; however, only population density was found to be significantly associated with increased risk of TB (p < 0.05). Molecular typing methods combined with spatial analysis suggest possible TB transmission. Early intervention to interrupt transmission may be most effective if targeted to hot zones of TB.
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Affiliation(s)
- Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiai-Yi, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chih-Da Wu
- Department of Forestry and Natural Resources, National Chiayi University, Chia-Yi, Taiwan
- The Center for Health and the Global Environment, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yen-Po Yeh
- Chang-Hua County Public Health Bureau, Changhua City, Taiwan
| | - Shiu-Ju Yang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chih-Hao Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ming-Ching Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ching-Fang Tsai
- Department of Medical Research, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Shian Lin
- Department of Internal Medicine, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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4
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Transposition mechanism, molecular characterization and evolution of IS6110, the specific evolutionary marker of Mycobacterium tuberculosis complex. Mol Biol Rep 2016; 44:25-34. [DOI: 10.1007/s11033-016-4084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
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In Vivo IS6110 Profile Changes in a Mycobacterium tuberculosis Strain as Determined by Tracking over 14 Years. J Clin Microbiol 2015; 53:2359-61. [PMID: 25948604 DOI: 10.1128/jcm.00607-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/28/2015] [Indexed: 11/20/2022] Open
Abstract
Transposition and homologous recombination of IS6110 appear in Mycobacterium tuberculosis along in vivo sequential infections. These events were checked in different clones of a successful strain, M. tuberculosis Zaragoza, with the focus on a variant in which integration of a copy of IS6110 in the origin of replication (oriC) region occurred.
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6
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Li G, Zhang J, Guo Q, Wei J, Jiang Y, Zhao X, Zhao LL, Liu Z, Lu J, Wan K. Study of efflux pump gene expression in rifampicin-monoresistant Mycobacterium tuberculosis clinical isolates. J Antibiot (Tokyo) 2015; 68:431-5. [PMID: 25690361 DOI: 10.1038/ja.2015.9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 10/28/2014] [Accepted: 01/19/2015] [Indexed: 11/09/2022]
Abstract
Rifampicin (RIF) resistance is a risk factor for poor outcome in tuberculosis (TB). In Mycobacterium tuberculosis, both target gene mutation and efflux pumps have major roles in the resistance to anti-TB drugs. This study aimed to determine whether RIF induces efflux pump activation in RIF-monoresistant M. tuberculosis strains. Here, we took advantage of 16 RIF-monoresistant M. tuberculosis clinical isolates to evaluate the expression of 27 putative drug efflux pump genes and measured the influence of four drug efflux pump inhibitors, carbonyl cyanide m-chlorophenyl hydrazone (CCCP), verapamil (VP), thioridazine (TZ) and chlorpromazine (CPZ), on the RIF MICs of these strains. Eight of the 16 RIF-monoresistant isolates carried mutations in rpoB and overexpressed one or two of the following putative efflux pump genes: Rv2333, drrB, drrC, Rv0842, bacA and efpA. CCCP, VP, TZ and CPZ lowered the RIF MICs greater than fourfold in 6, 12, 9 and 12 isolates, respectively. The lowered RIF MICs by VP and CPZ were identical and stronger than CCCP (P-values were all 0.033). In conclusion, the efflux pumps Rv2333, DrrB, DrrC, Rv0842, BacA and EfpA may have a role in RIF resistance in addition to classical mutations in the rpoB gene, and the addition of VP and CPZ could significantly increase RIF susceptibility in RIF-monoresistant M. tuberculosis.
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Affiliation(s)
- Guilian Li
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingrui Zhang
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China [3] Key Lab of Laboratory Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China [4] Laboratory, Gynecological and Obstetric Hospital in Shi Jiazhuang, Hebei, China
| | - Qian Guo
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China [3] Pathogenic Biology Institute, South of China University, Hengyang, Hunan, China
| | - Jianhao Wei
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China [3] Key Lab of Laboratory Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Yi Jiang
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiuqin Zhao
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Li-Li Zhao
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhiguang Liu
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jianxin Lu
- Key Lab of Laboratory Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Kanglin Wan
- 1] Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Dou HY, Chen YY, Kou SC, Su IJ. Prevalence of Mycobacterium tuberculosis strain genotypes in Taiwan reveals a close link to ethnic and population migration. J Formos Med Assoc 2014; 114:484-8. [PMID: 25542769 DOI: 10.1016/j.jfma.2014.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/10/2014] [Accepted: 07/21/2014] [Indexed: 01/02/2023] Open
Abstract
Taiwan is a relatively isolated island, serving as a mixing vessel for colonization by different waves of ethnic and migratory groups over the past 4 centuries. The potential transmission pattern of Mycobacterium tuberculosis in different ethnic and migratory populations remains to be elucidated. By using mycobacterial tandem repeat sequences as genetic markers, the prevalence of M. tuberculosis strains in Taiwan revealed a close link to the historical migration. Interestingly, the M. tuberculosis strain in the aborigines of Eastern and Central Taiwan had a dominance of the Haarlem (Dutch) strain while those in Southern Taiwan had a dominance of the East-African Indian (EAI) strain. The prevalence of different M. tuberculosis strains in specific ethnic populations suggests that M. tuberculosis transmission is limited and restricted to close contact. The prevalence of the Beijing modern strain in the young population causes a concern for M. tuberculosis control, because of high virulence and drug resistance. Furthermore, our data using molecular genotyping should provide valuable information on the historical study of the origin and migration of aborigines in Taiwan.
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Affiliation(s)
- Horng-Yunn Dou
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Yih-Yuan Chen
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Shu-Chen Kou
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Ih-Jen Su
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan.
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8
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Kato-Miyazawa M, Miyoshi-Akiyama T, Kanno Y, Takasaki J, Kirikae T, Kobayashi N. Genetic diversity of Mycobacterium tuberculosis isolates from foreign-born and Japan-born residents in Tokyo. Clin Microbiol Infect 2014; 21:248.e1-8. [PMID: 25595707 DOI: 10.1016/j.cmi.2014.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022]
Abstract
Sequences of the full genomes of 259 clinical isolates of Mycobacterium tuberculosis, obtained from foreign-born and Japan-born patients in Tokyo, Japan, were determined, and a phylogenetic tree constructed by concatenated single-nucleotide polymorphism (SNP) sequences. The 259 isolates were clustered into four clades: Lineage 2 (East Asian or "Beijing" genotype; n = 182, 70.3%), Lineage 4 (Euro-American, n = 46, 17.8%), Lineage 1 (Indo-Oceanic, n = 23, 8.9%), and Lineage 3 (East African-Indian, n = 8, 3.1%). Of the 259, 36 (13.9%) were resistant to at least one drug. There was no multi-drug-resistant isolate. Drug resistance was greater for the strains in Lineage 2 than the non-Lineage 2. The proportion of Lineage 2 isolates was significantly smaller in foreign-born (n = 43/91, 47.3%) than in Japan-born (n = 139/168, 82.7%) patients, whereas the proportion of Lineage 1 isolates was significantly larger in foreign-born (n = 19/91, 20.9%) than in Japan-born (n = 4/168, 2.4%) patients. We also found eight SNPs specific to the typical Beijing sub-genotype in Lineage 2, including 4 non-synonymous SNPs. Of the 259 isolates, 244 had strain-specific SNP(s) and small (1-30-bp) insertions and deletions (indels). The numbers of strain-specific SNPs and indels per isolate were significantly larger from foreign-born (median 89, range 0-520) than from Japan-born (median 23, range 0-415) (p 3.66E-15) patients. These results suggested that M. tuberculosis isolates from foreign-born patients had more genetic diversity than those from Japan-born patients.
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Affiliation(s)
| | - T Miyoshi-Akiyama
- Department of Infectious Diseases, Japan; Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Y Kanno
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - J Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - T Kirikae
- Department of Infectious Diseases, Japan.
| | - N Kobayashi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan; National Hospital Organization Tokyo National Hospital, Tokyo, Japan
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Barletta F, Vandelannoote K, Collantes J, Evans CA, Arévalo J, Rigouts L. Standardization of a TaqMan-based real-time PCR for the detection of Mycobacterium tuberculosis-complex in human sputum. Am J Trop Med Hyg 2014; 91:709-14. [PMID: 25114009 DOI: 10.4269/ajtmh.13-0603] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Real-time polymerase chain reaction (qPCR) was optimized for detecting Mycobacterium tuberculosis in sputum. Sputum was collected from patients (N = 112) with suspected pulmonary tuberculosis, tested by smear microscopy, decontaminated, and split into equal aliquots that were cultured in Löwenstein-Jensen medium and tested by qPCR for the small mobile genetic element IS6110. The human ERV3 sequence was used as an internal control. 3 of 112 (3%) qPCR failed. For the remaining 109 samples, qPCR diagnosed tuberculosis in 79 of 84 patients with culture-proven tuberculosis, and sensitivity was greater than microscopy (94% versus 76%, respectively, P < 0.05). The qPCR sensitivity was similar (P = 0.9) for smear-positive (94%, 60 of 64) and smear-negative (95%, 19 of 20) samples. The qPCR was negative for 24 of 25 of the sputa with negative microscopy and culture (diagnostic specificity 96%). The qPCR had 99.5% sensitivity and specificity for 211 quality control samples including 84 non-tuberculosis mycobacteria. The qPCR cost ∼5US$ per sample and provided same-day results compared with 2-6 weeks for culture.
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Affiliation(s)
- Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Koen Vandelannoote
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Jimena Collantes
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Carlton A Evans
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Jorge Arévalo
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Leen Rigouts
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
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10
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Chen YY, Chang JR, Huang WF, Hsu SC, Kuo SC, Sun JR, Dou HY. The pattern of cytokine production in vitro induced by ancient and modern Beijing Mycobacterium tuberculosis strains. PLoS One 2014; 9:e94296. [PMID: 24728339 PMCID: PMC3984122 DOI: 10.1371/journal.pone.0094296] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/14/2014] [Indexed: 12/20/2022] Open
Abstract
It is unclear to what extent the host-responses elicited by Beijing versus non-Beijing strains of Mycobacterium tuberculosis (MTB) contribute to the predominance of modern Beijing strains in Taiwan and some other Asian countries. The purpose of this study was to compare the expression profiles of virulence-related genes in human monocyte-derived macrophages infected in vitro with Beijing (ancient and modern strains) and non-Beijing strains (EAI strains) of MTB that are epidemic in Taiwan. We found that modern Beijing strains induced lower levels of pro-inflammatory cytokines, whereas EAI strains induced higher levels. Notably, the most prevalent modern Beijing sub-lineage, possessing intact RD150 and RD142 chromosomal regions, induced very low levels of pro-inflammatory cytokines, especially interleukin-1β. Moreover, in an intracellular growth assay, the survival of the same modern Beijing strain in human monocyte-derived macrophages was significantly higher than that of an ancient Beijing strain and an EAI strain. Taken together, these results may explain why modern Beijing strains of MTB predominate in Taiwan.
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Affiliation(s)
- Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Feng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shu-Ching Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jun-Ren Sun
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- * E-mail:
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Real-time PCR assay for rapid detection of epidemiologically and clinically significant Mycobacterium tuberculosis Beijing genotype isolates. J Clin Microbiol 2014; 52:1691-3. [PMID: 24523461 DOI: 10.1128/jcm.03193-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis Beijing genotype strains are rapidly disseminating, frequently hypervirulent, and multidrug resistant. Here, we describe a method for their rapid detection by real-time PCR that targets the specific IS6110 insertion in the dnaA-dnaN genome region. The method was evaluated with a geographically and genetically diverse collection representing areas in East Asia and the former Soviet Union in which the Beijing genotype is endemic and epidemic (i.e., major foci of its global propagation) and with clinical specimens.
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12
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Alonso H, Samper S, Martín C, Otal I. Mapping IS6110 in high-copy number Mycobacterium tuberculosis strains shows specific insertion points in the Beijing genotype. BMC Genomics 2013; 14:422. [PMID: 23800083 PMCID: PMC3701491 DOI: 10.1186/1471-2164-14-422] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis Beijing strains are characterized by a large number of IS6110 copies, suggesting the potential implication of this element in the virulence and capacity for rapid dissemination characteristic of this family. This work studies the insetion points of IS6110 in high-copy clinical isolates specifically focusing on the Beijing genotype. RESULTS In the present work we mapped the insertion points of IS6110 in all the Beijing strains available in the literature and in the DNA sequence databases. We generated a representative primer collection of the IS6110 locations, which was used to analyse 61 high-copy clinical isolates. A total of 440 points of insertion were identified and analysis of their flanking regions determined the exact location, the direct repeats (DRs), the orientation and the distance to neighboring genes of each copy of IS6110. We identified specific points of insertion in Beijing strains that enabled us to obtain a dendrogram that groups the Beijing genotype. CONCLUSIONS This work presents a detailed analysis of locations of IS6110 in high-copy clinical isolates, showing points of insertion present with high frequency in the Beijing family and absent in other strains.
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Affiliation(s)
- Henar Alonso
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, C/ Domingo Miral sn, 50009, Zaragoza, Spain
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13
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Chen YY, Chang JR, Huang WF, Kuo SC, Su IJ, Sun JR, Chiueh TS, Huang TS, Chen YS, Dou HY. Genetic diversity of the Mycobacterium tuberculosis Beijing family based on SNP and VNTR typing profiles in Asian countries. PLoS One 2012; 7:e39792. [PMID: 22808061 PMCID: PMC3395628 DOI: 10.1371/journal.pone.0039792] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/26/2012] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis (MTB) Beijing strain is highly virulent, drug resistant, and endemic over Asia. To explore the genetic diversity of this family in several different regions of eastern Asia, 338 Beijing strains collected in Taiwan (Republic of China) were analyzed by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and compared with published MIRU-VNTR profiles and by the Hunter-Gaston diversity index (HGDI) of Beijing strains from Japan and South Korea. The results revealed that VNTR2163b (HGDI>0.6) and five other loci (VNTR424, VNTR4052, VNTR1955, VNTR4156 and VNTR 2996; HGDI>0.3) could be used to discriminate the Beijing strains in a given geographic region. Analysis based on the number of VNTR repeats showed three VNTRs (VNTR424, 3192, and 1955) to be phylogenetically informative loci. In addition, to determine the geographic variation of sequence types in MTB populations, we also compared sequence type (ST) data of our strains with published ST profiles of Beijing strains from Japan and Thailand. ST10, ST22, and ST19 were found to be prevalent in Taiwan (82%) and Thailand (92%). Furthermore, classification of Beijing sublineages as ancient or modern in Taiwan was found to depend on the repeat number of VNTR424. Finally, phylogenetic relationships of MTB isolates in Taiwan, South Korea, and Japan were revealed by a minimum spanning tree based on MIRU-VNTR genotyping. In this topology, the MIRU-VNTR genotypes of the respective clusters were tightly correlated to other genotypic characters. These results are consistent with the hypothesis that clonal evolution of these MTB lineages has occurred.
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Affiliation(s)
- Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Feng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jun-Ren Sun
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Tzong-Shi Chiueh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Tsi-Shu Huang
- Department of Microbiology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yao-Shen Chen
- Department of Microbiology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
- * E-mail:
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Banu S, Mahmud AM, Rahman MT, Hossain A, Uddin MKM, Ahmed T, Khatun R, Akhanda W, Brosch R. Multidrug-resistant tuberculosis in admitted patients at a tertiary referral hospital of Bangladesh. PLoS One 2012; 7:e40545. [PMID: 22808189 PMCID: PMC3394739 DOI: 10.1371/journal.pone.0040545] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/08/2012] [Indexed: 11/21/2022] Open
Abstract
Background This study was set out to investigate the magnitude, patterns and molecular characterization of drug-resistant Mycobacterium tuberculosis strains at a tertiary referral hospital in Bangladesh. Methods Pulmonary tuberculosis (TB) patients admitted at National Institute of Diseases of the Chest and Hospital from February 2002 to September 2005 with or without previous history of TB and/or other complications were randomly interviewed. Among 265 participants enrolled, M. tuberculosis isolates from 189 patients were finally tested for susceptibility to rifampicin (RMP), isoniazid (INH), ethambutol (ETM) and streptomycin (STM). Genotyping of M. tuberculosis was done using deletion analysis and spoligotyping. Results Eighty-eight percent (n = 167) of the patients had history of previous anti-TB treatment while the remaining 12% were new TB cases. Of the 189 isolates, 9% were fully susceptible to the first line anti-TB drugs and 73.5% were multi-drug resistant TB. Other susceptibility results showed 79.4%, 77.2%, 76.7% and 78.8% resistance to INH, RMP, ETM and STM respectively. Multi-drug resistance was significantly higher among the 130 (78%) patients with previous history of anti-tuberculosis treatment (95% confidence interval, p = 0.001). Among the 189 analyzed isolates, 69% were classified as “modern” M. tuberculosis strains (i.e. TbD1- strains, lacking the M. tuberculosis-deletion region TbD1), whereas the remaining 31% were found to belong to the “ancestal” TbD1+ M. tuberculosis lineages. One hundred and five different spoligotype patterns were identified in which 16 clusters contained 100 strains and 89 strains had unique pattern. Strains with a spoligotype characteristic for the “Beijing” cluster were predominant (19%) and most of these strains (75%) were multi-drug resistant (MDR). Conclusions A high level of drug resistance observed among the re-treatment patients poses a threat of transmission of resistant strains to susceptible persons in the community. Proper counseling of patients and attention towards the completion of the anti-TB treatment is needed.
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Affiliation(s)
- Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.
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15
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Wu K, Dong D, Fang H, Levillain F, Jin W, Mei J, Gicquel B, Du Y, Wang K, Gao Q, Neyrolles O, Zhang J. An interferon-related signature in the transcriptional core response of human macrophages to Mycobacterium tuberculosis infection. PLoS One 2012; 7:e38367. [PMID: 22675550 PMCID: PMC3366933 DOI: 10.1371/journal.pone.0038367] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 05/03/2012] [Indexed: 11/23/2022] Open
Abstract
The W-Beijing family of Mycobacterium tuberculosis (Mtb) strains is known for its high-prevalence and -virulence, as well as for its genetic diversity, as recently reported by our laboratories and others. However, little is known about how the immune system responds to these strains. To explore this issue, here we used reverse engineering and genome-wide expression profiling of human macrophage-like THP-1 cells infected by different Mtb strains of the W-Beijing family, as well as by the reference laboratory strain H37Rv. Detailed data mining revealed that host cell transcriptome responses to H37Rv and to different strains of the W-Beijing family are similar and overwhelmingly induced during Mtb infections, collectively typifying a robust gene expression signature (“THP1r2Mtb-induced signature”). Analysis of the putative transcription factor binding sites in promoter regions of genes in this signature identified several key regulators, namely STATs, IRF-1, IRF-7, and Oct-1, commonly involved in interferon-related immune responses. The THP1r2Mtb-induced signature appeared to be highly relevant to the interferon-inducible signature recently reported in active pulmonary tuberculosis patients, as revealed by cross-signature and cross-module comparisons. Further analysis of the publicly available transcriptome data from human patients showed that the signature appears to be relevant to active pulmonary tuberculosis patients and their clinical therapy, and be tuberculosis specific. Thus, our results provide an additional layer of information at the transcriptome level on mechanisms involved in host macrophage response to Mtb, which may also implicate the robustness of the cellular defense system that can effectively fight against genetic heterogeneity in this pathogen.
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Affiliation(s)
- Kang Wu
- State Key Laboratory of Medical Genomics and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dandan Dong
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hai Fang
- State Key Laboratory of Medical Genomics and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Florence Levillain
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Wen Jin
- State Key Laboratory of Medical Genomics and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Mei
- Department of Tuberculosis Control, Shanghai Municipal CDC, Shanghai, China
| | - Brigitte Gicquel
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris, France
| | - Yanzhi Du
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- State Key Laboratory of Medical Genomics and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Olivier Neyrolles
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- * E-mail: (ON); (JZ)
| | - Ji Zhang
- State Key Laboratory of Medical Genomics and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (ON); (JZ)
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Garzelli C, Rindi L. Molecular epidemiological approaches to study the epidemiology of tuberculosis in low-incidence settings receiving immigrants. INFECTION GENETICS AND EVOLUTION 2012; 12:610-8. [DOI: 10.1016/j.meegid.2011.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
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Varma-Basil M, Kumar S, Arora J, Angrup A, Zozio T, Banavaliker JN, Singh UB, Rastogi N, Bose M. Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India. Mem Inst Oswaldo Cruz 2012; 106:524-35. [PMID: 21894371 DOI: 10.1590/s0074-02762011000500002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 06/06/2011] [Indexed: 11/22/2022] Open
Abstract
The aim of the present study was to compare polymerase chain reaction (PCR)-based methods--spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing--with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study.
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Affiliation(s)
- Mandira Varma-Basil
- Deptartment of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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18
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Mathema B, Kurepina N, Yang G, Shashkina E, Manca C, Mehaffy C, Bielefeldt-Ohmann H, Ahuja S, Fallows DA, Izzo A, Bifani P, Dobos K, Kaplan G, Kreiswirth BN. Epidemiologic consequences of microvariation in Mycobacterium tuberculosis. J Infect Dis 2012; 205:964-74. [PMID: 22315279 DOI: 10.1093/infdis/jir876] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Evidence from genotype-phenotype studies suggests that genetic diversity in pathogens have clinically relevant manifestations that can impact outcome of infection and epidemiologic success. We studied 5 closely related Mycobacterium tuberculosis strains that collectively caused extensive disease (n = 862), particularly among US-born tuberculosis patients. METHODS Representative isolates were selected using population-based genotyping data from New York City and New Jersey. Growth and cytokine/chemokine response were measured in infected human monocytes. Survival was determined in aerosol-infected guinea pigs. RESULTS Multiple genotyping methods and phylogenetically informative synonymous single nucleotide polymorphisms showed that all strains were related by descent. In axenic culture, all strains grew similarly. However, infection of monocytes revealed 2 growth phenotypes, slower (doubling ∼55 hours) and faster (∼25 hours). The faster growing strains elicited more tumor necrosis factor α and interleukin 1β than the slower growing strains, even after heat killing, and caused accelerated death of infected guinea pigs (∼9 weeks vs 24 weeks) associated with increased lung inflammation/pathology. Epidemiologically, the faster growing strains were associated with human immunodeficiency virus and more limited in spread, possibly related to their inherent ability to induce a strong protective innate immune response in immune competent hosts. CONCLUSIONS Natural variation, with detectable phenotypic changes, among closely related clinical isolates of M. tuberculosis may alter epidemiologic patterns in human populations.
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19
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Investigation on Mycobacterium tuberculosis diversity in China and the origin of the Beijing clade. PLoS One 2011; 6:e29190. [PMID: 22220207 PMCID: PMC3248407 DOI: 10.1371/journal.pone.0029190] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 11/22/2011] [Indexed: 12/02/2022] Open
Abstract
Background Investigation of the genetic diversity of Mycobacterium tuberculosis in China has shown that Beijing genotype strains play a dominant role in the tuberculosis (TB) epidemic. In order to examine the strain diversity in the whole country, and to study the evolutionary development of Beijing strains, we sought to genotype a large collection of isolates using different methods. Methodology/Principal Findings We applied a 15-loci VNTR typing analysis on 1,586 isolates from the Beijing municipality and 12 Chinese provinces or autonomous regions. The data was compared to that of 900 isolates from various other worldwide geographic regions outside of China. A total of 1,162/1,586 (73.2%) of the isolates, distributed into 472 VNTR types, were found to belong to the Beijing genotype family and this represented 56 to 94% of the isolates in each of the localizations. VNTR typing revealed that the majority of the non-Beijing isolates fall into two genotype families, which represented 17% of the total number of isolates, and seem largely restricted to China. A small number of East African Indian genotype strains was also observed in this collection. Ancient Beijing strains with an intact region of difference (RD) 181, as well as strains presumably resembling ancestors of the whole Beijing genotype family, were mainly found in the Guangxi autonomous region. Conclusions/Significance This is the largest M. tuberculosis VNTR-based genotyping study performed in China to date. The high percentage of Beijing isolates in the whole country and the presence in the South of strains representing early branching points may be an indication that the Beijing lineage originated from China, probably in the Guangxi region. Two modern lineages are shown here to represent the majority of non-Beijing Chinese isolates. The observed geographic distribution of the different lineages within China suggests that natural frontiers are major factors in their diffusion.
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20
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Hanekom M, Gey van Pittius N, McEvoy C, Victor T, Van Helden P, Warren R. Mycobacterium tuberculosis Beijing genotype: A template for success. Tuberculosis (Edinb) 2011; 91:510-23. [DOI: 10.1016/j.tube.2011.07.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 06/27/2011] [Accepted: 07/17/2011] [Indexed: 12/30/2022]
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21
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Characterization of microevolution events in Mycobacterium tuberculosis strains involved in recent transmission clusters. J Clin Microbiol 2011; 49:3771-6. [PMID: 21940467 DOI: 10.1128/jcm.01285-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Under certain circumstances, it is possible to identify clonal variants of Mycobacterium tuberculosis infecting a single patient, probably as a result of subtle genetic rearrangements in part of the bacillary population. We systematically searched for these microevolution events in a different context, namely, recent transmission chains. We studied the clustered cases identified using a population-based universal molecular epidemiology strategy over a 5-year period. Clonal variants of the reference strain defining the cluster were found in 9 (12%) of the 74 clusters identified after the genotyping of 612 M. tuberculosis isolates by IS6110 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive units-variable-number tandem repeat typing. Clusters with microevolution events were epidemiologically supported and involved 4 to 9 cases diagnosed over a 1- to 5-year period. The IS6110 insertion sites from 16 representative isolates of reference and microevolved variants were mapped by ligation-mediated PCR in order to characterize the genetic background involved in microevolution. Both intragenic and intergenic IS6110 locations resulted from these microevolution events. Among those cases of IS6110 locations in intergenic regions which could have an effect on the regulation of adjacent genes, we identified the overexpression of cytochrome P450 in one microevolved variant using quantitative real-time reverse transcription-PCR. Our results help to define the frequency with which microevolution can be expected in M. tuberculosis transmission chains. They provide a snapshot of the genetic background of these subtle rearrangements and identify an event in which IS6110-mediated microevolution in an isogenic background has functional consequences.
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22
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Millet J, Miyagi-Shiohira C, Yamane N, Mokrousov I, Rastogi N. High-resolution MIRU-VNTRs typing reveals the unique nature of Mycobacterium tuberculosis Beijing genotype in Okinawa, Japan. INFECTION GENETICS AND EVOLUTION 2011; 12:637-41. [PMID: 21723420 DOI: 10.1016/j.meegid.2011.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
Mycobacterium tuberculosis Beijing lineage is highly prevalent in Japan. The aim of the present study was to describe the population structure of the Beijing lineage in this country based on 12-, 15-, and 21-loci MIRU-VNTR genotyping schemes. The MIRU-VNTR patterns of Beijing strains from Okinawa, Ryukyu Islands were compared to those recently published from the Osaka-Kobe megalopolis of the main island of Japan, Honshu (Wada et al., 2009). We also compared proportions of "modern/typical" vs. "ancient/atypical" Beijing strains as defined by structure of the NTF locus. Contrarily to the 12-loci Minimum Spanning Tree (MST), the 15- and 21-loci trees allowed the distinction of two groups of strains in Okinawa. A 12-loci MIRU-VNTR pattern (223325173533) corresponding to MIRU international type MIT17 was identified as the most prevalent Beijing genotype in Japan. In the SITVIT2 database, this pattern was found to be disseminated worldwide and corresponded to the most widely distributed Beijing profile in East Asia and former USSR countries. A comparison of 15- and 21-loci MIRU-VNTR patterns showed that two loci (QUB-4156 and Mtub21) were most polymorphic in our study, and could be potential candidates to distinguish between NTF locus based subclassification of Beijing strains. High-resolution VNTR typing using 15- and 21-loci underlined an evolutionarily distinct "ancient/atypical" subpopulation of the Beijing genotype in Okinawa as well as a subgroup of strains closely related to "modern/typical" Beijing strains observed in Osaka/Kobe.
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Affiliation(s)
- Julie Millet
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes Cedex, Guadeloupe
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Faksri K, Drobniewski F, Nikolayevskyy V, Brown T, Prammananan T, Palittapongarnpim P, Prayoonwiwat N, Chaiprasert A. Genetic diversity of the Mycobacterium tuberculosis Beijing family based on IS6110, SNP, LSP and VNTR profiles from Thailand. INFECTION GENETICS AND EVOLUTION 2011; 11:1142-9. [PMID: 21515409 DOI: 10.1016/j.meegid.2011.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 04/04/2011] [Accepted: 04/08/2011] [Indexed: 01/23/2023]
Abstract
The Beijing family of Mycobacterium tuberculosis (MTB) has been shown to be highly virulent and is associated with tuberculosis outbreaks and drug resistance. To explore the evolutionary pathway of this genotype, 165 epidemiologically unlinked Beijing MTB isolates from Thailand were characterized based on IS6110, variable number of tandem repeats (VNTRs), region of differences (RDs) and single nucleotide polymorphisms (SNPs). Analysis based on VNTRs showed that 7 VNTRs were phylogenetically informative loci. Three of the seven VNTRs, 4156, 1982 and 1955, were promising markers for defining ancestral and modern Beijing sublineages. The evolutionary history of Beijing sublineages based on VNTR profiles showed dynamic changes in the repeat number, which also correlated with specific SNP STs. We constructed a refined, comprehensive phylogenetic tree based on multiple genetic markers from the Beijing strains from Thailand and combined the data with previous studies that were performed in South Africa and Japan. The phylogenetic tree showed how the modern Beijing and W-Beijing strains evolved from ancestral Beijing strains. The points at which the RD150 deletion occurred repeatedly were also demonstrated. The evolutionary scheme showed that most events were concordant with the SNP STs. Nevertheless, some SNPs used for sub-typing the Beijing family of MTB may not be irreversible, unique events.
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Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Prannok Road, Siriraj Hospital Siriraj Bangkoknoi, Bangkok 10700, Thailand
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Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype. INFECTION GENETICS AND EVOLUTION 2011; 11:587-97. [PMID: 21277396 DOI: 10.1016/j.meegid.2011.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 12/10/2010] [Accepted: 01/13/2011] [Indexed: 11/20/2022]
Abstract
The Beijing genotype family is an epidemiologically important sub-group of Mycobacterium tuberculosis. It has been suggested that the high frequency of the Beijing isolates in some areas could be explained by selective advantages. Some evidence suggests that the emerging and most frequently isolated "Typical Beijing" lineage has the ability to circumvent BCG-induced immunity. To investigate the phylogeny of the Beijing genotype of M. tuberculosis, the genome of six Beijing strains from three different countries was sequenced with next-generation sequencing. The phylogeny of these strains was established using single nucleotide polymorphisms (SNPs). The three Typical Beijing strains clustered very tightly in the Beijing phylogeny suggesting that Typical Beijing strains represent a monophyletic lineage and resulted from recent diversification. Typing of 150 M. tuberculosis strains with a subset of the SNPs and comparison of the IS6110 restriction-fragment length polymorphism (RFLP) patterns of these strains to a database of 1522 Beijing RFLP patterns revealed that about 80% of all Beijing strains belong to the Typical Beijing subclone, which indicates clonal expansion. To identify the genomic changes that are characteristic for all Typical Beijing strains and to reconstruct their most recent common ancestor, the presence of SNPs was assayed in other Beijing strains. We identified 51 SNPs that define the minimal set of polymorphisms for all Typical Beijing strains. Nonsynonymous polymorphisms in genes coding for the regulatory network were over-represented in this set of mutations. We suggest that alterations in the response to environmental signals may have enabled Typical Beijing strains to develop the emerging phenotype.
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25
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Chang JR, Lin CH, Tsai SF, Su IJ, Tseng FC, Chen YT, Chiueh TS, Sun JR, Huang TS, Chen YS, Dou HY. Genotypic analysis of genes associated with transmission and drug resistance in the Beijing lineage of Mycobacterium tuberculosis. Clin Microbiol Infect 2010; 17:1391-6. [PMID: 21091972 DOI: 10.1111/j.1469-0691.2010.03436.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Beijing genotype of Mycobacterium tuberculosis is an endemic lineage in East Asia that has disseminated worldwide. It is a major health concern, as it is geographically widespread and is considered to be hypervirulent. To elucidate its genetic diversity in Taiwan, phylogenetic reconstruction was performed using 338 M. tuberculosis Beijing family clinical isolates. Region-of-difference analysis revealed the strains from Taiwan to be distributed among six subgroups of a phylogenetic tree. Synonymous single nucleotide polymorphisms at 10 chromosomal positions were also analysed. Among the 338 isolates analysed for single-nucleotide polymorphisms by using mass spectrometry, the most frequent strain found was ST10 (53.3%), followed by ST19 (14.8%) and ST22 (14.5%). Tests of drug resistance showed that the sublineages ST10, ST19 and ST26 were over-represented in the multidrug-resistant population. The presence of mutations in putative genes coding for DNA repair enzymes, which could confer a mutator phenotype to facilitate spreading of the pathogen, did not demonstrate an association with multidrug resistance. Therefore, the DNA repair genes may be involved in transmission but not in drug resistance.
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Affiliation(s)
- J-R Chang
- Division of Infectious Diseases, National Health Research Institutes, Zhunan, Miaoli, Taiwan
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26
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Choi GE, Jang MH, Song EJ, Jeong SH, Kim JS, Lee WG, Uh Y, Roh KH, Lee HS, Shin JH, Ryoo NH, Kim YR, Jeong J, Kim JH, Lee SM, Yi J, Hwang SH, Kim HH, Lee EY, Chang CL, Kim MB, Kim YD. IS6110-restriction fragment length polymorphism and spoligotyping analysis of Mycobacterium tuberculosis clinical isolates for investigating epidemiologic distribution in Korea. J Korean Med Sci 2010; 25:1716-21. [PMID: 21165284 PMCID: PMC2995223 DOI: 10.3346/jkms.2010.25.12.1716] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/22/2010] [Indexed: 12/05/2022] Open
Abstract
The Beijing family of Mycobacterium tuberculosis has been emerging in the world. However, there are few nationwide data of genotypic distribution in Korea. This study aimed to identify the genotypic diversity of clinical isolates of M. tuberculosis and to demonstrate the population of Beijing family in Korea. We collected 96 clinical M. tuberculosis isolates from 11 university hospitals nationwide in Korea from 2008 to 2009. We observed 24 clusters in IS6110-RFLP analysis and 19 patterns in spoligotyping. Seventy-five isolates were confirmed to be Beijing family. Two isolates of the K strain and 12 isolates of the K family strain were also found. We found that drug resistance phenotypes were more strongly associated with Beijing family than non-Beijing family (P=0.003). This study gives an overview of the distribution of genotypes of M. tuberculosis in Korea. These findings indicate that we have to pay more attention to control of M. tuberculosis strains associated with the Beijing family.
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Affiliation(s)
- Go Eun Choi
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Mi Hee Jang
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Eun Ju Song
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
| | - Wee Gyo Lee
- Department of Laboratory Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hye Soo Lee
- Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Korea
| | - Nam Hee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Young Ree Kim
- Department of Laboratory Medicine, Cheju National University College of Medicine, Jeju, Korea
| | - Joseph Jeong
- Department of Laboratory Medicine, Ulsan University Hospital & Ulsan University College of Medicine, Ulsan, Korea
| | - Jee Hee Kim
- Department of Emergency Medical Technology, Kangwon National University, Samcheok, Korea
| | - Sun Min Lee
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Jongyoun Yi
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Sang Hyun Hwang
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Hyung Hoi Kim
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Eun Yup Lee
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Chulhun L. Chang
- Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea
| | - Moon-Bum Kim
- Department of Dermatology, School of Medicine, Pusan National University, Busan, Korea
| | - Yeong Dae Kim
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Pusan National University, Busan, Korea
- Medical Research Institute, Pusan National University, Busan, Korea
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27
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Abstract
In a 2-year prospective study of tuberculosis (TB) patients in China, the prevalences of non-Beijing strains of Mycobacterium tuberculosis varied between Shandong Province (20.6%), Shanghai (27.6%), and Sichuan Province (45.9%) (P < 0.005). These differences may be due to factors such as human migration, transmission, or diversification and adaptation of the mycobacteria to different hosts.
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Molecular epidemiology of Mycobacterium tuberculosis clinical isolates in Southwest Ireland. INFECTION GENETICS AND EVOLUTION 2010; 10:1110-6. [PMID: 20637901 DOI: 10.1016/j.meegid.2010.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 06/26/2010] [Accepted: 07/06/2010] [Indexed: 11/20/2022]
Abstract
Tuberculosis has had significant effects on Ireland over the past two centuries, causing persistently higher morbidity and mortality than in neighbouring countries until the last decade. This study describes the results of genotyping and drug susceptibility testing of 171 strains of Mycobacterium tuberculosis complex isolated between January 2004 and December 2006 in a region of Ireland centred on the city of Cork. Spoligotype comparisons were made with the SpolDB4 database and clustered 130 strains in 23 groups, forty-one strains showed unique Spoligotyping patterns. The commonest spoligotypes detected were ST0137 (X2) (16.9%), and ST0351 (15.8%) ('U' clade). The major spoligotype clades were X (26.2%), U (19.3%), T (15.2%), Beijing (5.9%), Haarlem (4.7%), LAM (4.1%), BOVIS (1.75%), with 12.9% unassigned strains. A 24-locus VNTR genotyping produced 15 clusters containing 49 isolates, with high discrimination index (HGDI>0.99). A combination of Spoligotyping and VNTR reduced the number of clustered isolates to 47 in 15 clusters (27.5%). This study identified ST351 as common among Irish nationals, and found a low rate of drug resistance with little evidence of transmission of drug resistant strains. Strain clustering was significantly associated with age under 55 years and Irish nationality. Only strains of Euro-American lineage formed clusters. Molecular typing did not completely coincide with the results of contact investigations.
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29
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Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories. J Bacteriol 2010; 192:3645-53. [PMID: 20472797 DOI: 10.1128/jb.00166-10] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The publication of the complete genome sequence for Mycobacterium tuberculosis H37Rv in 1998 has had a great impact on the research community. Nonetheless, it is suspected that genetic differences have arisen in stocks of H37Rv that are maintained in different laboratories. In order to assess the consistency of the genome sequences among H37Rv strains in use and the extent to which they have diverged from the original strain sequenced, we carried out whole-genome sequencing on six strains of H37Rv from different laboratories. Polymorphisms at 73 sites were observed, which were shared among the lab strains, though 72 of these were also shared with H37Ra and are likely to be due to sequencing errors in the original H37Rv reference sequence. An updated H37Rv genome sequence should be valuable to the tuberculosis research community as well as the broader microbial research community. In addition, several polymorphisms unique to individual strains and several shared polymorphisms were identified and shown to be consistent with the known provenance of these strains. Aside from nucleotide substitutions and insertion/deletions, multiple IS6110 transposition events were observed, supporting the theory that they play a significant role in plasticity of the M. tuberculosis genome. This genome-wide catalog of genetic differences can help explain any phenotypic differences that might be found, including a frameshift mutation in the mycocerosic acid synthase gene which causes two of the strains to be deficient in biosynthesis of the surface glycolipid phthiocerol dimycocerosate (PDIM). The resequencing of these six lab strains represents a fortuitous "in vitro evolution" experiment that demonstrates how the M. tuberculosis genome continues to evolve even in a controlled environment.
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30
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Parwati I, van Crevel R, van Soolingen D. Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains. THE LANCET. INFECTIOUS DISEASES 2010; 10:103-11. [PMID: 20113979 DOI: 10.1016/s1473-3099(09)70330-5] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The wide geographic distribution of one clade of Mycobacterium tuberculosis, the Beijing genotype family, and its genetic homogeneity, suggests that strains belonging to this grouping might have a selective advantage over other M tuberculosis strains. This hypothesis was addressed by reviewing molecular-epidemiological, experimental, and clinical studies. Beijing strains represent about 50% of strains in east Asia and at least 13% of strains worldwide. Their emergence might be linked to escape from BCG vaccination, and to multidrug resistance, which is associated with the Beijing genotype in many areas. Different animal models have shown Beijing strains to be more virulent, and to cause more histopathological changes, higher outgrowth, and increased mortality. At a molecular level, Beijing strains have specific properties in terms of protein and lipid structures and their interaction with the human immune system. Finally, the Beijing genotype has been linked to polymorphisms in immune genes, suggesting the possibility of human-mycobacterial co-evolution. The emergence of the Beijing genotype family might represent an evolutionary response of M tuberculosis to vaccination or antibiotic treatment, with an important negative impact on tuberculosis control. More research is needed to further unravel the mechanisms underlying the emergence of M tuberculosis Beijing genotype strains, and examine the implications for future control strategies.
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Affiliation(s)
- Ida Parwati
- Department of Clinical Pathology, Medical Faculty, Padjadjaran University, Dr Hasan Sadikin Hospital, Bandung, Indonesia.
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31
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McEvoy CRE, van Helden PD, Warren RM, van Pittius NCG. Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region. BMC Evol Biol 2009; 9:237. [PMID: 19769792 PMCID: PMC2758852 DOI: 10.1186/1471-2148-9-237] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 09/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PPE38 (Rv2352c) is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC) member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM). Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions. RESULTS We show that the ancestral MTBC PPE38 region comprises 2 homologous PPE genes (PPE38 and PPE71), separated by 2 esat-6 (esx)-like genes and that this structure derives from an esx/esx/PPE duplication in the common ancestor of M. tuberculosis and M. marinum. We also demonstrate that this region of the genome is hypervariable due to frequent IS6110 integration, IS6110-associated recombination, and homologous recombination and gene conversion events between PPE38 and PPE71. These mutations result in combinations of gene deletion, gene truncation and gene disruption in the majority of clinical isolates. These mutations were generally found to be IS6110 strain lineage-specific, although examples of additional within-lineage and even within-cluster mutations were observed. Furthermore, we provide evidence that the published M. tuberculosis H37Rv whole genome sequence is inaccurate regarding this region. CONCLUSION Our results show that this antigen-encoding region of the M. tuberculosis genome is hypervariable. The observation that numerous different mutations have become fixed within specific lineages demonstrates that this genomic region is undergoing rapid molecular evolution and that further lineage-specific evolutionary expansion and diversification has occurred subsequent to the lineage-defining mutational events. We predict that functional loss of these genes could aid immune evasion. Finally, we also show that the PPE38 region of the published M. tuberculosis H37Rv whole genome sequence is not representative of the ATCC H37Rv reference strain.
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Affiliation(s)
- Christopher RE McEvoy
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Nicolaas C Gey van Pittius
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
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32
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Population structure dynamics of Mycobacterium tuberculosis Beijing strains during past decades in Japan. J Clin Microbiol 2009; 47:3340-3. [PMID: 19710282 DOI: 10.1128/jcm.01061-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used 909 strains to compare the population structures of the Mycobacterium tuberculosis Beijing family between different birth-year cohorts in Japan. The results revealed that the spread of a modern sublineage that has high transmissibility is currently increasing, while the spread of an ancient sublineage, STK, has significantly decreased in younger generations.
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33
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Kremer K, van-der-Werf MJ, Au BKY, Anh DD, Kam KM, van-Doorn HR, Borgdorff MW, van-Soolingen D. Vaccine-induced immunity circumvented by typical Mycobacterium tuberculosis Beijing strains. Emerg Infect Dis 2009; 15:335-9. [PMID: 19193289 PMCID: PMC2657620 DOI: 10.3201/eid1502.080795] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The frequency of typical and atypical Beijing strains of Mycobacterium tuberculosis was determined in the Netherlands; Vietnam; and Hong Kong Special Administrative Region, People's Republic of China. The strains' associations with drug resistance, M. bovis BCG vaccination, and patient characteristics were assessed. BCG vaccination may have positively selected the prevalent typical Beijing strains.
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Affiliation(s)
- Kristin Kremer
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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34
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Turcios L, Casart Y, Florez I, de Waard J, Salazar L. Characterization of IS6110 insertions in the dnaA–dnaN intergenic region of Mycobacterium tuberculosis clinical isolates. Clin Microbiol Infect 2009; 15:200-3. [DOI: 10.1111/j.1469-0691.2008.02107.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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35
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Population structure analysis of the Mycobacterium tuberculosis Beijing family indicates an association between certain sublineages and multidrug resistance. Antimicrob Agents Chemother 2008; 52:3805-9. [PMID: 18694954 DOI: 10.1128/aac.00579-08] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our population-based study of the Mycobacterium tuberculosis Beijing family examined the frequency of occurrence of each sublineage of this family, classified by using 10 synonymous single-nucleotide polymorphisms. The results revealed the overabundance of two evolutionary sublineages in a population of multidrug-resistant and extensively drug-resistant tuberculosis bacteria.
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36
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Casart Y, Turcios L, Florez I, Jaspe R, Guerrero E, de Waard J, Aguilar D, Hérnandez-Pando R, Salazar L. IS6110 in oriC affects the morphology and growth of Mycobacterium tuberculosis and attenuates virulence in mice. Tuberculosis (Edinb) 2008; 88:545-52. [PMID: 18534910 DOI: 10.1016/j.tube.2008.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 03/27/2008] [Accepted: 03/27/2008] [Indexed: 10/22/2022]
Abstract
The IS6110 element is widely used in studies of molecular epidemiology of tuberculosis and it is considered the gold standard for genotyping Mycobacterium tuberculosis strains. Because of its high frequency of transposition, IS6110 is probably a major contributor to the evolution of M. tuberculosis. Nevertheless, very few studies of the effect of IS6110 insertions on the virulence of M. tuberculosis have been reported. We analysed two isogenic groups of M. tuberculosis strains isolated from the sputa of two patients. Strains belonging to the same isogenic group differed from one another by one IS6110-oriC hybridising band, but they showed identical spoligo and MIRU-VNTR profiles. Isogenic strains containing the IS6110 element in oriC exhibited a diminished growth rate and average dimensions of the bacilli were modified; moreover, they were less virulent in a mouse model.
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Affiliation(s)
- Yveth Casart
- Departamento de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Km 11 Carretera Panamericana, Estado Miranda, Venezuela
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37
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Thorne N, Evans JT, Smith EG, Hawkey PM, Gharbia S, Arnold C. An IS6110-targeting fluorescent amplified fragment length polymorphism alternative to IS6110 restriction fragment length polymorphism analysis for Mycobacterium tuberculosis DNA fingerprinting. Clin Microbiol Infect 2007; 13:964-70. [PMID: 17803750 DOI: 10.1111/j.1469-0691.2007.01783.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A rapid, simple and highly discriminatory DNA fingerprinting methodology which produces data that can be easily interpreted, compared and transported is the ultimate goal for studying the epidemiology of Mycobacterium tuberculosis. A novel TaqI fluorescent amplified fragment length polymorphism (fAFLP) approach to M. tuberculosis DNA fingerprinting that targeted the variable IS6110 marker was developed in this study. The new method was tested for specificity and reproducibility, and compared with the standard reference IS6110 restriction fragment length polymorphism (RFLP) method for a panel of 78 isolates. Clustering conflicts between the two methods were resolved using mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) data. Comparison with an in-silico digestion of strain H37Rv showed that fAFLP-detected fragments were highly specific in vitro. The reproducibility of repeated digestions of strain H37Rv was 100%. Clustering results obtained by fAFLP and RFLP were highly congruent, with fAFLP allocating 97% of RFLP-clustered isolates to the same eight clusters as RFLP. Two single-copy isolates that had been clustered by RFLP were not clustered by fAFLP, but the MIRU-VNTR patterns of these isolates were different, indicating that the RFLP data had falsely clustered these isolates. Analysis by fAFLP will allow rapid screening of isolates to confirm or refute epidemiological links, and thereby provide insights into the frequency, conservation and consequences of specific transposition events.
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Affiliation(s)
- N Thorne
- Applied and Functional Genomics, Centre for Infections, Health Protection Agency, London, UK
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38
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Lazzarini LCO, Huard RC, Boechat NL, Gomes HM, Oelemann MC, Kurepina N, Shashkina E, Mello FCQ, Gibson AL, Virginio MJ, Marsico AG, Butler WR, Kreiswirth BN, Suffys PN, Lapa E Silva JR, Ho JL. Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol 2007; 45:3891-902. [PMID: 17898156 PMCID: PMC2168543 DOI: 10.1128/jcm.01394-07] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current study evaluated Mycobacterium tuberculosis isolates from Rio de Janeiro, Brazil, for genomic deletions. One locus in our panel of PCR targets failed to amplify in approximately 30% of strains. A single novel long sequence polymorphism (>26.3 kb) was characterized and designated RD(Rio). Homologous recombination between two similar protein-coding genes is proposed as the mechanism for deleting or modifying 10 genes, including two potentially immunogenic PPE proteins. The flanking regions of the RD(Rio) locus were identical in all strains bearing the deletion. Genetic testing by principal genetic group, spoligotyping, variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR), and IS6110-based restriction fragment length polymorphism analysis cumulatively support the idea that RD(Rio) strains are derived from a common ancestor belonging solely to the Latin American-Mediterranean spoligotype family. The RD(Rio) lineage is therefore the predominant clade causing tuberculosis (TB) in Rio de Janeiro and, as indicated by genotypic clustering in MIRU-VNTR analysis, the most significant source of recent transmission. Limited retrospective reviews of bacteriological and patient records showed a lack of association with multidrug resistance or specific risk factors for TB. However, trends in the data did suggest that RD(Rio) strains may cause a form of TB with a distinct clinical presentation. Overall, the high prevalence of this genotype may be related to enhanced virulence, transmissibility, and/or specific adaptation to a Euro-Latin American host population. The identification of RD(Rio) strains outside of Brazil points to the ongoing intercontinental dissemination of this important genotype. Further studies are needed to determine the differential strain-specific features, pathobiology, and worldwide prevalence of RD(Rio) M. tuberculosis.
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Affiliation(s)
- Luiz Claudio Oliveira Lazzarini
- Department of Medicine, Division of International Medicine and Infectious Diseases, Cornell University, Joan and Sanford I Weill Medical College, New York, NY 10021, USA
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39
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McEvoy CRE, Falmer AA, Gey van Pittius NC, Victor TC, van Helden PD, Warren RM. The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2007; 87:393-404. [PMID: 17627889 DOI: 10.1016/j.tube.2007.05.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 05/15/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
Members of the Mycobacterium tuberculosis complex contain the transposable element IS6110 which, due to its high numerical and positional polymorphism, has become a widely used marker in epidemiological studies. Here, we review the evidence that IS6110 is not simply a passive or 'junk' DNA sequence, but that, through its transposable activity, it is able to generate genotypic variation that translates into strain-specific phenotypic variation. We also speculate on the role that this variation has played in the evolution of M. tuberculosis and conclude that the presence of a moderate IS6110 copy number within the genome may provide the pathogen with a selective advantage that has aided its virulence.
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Affiliation(s)
- Christopher R E McEvoy
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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40
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Asgharzade M, Shahbabian K, Samadi Kaf H, Rafi A. Use of DNA Fingerprinting in Identifying the Source Case of Tuberculosis in East Azarbaijan Province of Iran. JOURNAL OF MEDICAL SCIENCES 2007. [DOI: 10.3923/jms.2007.418.421] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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Asgharzade M, Yousefee S, Kafil HS, Nahaei MR, Ansarin K, Akhi MT. Comparing Transmission of Mycobacterium tuberculosis in East Azarbaijan and West Azarbaijan Provinces of Iran by Using IS6110-RFLP Method. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/biotech.2007.273.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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42
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Mokrousov I, Jiao WW, Sun GZ, Liu JW, Valcheva V, Li M, Narvskaya O, Shen AD. Evolution of drug resistance in different sublineages of Mycobacterium tuberculosis Beijing genotype. Antimicrob Agents Chemother 2006; 50:2820-3. [PMID: 16870777 PMCID: PMC1538659 DOI: 10.1128/aac.00324-06] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared the population structure and drug resistance patterns of the Mycobacterium tuberculosis strains currently circulating in the Beijing area of China. One hundred thirteen of 123 strains belonged to the Beijing family genotypes defined by spoligotyping. The Beijing genotype strains were further subdivided into old and modern sublineages on the basis of NTF locus analysis. A stronger association with resistance to the more recently introduced antituberculosis drugs has been observed for old versus modern strains of the Beijing genotype, suggesting that its different sublineages may differ in their mechanisms of adaptation to drug selective pressure.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira Street, 197101 St. Petersburg, Russia.
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43
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Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev 2006; 19:658-85. [PMID: 17041139 PMCID: PMC1592690 DOI: 10.1128/cmr.00061-05] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.
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Affiliation(s)
- Barun Mathema
- Tuberculosis Center, Public Health Research Institute, Newark, NJ 07103, USA.
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44
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Abstract
The genotype, endemic in some areas and emerging in others, may be associated with drug-resistance. Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype’s prevalence worldwide, trends over time and with age, and associations with drug resistance. We found 4 patterns for Beijing/W genotype tuberculosis (TB): 1) endemic, not associated with drug resistance (high level in most of East Asia, lower level in parts of the United States); 2) epidemic, associated with drug resistance (high level in Cuba, the former Soviet Union, Vietnam, and South Africa, lower level in parts of Western Europe); 3) epidemic but drug sensitive (Malawi, Argentina); and 4) very low level or absent (parts of Europe, Africa). This study confirms that Beijing/W genotype TB is an emerging pathogen in several areas and a predominant endemic strain in others; it is frequently associated with drug resistance.
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45
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Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ. Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 2006; 19:512-30. [PMID: 16847083 PMCID: PMC1539107 DOI: 10.1128/cmr.00025-05] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nosocomial infections are an important source of morbidity and mortality in hospital settings, afflicting an estimated 2 million patients in United States each year. This number represents up to 5% of hospitalized patients and results in an estimated 88,000 deaths and 4.5 billion dollars in excess health care costs. Increasingly, hospital-acquired infections with multidrug-resistant pathogens represent a major problem in patients. Understanding pathogen relatedness is essential for determining the epidemiology of nosocomial infections and aiding in the design of rational pathogen control methods. The role of pathogen typing is to determine whether epidemiologically related isolates are also genetically related. To determine molecular relatedness of isolates for epidemiologic investigation, new technologies based on DNA, or molecular analysis, are methods of choice. These DNA-based molecular methodologies include pulsed-field gel electrophoresis (PFGE), PCR-based typing methods, and multilocus sequence analysis. Establishing clonality of pathogens can aid in the identification of the source (environmental or personnel) of organisms, distinguish infectious from noninfectious strains, and distinguish relapse from reinfection. The integration of molecular typing with conventional hospital epidemiologic surveillance has been proven to be cost-effective due to the associated reduction in the number of nosocomial infections. Cost-effectiveness is maximized through the collaboration of the laboratory, through epidemiologic typing, and the infection control department during epidemiologic investigations.
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Affiliation(s)
- Aparajita Singh
- Department of Medicine, Section of Infectious Diseases, Henry Ford Hospital, Wayne State University School of Medicine, Detroit, MI 48202, USA
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46
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Rao KR, Ahmed N, Srinivas S, Sechi LA, Hasnain SE. Rapid identification of Mycobacterium tuberculosis Beijing genotypes on the basis of the mycobacterial interspersed repetitive unit locus 26 signature. J Clin Microbiol 2006; 44:274-7. [PMID: 16390989 PMCID: PMC1351955 DOI: 10.1128/jcm.44.1.274-277.2006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis Beijing strains are prevalent in many parts of the world and often give rise to large institutional outbreaks. Such highly transmissible strains, often associated with multidrug resistance, are likely underrepresented in outbreaks reported from developing countries, mainly due to nonavailability of fast detection methods suitable in epidemiological surveillance studies. We evaluated a PCR assay based on amplification of mycobacterial interspersed repetitive unit locus 26 as a stand-alone method for unambiguous identification of Beijing strains. The method was used on blinded samples from 10 standard strains whose Beijing status was already confirmed by spoligotyping. All 10 strains were accurately identified, and their profiles were corroborated successfully with spoligotypes. The method was also applied to 70 different non-Beijing clinical isolates from different countries to allow discrimination of isolates. Owing to its accuracy, simplicity, and rapidity, the assay can be employed in laboratory-level testing of isolates linked to certain outbreaks. The test can also be adopted for direct application on clinical samples to save time on culturing bacilli for genotyping.
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Affiliation(s)
- K Rajender Rao
- Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, India
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Surikova OV, Voitech DS, Kuzmicheva G, Tatkov SI, Mokrousov IV, Narvskaya OV, Rot MA, van Soolingen D, Filipenko ML. Efficient differentiation of Mycobacterium tuberculosis strains of the W-Beijing family from Russia using highly polymorphic VNTR loci. Eur J Epidemiol 2006; 20:963-74. [PMID: 16284875 DOI: 10.1007/s10654-005-3636-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2005] [Indexed: 10/25/2022]
Abstract
The W-Beijing family is a widespread Mycobacterium tuberculosis clonal lineage that frequently causes epidemic outbreaks. This family is genetically homogeneous and conserved, so ETR-VNTR (exact tandem repeat-variable number of tandem repeats) typing is insufficient for strain differentiation, due to a common ETR-A to E profile (42435). This leads to the false clustering in molecular epidemiological studies, especially in the regions of predominance of the W-Beijing family. In this study, we searched for VNTR loci with a high evolutionary rate of polymorphism in the W-Beijing genome. Here we further evaluated VNTR typing on a set of 99 Mycobacterium tuberculosis clinical isolates and reference strains. These isolates were characterized and classified into several genotype families based on three ETR loci (A, C, E) and eight additional loci [previously described as QUB (Queen's University Belfast) or MIRU (Mycobacterial Interspersed Repetitive Units) or Mtubs]. Ninety-nine strains were divided into 74 VNTR-types, 51 isolates of the W-Beijing family identified by IS6110 RFLP-typing (the restriction fragment length polymorphism-typing) and/or spoligotyping were subdivided into 30 VNTR-types. HGDI (the Hunter-Gaston discriminatory index) for all studied loci was close to that of IS6110 RFLP typing, a "gold standard" method for subtyping M. tuberculosis complex strains. The QUB 26 and QUB 18 loci located in the PPE genes were highly polymorphic and more discriminative than other loci (HGDI is 0.8). Statistically significant increase of tandem repeats number in loci ETR-A, -E, QUB 26, QUB 18, QUB 11B, Mtub21 was revealed in the W-Beijing group compared to genetically divergent non-W-Beijing strains. Thirty-six isolates were subjected to IS6110 RFLP typing. The congruence between results of the IS6110 RFLP typing and 11-loci VNTR typing was estimated on 23 isolates of the W-Beijing family. These isolates were subdivided into 9 IS6110-RFLP types and 13 VNTR types. The poor profiles correlation (0.767) reflects the differences in the rate and type of evolution between genome regions targeted by IS6110-RFLP and VNTR typing. VNTR typing in proposed format is powerful tool for discrimination of M. tuberculosis strains with different level of genetic relationship.
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Affiliation(s)
- O V Surikova
- Pharmacogenomics Group, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
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48
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Gibson A, Brown T, Baker L, Drobniewski F. Can 15-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis provide insight into the evolution of Mycobacterium tuberculosis? Appl Environ Microbiol 2006; 71:8207-13. [PMID: 16332804 PMCID: PMC1317395 DOI: 10.1128/aem.71.12.8207-8213.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.
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Affiliation(s)
- Andrea Gibson
- Mycobacterium Reference Unit, Health Protection Agency, Barts and The London Queen Mary's School of Medicine and Dentistry, London, United Kingdom
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Freeman R, Kato-Maeda M, Hauge KA, Horan KL, Oren E, Narita M, Wallis CK, Cave D, Nolan CM, Small PM, Cangelosi GA. Use of rapid genomic deletion typing to monitor a tuberculosis outbreak within an urban homeless population. J Clin Microbiol 2005; 43:5550-4. [PMID: 16272485 PMCID: PMC1287805 DOI: 10.1128/jcm.43.11.5550-5554.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Beginning in mid-2002, a large tuberculosis outbreak occurred among homeless persons in King County, Washington. In order to further monitor the outbreak following its peak in 2003, Mycobacterium tuberculosis isolates from all new King County tuberculosis (TB) patients in 2004 and the first half of 2005 (n = 220) were genotyped by using a rapid comparative genomics-based (genomic deletion-typing) approach, with confirmation by mycobacterial interspersed repetitive units and repetitive-sequence-based PCR (rep-PCR). Results were compared to retrospective genotypic data from 1995 to 2003. The outbreak strain SBRI9, which was not seen among King County homeless persons prior to 2002, accounted for 16 out of 30 TB cases (53%) within this population in 2002. This trend continued with 27 out of 35 cases (77%) caused by the outbreak strain in 2003, 11 out of 13 cases (85%) caused by the outbreak strain in 2004, and 4 out of 10 cases (40%) caused by the outbreak strain in the first 5 months of 2005. Thus, the outbreak strain remained well established within this homeless population throughout the study period. At least four SBRI9 cases were in people who had previously been infected by other strains. The novel PCR-based strain-typing approach used in this investigation proved to be cost-effective and very rapid. In most cases, it was possible to analyze DNA extracted directly from primary isolation (Mycobacterium growth indicator tube) cultures submitted by clinical laboratories, a feature that markedly reduced the delay between diagnosis and strain typing results. This rapid turnaround facilitated public health efforts to prevent new outbreaks involving this strain.
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Affiliation(s)
- Robert Freeman
- Seattle Biomedical Research Institute, 307 Westlake Avenue N, Suite 500, Seattle, WA 98107-5219, USA
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Mokrousov I, Ly HM, Otten T, Lan NN, Vyshnevskyi B, Hoffner S, Narvskaya O. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: clues from human phylogeography. Genome Res 2005; 15:1357-64. [PMID: 16169923 PMCID: PMC1240077 DOI: 10.1101/gr.3840605] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 07/12/2005] [Indexed: 11/25/2022]
Abstract
We suggest that the evolution of the population structure of microbial pathogens is influenced by that of modern humans. Consequently, the timing of hallmark changes in bacterial genomes within the last 100,000 yr may be attempted by comparison with relevant human migrations. Here, we used a lineage within Mycobacterium tuberculosis, a Beijing genotype, as a model and compared its phylogeography with human demography and Y chromosome-based phylogeography. We hypothesize that two key events shaped the early history of the Beijing genotype: (1) its Upper Palaeolithic origin in the Homo sapiens sapiens K-M9 cluster in Central Asia, and (2) primary Neolithic dispersal of the secondary Beijing NTF::IS6110 lineage by Proto-Sino-Tibetan farmers within east Asia (human O-M214/M122 haplogroup). The independent introductions of the Beijing strains from east Asia to northern Eurasia and South Africa were likely historically recent, whereas their differential dissemination within these areas has been influenced by demographic and climatic factors.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia.
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