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Tuberculosis attributed to transmission within healthcare facilities, Botswana—The Kopanyo Study. Infect Control Hosp Epidemiol 2022; 43:1603-1609. [DOI: 10.1017/ice.2021.517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Objective:
Healthcare facilities are a well-known high-risk environment for transmission of M. tuberculosis, the etiologic agent of tuberculosis (TB) disease. However, the link between M. tuberculosis transmission in healthcare facilities and its role in the general TB epidemic is unknown. We estimated the proportion of overall TB transmission in the general population attributable to healthcare facilities.
Methods:
We combined data from a prospective, population-based molecular epidemiologic study with a universal electronic medical record (EMR) covering all healthcare facilities in Botswana to identify biologically plausible transmission events occurring at the healthcare facility. Patients with M. tuberculosis isolates of the same genotype visiting the same facility concurrently were considered an overlapping event. We then used TB diagnosis and treatment data to categorize overlapping events into biologically plausible definitions. We calculated the proportion of overall TB cases in the cohort that could be attributable to healthcare facilities.
Results:
In total, 1,881 participants had TB genotypic and EMR data suitable for analysis, resulting in 46,853 clinical encounters at 338 healthcare facilities. We identified 326 unique overlapping events involving 370 individual patients; 91 (5%) had biologic plausibility for transmission occurring at a healthcare facility. A sensitivity analysis estimated that 3%–8% of transmission may be attributable to healthcare facilities.
Conclusions:
Although effective interventions are critical in reducing individual risk for healthcare workers and patients at healthcare facilities, our findings suggest that development of targeted interventions aimed at community transmission may have a larger impact in reducing TB.
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Lekko YM, Ooi PT, Omar S, Mazlan M, Ramanoon SZ, Jasni S, Jesse FFA, Che-Amat A. Mycobacterium tuberculosis complex in wildlife: Review of current applications of antemortem and postmortem diagnosis. Vet World 2020; 13:1822-1836. [PMID: 33132593 PMCID: PMC7566238 DOI: 10.14202/vetworld.2020.1822-1836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a chronic inflammatory and zoonotic disease caused by Mycobacterium tuberculosis complex (MTBC) members, which affects various domestic animals, wildlife, and humans. Some wild animals serve as reservoir hosts in the transmission and epidemiology of the disease. Therefore, the monitoring and surveillance of both wild and domestic hosts are critical for prevention and control strategies. For TB diagnosis, the single intradermal tuberculin test or the single comparative intradermal tuberculin test, and the gamma-interferon test, which is regarded as an ancillary test, are used. Postmortem examination can identify granulomatous lesions compatible with a diagnosis of TB. In contrast, smears of the lesions can be stained for acid-fast bacilli, and samples of the affected organs can be subjected to histopathological analyses. Culture is the gold standard test for isolating mycobacterial bacilli because it has high sensitivity and specificity compared with other methods. Serology for antibody detection allows the testing of many samples simply, rapidly, and inexpensively, and the protocol can be standardized in different laboratories. Molecular biological analyses are also applicable to trace the epidemiology of the disease. In conclusion, reviewing the various techniques used in MTBC diagnosis can help establish guidelines for researchers when choosing a particular diagnostic method depending on the situation at hand, be it disease outbreaks in wildlife or for epidemiological studies. This is because a good understanding of various diagnostic techniques will aid in monitoring and managing emerging pandemic threats of infectious diseases from wildlife and also preventing the potential spread of zoonotic TB to livestock and humans. This review aimed to provide up-to-date information on different techniques used for diagnosing TB at the interfaces between wildlife, livestock, and humans.
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Affiliation(s)
- Yusuf Madaki Lekko
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Maiduguri, 1069 PMB, Maiduguri, Borno State, Nigeria
| | - Peck Toung Ooi
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sharina Omar
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mazlina Mazlan
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Zubaidah Ramanoon
- Department of Farm and Exotic Animal Medicine and Surgery, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sabri Jasni
- Department of Paraclinical, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Faez Firdaus Abdullah Jesse
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Azlan Che-Amat
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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3
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On sunspots, click science and molecular iconography. Tuberculosis (Edinb) 2018; 110:91-95. [PMID: 29779780 DOI: 10.1016/j.tube.2018.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023]
Abstract
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools. Here, I present a critical essay on hot practical aspects related to the use of SITVIT_WEB and MIRU-VNTRplus, in particular, partly inadequate (sub)clade assignment due to imperfect decision rules, partly outdated methodological options offered to the users that permit to build scientifically unsound phylogenies from spoligotyping data. A confusing terminology, misclassification and false clustering are not abstract issues but make a scientific discussion meaningless, and I propose some courses for improvement.
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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: 36] [Impact Index Per Article: 5.1] [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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5
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Ahlstrom C, Barkema HW, Stevenson K, Zadoks RN, Biek R, Kao R, Trewby H, Haupstein D, Kelton DF, Fecteau G, Labrecque O, Keefe GP, McKenna SLB, De Buck J. Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level. BMC Genomics 2015; 16:161. [PMID: 25765045 PMCID: PMC4356054 DOI: 10.1186/s12864-015-1387-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/24/2015] [Indexed: 01/14/2023] Open
Abstract
Background Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne’s disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates. Results Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including “bison type” isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1–2 to 239–240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd. Conclusions The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne’s disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.
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Affiliation(s)
| | | | | | - Ruth N Zadoks
- Moredun Research Institute, Penicuik, Scotland. .,University of Glasgow, Glasgow, Scotland.
| | - Roman Biek
- University of Glasgow, Glasgow, Scotland.
| | | | | | | | | | | | - Olivia Labrecque
- Laboratoire d'épidémiosurveillance animale du Québec, Saint-Hyacinthe, Québec, Canada.
| | - Greg P Keefe
- University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.
| | - Shawn L B McKenna
- University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.
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6
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Bacteriological diagnosis and molecular strain typing of Mycobacterium bovis and Mycobacterium caprae. Res Vet Sci 2014; 97 Suppl:S30-43. [DOI: 10.1016/j.rvsc.2014.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 04/08/2014] [Accepted: 04/24/2014] [Indexed: 11/24/2022]
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7
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Chiou CS. Multilocus variable-number tandem repeat analysis as a molecular tool for subtyping and phylogenetic analysis of bacterial pathogens. Expert Rev Mol Diagn 2014; 10:5-7. [DOI: 10.1586/erm.09.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Insights into the origin, emergence, and current spread of a successful Russian clone of Mycobacterium tuberculosis. Clin Microbiol Rev 2013; 26:342-60. [PMID: 23554420 DOI: 10.1128/cmr.00087-12] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Mycobacterium tuberculosis variant Beijing B0/W148 is regarded as a successful clone of M. tuberculosis that is widespread in the former Soviet Union and respective immigrant communities. Understanding the pathobiology and phylogeography of this notorious strain may help to clarify its origin and evolutionary history and the driving forces behind its emergence and current dissemination. I present the first review and analysis of all available data on the subject. In spite of the common perception of the omnipresence of B0/W148 across post-Soviet countries, its geographic distribution shows a peculiar clinal gradient. Its frequency peaks in Siberian Russia and, to a lesser extent, in the European part of the former Soviet Union. In contrast, the frequency of B0/W148 is sharply decreased in the Asian part of the former Soviet Union, and it is absent in autochthonous populations elsewhere in the world. Placing the molecular, clinical, and epidemiological features in a broad historical, demographic, and ecological context, I put forward two interdependent hypotheses. First, B0/W148 likely originated in Siberia, and its primary dispersal was driven by a massive population outflow from Siberia to European Russia in the 1960s to 1980s. Second, a historically recent, phylogenetically demonstrated successful dissemination of the Beijing B0/W148 strain was triggered by the advent and wide use of modern antituberculosis (anti-TB) drugs and was due to the remarkable capacity of this strain to acquire drug resistance. In contrast, there is some indication, but not yet systematic proof, of an enhanced virulence of this strain.
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Ragheb MN, Ford CB, Chase MR, Lin PL, Flynn JL, Fortune SM. The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection. BMC Genomics 2013; 14:145. [PMID: 23496945 PMCID: PMC3635867 DOI: 10.1186/1471-2164-14-145] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/26/2013] [Indexed: 11/25/2022] Open
Abstract
Background Mycobacterial interspersed repetitive units (MIRUs) are minisatellites within the Mycobacterium tuberculosis (Mtb) genome. Copy number variation (CNV) in MIRU loci is used for epidemiological typing, making the rate of variation important for tracking the transmission of Mtb strains. In this study, we developed and assessed a whole-genome sequencing (WGS) approach to detect MIRU CNV in Mtb. We applied this methodology to a panel of Mtb strains isolated from the macaque model of tuberculosis (TB), the animal model that best mimics human disease. From these data, we have estimated the rate of MIRU variation in the host environment, providing a benchmark rate for future epidemiologic work. Results We assessed variation at the 24 MIRU loci used for typing in a set of Mtb strains isolated from infected cynomolgus macaques. We previously performed WGS of these strains and here have applied both read depth (RD) and paired-end mapping (PEM) metrics to identify putative copy number variants. To assess the relative power of these approaches, all MIRU loci were resequenced using Sanger sequencing. We detected two insertion/deletion events both of which could be identified as candidates by PEM criteria. With these data, we estimate a MIRU mutation rate of 2.70 × 10-03 (95% CI: 3.30 × 10-04- 9.80 × 10-03) per locus, per year. Conclusion Our results represent the first experimental estimate of the MIRU mutation rate in Mtb. This rate is comparable to the highest previous estimates gathered from epidemiologic data and meta-analyses. Our findings allow for a more rigorous interpretation of data gathered from MIRU typing.
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Affiliation(s)
- Mark N Ragheb
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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10
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Nguyen VAT, Choisy M, Nguyen DH, Tran THT, Pham KLT, Thi Dinh PT, Philippe J, Nguyen TS, Ho ML, Van Tran S, Bañuls AL, Dang DA. High prevalence of Beijing and EAI4-VNM genotypes among M. tuberculosis isolates in northern Vietnam: sampling effect, rural and urban disparities. PLoS One 2012; 7:e45553. [PMID: 23029091 PMCID: PMC3454422 DOI: 10.1371/journal.pone.0045553] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/21/2012] [Indexed: 11/26/2022] Open
Abstract
A total of 221 isolates of M. tuberculosis were sampled from hospitals and the general population in the northern plain of Vietnam, one of the most populated region of the country. Genotypic composition and diversity were characterized, and we investigated how they are affected by sampling (hospital vs. general population), correcting for potential confounding effects (location, age and gender of the patients). Spoligotyping and 12 MIRU-VNTR typing were used as first line. Then 15 MIRU-VNTR standard set was used, making 21 MIRU-VNTR typing for the clustered isolates. Result showed that 8 lineages and 13 sub-lineages were circulating in the region. The most predominant lineages were Beijing (38.5%) and EAI (38.5%). Others appeared with small proportions H (1.4%), LAM (1.8%), T (8.1%), X (0.9%), MANU (2.3%), and Zero (0.4%). Higher clustering rate was found in the hospital samples (17.9% in urban and 19.2% in rural areas) compared to the population ones (0%). The typical Vietnamese EAI4-VNM sub-lineage of EAI lineage accounted for 67% of EAI strains and was associated with older ages. Beijing genotypes were associated with younger, urban population and were characterized by high clustering rates. These characteristics strongly suggest that Beijing strains are invading the population, replacing the local EAI-VNM4, thus predicting a more serious tuberculosis situation in the future in the absence of more effective control strategies.
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Affiliation(s)
- Van Anh Thi Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
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11
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Ozcaglar C, Shabbeer A, Kurepina N, Rastogi N, Yener B, Bennett KP. Inferred spoligoforest topology unravels spatially bimodal distribution of mutations in the DR region. IEEE Trans Nanobioscience 2012; 11:191-202. [PMID: 22987125 DOI: 10.1109/tnb.2012.2213265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Biomarkers of Mycobacterium tuberculosis complex (MTBC) mutate over time. Among the biomarkers of MTBC, spacer oligonucleotide type (spoligotype) and mycobacterium interspersed repetitive unit (MIRU) patterns are commonly used to genotype clinical MTBC strains. In this study, we present an evolution model of spoligotype rearrangements using MIRU patterns to disambiguate the ancestors of spoligotypes. We use a large patient dataset from the United States Centers for Disease Control and Prevention (CDC) to generate this model. Based on the contiguous deletion assumption and rare observation of convergent evolution, we first generate the most parsimonious forest of spoligotypes, called a spoligoforest, using three genetic distance measures. An analysis of topological attributes of the spoligoforest and number of variations at the direct repeat (DR) locus of each strain reveals interesting properties of deletions in the DR region. First, we compare our mutation model to existing mutation models of spoligotypes and find that our mutation model produces as many within-lineage mutation events as other models, with slightly higher segregation accuracy. Second, based on our mutation model, the number of descendant spoligotypes follows a power law distribution. Third, contrary to prior studies, the power law distribution does not plausibly fit to the mutation length frequency. Moreover, we find that the total number of mutation events at consecutive spacers follows a spatially bimodal distribution. The two modes are spacers 13 and 40, which are hotspots for chromosomal rearrangements, and the change point is spacer 34, which is absent in most MTBC strains. Based on this observation, we built two alternative models for mutation length frequency: the Starting Point Model (SPM) and the Longest Block Model (LBM). Both models are plausibly good fits to the mutation length frequency distribution, as verified by the goodness-of-fit test. We also apply SPM and LBM to a dataset from Institut Pasteur de Guadeloupe and verify that these models hold for different strain datasets.
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Affiliation(s)
- Cagri Ozcaglar
- Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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12
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Aandahl RZ, Reyes JF, Sisson SA, Tanaka MM. A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis. PLoS Comput Biol 2012; 8:e1002573. [PMID: 22761563 PMCID: PMC3386166 DOI: 10.1371/journal.pcbi.1002573] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 05/04/2012] [Indexed: 11/18/2022] Open
Abstract
Variable numbers of tandem repeats (VNTR) typing is widely used for studying the bacterial cause of tuberculosis. Knowledge of the rate of mutation of VNTR loci facilitates the study of the evolution and epidemiology of Mycobacterium tuberculosis. Previous studies have applied population genetic models to estimate the mutation rate, leading to estimates varying widely from around to per locus per year. Resolving this issue using more detailed models and statistical methods would lead to improved inference in the molecular epidemiology of tuberculosis. Here, we use a model-based approach that incorporates two alternative forms of a stepwise mutation process for VNTR evolution within an epidemiological model of disease transmission. Using this model in a Bayesian framework we estimate the mutation rate of VNTR in M. tuberculosis from four published data sets of VNTR profiles from Albania, Iran, Morocco and Venezuela. In the first variant, the mutation rate increases linearly with respect to repeat numbers (linear model); in the second, the mutation rate is constant across repeat numbers (constant model). We find that under the constant model, the mean mutation rate per locus is (95% CI: ,)and under the linear model, the mean mutation rate per locus per repeat unit is (95% CI: ,). These new estimates represent a high rate of mutation at VNTR loci compared to previous estimates. To compare the two models we use posterior predictive checks to ascertain which of the two models is better able to reproduce the observed data. From this procedure we find that the linear model performs better than the constant model. The general framework we use allows the possibility of extending the analysis to more complex models in the future. Genetically typing the bacterium responsible for tuberculosis is useful for understanding the evolutionary and epidemiological characteristics of the disease. Typing methods based on variable number tandem repeat (VNTR) loci are increasingly being used. These loci, which are composed of repeated units, mutate by increasing or decreasing in the number of these repeats. Knowledge of the mutation rate of molecular markers facilitates the epidemiological interpretation of the observed genetic variation in a sample of bacterial isolates. Few studies have examined the rate of mutation at these markers and estimates to date have varied considerably. To address this problem we develop a stochastic model of evolution of these markers and then estimate their mutation rate using approximate Bayesian computation. We examine two alternative forms of the mutation process. The observed data are from four published data sets of tuberculosis bacterial isolates sampled in Albania, Iran, Morocco and Venezuela. We find that these markers have fairly high rates of mutation compared with estimates from previous studies.
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Affiliation(s)
- R. Zachariah Aandahl
- School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia
- Evolution & Ecology Research Centre and School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Josephine F. Reyes
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Scott A. Sisson
- School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark M. Tanaka
- Evolution & Ecology Research Centre and School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail:
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13
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Reyes JF, Chan CHS, Tanaka MM. Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:811-8. [PMID: 21683165 DOI: 10.1016/j.meegid.2011.05.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 05/21/2011] [Accepted: 05/22/2011] [Indexed: 11/24/2022]
Abstract
Homoplasy is the occurrence of genotypes that are identical by state but not by descent. It arises through a number of means including convergent and reverse evolution, and horizontal gene transfer. When using molecular markers that are based on sequences possessing a finite number of character states, such as VNTR or spoligotypes, this is an unavoidable phenomenon. Here we discuss the extent of homoplasy and its impact on inferences drawn from spoligotypes and VNTR in epidemiological studies of tuberculosis. To further explore this problem, we developed a computer simulation model combining the processes of mutation and transmission. Our results show that while the extent of homoplasy is not negligible, its effect on the proportion of isolates clustered ("n-1 method") is likely to be relatively low for spoligotyping. For VNTR-typing, homoplasy occurs at a low rate provided the number of loci used is high and the mutation rate is relatively high. However, deep phylogenetic inferences using spoligotypes or VNTRs with a small number of loci are likely to be unreliable.
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Affiliation(s)
- Josephine F Reyes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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14
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Supply P, Niemann S, Wirth T. On the mutation rates of spoligotypes and variable numbers of tandem repeat loci of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 11:251-2. [DOI: 10.1016/j.meegid.2010.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 12/16/2010] [Indexed: 11/29/2022]
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15
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Mutation rate of VNTR loci in Mycobacterium tuberculosis: response to Supply et al. INFECTION GENETICS AND EVOLUTION 2011; 11:1189-90; discussion 1191-2. [PMID: 21295160 DOI: 10.1016/j.meegid.2011.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 01/14/2011] [Indexed: 11/22/2022]
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16
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Ozcaglar C, Shabbeer A, Kurepina N, Yener B, Bennett KP. Data-driven insights into deletions of Mycobacterium tuberculosis complex chromosomal DR region using spoligoforests. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2011:75-82. [PMID: 22343484 PMCID: PMC3279189 DOI: 10.1109/bibm.2011.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biomarkers of Mycobacterium tuberculosis complex (MTBC) mutate over time. Among the biomarkers of MTBC, spacer oligonucleotide type (spoligotype) and Mycobacterium Interspersed Repetitive Unit (MIRU) patterns are commonly used to genotype clinical MTBC strains. In this study, we present an evolution model of spoligotype rearrangements using MIRU patterns to disambiguate the ancestors of spoligotypes, in a large patient dataset from the United States Centers for Disease Control and Prevention (CDC). Based on the contiguous deletion assumption and rare observation of convergent evolution, we first generate the most parsimonious forest of spoligotypes, called a spoligoforest, using three genetic distance measures. An analysis of topological attributes of the spoligoforest and number of variations at the direct repeat (DR) locus of each strain reveals interesting properties of deletions in the DR region. First, we compare our mutation model to existing mutation models of spoligotypes and find that our mutation model produces as many within-lineage mutation events as other models, with slightly higher segregation accuracy. Second, based on our mutation model, the number of descendant spoligotypes follows a power law distribution. Third, contrary to prior studies, the power law distribution does not plausibly fit to the mutation length frequency. Finally, the total number of mutation events at consecutive DR loci follows a bimodal distribution, which results in accumulation of shorter deletions in the DR region. The two modes are spacers 13 and 40, which are hotspots for chromosomal rearrangements. The change point in the bimodal distribution is spacer 34, which is absent in most MTBC strains. This bimodal separation results in accumulation of shorter deletions, which explains why a power law distribution is not a plausible fit to the mutation length frequency.
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Affiliation(s)
- Cagri Ozcaglar
- Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY
| | - Amina Shabbeer
- Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY
| | | | - Bülent Yener
- Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY
| | - Kristin P. Bennett
- Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY
- Mathematical Sciences Department, Rensselaer Polytechnic Institute, Troy, NY
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Reyes JF, Tanaka MM. Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2010; 10:1046-51. [DOI: 10.1016/j.meegid.2010.06.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 06/24/2010] [Accepted: 06/24/2010] [Indexed: 01/14/2023]
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Mycobacterium bovis BCG-Russia clinical isolate with noncanonical spoligotyping profile. J Clin Microbiol 2010; 48:4686-7. [PMID: 20881181 DOI: 10.1128/jcm.01368-10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D. High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster. J Clin Microbiol 2010; 48:3403-6. [PMID: 20592143 PMCID: PMC2937716 DOI: 10.1128/jcm.00370-10] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/19/2010] [Accepted: 06/22/2010] [Indexed: 01/20/2023] Open
Abstract
To investigate whether genome sequencing yields more useful markers than those currently used to study the epidemiology of tuberculosis, it was applied to three Mycobacterium tuberculosis isolates of the Harlingen outbreak. Our findings suggest that single nucleotide polymorphisms can be used to identify transmission chains in restriction fragment length polymorphism clusters.
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Affiliation(s)
- Anita C. Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Kristin Kremer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Olaf Daviena
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Albert Kiers
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Martin J. Boeree
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Roland J. Siezen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, Netherlands, Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden, Netherlands, University Centre for Chronic Diseases, Department of Pulmonary Disease, Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
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Valcheva V, Mokrousov I, Panaiotov S, Bachiiska E, Zozio T, Sola C, Markova N, Rastogi N. Bulgarian specificity and controversial phylogeography of Mycobacterium tuberculosis spoligotype ST 125__BGR. ACTA ACUST UNITED AC 2010; 59:90-9. [PMID: 20402768 DOI: 10.1111/j.1574-695x.2010.00667.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The local specificity of bacterial clones may be explained by long-term presence or recent importation/fast dissemination in an area. Mycobacterium tuberculosis spoligotype ST125, noticeably prevalent among Bulgaria-specific spoligotypes, has a characteristically 'abridged' profile and an uncertain clade position [Latin-American-Mediterranean (LAM)/S]. A comparison with the SITVIT2 database (Institut Pasteur de Guadeloupe) demonstrated its high gradient in Bulgaria (14.3%) compared with the negligible presence in the rest of the world. Further typing of all available Bulgarian ST125 strains revealed that they: (i) monophyletically clustered in 21-mycobacterial interspersed repetitive units (MIRU)-loci tree of all Bulgarian strains; (ii) grouped closely with the ST34 spoligotype, a prototype of the S family; and (iii) did not harbor a LAM-specific IS6110 insertion. Comparison of the 21-MIRU-based network with geographic data revealed a complex dissemination pattern of ST125 in Bulgaria. Interestingly, this variable number of tandem repeats (VNTR) network remarkably corroborated with a recent hypothesis of single repeat loss as the primary mode of evolution of VNTR loci in M. tuberculosis. In conclusion, M. tuberculosis spoligotype ST125 is phylogeographically specific for Bulgaria. This spoligotype was not associated with drug resistance or increased transmissibility; its prevalence in Bulgaria can rather be attributed to the historical circulation in the country, having led, speculatively, to adaptation to the local human population.
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Affiliation(s)
- Violeta Valcheva
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe, France
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Schürch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D. The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale. INFECTION GENETICS AND EVOLUTION 2010; 10:108-14. [DOI: 10.1016/j.meegid.2009.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 11/24/2022]
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First insight into genetic diversity of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variable-number tandem-repeat analysis and spoligotyping reveals the presence of beijing multidrug-resistant isolates. J Clin Microbiol 2009; 47:1581-4. [PMID: 19279172 DOI: 10.1128/jcm.02284-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized a set of 100 Mycobacterium tuberculosis complex clinical isolates from tuberculosis (TB) patients in Albania, typing them with a 24-locus variable-number tandem-repeat-spoligotyping scheme. Depending on the cluster definition, 43 to 49 patients were distributed into 15 to 16 clusters which were likely to be epidemiologically linked, indicative of a recent transmission rate of 28 to 34%. This result suggests that TB is under control in Albania. However, two multidrug-resistant (MDR) Beijing genotypes harboring the same S531A mutation on the rpoB gene were also found, suggesting a potential recent transmission of MDR TB. Three brand new genotypes, Albania-1 to Albania-3, are also described.
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Wada T, Iwamoto T, Maeda S. Genetic diversity of the Mycobacterium tuberculosis Beijing family in East Asia revealed through refined population structure analysis. FEMS Microbiol Lett 2008; 291:35-43. [PMID: 19054072 DOI: 10.1111/j.1574-6968.2008.01431.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The Beijing/W family is the endemic lineage of Mycobacterium tuberculosis in East Asia: it has disseminated worldwide. To elucidate its genetic diversity in Japan, phylogenetic reconstruction was performed using 403 M. tuberculosis Beijing family clinical isolates. Variable number of tandem repeats analysis revealed the strains from Japan to be dispersed mainly among five subgroups in a phylogenetic tree. Interestingly, the genotypes of the strains from China and Mongolia were restricted mainly to a single branch; they exhibited high clonality. IS6110 insertion in the NTF region was also analyzed. The majority (78.6%) of Japanese isolates belonged to the ancient sublineage. The modern Beijing strains were observed to correspond to the branch containing the foreign strains, although the ancient Beijing strains were dispersed among the tree's other branches. Our results reflect the singular genetic diversity and the epidemiological pattern of Beijing M. tuberculosis in Japan.
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Affiliation(s)
- Takayuki Wada
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan.
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Valcheva V, Mokrousov I, Narvskaya O, Rastogi N, Markova N. Molecular snapshot of drug-resistant and drug-susceptible Mycobacterium tuberculosis strains circulating in Bulgaria. INFECTION GENETICS AND EVOLUTION 2008; 8:657-63. [DOI: 10.1016/j.meegid.2008.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 11/26/2022]
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Mokrousov I. Genetic geography of Mycobacterium tuberculosis Beijing genotype: a multifacet mirror of human history? INFECTION GENETICS AND EVOLUTION 2008; 8:777-85. [PMID: 18691674 DOI: 10.1016/j.meegid.2008.07.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 07/03/2008] [Accepted: 07/04/2008] [Indexed: 11/26/2022]
Abstract
The Beijing genotype of Mycobacterium tuberculosis has been shown in many settings to be hypervirulent and associated with multi-drug resistance. Its presently global and rapid dissemination makes it an important issue of public health. Here, I present a significantly enlarged update of the MIRU-VNTR global database of the M. tuberculosis Beijing genotype (11 loci). I further attempted to link the observed mycobacterial diversity with relevant events of the known human history. Large water masses have been the most efficient and drastic generators of the genetic divergence between human populations. The same situation appears true also for M. tuberculosis, which general diversity pattern amazingly resembles that of its human host. At the same time, less expected affinities observed between distant populations of M. tuberculosis may reflect hidden patterns of human migrations or yet unknown epidemiological links between distant regions.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg 197101, Russia.
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