1
|
Xia H, van den Hof S, Cobelens F, Zhou Y, Zhao B, Wang S, Zhao Y. Value of pyrazinamide for composition of new treatment regimens for multidrug-resistant Mycobacterium tuberculosis in China. BMC Infect Dis 2020; 20:19. [PMID: 31910878 PMCID: PMC6947908 DOI: 10.1186/s12879-020-4758-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/31/2019] [Indexed: 11/29/2022] Open
Abstract
Background Pyrazinamide still may be a useful drug for treatment of rifampin-resistant (RR-TB) or multidrug-resistant tuberculosis (MDR-TB) in China while awaiting scale up of new drugs and regimens including bedaquiline and linezolid. The level of pyrazinamide resistance among MDR-TB patients in China is not well established. Therefore, we assessed pyrazinamide resistance in a representative sample and explored determinants and patterns of pncA mutations. Methods MDR-TB isolates from the 2007 national drug resistance survey of China were sub-cultured and examined for pyrazinamide susceptibility by BACTEC MGIT 960 method. pncA mutations were identified by sequencing. Characteristics associated with pyrazinamide resistance were analyzed using univariable and multivariable log-binominal regression. Results Of 401 MDR-TB isolates, 324 were successfully sub-cultured and underwent drug susceptibility testing. Pyrazinamide resistance was prevalent in 40.7% of samples, similarly among new and previously treated MDR-TB patients. Pyrazinamide resistance in MDR-TB patients was associated with lower age (adjusted OR 0.54; 95% CI, 0.34–0.87 for those aged ≧60 years compared to < 40 years). Pyrazinamide resistance was not associated with gender, residential area, previous treatment history and Beijing genotype. Of 132 patients with pyrazinamide resistant MDR-TB, 97 (73.5%) had a mutation in the pncA gene; with 61 different point mutations causing amino acid change, and 11 frameshifts in the pncA gene. The mutations were scattered throughout the whole pncA gene and no hot spot region was identified. Conclusions Pyrazinamide resistance among MDR-TB patients in China is common, although less so in elderly patients. Therefore, pyrazinamide should only be used for treatment of RR/MDR-TB in China if susceptibility is confirmed. Molecular testing for detection of pyrazinamide resistance only based on pncA mutations has certain value for the rapid detection of pyrazinamide resistance in MDR-TB strains but other gene mutations conferring to pyrazinamide resistance still need to be explored to increase its predictive ability .
Collapse
Affiliation(s)
- Hui Xia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Susan van den Hof
- KNCV Tuberculosis Foundation, The Hague, The Netherlands.,National Institute of Public Health and the Environment, Centre for Infectious Disease Epidemiology and Surveillance, Bilthoven, The Netherlands
| | - Frank Cobelens
- Department of Global Health and Amsterdam Institute for Global Health and Development, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Yang Zhou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
2
|
Mulholland CV, Shockey AC, Aung HL, Cursons RT, O'Toole RF, Gautam SS, Brites D, Gagneux S, Roberts SA, Karalus N, Cook GM, Pepperell CS, Arcus VL. Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific. Front Microbiol 2019; 10:2778. [PMID: 31921003 PMCID: PMC6915100 DOI: 10.3389/fmicb.2019.02778] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of Mtb remains largely unexplored. Here, we investigated the evolutionary history of the Euro-American L4.4 sublineage and its dispersal to the South Pacific. Using a phylodynamics approach and a dataset of 236 global Mtb L4.4 genomes we have traced the origins and dispersal of L4.4 strains to New Zealand. These strains are predominantly found in indigenous Māori and Pacific people and we identify a clade of European, likely French, origin that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests the expansion of European trade networks in the early 19th century drove the dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the expansion and dispersal of Mtb in the South Pacific and provide a striking example of the role of historical European migrations in the global dispersal of Mtb.
Collapse
Affiliation(s)
- Claire V Mulholland
- School of Science, University of Waikato, Hamilton, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Htin L Aung
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ray T Cursons
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Ronan F O'Toole
- School of Medicine, University of Tasmania, Hobart, TAS, Australia.,School of Molecular Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Sanjay S Gautam
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | | | - Gregory M Cook
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Vickery L Arcus
- School of Science, University of Waikato, Hamilton, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
3
|
Shockey AC, Dabney J, Pepperell CS. Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria. Front Genet 2019; 10:477. [PMID: 31214242 PMCID: PMC6558051 DOI: 10.3389/fgene.2019.00477] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.
Collapse
Affiliation(s)
- Abigail C. Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Jesse Dabney
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
4
|
Mortimer TD, Weber AM, Pepperell CS. Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis. mSystems 2018; 3:e00108-17. [PMID: 29404424 PMCID: PMC5790871 DOI: 10.1128/msystems.00108-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis. Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis, we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant M. tuberculosis. A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in M. tuberculosis and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in M. tuberculosis is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of M. tuberculosis isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant M. tuberculosis to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in M. tuberculosis and other clonal pathogens.
Collapse
Affiliation(s)
- Tatum D. Mortimer
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Alexandra M. Weber
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| |
Collapse
|
5
|
Sengstake S, Bergval IL, Schuitema AR, de Beer JL, Phelan J, de Zwaan R, Clark TG, van Soolingen D, Anthony RM. Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia. BMC Infect Dis 2017; 17:491. [PMID: 28697808 PMCID: PMC5506614 DOI: 10.1186/s12879-017-2594-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/05/2017] [Indexed: 11/28/2022] Open
Abstract
Background The ongoing epidemic of multidrug-resistant tuberculosis (MDR-TB) in Georgia highlights the need for more effective control strategies. A new regimen to treat MDR-TB that includes pyrazinamide (PZA) is currently being evaluated and PZA resistance status will largely influence the success of current and future treatment strategies. PZA susceptibility testing was not routinely performed at the National Reference Laboratory (NRL) in Tbilisi between 2010 and September 2015. We here provide a first insight into the prevalence of PZA resistant TB in this region. Methods Phenotypic susceptibility to PZA was determined in a convenience collection of well-characterised TB patient isolates collected at the NRL in Tbilisi between 2012 and 2013. In addition, the pncA gene was sequenced and whole genome sequencing was performed on two isolates. Results Out of 57 isolates tested 33 (57.9%) showed phenotypic drug resistance to PZA and had a single pncA mutation. All of these 33 isolates were MDR-TB strains. pncA mutations were absent in all but one of the 24 PZA susceptible isolate. In total we found 18 polymorphisms in the pncA gene. From the two major MDR-TB clusters represented (94–32 and 100–32), 10 of 15, 67.0% and 13 of 14, 93.0% strains, respectively were PZA resistant. We also identified a member of the potentially highly transmissive clade A strain carrying the characteristic I6L substitution in PncA. Another strain with the same MLVA type as the clade A strain acquired a different mutation in pncA and was genetically more distantly related suggesting that different branches of this particular lineage have been introduced into this region. Conclusion In this high MDR-TB setting more than half of the tested MDR-TB isolates were resistant to PZA. As PZA is part of current and planned MDR-TB treatment regimens this is alarming and deserves the attention of health authorities. Based on our typing and sequence analysis results we conclude that PZA resistance is the result of primary transmission as well as acquisition within the patient and recommend prospective genotyping and PZA resistance testing in high MDR-TB settings. This is of utmost importance in order to preserve bacterial susceptibility to PZA to help protect (new) second line drugs in PZA containing regimens.
Collapse
Affiliation(s)
- Sarah Sengstake
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands. .,Unit of Mycobacteriology, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium.
| | - Indra L Bergval
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands.,Centre for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Anja R Schuitema
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands
| | - Jessica L de Beer
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Jody Phelan
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
| | - Rina de Zwaan
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Taane G Clark
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.,Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
| | - Dick van Soolingen
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Richard M Anthony
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands.,Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| |
Collapse
|
6
|
Evolution of Mycobacterium tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 783:81-91. [DOI: 10.1007/978-1-4614-6111-1_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
7
|
Bergval I, Sengstake S, Brankova N, Levterova V, Abadía E, Tadumaze N, Bablishvili N, Akhalaia M, Tuin K, Schuitema A, Panaiotov S, Bachiyska E, Kantardjiev T, de Zwaan R, Schürch A, van Soolingen D, van ‘t Hoog A, Cobelens F, Aspindzelashvili R, Sola C, Klatser P, Anthony R. Combined species identification, genotyping, and drug resistance detection of Mycobacterium tuberculosis cultures by MLPA on a bead-based array. PLoS One 2012; 7:e43240. [PMID: 22916230 PMCID: PMC3423362 DOI: 10.1371/journal.pone.0043240] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/18/2012] [Indexed: 11/29/2022] Open
Abstract
The population structure of Mycobacterium tuberculosis is typically clonal therefore genotypic lineages can be unequivocally identified by characteristic markers such as mutations or genomic deletions. In addition, drug resistance is mainly mediated by mutations. These issues make multiplexed detection of selected mutations potentially a very powerful tool to characterise Mycobacterium tuberculosis. We used Multiplex Ligation-dependent Probe Amplification (MLPA) to screen for dispersed mutations, which can be successfully applied to Mycobacterium tuberculosis as was previously shown. Here we selected 47 discriminative and informative markers and designed MLPA probes accordingly to allow analysis with a liquid bead array and robust reader (Luminex MAGPIX technology). To validate the bead-based MLPA, we screened a panel of 88 selected strains, previously characterised by other methods with the developed multiplex assay using automated positive and negative calling. In total 3059 characteristics were screened and 3034 (99.2%) were consistent with previous molecular characterizations, of which 2056 (67.2%) were directly supported by other molecular methods, and 978 (32.0%) were consistent with but not directly supported by previous molecular characterizations. Results directly conflicting or inconsistent with previous methods, were obtained for 25 (0.8%) of the characteristics tested. Here we report the validation of the bead-based MLPA and demonstrate its potential to simultaneously identify a range of drug resistance markers, discriminate the species within the Mycobacterium tuberculosis complex, determine the genetic lineage and detect and identify the clinically most relevant non-tuberculous mycobacterial species. The detection of multiple genetic markers in clinically derived Mycobacterium tuberculosis strains with a multiplex assay could reduce the number of TB-dedicated screening methods needed for full characterization. Additionally, as a proportion of the markers screened are specific to certain Mycobacterium tuberculosis lineages each profile can be checked for internal consistency. Strain characterization can allow selection of appropriate treatment and thereby improve treatment outcome and patient management.
Collapse
Affiliation(s)
- Indra Bergval
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Sarah Sengstake
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Nadia Brankova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Edgar Abadía
- Institute of Genetics and Microbiology UMR 8621 CNRS/UPS11, Orsay, France
- Venezuelan Institute of Scientific Research, Caracas, Venezuela
| | - Nino Tadumaze
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Nino Bablishvili
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Maka Akhalaia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Kiki Tuin
- MRC-Holland, Amsterdam, The Netherlands
| | - Anja Schuitema
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Todor Kantardjiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Rina de Zwaan
- Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anita Schürch
- Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Departments of Microbiology and of Pulmonary Diseases, Radboud University Nijmegen Medical Centre/University Lung Centre Dekkerswald, Nijmegen, The Netherlands
| | - Anja van ‘t Hoog
- Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | - Frank Cobelens
- Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | - Rusudan Aspindzelashvili
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Christophe Sola
- Institute of Genetics and Microbiology UMR 8621 CNRS/UPS11, Orsay, France
| | - Paul Klatser
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Richard Anthony
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
8
|
Borrell S, Gagneux S. Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis. Clin Microbiol Infect 2011; 17:815-20. [PMID: 21682802 DOI: 10.1111/j.1469-0691.2011.03556.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mycobacterium tuberculosis harbours little DNA sequence diversity compared with other bacteria. However, there is mounting evidence that strain-to-strain variation in this organism has been underestimated. We review our current understanding of the genetic diversity among M. tuberculosis clinical strains and discuss the relevance of this diversity for the ongoing global epidemics of drug-resistant tuberculosis. Based on findings in other bacteria, we propose that epistatic interactions between pre-existing differences in strain genetic background, acquired drug-resistance-conferring mutations and compensatory changes could play a role in the emergence and spread of drug-resistant M. tuberculosis.
Collapse
Affiliation(s)
- S Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland University of Basel, Basel, Switzerland
| | | |
Collapse
|
9
|
Dispersal of Mycobacterium tuberculosis via the Canadian fur trade. Proc Natl Acad Sci U S A 2011; 108:6526-31. [PMID: 21464295 DOI: 10.1073/pnas.1016708108] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Patterns of gene flow can have marked effects on the evolution of populations. To better understand the migration dynamics of Mycobacterium tuberculosis, we studied genetic data from European M. tuberculosis lineages currently circulating in Aboriginal and French Canadian communities. A single M. tuberculosis lineage, characterized by the DS6(Quebec) genomic deletion, is at highest frequency among Aboriginal populations in Ontario, Saskatchewan, and Alberta; this bacterial lineage is also dominant among tuberculosis (TB) cases in French Canadians resident in Quebec. Substantial contact between these human populations is limited to a specific historical era (1710-1870), during which individuals from these populations met to barter furs. Statistical analyses of extant M. tuberculosis minisatellite data are consistent with Quebec as a source population for M. tuberculosis gene flow into Aboriginal populations during the fur trade era. Historical and genetic analyses suggest that tiny M. tuberculosis populations persisted for ∼100 y among indigenous populations and subsequently expanded in the late 19th century after environmental changes favoring the pathogen. Our study suggests that spread of TB can occur by two asynchronous processes: (i) dispersal of M. tuberculosis by minimal numbers of human migrants, during which small pathogen populations are sustained by ongoing migration and slow disease dynamics, and (ii) expansion of the M. tuberculosis population facilitated by shifts in host ecology. If generalizable, these migration dynamics can help explain the low DNA sequence diversity observed among isolates of M. tuberculosis and the difficulties in global elimination of tuberculosis, as small, widely dispersed pathogen populations are difficult both to detect and to eradicate.
Collapse
|
10
|
Benedetti A, Menzies D, Behr MA, Schwartzman K, Jin Y. How close is close enough? Exploring matching criteria in the estimation of recent transmission of tuberculosis. Am J Epidemiol 2010; 172:318-26. [PMID: 20576754 DOI: 10.1093/aje/kwq124] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
If Mycobacterium tuberculosis isolates from 2 people have the same genotype, transmission may have occurred between them. Genotyping based on the insertion sequence IS6110 uses identical restriction fragment length polymorphisms ("fingerprints") to infer transmission. However, once transmission has occurred, the genotypes may mutate, resulting in divergent fingerprints. Estimation of the proportion of tuberculosis (TB) cases due to recent transmission includes 3 approaches to determine if genotypes match: exact matching (assumes no fingerprint change); band-addition, band-loss, band-shift matching (ad hoc attempt to account for fingerprint changes); and genetic distance (directly accounts for fingerprint changes). Via simulation study, the authors varied the fingerprint change rate, level of recent transmission, and background genetic heterogeneity and estimated sensitivity, specificity, and bias of the recent transmission index by matching method. For exact matching, specificity was always high, but sensitivity decreased as the change rate increased. For band-addition, band-loss, band-shift matching, specificity decreased as genetic diversity decreased, and sensitivity remained high as the change rate increased. Genetic distance offered a compromise between the 2. Results from this study suggest that interpretation of the recent transmission index and the resulting necessary public health interventions will vary according to how researchers account for spontaneous mutation when estimating transmission from genotyping data.
Collapse
Affiliation(s)
- Andrea Benedetti
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada.
| | | | | | | | | |
Collapse
|
11
|
Mycobacterium tuberculosis in Ontario, Canada: Insights from IS6110 restriction fragment length polymorphism and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping. J Clin Microbiol 2009; 47:2651-4. [PMID: 19494075 DOI: 10.1128/jcm.01946-08] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A collection of 1,308 clinical Mycobacterium tuberculosis isolates from Ontario, Canada, was genotyped by IS6110 restriction fragment length polymorphism (RFLP) and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. RFLP or >12 MIRU-VNTR loci were necessary for resolution of Indo-Oceanic strains. The low clustering rate and high strain diversity indicate that, in Ontario, most tuberculosis results from reactivation of latent infections.
Collapse
|
12
|
Major Mycobacterium tuberculosis lineages associate with patient country of origin. J Clin Microbiol 2009; 47:1119-28. [PMID: 19213699 DOI: 10.1128/jcm.02142-08] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over recent years, there has been an increasing acknowledgment of the diversity that exists among Mycobacterium tuberculosis clinical isolates. To facilitate comparative studies aimed at deciphering the relevance of this diversity to human disease, an unambiguous and easily interpretable method of strain classification is required. Presently, the most effective means of assigning isolates into a series of unambiguous lineages is the method of Gagneux et al. (S. Gagneux et al., Proc. Natl. Acad. Sci. USA 103:2869-2873, 2006) that involves the PCR-based detection of large sequence polymorphisms (LSPs). In this manner, isolates are classified into six major lineages, the majority of which display a high degree of geographic restriction. Here we describe an independent replicate of the Gagneux study carried out on 798 isolates collected over a 6-year period from mostly foreign-born patients resident on the island of Montreal, Canada. The original trends in terms of bacterial genotype and patient ethnicity are remarkably conserved within this Montreal cohort, even though the patient distributions between the two populations are quite distinct. In parallel with the LSP analysis, we also demonstrate that "clustered" tuberculosis (TB) cases defined through restriction fragment length polymorphism (RFLP) analysis (for isolates with >or=6 IS6110 copies) or RFLP in combination with spoligotyping (for isolates with <6 IS6110 copies) do not stray across the LSP-defined lineage boundaries. However, our data also demonstrate the poor discriminatory power of either RFLP or spoligotyping alone for these low-IS6110-copy-number isolates. We believe that this independent validation of the LSP method should encourage researchers to adopt this system in investigations aimed at elucidating the role of strain variation in TB.
Collapse
|
13
|
Sheline KD, France AM, Talarico S, Foxman B, Zhang L, Marrs CF, Bates JH, Cave MD, Yang Z. Does the lipR gene of tubercle bacilli have a role in tuberculosis transmission and pathogenesis? Tuberculosis (Edinb) 2008; 89:114-9. [PMID: 19027362 DOI: 10.1016/j.tube.2008.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 09/28/2008] [Accepted: 09/29/2008] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis lipases, a diverse class of enzymes involved in lipid metabolism, may have an important role in tuberculosis (TB) pathogenesis. We explored the association of large sequence polymorphism (LSP) in one of the M. tuberculosis lipase-encoding genes, lipR (Rv3084), with patient characteristics using a population-based sample of clinical isolates to elucidate the potential role of lipR in TB pathogenesis. LSP in lipR was found in 104 (15.6%) of 665 isolates, of which 96% belonged to principal genetic group 3. When linkage by molecular type and epidemiologic evidence were compared, molecularly clustered cases infected with a lipR LSP isolate were more often epidemiologically linked than clustered cases infected with a lipR wild-type isolate. Further epidemiologic and functional studies are necessary to determine if the association between this lipR LSP and recent transmission we identified in this population reflects a functional role of lipR in TB transmission and pathogenesis or other unidentified mechanisms.
Collapse
Affiliation(s)
- Katherine D Sheline
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Brassard P, Henry KA, Schwartzman K, Jomphe M, Olson SH. Geography and genealogy of the human host harbouring a distinctive drug-resistant strain of tuberculosis. INFECTION GENETICS AND EVOLUTION 2007; 8:247-57. [PMID: 18316250 DOI: 10.1016/j.meegid.2007.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 11/28/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
Abstract
For a strain of Mycobacterium tuberculosis mono-resistant to pyrazinamide (PZA), we report the geographic distribution within Quebec of the 77 cases diagnosed during 1990-2000. Known as the Quebec mutation (or the pncA deletion), the strain is rare in urban areas and showed an unexpected concentration in Mauricie, one of the 16 health districts of the province, with a cluster of 10 cases situated in a rural area of 35-km radius. The cases occurred among people >50 (98%), of French Canadian origins (90%), and are understood to have arisen by reactivation. The rarity in Montreal and smaller cities is explained by the youthfulness of massive postwar migrations. To reach back into the history of settlement, we examined genealogies: 92,429 ancestral marriages for 32 of the 77 PZA-resistant isolates and 226,535 for a set of 85 controls with isolates of more diverse mycobacterial strains. Genealogical analysis showed no salient common ancestor for the cases, and kinship among them was no greater than observed in control samples from the same regions. But it identified an unsuspected geographical region as the site of ancestral concentrations prior to 1840, for both resistant strains and controls. The following scenario is proposed for the resistant strain: endemic in a specific geographical region by 1800, it dispersed with families moving into regions opened to settlement in the 1840s and 1850s, among them Mauricie, where dispersion was intensified by seasonal mobility of labour in logging, milling and marketing timber. In high-incidence areas, it is difficult to distinguish cases of reactivation from recent infections, but the low-incidence context allows us to observe a 200-year trajectory of a distinctive drug-resistant strain of M. tuberculosis.
Collapse
Affiliation(s)
- Paul Brassard
- Department of Medicine, McGill University Health Center, Royal Victoria Hospital, Montréal, Québec, Canada H3A 1A1.
| | | | | | | | | |
Collapse
|
15
|
Haddad MB, Diem LA, Cowan LS, Cave MD, Bettridge J, Yun L, Winkler CS, Ingman DD, Oemig TV, Lynch A, Montero JT, McCombs SB, Ijaz K. Tuberculosis genotyping in six low-incidence States, 2000-2003. Am J Prev Med 2007; 32:239-43. [PMID: 17236744 DOI: 10.1016/j.amepre.2006.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/03/2006] [Accepted: 10/27/2006] [Indexed: 11/18/2022]
Abstract
BACKGROUND As tuberculosis incidence declines in the United States, a new tool for TB control efforts is Mycobacterium tuberculosis genotyping. Colorado, Iowa, Montana, New Hampshire, West Virginia, and Wisconsin began routine genotyping of all culture-confirmed TB cases in October 2000. METHODS M. tuberculosis isolates from cases reported October 2000 through December 2003 were genotyped by spoligotyping, mycobacterial interspersed repetitive units, and IS6110-based restriction fragment length polymorphism methods. Genotyping results were linked to demographic variables from national surveillance records. Patients who were in genotype clusters were interviewed and their records reviewed to determine possible transmission links among clustered patients. Final analysis was completed during April 2004 through June 2005. RESULTS Of 971 reported TB cases, 774 (80%) were culture-confirmed, of which 728 (94%) were genotyped. Most genotyped isolates (634 [87%]) were unique. Within 36 clusters linking 94 individuals, four clusters involved both U.S.- and foreign-born individuals. For eight clusters, genotyping results led to the discovery of previously unsuspected transmission. Transmission links between individuals were established in 21 (58%) of the 36 clusters. CONCLUSIONS In these six low-incidence states, most isolates had unique genotypes, suggesting that most cases arose from activation of latent infection. Few TB clusters involved the foreign-born. For 58% of genotype clusters, epidemiologic investigation ascertained that clustering represented recent M. tuberculosis transmission.
Collapse
Affiliation(s)
- Maryam B Haddad
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Gopaul KK, Brown TJ, Gibson AL, Yates MD, Drobniewski FA. Progression toward an improved DNA amplification-based typing technique in the study of Mycobacterium tuberculosis epidemiology. J Clin Microbiol 2006; 44:2492-8. [PMID: 16825370 PMCID: PMC1489471 DOI: 10.1128/jcm.01428-05] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While high-copy-number IS6110-based restriction fragment length polymorphism (HCN-RFLP) is the gold standard for typing most Mycobacterium tuberculosis strains, the time taken for culturing and low throughput make it impractical for large-scale prospective typing of large numbers of isolates. The development of a new method, mycobacterial interspersed repetitive units (MIRU), a variation of the original variable-number tandem repeat (VNTR) technique, may provide a viable alternative. Panels based on the original 12-loci MIRU (12MIRU), a combination of 12MIRU and remaining ETR loci (15MIRU-VNTR), and an extended panel with an additional 10 novel regions (25VNTR) were used to study three populations with varying degrees of epidemiological data. MIRU discrimination increased with panel size and the addition of spoligotyping. Combining these two techniques enabled a reduction in the panel size from 25 to 14 loci without a significant loss in discrimination. However, 25VNTR alone or in combination with spoligotyping still possessed weaker discrimination than RFLP for high-copy-number isolates.
Collapse
Affiliation(s)
- Krishna K Gopaul
- Health Protection Agency Mycobacterium Reference Unit, Clinical Research Centre, Barts and the London Medical School, Queen Mary College, University of London, 2 Newark St., London E1 2AT, United Kingdom
| | | | | | | | | |
Collapse
|
17
|
Viana-Niero C, Rodriguez CAR, Bigi F, Zanini MS, Ferreira-Neto JS, Cataldi A, Leão SC. Identification of an IS6110 insertion site in plcD, the unique phospholipase C gene of Mycobacterium bovis. J Med Microbiol 2006; 55:451-457. [PMID: 16533994 DOI: 10.1099/jmm.0.46364-0] [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: 11/18/2022] Open
Abstract
The IS6110 repetitive element is present in multiple copies in most Mycobacterium tuberculosis complex bacteria, except for Mycobacterium bovis strains, which usually contain a single copy of IS6110 located on a 1·9 kb PvuII fragment of the direct repeat region. IS6110 transposition can disrupt coding regions and is a major force of genomic variation. In a previous work it was demonstrated that phospholipase C genes are preferential loci for IS6110 transposition in M. tuberculosis clinical strains. Bacterial phospholipase C enzymes participate in pathogenic mechanisms used by different organisms, and have been implicated in intracellular survival, cytolysis and cell-to-cell spread. Four phospholipase C genes (plcA, plcB, plcC and plcD) were detected in the genomes of M. tuberculosis, Mycobacterium africanum, Mycobacterium microti and ‘Mycobacterium canettii’. M. bovis and the vaccine strain M. bovis Bacillus Calmette–Guérin contain only the plcD gene. In the present work, the existence of IS6110 insertions within plcD, the unique phospholipase C gene of M. bovis, has been investigated by PCR, Southern blot hybridization and sequencing analysis. In 18 (7·3 %) of 245 isolates analysed, the plcD gene was interrupted by the insertion of one copy of IS6110, which in all cases was transposed in the same orientation and at the same position, 1 972 894, relative to the genome of M. bovis AF2122/97. These 18 isolates were distributed in 6 different spoligotype patterns and contained 4 to 8 IS6110 copies. In contrast, strains showing an intact plcD gene contained one (87 %), two (9·4 %) or three (2·4 %) IS6110 copies, and only a single isolate (1·2 %) had four IS6110 copies. The implications of plcD gene disruption in M. bovis have not been fully investigated, but no differences in the organ distribution of the disease were detected when animals infected with strains from the same spoligotype patterns bearing plcD : : IS6110 and intact plcD were compared.
Collapse
Affiliation(s)
- Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu 862 3° andar, São Paulo, CEP 04023-062, Brazil
| | - Cesar Alejandro Rosales Rodriguez
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Professor Dr Orlando Marques de Paiva 87, São Paulo, CEP 05508-900, Brazil
| | - Fabiana Bigi
- Instituto de Microbiología y Zoología Agrícola del CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Castelar, Buenos Aires, Argentina
| | - Marcos Santos Zanini
- Centro de Ciências Agrárias, Universidade Federal do Espírito Santo, PO Box 16, Alegre, Espírito Santo, Brazil
| | - José Soares Ferreira-Neto
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Professor Dr Orlando Marques de Paiva 87, São Paulo, CEP 05508-900, Brazil
| | - Angel Cataldi
- Instituto de Microbiología y Zoología Agrícola del CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Castelar, Buenos Aires, Argentina
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu 862 3° andar, São Paulo, CEP 04023-062, Brazil
| |
Collapse
|
18
|
Mostowy S, Inwald J, Gordon S, Martin C, Warren R, Kremer K, Cousins D, Behr MA. Revisiting the evolution of Mycobacterium bovis. J Bacteriol 2005; 187:6386-95. [PMID: 16159772 PMCID: PMC1236643 DOI: 10.1128/jb.187.18.6386-6395.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Though careful consideration has been placed towards genetic characterization of tubercle bacillus isolates causing disease in humans, those causing disease predominantly among wild and domesticated mammals have received less attention. In contrast to Mycobacterium tuberculosis, whose host range is largely specific to humans, M. bovis and "M bovis-like" organisms infect a broad range of animal species beyond their most prominent host in cattle. To determine whether strains of variable genomic content are associated with distinct distributions of disease, the DNA contents of M. bovis or M. bovis-like isolates from a variety of hosts were investigated via Affymetrix GeneChip. Consistent with previous genomic analysis of the M. tuberculosis complex (MTC), large sequence polymorphisms of putative diagnostic and biological consequence were able to unambiguously distinguish interrogated isolates. The distribution of deleted regions indicates organisms genomically removed from M. bovis and also points to structured genomic variability within M. bovis. Certain genomic profiles spanned a variety of hosts but were clustered by geography, while others associated primarily with host type. In contrast to the prevailing assumption that M. bovis has broad host capacity, genomic profiles suggest that distinct MTC lineages differentially infect a variety of mammals. From this, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC.
Collapse
Affiliation(s)
- Serge Mostowy
- McGill University Health Centre, Montreal, Quebec, Canada
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Behr MA. Polyclonal tuberculosis and the emergence of drug resistance. Am J Respir Crit Care Med 2005; 172:521-2. [PMID: 16120715 DOI: 10.1164/rccm.2506008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
20
|
Abstract
This article introduces the tools and terminology used for the classification of specific isolates of the Mycobacterium tuberculosis complex (MTC). The utility of these tools and terminology is illustrated by discussing work from independent laboratories that have established a genome-based phylogeny for the MTC. It considers the use of these markers to distinguish atypical isolates not conforming to attributes of traditional MTC members. Finally, it discusses the current genomic evidence regarding the origin and evolution of M. tuberculosis in the context of its relevance for tuberculosis control in humans and other mammalian hosts.
Collapse
Affiliation(s)
- Serge Mostowy
- McGill University Health Centre, 1650 Cedar Avenue, Montreal, QC H3G 1A4, Canada
| | | |
Collapse
|
21
|
Daley CL. Molecular Epidemiology: A Tool for Understanding Control of Tuberculosis Transmission. Clin Chest Med 2005; 26:217-31, vi. [PMID: 15837107 DOI: 10.1016/j.ccm.2005.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the primary goals of tuberculosis control programs is to interrupt the transmission of Mycobacterium tuberculosis. The development of several genotyping tools has allowed tracking of strains of M. tuberculosis as they spread through communities. Studies that have combined the use of genotyping with conventional epidemiologic investigation have increased the understanding of the transmission and pathogenesis of tuberculosis. This article reviews some of the lessons learned using these new epidemiologic tools.
Collapse
Affiliation(s)
- Charles L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Medical and Research Center, 1400 Jackson Street, Denver, CO 80206, USA.
| |
Collapse
|
22
|
Malik ANJ, Godfrey-Faussett P. Effects of genetic variability of Mycobacterium tuberculosis strains on the presentation of disease. THE LANCET. INFECTIOUS DISEASES 2005; 5:174-83. [PMID: 15766652 DOI: 10.1016/s1473-3099(05)01310-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The nature of the variability in the clinical and epidemiological consequences of Mycobacterium tuberculosis infection remains poorly understood. Environmental and host factors that contribute to the outcome of infection and disease presentation are well recognised, but the role of bacterial factors has been more elusive. The rapid increase in the understanding of the molecular basis of M tuberculosis over the past decades has revived research into its pathogenesis. DNA fingerprinting techniques have been used to distinguish between strains of M tuberculosis, and efforts to characterise the strains present within populations have led to increased understanding of their global distribution. This research has shown that in certain areas a small number of strains are causing a disproportionate number of cases of the disease. The sequencing of the complete genome of M tuberculosis has accelerated the development of molecular techniques to differentiate strains according to their genetic polymorphisms. Investigation into the reasons why some strains are predominant by genetic strain-typing techniques may clarify which bacterial factors contribute to disease. This knowledge has the potential to influence control and prevention strategies for tuberculosis in the future. However, there are still limitations in these techniques and their results. This review discusses molecular epidemiology and genetic studies, and their contribution to the understanding of the links between genotypic and phenotypic characteristics of M tuberculosis strains.
Collapse
|
23
|
Scott AN, Menzies D, Tannenbaum TN, Thibert L, Kozak R, Joseph L, Schwartzman K, Behr MA. Sensitivities and specificities of spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat typing methods for studying molecular epidemiology of tuberculosis. J Clin Microbiol 2005; 43:89-94. [PMID: 15634955 PMCID: PMC540143 DOI: 10.1128/jcm.43.1.89-94.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of PCR-based genotyping modalities (spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat [MIRU-VNTR] typing) offers promise for real-time molecular epidemiological studies of tuberculosis (TB). However, the utility of these methods depends on their capacity to appropriately classify isolates. To determine the operating parameters of spoligotyping and MIRU-VNTR typing, we have compared results generated by these newer tests to the standard typing method, IS6110 restriction fragment length polymorphism, in analyses restricted to high-copy-number IS6110 isolates. Sensitivities of the newer tests were estimated as the percentages of isolates with identical IS6110 fingerprints that had identical spoligotypes and MIRU-VNTR types. The specificities of these tests were estimated as the percentages of isolates with unique IS6110 fingerprints that had unique spoligotypes and MIRU-VNTR types. The sensitivity of MIRU-VNTR typing was 52% (95% confidence interval [CI], 31 to 72%), and the sensitivity of spoligotyping was 83% (95% CI, 63 to 95%). The specificity of MIRU-VNTR typing was 56% (95% CI, 51 to 62%), and the specificity of spoligotyping was 40% (95% CI, 35 to 46%). The proportion of isolates estimated to be due to recent transmission was 4% by identical IS6110 patterns, 19% by near-identical IS6110 patterns, 33% by MIRU-VNTR typing, and 53% by spoligotyping. The low calculated specificities of spoligotyping and MIRU-VNTR typing led to misclassification of cases, inflated estimates of TB transmission, and low positive predictive values, suggesting that these techniques have unsuitable operating parameters for population-based molecular epidemiology studies.
Collapse
Affiliation(s)
- Allison N Scott
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447475 DOI: 10.1002/cfg.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|