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Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. BMC Genomics 2019; 20:917. [PMID: 31791238 PMCID: PMC6889575 DOI: 10.1186/s12864-019-6267-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/06/2019] [Indexed: 12/26/2022] Open
Abstract
Background Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
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Affiliation(s)
- Kwanho Jeong
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Alejandra Muñoz-Bodnar
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Current address: Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lucie Poulin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Laboratoire de Biologie et de Pathologie Végétales, Université de Nantes, Nantes, France
| | - Luis Miguel Rodriguez-R
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lionel Gagnevin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Christian Vernière
- CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France.,CIRAD, UMR BGPI, 34398, Montpellier, France
| | | | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.
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Dou HY, Chen YY, Kou SC, Su IJ. Prevalence of Mycobacterium tuberculosis strain genotypes in Taiwan reveals a close link to ethnic and population migration. J Formos Med Assoc 2014; 114:484-8. [PMID: 25542769 DOI: 10.1016/j.jfma.2014.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/10/2014] [Accepted: 07/21/2014] [Indexed: 01/02/2023] Open
Abstract
Taiwan is a relatively isolated island, serving as a mixing vessel for colonization by different waves of ethnic and migratory groups over the past 4 centuries. The potential transmission pattern of Mycobacterium tuberculosis in different ethnic and migratory populations remains to be elucidated. By using mycobacterial tandem repeat sequences as genetic markers, the prevalence of M. tuberculosis strains in Taiwan revealed a close link to the historical migration. Interestingly, the M. tuberculosis strain in the aborigines of Eastern and Central Taiwan had a dominance of the Haarlem (Dutch) strain while those in Southern Taiwan had a dominance of the East-African Indian (EAI) strain. The prevalence of different M. tuberculosis strains in specific ethnic populations suggests that M. tuberculosis transmission is limited and restricted to close contact. The prevalence of the Beijing modern strain in the young population causes a concern for M. tuberculosis control, because of high virulence and drug resistance. Furthermore, our data using molecular genotyping should provide valuable information on the historical study of the origin and migration of aborigines in Taiwan.
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Affiliation(s)
- Horng-Yunn Dou
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Yih-Yuan Chen
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Shu-Chen Kou
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Ih-Jen Su
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan.
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3
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Chen YY, Chang JR, Huang WF, Hsu SC, Kuo SC, Sun JR, Dou HY. The pattern of cytokine production in vitro induced by ancient and modern Beijing Mycobacterium tuberculosis strains. PLoS One 2014; 9:e94296. [PMID: 24728339 PMCID: PMC3984122 DOI: 10.1371/journal.pone.0094296] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/14/2014] [Indexed: 12/20/2022] Open
Abstract
It is unclear to what extent the host-responses elicited by Beijing versus non-Beijing strains of Mycobacterium tuberculosis (MTB) contribute to the predominance of modern Beijing strains in Taiwan and some other Asian countries. The purpose of this study was to compare the expression profiles of virulence-related genes in human monocyte-derived macrophages infected in vitro with Beijing (ancient and modern strains) and non-Beijing strains (EAI strains) of MTB that are epidemic in Taiwan. We found that modern Beijing strains induced lower levels of pro-inflammatory cytokines, whereas EAI strains induced higher levels. Notably, the most prevalent modern Beijing sub-lineage, possessing intact RD150 and RD142 chromosomal regions, induced very low levels of pro-inflammatory cytokines, especially interleukin-1β. Moreover, in an intracellular growth assay, the survival of the same modern Beijing strain in human monocyte-derived macrophages was significantly higher than that of an ancient Beijing strain and an EAI strain. Taken together, these results may explain why modern Beijing strains of MTB predominate in Taiwan.
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Affiliation(s)
- Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Feng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shu-Ching Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jun-Ren Sun
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- * E-mail:
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4
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Chen YY, Chang JR, Huang WF, Kuo SC, Su IJ, Sun JR, Chiueh TS, Huang TS, Chen YS, Dou HY. Genetic diversity of the Mycobacterium tuberculosis Beijing family based on SNP and VNTR typing profiles in Asian countries. PLoS One 2012; 7:e39792. [PMID: 22808061 PMCID: PMC3395628 DOI: 10.1371/journal.pone.0039792] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/26/2012] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis (MTB) Beijing strain is highly virulent, drug resistant, and endemic over Asia. To explore the genetic diversity of this family in several different regions of eastern Asia, 338 Beijing strains collected in Taiwan (Republic of China) were analyzed by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and compared with published MIRU-VNTR profiles and by the Hunter-Gaston diversity index (HGDI) of Beijing strains from Japan and South Korea. The results revealed that VNTR2163b (HGDI>0.6) and five other loci (VNTR424, VNTR4052, VNTR1955, VNTR4156 and VNTR 2996; HGDI>0.3) could be used to discriminate the Beijing strains in a given geographic region. Analysis based on the number of VNTR repeats showed three VNTRs (VNTR424, 3192, and 1955) to be phylogenetically informative loci. In addition, to determine the geographic variation of sequence types in MTB populations, we also compared sequence type (ST) data of our strains with published ST profiles of Beijing strains from Japan and Thailand. ST10, ST22, and ST19 were found to be prevalent in Taiwan (82%) and Thailand (92%). Furthermore, classification of Beijing sublineages as ancient or modern in Taiwan was found to depend on the repeat number of VNTR424. Finally, phylogenetic relationships of MTB isolates in Taiwan, South Korea, and Japan were revealed by a minimum spanning tree based on MIRU-VNTR genotyping. In this topology, the MIRU-VNTR genotypes of the respective clusters were tightly correlated to other genotypic characters. These results are consistent with the hypothesis that clonal evolution of these MTB lineages has occurred.
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Affiliation(s)
- Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Feng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jun-Ren Sun
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Tzong-Shi Chiueh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Tsi-Shu Huang
- Department of Microbiology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yao-Shen Chen
- Department of Microbiology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
- * E-mail:
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5
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Strain Typing Using Multiple “Variable Number of Tandem Repeat” Analysis and Genetic Element CRISPR. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Schürch AC, Kremer K, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D. Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis. J Clin Microbiol 2011; 49:1318-22. [PMID: 21325559 PMCID: PMC3122804 DOI: 10.1128/jcm.01848-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 02/04/2011] [Indexed: 11/20/2022] Open
Abstract
The "Harlingen" IS6110 restriction fragment length polymorphism (RFLP) cluster has linked over 100 tuberculosis cases in The Netherlands since 1993. Four Mycobacterium tuberculosis isolates that were epidemiologically linked to this cluster had different spoligotype patterns, as well as slightly divergent IS6110 profiles, compared to the majority of the isolates. Sequencing of the direct repeat (DR) locus revealed sequence polymorphisms at the putative deletion sites. These deletion footprints provided evidence for independent deletions of the central region of the DR locus in three isolates, while the different genotype of the fourth isolate was explained by transmission. Our finding suggests that convergent deletions in the DR locus occur frequently. However, deletion footprints are not suitable to detect convergent deletions in the DR because they seem to be exceptional. Deletion footprints in the DR were not described previously, and we did not observe them in any public M. tuberculosis complex sequences. We conclude that preferential deletions in the DR loci of closely related strains are usually an unnoted event that interferes with clustering of closely related strains.
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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 (CIb), Laboratory for Infectious Disease and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen
| | - Kristin Kremer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Infectious Disease and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven
| | - Albert Kiers
- Department of Tuberculosis Control GGD Fryslân, P.O. Box 601, 8901 BK Leeuwarden
| | - Martin J. Boeree
- 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
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 9101, 6500 HB Nijmegen
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Infectious Disease and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven
- 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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7
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Drug resistant Mycobacterium tuberculosis of the Beijing genotype does not spread in Sweden. PLoS One 2010; 5:e10893. [PMID: 20531942 PMCID: PMC2878347 DOI: 10.1371/journal.pone.0010893] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 05/05/2010] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Drug resistant (DR) and multi-drug resistant (MDR) tuberculosis (TB) is increasing worldwide. In some parts of the world 10% or more of new TB cases are MDR. The Beijing genotype is a distinct genetic lineage of Mycobacterium tuberculosis, which is distributed worldwide, and has caused large outbreaks of MDR-TB. It has been proposed that certain lineages of M. tuberculosis, such as the Beijing lineage, may have specific adaptive advantages. We have investigated the presence and transmission of DR Beijing strains in the Swedish population. METHODOLOGY/PRINCIPAL FINDINGS All DR M. tuberculosis complex isolates between 1994 and 2008 were studied. Isolates that were of Beijing genotype were investigated for specific resistance mutations and phylogenetic markers. Seventy (13%) of 536 DR strains were of Beijing genotype. The majority of the patients with Beijing strains were foreign born, and their country of origin reflects the countries where the Beijing genotype is most prevalent. Multidrug-resistance was significantly more common in Beijing strains than in non-Beijing strains. There was a correlation between the Beijing genotype and specific resistance mutations in the katG gene, the mabA-inhA-promotor and the rpoB gene. By a combined use of RD deletions, spoligotyping, IS1547, mutT gene polymorphism and Rv3135 gene analysis the Beijing strains could be divided into 11 genomic sublineages. Of the patients with Beijing strains 28 (41%) were found in altogether 10 clusters (2-5 per cluster), as defined by RFLP IS6110, while 52% of the patients with non-Beijing strains were in clusters. By 24 loci MIRU-VNTR 31 (45%) of the patients with Beijing strains were found in altogether 7 clusters (2-11 per cluster). Contact tracing established possible epidemiological linkage between only two patients with Beijing strains. CONCLUSIONS/SIGNIFICANCE Although extensive outbreaks with non-Beijing TB strains have occurred in Sweden, Beijing strains have not taken hold, in spite of the proximity to high prevalence countries such as Russia and the Baltic countries. The Beijing sublineages so far introduced in Sweden may not be adapted to spread in the Scandinavian population.
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Nikolayevskyy VV, Brown TJ, Bazhora YI, Asmolov AA, Balabanova YM, Drobniewski FA. Molecular epidemiology and prevalence of mutations conferring rifampicin and isoniazid resistance in Mycobacterium tuberculosis strains from the southern Ukraine. Clin Microbiol Infect 2007; 13:129-138. [PMID: 17328724 DOI: 10.1111/j.1469-0691.2006.01583.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Understanding the molecular epidemiology of tuberculosis (TB) and mutations in genes associated with drug resistance may contribute to the development of appropriate interventions to improve tuberculosis control. A structured questionnaire was used to collect basic epidemiological data from 589 patients with radiologically confirmed TB in the Odessa and Nikolaev regions of the Ukraine in 2003-2004. A non-commercial reverse hybridisation assay and DNA sequencing were used to detect mutations associated with rifampicin and isoniazid resistance. Genotyping was performed using multilocus variable number tandem repeat (VNTR) typing and spoligotyping. Mutations conferring rifampicin and isoniazid resistance were detected in 32.9% and 44.0%, respectively, of 225 Mycobacterium tuberculosis isolates from individual consecutive patients. Mutations in codon 531 and codon 315 of the rpoB and katG genes, respectively, were predominant among drug-resistant isolates. Multidrug (MDR) resistance rates were significantly higher among former prison inmates compared with non-prisoners (54.8% vs. 27.3%; RR 2.01; 95% CI 1.35-2.97) and the prevalence of mutations was higher in Beijing strains sharing the VNTR signature 223325173533424 than in other Beijing strains (71.4% vs. 45.7%; RR 1.74; 95% CI 1.17-2.57), suggesting that this group may be responsible for rapid transmission of MDR TB in the southern Ukraine.
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Affiliation(s)
- V V Nikolayevskyy
- HPA Mycobacterium Reference Unit, Institute of Cell and Molecular Sciences, Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, London, UK; Odessa State Medical University, Odessa, the Ukraine
| | - T J Brown
- HPA Mycobacterium Reference Unit, Institute of Cell and Molecular Sciences, Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, London, UK
| | - Y I Bazhora
- Odessa State Medical University, Odessa, the Ukraine
| | - A A Asmolov
- Odessa State Medical University, Odessa, the Ukraine
| | - Y M Balabanova
- HPA Mycobacterium Reference Unit, Institute of Cell and Molecular Sciences, Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, London, UK
| | - F A Drobniewski
- HPA Mycobacterium Reference Unit, Institute of Cell and Molecular Sciences, Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, London, UK.
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Nikolayevskyy V, Gopaul K, Balabanova Y, Brown T, Fedorin I, Drobniewski F. Differentiation of tuberculosis strains in a population with mainly Beijing-family strains. Emerg Infect Dis 2006; 12:1406-13. [PMID: 17073090 PMCID: PMC3294723 DOI: 10.3201/eid1209.041263] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A new panel of 25 VNTR-MIRU loci differentiates Beijing-family TB strains better than a panel of 15. A high prevalence of tuberculosis (TB) isolates that are genetically homogenous and from the Beijing family has been reported in Russia. To map TB transmission caused by these strains, new genotyping systems are needed. Mycobacterial interspersed repetitive units (MIRUs) offer the possibility of rapid PCR-based typing with comparable discrimination to IS6110 restriction fragment length polymorphism techniques. Spoligotyping and detection of IS6110 insertion in the dnaA-dnaN region were used to identify Beijing strains in 187 Mycobacterium tuberculosis isolates from Samara, Russia. The Beijing isolates were analyzed by using 12-MIRU and 3–exact tandem repeats (ETR) loci and by an expanded set of 10 additional variable number tandem repeats loci. The expanded set of 25 MIRUs provided better discrimination than the original set of 15 (Hunter-Gaston diversity index 0.870 vs 0.625). Loci MIRU 26, 1982, and 3232 were the most polymorphic in Beijing isolates.
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Affiliation(s)
| | - Krishna Gopaul
- Barts and the London School of Medicine, University of London, London, United Kingdom
| | - Yanina Balabanova
- Barts and the London School of Medicine, University of London, London, United Kingdom
- Samara Regional Tuberculosis Service, Samara, Russia
| | - Timothy Brown
- Barts and the London School of Medicine, University of London, London, United Kingdom
| | - Ivan Fedorin
- Samara Regional Tuberculosis Service, Samara, Russia
| | - Francis Drobniewski
- Barts and the London School of Medicine, University of London, London, United Kingdom
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Vitol I, Driscoll J, Kreiswirth B, Kurepina N, Bennett KP. Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. INFECTION GENETICS AND EVOLUTION 2006; 6:491-504. [PMID: 16632413 DOI: 10.1016/j.meegid.2006.03.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 03/13/2006] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
We present a novel approach for analysis of Mycobacterium tuberculosis complex (MTC) strain genotyping data. Our work presents a first step in an ongoing project dedicated to the development of decision support tools for tuberculosis (TB) epidemiologists exploiting both genotyping and epidemiological data. We focus on spacer oligonucleotide typing (spoligotyping), a genotyping method based on analysis of a direct repeat (DR) locus. We use mixture models to identify strain families of MTC based on their spoligotyping patterns. Our algorithm, SPOTCLUST, incorporates biological information on spoligotype evolution, without attempting to derive the full phylogeny of MTC. We applied our algorithm to 535 different spoligotype patterns identified among 7166 MTC strains isolated between 1996 and 2004 from New York State TB patients. Two models were employed and validated: a 36-component model based on global spoligotype database SpolDB3, and a randomly initialized model (RIM) containing 48 components. Our analysis both confirmed previously expert-defined families of MTC strains and suggested certain new families. SPOTCLUST, which is available online, can be further improved by incorporating data obtained using additional strain genetic markers and epidemiological information. We demonstrate on New York City (NYC) patient data how the resulting models can potentially form the basis of TB control tools using genotyping.
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Affiliation(s)
- Inna Vitol
- Computer Science Department, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180, USA.
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Colborn JM, Koita OA, Cissé O, Bagayoko MW, Guthrie EJ, Krogstad DJ. Identifying and quantifying genotypes in polyclonal infections due to single species. Emerg Infect Dis 2006; 12:475-82. [PMID: 16704787 PMCID: PMC3291430 DOI: 10.3201/eid1203.05057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The combination of real-time PCR and capillary electrophoresis permits the rapid identification and quantification of pathogen genotypes. Simultaneous infection with multiple pathogens of the same species occurs with HIV, hepatitis C, Epstein-Barr virus, dengue, tuberculosis, and malaria. However, available methods do not distinguish among or quantify pathogen genotypes in individual patients; they also cannot test for novel insertions and deletions in genetically modified organisms. The strategy reported here accomplishes these goals with real-time polymerase chain reaction (PCR) and capillary electrophoresis. Real-time PCR with allotype-specific primers defines the allotypes (strains) present and the intensity of infection (copy number). Capillary electrophoresis defines the number of genotypes within each allotype and the intensity of infection by genotype. This strategy can be used to study the epidemiology of emerging infectious diseases with simultaneous infection by multiple genotypes, as demonstrated here with malaria. It also permits testing for insertions or deletions in genetically modified organisms that may be used for bioterrorism.
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Affiliation(s)
- James M. Colborn
- Tulane University Health Sciences Center, New Orleans, Louisiana, USA
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12
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Mokrousov I, Narvskaya O, Limeschenko E, Vyazovaya A. Efficient discrimination within a Corynebacterium diphtheriae epidemic clonal group by a novel macroarray-based method. J Clin Microbiol 2005; 43:1662-8. [PMID: 15814981 PMCID: PMC1081353 DOI: 10.1128/jcm.43.4.1662-1668.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large diphtheria epidemic in the 1990s in Russia and neighboring countries was caused by a clonal group of closely related Corynebacterium diphtheriae strains (ribotypes Sankt-Peterburg and Rossija). In the recently published complete genome sequence of C. diphtheriae strain NCTC13129, representative of the epidemic clone (A. M. Cerdeno-Tarraga et al., Nucleic Acids Res. 31:6516-6523, 2003), we identified in silico two direct repeat (DR) loci 39 kb downstream and 180 kb upstream of the oriC region, consisting of minisatellite (27- to 36-bp) alternating DRs and variable spacers. We designated these loci DRA and DRB, respectively. A reverse-hybridization macroarray-based method has been developed to study polymorphism (the presence or absence of 21 different spacers) in the larger DRB locus. We name it spoligotyping (spacer oligonucleotide typing), analogously to a similar method of Mycobacterium tuberculosis genotyping. The method was evaluated with 154 clinical strains of the C. diphtheriae epidemic clone from the St. Petersburg area in Russia from 1997 to 2002. By comparison with the international ribotype database (Institut Pasteur, Paris, France), these strains were previously identified as belonging to ribotypes Sankt-Peterburg (n = 79) and Rossija (n = 75). The 154 strains were subdivided into 34 spoligotypes: 14 unique strains and 20 types shared by 2 to 46 strains; the Hunter Gaston discriminatory index (HGDI) was 0.85. DRB locus-based spoligotyping allows fast and efficient discrimination within the C. diphtheriae epidemic clonal group and is applicable to both epidemiological investigations and phylogenetic reconstruction. The results are easy to interpret and can be presented and stored in a user-friendly digital database (Excel file), allowing rapid type determination of new strains.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14, Mira St., St. Petersburg 197101, Russia. [corrected]
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13
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Niobe-Eyangoh SN, Kuaban C, Sorlin P, Thonnon J, Vincent V, Gutierrez MC. Molecular characteristics of strains of the cameroon family, the major group of Mycobacterium tuberculosis in a country with a high prevalence of tuberculosis. J Clin Microbiol 2005; 42:5029-35. [PMID: 15528691 PMCID: PMC525220 DOI: 10.1128/jcm.42.11.5029-5035.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A preliminary investigation of the genetic biodiversity of Mycobacterium tuberculosis complex strains in Cameroon, a country with a high prevalence of tuberculosis, described a group of closely related M. tuberculosis strains (the Cameroon family) currently responsible for more than 40% of smear-positive pulmonary tuberculosis cases. Here, we used various molecular methods to study the genetic characteristics of this family of strains. Cameroon family M. tuberculosis strains (i) are part of the major genetic group 2 and lack the TbD1 region like other families of epidemic strains, (ii) lack spacers 23, 24, and 25 in their direct repeat (DR) region, (iii) have an identical number of repeats in 8 of 12 variable-number tandem repeats of mycobacterial interspersed repetitive unit (MIRU-VNTR) loci, (iv) have similar IS6110-restriction fragment length polymorphism (RFLP) multiband patterns (10 to 15 copies) with seven common IS6110 bands, (v) do not have an IS6110 element in their DR locus, and (vi) have four IS6110 elements in open reading frames (adenylate cyclase, phospholipase C, moeY, and ATP binding genes). Analysis by spoligotyping, MIRU-VNTR, and IS6110-RFLP typing methods revealed differences not observed in previous studies; polymorphism as assessed by MIRU-VNTR typing was lower than suggested by spoligotyping, and in rare cases, strains with identical IS6110-RFLP patterns had spoligotypes differing by as much as 15 spacers. Our findings confirm the recent expansion of this family in Cameroon and indicate that the interpretation of molecular typing results has to be adapted to the characteristics of the strain population within each setting. The knowledge of this particular genotype, with its large involvement in tuberculosis in Cameroon, allows greater refinement of tuberculosis transmission studies by interpreting data in the context of this geographic area.
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Affiliation(s)
- Sara Ngo Niobe-Eyangoh
- Centre National de Référence des Mycobactéries, Institut Pasteur, 25 rue du Dr Roux, 75724 Cedex 15, Paris, France
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Kremer K, Glynn JR, Lillebaek T, Niemann S, Kurepina NE, Kreiswirth BN, Bifani PJ, van Soolingen D. Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers. J Clin Microbiol 2004; 42:4040-9. [PMID: 15364987 PMCID: PMC516354 DOI: 10.1128/jcm.42.9.4040-4049.2004] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2003] [Revised: 01/13/2004] [Accepted: 05/18/2004] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis Beijing genotype strains are highly prevalent in Asian countries and in the territory of the former Soviet Union. They are increasingly reported in other areas of the world and are frequently associated with tuberculosis outbreaks and drug resistance. Beijing genotype strains, including W strains, have been characterized by their highly similar multicopy IS6110 restriction fragment length polymorphism (RFLP) patterns, deletion of spacers 1 to 34 in the direct repeat region (Beijing spoligotype), and insertion of IS6110 in the genomic dnaA-dnaN locus. In this study the suitability and comparability of these three genetic markers to identify members of the Beijing lineage were evaluated. In a well-characterized collection of 1,020 M. tuberculosis isolates representative of the IS6110 RFLP genotypes found in The Netherlands, strains of two clades had spoligotypes characteristic of the Beijing lineage. A set of 19 Beijing reference RFLP patterns was selected to retrieve all Beijing strains from the Dutch database. These reference patterns gave a sensitivity of 98.1% and a specificity of 99.7% for identifying Beijing strains (defined by spoligotyping) in an international database of 1,084 strains. The usefulness of the reference patterns was also assessed with large DNA fingerprint databases in two other European countries and for identification strains from the W lineage found in the United States. A standardized definition for the identification of M. tuberculosis strains belonging to the Beijing/W lineage, as described in this work, will facilitate further studies on the spread and characterization of this widespread genotype family of M. tuberculosis strains.
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Affiliation(s)
- Kristin Kremer
- Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
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15
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Mokrousov I, Narvskaya O, Limeschenko E, Vyazovaya A, Otten T, Vyshnevskiy B. Analysis of the allelic diversity of the mycobacterial interspersed repetitive units in Mycobacterium tuberculosis strains of the Beijing family: practical implications and evolutionary considerations. J Clin Microbiol 2004; 42:2438-44. [PMID: 15184416 PMCID: PMC427846 DOI: 10.1128/jcm.42.6.2438-2444.2004] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A study set comprised 44 Mycobacterium tuberculosis strains of the Beijing family selected for their representativeness among those previously characterized by IS6110-RFLP and spoligotyping (Northwest Russia, 1997 to 2003). In the present study, these strains were subjected to mycobacterial interspersed repetitive units (MIRU) typing to assess a discriminatory power of the 12-MIRU-loci scheme (P. Supply et al., J. Clin. Microbiol. 39:3563-3571, 2001). The 44 Russian Beijing strains were subdivided into 12 MIRU types with identical profiles: 10 unique strains and two major types shared by 10 and 24 strains. Thus, basically, two distinct sublineages appear to shape the evolution of the Beijing strains in Russia. Most of the MIRU loci were found to be (almost) monomorphic in the Russian Beijing strains; the Hunter-Gaston discriminatory index (HGDI) for all 12 loci taken together was 0.65, whereas MIRU26 (the most variable in our study) showed a moderate level of discrimination (0.49). The results were compared against all available published MIRU profiles of Beijing strains from Russia (3 strains) and other geographic areas (51 strains in total), including South Africa (38 strains), East Asia (7 strains), and the United States (4 strains). A UPGMA (unweighted pair-group method with arithmetic averages)-based tree was constructed. Interestingly, no MIRU types were shared by Russian and South African strains (the two largest samples in this analysis), whereas both major Russian types included also isolates from other locations (United States and/or East Asia). This implies the evolution of the Beijing genotype to be generally strictly clonal, although a possibility of a convergent evolution of the MIRU loci cannot be excluded. We propose a dissemination of the prevailing local Beijing clones to have started earlier in South Africa rather than in Russia since more monomorphic loci were identified in Russian samples than in South African samples (mean HGDI scores, 0.08 versus 0.17). To conclude, we suggest to use a limited number of MIRUs for preliminary subdivision of Beijing strains in Russian (loci 26 + 31), South African (10 + 26 + 39), and global settings (10 + 26 + 39).
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Affiliation(s)
- Igor Mokrousov
- Pasteur Institute, 14, Mira St., St. Petersburg 197101, Russia.
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16
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Mokrousov I, Otten T, Vyazovaya A, Limeschenko E, Filipenko ML, Sola C, Rastogi N, Steklova L, Vyshnevskiy B, Narvskaya O. PCR-based methodology for detecting multidrug-resistant strains of Mycobacterium tuberculosis Beijing family circulating in Russia. Eur J Clin Microbiol Infect Dis 2003; 22:342-8. [PMID: 12783278 DOI: 10.1007/s10096-003-0944-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Beijing genotype of Mycobacterium tuberculosis has been identified in 40-50% of the clinical isolates studied in Russia during the last decade. This genotype has been reported to be associated with multiple drug resistance and possesses some significant pathogenic properties. Therefore, early identification of such strains is of extreme importance in the timely detection of drug resistance. The present study was performed on 354 strains isolated in Russia from 1996 to 2002 and previously characterised by IS 6110-restriction fragment length polymorphism (RFLP) typing and spoligotyping. These strains included 198 Beijing family strains and 156 strains of other genotypes (IS 6110-RFLP profiles). A subsequent polymerase chain reaction (PCR) analysis with IS 6110-derived outwardly oriented primers (IS 6110-PCR) easily discriminated the Beijing strains from non-Beijing strains. The multiplex allele-specific (MAS)-PCR assays were further used to detect mutations in katG315 and rpoB531, associated with resistance to isoniazid and rifampin, respectively. The katG315 and rpoB531 mutations were found to be more prevalent among Beijing (96.8% and 77.3%) than among non-Beijing strains (85.7% and 28%). Consequently, we propose a two-step methodology based on routine PCR and simple agarose gel electrophoresis in order to detect (i) a Beijing family strain using IS 6110-PCR, and, (ii) its possible resistance to the major anti-tuberculosis drugs using specific MAS-PCR assays.
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Affiliation(s)
- I Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira Street, 197101 St. Petersburg, Russia.
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Warren RM, Streicher EM, Sampson SL, van der Spuy GD, Richardson M, Nguyen D, Behr MA, Victor TC, van Helden PD. Microevolution of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. J Clin Microbiol 2002; 40:4457-65. [PMID: 12454136 PMCID: PMC154636 DOI: 10.1128/jcm.40.12.4457-4465.2002] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The direct repeat (DR) region has been determined to be an important chromosomal domain for studying the evolution of Mycobacterium tuberculosis. Despite this, very little is known about microevolutionary events associated with clonal expansion and how such events influence the interpretation of both restriction fragment length polymorphism (RFLP) and spoligotype data. This study examined the structure of the DR region in three independently evolving lineages of M. tuberculosis with a combination of DR-RFLP, spoligotyping, and partial DNA sequencing. The results show that the duplication of direct variable repeat (DVR) sequences and single-nucleotide polymorphisms is rare; conversely, the deletion of DVR sequences and IS6110-mediated mutation is observed frequently. Deletion of either single or contiguous DVR sequences was observed. The deletion of adjacent DVR sequences occurred in a dependent manner rather than as an accumulation of independent events. Insertion of IS6110 into either the direct repeat or spacer sequences influenced the spoligotype pattern, resulting in apparent deletion of DVR sequences. Homologous recombination between adjacent IS6110 elements led to extensive deletion in the DR region, again demonstrating a dependent evolutionary mechanism. Different isolates from the same strain family and isolates from different strain families were observed to converge to the same spoligotype pattern. In conclusion, the binary data of the spoligotype are unable to provide sufficient information to accurately establish genotypic relationships between certain clinical isolates of M. tuberculosis. This has important implications for molecular epidemiologic strain tracking and for the application of spoligotype data to phylogenetic analysis of M. tuberculosis isolates.
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Affiliation(s)
- R. M. Warren
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - E. M. Streicher
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - S. L. Sampson
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - G. D. van der Spuy
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - M. Richardson
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - D. Nguyen
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - M. A. Behr
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - T. C. Victor
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - P. D. van Helden
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
- Corresponding author. Mailing address: MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa. Phone: 27 21 9389401. Fax: 27 21 9389467. E-mail:
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