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Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR. Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system. eLife 2019; 8:e45833. [PMID: 31843054 PMCID: PMC6917503 DOI: 10.7554/elife.45833] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023] Open
Abstract
Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown. In Britain, the role of badgers in infection persistence in cattle is highly contentious, despite decades of research and control efforts. We applied Bayesian phylogenetic and machine-learning approaches to bacterial genome data to quantify the roles of badgers and cattle in M. bovis infection dynamics in the presence of data biases. Our results suggest that transmission occurs more frequently from badgers to cattle than vice versa (10.4x in the most likely model) and that within-species transmission occurs at higher rates than between-species transmission for both. If representative, our results suggest that control operations should target both cattle and badgers.
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Affiliation(s)
- Joseph Crispell
- School of Veterinary Medicine, Veterinary Sciences CentreUniversity College DublinDublinIreland
| | - Clare H Benton
- National Wildlife Management CentreAnimal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Daniel Balaz
- Roslin InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)CambridgeUnited Kingdom
| | - Assel Ahkmetova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Adrian Allen
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Eleanor L Presho
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | - James Dale
- Animal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Glyn Hewinson
- Centre for Bovine Tuberculosis, Institute of Biological, Environmental and Rural SciencesUniversity of AberystwythAberystwythUnited Kingdom
| | | | | | - Robin A Skuce
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | | | - Daniel J Wilson
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population HealthUniversity of OxfordOxfordUnited Kingdom
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Richard J Delahay
- National Wildlife Management CentreAnimal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Rowland Raymond Kao
- Roslin InstituteUniversity of EdinburghEdinburghUnited Kingdom
- Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUnited Kingdom
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Kalo D, Kant S, Srivastava K, Sharma AK. Assess drug resistance pattern and genetic profile of Mycobacterium tuberculosis clinical isolates by molecular typing methods using direct repeats and IS6110 in pulmonary tuberculosis cases. Lung India 2017; 34:155-159. [PMID: 28360464 PMCID: PMC5351358 DOI: 10.4103/0970-2113.201314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background: Tuberculosis (TB), a highly contagious disease that sees no gender, age, or race is mainly a disease of lungs. According to World Health Organization, a TB patient can be completely cured with 6–9 months of anti-TB treatment under directly observed treatment short course. Objectives: The aim of this study was to check the mono, multi- and triple-drug resistance to first line drugs (FLDs) among TB patients and to access their genetic profile using DR 3074, DR 0270, DR 0642, DR 2068, and DR 4110 using molecular techniques. Material and Methods: To gain a better understanding of drug resistant TB, we characterized 121 clinical isolates recovered from 159 drug resistant pulmonary tuberculosis patients by IS6110 genotyping. MTB isolates recovered from HIV- negative, and smear positive cases of both genders, age varied from 18 to 70 years with drug resistant-TB that was refractory to chemotherapy given for > 12 months. Of a total of 159 sputum smear positive patients sum number of male and female patients was 121 (76.10%) and 38 (23.89%), respectively. Among these patients, number of literate and illiterate patients were 123 (77.3%) and 36 (22.6%). 25 (15.7%) patients had farming as their occupation, 80 (50.3%) had nonagricultural occupation and 54 (33.9%) women were housewives. Results: Mono drug resistant, multi-drug resistant, and totally drug resistant (TDR) cases of TB were calculated as 113.83%, 125.1%, and 67.9%. Isoniazid showed the highest percentage of resistance among the patients. Conclusion: Any noncompliance to TB medications, lack of knowledge, and poor management in health centers, etc., results in the emergence of deadly direct repeat forms of TB, which are further complicated and complex to treat.
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Affiliation(s)
- Deepika Kalo
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Kanchan Srivastava
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Ajay K Sharma
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, India
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3
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Bacteriological diagnosis and molecular strain typing of Mycobacterium bovis and Mycobacterium caprae. Res Vet Sci 2014; 97 Suppl:S30-43. [DOI: 10.1016/j.rvsc.2014.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 04/08/2014] [Accepted: 04/24/2014] [Indexed: 11/24/2022]
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Ramos DF, Tavares L, da Silva PEA, Dellagostin OA. Molecular typing of Mycobacterium bovis isolates: a review. Braz J Microbiol 2014; 45:365-72. [PMID: 25242917 PMCID: PMC4166258 DOI: 10.1590/s1517-83822014005000045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 09/09/2013] [Indexed: 01/21/2023] Open
Abstract
Mycobacterium bovis is the main causative agent of animal tuberculosis (TB) and it may cause TB in humans. Molecular typing of M. bovis isolates provides precise epidemiological data on issues of inter- or intra-herd transmission and wildlife reservoirs. Techniques used for typing M. bovis have evolved over the last 2 decades, and PCR-based methods such as spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) have been extensively used. These techniques can provide epidemiological information about isolates of M. Bovis that may help control bovine TB by indicating possible links between diseased animals, detecting and sampling outbreaks, and even demonstrating cases of laboratory cross-contamination between samples. This review will focus on techniques used for the molecular typing of M. bovis and discuss their general aspects and applications.
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Affiliation(s)
- Daniela Fernandes Ramos
- Núcleo de Biotecnologia Universidade Federal de Pelotas PelotasRS Brazil Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Lucas Tavares
- Núcleo de Biotecnologia Universidade Federal de Pelotas PelotasRS Brazil Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Pedro Eduardo Almeida da Silva
- Faculdade de Medicina Universidade Federal de Rio Grande Rio GrandeRS Brazil Faculdade de Medicina, Universidade Federal de Rio Grande, Rio Grande, RS, Brazil
| | - Odir Antônio Dellagostin
- Núcleo de Biotecnologia Universidade Federal de Pelotas PelotasRS Brazil Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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Garbaccio S, Macias A, Shimizu E, Paolicchi F, Pezzone N, Magnano G, Zapata L, Abdala A, Tarabla H, Peyru M, Caimi K, Zumárraga M, Canal A, Cataldi A. Association between spoligotype-VNTR types and virulence of Mycobacterium bovis in cattle. Virulence 2014; 5:297-302. [PMID: 24398919 DOI: 10.4161/viru.27193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium bovis is the causative agent of bovine tuberculosis, a disease that affects approximately 5% of Argentine cattle. The aim of this research was to study if it is possible to infer the degree of virulence of different M. bovis genotypes based on scorified observations of tuberculosis lesions in cattle. In this study, we performed association analyses between several parameters with tuberculosis lesions: M. bovis genotype, degree of progression of tuberculosis, and animal age. For this purpose, the genotype was determined by spoligotyping and the degree of bovine tuberculosis gross lesion was quantified with a score based on clinical observations (number, size, and location of granulomas along with histopathologic features). This study was performed with naturally infected cattle of slaughterhouses from three provinces in Argentina. A total of 265 M. bovis isolates were obtained from 378 pathological lesion samples and 192 spoligotyping and VNTR (based on ETR sequences) typing patterns were obtained. SB0140 was the most predominant spoligotype, followed by SB0145. The spoligotype with the highest lesion score was SB0273 (median score of 27 ± 4.46), followed by SB0520 (18 ± 5.8). Furthermore, the most common spoligotype, SB0140, had a median score of 11 ± 0.74. Finally, the spoligotype with the lowest score was SB0145 (8 ± 1.0). ETR typing of SB0140, SB0145, SB0273, and SB0520 did not subdivide the lesion scores in those spoligotypes. In conclusion, SB0273 and SB0520 were the spoligotypes with the strongest association with hypervirulence and both spoligotypes were only found in Río Cuarto at the south of Córdoba province. Interestingly, there is no other report of any of these spoligotyes in Latin America.
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Affiliation(s)
- Sergio Garbaccio
- Pathobiology Institute; CICVyA-INTA; Castelar, Buenos Aires, Argentina
| | - Analía Macias
- School of Agronomy and Veterinary; National University of Río Cuarto; Córdoba, Argentina
| | - Ernesto Shimizu
- Bacteriology Laboratory; EEA-INTA Balcarce; School of Agricultural Sciences; National University of Mar del Plata; Buenos Aires, Argentina
| | - Fernando Paolicchi
- Bacteriology Laboratory; EEA-INTA Balcarce; School of Agricultural Sciences; National University of Mar del Plata; Buenos Aires, Argentina
| | - Natalia Pezzone
- Department of Basic Pathology; School of Veterinaries Sciences; National University of the Littoral; Santa Fe, Argentina
| | - Gabriel Magnano
- School of Agronomy and Veterinary; National University of Río Cuarto; Córdoba, Argentina
| | - Laura Zapata
- School of Agronomy and Veterinary; National University of Río Cuarto; Córdoba, Argentina
| | | | | | - Maite Peyru
- General Direction of Animal Production; Secretary of Production; Entre Ríos, Argentina
| | - Karina Caimi
- Biotechnology Institute; CICVyA-INTA; Castelar, Buenos Aires, Argentina
| | - Martín Zumárraga
- Biotechnology Institute; CICVyA-INTA; Castelar, Buenos Aires, Argentina
| | - Ana Canal
- Department of Basic Pathology; School of Veterinaries Sciences; National University of the Littoral; Santa Fe, Argentina
| | - Angel Cataldi
- Biotechnology Institute; CICVyA-INTA; Castelar, Buenos Aires, Argentina
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6
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Genotypic characterization by spoligotyping and VNTR typing of Mycobacterium bovis and Mycobacterium caprae isolates from cattle of Tunisia. Trop Anim Health Prod 2013; 46:305-11. [PMID: 24158359 DOI: 10.1007/s11250-013-0488-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
This work is an approach to the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) bovine infections in Tunisia. A total of 35 MTBC isolates from both lateral retropharyngeal lymph node samples of cattle slaughtered in different Tunisian regions were genotyped by spoligotyping and variable number tandem repeat typing (VNTR)-typing. Spoligotyping allowed to identify two profiles not previously registered, namely SB2024, a Mycobacterium caprae isolate from Nabeul Region (North East Tunisia), the first description of this species in the country, and SB2025 (Mycobacterium bovis) from Sfax Region (Southern Tunisia). A second M. caprae isolate with a spoligotyping profile previously described in Europe mainland, SB0418, was also isolated from a bovine of Sfax region. Both isolates suggest the possibility of a widespread distribution of this species in the country. The predominant spoligotype was SB0120, present in all Tunisian regions selected for the study but Nabeul. Molecular typing also allowed to describe a mixed infection caused by two different M. bovis isolates (SB0120 and SB0848) in the same animal. VNTR typing was highly discriminant by testing a panel of six loci. Loci QUB3232 and QUB11b were the most discriminant, whereas ETR-D and QUB11a had the lower diversity index. The value of allelic diversity can significantly vary among countries; thus, it is important to standardize a panel of loci for future inter-laboratory comparisons. Although VNTR typing proved to be useful for an efficient discrimination among MTBC isolates, especially in combination with spoligotyping, further studies are needed in order to assess the genetic diversity of the MTBC in Tunisia.
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8
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Rodríguez S, Romero B, Bezos J, de Juan L, Álvarez J, Castellanos E, Moya N, Lozano F, González S, Sáez-Llorente JL, Mateos A, Domínguez L, Aranaz A. High spoligotype diversity within a Mycobacterium bovis population: Clues to understanding the demography of the pathogen in Europe. Vet Microbiol 2010; 141:89-95. [PMID: 19720476 DOI: 10.1016/j.vetmic.2009.08.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 07/09/2009] [Accepted: 08/03/2009] [Indexed: 10/20/2022]
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9
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Jeon BY, Je S, Park J, Kim Y, Lee EG, Lee H, Seo S, Cho SN. Variable number tandem repeat analysis of Mycobacterium bovis isolates from Gyeonggi-do, Korea. J Vet Sci 2008; 9:145-53. [PMID: 18487935 PMCID: PMC2839091 DOI: 10.4142/jvs.2008.9.2.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine tuberculosis (TB) is a major zoonosis that's caused by Mycobacterium bovis (M. bovis). Being able to detect M. bovis is important to control bovine TB. We applied a molecular technique, the variable number tandem repeat (VNTR) typing method, to identify and distinguish the M. bovis isolates from Gyeonggi-do, Korea. From 2003 to 2004, 59 M. bovis clinical strains were isolated from dairy cattle in Gyeonggi-do, Korea, and these cattle had tuberculosis- like lesions. Twenty-four published MIRUVNTR markers were applied to the M. bovis isolates and ten of them showed allelic diversity. The most discriminatory locus for the M. bovis isolates in Korea was QUB 3336 (h = 0.64). QUB 26 and MIRU 31 also showed high discriminative power (h = 0.35). The allelic diversity by the combination of all VNTR loci was 0.86. Six loci (MIRU 31, ETR-A and QUB-18, -26, -3232, -3336) displayed valuable allelic diversity. Twelve genotypes were identified from the 59 M. bovis isolates that originated from 20 cattle farms that were dispersed throughout the region of Gyenggi-do. Two genotypes [designation index (d.i.) = e, g] showed the highest prevalence (20% of the total farms). For the multiple outbreaks on three farms, two successive outbreaks were caused by the same genotype at two farms. Interestingly, the third outbreak at one farm was caused by both a new genotype and a previous genotype. In conclusion, this study suggests that MIRU-VNTR typing is useful to identify and distinguish the M. bovis isolates from Gyeonggi-do, Korea.
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Affiliation(s)
- Bo- Young Jeon
- Department of Microbiology and the Brain Korea 21 Project for the Medical Sciences, Yonsei University College of Medicine, Seoul 120-752, Korea
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10
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Javed MT, Aranaz A, de Juan L, Bezos J, Romero B, Alvarez J, Lozano C, Mateos A, Domínguez L. Improvement of spoligotyping with additional spacer sequences for characterization of Mycobacterium bovis and M. caprae isolates from Spain. Tuberculosis (Edinb) 2007; 87:437-45. [PMID: 17569586 DOI: 10.1016/j.tube.2007.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Revised: 04/19/2007] [Accepted: 04/21/2007] [Indexed: 11/24/2022]
Abstract
Spoligotyping is a typing tool used worldwide for epidemiological studies on Mycobacterium tuberculosis complex organisms; however it has received little attention regarding improvement of its discriminatory power (DP). In this study, we have evaluated a spoligotyping membrane prepared with 25 novel spacer sequences selected from a previous study [van der Zanden AG, Kremer K, Schouls LM. Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides. J Clin Microbiol 2002;40:4628-39] on 308 M. bovis and 88 M. caprae Spanish isolates in comparison with the traditional spoligotyping membrane. The results obtained by combining the two membranes together revealed an improvement of 45 patterns instead of 31. The spacers used in the second membrane were able to distinguish 8 out of the 16 M. bovis types that had more than one isolate. Seven of these types were differentiated into two subtypes with the second-generation membrane, while spb-7, the most prevalent in Spain, was further differentiated into eight subtypes. This second-generation membrane also differentiates M. bovis from M. caprae. A set of 39 spacers (1, 2, 4-8, 10-15, 17-21, 23, 26-32, 37, 44-49, 51-54, 56 and 57) contain all the DP for both M. bovis and M. caprae isolates; and a set of 35 spacers (1, 2, 4-8, 10-15, 17-21, 26-32, 37, 44-48, 52-54 and 57) had all the DP for the M. bovis isolates. Our results show that the research on new spacers and the design of a new membrane may be useful for epidemiological studies of M. bovis and M. caprae isolates.
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Affiliation(s)
- M Tariq Javed
- Grupo de Vigilancia Sanitaria Veterinaria, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
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11
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Romero B, Aranaz A, de Juan L, Alvarez J, Bezos J, Mateos A, Gómez-Mampaso E, Domínguez L. Molecular epidemiology of multidrug-resistant Mycobacterium bovis isolates with the same spoligotyping profile as isolates from animals. J Clin Microbiol 2006; 44:3405-8. [PMID: 16954286 PMCID: PMC1594710 DOI: 10.1128/jcm.00730-06] [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
PCR-based characterization techniques have been adopted in most laboratories for Mycobacterium bovis typing. We report a molecular characterization of human multidrug-resistant M. bovis isolates and three bovine isolates that share the spoligotyping profile. The analysis of the direct repeat region showed that both groups differed in the presence of spacers not included in the current membrane. They were also distinguished by two out of the nine mycobacterial interspersed repetitive unit variable-number tandem repeat loci tested, indicating that the human infection was not acquired from the cattle from which isolates were obtained. These results highlight that a combination of techniques is required for appropriate discrimination, even for those spoligotypes that have a low frequency.
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Affiliation(s)
- Beatriz Romero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
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12
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Kremer K, Arnold C, Cataldi A, Gutiérrez MC, Haas WH, Panaiotov S, Skuce RA, Supply P, van der Zanden AGM, van Soolingen D. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 2005; 43:5628-38. [PMID: 16272496 PMCID: PMC1287774 DOI: 10.1128/jcm.43.11.5628-5638.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/18/2005] [Accepted: 06/23/2005] [Indexed: 11/20/2022] Open
Abstract
In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.
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Affiliation(s)
- Kristin Kremer
- Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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13
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Gori A, Bandera A, Marchetti G, Degli Esposti A, Catozzi L, Nardi GP, Gazzola L, Ferrario G, van Embden JDA, van Soolingen D, Moroni M, Franzetti F. Spoligotyping and Mycobacterium tuberculosis. Emerg Infect Dis 2005. [PMID: 16102314 PMCID: PMC3320497 DOI: 10.3201/1108.040982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Speed of spoligotyping could be a benefit in the clinical setting. We evaluated the clinical usefulness of spoligotyping, a polymerase chain reaction–based method for simultaneous detection and typing of Mycobacterium tuberculosis strains, with acid-fast bacilli–positive slides from clinical specimens or mycobacterial cultures. Overall sensitivity and specificity were 97% and 95% for the detection of M. tuberculosis and 98% and 96% when used with clinical specimens. Laboratory turnaround time of spoligotyping was less than that for culture identification by a median of 20 days. In comparison with IS6110-based restriction fragment length polymorphism typing, spoligotyping overestimated the number of isolates with identical DNA fingerprints by ≈50%, but showed a 100% negative predictive value. Spoligotyping resulted in the modification of ongoing antimycobacterial treatment in 40 cases and appropriate therapy in the absence of cultures in 11 cases. The rapidity of this method in detection and typing could make it useful in the management of tuberculosis in a clinical setting.
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Affiliation(s)
- Andrea Gori
- Institute of Infectious Diseases, L. Sacco Hospital, University of Milan, Milan, Italy.
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14
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Gori A, Esposti AD, Bandera A, Mezzetti M, Sola C, Marchetti G, Ferrario G, Salerno F, Goyal M, Diaz R, Gazzola L, Codecasa L, Penati V, Rastogi N, Moroni M, Franzetti F. Comparison between spoligotyping and IS6110 restriction fragment length polymorphisms in molecular genotyping analysis of Mycobacterium tuberculosis strains. Mol Cell Probes 2005; 19:236-44. [PMID: 16038791 DOI: 10.1016/j.mcp.2005.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Accepted: 01/05/2005] [Indexed: 11/23/2022]
Abstract
Spoligotyping was compared with RFLP fingerprinting analysis in the identification of Mycobacterium tuberculosis strains. Spoligotyping sensitivity was 97.6% with a specificity of 47%. The global probability for two strains clustered with spoligotyping to be clustered also with RFLP analysis was 33%; the probability for two strains clustered with RFLP analysis to be clustered also with spoligotyping analysis was 95%. However, comparing the two methods in five outbreak episodes, full concordance was evidenced between spoligotyping and RFLP. Moreover, we evaluated the presence of our 17 largest spoligotyping clusters in spoligotyping databases from Caribbean countries, London and Cuba. Only five out of 17 patterns were present in all the cohorts. The conditional probability comparing spoligotyping and RFLP methods related to these patterns resulted in very low concordance (range from 2 to 38%). In conclusion, we confirm that spoligotyping when used alone overestimates the number of recent transmission and does not represent a suitable method for wide clinical practice application. However, it allows to get a first good picture of strain identity in a new setting and in more localized or confined settings, the probability of reaching the same result compared to RFLP was 100% confirming the usefulness of spoligotyping in the management of epidemic events, especially in hospitals, prisons and close communities.
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Affiliation(s)
- Andrea Gori
- Institute of Infectious Diseases and Tropical Medicine, Luigi Sacco Hospital, University of Milan, Via G.B.Grassi 74, Milan 20157, Italy.
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15
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Gori A, Bandera A, Marchetti G, Degli Esposti A, Catozzi L, Nardi GP, Gazzola L, Ferrario G, van Embden JDA, van Soolingen D, Moroni M, Franzetti F. Spoligotyping andMycobacterium tuberculosis. Emerg Infect Dis 2005; 11:1242-8. [PMID: 16102314 PMCID: PMC3320497 DOI: 10.3201/eid1108.040982] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We evaluated the clinical usefulness of spoligotyping, a polymerase chain reaction-based method for simultaneous detection and typing of Mycobacterium tuberculosis strains, with acid-fast bacilli-positive slides from clinical specimens or mycobacterial cultures. Overall sensitivity and specificity were 97% and 95% for the detection of M. tuberculosis and 98% and 96% when used with clinical specimens. Laboratory turnaround time of spoligotyping was less than that for culture identification by a median of 20 days. In comparison with IS6110-based restriction fragment length polymorphism typing, spoligotyping overestimated the number of isolates with identical DNA fingerprints by approximately 50%, but showed a 100% negative predictive value. Spoligotyping resulted in the modification of ongoing antimycobacterial treatment in 40 cases and appropriate therapy in the absence of cultures in 11 cases. The rapidity of this method in detection and typing could make it useful in the management of tuberculosis in a clinical setting.
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Affiliation(s)
- Andrea Gori
- Institute of Infectious Diseases, L. Sacco Hospital, University of Milan, Milan, Italy.
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Warren RM, Victor TC, Streicher EM, Richardson M, van der Spuy GD, Johnson R, Chihota VN, Locht C, Supply P, van Helden PD. Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers. J Clin Microbiol 2005; 42:5774-82. [PMID: 15583312 PMCID: PMC535222 DOI: 10.1128/jcm.42.12.5774-5782.2004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the clonal expansion of Mycobacterium tuberculosis and accurate identification of predominant evolutionary lineages in this species remain limited, especially with regard to low-IS6110-copy-number strains. In this study, 170 M. tuberculosis isolates with </=6 IS6110 insertions identified in Cape Town, South Africa, were characterized by principal genetic grouping, restriction fragment length polymorphism analysis, spoligotyping, IS6110 insertion site mapping, and variable-number tandem repeat (VNTR) typing. These analyses indicated that all but one of the isolates analyzed were members of principal genetic group 2 and of the same low-IS6110-copy-number lineage. The remaining isolate was a member of principal genetic group 1 and a different low-IS6110-copy-number lineage. Phylogenetic reconstruction suggests clonal expansion through sequential acquisition of additional IS6110 copies, expansion and contraction of VNTR sequences, and the deletion of specific direct-variable-repeat sequences. Furthermore, comparison of the genotypic data of 91 representative low-IS6110-copy-number isolates from Cape Town, other southern African regions, Europe, and the United States suggests that certain low-IS6110-copy-number strain spoligotypes and IS6110 fingerprints were acquired in the distant past. These clones have subsequently become widely disseminated and now play an important role in the global tuberculosis epidemic.
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Affiliation(s)
- R M Warren
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, University of Stellenbosch, P.O. Box 19063, Tygerberg, 7505, South Africa.
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17
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Aranaz A, De Juan L, Montero N, Sánchez C, Galka M, Delso C, Alvarez J, Romero B, Bezos J, Vela AI, Briones V, Mateos A, Domínguez L. Bovine tuberculosis (Mycobacterium bovis) in wildlife in Spain. J Clin Microbiol 2004; 42:2602-8. [PMID: 15184440 PMCID: PMC427808 DOI: 10.1128/jcm.42.6.2602-2608.2004] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium bovis infection in wildlife and feral species is a potential source of infection for livestock and a threat to protected and endangered species. The aim of this study was to identify Spanish wild animal species infected with M. bovis through bacteriological culture and spacer oligonucleotide typing (spoligotyping) of isolates for epidemiological purposes. This study included samples from red deer (Cervus elaphus), fallow deer (Dama dama), wild boar (Sus scrofa), Iberian lynx (Lynx pardina), hare (Lepus europaeus), and cattle (Bos taurus). They were collected in several geographical areas that were selected for their unique ecological value and/or known relationships between wildlife and livestock. In the areas included in this survey, M. bovis strains with the same spoligotyping pattern were found infecting several wild species and livestock, which indicates an epidemiological link. A locally predominant spoligotype was found in these areas. Better understanding of the transmission and distribution of disease in these populations will permit more precise targeting of control measures.
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Affiliation(s)
- Alicia Aranaz
- Departamento de Sanidad Animal, Facultad de Veterinaria, U.C.M., Av. Puerta de Hierro s/n, 28040 Madrid, Spain.
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18
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19
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Parra A, Fernández-Llario P, Tato A, Larrasa J, García A, Alonso JM, Hermoso de Mendoza M, Hermoso de Mendoza J. Epidemiology of Mycobacterium bovis infections of pigs and wild boars using a molecular approach. Vet Microbiol 2003; 97:123-33. [PMID: 14637044 DOI: 10.1016/j.vetmic.2003.08.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A molecular epidemiological approach was applied to establishing a possible role for the wild boar as a natural reservoir of Mycobacterium bovis in Sierra de Villuercas, Western Spain; an area free of farmed cattle and wild deer populations. Spoligo and VNTR typing were used over a three year period to study the epidemiological relationship between the occurrence of bovine tuberculosis (TB) in extensively bred Iberian pigs and indigenous wild boar. The 37 sampled wild boar showed different degree of calcified granulomatous lesions in retropharyngeal, mediastinal and pulmonary lymph nodes. The 25 sampled Iberian pigs showed calcified lesions, mainly in the respiratory tract. Lesions located in the mesenteric lymph nodes appeared secondarily. M. bovis was isolated from all affected animals. Twenty-five and 37 isolates of M. bovis were obtained from domestic pigs and wild boar, respectively. Our findings provide evidence that supports the possibility of cross infection between wild boar and domestic pig populations. This is contrary to the generally held belief that swine represent an epidemiological dead end host and play no role in the epidemiology of M. bovis.
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Affiliation(s)
- A Parra
- Cátedra de Patología Infecciosa y Epidemiología, Departamento de Medicina y Sanidad Animal, Facultad de Veterinaria de Cáceres, UEX, Avda. de la Universidad s/n, 10071 Cáceres, Spain.
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20
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Roring S, Scott A, Brittain D, Walker I, Hewinson G, Neill S, Skuce R. Development of variable-number tandem repeat typing of Mycobacterium bovis: comparison of results with those obtained by using existing exact tandem repeats and spoligotyping. J Clin Microbiol 2002; 40:2126-33. [PMID: 12037076 PMCID: PMC130792 DOI: 10.1128/jcm.40.6.2126-2133.2002] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Various genetic markers have been exploited for fingerprinting the Mycobacterium tuberculosis complex (MTBC) in molecular epidemiological studies, mainly through identifying restriction fragment length polymorphisms (RFLP). In large-scale studies, RFLP typing has practical processing and analysis limitations; therefore, attempts have been made to move towards PCR-based typing techniques. Spoligotyping (spacer oligotyping) and, more recently, variable-number tandem repeat (VNTR) typing have provided PCR-derived typing techniques. This study describes the identification and characterization of novel VNTR loci, consisting of tandem repeats in the size range of 53 to 59 bp in the MTBC, and their assessment as typing tools in 47 Mycobacterium bovis field isolates and nine MTBC strains. Spoligotyping and the previously described set of exact tandem repeats (ETRs) (R. Frothingham and W. A. Meeker-O'Connell, Microbiology 144:1189-1196, 1998) were also applied to the same panel of isolates. The allelic diversity of the individual VNTR loci was calculated, and a comparison of the novel VNTRs was made against the results obtained by spoligotyping and the existing set of ETRs. Eleven unique spoligotypes were discriminated in the panel of 47 M. bovis isolates. Greater resolution was obtained through the combination of the most-discriminating VNTRs from both sets. Considerable discrimination was achieved, with the 47 M. bovis isolates resolved into 14 unique profiles, while all nine MTBC isolates were uniquely differentiated. The novel VNTR markers described increased the discrimination possible in strain typing of M. bovis, with the added benefit of an intuitive digital nomenclature, with the allele copy number of the individual VNTRs providing a profile. VNTR typing was shown to be a valuable technique with great potential for further development and application to epidemiological tracing of tuberculosis transmissions.
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Affiliation(s)
- Solvig Roring
- Department of Veterinary Science, Queen's University Belfast, Belfast, Northern Ireland.
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21
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Skuce RA, McCorry TP, McCarroll JF, Roring SMM, Scott AN, Brittain D, Hughes SL, Hewinson RG, Neill SD. Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets. MICROBIOLOGY (READING, ENGLAND) 2002; 148:519-528. [PMID: 11832515 DOI: 10.1099/00221287-148-2-519] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The lack of a convenient high-resolution strain-typing method has hampered the application of molecular epidemiology to the surveillance of bacteria of the Mycobacterium tuberculosis complex, particularly the monitoring of strains of Mycobacterium bovis. With the recent availability of genome sequences for strains of the M. tuberculosis complex, novel PCR-based M. tuberculosis-typing methods have been developed, which target the variable-number tandem repeats (VNTRs) of minisatellite-like mycobacterial interspersed repetitive units (MIRUs), or exact tandem repeats (ETRs). This paper describes the identification of seven VNTR loci in M. tuberculosis H37Rv, the copy number of which varies in other strains of the M. tuberculosis complex. Six of these VNTRs were applied to a panel of 100 different M. bovis isolates, and their discrimination and correlation with spoligotyping and an established set of ETRs were assessed. The number of alleles varied from three to seven at the novel VNTR loci, which differed markedly in their discrimination index. There was positive correlation between spoligotyping, ETR- and VNTR-typing. VNTR-PCR discriminates well between M. bovis strains. Thirty-three allele profiles were identified by the novel VNTRs, 22 for the ETRs and 29 for spoligotyping. When VNTR- and ETR-typing results were combined, a total of 51 different profiles were identified. Digital nomenclature and databasing were intuitive. VNTRs were located both in intergenic regions and annotated ORFs, including PPE (novel glycine-asparigine-rich) proteins, a proposed source of antigenic variation, where VNTRs potentially code repeating amino acid motifs. VNTR-PCR is a valuable tool for strain typing and for the study of the global molecular epidemiology of the M. tuberculosis complex. The novel VNTR targets identified in this study should additionally increase the power of this approach.
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Affiliation(s)
- Robin A Skuce
- Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1
| | - Thomas P McCorry
- The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2
| | - Julie F McCarroll
- Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1
| | - Solvig M M Roring
- The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2
| | - Alistair N Scott
- The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2
| | - David Brittain
- Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1
| | - Stephen L Hughes
- Veterinary Laboratories Agency, Department for Environment, Food and Rural Affairs, Weybridge, Surrey KT15 3NB, UK3
| | - R Glyn Hewinson
- Veterinary Laboratories Agency, Department for Environment, Food and Rural Affairs, Weybridge, Surrey KT15 3NB, UK3
| | - Sydney D Neill
- The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2
- Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1
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22
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Haddad N, Ostyn A, Karoui C, Masselot M, Thorel MF, Hughes SL, Inwald J, Hewinson RG, Durand B. Spoligotype diversity of Mycobacterium bovis strains isolated in France from 1979 to 2000. J Clin Microbiol 2001; 39:3623-32. [PMID: 11574583 PMCID: PMC88399 DOI: 10.1128/jcm.39.10.3623-3632.2001] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Accepted: 08/04/2001] [Indexed: 11/20/2022] Open
Abstract
The molecular fingerprints of 1,349 isolates of Mycobacterium bovis received between 1979 and August 2000 at Agence Française de Sécurité Sanitaire des Aliments (Afssa) have been obtained by spoligotyping. The majority of the isolates (1,266) were obtained from cattle living in France. An apparently high level of heterogeneity was observed between isolates. One hundred sixty-one spoligotypes were observed in total, of which 153 were from French isolates. The two predominant spoligotypes, designated BCG-like and GB54, accounted for 26 and 12% of the isolates, respectively. In addition, 84% of the spoligotypes were found fewer than 10 times. Analysis of the results by clustering and parsimony-based algorithms revealed that the majority of the spoligotypes were closely related. The predominant spoligotype was identical to that of the vaccine strain Mycobacterium bovis BCG, which was isolated in France at the end of the 19th century. Some spoligotypes were closely associated with restricted geographical areas. Interestingly, some spoligotypes, which were frequently observed in France, were also observed in neighboring countries. Conversely, few spoligotypes were common to France and England, and those that were shared were observed at very different frequencies. This last point illustrates the potential role for an international data bank, which could help trace the spread of M. bovis across national borders.
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Affiliation(s)
- N Haddad
- Secteur des Mycobactéries, Unité des Zoonoses Bactériennes, Agence Française de Sécurité Sanitaire des Aliments, Maisons-Alfort, France.
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23
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Gordon SV, Eiglmeier K, Garnier T, Brosch R, Parkhill J, Barrell B, Cole ST, Hewinson RG. Genomics of Mycobacterium bovis. Tuberculosis (Edinb) 2001; 81:157-63. [PMID: 11463237 DOI: 10.1054/tube.2000.0269] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The imminent completion of the genome sequence of Mycobacterium bovis will reveal the genetic blueprint for this most successful pathogen. Comparative analysis with the genome sequences of M. tuberculosis and M. bovis BCG promises to expose the genetic basis for the phenotypic differences between the tubercle bacilli, offering unparalleled insight into the virulence factors of the M. tuberculosis complex. Initial analysis of the sequence data has already revealed a novel deletion from M. bovis, as well as identifying variation in members of the PPE family of proteins. As the study of bacterial pathogenicity enters the postgenomic phase, the genome sequence of M. bovis promises to serve as a cornerstone of mycobacterial genetics.
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Affiliation(s)
- S V Gordon
- Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey, UK.
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24
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Skuce RA, Neill SD. Molecular epidemiology of Mycobacterium bovis: exploiting molecular data. Tuberculosis (Edinb) 2001; 81:169-75. [PMID: 11463239 DOI: 10.1054/tube.2000.0270] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
'Molecular epidemiology' is defined as the integration of conventional epidemiological approaches with molecular techniques to track specific strains of pathogens in order to understand the distribution of disease in populations. It has become a very powerful tool in the study of Mycobacterium tuberculosis and human tuberculosis, where it has been exploited to provide 'added value' to conventional epidemiological approaches (contact tracing) and has often challenged accepted dogmas. It has been used to confirm epidemiologically suspected transmission, to detect epidemiologically unsuspected transmission, to identify risk factors and environments where transmission is occurring, to detect laboratory errors and to monitor the efficacy of tuberculosis control programmes. For Mycobacterium bovis and bovine tuberculosis, molecular epidemiology has a key role to play in providing more precise epidemiological data on the issues of interbovine transmission and the role of wildlife reservoirs in disease maintenance and transmission. M. bovis strains may also differ in key biological properties, such as virulence, transmissibility, stability and antigenic variation, which may help to explain field observations. There may be correlation between strain type and 'herd level' factors such as breakdown size etc. Molecular 'strain typing' studies have provided useful information in several countries, notably New Zealand, where strain typing data is used as an integral part of M. bovis control schemes, to influence the level of herd testing or wildlife control and to define the extent and spread of infected wildlife. This presentation will review the methods and approaches currently appropriate for M. bovis strain typing and will review selected applications as well as discussing future perspectives and challenges for the application of molecular epidemiology to bovine tuberculosis.
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Affiliation(s)
- R A Skuce
- Veterinary Sciences Division, Stormont, Belfast, BT4 3SD, UK.
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25
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Zanini MS, Moreira EC, Lopes MT, Oliveira RS, Leão SC, Fioravanti RL, Roxo E, Zumarraga M, Romano MI, Cataldi A, Salas CE. Mycobacterium bovis: polymerase chain reaction identification in bovine lymphonode biopsies and genotyping in isolates from Southeast Brazil by spolygotyping and restriction fragment length polymorphism. Mem Inst Oswaldo Cruz 2001; 96:809-13. [PMID: 11562707 DOI: 10.1590/s0074-02762001000600012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Diagnosis of the Mycobacterium tuberculosis complex by direct PCR of mediastinal lymphnode DNA and microbiological tests were compared in cattle suspicious of bearing tuberculous-like lesions detected during slaughter. The PCR procedure applied on DNA samples (n=54) obtained by adding alpha -casein into the thiocyanate extraction mix was positive in 70% of the samples. PCR confirmed the identification of 23 samples (100%) that grew in culture, 9 samples (60%) that failed to grow in culture, plus 6 (37.5%) samples that resulted in growth of bacterial contaminants. Genotyping by IS6110-RFLP and DR-spoligotyping analysis of seven samples revealed the presence of several polimorphisms. Seven of the isolates contained multiple copies of IS6110, thus defining the existence of five singular genotypes.
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Affiliation(s)
- M S Zanini
- Escola de Veterinária, ICB, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brasil
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26
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Van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J Intern Med 2001; 249:1-26. [PMID: 11168781 DOI: 10.1046/j.1365-2796.2001.00772.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the last decade, DNA fingerprint techniques have become available to study the interperson transmission of tuberculosis and other mycobacterial infections. These methods have facilitated epidemiological studies at a population level. In addition, the species identification of rarely encountered mycobacteria has improved significantly. This article describes the state of the art of the main molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.
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MESH Headings
- Animals
- Contact Tracing
- DNA Fingerprinting
- DNA, Bacterial/genetics
- Genetics, Microbial/trends
- Genotype
- Humans
- Molecular Epidemiology/methods
- Mycobacterium/classification
- Mycobacterium/genetics
- Mycobacterium/isolation & purification
- Mycobacterium Infections, Nontuberculous/epidemiology
- Mycobacterium Infections, Nontuberculous/genetics
- Mycobacterium Infections, Nontuberculous/transmission
- Mycobacterium tuberculosis/genetics
- Nontuberculous Mycobacteria/genetics
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Transformation, Bacterial
- Tuberculosis/epidemiology
- Tuberculosis/genetics
- Tuberculosis/transmission
- Tuberculosis, Multidrug-Resistant/epidemiology
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Affiliation(s)
- D Van Soolingen
- Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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27
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Njanpop-Lafourcade BM, Inwald J, Ostyn A, Durand B, Hughes S, Thorel MF, Hewinson G, Haddad N. Molecular typing of Mycobacterium bovis isolates from Cameroon. J Clin Microbiol 2001; 39:222-7. [PMID: 11136775 PMCID: PMC87706 DOI: 10.1128/jcm.39.1.222-227.2001] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to gain a better understanding of the molecular epidemiology of Mycobacterium bovis isolates in Cameroon, 75 isolates of M. bovis collected in three provinces of northern Cameroon were studied by spoligotyping. For 65 of these isolates, typing was also carried out by pulsed-field gel electrophoresis (PFGE) with DraI, and 18 of the isolates were also typed by restriction fragment length polymorphism (RFLP) analysis with probe IS6110-RHS. Molecular typing of the isolates by these techniques revealed a high degree of homogeneity, with 10 spoligotypes for 75 isolates, four PFGE profiles for 65 isolates, and three RFLP types for 18 isolates. Some types were present in the three different provinces, while some were confined to one or two areas. These results suggest that geographical mapping of M. bovis strains could be helpful for the control of bovine tuberculosis at the regional level. An interesting feature of all the spoligotypes was the absence of spacer 30, suggesting a common origin for all of the Cameroon isolates tested; an evolutionary scenario for the isolates is discussed. In addition, a comparison of the three techniques showed that for M. bovis strain differentiation in Cameroon and in surrounding countries, spoligotyping would be a more discriminating and practical tool for molecular typing than the other two techniques used in this study.
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Affiliation(s)
- B M Njanpop-Lafourcade
- Secteur des Mycobactéries, Unité des Zoonoses Bactériennes, Agence Française de Sécurité Sanitaire des Aliments Alfort, Maisons-Alfort, France
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28
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O'Brien R, Danilowicz BS, Bailey L, Flynn O, Costello E, O'Grady D, Rogers M. Characterization of the Mycobacterium bovis restriction fragment length polymorphism DNA probe pUCD and performance comparison with standard methods. J Clin Microbiol 2000; 38:3362-9. [PMID: 10970384 PMCID: PMC87387 DOI: 10.1128/jcm.38.9.3362-3369.2000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the newly described Mycobacterium bovis restriction fragment length polymorphism (RFLP) typing probe pUCD was characterized by sequence analysis and the previously observed polymorphic banding pattern was reproduced with a combination of three oligonucleotide probes in a single, mixed hybridization. In addition, the ability of pUCD to distinguish between 299 M. bovis isolates from the Republic of Ireland was assessed in relation to established methods and a statistical function for objective comparison of RFLP probes was derived. It was found that typing with pUCD alone produced greater discrimination between M. bovis isolates than typing with the commonly used mycobacterial DNA probes IS6110, PGRS, and DR and also by the spoligotyping technique. pUCD and DR in combination produced the highest level of discrimination while maintaining a high level of concordance with known epidemiological data relating to the samples. The reduction of pUCD to the level of oligonucleotides should in future allow pUCD and DR to be included together in a mixed hybridization, thus producing a high level of M. bovis strain type discrimination from a single round of RFLP analysis.
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Affiliation(s)
- R O'Brien
- National Agricultural and Veterinary Biotechnology Centre, University College Dublin, Ballsbridge, Dublin 4, Ireland.
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29
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Roring S, Hughes MS, Skuce RA, Neill SD. Simultaneous detection and strain differentiation of Mycobacterium bovis directly from bovine tissue specimens by spoligotyping. Vet Microbiol 2000; 74:227-36. [PMID: 10808091 DOI: 10.1016/s0378-1135(00)00189-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Culture of Mycobacterium bovis is used routinely to support field diagnosis of bovine tuberculosis; however, this method is slow. Rapid detection and strain-typing of M. bovis directly from 37 lesioned bovine lymph node specimens was performed by the polymerase chain reaction (PCR) based method, spoligotyping. Mycobacterial DNA was extracted from the specimens using a nucleic acid sequence capture technique. Two sets of specimens were tested, the first set comprising 16 decontaminated tissue homogenates from lesioned lymph node specimens which had been processed for BACTEC culture and a second set of 21 non-decontaminated lesioned lymph node specimens. Both sets of specimens had been frozen before analysis. Sequence capture PCR enabled detection and strain-typing of M. bovis directly from 15 of the 16 decontaminated homogenates and all 21 of the non-decontaminated tissues. Four spoligotype (ST) patterns were obtained from each set; ST1, ST2, ST3 and ST16 were detected in the decontaminated specimens and ST1, ST2, ST11 and ST14 in the non-decontaminated specimens. For both sets of specimens, ST1 was the predominant strain type detected. ST patterns obtained from the BACTEC cultures of the decontaminated specimens were in agreement with those obtained directly from the tissue. The sensitivity of detection by sequence capture-PCR compared very favourably with that of BACTEC culture. ST patterns were obtained directly from tissues of 34 of the 35 culture positive specimens and the two culture negative specimens. DNA extraction from the 21 non-decontaminated specimens involved an initial stomaching treatment. An assessment of sequence capture on both liquid alone and liquid and tissue homogenate combined, following stomaching, indicated that PCR was less successful on the liquid component alone.
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Affiliation(s)
- S Roring
- Queen's University of Belfast, Stoney Road, Stormont, Belfast, UK
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30
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O'Brien R, Flynn O, Costello E, O'Grady D, Rogers M. Identification of a novel DNA probe for strain typing Mycobacterium bovis by restriction fragment length polymorphism analysis. J Clin Microbiol 2000; 38:1723-30. [PMID: 10790088 PMCID: PMC86571 DOI: 10.1128/jcm.38.5.1723-1730.2000] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine tuberculosis caused by Mycobacterium bovis remains a significant disease of farmed cattle in many countries despite ongoing tuberculosis eradication programs. Molecular typing methods such as restriction fragment length polymorphism (RFLP) analysis and spoligotyping have been used to identify related herd breakdowns in an attempt to identify more precisely the route of infection into cattle herds and to trace the transmission of bovine tuberculosis. A recent geographical survey of Irish M. bovis isolates demonstrated that a significant proportion of isolates ( approximately 20%) exhibit a common strain type, limiting the value of current strain typing methods as an epidemiological tool. We have identified and cloned a region of the M. bovis genome, pUCD, which generates a clear, highly polymorphic banding pattern when used as an RFLP probe on AluI restriction-digested M. bovis genomic DNA and which effectively subdivides this common strain type. When used to type 60 Irish M. bovis isolates, pUCD exhibited greater discriminatory power than the commonly used mycobacterial RFLP probes IS6110, PGRS, and DR and detected an equivalent number of strain types to a combination of these three probes. pUCD also detected significantly more strain types than the spoligotyping technique, while maintaining a high level of concordance between epidemiologically related and unrelated herd breakdowns. The polymorphic element within pUCD remains to be fully characterized, however the potential for this probe to greatly decrease the workload necessary to genotype M. bovis by RFLP analysis is compelling.
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Affiliation(s)
- R O'Brien
- National Agricultural and Veterinary Biotechnology Centre, University College Dublin, Belfield, Dublin 4, Ireland.
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31
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Costello E, O'Grady D, Flynn O, O'Brien R, Rogers M, Quigley F, Egan J, Griffin J. Study of restriction fragment length polymorphism analysis and spoligotyping for epidemiological investigation of Mycobacterium bovis infection. J Clin Microbiol 1999; 37:3217-22. [PMID: 10488180 PMCID: PMC85531 DOI: 10.1128/jcm.37.10.3217-3222.1999] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Restriction fragment length polymorphism (RFLP) analysis with probes derived from the insertion element IS6110, the direct repeat sequence, and the polymorphic GC-rich sequence (PGRS) and a PCR-based typing method called spacer oligonucleotide typing (spoligotyping) were used to strain type Mycobacterium bovis isolates from the Republic of Ireland. Results were assessed for 452 isolates which were obtained from 233 cattle, 173 badgers, 33 deer, 7 pigs, 5 sheep, and 1 goat. Eighty-five strains were identified by RFLP analysis, and 20 strains were identified by spoligotyping. Twenty percent of the isolates were the most prevalent RFLP type, while 52% of the isolates were the most prevalent spoligotype. Both the prevalent RFLP type and the prevalent spoligotype were identified in isolates from all animal species tested and had a wide geographic distribution. Isolates of some RFLP types and some spoligotypes were clustered in regions consisting of groups of adjoining counties. The PGRS probe gave better differentiation of strains than the IS6110 or DR probes. The majority of isolates from all species carried a single IS6110 copy. In four RFLP types IS6110 polymorphism was associated with deletion of fragments equivalent in size to one or two direct variable repeat sequences. The same range and geographic distribution of strains were found for the majority of isolates from cattle, badgers, and deer. This suggests that transmission of infection between these species is a factor in the epidemiology of M. bovis infection in Ireland.
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Affiliation(s)
- E Costello
- Central Veterinary Research Laboratory, Abbotstown, Castleknock, Dublin 15, Ireland.
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Serraino A, Marchetti G, Sanguinetti V, Rossi MC, Zanoni RG, Catozzi L, Bandera A, Dini W, Mignone W, Franzetti F, Gori A. Monitoring of transmission of tuberculosis between wild boars and cattle: genotypical analysis of strains by molecular epidemiology techniques. J Clin Microbiol 1999; 37:2766-71. [PMID: 10449449 PMCID: PMC85373 DOI: 10.1128/jcm.37.9.2766-2771.1999] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An epidemiological survey for the monitoring of bovine tuberculosis transmission was carried out in western Liguria, a region in northern Italy. Fifteen Mycobacterium bovis strains were isolated from 63 wild boar samples (62 from mandibular lymph nodes and 1 from a liver specimen). Sixteen mediastinal lymph nodes of 16 head of cattle were collected, and 15 Mycobacterium bovis strains were subsequently cultured. All M. bovis strains isolated from cattle and wild boars were genotyped by spoligotyping and by restriction fragment length polymorphism (RFLP) analysis with the IS6110 and IS1081 probes. All M. bovis strains showed the typical spoligotype characterized by the absence of the 39 to 43 spacers in comparison with the number in M. tuberculosis. A total of nine different clusters were identified by spoligotyping. The largest cluster included 9 strains isolated from wild boars and 11 strains isolated from cattle, thus confirming the possibility of transmission between the two animal species. Fingerprinting by RFLP analysis with the IS6110 probe showed an identical single-band pattern for 29 of 30 strains analyzed, and only 1 strain presented a five-band pattern. The use of IS1081 as a second probe was useful for differentiation of M. bovis from M. bovis BCG but not for differentiation among M. bovis strains, which presented the same undifferentiated genomic profile. In relation to the epidemiological investigation, we hypothesized that the feeding in pastures contaminated by cattle discharges could represent the most probable route of transmission of M. bovis between the two animal species. In conclusion, our results confirmed the higher discriminatory power of spoligotyping in relation to that of RFLP analysis for the differentiation of M. bovis genomic profiles. Our data showed the presence of a common M. bovis genotype in both cattle and wild boars, confirming the possible interspecies transmission of M. bovis.
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Affiliation(s)
- A Serraino
- Department of Veterinary Public Health and Animal Pathology, University of Bologna, Bologna, Italy
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Bauer J, Andersen AB, Kremer K, Miörner H. Usefulness of spoligotyping To discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultured in Denmark. J Clin Microbiol 1999; 37:2602-6. [PMID: 10405409 PMCID: PMC85294 DOI: 10.1128/jcm.37.8.2602-2606.1999] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis complex strains cultured in Denmark have been analyzed by IS6110 restriction fragment length polymorphism (RFLP) on a routine basis from 1992 and onwards. Due to the influx of immigrants with tuberculosis, the number of strains harboring only one to five copies of IS6110 has increased steadily. Since the discriminatory power of IS6110 fingerprinting for such strains is poor, we have performed additional genotyping of all low-copy-number strains by the recently described PCR-based method known as spoligotyping. A total of 311 clinical strains were typed: 14 Mycobacterium bovis BCG, 48 M. bovis, and 249 M. tuberculosis strains. Spoligotyping correctly differentiated M. bovis and M. bovis BCG from M. tuberculosis strains, but it did not differentiate M. bovis from M. bovis BCG. All M. bovis BCG strains exhibited identical spoligotype patterns. The discriminatory power of spoligotyping of low-copy-number M. tuberculosis strains was higher than that of IS6110 fingerprinting. Based on RFLP typing solely, 83% of the low-copy-number M. tuberculosis strains were found to form part of a cluster, and 75% were found to form a cluster on the basis of spoligotyping. When the two techniques were combined, the amount of clustering decreased to 55%. The combination of these two techniques might be valuable in studying the epidemiology of M. tuberculosis strains harboring few copies of the IS6110 element.
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Affiliation(s)
- J Bauer
- Department of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
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Sechi LA, Leori G, Lollai SA, Duprè I, Molicotti P, Fadda G, Zanetti S. Different strategies for molecular differentiation of Mycobacterium bovis strains isolated in Sardinia, Italy. Appl Environ Microbiol 1999; 65:1781-5. [PMID: 10103282 PMCID: PMC91252 DOI: 10.1128/aem.65.4.1781-1785.1999] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Different genetic markers were used to analyze 22 Mycobacterium bovis strains isolated from cattle in Sardinia and one human isolate. IS6110 DNA fingerprinting differentiated the strains into six patterns, whereas with enterobacterial repetitive consensus sequence primers produced seven clusters. PCR ribotyping followed by digestion with HaeIII and PvuII produced five and seven patterns, respectively. PCR with the (GTG)5 oligonucleotide primer showed the best discriminatory power, generating eight clusters among the strains analyzed.
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Affiliation(s)
- L A Sechi
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia Sperimentale e Clinica, Università degli studi di Sassari, 07100 Sassari, Italy.
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