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Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, Robinson E, Walker T, Campbell C. A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study. EBioMedicine 2018; 34:122-130. [PMID: 30077721 PMCID: PMC6116353 DOI: 10.1016/j.ebiom.2018.07.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/24/2022] Open
Abstract
Background Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing is widely used in high-income countries to determine Mycobacterium tuberculosis relatedness. Whole-genome sequencing (WGS) is known to deliver greater specificity, but no quantitative prospective comparison has yet been undertaken. Methods We studied isolates from the English Midlands, sampled consecutively between 1 January 2012 and 31 December 2015. In addition to routinely performed MIRU-VNTR typing, DNA was extracted from liquid cultures and sequenced using Illumina technology. Demographic and epidemiological data for the relevant patients were extracted from the Enhanced Tuberculosis Surveillance system run by Public Health England. Closely related samples, defined using a threshold of five single nucleotide variants (SNVs), were compared to samples with identical MIRU-VNTR profiles, to samples from individuals with shared epidemiological risk factors, and to those with both characteristics. Findings 1999 patients were identified for whom at least one M. tuberculosis isolate had been MIRU-VNTR typed and sequenced. Comparing epidemiological risk factors with close genetic relatedness, only co-residence had a positive predictive value of over 5%. Excluding co-resident individuals, 18.6% of patients with identical MIRU-VNTR profiles were within 5 SNVs. Where patients also shared social risk factors and ethnic group, this rose to 48%. Only 8% of MIRU-VNTR linked pairs in lineage 1 were within 5 SNV, compared to 31% in lineage 4. Interpretation In the setting studied, this molecular epidemiological study shows MIRU-VNTR typing and epidemiological risk factors are poorly predictive of close genomic relatedness, assessed by SNV. MIRU-VNTR performance varies markedly by lineage. Funding Public Health England, Health Innovation Challenge Fund, NIHR Health Protection Research Unit Oxford, NIHR Oxford Biomedical Research Centre. M. tuberculosis relatedness was measured by MIRU-VNTR typing and single nucleotide variants (SNV). In consecutive isolates in England, only 20% of samples with identical MIRU-VNTR profiles were within 5 SNVs. MIRU-VNTR is more predictive of close relatedness in lineage 4 (Euro-American) lineages than in other lineages.
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Affiliation(s)
- David H Wyllie
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; Public Health England Academic Collaborating Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK.
| | - Jennifer A Davidson
- Tuberculosis Section, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - E Grace Smith
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Priti Rathod
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Esther Robinson
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Tim Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Colin Campbell
- Tuberculosis Section, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Toka Özer T, Yula E, Doğan M, Baskın H. Determination of antibiotic resistance and high-performance liquid chromatography profiles for Mycobacterium species. J Clin Lab Anal 2018; 32:e22459. [PMID: 29701251 DOI: 10.1002/jcla.22459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Incidence of mycobacterial infections has been increasing. However, diagnosis and treatment of mycobacterial infections can be difficult. The aim of this study was to investigate high-performance liquid chromatography (HPLC) analysis of the mycolic acids for rapid identification and dendrogram cluster analysis of mycobacterium species. METHODS Clinical specimens received for mycobacterial culture and antimicrobial susceptibility test were processed by standard laboratory protocols. Positive cultures were analyzed with HPLC method. Mycolic acid analysis with HPLC was used for diagnosis of tuberculosis and other mycobacterial infections. These reports were compared with Sherlock Library mycobacterial species, and the similarity index was analyzed. This value was formed by a software in multidimensional space that was the calculation of the average distance between the nearest library profile and unknown profile. RESULTS The ninety-two samples were identified as M. tuberculosis. (similarity index between 0.593 and 0.994). One of the other strains was identified as M. avium intracellulare (strain No. 82) (SI = 0.906); one of them was identified as M. interjectum (strain no. 89) (SI = 0.644). Total 94 samples were identified, and dendrogram was applied to these samples. Profile A (10.6%), profile B (59.6%), profile C (11.7%), profile D (3.2%), and other profiles as single different profiles were identified. Rates for each as 1% (89, 94, 1, 82, 26, 42, 32, 41, 100, 43, 47, 44, 40, 35). CONCLUSION High-performance liquid chromatography is a useful, rapid, reliable, and practical method for diagnosis of mycobacterium species.
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Affiliation(s)
- Türkan Toka Özer
- Department of Medical Microbiology, Konya Hospital, Konya, Turkey
| | - Erkan Yula
- QMEL Medicine & Publishing Agency, İstanbul, Turkey
| | - Metin Doğan
- Department of Medical Microbiology, Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
| | - Hüseyin Baskın
- Department of Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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Pouseele H, Supply P. Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Hingley-Wilson SM, Casey R, Connell D, Bremang S, Evans JT, Hawkey PM, Smith GE, Jepson A, Philip S, Kon OM, Lalvani A. Undetected multidrug-resistant tuberculosis amplified by first-line therapy in mixed infection. Emerg Infect Dis 2014; 19:1138-41. [PMID: 23764343 DOI: 10.3201/1907.130313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infections with >1 Mycobacterium tuberculosis strain(s) are underrecognized. We show, in vitro and in vivo, how first-line treatment conferred a competitive growth advantage to amplify a multidrug-resistant M. tuberculosis strain in a patient with mixed infection. Diagnostic techniques that identify mixed tubercle bacilli populations are needed to curb the spread of multidrug resistance.
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Hingley-Wilson SM, Casey R, Connell D, Bremang S, Evans JT, Hawkey PM, Smith GE, Jepson A, Philip S, Kon OM, Lalvani A. Undetected multidrug-resistant tuberculosis amplified by first-line therapy in mixed infection. Emerg Infect Dis 2014. [PMID: 23764343 PMCID: PMC3713993 DOI: 10.3201/eid1907.130313] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Infections with >1 Mycobacterium tuberculosis strain(s) are underrecognized. We show, in vitro and in vivo, how first-line treatment conferred a competitive growth advantage to amplify a multidrug-resistant M. tuberculosis strain in a patient with mixed infection. Diagnostic techniques that identify mixed tubercle bacilli populations are needed to curb the spread of multidrug resistance.
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Mycobacterium tuberculosis is the causative agent of tuberculosis in the southern ecological zones of Cameroon, as shown by genetic analysis. BMC Infect Dis 2013; 13:431. [PMID: 24028382 PMCID: PMC3851856 DOI: 10.1186/1471-2334-13-431] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 09/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) is a major cause of mortality and suffering worldwide, with over 95% of TB deaths occurring in low- and middle-income countries. In recent years, molecular typing methods have been widely used in epidemiological studies to aid the control of TB, but this usage has not been the case with many African countries, including Cameroon. The aims of the present investigation were to identify and evaluate the diversity of the Mycobacterium tuberculosis complex (MTBC) isolates circulating in two ecological zones of Cameroon, seven years after the last studies in the West Region, and after the re-organization of the National TB Control Program (NTBCP). These were expected to shed light also on the transmission of TB in the country. The study was conducted from February to July 2009. During this period, 169 patients with symptomatic disease and with sputum cultures that were positive for MTBC were randomly selected for the study from amongst 964 suspected patients in the savannah mosaic zone (West and North West regions) and the tropical rainforest zone (Central region). After culture and diagnosis, DNA was extracted from each of the MTBC isolates and transported to the BecA-ILRI Hub in Nairobi, Kenya for molecular analysis. Methods Genetic characterization was done by mycobacterial interspersed repetitive unit–variable number tandem repeat typing (MIRU-VNTR) and Spoligotyping. Results Molecular analysis showed that all TB cases reported in this study were caused by infections with Mycobacterium tuberculosis (98.8%) and Mycobacterium africanum (M. africanum) (1.2%) respectively. We did not detect any M. bovis. Comparative analyses using spoligotyping revealed that the majority of isolates belong to major clades of M. tuberculosis: Haarlem (7.6%), Latin American-Mediterranean (34.4%) and T clade (26.7%); the remaining isolates (31.3%) where distributed among the minor clades. The predominant group of isolates (34.4%) corresponded to spoligotype 61, previously described as the “Cameroon family. Further analysis based on MIRU-VNTR profiles had greater resolving power than spoligotyping and defined additional genotypes in the same spoligotype cluster. Conclusion The molecular characterization of MTBC strains from humans in two ecological regions of Cameroon has shown that M. tuberculosis sensu stricto is the predominant agent of TB cases in the zones. Three decades ago, TB was reported to be caused by M. africanum in 56.0% of cases. The present findings are consistent with a major shift in the prevalence of M. tuberculosis in Cameroon.
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Combination of multiplex PCR with denaturing high-performance liquid chromatography for rapid detection of Mycobacterium genus and simultaneous identification of the Mycobacterium tuberculosis complex. Diagn Microbiol Infect Dis 2013; 77:53-7. [DOI: 10.1016/j.diagmicrobio.2013.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/22/2013] [Accepted: 06/01/2013] [Indexed: 11/17/2022]
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9
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Jiang Y, Liu HC, Zheng H, Dou X, Tang B, Zhao XQ, Zhu Y, Lu B, Wang S, Dong HY, Zhang YY, Zhao G, Wan K. 19-VNTR loci used in genotyping Chinese clinical Mycobacterium tuberculosis complex strains and in association with spoligotyping. J Basic Microbiol 2013; 53:562-80. [PMID: 23322548 DOI: 10.1002/jobm.201200230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/27/2012] [Indexed: 11/07/2022]
Abstract
Recently, tandem repeat typing has emerged as a rapid and easy method for the molecular epidemiology of the Mycobacterium tuberculosis (M. tuberculosis) complex. In this study, a collection of 19 VNTRs incorporating 15 previously described loci and 4 newly evaluated markers were used to genotype 206 Chinese M. tuberculosis isolates and 9 BCG strains. The discriminatory power was evaluated and compared with that obtained by Spoligotyping. It turned out that 15-locus VNTR could be very useful in M. tuberculosis complex strains genotyping in China. The 4 newly evaluated loci were proved informative and could be useful for future epidemiology studies, especially in Beijing family strains. In addition, a unique pattern of the latter 4 loci were found in Chinese BCG strains.
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Affiliation(s)
- Yi Jiang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing, PR China
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Pareek M, Evans J, Innes J, Smith G, Hingley-Wilson S, Lougheed KE, Sridhar S, Dedicoat M, Hawkey P, Lalvani A. Ethnicity and mycobacterial lineage as determinants of tuberculosis disease phenotype. Thorax 2012; 68:221-9. [PMID: 23019255 DOI: 10.1136/thoraxjnl-2012-201824] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Emerging evidence suggests that Mycobacterium tuberculosis (Mtb) lineage and host ethnicity can determine tuberculosis (TB) clinical disease patterns but their relative importance and interaction are unknown. METHODS We evaluated prospectively collected TB surveillance and Mtb strain typing data in an ethnically heterogeneous UK population. Lineage assignment was denoted using 15-loci mycobacterial interspersed repetitive units containing variable numbers of tandem repeats (MIRU-VNTR) and MIRU-VNTRplus. Geographical and ethnic associations of the six global Mtb lineages were identified and the influence of lineage and demographic factors on clinical phenotype were assessed using multivariate logistic regression. RESULTS Data were available for 1070 individuals with active TB which was pulmonary only, extrapulmonary only and concurrent pulmonary-extrapulmonary in 52.1%, 36.9% and 11.0% respectively. The most prevalent lineages were Euro-American (43.7%), East African Indian (30.2%), Indo-Oceanic (13.6%) and East Asian (12.2%) and were geo-ethnically restricted with, for example, Indian subcontinent ethnicity inversely associated with Euro-American lineage (OR 0.23; 95% CI 0.14 to 0.39) and positively associated with the East African-Indian lineage (OR 4.04; 95% CI 2.19 to 7.45). Disease phenotype was most strongly associated with ethnicity (OR for extrathoracic disease 21.14 (95% CI 6.08 to 73.48) for Indian subcontinent and 14.05 (3.97 to 49.65) for Afro-Caribbean), after adjusting for lineage. With East Asian lineage as the reference category, the Euro-American (OR 0.54; 95% CI 0.32 to 0.91) and East-African Indian (OR 0.50; 95% CI 0.29 to 0.86) lineages were negatively associated with extrathoracic disease, compared with pulmonary disease, after adjusting for ethnicity. CONCLUSIONS Ethnicity is a powerful determinant of clinical TB phenotype independently of mycobacterial lineage and the role of ethnicity-associated factors in pathogenesis warrants investigation.
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Affiliation(s)
- Manish Pareek
- Tuberculosis Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
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11
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First worldwide proficiency study on variable-number tandem-repeat typing of Mycobacterium tuberculosis complex strains. J Clin Microbiol 2011; 50:662-9. [PMID: 22170917 DOI: 10.1128/jcm.00607-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future.
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Systematic survey of clonal complexity in tuberculosis at a populational level and detailed characterization of the isolates involved. J Clin Microbiol 2011; 49:4131-7. [PMID: 21956991 DOI: 10.1128/jcm.05203-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clonally complex infections by Mycobacterium tuberculosis are progressively more accepted. Studies of their dimension in epidemiological scenarios where the infective pressure is not high are scarce. Our study systematically searched for clonally complex infections (mixed infections by more than one strain and simultaneous presence of clonal variants) by applying mycobacterial interspersed repetitive-unit (MIRU)-variable-number tandem-repeat (VNTR) analysis to M. tuberculosis isolates from two population-based samples of respiratory (703 cases) and respiratory-extrapulmonary (R+E) tuberculosis (TB) cases (71 cases) in a context of moderate TB incidence. Clonally complex infections were found in 11 (1.6%) of the respiratory TB cases and in 10 (14.1%) of those with R+E TB. Among the 21 cases with clonally complex TB, 9 were infected by 2 independent strains and the remaining 12 showed the simultaneous presence of 2 to 3 clonal variants. For the 10 R+E TB cases with clonally complex infections, compartmentalization (different compositions of strains/clonal variants in independent infected sites) was found in 9 of them. All the strains/clonal variants were also genotyped by IS6110-based restriction fragment length polymorphism analysis, which split two MIRU-defined clonal variants, although in general, it showed a lower discriminatory power to identify the clonal heterogeneity revealed by MIRU-VNTR analysis. The comparative analysis of IS6110 insertion sites between coinfecting clonal variants showed differences in the genes coding for a cutinase, a PPE family protein, and two conserved hypothetical proteins. Diagnostic delay, existence of previous TB, risk for overexposure, and clustered/orphan status of the involved strains were analyzed to propose possible explanations for the cases with clonally complex infections. Our study characterizes in detail all the clonally complex infections by M. tuberculosis found in a systematic survey and contributes to the characterization that these phenomena can be found to an extent higher than expected, even in an unselected population-based sample lacking high infective pressure.
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García de Viedma D, Mokrousov I, Rastogi N. Innovations in the molecular epidemiology of tuberculosis. Enferm Infecc Microbiol Clin 2011; 29 Suppl 1:8-13. [DOI: 10.1016/s0213-005x(11)70012-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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McMurray CL, Hardy KJ, Hawkey PM. Rapid, automated epidemiological typing of methicillin-resistant Staphylococcus aureus. J Microbiol Methods 2009; 80:109-11. [PMID: 19895854 DOI: 10.1016/j.mimet.2009.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 10/21/2009] [Accepted: 10/26/2009] [Indexed: 11/29/2022]
Abstract
The QIAxcel is an accurate, automated DNA sizing system that can be used as an alternative to agarose gel electrophoresis for rapid, high throughput epidemiological typing of methicillin-resistant Staphylococcus aureus using staphylococcal interspersed repeating unit (SIRU) typing.
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Affiliation(s)
- Claire L McMurray
- Heart of England NHS Foundation Trust, Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, United Kingdom.
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Mallard K, Sharaf Eldin GS, McNerney R. ScreenTape as a tool for the rapid differentiation of Mycobacterium tuberculosis isolates. J Med Microbiol 2009; 58:1266-1268. [PMID: 19541780 DOI: 10.1099/jmm.0.008219-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kim Mallard
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Ruth McNerney
- London School of Hygiene and Tropical Medicine, London, UK
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Brown TJ, Nikolayevskyy VN, Drobniewski FA. Typing Mycobacterium tuberculosis using variable number tandem repeat analysis. Methods Mol Biol 2009; 465:371-394. [PMID: 20560063 DOI: 10.1007/978-1-59745-207-6_25] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
DNA-based typing has contributed to the understanding of M. tuberculosis epidemiology and evolution. IS6110 RFLP was the first method described and has been used in many epidemiologic investigations. Technological difficulties have hampered the widespread establishment of this method, and it has been found to be of little use in evolutionary studies. PCR-based methods such as spoligotyping and variable number tandem repeat (VNTR) analysis largely overcome these difficulties. Spoligotyping alone is of limited value in epidemiologic investigations due to low discrimination but can be useful in evolutionary studies. Panels of VNTR loci selected from the 59 polymorphic VNTRs described to date have been shown to be useful in both epidemiologic and evolutionary studies. A VNTR type is identified by, first, amplifying a series of PCR fragments each encompassing a different VNTR locus and, second, determining the PCR fragment sizes from which the number of repeats present is calculated. The repeat number present at a series of loci is used as numerical code to describe a type. This chapter describes a high-throughput automated method for VNTR analysis at 15 loci using a capillary fragment analyzer and a manual method using agarose gel analysis.
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Affiliation(s)
- T J Brown
- HPA MRU, Queen Mary's School of Medicine and Dentistry, 2 Newark Street, London E1 2AT, UK.
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Nazaret S, Assade F, Brothier E, Freydière AM, Bellon G, Cournoyer B. RISA–HPLC analysis of lung bacterial colonizers of cystic fibrosis children. J Microbiol Methods 2009; 76:58-69. [DOI: 10.1016/j.mimet.2008.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/05/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
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Evans JT, Parveen A, Smith GE, Xu L, Chan EWC, Chan RCY, Hawkey PM. Application of denaturing HPLC to rapidly identify rifampicin-resistant Mycobacterium tuberculosis in low- and high-prevalence areas. J Antimicrob Chemother 2008; 63:295-301. [DOI: 10.1093/jac/dkn506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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DeRiemer K, de Jong BC. Catch Them While You Can! Am J Respir Crit Care Med 2008; 178:5-6. [DOI: 10.1164/rccm.200804-589ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Bouke C. de Jong
- New York University
New York, New York
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MRC Laboratories
Banjul, The Gambia
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Djelouadji Z, Arnold C, Gharbia S, Raoult D, Drancourt M. Multispacer sequence typing for Mycobacterium tuberculosis genotyping. PLoS One 2008; 3:e2433. [PMID: 18560597 PMCID: PMC2413405 DOI: 10.1371/journal.pone.0002433] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 04/16/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genotyping methods developed to survey the transmission dynamics of Mycobacterium tuberculosis currently rely on the interpretation of restriction and amplification profiles. Multispacer sequence typing (MST) genotyping is based on the sequencing of several intergenic regions selected after complete genome sequence analysis. It has been applied to various pathogens, but not to M. tuberculosis. METHODS AND FINDINGS In M. tuberculosis, the MST approach yielded eight variable intergenic spacers which included four previously described variable number tandem repeat loci, one single nucleotide polymorphism locus and three newly evaluated spacers. Spacer sequence stability was evaluated by serial subculture. The eight spacers were sequenced in a collection of 101 M. tuberculosis strains from five phylogeographical lineages, and yielded 29 genetic events including 13 tandem repeat number variations (44.82%), 11 single nucleotide mutations (37.93%) and 5 deletions (17.24%). These 29 genetic events yielded 32 spacer alleles or spacer-types (ST) with an index of discrimination of 0.95. The distribution of M. tuberculosis isolates into ST profiles correlated with their assignment into phylogeographical lineages. Blind comparison of a further 93 M. tuberculosis strains by MST and restriction fragment length polymorphism-IS6110 fingerprinting and mycobacterial interspersed repetitive units typing, yielded an index of discrimination of 0.961 and 0.992, respectively. MST yielded 41 different profiles delineating 16 related groups and proved to be more discriminatory than IS6110-based typing for isolates containing < 8 IS6110 copies (P<0.0003). MST was successfully applied to 7/10 clinical specimens exhibiting a Cts < or = 42 cycles in internal transcribed spacer-real time PCR. CONCLUSIONS These results support MST as an alternative, sequencing-based method for genotyping low IS6110 copy-number M. tuberculosis strains. The M. tuberculosis MST database is freely available (http://ifr48.timone.univ-mrs.fr/MST_MTuberculosis/mst).
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Affiliation(s)
- Zoheira Djelouadji
- Unité des Rickettsies CNRS UMR6236, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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21
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Thorne N, Evans JT, Smith EG, Hawkey PM, Gharbia S, Arnold C. An IS6110-targeting fluorescent amplified fragment length polymorphism alternative to IS6110 restriction fragment length polymorphism analysis for Mycobacterium tuberculosis DNA fingerprinting. Clin Microbiol Infect 2007; 13:964-70. [PMID: 17803750 DOI: 10.1111/j.1469-0691.2007.01783.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A rapid, simple and highly discriminatory DNA fingerprinting methodology which produces data that can be easily interpreted, compared and transported is the ultimate goal for studying the epidemiology of Mycobacterium tuberculosis. A novel TaqI fluorescent amplified fragment length polymorphism (fAFLP) approach to M. tuberculosis DNA fingerprinting that targeted the variable IS6110 marker was developed in this study. The new method was tested for specificity and reproducibility, and compared with the standard reference IS6110 restriction fragment length polymorphism (RFLP) method for a panel of 78 isolates. Clustering conflicts between the two methods were resolved using mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) data. Comparison with an in-silico digestion of strain H37Rv showed that fAFLP-detected fragments were highly specific in vitro. The reproducibility of repeated digestions of strain H37Rv was 100%. Clustering results obtained by fAFLP and RFLP were highly congruent, with fAFLP allocating 97% of RFLP-clustered isolates to the same eight clusters as RFLP. Two single-copy isolates that had been clustered by RFLP were not clustered by fAFLP, but the MIRU-VNTR patterns of these isolates were different, indicating that the RFLP data had falsely clustered these isolates. Analysis by fAFLP will allow rapid screening of isolates to confirm or refute epidemiological links, and thereby provide insights into the frequency, conservation and consequences of specific transposition events.
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Affiliation(s)
- N Thorne
- Applied and Functional Genomics, Centre for Infections, Health Protection Agency, London, UK
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22
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Evans JT, Smith EG, Banerjee A, Smith RM, Dale J, Innes JA, Hunt D, Tweddell A, Wood A, Anderson C, Hewinson RG, Smith NH, Hawkey PM, Sonnenberg P. Cluster of human tuberculosis caused by Mycobacterium bovis: evidence for person-to-person transmission in the UK. Lancet 2007; 369:1270-1276. [PMID: 17434402 DOI: 10.1016/s0140-6736(07)60598-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Despite a recent resurgence in the incidence of bovine tuberculosis in UK cattle herds, no associated rise in the number of cases in man has been noted. Disease due to human Mycobacterium bovis infection usually occurs in older patients, in whom drinking unpasteurised milk in the past is the probable source of infection. Person-to-person transmission is very rare. METHODS After identification of two epidemiologically-linked cases of human M bovis infection through routine laboratory and surveillance activities, all patients identified with M bovis infection in the Midlands from 2001-05 (n=20) were assessed by DNA fingerprinting (MIRU-VNTR and spoligotyping), with additional interviews for patients with a clustered strain. FINDINGS A cluster of six cases was identified. All clustered cases were young and UK-born; five patients had pulmonary disease, and one patient died due to M bovis meningitis, with four patients possessing factors predisposing to tuberculosis. All patients had common social links through visits to bars in two different areas. With the exception of the first case, there was an absence of zoonotic links or consumption of unpasteurised dairy products, suggesting that person-to-person transmission had occurred. INTERPRETATION This report of several instances of M bovis transmission between people in a modern urban setting emphasises the need to maintain control measures for human and bovine tuberculosis. Transmission and subsequent disease was probably due to a combination of host and environmental factors. Prospective surveillance and DNA fingerprinting identified the cluster, enabling health protection teams to set up control measures and prevent further transmission.
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Affiliation(s)
- Jason T Evans
- Regional Centre for Mycobacteriology, West Midlands Public Health Laboratory, Health Protection Agency, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK.
| | - E Grace Smith
- Regional Centre for Mycobacteriology, West Midlands Public Health Laboratory, Health Protection Agency, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Ashis Banerjee
- Health Protection Agency Regional Surveillance Unit (West Midlands), Birmingham, UK
| | - Robert Mm Smith
- Zoonoses Surveillance Unit, National Public Health Service for Wales, Communicable Disease Surveillance Centre, Cardiff, UK
| | - James Dale
- TB Research Group, Veterinary Laboratories Agency, Weybridge, UK
| | - John A Innes
- Birmingham Chest Clinic, Heart of England NHS Foundation Trust, Birmingham, UK
| | - David Hunt
- Health Protection Agency Regional Surveillance Unit (West Midlands), Birmingham, UK
| | - Alan Tweddell
- Herefordshire and Worcestershire Health Protection Unit, UK
| | - Annette Wood
- Birmingham and Solihull Health Protection Unit, UK
| | - Charlotte Anderson
- Tuberculosis Section, Health Protection Agency Centre for Infections, London, UK
| | - R Glyn Hewinson
- TB Research Group, Veterinary Laboratories Agency, Weybridge, UK
| | - Noel H Smith
- TB Research Group, Veterinary Laboratories Agency, Weybridge, UK
| | - Peter M Hawkey
- Regional Centre for Mycobacteriology, West Midlands Public Health Laboratory, Health Protection Agency, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK; Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, UK
| | - Pam Sonnenberg
- Tuberculosis Section, Health Protection Agency Centre for Infections, London, UK; Department of Primary Care and Population Sciences, University College London, London, UK
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23
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Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 2006; 44:4498-510. [PMID: 17005759 PMCID: PMC1698431 DOI: 10.1128/jcm.01392-06] [Citation(s) in RCA: 997] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular typing based on 12 loci containing variable numbers of tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTRs) has been adopted in combination with spoligotyping as the basis for large-scale, high-throughput genotyping of Mycobacterium tuberculosis. However, even the combination of these two methods is still less discriminatory than IS6110 fingerprinting. Here, we define an optimized set of MIRU-VNTR loci with a significantly higher discriminatory power. The resolution and the stability/robustness of 29 loci were analyzed, using a total of 824 tubercle bacillus isolates, including representatives of the main lineages identified worldwide so far. Five loci were excluded for lack of robustness and/or stability in serial isolates or isolates from epidemiologically linked patients. The use of the 24 remaining loci increased the number of types by 40%--and by 23% in combination with spoligotyping--among isolates from cosmopolitan origins, compared to those obtained with the original set of 12 loci. Consequently, the clustering rate was decreased by fourfold--by threefold in combination with spoligotyping--under the same conditions. A discriminatory subset of 15 loci with the highest evolutionary rates was then defined that concentrated 96% of the total resolution obtained with the full 24-locus set. Its predictive value for evaluating M. tuberculosis transmission was found to be equal to that of IS6110 restriction fragment length polymorphism typing, as shown in a companion population-based study. This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies.
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Affiliation(s)
- Philip Supply
- INSERM U629, Institut Pasteur de Lille, 1, rue du Prof. Calmette, F-59019 Lille Cedex, France.
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24
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Jury F, Al-Mahrous M, Apostolou M, Sandiford S, Fox A, Ollier W, Upton M. Rapid cost-effective subtyping of meticillin-resistant Staphylococcus aureus by denaturing HPLC. J Med Microbiol 2006; 55:1053-1060. [PMID: 16849725 DOI: 10.1099/jmm.0.46409-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The importance of meticillin-resistant Staphylococcus aureus (MRSA) in hospital-acquired infection is widely acknowledged. The UK government has stated that MRSA bloodstream infection rates will have to be halved by 2008. Such radical improvements will require advances on several fronts. Screening for MRSA in high-risk patients on arrival at hospital allows isolation of carriers and reduces transmission to staff and other patients. Concurrent subtyping of MRSA could also inform outbreak investigations and long-term epidemiological studies. The variability within the staphylococcal protein A, or spaA, gene-repeat region can be used as a marker of short- and long-term genetic variation. A novel application is described of denaturing HPLC (DHPLC) for rapid, inexpensive characterization of spaA gene amplification products, without the need for DNA sequence determination. The method allowed rapid and precise sizing of spaA gene-repeat regions from 99 S. aureus strains and was combined with heteroduplex analysis, using reference PCR products, to indicate the spa type of the test isolate. The method allowed subtyping of strains in less than 5 h from receipt of a primary isolation plate. When applied to an outbreak that occurred during this study, the authors were able to demonstrate relatedness of the isolates more than 5 days before results were received from a reference laboratory. If combined with direct amplification from swabs, DHPLC analysis of spaA gene variation could prove extremely valuable in outbreak investigation and MRSA surveillance.
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Affiliation(s)
- F Jury
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
| | - M Al-Mahrous
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - M Apostolou
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - S Sandiford
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - A Fox
- Health Protection Agency (HPA) North West Laboratory, Manchester Medical Microbiology Partnership, Clinical Sciences Building 2, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - W Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
| | - M Upton
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
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25
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Xu L, Ensor V, Gossain S, Nye K, Hawkey P. Rapid and simple detection of blaCTX-M genes by multiplex PCR assay. J Med Microbiol 2006; 54:1183-1187. [PMID: 16278432 DOI: 10.1099/jmm.0.46160-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel multiplex PCR assay is described (CTX-Mplex PCR) that allows rapid detection of bla(CTX-M) genes and discrimination between groups 1, 2, 9 and 25/26. The specificity and sensitivity of the assay were evaluated with 10 control strains and then applied to 62 clinical isolates. The multiplex PCR detected and classified bla(CTX-M) genes with 100 % accuracy. The utilization of a denaturing HPLC WAVE system to size the PCR products automatically from the multiplex PCR enhances the assay by saving time and costs.
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Affiliation(s)
- Li Xu
- Health Protection Agency West Midlands Public Health Laboratory, Birmingham Heartlands & Solihull NHS Trust, Birmingham B9 5SS, UK 2Division of Immunity and Infection, University of Birmingham, UK
| | - Vicki Ensor
- Health Protection Agency West Midlands Public Health Laboratory, Birmingham Heartlands & Solihull NHS Trust, Birmingham B9 5SS, UK 2Division of Immunity and Infection, University of Birmingham, UK
| | - Savita Gossain
- Health Protection Agency West Midlands Public Health Laboratory, Birmingham Heartlands & Solihull NHS Trust, Birmingham B9 5SS, UK 2Division of Immunity and Infection, University of Birmingham, UK
| | - Kathy Nye
- Health Protection Agency West Midlands Public Health Laboratory, Birmingham Heartlands & Solihull NHS Trust, Birmingham B9 5SS, UK 2Division of Immunity and Infection, University of Birmingham, UK
| | - Peter Hawkey
- Health Protection Agency West Midlands Public Health Laboratory, Birmingham Heartlands & Solihull NHS Trust, Birmingham B9 5SS, UK 2Division of Immunity and Infection, University of Birmingham, UK
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26
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Hardy KJ, Oppenheim BA, Gossain S, Gao F, Hawkey PM. Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains. J Clin Microbiol 2006; 44:271-3. [PMID: 16390988 PMCID: PMC1351958 DOI: 10.1128/jcm.44.1.271-273.2006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.
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Affiliation(s)
- Katherine J Hardy
- West Midlands Public Health Laboratory, Health Protection Agency, Heartlands Hospital, Bordesley Green East, Birmingham, UK. Katie.Hardy@heartofengland
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