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Jutzeler KS, Platt RN, Li X, Morales M, Diaz R, Le Clec'h W, Chevalier FD, Anderson TJC. Rapid phenotypic and genotypic change in a laboratory schistosome population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606850. [PMID: 39149304 PMCID: PMC11326245 DOI: 10.1101/2024.08.06.606850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Background Genomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, Mycobacterium tuberculosis and Salmonella spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian Schistosoma mansoni population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocysts number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host. In 2021 we observed a rapid change in SmBRE parasite phenotypes, with a ∼10x increase in cercarial production and ∼4x increase in worm burden. Methods To determine the underlying genomic cause of these changes, we sequenced pools of SmBRE adults collected during parasite maintenance between 2015 and 2023. We also sequenced another parasite population (SmLE) maintained alongside SmBRE without phenotypic changes. Results While SmLE allele frequencies remained stable over the eight-year period, we observed sudden changes in allele frequency across the genome in SmBRE between July 2021 and February 2023, consistent with expectations of laboratory contamination. (i) SmLE-specific alleles rose in the SmBRE population from 0 to 41-46% across the genome between September and October 2021, documenting the timing and magnitude of the contamination event. (ii) After contamination, strong selection ( s = ∼0.23) drove replacement of low fitness SmBRE with high fitness SmLE alleles. (iii) Allele frequency changed rapidly across the whole genome, except for a region on chromosome 4 where SmBRE alleles remained at high frequency. Conclusions We were able to detect contamination in this case because SmBRE shows distinctive phenotypes. However, this would likely have been missed with phenotypically similar parasites. These results provide a cautionary tale about the importance of tracking the identity of parasite populations, but also showcase a simple approach to monitor changes within populations using molecular profiling of pooled population samples to characterize fixed single nucleotide polymorphisms. We also show that genetic drift results in continuous change even in the absence of contamination, causing parasites maintained in different labs (or sampled from the same lab at different times) to diverge.
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Cooke DM, Clarke C, Kerr TJ, Warren RM, Witte C, Miller MA, Goosen WJ. Detection of Mycobacterium bovis in nasal swabs from communal goats ( Capra hircus) in rural KwaZulu-Natal, South Africa. Front Microbiol 2024; 15:1349163. [PMID: 38419629 PMCID: PMC10899470 DOI: 10.3389/fmicb.2024.1349163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Animal tuberculosis, caused by Mycobacterium bovis, presents a significant threat to both livestock industries and public health. Mycobacterium bovis tests rely on detecting antigen specific immune responses, which can be influenced by exposure to non-tuberculous mycobacteria, test technique, and duration and severity of infection. Despite advancements in direct M. bovis detection, mycobacterial culture remains the primary diagnostic standard. Recent efforts have explored culture-independent PCR-based methods for identifying mycobacterial DNA in respiratory samples. This study aimed to detect M. bovis in nasal swabs from goats (Capra hircus) cohabiting with M. bovis-infected cattle in KwaZulu-Natal, South Africa. Nasal swabs were collected from 137 communal goats exposed to M. bovis-positive cattle and 20 goats from a commercial dairy herd without M. bovis history. Swabs were divided into three aliquots for analysis. The first underwent GeneXpert® MTB/RIF Ultra assay (Ultra) screening. DNA from the second underwent mycobacterial genus-specific PCR and Sanger sequencing, while the third underwent mycobacterial culture followed by PCR and sequencing. Deep sequencing identified M. bovis DNA in selected Ultra-positive swabs, confirmed by region-of-difference (RD) PCR. Despite no other evidence of M. bovis infection, viable M. bovis was cultured from three communal goat swabs, confirmed by PCR and sequencing. Deep sequencing of DNA directly from swabs identified M. bovis in the same culture-positive swabs and eight additional communal goats. No M. bovis was found in commercial dairy goats, but various NTM species were detected. This highlights the risk of M. bovis exposure or infection in goats sharing pastures with infected cattle. Rapid Ultra screening shows promise for selecting goats for further M. bovis testing. These techniques may enhance M. bovis detection in paucibacillary samples and serve as valuable research tools.
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Affiliation(s)
- Deborah M. Cooke
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Charlene Clarke
- Faculty of Natural and Agricultural Sciences, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Tanya J. Kerr
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Carmel Witte
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
- The Center for Wildlife Studies, South Freeport, ME, United States
| | - Michele A. Miller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Wynand J. Goosen
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
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de Neeling AJ, Jonckers Nieboer LF, Mulder A, Mariman R, Anthony RM, van Soolingen D. Tracking Mycobacterium tuberculosis sequencing samples using unique spikes of random DNA. J Microbiol Methods 2022; 197:106482. [PMID: 35551970 DOI: 10.1016/j.mimet.2022.106482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
In the Netherlands, local laboratories are involved in the primary diagnosis of tuberculosis. Positive Mycobacterium tuberculosis complex cultures are sent to the National Institute for Public Health and the Environment (RIVM) for species identification, epidemiological typing, and screening for resistance by Whole Genome Sequencing (WGS). Occasional sample-swaps and cross-contaminations are known to occur in the diagnostic procedures. Such errors may lead to incorrect diagnoses resulting in the unnecessary or sub-optimal treatment of patients. Internal controls throughout the process ideally allow the early detection of such mistakes.
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Affiliation(s)
- Albert J de Neeling
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
| | - Lucia F Jonckers Nieboer
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Arnout Mulder
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rob Mariman
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Richard M Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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AYDIN E, TARHAN G, ŞAHİN F, EREN S. Molecular epidemiological typing of M. tuberculosis isolates isolated from Turkey's Eastern Anatolia with in house PCR method. CUKUROVA MEDICAL JOURNAL 2022. [DOI: 10.17826/cumj.997873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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5
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Asgharzadeh M, Ozma MA, Rashedi J, Poor BM, Agharzadeh V, Vegari A, Shokouhi B, Ganbarov K, Ghalehlou NN, Leylabadlo HE, Kafil HS. False-Positive Mycobacterium tuberculosis Detection: Ways to Prevent Cross-Contamination. Tuberc Respir Dis (Seoul) 2020; 83:211-217. [PMID: 32578410 PMCID: PMC7362751 DOI: 10.4046/trd.2019.0087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 01/17/2023] Open
Abstract
The gold standard method for diagnosis of tuberculosis is the isolation of Mycobacterium tuberculosis through culture, but there is a probability of cross-contamination in simultaneous cultures of samples causing false-positives. This can result in delayed treatment of the underlying disease and drug side effects. In this paper, we reviewed studies on falsepositive cultures of M. tuberculosis. Rate of occurrence, effective factors, and extent of false-positives were analyzed. Ways to identify and reduce the false-positives and management of them are critical for all laboratories. In most cases, falsepositive is occurring in cases with only one positive culture but negative direct smear. The three most crucial factors in this regard are inappropriate technician function, contamination of reagents, and aerosol production. Thus, to reduce false-positives, good laboratory practice, as well as use of whole-genome sequencing or genotyping of all positive culture samples with a robust, extra pure method and rapid response, are essential for minimizing the rate of false-positives. Indeed, molecular approaches and epidemiological surveillance can provide a valuable tool besides culture to identify possible false positives.
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Affiliation(s)
- Mohammad Asgharzadeh
- Biotechnology Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalil Rashedi
- Tuberculosis and Lung Diseases Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavi Poor
- Tuberculosis and Lung Diseases Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Agharzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Vegari
- Department of Medical Physics, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Behrooz Shokouhi
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | | | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Bastian I, Shephard L, Lumb R. Revised guidelines for Australian laboratories performing mycobacteriology testing. ACTA ACUST UNITED AC 2020; 44. [PMID: 31940451 DOI: 10.33321/cdi.2020.44.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/27/2021] [Indexed: 11/20/2022]
Abstract
Mycobacteriology laboratories play a key role in tuberculosis (TB) control by providing phenotypic and molecular diagnostics, by performing molecular typing to aid contact tracing, and by supporting research and similar laboratories in Australia's neighbouring countries where TB is prevalent. The National Tuberculosis Advisory Committee (NTAC) published a set of laboratory guidelines in 2006 aiming to document the infrastructure, equipment, staffing and work practices required for safe high-quality work in Australian mycobacteriology laboratories. These revised guidelines have the same aims and have been through a similar extensive consultative peer-review process involving the Mycobacterium Reference Laboratory (MRL) network, the Mycobacterium Special Interest Group (SIG) of the Australian Society for Microbiology (ASM), and other relevant national bodies. This revised document contains several significant changes reflecting the publication of new biosafety guidelines and tuberculosis standards by various national and international organisations, technology developments - such as the MPT64-based immunochromatographic tests (ICTs) and the Xpert MTB/RIF assay, and updated work practices in mycobacteriology laboratories. The biosafety recommendations affirm the latest Australian/New Zealand Standard 2243.3: 2010 and promote a biorisk assessment approach that, in addition to the risk categorisation of the organism, also considers the characteristics of the procedure being performed. Using this biorisk assessment approach, limited manipulations, such as Ziehl-Neelsen (ZN) microscopy, MPT64 ICTs, and culture inactivation/DNA extraction for molecular testing, may be performed on a positive TB culture in a PC2 laboratory with additional features and work practices. Other significant changes include recommendations on the integration of MPT64 ICTs and novel molecular tests into TB laboratory workflows to provide rapid accurate results that improve the care of TB patients. This revised document supersedes the original 2006 publication. NTAC will periodically review these guidelines and provide updates as new laboratory technologies become available.
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Affiliation(s)
- Ivan Bastian
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
| | - Lisa Shephard
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
| | - Richard Lumb
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
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Barac A, Karimzadeh-Esfahani H, Pourostadi M, Rahimi MT, Ahmadpour E, Rashedi J, Mahdavipoor B, Kafil HS, Spotin A, Abate KH, Mathioudakis AG, Asgharzadeh M. Laboratory Cross-Contamination of Mycobacterium tuberculosis: A Systematic Review and Meta-analysis. Lung 2019; 197:651-661. [PMID: 31203380 DOI: 10.1007/s00408-019-00241-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/24/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Microbiological cultures are the mainstay of the diagnosis of tuberculosis (TB). False-positive TB results lead to significant unnecessary therapeutic and economic burden and are frequently caused by laboratory cross-contamination. The aim of this meta-analysis was to quantify the prevalence of laboratory cross-contamination. METHODS Through a systematic review of five electronic databases, we identified studies reporting rates of laboratory cross-contamination, confirmed by molecular techniques in TB cultures. We evaluated the quality of the identified studies using the National Institute of Health (NIH) Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies, and conducted a meta-analysis using standard methodology recommended by the Cochrane Collaboration. RESULTS Based on 31 eligible studies evaluating 29,839 TB cultures, we found that 2% (95% confidence intervals [CI] 1-2%) of all positive TB cultures represent false-positive results secondary to laboratory cross-contamination. More importantly, we evaluated the rate of laboratory cross-contamination in cases where a single-positive TB culture was available in addition to at least one negative TB culture, and we found a rate of 15% (95% CI 6-33%). Moreover, 9.2% (91/990) of all patients with a preliminary diagnosis of TB had false-positive results and received unnecessary and potentially harmful treatments. CONCLUSIONS Our results highlight a remarkably high prevalence of false-positive TB results as a result of laboratory cross-contamination, especially in single-positive TB cultures, leading to the administration of unnecessary, harmful treatments. The need for the adoption of strict technical standards for mycobacterial cultures cannot be overstated.
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Affiliation(s)
- Aleksandra Barac
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Mahya Pourostadi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ehsan Ahmadpour
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Jalil Rashedi
- Tuberculosis and Lung Disease Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavipoor
- Department of Laboratory Science, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Parasitology, School of Medical Sciences, Tarbiat Modarres University, Tehran, Iran
| | - Hossein Samadi Kafil
- Department of Microbiology, Tabriz University of Medical Sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Adel Spotin
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Alexander G Mathioudakis
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester, Manchester, UK. .,North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
| | - Mohammad Asgharzadeh
- Faculty of Paramedicine, Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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8
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A case of Mycobacterium tuberculosis laboratory cross-contamination. J Infect Chemother 2019; 25:610-614. [PMID: 30982725 DOI: 10.1016/j.jiac.2019.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/08/2019] [Accepted: 03/13/2019] [Indexed: 11/23/2022]
Abstract
SETTING A laboratory cross-contamination event was suspected because Mycobacterium tuberculosis was unexpectedly detected at a high incidence in the cultures of several clinical specimens at the National Hospital Organization, Tokyo National Hospital, Japan. OBJECTIVE To describe a case of Mycobacterium tuberculosis laboratory cross-contamination. DESIGN We reviewed the medical records of 20 patients whose clinical specimens were suspected to have been contaminated by Mycobacterium tuberculosis. Variable number of tandem repeat analysis with 15 loci, the Japan Anti-Tuberculosis Association-12, and three additional hyper-variable loci, was performed to identify the cross-contamination event. RESULTS The clinical, laboratory, and variable number of tandem repeat data revealed that the cross-contamination had possibly originated from one strongly positive specimen, resulting in false-positive results in 11 other specimens, including a case treated with anti-tuberculosis drugs. CONCLUSION Clinical and laboratory data must be re-evaluated when cross-contamination is suspected and variable number of tandem repeat analysis should be used to confirm cross-contamination. Furthermore, original isolates should be stored appropriately, without sub-culturing and genotyping should be performed at the earliest possible for better utilization of variable number of tandem repeat for the identification of cross-contamination.
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Sensitivity and specificity of routine diagnostic work-up for tuberculosis in lung clinics in Yogyakarta, Indonesia: a cohort study. BMC Public Health 2019; 19:363. [PMID: 30940123 PMCID: PMC6444523 DOI: 10.1186/s12889-019-6658-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Establishing a correct diagnosis is challenging. We aimed to investigate the sensitivity and specificity of routine tuberculosis (TB) diagnostic work-up in lung clinics in Indonesia, a country with the third highest TB burden and the second highest gap between notifications of TB cases and the best estimate of incident cases in the world. Methods In the lung clinics of the Province of Yogyakarta, Indonesia, we recruited all consecutive patients with symptoms suggesting TB, aged ≥18 years. Routine TB examination consisted of clinical evaluation, sputum smear microscopy, and chest radiography. For research purposes, we added sputum culture, Human Immunodeficiency Virus (HIV) testing, and follow-up for 1.5 years or 2.5 years if culture results disagreed with the initial clinical diagnosis. The initial diagnosis was considered incorrect if patients did not respond to treatment. We calculated sensitivity and specificity of the TB routine examination using culture and a composite reference standard (CRS – a combination of routine examination, culture, and follow-up) as the reference standards. All analyses were conducted with IBM SPSS Statistics 25 (IBM Corp., Armonk, NY, USA). Results Between 2013 and 2015, we included 360 participants, and 21 were excluded due to incomplete data. Among those analyzed, 115 were initially diagnosed with smear-positive TB, 12 with smear-negative TB, and 212 non-TB. In 15 study participants, the diagnosis was changed after median 45 (range: 14–870) days; 14 participants initially not diagnosed with TB were later diagnosed with TB, while one subject initially diagnosed with TB actually did not have TB. Compared with culture and CRS, TB routine examination had sensitivity of 85% (95%CI: 77–91) and 90% (95%CI: 84–94), and specificity of 86.3% (95%CI: 81–91) and 99.5% (95%CI: 97–100), respectively. Conclusions A combination of clinical evaluation with sputum microscopy and chest radiography provided high sensitivity and specificity in diagnosing TB in lung clinics; in only 4.4% the diagnosis was incorrect. There is a need to improve routine TB diagnostic work by using clinical evaluation, sputum smear microscopy, and chest radiography all together in other settings, such as in primary health centers. Trial registration NCT02219945, clinicaltrials.gov. Registered 19 August 2014 (retrospectively registered).
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Datta S, Gonzales-Huerta LE, Evans CA. The Potential for Testing Stool to Reduce Tuberculosis Missed Diagnoses and Misdiagnoses. Am J Trop Med Hyg 2018; 99:243-245. [PMID: 30076698 PMCID: PMC6090364 DOI: 10.4269/ajtmh.18-0507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Sumona Datta
- Section of Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health Research, London, United Kingdom;,Innovation for Health and Development (IFHAD), Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru;,Innovación Por la Salud Y Desarrollo (IPSYD), Asociación Benéfica PRISMA, Lima, Peru
| | - Luis E. Gonzales-Huerta
- Section of Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health Research, London, United Kingdom;,Innovation for Health and Development (IFHAD), Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru;,Innovación Por la Salud Y Desarrollo (IPSYD), Asociación Benéfica PRISMA, Lima, Peru
| | - Carlton A. Evans
- Section of Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health Research, London, United Kingdom;,Innovation for Health and Development (IFHAD), Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru;,Innovación Por la Salud Y Desarrollo (IPSYD), Asociación Benéfica PRISMA, Lima, Peru,Address correspondence to Carlton A. Evans, Section of Infectious Diseases and Immunity, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom. E-mail:
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Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria. Clin Microbiol Rev 2018; 31:31/2/e00038-17. [PMID: 29386234 DOI: 10.1128/cmr.00038-17] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.
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12
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Clonal Complexity in Mycobacterium tuberculosis Can Hamper Diagnostic Procedures. J Clin Microbiol 2017; 55:1388-1395. [PMID: 28202799 DOI: 10.1128/jcm.00149-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/07/2017] [Indexed: 11/20/2022] Open
Abstract
Clonal complexity is increasingly accepted in Mycobacterium tuberculosis infection, including mixed infections by ≥2 strains, which usually occur in settings with a high burden of tuberculosis and/or a high risk of overexposure to infected patients. Mixed infections can hamper diagnostic procedures; obtaining an accurate antibiogram is difficult when the susceptibility patterns of the strains differ. Here, we show how mixed infections can also prove challenging for other diagnostic procedures, even outside settings where mixed infections are traditionally expected. We show how an unnoticed mixed infection in an HIV-positive patient diagnosed in Madrid, Spain, with differences in the representativeness of the coinfecting strains in different sputum samples, markedly complicated the resolution of a laboratory cross-contamination false positivity alert.
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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Morgen EK, Naugler C. Inappropriate repeats of six common tests in a Canadian city: a population cohort study within a laboratory informatics framework. Am J Clin Pathol 2015; 144:704-12. [PMID: 26486733 DOI: 10.1309/ajcpyxdaus2f8xjy] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To identify inappropriate repeats of six common laboratory tests in a population sample of patients, using highly specific criteria based only on repeat time and test value. METHODS We used a laboratory informatics database to conduct a retrospective cohort study using a population sample of 103,000 patients in the city of Calgary with an index test in 2010 and uniform follow-up of 1 year. We examined six tests (cholesterol, hemoglobin A1c, thyroid-stimulating hormone, vitamin B12, vitamin D, and ferritin) with consensus-based or easily justified criteria for inappropriate repeats based solely on time to repeat and the index test value. RESULTS The percentages of tests repeated at 3, 6, and 12 months were 11%, 23%, and 41%, respectively. In total, 16% of these six tests were inappropriately repeated, representing an annual internal cost of $0.6 to $2.2 million Canadian dollars and corresponding to population-scaled national estimates for Canada and the United States of $160 million and $2.4 billion, respectively. CONCLUSIONS Objective definitions based on repeated testing identified 16% of six studied tests as inappropriate, delineating a subset of inappropriate testing that is well suited to automated identification and intervention and that provides a likely lower bound on the true burden of inappropriate testing.
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Laboratory cross-contamination of Mycobacterium tuberculosis in Northwest of Iran. EGYPTIAN JOURNAL OF CHEST DISEASES AND TUBERCULOSIS 2015. [DOI: 10.1016/j.ejcdt.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Johnson MG, Lindsey PH, Harvey CF, Bradley KK. Recognizing Laboratory Cross-Contamination. Chest 2013; 144:319-322. [DOI: 10.1378/chest.12-2294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Lee MR, Chung KP, Chen WT, Huang YT, Lee LN, Yu CJ, Teng LJ, Hsueh PR, Yang PC, Luh KT. Epidemiologic surveillance to detect false-positive Mycobacterium tuberculosis cultures. Diagn Microbiol Infect Dis 2012; 73:343-9. [PMID: 22705229 DOI: 10.1016/j.diagmicrobio.2012.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/29/2012] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
Abstract
This study was aimed to investigate the ability of potential indices from epidemiologic surveillance to detect false-positive cultures of Mycobacterium tuberculosis (MTB). All clinical specimens for mycobacterial culture from April 1 to August 31, 2010, were reviewed. Single-positive cultures without relevant clinical and pathologic information were categorized as suspected false-positive cultures. Genotyping methods were used to confirm false-positive cultures. The performance of epidemiologic surveillance indices to detect potential false-positive cultures was evaluated. A total of 14,462 specimens were sent to the laboratory and 214 batches were processed in 107 work days (average 67.6 specimens per batch, ranging from 21 to 130 specimens per batch). Seventy-one single-positive cultures were identified, among which 5 cultures of multidrug-resistant MTB in 1 batch were false-positive, confirmed by genotyping methods. Epidemiologic surveillance with statistical process control charts for single-positive cultures per day showed good performance in epidemiologic surveillance. The false-positive rate was 38.5% in the 13 potential false-positive cultures according to the statistical process control chart for single-positive cultures per day. Although the incidence of tuberculous disease is high in Taiwan, clustering of multidrug-resistant MTB in 1 batch or clustering of single-positive cultures still suggested the occurrence of false-positive MTB cultures. Therefore, epidemiologic surveillance for the clustering of single-positive cultures with the statistical process control chart could be used to monitor the occurrence of false-positive results.
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Affiliation(s)
- Meng-Rui Lee
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Lai CC, Tan CK, Lin SH, Liao CH, Chou CH, Huang YT, Hsueh PR. Molecular Evidence of False-Positive Cultures for Mycobacterium tuberculosis in a Taiwanese Hospital With a High Incidence of TB. Chest 2010; 137:1065-70. [DOI: 10.1378/chest.09-1878] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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van Kampen SC, Anthony RM, Klatser PR. The realistic performance achievable with mycobacterial automated culture systems in high and low prevalence settings. BMC Infect Dis 2010; 10:93. [PMID: 20385000 PMCID: PMC2862026 DOI: 10.1186/1471-2334-10-93] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 04/12/2010] [Indexed: 11/30/2022] Open
Abstract
Background Diagnostic tests are generally used in situations with similar pre-test probability of disease to where they were developed. When these tests are applied in situations with very different pre-test probabilities of disease, it is informative to model the likely implications of known characteristics of test performance in the new situation. This is the case for automated Mycobacterium tuberculosis (MTB) liquid culture systems for tuberculosis case detection which were developed and are widely used in low burden settings but are only beginning to be applied on a large scale in high burden settings. Methods Here we model the performance of MTB liquid culture systems in high and low tuberculosis (TB) prevalence settings using detailed published data concentrating on the likely frequency of cross-contamination events. Results Our model predicts that as the TB prevalence in the suspect population increases there is an exponential increase in the risk of MTB cross-contamination events expected in otherwise negative samples, even with equivalent technical performance of the laboratories. Quality control and strict cross-contamination measures become increasingly critical as the burden of MTB infection among TB suspects increases. Even under optimal conditions the realistically achievable specificity of these systems in high burden settings will likely be significantly below that obtained in low TB burden laboratories. Conclusions Liquid culture systems can play a valuable role in TB case detection in laboratories in high burden settings, but laboratory workers, policy makers and clinicians should be aware of the increased risks, independent of laboratory proficiency, of cross-contamination events in high burden settings.
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Affiliation(s)
- Sanne C van Kampen
- VU University Amsterdam, Faculty of Earth and Life Sciences, De Boelenlaan 1085, 1081 HV Amsterdam, The Netherlands
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Abstract
OBJECTIVE To estimate rates of recurrent tuberculosis due to reinfection and relapse, by HIV status, in a general population. DESIGN Long-term cohort study in Karonga district, rural Malawi. METHODS All tuberculosis patients with culture-proven disease in Karonga district were followed up after treatment. HIV testing was offered and all Mycobacterium tuberculosis isolates were fingerprinted using IS6110 RFLP. Fingerprints from initial and recurrent disease episodes were compared to distinguish relapse and reinfection: a second episode was considered a relapse if the fingerprint was identical or differed by only 1-4 bands and was the first occurrence of that pattern in the population. Rates of and risk factors for recurrence, reinfection disease, and relapse were estimated using survival analysis and Poisson regression. RESULTS Five hundred and eighty-four culture-positive episodes of tuberculosis were diagnosed and treatment was completed during 1995-2003 in patients with known HIV status; 53 culture-positive recurrences occurred by May 2005. Paired fingerprints were available for 39 of these. Reinfections accounted for 1/16 recurrences in HIV-negative and 12/23 in HIV-positive individuals. Rates of relapse were similar in HIV-positive and HIV-negative individuals. Using multiple imputation to allow for missing fingerprint information, the rate of reinfection disease in HIV-positive individuals was 2.2/100 person-years, and in HIV-negative individuals 0.4/100 person-years. CONCLUSIONS HIV increases the rate of recurrent tuberculosis in this setting by increasing the rate of reinfection disease, not relapse.
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Schürch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D. The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale. INFECTION GENETICS AND EVOLUTION 2010; 10:108-14. [DOI: 10.1016/j.meegid.2009.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 11/24/2022]
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De Lappe N, Connor JO, Doran G, Devane G, Cormican M. Role of subtyping in detecting Salmonella cross contamination in the laboratory. BMC Microbiol 2009; 9:155. [PMID: 19646244 PMCID: PMC2727516 DOI: 10.1186/1471-2180-9-155] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 07/31/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the exception of M. tuberculosis, little has been published on the problems of cross-contamination in bacteriology laboratories. We performed a retrospective analysis of subtyping data from the National Salmonella Reference Laboratory (Ireland) from 2000-2007 to identify likely incidents of laboratory cross contamination. METHODS Serotyping and antimicrobial susceptibility testing was performed on all Salmonella isolates received in the NSRL. Phage typing was performed on all S. Typhimurium and S. Enteritidis isolates while multi-locus variance analysis (MLVA) was performed on selected S. Typhimurium isolates. Pulsed field gel electrophoresis (PFGE) using the PulseNet standard protocol was performed on selected isolates of various serovars. RESULTS Twenty-three incidents involving fifty-six isolates were identified as likely to represent cross contamination. The probable sources of contamination identified were the laboratory positive control isolate (n = 13), other test isolates (n = 9) or proficiency test samples (n = 1). CONCLUSION The scale of laboratory cross-contamination in bacteriology is most likely under recognized. Testing laboratories should be aware of the potential for cross-contamination, regularly review protocols to minimize its occurrence and consider it as a possibility when unexpected results are obtained.
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Affiliation(s)
- Niall De Lappe
- National Salmonella Reference Laboratory, Department of Medical Microbiology, Galway University Hospitals, Galway, Ireland.
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Djelouadji Z, Orehek J, Drancourt M. Rapid detection of laboratory cross-contamination with Mycobacterium tuberculosis using multispacer sequence typing. BMC Microbiol 2009; 9:47. [PMID: 19257895 PMCID: PMC2653047 DOI: 10.1186/1471-2180-9-47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 03/03/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to culture Mycobacterium tuberculosis from clinical specimens serves as the gold standard for the diagnosis of tuberculosis. However, a number of false-positive diagnoses may be due to cross-contamination of such specimens. We herein investigate such episode of cross-contamination by using a technique known as multispacer sequence typing (MST). This technique was applied to six M. tuberculosis isolates prepared within the same laboratory over a two-week period of time. RESULTS MST analysis indicated a unique and common sequence profile between a strain isolated from a patient with proven pulmonary tuberculosis and a strain isolated from a patient diagnosed with lung carcinoma. Using this approach, we were able to provide a clear demonstration of laboratory cross-contamination within just four working days. Further epidemiological investigations revealed that the two isolates were processed for culture on the same day. CONCLUSION The application of MST has been demonstrated to serve as a rapid and efficient method to investigate cases of possible cross-contamination with M. tuberculosis.
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Affiliation(s)
- Zoheira Djelouadji
- Faculté de Médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, IFR 48, Marseille, France
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Ce que le génome de Mycobacterium tuberculosis nous a appris. Rev Mal Respir 2008. [DOI: 10.1016/s0761-8425(08)56010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Tuberculosis testing in deer ‐ Scientific Opinion of the Panel on Animal Health and Welfare. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Martín A, Herranz M, Lirola MM, Fernández RF, Bouza E, García de Viedma D. Optimized molecular resolution of cross-contamination alerts in clinical mycobacteriology laboratories. BMC Microbiol 2008; 8:30. [PMID: 18275600 PMCID: PMC2291055 DOI: 10.1186/1471-2180-8-30] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 02/14/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The phenomenon of misdiagnosing tuberculosis (TB) by laboratory cross-contamination when culturing Mycobacterium tuberculosis (MTB) has been widely reported and it has an obvious clinical, therapeutic and social impact. The final confirmation of a cross-contamination event requires the molecular identification of the same MTB strain cultured from both the potential source of the contamination and from the false-positive candidate. The molecular tool usually applied in this context is IS6110-RFLP which takes a long time to provide an answer, usually longer than is acceptable for microbiologists and clinicians to make decisions. Our purpose in this study is to evaluate a novel PCR-based method, MIRU-VNTR as an alternative to assure a rapid and optimized analysis of cross-contamination alerts. RESULTS MIRU-VNTR was prospectively compared with IS6110-RFLP for clarifying 19 alerts of false positivity from other laboratories. MIRU-VNTR highly correlated with IS6110-RFLP, reduced the response time by 27 days and clarified six alerts unresolved by RFLP. Additionally, MIRU-VNTR revealed complex situations such as contamination events involving polyclonal isolates and a false-positive case due to the simultaneous cross-contamination from two independent sources. CONCLUSION Unlike standard RFLP-based genotyping, MIRU-VNTR i) could help reduce the impact of a false positive diagnosis of TB, ii) increased the number of events that could be solved and iii) revealed the complexity of some cross-contamination events that could not be dissected by IS6110-RFLP.
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Affiliation(s)
- Ana Martín
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital Gregorio Marañón, Universidad Complutense, Madrid, CIBER-Enfermedades Respiratorias CIBERES, Spain.
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Asgharzade M, Yousefee S, Kafil HS, Nahaei MR, Ansarin K, Akhi MT. Comparing Transmission of Mycobacterium tuberculosis in East Azarbaijan and West Azarbaijan Provinces of Iran by Using IS6110-RFLP Method. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/biotech.2007.273.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Cook VJ, Stark G, Roscoe DL, Kwong A, Elwood RK. Investigation of suspected laboratory cross-contamination: interpretation of single smear-negative, positive cultures for Mycobacterium tuberculosis. Clin Microbiol Infect 2006; 12:1042-5. [PMID: 16961647 DOI: 10.1111/j.1469-0691.2006.01517.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: 11/29/2022]
Abstract
Restriction fragment length polymorphism (RFLP) analysis can be used to assess genetic relatedness of Mycobacterium tuberculosis isolates. This study reports a collaborative investigation of false-positive cultures for M. tuberculosis, suspected when the DNA fingerprint from an index case matched an epidemiologically improbable source case. RFLP analysis matched fingerprints in ten of 16 cases of suspected laboratory contamination to four separate smear-positive sources that were processed on the same day in the same laboratory. All single smear-negative, positive cultures processed on the same day as smear-positive specimens should be reviewed on a case-by-case basis to identify possible false-positive cultures.
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Affiliation(s)
- V J Cook
- Division of TB Control, British Columbia Centre for Disease Control, Vancouver, Canada.
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Martínez M, García de Viedma D, Alonso M, Andrés S, Bouza E, Cabezas T, Cabeza I, Reyes A, Sánchez-Yebra W, Rodríguez M, Sánchez MI, Rogado MC, Fernández R, Peñafiel T, Martínez J, Barroso P, Lucerna MA, Diez LF, Gutiérrez C. Impact of laboratory cross-contamination on molecular epidemiology studies of tuberculosis. J Clin Microbiol 2006; 44:2967-9. [PMID: 16891518 PMCID: PMC1594630 DOI: 10.1128/jcm.00754-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory cross-contamination by Mycobacterium tuberculosis is known to be responsible for the misdiagnosis of tuberculosis, but its impact on other contexts has not been analyzed. We present the findings of a molecular epidemiology analysis in which the recent transmission events identified by a genotyping reference center were overestimated as a result of unnoticed laboratory cross-contamination in the original diagnostic laboratories.
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Moore DAJ, Caviedes L, Gilman RH, Coronel J, Arenas F, LaChira D, Salazar C, Carlos Saravia J, Oberhelman RA, Hollm-Delgado MG, Escombe AR, Evans CAW, Friedland JS. Infrequent MODS TB culture cross-contamination in a high-burden resource-poor setting. Diagn Microbiol Infect Dis 2006; 56:35-43. [PMID: 16678991 PMCID: PMC2912514 DOI: 10.1016/j.diagmicrobio.2006.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 03/09/2006] [Accepted: 03/12/2006] [Indexed: 11/25/2022]
Abstract
One obstacle to wider use of rapid liquid culture-based tuberculosis diagnostics such as the microscopic observation drug susceptibility (MODS) assay is concern about cross-contamination. We investigated the rate of laboratory cross-contamination in MODS, automated MBBacT, and Lowenstein-Jensen (LJ) cultures performed in parallel, through triangulation of microbiologic (reculturing stored samples), molecular (spoligotype/RFLP), and clinical epidemiologic data. At least 1 culture was positive for Mycobacterium tuberculosis for 362 (11%) of 3416 samples; 53 were regarded as potential cross-contamination suspects. Cross-contamination accounted for 17 false-positive cultures from 14 samples representing 0.41% (14/3416) and 0.17% (17/10248) of samples and cultures, respectively. Positive predictive values for MODS, MBBacT (bioMérieux, Durham, NC), and LJ were 99.1%, 98.7%, and 99.7%, and specificity was 99.9% for all 3. Low rates of cross-contamination are achievable in mycobacterial laboratories in resource-poor settings even when a large proportion of samples are infectious and highly sensitive liquid culture-based diagnostics such as MODS are used.
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Affiliation(s)
- David A J Moore
- Department of Infectious Diseases and Immunity, Imperial College London Wellcome Centre for Clinical Tropical Medicine, W12 0NN London, UK.
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Yan JJ, Jou R, Ko WC, Wu JJ, Yang ML, Chen HM. The use of variable-number tandem-repeat mycobacterial interspersed repetitive unit typing to identify laboratory cross-contamination with Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2005; 52:21-8. [PMID: 15878438 DOI: 10.1016/j.diagmicrobio.2004.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Revised: 11/23/2004] [Indexed: 10/25/2022]
Abstract
A retrospective study including 515 Mycobacterium tuberculosis isolates from 215 patients was conducted to investigate possible laboratory contamination with M. tuberculosis over a 1-year period in a university hospital. All cultures underwent variable-number tandem-repeat (VNTR) typing. Cultures suspected of being contaminated in the VNTR analysis and possible sources of contamination underwent mycobacterial interspersed repetitive unit (MIRU) typing further. Overall, 8 (3.7%) cases of 215 patients were considered possible false-positives. Five (2.3%) cultures might be contaminated during initial batching processing, and 1 (0.5%) and 4 (1.9%) cultures of them were further classified as presumed and possible cases, respectively, of cross-contamination on clinical grounds. Three (1.4%) cultures might be contaminated by cultures that had been processed in species identification procedures in the same laminar-flow hood. The 2-step strategy using VNTR and MIRU analyses in combination in this study appears to be a valuable means for the study of false-positive cultures.
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Affiliation(s)
- Jing-Jou Yan
- Department of Pathology, National Cheng Kung University Hospital, Tainan 70428, Taiwan.
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Piersimoni C, Mandler F, Marchetti D, Molinari GL, Riva R, Tortoli E, Tronci M, Scarparo C. Mycobacterial testing in hospital laboratories: results from a questionnaire survey in Italy. Clin Microbiol Infect 2004; 10:1014-7. [PMID: 15522007 DOI: 10.1111/j.1469-0691.2004.00950.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Between 1999 and 2001, 355 hospital laboratories in Italy were asked to complete a questionnaire addressing mycobacterial test methods, 1-year workloads and laboratory safety features. Analysis of the data showed that rapid methods for mycobacterial testing were being used by most larger laboratories; however, sub-optimal methods were still in use in small and medium-size laboratories. In a country such as Italy, which has a low prevalence of tuberculosis cases, implementation of rapid technologies, combined with regionalisation of mycobacterial diagnostic services, seems to be the most reasonable and cost-effective strategy.
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Affiliation(s)
- C Piersimoni
- Mycobacteria Committee, Italian Association of Clinical Microbiology (AMCLI), Milan, Italy.
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Recognition of Misdiagnosed Tuberculosis in a Bone Marrow Transplant Recipient Leads to Identification of "Pseudotuberculosis" Due to Laboratory Contamination. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2004. [DOI: 10.1097/01.idc.0000144899.20580.4d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Dahle UR, Sandven P, Heldal E, Caugant DA. Continued low rates of transmission of Mycobacterium tuberculosis in Norway. J Clin Microbiol 2003; 41:2968-73. [PMID: 12843028 PMCID: PMC165220 DOI: 10.1128/jcm.41.7.2968-2973.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2002] [Accepted: 03/30/2003] [Indexed: 11/20/2022] Open
Abstract
In this study, we determined the genetic diversity of Mycobacterium tuberculosis isolated in Norway from 1999 to 2001. The results were compared to those for strains isolated from 1994 to 1998. A total of 818 patients were diagnosed with tuberculosis (TB) during the last 3-year period. Of these cases, 576 (70%) were verified by culturing, and strains from 551 patients (96%) were analyzed by the IS6110 restriction fragment length polymorphism (RFLP) method. We excluded 13 strains (2.4%) from the analyses, since they were found to represent false-positive samples. A total of 67 strains (12%) that carried fewer than five copies of IS6110 were analyzed by spoligotyping. The strains were from 157 patients (29%) of Norwegian origin and 381 patients (71%) of foreign origin. The rate of diversity among all of the strains was 90%, while in 1994 to 1998 it was 87%. Clusters were assumed to have arisen from recent transmission; the degree of such transmission was 10% in 1999 to 2001, while for the whole 8-year period (1994 to 2001), it was 11%. Of the 109 patients diagnosed as being part of a cluster in 1999 to 2001, 89 were infected with a strain that carried more than four copies of IS6110. Among these 89 patients, 52 (58%) were infected with a strain that had already been identified in 1994 to 1998. The results indicated that most cases of TB in Norway were due to the import of new strains rather than to transmission within the country. This finding demonstrates that screening of immigrants for TB upon arrival in Norway needs to be improved. Outbreaks, however, were caused mainly by strains that have been circulating in Norway for many years.
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Affiliation(s)
- Ulf R Dahle
- Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway.
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Carroll NM, Richardson M, van Helden PD. Criteria for identification of cross-contamination of cultures of Mycobacterium tuberculosis in routine microbiology laboratories. J Clin Microbiol 2003; 41:2269; author reply 269-70. [PMID: 12734301 PMCID: PMC154733 DOI: 10.1128/jcm.41.5.2269-2270.2003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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