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Bissonnette N, Brousseau JP, Ollier S, Byrne AS, Ibeagha-Awemu EM, Tahlan K. Systematic assessment of the reliability of quantitative PCR assays targeting IS900 for the detection of Mycobacterium avium ssp. paratuberculosis presence in animal and environmental samples. J Dairy Sci 2024:S0022-0302(24)00788-4. [PMID: 38754821 DOI: 10.3168/jds.2023-24566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the bacterium responsible for causing Johne's Disease (JD), which is endemic to dairy cattle and also incriminated in the etiology of Crohn's disease. The difficulty in diagnosing asymptomatic cows for JD makes this disease hard to control. JD is considered a priority under the One Health approach to prevent the spread of the causative agent to humans. Environmental screening is a strategic approach aimed at identifying dairy herds with animals infected with MAP. It serves as the initial step toward implementing more intensive actions to control the disease. Quantitative polymerase chain reaction (qPCR) technology is widely used for diagnosis. Given that genome sequencing is now much more accessible than ever before, it is possible to target regions of the MAP genome that allow for the greatest diagnostic sensitivity and specificity. The aim of this study was to identify among the published qPCR assays targeting IS900 the more cost-effective options to detect MAP and to validate them in the diagnostic context of JD disease. MAP IS900 is a prime target because it is a multicopy genetic element. A total of 136 publications have reported on the use of IS900 qPCR assays over the past 3 decades. Among these records, 29 used the SYBR Green chemistry and TaqMan technology was used in 107 reports. Aside from the 9 reports using commercial assays, 72 TaqMan reports cited previously published work, leaving us with 27 TaqMan qPCR designs. Upon closer examination, 5 TaqMan designs contained mismatches in primer or probe sequences. Additionally, others exhibited high similarity to environmental microorganisms or non-MAP mycobacteria. We assessed the performance of 6 IS900 qPCR designs and their sensitivity when applied to clinical or environmental samples, which varied from 4 to 56 fold overall. Additionally, we provide recommendations for testing clinical and environmental samples, as certain strategies used previously should be avoided due to poor qPCR design (e.g., the presence of mismatches) or a lack of specificity.
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Affiliation(s)
- N Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8.
| | - J-P Brousseau
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - S Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - A S Byrne
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada A1C 5S7
| | - E M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - K Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada A1C 5S7
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Development of a reference standard for the detection and quantification of Mycobacterium avium subsp. paratuberculosis by quantitative PCR. Sci Rep 2021; 11:11622. [PMID: 34078951 PMCID: PMC8172567 DOI: 10.1038/s41598-021-90789-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/12/2021] [Indexed: 01/09/2023] Open
Abstract
Quantitative PCR (qPCR) has become a frequently employed direct method for the detection and quantification of Mycobacterium avium subsp. paratuberculosis (MAP). The quantity of MAP determined by qPCR, however, may be affected by the type of qPCR quantification standard used (PCR product, plasmid, genomic DNA) and the way in which standard DNA quantity is determined (absorbance, fluorescence). In practice, this can be reflected in the inability to properly compare quantitative data from the same qPCR assays in different laboratories. Thus, the aim of this study was to prepare a prototype of an international MAP reference standard, which could be used to calibrate routinely used qPCR quantification standards in various laboratories to promote clinical data comparability. Considering stability, storage and shipment issues, a lyophilised fecal suspension artificially contaminated with a MAP reference strain was chosen as the most suitable form of the standard. The effect of five types of lyophilisation matrices on standard stability was monitored on 2-weeks interval basis for 4 months by F57 qPCR. The lyophilisation matrix with 10% skimmed milk provided the best recovery and stability in time and was thus selected for subsequent comparative testing of the standard involving six diagnostic and research laboratories, where DNA isolation and qPCR assay procedures were performed with the parallel use of the identical supplied genomic DNA solution. Furthermore, the effect of storage conditions on the standard stability was tested for at least 6 months. The storage at room temperature in the dark and under light, at + 4 °C, - 20 °C and - 80 °C showed no significant changes in the stability, and also no substantial changes in MAP viability were found using phage amplification assay. The prepared MAP quantification standard provided homogeneous and reproducible results demonstrating its suitability for utilisation as an international reference qPCR standard.
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Heidarian F, Alebouyeh M, Shahrokh S, Balaii H, Zali MR. Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction. Curr Res Transl Med 2019; 67:41-50. [PMID: 30685379 DOI: 10.1016/j.retram.2019.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE OF THE STUDY In this study we investigated the presence and relative abundance of important genera of the gut microbiota in IBD patients and their role in induction of IL8 in a cell culture model. PATIENTS AND METHODS Stool samples of IBD patients and healthy controls were collected and relative diversity of thirteen bacterial families was measured using quantitative real-time PCR assay. Moreover, filtrate of the stool samples was used for treatment of HT-29 cell line to analyze involvement of diversity of the fecal bacterial communities in the extent of IL8 induction. RESULTS Bacteroides, Faecalibacterium prausnitzii, Prevotella spp., and Methanobrevibacterium were significantly less abundant in IBD patients (UC, N = 22; CD, N = 7) compared with control group (N = 29). Increase in relative amounts of Haemophilus, Streptococcus spp., and H. pylori were detected in IBD patients, which was not statistically significant. Relative decrease in amount of Bacteroides spp., Faecalibacterium prausnitzii, and Prevotella spp. were found in UC patients with disease activity score greater than 4; however, higher levels of Streptococcus and Haemophilus were detected in the patients who were at flares. A relationship between the reduction of Haemophilus spp. and higher BMI was shown in IBD patients. Expression of IL8 was significantly higher in the treated cells by the fecal inoculates of IBD patients. Increase in relative amounts of Enterobacteriacea showed a correlation with the higher level of IL8 induction in both groups. CONCLUSIONS These results showed that changes in the fecal microbiota composition could affect disease activity, BMI, and IL8 induction.
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Affiliation(s)
- Farnaz Heidarian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Alebouyeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedieh Balaii
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Thirumalapura NR, Feria W, Tewari D. Comparison of three DNA extraction methods for molecular confirmation of Mycobacterium avium subspecies paratuberculosis from the VersaTrek™ liquid cultures of bovine fecal samples. J Microbiol Methods 2018; 152:27-30. [PMID: 30031737 DOI: 10.1016/j.mimet.2018.07.012] [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: 04/17/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
Abstract
We evaluated three DNA extraction methods for confirmation of Mycobacterium avium subspecies paratuberculosis from liquid cultures of bovine feces. Use of DNA Extract All Reagents Kit™ resulted in efficient extraction of amplifiable DNA from higher proportion (96.29%) of known positive samples compared to Chelex-100 resin (25.92%) and polyethylene glycol (0%).
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Affiliation(s)
- Nagaraja R Thirumalapura
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, United States.
| | - Willard Feria
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, United States
| | - Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, United States.
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Park HT, Park HE, Cho YI, Kim EH, Jung M, Shin SW, Lee SH, Kim DY, Yoo HS. Potential biomarkers as an indicator of vertical transmission of Johne's disease in a Korean native cattle farm. J Vet Sci 2018; 18:343-349. [PMID: 28385000 PMCID: PMC5583422 DOI: 10.4142/jvs.2017.18.s1.343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 01/19/2017] [Accepted: 02/07/2017] [Indexed: 01/09/2023] Open
Abstract
Paratuberculosis (PTB) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is one of the most widespread and economically important diseases in cattle. After birth, calves are raised with natural breast feeding without separation from their mothers in most Korean native cattle (Hanwoo breed) farms. Vertical transmission of PTB has been reported, but the exact PTB infection route has not been revealed in Hanwoo farms. Calves of MAP seropositive dams were tested for MAP presence and MAP antibodies in feces and tissues. MAP was detected in calf tissues by using polymerase chain reaction. Expressions of genes reported to be prognostic biomarkers of MAP infection changed in both calves and cows (p < 0.05). Expression of two genes (HGF and SERPINE1) were significantly decreased in MAP-infected cattle and their offspring (p < 0.01). The results suggest that biomarker gene expression profiles can be useful in detecting early stage MAP infection. Based on the results, complete eradication of MAP may be possible if accurate diagnostic methods to detect infected calves are added to the current PTB eradication strategy, which, because infected individuals are likely to develop into fecal MAP shedders at any time, includes isolation of new born calves and feeding sterilized colostrum.
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Affiliation(s)
- Hong-Tae Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hyun-Eui Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Yong-Il Cho
- Department of Animal Science & Technology, Suncheon National University, Suncheon 57922, Korea
| | - Eui-Hyung Kim
- National Institute of Animal Science, Rural Development Administration, Pyeongchang 25340, Korea
| | - Myunghwan Jung
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Seung Won Shin
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Su-Hyung Lee
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Dae-Yong Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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6
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Hahn N, Failing K, Eisenberg T, Schlez K, Zschöck PM, Donat K, Einax E, Köhler H. Evaluation of different diagnostic methods for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples. BMC Vet Res 2017; 13:259. [PMID: 28821251 PMCID: PMC5563032 DOI: 10.1186/s12917-017-1173-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/09/2017] [Indexed: 11/29/2022] Open
Abstract
Background Environmental sampling based on boot swabs and/or liquid manure samples is an upcoming strategy for the identification of paratuberculosis (paraTB) positive herds, but only limited data are available regarding the diagnostic performance of molecular detection methods (qPCR) versus faecal culture (FC) for this purpose. In the present study, the test characteristics of two different qPCR protocols (A and B) and a standardized FC protocol, for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples were evaluated. Results In 19 paraTB unsuspicious and 58 paraTB positive herds boot swabs and liquid manure were sampled simultaneously and analyzed in three different diagnostic laboratories. Using boot swabs and liquid manure, a substantial to excellent accordance was found between both qPCRs, for boot swabs also with culture, while for liquid manure the detection rate of culture was decreased after prolonged storage at −20 °C. The quantitative results of both qPCR methods correlated well for the same sample and also for boot swabs and liquid manure from the same herd. When cut-off threshold cycle (CT-)-values were applied as recommended by the manufacturers, herd level specificity (Sp) of qPCR B was below 100% for boot swabs and for both qPCRs for liquid manure. A decreased herd level sensitivity was encountered after adjustment of Sp to 100% and re-calculation of the cut-off CT-values. Conclusions qPCR is equally suitable as bacterial culture for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples. Both matrices represent easily accessible composite environmental samples which can be tested with reliable results. The data encourage qPCR testing of composite environmental samples for paraTB herd diagnosis.
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Affiliation(s)
- Nathalie Hahn
- Animal Health Service, Thuringian Animal Diseases Fund, Jena, Thuringia, Germany
| | - Klaus Failing
- Unit for Biomathematics and Data Processing, Justus-Liebig-University, Gießen, Hesse, Germany
| | - Tobias Eisenberg
- Department Veterinary Medicine, Hessian State Laboratory, Gießen, Hesse, Germany
| | - Karen Schlez
- Department Veterinary Medicine, Hessian State Laboratory, Gießen, Hesse, Germany
| | | | - Karsten Donat
- Animal Health Service, Thuringian Animal Diseases Fund, Jena, Thuringia, Germany
| | - Esra Einax
- Animal Health Service, Thuringian Animal Diseases Fund, Jena, Thuringia, Germany
| | - Heike Köhler
- Institute for Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Thuringia, Germany.
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7
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Ravva SV, Harden LA, Sarreal CZ. Characterization and Differentiation of Mycobacterium avium subsp. paratuberculosis from Other Mycobacteria Using Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Front Cell Infect Microbiol 2017; 7:297. [PMID: 28713782 PMCID: PMC5491938 DOI: 10.3389/fcimb.2017.00297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/16/2017] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease in cattle, is responsible for significant economic losses to the US dairy industry. The pathogen has also been associated with chronic human diseases like Crohn's disease, type 1 diabetes and multiple sclerosis. Determining causation requires rapid characterization and source tracking the pathogen. Here, we used matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to characterize and differentiate strains of MAP from 14 other species of Mycobacterium from bovine, human, and environmental sources. Lysates from cells disrupted by bead beating in TFA-acetonitrile solution were analyzed by MALDI-TOF. MAP strains were differentiated by mass spectral profiles that are distinct from each other and from other Mycobacterium species. Cluster analysis of spectral profiles indicates two distinct clusters, one dominated by the members of avium complex and a second group dominated by members of fortuitum and parafortuitum complexes. We believe that MALDI-TOF methods can be used to differentiate and source-track MAP strains.
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Affiliation(s)
- Subbarao V Ravva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of AgricultureAlbany, CA, United States
| | - Leslie A Harden
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of AgricultureAlbany, CA, United States
| | - Chester Z Sarreal
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of AgricultureAlbany, CA, United States
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8
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Daems D, Knez K, Delport F, Spasic D, Lammertyn J. Real-time PCR melting analysis with fiber optic SPR enables multiplex DNA identification of bacteria. Analyst 2017; 141:1906-11. [PMID: 26881275 DOI: 10.1039/c5an02342d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fiber optic surface plasmon resonance (FO-SPR) technology was developed that enables simultaneous quantification and identification of multiple DNA targets on the same platform. The bioassay was based on the hybridization/melting of DNA-coated Au nanoparticles on the FO-SPR sensor when targets are present. The multiplex concept was successfully demonstrated on two related bacteria and for detection of multiple mutations in sequences. In conclusion, FO-SPR technology shows a great potential as a next generation in vitro diagnostics tool.
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Affiliation(s)
- D Daems
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - K Knez
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - F Delport
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - D Spasic
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - J Lammertyn
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
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Utility of Real-Time Quantitative Polymerase Chain Reaction in Detecting Mycobacterium tuberculosis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1058579. [PMID: 28168192 PMCID: PMC5266798 DOI: 10.1155/2017/1058579] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/20/2016] [Indexed: 11/18/2022]
Abstract
This study aimed to assess the value of real-time quantitative polymerase chain reaction (RT-qPCR) for the detection of Mycobacterium tuberculosis (MTB). Samples from 192 patients with suspected MTB were examined by RT-qPCR and an improved Löwenstein-Jensen (L-J) culture method. To evaluate the diagnostic usefulness of RT-qPCR in detecting MTB, a receiver operating characteristic (ROC) curve for RT-qPCR was generated, and the area under the curve (AUC) as well as a cutoff value was calculated. Using the L-J culture method as the gold standard, accuracy of the RT-qPCR method for detecting MTB was 92.7%, with sensitivity and specificity of 62.5% and 97.02%, respectively. In comparison with the improved L-J culture method, the AUC of RT-qPCR ROC curve was 0.957, which was statistically significant (p < 0.001). The Youden Index reached the maximum value (0.88) for gene copy number of 794.5 IU/mL, which was used as the cutoff value. RT-qPCR detection of MTB yielded results consistent with those of the improved L-J culture method, with high accuracy. RT-qPCR may be used as an auxiliary method for etiological diagnosis of tuberculosis.
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Selim AM, Gaede W. Comparative Evaluation of PCR Assay for Direct Detection of Mycobacterium avium subsp. paratuberculosis in Ruminant. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ajava.2015.761.771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Shin MK, Shin SW, Jung M, Park H, Park HE, Yoo HS. Host gene expression for Mycobacterium avium subsp. paratuberculosis infection in human THP-1 macrophages. Pathog Dis 2015; 73:ftv031. [PMID: 25877879 DOI: 10.1093/femspd/ftv031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2015] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, which causes considerable economic loss in the dairy industry and has a possible relationship to Crohn's disease (CD) in humans. As MAP has been detected in retail pasteurized milk samples, its transmission via milk is of concern. Despite its possible role in the etiology of CD, there have been few studies examining the interactions between MAP and human cells. In the current study, we applied Ingenuity Pathway Analysis to the transcription profiles generated from a murine model with MAP infection as part of a previously conducted study. Twenty-one genes were selected as potential host immune responses, compared with the transcriptional profiles in naturally MAP-infected cattle, and validated in MAP-infected human monocyte-derived macrophage THP-1 cells. Of these, the potential host responses included up-regulation of genes related to immune response (CD14, S100A8, S100A9, LTF, HP and CHCIL3), up-regulation of Th1-polarizing factor (CCL4, CCL5, CXCL9 and CXCL10), down-regulation of genes related to metabolism (ELANE, IGF1, TCF7L2 and MPO) and no significant response of other genes (GADD45a, GPNMB, HMOX1, IFNG and NQO1) in THP-1 cells infected with MAP.
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Affiliation(s)
- Min-Kyoung Shin
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Korea Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 1Z3, Canada
| | - Seung Won Shin
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Korea
| | - Myunghwan Jung
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Korea
| | - Hongtae Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Korea
| | - Hyun-Eui Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Korea
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Korea Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, 232-916, Korea
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12
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Chern EC, King D, Haugland R, Pfaller S. Evaluation of quantitative polymerase chain reaction assays targeting Mycobacterium avium, M. intracellulare, and M. avium subspecies paratuberculosis in drinking water biofilms. JOURNAL OF WATER AND HEALTH 2015; 13:131-9. [PMID: 25719473 DOI: 10.2166/wh.2014.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mycobacterium avium (MA), Mycobacterium intracellulare (MI), and Mycobacterium avium subsp. paratuberculosis (MAP) are difficult to culture due to their slow growing nature. A quantitative polymerase chain reaction (qPCR) method for the rapid detection of MA, MI, and MAP can be used to provide data supporting drinking water biofilms as potential sources of human exposure. The aim of this study was to characterize two qPCR assays targeting partial 16S rRNA gene sequences of MA and MI and use these assays, along with two previously reported MAP qPCR assays (IS900 and Target 251), to investigate Mycobacterium occurrence in kitchen faucet biofilms. MA and MI qPCR assays demonstrated 100% specificity and sensitivity when evaluated against 18 non-MA complex, 76 MA, and 17 MI isolates. Both assays detected approximately 1,000 cells from a diluted cell stock inoculated on a sampling swab 100% of the time. DNA analysis by qPCR indicated that 35.3, 56.9 and 11.8% of the 51 kitchen faucet biofilm samples collected contained MA, MI, and MAP, respectively. This study introduces novel qPCR assays designed to specifically detect MA and MI in biofilm. Results support the use of qPCR as an alternative to culture for detection and enumeration of MA, MI, and MAP in microbiologically complex samples.
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Affiliation(s)
- Eunice C Chern
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Dawn King
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Richard Haugland
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Stacy Pfaller
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
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13
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Effective DNA extraction method to improve detection of Mycobacterium avium subsp. paratuberculosis in bovine feces. ACTA ACUST UNITED AC 2014. [DOI: 10.14405/kjvr.2014.54.1.55] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Su Y, Wang S, Guo J, Xue B, Xu L, Que Y. A TaqMan real-time PCR assay for detection and quantification of Sporisorium scitamineum in sugarcane. ScientificWorldJournal 2013; 2013:942682. [PMID: 24228020 PMCID: PMC3819024 DOI: 10.1155/2013/942682] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/04/2013] [Indexed: 11/18/2022] Open
Abstract
Sporisorium scitamineum is a fungal smut pathogen epidemic in sugarcane producing areas. Early detection and proper identification of the smut are an essential requirement in its management practice. In this study, we developed a TaqMan real-time PCR assay using specific primers (bEQ-F/bEQ-R) and a TaqMan probe (bEQ-P) which were designed based on the bE (b East mating type) gene (Genbank Accession no. U61290.1). This method was more sensitive (a detection limit of 10 ag pbE DNA and 0.8 ng sugarcane genomic DNA) than that of conventional PCR (10 fg and 100 ng, resp.). Reliability was demonstrated through the positive detection of samples collected from artificially inoculated sugarcane plantlets (FN40). This assay was capable of detecting the smut pathogen at the initial stage (12 h) of infection and suitable for inspection of sugarcane pathogen-free seed cane and seedlings. Furthermore, quantification of pathogen was verified in pathogen-challenged buds in different sugarcane genotypes, which suggested its feasibility for evaluation of smut resistance in different sugarcane genotypes. Taken together, this novel assay can be used as a diagnostic tool for sensitive, accurate, fast, and quantitative detection of the smut pathogen especially for asymptomatic seed cane or plants and evaluation of smut resistance of sugarcane genotypes.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shanshan Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bantong Xue
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Karunasena E, Kurkure PC, Lackey RD, McMahon KW, Kiernan EP, Graham S, Alabady MS, Campos DL, Tatum OL, Brashears MM. Effects of the probiotic Lactobacillus animalis in murine Mycobacterium avium subspecies paratuberculosis infection. BMC Microbiol 2013; 13:8. [PMID: 23324647 PMCID: PMC3563475 DOI: 10.1186/1471-2180-13-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/07/2013] [Indexed: 01/29/2023] Open
Abstract
Background MAP is a suspected zoonotic pathogen and the causative agent of Johne’s Disease in cattle and other ruminant animals. With over $1 billion dollars in loss to the dairy industry due to Johne’s Disease, efforts to eliminate or reduce MAP from cattle are of importance. The purpose of this study was to determine if daily intake of probiotics could eliminate or reduce Johne’s Disease associated symptoms and pathogenesis by MAP. Post infection, animals are often asymptomatic carriers with limited shedding of the pathogen, proving early detection to be difficult. Disease and symptoms often appear 3–4 years after infection with antibiotic treatment proving ineffective. Symptoms include chronic gastrointestinal inflammation leading to severe weight-loss from poor feed and water intake cause a wasting disease. These symptoms are similar to those found in individuals with Crohn’s Disease (CD); MAP has been implicated by not proven to be the causative agent of CD. Probiotics administered to livestock animals, including dairy and beef cattle have demonstrated improvements in cattle performance and health. Our objectives included determining the benefits of Lactobacillus animalis (strain name: NP-51) in MAP infected BALB/c mice by evaluating systemic and gastrointestinal response by the host and gut microbiota. Male and female animals were fed 1×106 CFU/g probiotics in sterile, powdered mouse chow daily and infected with 1 × 107 CFU/ml MAP and compared to controls. Animals were evaluated for 180 days to assess acute and chronic stages of disease, with sample collection from animals every 45 days. MAP concentrations from liver and intestinal tissues were examined using real time-PCR methods and the expression of key inflammatory markers were measured during MAP infection (interferon-gamma [IFN-Υ], Interleukin-1α, IL-12, IL-10, IL-6, and Tumor necrosis factor alpha [TNF-α]). Results Our results demonstrate administration of probiotics reduces production of IFN-Υ and IL-6 while increasing TNF-α and IL-17 in chronic disease; healthful immune responses that reduce chronic inflammation associated to MAP infection. Conclusions We observed that the immune system’s response in the presence of probiotics to MAP contributes towards host health by influencing the activity of the immune system and gut microbial populations.
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Affiliation(s)
- Enusha Karunasena
- Virginia Tech, MC 0477, Washington Street, Blacksburg, VA 24061, USA.
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16
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Kralik P, Beran V, Pavlik I. Enumeration of Mycobacterium avium subsp. paratuberculosis by quantitative real-time PCR, culture on solid media and optical densitometry. BMC Res Notes 2012; 5:114. [PMID: 22357065 PMCID: PMC3305647 DOI: 10.1186/1756-0500-5-114] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/22/2012] [Indexed: 11/23/2022] Open
Abstract
Background Different approaches are used for determining the number of Mycobacterium avium subsp. paratuberculosis (MAP) cells in a suspension. The majority of them are based upon culture (determination of CFU) or visual/instrumental direct counting of MAP cells. In this study, we have compared the culture method with a previously published F57 based quantitative real-time PCR (F57qPCR) method, to determine their relative abilities to count the number of three different MAP isolates in suspensions with the same optical densities (OD). McFarland turbidity standards were also compared with F57qPCR and culture, due to its frequent inclusion and use in MAP studies. Findings The numbers of MAP in two-fold serial dilutions of isolates with respective OD measurements were determined by F57qPCR and culture. It was found that culture provided lower MAP CFU counts by approximately two log10, compared to F57qPCR. The McFarland standards (as defined for E. coli) showed an almost perfect fit with the enumeration of MAP performed by F57qPCR. Conclusions It is recommended to use culture and/or qPCR estimations of MAP numbers in experiments where all subsequent counts are performed using the same method. It is certainly not recommended the use of culture as the standard for qPCR experiments and vice versa.
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Affiliation(s)
- Petr Kralik
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic.
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17
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Ravva SV, Sarreal CZ, Mandrell RE. Bacterial communities in aerosols and manure samples from two different dairies in central and Sonoma valleys of California. PLoS One 2011; 6:e17281. [PMID: 21364996 PMCID: PMC3041799 DOI: 10.1371/journal.pone.0017281] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 01/28/2011] [Indexed: 11/19/2022] Open
Abstract
Aerosols have been suspected to transport food pathogens and contaminate fruits and vegetables grown in close proximity to concentrated animal feeding operations, but studies are lacking that substantiate such transport. To monitor the potential transport of bacteria originated from fresh or dry manure through aerosols on a dairy, we identified by 16S rRNA sequencing, bacteria in aerosols collected within 2 to 3 meters from dairy cows at two dairies. Gram-positive Firmicutes were predominant in aerosols from a dairy in Sonoma, California, and surrounded by vineyards, in contrast to sequences of Gram-negative Proteobacteria predominant in aerosols from a dairy in Modesto, California, also surrounded by other dairies. Although Firmicutes represented approximately 50% of the 10 most abundant sequences, aerosols from the Sonoma dairy also contained sequences of Bacteriodetes and Actinobacteria, identified previously with animal feces. While none of the top 10 sequences from fresh or dry manure from Modesto dairy were detected in aerosols, two of the sequences from the phylum Bacteriodetes and one from class Clostridia from fresh manure were detected in aerosols from Sonoma. Interestingly, none of the sequences from dry manure were in the top 10 sequences in aerosols from both dairies. The 10 most abundant sequences in aerosols from the Modesto dairy were all from Proteobacteria and nearly half of them were from genus Massilia, which have been isolated previously from immune-compromised people and aerosols. We conclude that the predominant bacteria in aerosols are diverse among locations and that they do not reflect the predominant species of bacteria present in cow feces and/or in close proximity to cows. These results suggest that the aerosol sequences did not originate from manure. Large volumes of aerosols would be required to determine if bacterial sequences from aerosols could be used to track bacteria in manure to crops grown in proximity.
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Affiliation(s)
- Subbarao V. Ravva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, United States Department of Agriculture, Albany, California, United States of America
- * E-mail:
| | - Chester Z. Sarreal
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, United States Department of Agriculture, Albany, California, United States of America
| | - Robert E. Mandrell
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, United States Department of Agriculture, Albany, California, United States of America
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18
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Timms VJ, Gehringer MM, Mitchell HM, Daskalopoulos G, Neilan BA. How accurately can we detect Mycobacterium avium subsp. paratuberculosis infection? J Microbiol Methods 2011; 85:1-8. [PMID: 21281678 DOI: 10.1016/j.mimet.2011.01.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/20/2011] [Accepted: 01/24/2011] [Indexed: 01/03/2023]
Abstract
Mycobacteria have thwarted detection by scientists for centuries. Mycobacterium paratuberculosis is one of the most fastidious of the Mycobacteriaceae, and has been implicated in both animal and human diseases. In domestic livestock, M. paratuberculosis has been associated with Johne's disease, which given its increasing incidence, is currently a cause for concern, due to the potential for M. paratuberculosis to enter our food chain. In addition, a tenuous link has been reported between M. paratuberculosis and Crohn's disease, however evidence to support this link is hampered by the lack of accurate methodologies for detection of M. paratuberculosis in humans. This review compares the sensitivity and specificity of traditional and more recent techniques to the culture and molecular detection of M. paratuberculosis. While serology and culture are popular choices for the livestock industry they have not produced useful data for human infection. Although the advent of molecular biology has enabled faster diagnosis of M. paratuberculosis in human infection, there is currently no gold standard such as culture on which to validate these findings. Even with DNA/RNA detection methods, there is the ever present issue of the genetic relatedness of M. paratuberculosis to other mycobacteria of the Mycobacterium avium complex, some of which also infect humans with very different pathological outcomes. Recent developments in this field include more rapid methods of M. paratuberculosis culture as well as the development of more accurate and sensitive PCR assays. The application of these techniques should offer a greater insight as to the role of M. paratuberculosis in human gastrointestinal diseases.
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Affiliation(s)
- Verlaine J Timms
- School of Biotechnology and Biomolecular Science, University of NSW, Sydney, NSW 2052, Australia.
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19
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Zhang MZ, Zhang S. An Efficient DNA Extraction Method for Polymerase Chain Reaction–Based Detection of Mycobacterium Avium Subspecies Paratuberculosis in Bovine Fecal Samples. J Vet Diagn Invest 2011; 23:41-8. [DOI: 10.1177/104063871102300106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Due to the lipid rich cell wall of Mycobacterium avium subspecies paratuberculosis (MAP), the complex nature of bovine feces, and intermittent organism shedding by infected cattle, it is difficult to recover a sufficient amount of high-quality MAP DNA from fecal samples, directly affecting the sensitivity of downstream polymerase chain reaction (PCR) tests. In the current study, a DNA extraction method, designated the Mississippi Veterinary Research and Diagnostic Laboratory (MVRDL) method, was developed for PCR-based detection of MAP in bovine fecal samples. The MVRDL method combined multiple procedures, including chemical pretreatment, 1-tube cell lysis and extraction, chelex matrix absorption, and mini-column purification. The DNA yield and purity, as measured by spectrophotometry, was 3.36 fg per colony forming unit (CFU) MAP and A260/280 absorbance ratio of 2, respectively. This method was further evaluated by real-time PCR. A linear correlation was found between cycle-threshold (Ct) and log input CFU (ranging from 7.2 to 7.2 × 107 CFU per ml or CFU per g). The detection limit of the real-time PCR assay was 3 CFU per ml of MAP culture or per g of MAP-spiked feces. In addition, the MVRDL method was validated by performing 7 Johne's direct fecal PCR proficiency tests administered by the National Veterinary Service Laboratories. Based on culture results as the “gold standard,” the specificity of MVRDL PCR was 100%, and the sensitivity was 98.46% for samples containing more than 1.5 CFU per tube of fecal cultures. To the authors' knowledge, this is the most efficient MAP DNA extraction method in comparison with all previously published protocols.
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Affiliation(s)
- Michael Z. Zhang
- Mississippi Veterinary Research and Diagnostic Laboratory, Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Pearl, MS
| | - Shuping Zhang
- Yhe Department of Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX
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20
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Jafarzadeh SR, Johnson WO, Utts JM, Gardner IA. Bayesian estimation of the receiver operating characteristic curve for a diagnostic test with a limit of detection in the absence of a gold standard. Stat Med 2010; 29:2090-106. [DOI: 10.1002/sim.3975] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Assessment of food as a source of exposure to Mycobacterium avium subspecies paratuberculosis (MAP). J Food Prot 2010; 73:1357-97. [PMID: 20615354 DOI: 10.4315/0362-028x-73.7.1357] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The National Advisory Committee on Microbiological Criteria for Foods assessed the importance of food as a source of exposure to Mycobacterium avium subspecies paratuberculosis (MAP). MAP is the causative agent of Johne's disease, which affects primarily the small intestine of all ruminants. The significance of MAP as a human pathogen is unknown and is being investigated by several research groups. This document also reviews the efficacy of current detection methods, processing interventions, and MAP inactivation. Research needs related to MAP are provided. The Committee reached the following conclusions: current methods for detection of MAP have significant limitations, and a standard method for the detection of viable MAP cells is needed. Aside from MAP-infected domestic ruminant animals, the organism is found infrequently. If MAP in cattle is controlled, the source of MAP in other animals, food, and water may largely be eliminated. Milk, particularly raw milk, may be a likely food source for human exposure to MAP. Given the prevalence of MAP in U.S. cattle herds, ground beef may be a potential source of MAP. Although humans may be exposed to MAP through a variety of routes, including food and the environment, the frequency and amount of exposure will require additional research.
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Affiliation(s)
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- U.S. Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, Washington, DC 20250-3700, USA
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22
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Specific detection of unamplified mycobacterial DNA by use of fluorescent semiconductor quantum dots and magnetic beads. J Clin Microbiol 2010; 48:2830-5. [PMID: 20554817 DOI: 10.1128/jcm.00185-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we present the development of a specific DNA detection method using fluorescent semiconductor quantum dots (QDs) and magnetic beads (MBs) for fast detection of Mycobacterium spp., dispensing with the need for DNA amplification. Two biotinylated oligonucleotide probes were used to recognize and detect specific complementary mycobacterial target DNA through a sandwich hybridization reaction. Cadmium selenite QDs conjugated with streptavidin and species-specific probes were used to produce a fluorescent signal. MBs conjugated with streptavidin and a genus-specific probe were used to isolate and concentrate the DNA targets. The application of the proposed method to isolated bacteria produced the expected result in all cases. The minimum detection limit of the assay was defined as 12.5 ng of DNA diluted in a sample volume of 20 microl. In order to obtain an indication of the method's performance with clinical samples, we applied the optimized assay to the detection of Mycobacterium tuberculosis in DNA isolated from bronchoalveolar lavage specimens from patients with tuberculosis and Mycobacterium avium subsp. paratuberculosis in DNA isolated from feces and paraffin-embedded tissues in comparison with culture, Ziehl-Neelsen staining, and real-time PCR. The concordance of these methods compared to the proposed method with regard to positive and negative samples varied between 53.84% and 87.23% and between 84.61% and 100%, respectively. The overall accuracy of the QD assay compared to real-time PCR was 70 to 90% depending on the type of clinical material. The proposed diagnostic assay offers a simple, rapid, specific, and cost-effective method for direct detection and identification of mycobacterial DNA in clinical samples.
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23
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Pozzato N, Stefani E, Capello K, Muliari R, Vicenzoni G. Mycobacterium avium subsp. paratuberculosis as a template in the evaluation of automated kits for DNA extraction from bovine organs. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0423-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Liandris E, Gazouli M, Andreadou M, Čomor M, Abazovic N, Sechi LA, Ikonomopoulos J. Direct detection of unamplified DNA from pathogenic mycobacteria using DNA-derivatized gold nanoparticles. J Microbiol Methods 2009; 78:260-4. [PMID: 19539667 DOI: 10.1016/j.mimet.2009.06.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 06/01/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
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25
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One-step real-time quantitative PCR assays for the detection and field study of Sacbrood honeybee and Acute bee paralysis viruses. J Virol Methods 2009; 161:240-6. [PMID: 19559729 DOI: 10.1016/j.jviromet.2009.06.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 06/12/2009] [Accepted: 06/16/2009] [Indexed: 11/21/2022]
Abstract
Two one-step real-time RT-PCR assays, based on SYBR Green (SG) chemistry, were developed or adapted respectively, for the detection, differentiation, and quantitation of two important honeybee viruses: Sacbrood virus (SBV) and Acute bee paralysis virus (ABPV). Both reactions were optimized to yield the highest sensitivity and specificity. The genome equivalent copies (GEC) detection limit per reaction was 389.3 for the ABPV RT-PCR. The GEC detection limit per reaction was 298.9 for the SBV RT-PCR. Viral detection and identification were confirmed by melting curve analysis and sequencing of the PCR products. Both techniques were used to evaluate Spanish field samples and establish the distribution of these viruses. Acute bee paralysis virus was not detected, and Sacbrood virus was present at low frequencies. The one-step real-time SG RT-PCR methods are fast, accurate, and useful for detecting and quantifying these honeybee viruses, which cause inapparent infections and contribute to the increasing depopulation of honeybee colonies.
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26
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Wen Z, Yu L, Yang W, Wang J, Zhao J, Li N, Lu J, Li J. Detection of viral aerosols by use of real-time quantitative PCR. AEROBIOLOGIA 2009; 25:65-73. [PMID: 32214624 PMCID: PMC7087933 DOI: 10.1007/s10453-009-9110-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 01/09/2009] [Indexed: 05/14/2023]
Abstract
PCR quantification is regarded as one of the most promising techniques for real-time identification of bio-aerosols. We have, therefore, validated a QPCR assay for quantification of a viral aerosol sample using the double-stranded DNA-binding dye SYBR green I, an economical alternative for quantification of target microorganisms. To achieve this objective we used mycobacteriophage D29 as model organism. Phage D29 aerosol was produced in an aerosol cabinet and then collected by use of an AGI liquid sampler. A standard curve was created by use of purified genomic DNA from the phage in liquid culture of known concentration measured by titration. To prevent false-positive results caused by formation of primer-dimers, an additional data-acquisition step was added to the three-step QPCR procedure; the new technique was called four-step QPCR. The standard curve was then used to quantify the total amount of phage D29 in liquid culture and aerosol samples. For liquid culture samples there was no significant difference (P > 0.05) between results from quantification of the virus using double-agar culture and QPCR. For aerosol samples, however, the result determined by the QPCR method was significantly (P < 0.05) higher than that from the double-agar culture method. The four-step SYBR green I QPCR method is a quick quantitative method for mycobacteriophage D29 aerosol. We believe that QPCR using SYBR green I dye will be an economical method for detection of airborne bio-aerosols.
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Affiliation(s)
- Zhanbo Wen
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Long Yu
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Wenhui Yang
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Jie Wang
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Jianjun Zhao
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Na Li
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Jianchun Lu
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
| | - Jinsong Li
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 100071 Beijing, People’s Republic of China
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27
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Nelli RK, Graham E, Dunham SP, Taylor DJ. Real-time PCR identification of Mycobacterium avium
subspecies paratuberculosis
in ovine and bovine tissues. Vet Rec 2008; 163:422-3. [DOI: 10.1136/vr.163.14.422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- R. K. Nelli
- Institute of Comparative Medicine; Faculty of Veterinary Medicine; University of Glasgow; Bearsden Glasgow G61 1QH
| | - E. Graham
- Institute of Comparative Medicine; Faculty of Veterinary Medicine; University of Glasgow; Bearsden Glasgow G61 1QH
| | - S. P. Dunham
- Institute of Comparative Medicine; Faculty of Veterinary Medicine; University of Glasgow; Bearsden Glasgow G61 1QH
| | - D. J. Taylor
- Institute of Comparative Medicine; Faculty of Veterinary Medicine; University of Glasgow; Bearsden Glasgow G61 1QH
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28
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Prevalence on beef carcasses of Mycobacterium avium subsp. paratuberculosis DNA. Int J Food Microbiol 2008; 124:291-4. [DOI: 10.1016/j.ijfoodmicro.2008.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 02/22/2008] [Accepted: 03/24/2008] [Indexed: 11/20/2022]
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29
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Li W, Li D, Twieg E, Hartung JS, Levy L. Optimized Quantification of Unculturable Candidatus Liberibacter Spp. in Host Plants Using Real-Time PCR. PLANT DISEASE 2008; 92:854-861. [PMID: 30769724 DOI: 10.1094/pdis-92-6-0854] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Citrus huanglongbing (HLB) is caused by the phloem-limited and psyllid-vectored Candidatus Liberibacter spp. and is a destructive disease of citrus that is rapidly increasing in importance. The disease was reported recently in the principle citrus-producing areas of São Paulo, Brazil in 2004 and in Florida in 2005. A variety of laboratory methods have been developed to confirm a symptom-based disease diagnosis or for the detection or identification of the pathogen; however, no quantitative information has been available on the pathogen titer in either host or vector interactions because the pathogen remains unculturable in artificial media. We previously developed a quantitative polymerase chain reaction (PCR)-based assay for detection of Ca. Liberibacter spp. and, in this study, we evaluated the effects of sample composition on quantification of the pathogen in citrus plants by TaqMan real-time PCR. Standard curves were established using cloned plasmids containing target DNA from the pathogen and with total DNA samples from field-grown HLB-infected citrus plants. Regression analysis showed that a standard curve established with DNA extracted from naturally infected field-grown plants was more accurate than the standard curve constructed from plasmids containing the amplification targets as cloned inserts. Nontarget DNA and putative PCR inhibitors from citrus plants decreased the sensitivity and the amplification efficiency of real-time PCR when plasmids provided the template target in "spiked" healthy citrus DNA extracts. This effect varied among plant tissue types, citrus species, and geographic locations. Based on these sample effects, a universal standard curve has been established for quantification of the pathogen in various citrus tissues of different citrus species planted in different geographic locations. Sample storage at 4°C for 2 months prior to PCR assay did not affect subsequent quantification of the pathogen. The validated quantitative real-time PCR method and the universal standard curve will be very useful for studies of host-pathogen interactions and epidemiology, and in the development of control strategies for the disease.
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Affiliation(s)
- Wenbin Li
- National Plant Germplasm and Biotechnology Laboratory, United States Department of Agriculture-Animal and Plant Health Inspection Service (USDA-APHIS)-PPQ-CPHST, Beltsville, MD 20705
| | - Dayan Li
- Harvard University, Cambridge, MA 02138
| | - Elizabeth Twieg
- National Plant Germplasm and Biotechnology Laboratory, USDA-APHIS-PPQ-CPHST
| | - John S Hartung
- USDA-Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705
| | - Laurene Levy
- National Plant Germplasm and Biotechnology Laboratory, United States Department of Agriculture-Animal and Plant Health Inspection Service (USDA-APHIS)-PPQ-CPHST, Beltsville, MD 20705
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Zwart MP, van Oers MM, Cory JS, van Lent JW, van der Werf W, Vlak JM. Development of a quantitative real-time PCR for determination of genotype frequencies for studies in baculovirus population biology. J Virol Methods 2008; 148:146-54. [DOI: 10.1016/j.jviromet.2007.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/17/2007] [Accepted: 10/26/2007] [Indexed: 11/15/2022]
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31
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McCrea JK, Liu C, Ng LK, Wang G. Detection of the Escherichia coli pathogenic gene eae with three real-time polymerase chain reaction methods. Can J Microbiol 2007; 53:398-403. [PMID: 17538649 DOI: 10.1139/w06-148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Several real-time polymerase chain reaction (PCR) methods are currently available to rapidly detect the presence of a specific DNA sequence. When used for detection of pathogenic organisms, the turnaround time for PCR-based methods is much lower than for traditional culture techniques. This study compared the sensitivity of three real-time PCR methods when detecting the Escherichia coli pathogenic gene eae to determine which method is most effective in identifying very low levels of the organism. The three methods were used to detect the eae gene over a range of DNA concentrations. The differences in sensitivity were statistically significant (p<0.05), and SYBR Green I PCR was found to have the lowest detection limit of the three; LUX primers had the highest detection limit. Therefore, using a defined DNA concentration for detecting the eae gene, SYBR Green I is the best alternative.
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32
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Cook KL, Britt JS. Optimization of methods for detecting Mycobacterium avium subsp. paratuberculosis in environmental samples using quantitative, real-time PCR. J Microbiol Methods 2006; 69:154-60. [PMID: 17257697 DOI: 10.1016/j.mimet.2006.12.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 12/13/2006] [Accepted: 12/21/2006] [Indexed: 11/28/2022]
Abstract
Detection of Johne's disease, an enteric infection of cattle caused by Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis), has been impeded by the lack of rapid, reliable detection methods. The goal of this study was to optimize methodologies for detecting M. paratuberculosis in manure from an infected dairy cow or in contaminated soil samples using a quantitative, real-time PCR (QRT-PCR) based analysis. Three different nucleic acid extraction techniques, the efficiency of direct versus indirect sample extraction, and sample pooling were assessed. The limit of detection was investigated by adding dilutions of M. paratuberculosis to soil. Results show that the highest yield (19.4+/-2.3 microg(-1) DNA extract) and the highest copy number of the targeted M. paratuberculosis IS900 sequence (1.3+/-0.2x10(8) copies g(-1) manure) were obtained with DNA extracted from manure using Qbiogene's Fast DNA Spin kit for soil. Pooling ten samples of M. paratuberculosis-contaminated soil improved the limit of detection ten fold (between 20 and 115 M. paratuberculosis cells g(-1) soil). Detection was between 65% and 95% higher when samples were extracted directly using bead-beating than when using pre-treatment with cell extraction buffers. The final soil-sampling and extraction regime was applied for detection of M. paratuberculosis in pasture soil after the removal of a M. paratuberculosis culture positive dairy cow. M. paratuberculosis remained in the pasture soil for more than 200 days. Results from these studies suggest that DNA extraction method, sampling protocol and PCR conditions each critically influence the outcome and validity of the QRT-PCR analysis of M. paratuberculosis concentrations in environmental samples.
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Affiliation(s)
- Kimberly L Cook
- AWMRU, USDA-ARS, 230 Bennett Lane, Bowling Green, KY 42104, USA.
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Herthnek D, Bölske G. New PCR systems to confirm real-time PCR detection of Mycobacterium avium subsp. paratuberculosis. BMC Microbiol 2006; 6:87. [PMID: 17020599 PMCID: PMC1609169 DOI: 10.1186/1471-2180-6-87] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 10/04/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Johne's disease, a serious chronic form of enteritis in ruminants, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). As the organism is very slow-growing and fastidious, several PCR-based methods for detection have been developed, based mainly on the MAP-specific gene IS900. However, because this gene is similar to genes in other mycobacteria, there is a need for sensitive and reliable methods to confirm the presence of MAP. As described here, two new real-time PCR systems on the IS900 gene and one on the F57 gene were developed and carefully validated on 267 strains and 56 positive clinical faecal samples. RESULTS Our confirmatory PCR systems on IS900 were found sensitive and specific, only yielding weak false positive reactions in one strain for each system. The PCR system on F57 did not elicit any false positives and was only slightly less sensitive than our primary IS900-system. DNA from both naturally infected and spiked faeces that tested positive with our primary system could be confirmed with all new systems, except one low-level infected sample that tested negative with the F57 system. CONCLUSION We recommend using the newly constructed DH3 PCR system on the F57 gene as the primary confirmatory test for PCR positives, but should it fail due to its lower sensitivity, the DH1 and DH2 PCR systems should be used.
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Affiliation(s)
- David Herthnek
- National Veterinary Institute (SVA), Department of Bacteriology, SE-751 89 Uppsala, Sweden
| | - Göran Bölske
- National Veterinary Institute (SVA), Department of Bacteriology, SE-751 89 Uppsala, Sweden
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