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Morka K, Bystroń J, Bania J, Korzeniowska-Kowal A, Korzekwa K, Guz-Regner K, Bugla-Płoskońska G. Identification of Yersinia enterocolitica isolates from humans, pigs and wild boars by MALDI TOF MS. BMC Microbiol 2018; 18:86. [PMID: 30119648 PMCID: PMC6098659 DOI: 10.1186/s12866-018-1228-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/06/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Yersinia enterocolitica is widespread within the humans, pigs and wild boars. The low isolation rate of Y. enterocolitica from food or environmental and clinical samples may be caused by limited sensitivity of culture methods. The main goal of present study was identification of presumptive Y. enterocolitica isolates using MALDI TOF MS. The identification of isolates may be difficult due to variability of bacterial strains in terms of biochemical characteristics. This work emphasizes the necessity of use of multiple methods for zoonotic Y. enterocolitica identification. RESULTS Identification of Y. enterocolitica isolates was based on MALDI TOF MS, and verified by VITEK® 2 Compact and PCR. There were no discrepancies in identification of all human' and pig' isolates using MALDI TOF MS and VITEK® 2 Compact. However three isolates from wild boars were not decisively confirmed as Y. enterocolitica. MALDI TOF MS has identified the wild boar' isolates designated as 3dz, 4dz, 8dz as Y. enterocolitica with a high score of matching with the reference spectra of MALDI Biotyper. In turn, VITEK® 2 Compact identified 3dz and 8dz as Y. kristensenii, and isolate 4dz as Y. enterocolitica. The PCR for Y. enterocolitica 16S rDNA for these three isolates was negative, but the 16S rDNA sequence analysis identified these isolates as Y. kristensenii (3dz, 4dz) and Y. pekkanenii (8dz). The wild boar' isolates 3dz, 4dz and 8dz could not be classified using biotyping. The main bioserotype present within pigs and human faeces was 4/O:3. It has been shown that Y. enterocolitica 1B/O:8 can be isolated from human faeces using ITC/CIN culturing. CONCLUSION The results of our study indicate wild boars as a reservoir of new and atypical strains of Yersinia, for which protein and biochemical profiles are not included in the MALDI Biotyper or VITEK® 2 Compact databases. Pigs in the south-west Poland are the reservoir for pathogenic Y. enterocolitica strains. Four biochemical features included in VITEK® 2 Compact known to be common with Wauters scheme were shown to produce incompatible results, thus VITEK® 2 Compact cannot be applied in biotyping of Y. enterocolitica.
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Affiliation(s)
- Katarzyna Morka
- Department of Microbiology, Faculty of Biological Sciences, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Jarosław Bystroń
- Faculty of Veterinary Medicine, Department of Food Hygiene and Consumer Health Protection, Wroclaw University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Jacek Bania
- Faculty of Veterinary Medicine, Department of Food Hygiene and Consumer Health Protection, Wroclaw University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Agnieszka Korzeniowska-Kowal
- Polish Collection of Microorganisms, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wrocław, Poland
| | - Kamila Korzekwa
- Department of Microbiology, Faculty of Biological Sciences, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Katarzyna Guz-Regner
- Department of Microbiology, Faculty of Biological Sciences, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Gabriela Bugla-Płoskońska
- Department of Microbiology, Faculty of Biological Sciences, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148 Wrocław, Poland
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Petsios S, Fredriksson-Ahomaa M, Sakkas H, Papadopoulou C. Conventional and molecular methods used in the detection and subtyping of Yersinia enterocolitica in food. Int J Food Microbiol 2016; 237:55-72. [DOI: 10.1016/j.ijfoodmicro.2016.08.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 07/28/2016] [Accepted: 08/11/2016] [Indexed: 01/08/2023]
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Culture-independent quantification of Salmonella enterica in carcass gauze swabs by flotation prior to real-time PCR. Int J Food Microbiol 2011; 145 Suppl 1:S103-9. [DOI: 10.1016/j.ijfoodmicro.2010.03.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 03/16/2010] [Accepted: 03/30/2010] [Indexed: 11/21/2022]
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LAZARTE OTERO VALERIA, LUCERO ESTRADA CECILIA, FAVIER GABRIELAISABEL, VELÁZQUEZ LIDIA, ESCUDERO MARÍAESTHER, STEFANINI DE GUZMÁN ANAMARÍA. DETECTION AND SURVIVAL OF YERSINIA ENTEROCOLITICA IN GOAT CHEESE PRODUCED IN SAN LUIS, ARGENTINA. J Food Saf 2010. [DOI: 10.1111/j.1745-4565.2010.00256.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella. BMC Microbiol 2009; 9:85. [PMID: 19422711 PMCID: PMC2692855 DOI: 10.1186/1471-2180-9-85] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 05/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the major sources of human Salmonella infections is meat. Therefore, efficient and rapid monitoring of Salmonella in the meat production chain is necessary. Validation of alternative methods is needed to prove that the performance is equal to established methods. Very few of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal) of a same-day, non-commercial real-time PCR method for detection of Salmonella in meat and carcass swabs. RESULTS The comparative trial was performed against a reference method (NMKL-71:5, 1999) using artificially and naturally contaminated samples (60 minced veal and pork meat samples, 60 poultry neck-skins, and 120 pig carcass swabs). The relative accuracy was 99%, relative detection level 100%, relative sensitivity 103% and relative specificity 100%. The collaborative trial included six laboratories testing minced meat, poultry neck-skins, and carcass swabs as un-inoculated samples and samples artificially contaminated with 1-10 CFU/25 g, and 10-100 CFU/25 g. Valid results were obtained from five of the laboratories and used for the statistical analysis. Apart from one of the non-inoculated samples being false positive with PCR for one of the laboratories, no false positive or false negative results were reported. Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially contaminated with Salmonella. There was no significant difference in the results obtained by the two methods. CONCLUSION The real-time PCR method for detection of Salmonella in meat and carcass swabs was validated in comparative and collaborative trials according to NordVal recommendations. The PCR method was found to perform well. The test is currently being implemented for screening of several hundred thousand samples per year at a number of major Danish slaughterhouses to shorten the post-slaughter storage time and facilitate the swift export of fresh meat.
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Rådström P, Löfström C, Lövenklev M, Knutsson R, Wolffs P. Strategies for overcoming PCR inhibition. ACTA ACUST UNITED AC 2008; 2008:pdb.top20. [PMID: 21356797 DOI: 10.1101/pdb.top20] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTIONThe use of conventional and real-time PCR is to some extent restricted by the presence of PCR inhibitors. This is particularly so when the techniques are applied directly to complex biological samples such as clinical, environmental, or food samples for the detection of microorganisms. PCR inhibitors can originate from the sample itself, or as a result of the method used to collect or otherwise prepare the sample. Either way, inhibitors can dramatically reduce the sensitivity and amplification efficiency of PCR. This article discusses methods of reducing inhibition and designing reliable and sensitive conventional and real-time PCR experiments.
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Handschur M, Karlic H, Hertel C, Pfeilstöcker M, Haslberger AG. Preanalytic removal of human DNA eliminates false signals in general 16S rDNA PCR monitoring of bacterial pathogens in blood. Comp Immunol Microbiol Infect Dis 2008; 32:207-19. [PMID: 18261798 DOI: 10.1016/j.cimid.2007.10.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/17/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022]
Abstract
PCR detection of microbial pathogens in blood from patients is a promising issue for rapid diagnosis of sepsis and early targeted therapy. However, for PCR assays detecting all bacterial groups, broad range primers, in particular the 16S rDNA targeting primers have to be used. Upcoming false signals and reduced sensitivity are a common problem as a consequence of unspecific amplification reactions with the human DNA background. Here we show that, using total DNA extracts from blood, unspecific signals occurred in general 16S rDNA PCRs as a result of the amplification of human sequences. To address this problem, we developed a protocol by which the human background DNA is removed and bacterial DNA is enriched during sample preparation, a method we termed background-free enrichment method (BFEM). In general, we aimed to exclude false signals due to the human background DNA yielded from 16S rDNA PCR, Real-Time-PCR and IGS-PCR analyses. We applied the BFEM to the analysis of blood samples from 22 patients and obtained results similar to standard blood culture methods. The BFEM allows specific and sensitive detection of pathogens in downstream PCR assays and is easy to handle due to the quick sample preparation procedure. Thus, the BFEM contributes to the generation of replicable and more reliable data in general 16S rDNA PCR assays.
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Affiliation(s)
- Michael Handschur
- Ludwig Boltzmann Institute for Leukemia Research and Hematology, Vienna, Austria
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Freitas EID, Lemos AAD, Marin VA. Validação de métodos alternativos qualitativos na detecção de patógenos alimentares. CIENCIA & SAUDE COLETIVA 2006. [DOI: 10.1590/s1413-81232006000400028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
As Doenças de Origem Alimentar (DOA) são um perigo de grande relevância para a saúde humana e para a economia dos indivíduos, famílias e nações. O risco de disseminação de microrganismos patogênicos vem crescendo continuamente, e programas de controle de qualidade microbiológica são empregados em toda a cadeia de produção alimentar a fim de minimizar o risco de infecção e/ou intoxicação. A utilização de métodos de detecção alternativos de microrganismos é uma das ferramentas que podem ser utilizadas para garantir a segurança microbiológica dos produtos. Contudo, para que a metodologia utilizada forneça resultados confiáveis é necessário que ela seja validada. A validação deve garantir, por meio de estudos experimentais, que o método atenda às exigências das aplicações analíticas, assegurando a confiabilidade dos resultados, devendo apresentar níveis adequados de acurácia, precisão, limite de detecção, robustez, repetitividade, reprodutibilidade, especificidade, linearidade e exatidão. Embora existam diversos guias descrevendo a validação de métodos analíticos, comparativamente, pouco se tem dito a respeito da validação de métodos microbiológicos e, menos ainda, de métodos moleculares. O objetivo deste trabalho é fazer uma revisão dos parâmetros necessários para validação de métodos alternativos qualitativos na detecção de patógenos alimentares.
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Lund M, Madsen M. Strategies for the inclusion of an internal amplification control in conventional and real time PCR detection of Campylobacter spp. in chicken fecal samples. Mol Cell Probes 2005; 20:92-9. [PMID: 16330185 DOI: 10.1016/j.mcp.2005.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 10/07/2005] [Indexed: 11/20/2022]
Abstract
To illustrate important issues in optimization of a PCR assay with an internal control four different primer combinations for conventional PCR, two non-competitive and two competitive set-ups for real time PCR were used for detection of Campylobacter spp. in chicken faecal samples. In the conventional PCR assays the internal control was genomic DNA from Yersinia ruckeri, which is not found in chicken faeces. This internal control was also used in one of the set ups in real time PCR. In the three other set-ups different DNA fragments of 109 bp length prepared from two oligos of each 66 bp by a simple extension reaction was used. All assays were optimized to avoid loss of target sensitivity due to the presence of the internal control by adjusting the amount of internal control primers in the duplex assays and the amount of internal control in all assays. Furthermore, the assays were tested against faecal inhibitors to ensure that the internal control and the target PCR had the same sensitivity towards inhibitors.
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Affiliation(s)
- M Lund
- Danish Institute for Food and Veterinary Research (DFVF), Arhus N, Denmark.
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Mayoral MB, Martín R, Sanz A, Hernández PE, González I, García T. Detection of Kluyveromyces marxianus and other spoilage yeasts in yoghurt using a PCR-culture technique. Int J Food Microbiol 2005; 105:27-34. [PMID: 16026876 DOI: 10.1016/j.ijfoodmicro.2005.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/26/2005] [Accepted: 06/09/2005] [Indexed: 11/30/2022]
Abstract
A combined PCR-culture technique was developed for the detection of viable yeasts in yoghurt samples. Yoghurt samples were inoculated with either viable or heat-inactivated Kluyveromyces marxianus cells, and analyzed before and after incubation for 24 h at 25 degrees C under agitation. DNA was extracted from the samples and amplified using yeast-specific primers targeted at the gene coding for the 18S rRNA. A 251-bp fragment was amplified by the Polymerase Chain Reaction from the yoghurt samples containing initial yeasts counts of 10 cfu g(-1) or higher, whereas no PCR product was generated from control uninoculated yoghurt samples. Comparison of PCR results obtained before and after the incubation step was used to assess yeast viability. Viability was also confirmed by plating on Sabouraud-Dextrose-Chloramphenicol Agar. Moreover, comparison of the results obtained using PCR-culture and plate count methods for the analysis of commercial yoghurt samples, demonstrated that the PCR-culture technique developed in this work can be very useful for the rapid detection of viable spoilage yeasts in dairy industries.
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Affiliation(s)
- María Belén Mayoral
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Spain
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Rodríguez-Lázaro D, D'Agostino M, Herrewegh A, Pla M, Cook N, Ikonomopoulos J. Real-time PCR-based methods for detection of Mycobacterium avium subsp. paratuberculosis in water and milk. Int J Food Microbiol 2005; 101:93-104. [PMID: 15878410 DOI: 10.1016/j.ijfoodmicro.2004.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 09/18/2004] [Accepted: 09/20/2004] [Indexed: 10/25/2022]
Abstract
A real-time PCR assay for quantitative detection of Mycobacterium avium paratuberculosis has been developed. It targets and amplifies sequences from the IS900 insertion element which is specific for this bacterium, and includes an internal amplification control. The assay was tested against 18 isolates of M. avium paratuberculosis, 17 other mycobacterial strains, and 25 non-mycobacterial strains, and was fully selective. It is capable of detecting <3 genomic DNA copies with 99% probability or alternatively, using cells directly in the reaction, 12 cells can be detected with 99% probability. Using prior centrifugation, the assay was able to consistently and quantifiably detect 10(2) M. avium paratuberculosis cells in 20 ml artificially contaminated drinking water. With a simple detergent and enzymatic sample pretreatment before centrifugation and nucleic acid extraction, the assay was able to consistently detect 10(2) M. avium paratuberculosis in 20 ml artificially contaminated semi-skimmed milk. The assay will be a useful addition to the range of diagnostic tools available for the study of M. avium paratuberculosis.
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Josefsen MH, Jacobsen NR, Hoorfar J. Enrichment followed by quantitative PCR both for rapid detection and as a tool for quantitative risk assessment of food-borne thermotolerant campylobacters. Appl Environ Microbiol 2004; 70:3588-92. [PMID: 15184161 PMCID: PMC427791 DOI: 10.1128/aem.70.6.3588-3592.2004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As part of a large international project for standardization of PCR (Food-PCR; www.pcr.dk), a multiplex, multiplatform, ready-to-go enrichment followed by a real-time PCR method, including an internal amplification control, was developed for detection of food-borne thermotolerant campylobacters in chickens. Chicken rinse samples were enriched in Bolton broth for 20 h, a simple and rapid (1-h) resin-based DNA extraction was performed, and DNA samples were then tested with two instrument platforms: ABI-PRISM 7700 and RotorGene 3000. The method was validated against an International Standard Organization (ISO)-based culture method by testing low, medium, and high levels of 12 spiked and 66 unspiked, presumably naturally contaminated, chicken rinse samples. In the RotorGene, a positive PCR response was detected in 40 samples of the 66. This was in complete agreement with the enriched ISO culture. The ABI-PRISM 7700 missed one culture-positive sample. Positive samples contained 10(2) to 10(7) CFU/ml after enrichment in Bolton broth. In the enriched samples a detection probability of 95% was obtained at levels of 1 x 10(3) and 2 x 10(3) CFU/ml in the RotorGene and ABI-PRISM, respectively. The amplification efficiency in both platforms was 90%, although the linear range of amplification of purified genomic DNA was 1.5 x 10(1) to 1 x 10(7) (R(2) = 1.00) for the RotorGene and 10(3) to 10(7) (R(2) = 0.99) for the ABI-PRISM. In RotorGene and ABI-PRISM the levels of precision of detection as determined by standard deviation (coefficients of variation) of 6-carboxyfluorescein (FAM) threshold cycle (Ct) values were 0.184 to 0.417 (0.65 to 2.57%) and 0.119 to 0.421 (0.59 to 1.82%), respectively. The results showed a correlation (R(2)) of 0.94 between the target FAM Ct values and CFU per milliliter of enriched naturally contaminated chicken samples, which indicates PCR's additional potential as a tool for quantitative risk assessment. Signal from the internal amplification control was detected in all culture-negative samples (VIC Ct: 23.1 to 28.1). The method will be taken further and validated in an international collaborative trial with regard to standardization.
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Affiliation(s)
- M H Josefsen
- Danish Institute for Food and Veterinary Research, DK-1790 Copenhagen V, Denmark
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RodrÃguez-Lázaro D, Lloyd J, Herrewegh A, Ikonomopoulos J, D'Agostino M, Pla M, Cook N. A molecular beacon-based real-time NASBA assay for detection ofMycobacterium aviumsubsp.paratuberculosisin water and milk. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09686.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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D'Agostino M, Wagner M, Vazquez-Boland JA, Kuchta T, Karpiskova R, Hoorfar J, Novella S, Scortti M, Ellison J, Murray A, Fernandes I, Kuhn M, Pazlarova J, Heuvelink A, Cook N. A validated PCR-based method to detect Listeria monocytogenes using raw milk as a food model--towards an international standard. J Food Prot 2004; 67:1646-55. [PMID: 15330529 DOI: 10.4315/0362-028x-67.8.1646] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A PCR assay with an internal amplification control was developed for Listeria monocytogenes. The assay has a 99% detection probability of seven cells per reaction. When tested against 38 L. monocytogenes strains and 52 nontarget strains, the PCR assay was 100% inclusive (positive signal from target) and 100% exclusive (no positive signal from nontarget). The assay was then evaluated in a collaborative trial involving 12 European laboratories, where it was tested against an additional 14 target and 14 nontarget strains. In that trial, the inclusivity was 100% and the exclusivity was 99.4%, and both the accordance (repeatability) and the concordance (reproducibility) were 99.4%. The assay was incorporated within a method for the detection of L. monocytogenes in raw milk, which involves 24 h of enrichment in half-Fraser broth followed by 16 h of enrichment in a medium that can be added directly into the PCR. The performance characteristics of the PCR-based method were evaluated in a collaborative trial involving 13 European laboratories. In that trial, a specificity value (percentage of correct identification of blank samples) of 81.8% was obtained; the accordance was 87.9%, and the concordance was 68.1%. The sensitivity (correct identification of milk samples inoculated with 20 to 200 L. monocytogenes cells per 25 ml) was 89.4%, the accordance was 81.2%, and the concordance was 80.7%. This method provides a basis for the application of routine PCR-based analysis to dairy products and other foodstuffs and should be appropriate for international standardization.
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Affiliation(s)
- M D'Agostino
- DEFRA Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK
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Wolffs P, Knutsson R, Norling B, Rådström P. Rapid quantification of Yersinia enterocolitica in pork samples by a novel sample preparation method, flotation, prior to real-time PCR. J Clin Microbiol 2004; 42:1042-7. [PMID: 15004051 PMCID: PMC356873 DOI: 10.1128/jcm.42.3.1042-1047.2004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of real-time PCR thermal cycles in the late 1990s has opened up the possibility of accurate quantification of microorganisms in clinical, environmental, and food samples. However, a lack of suitable sample preparation methods that allow rapid quantification of the nucleic acids, remove PCR inhibitors, and prevent false-positive results due to DNA originating from dead cells has limited the use of quantitative PCR. We have used for the first time a new variant of density gradient centrifugation, called flotation, as a user-friendly sample preparation method prior to PCR. This paper describes the use of this sample preparation method, without DNA purification, for direct detection and quantification of Yersinia enterocolitica in PCR-inhibitory meat juice from pork. Flotation combined with qPCR could overcome PCR interference in juice from pork, as was shown by amplification efficiencies of 1.006 +/- 0.021 and 1.007 +/- 0.025, which are comparable to the amplification efficiency obtained for purified DNA samples (1.005 +/- 0.059). Applying flotation to meat juice samples containing natural background flora and spiked with different levels of Y. enterocolitica showed that direct quantification of Y. enterocolitica was possible down to a level of at least 4.2 x 10(3) CFU per ml of meat juice, even in the presence of 10(6) CFU of background flora per ml. Finally, the results showed that samples containing large amounts of Y. enterocolitica DNA did not result in a positive PCR signal. This indicates that the risk of false-positive results due to detection of DNA originating from dead cells can be greatly reduced by using flotation prior to PCR.
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Affiliation(s)
- Petra Wolffs
- Applied Microbiology, Lund Institute of Technology, Lund University, SE-221 00 Lund, Sweden
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Löfström C, Knutsson R, Axelsson CE, Rådström P. Rapid and specific detection of Salmonella spp. in animal feed samples by PCR after culture enrichment. Appl Environ Microbiol 2004; 70:69-75. [PMID: 14711627 PMCID: PMC321250 DOI: 10.1128/aem.70.1.69-75.2004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A PCR procedure has been developed for routine analysis of viable Salmonella spp. in feed samples. The objective was to develop a simple PCR-compatible enrichment procedure to enable DNA amplification without any sample pretreatment such as DNA extraction or cell lysis. PCR inhibition by 14 different feed samples and natural background flora was circumvented by the use of the DNA polymerase Tth. This DNA polymerase was found to exhibit a high level of resistance to PCR inhibitors present in these feed samples compared to DyNAzyme II, FastStart Taq, Platinum Taq, Pwo, rTth, Taq, and Tfl. The specificity of the Tth assay was confirmed by testing 101 Salmonella and 43 non-Salmonella strains isolated from feed and food samples. A sample preparation method based on culture enrichment in buffered peptone water and DNA amplification with Tth DNA polymerase was developed. The probability of detecting small numbers of salmonellae in feed, in the presence of natural background flora, was accurately determined and found to follow a logistic regression model. From this model, the probability of detecting 1 CFU per 25 g of feed in artificially contaminated soy samples was calculated and found to be 0.81. The PCR protocol was evaluated on 155 naturally contaminated feed samples and compared to an established culture-based method, NMKL-71. Eight percent of the samples were positive by PCR, compared with 3% with the conventional method. The reasons for the differences in sensitivity are discussed. Use of this method in the routine analysis of animal feed samples would improve safety in the food chain.
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Affiliation(s)
- Charlotta Löfström
- Department of Applied Microbiology, Lund Institute of Technology, Lund University, SE-221 00 Lund. AnalyCen Nordic AB, SE-531 19 Lidköping, Sweden
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Abdulmawjood A, Bülte M, Cook N, Roth S, Schönenbrücher H, Hoorfar J. Toward an international standard for PCR-based detection of Escherichia coli O157. J Microbiol Methods 2003; 55:775-86. [PMID: 14607420 DOI: 10.1016/j.mimet.2003.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
As part of a major European research project, a diagnostic PCR assay, including an internal amplification control, was developed and validated in a collaborative trial for the detection of Escherichia coli O157. The assay is based on amplification of sequences of the rfbE O157 gene. The collaborative trial, including 12 international laboratories, was carried out in two phases: phase (a) was performed with identical PCR reagents, including the internal control, provided by the sending laboratory; phase (b) was performed on the same samples and internal control but using in-house PCR reagents of own choice. Phase (a) showed an inclusivity (detection of target strains) of 96.8% and the exclusivity (negative response from nontarget strains) was 100%. The overall performance resulted of phase (a) in an accordance of 98.8, concordance of 98.6, and a concordance odds ratio of 1.11. Phase (b) results showed an accuracy of 100% with all partners and by using different polymerase types and thermocycler models. This indicates that the assay, under consideration as an international standard, was just as reproducible between laboratories, as repeatable within a laboratory. The assay is taken further for validation on carcass-rinse samples.
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Affiliation(s)
- A Abdulmawjood
- Institute of Veterinary Food Sciences, Justus-Liebig-University, Frankfurter strasse 92, 35392 Giessen, Germany
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18
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Josefsen MH, Lambertz ST, Jensen S, Hoorfar J. Food-PCR. Validation and standardization of diagnostic PCR for detection of Yersinia enterocolitica and other foodborne pathogens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2003; 529:443-9. [PMID: 12756806 DOI: 10.1007/0-306-48416-1_88] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Malorny B, Tassios PT, Rådström P, Cook N, Wagner M, Hoorfar J. Standardization of diagnostic PCR for the detection of foodborne pathogens. Int J Food Microbiol 2003; 83:39-48. [PMID: 12672591 DOI: 10.1016/s0168-1605(02)00322-7] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In vitro amplification of nucleic acids using the polymerase chain reaction (PCR) has become, since its discovery in the 1980s, a powerful diagnostic tool for the analysis of microbial infections as well as for the analysis of microorganisms in food samples. However, despite its potential, PCR has neither gained wide acceptance in routine diagnostics nor been widely incorporated in standardized methods. Lack of validation and standard protocols, as well as variable quality of reagents and equipment, influence the efficient dissemination of PCR methodology from expert research laboratories to end-user laboratories. Moreover, the food industry understandably requires and expects officially approved standards. Recognizing this, in 1999, the European Commission approved the research project, FOOD-PCR (http://www.PCR.dk), which aims to validate and standardize the use of diagnostic PCR for the detection of pathogenic bacteria in foods. The present review focuses on the harmonization procedure and standardization criteria for detection of foodborne pathogens by PCR. The progress of standardization so far and future perspectives of diagnostic PCR are discussed.
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Affiliation(s)
- Burkhard Malorny
- Federal Institute for Health Protection of Consumers and Veterinary Medicine, Diedersdorfer Weg 1, 12277 Berlin, Germany.
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Cook N. The use of NASBA for the detection of microbial pathogens in food and environmental samples. J Microbiol Methods 2003; 53:165-74. [PMID: 12654488 DOI: 10.1016/s0167-7012(03)00022-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The isothermal amplification method nucleic acid sequence-based amplification (NASBA), which amplifies RNA, has been reported as useful for the detection of microbial pathogens in food and environmental samples. Methods have been published for Campylobacter spp., Listeria monocytogenes and Salmonella enterica ser. Enteritidis in various foods and for Cryptosporidium parvum in water. Both 16S rRNA and various mRNAs have been used as target molecules for detection; the latter may have advantages in allowing specific detection of viable cells. Most of the methods to detect pathogens in foods have employed enrichment in nutrient medium prior to NASBA, as this can ensure sensitivity of detection and encourage the detection of only viable target cells. Although a relatively recent method, NASBA has the potential for adoption as a diagnostic tool for environmental pathogens.
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Affiliation(s)
- Nigel Cook
- DEFRA Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK.
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Marie Yeung P, DePaola A, Kaysner C, Boor K. A PCR Assay for Specific Detection of the Pandemic Vibrio parahaemolyticus O3:K6 Clone from Shellfish. J Food Sci 2003. [DOI: 10.1111/j.1365-2621.2003.tb09667.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Malorny B, Hoorfar J, Bunge C, Helmuth R. Multicenter validation of the analytical accuracy of Salmonella PCR: towards an international standard. Appl Environ Microbiol 2003; 69:290-6. [PMID: 12514007 PMCID: PMC152403 DOI: 10.1128/aem.69.1.290-296.2003] [Citation(s) in RCA: 341] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As part of a major international project for the validation and standardization of PCR for detection of five major food-borne pathogens, four primer sets specific for Salmonella species were evaluated in-house for their analytical accuracy (selectivity and detection limit) in identifying 43 Salmonella spp. and 47 non-Salmonella strains. The most selective primer set was found to be 139-141 (K. Rahn, S. A. De Grandis, R. C. Clarke, S. A. McEwen, J. E. Galán, C. Ginocchio, R. Curtiss III, and C. L. Gyles, Mol. Cell. Probes 6:271-279, 1992), which targets the invA gene. An extended determination of selectivity by using 364 strains showed that the inclusivity was 99.6% and the exclusivity was 100% for the invA primer set. To indicate possible PCR inhibitors derived from the sample DNA, an internal amplification control (IAC), which was coamplified with the invA target gene, was constructed. In the presence of 300 DNA copies of the IAC, the detection probability for primer set 139-141 was found to be 100% when a cell suspension containing 10(4) CFU/ml was used as the template in the PCR (50 CFU per reaction). The primer set was further validated in an international collaborative study that included 16 participating laboratories. Analysis with 28 coded ("blind") DNA samples revealed an analytical accuracy of 98%. Thus, a simple PCR assay that is specific for Salmonella spp. and amplifies a chromosomal DNA fragment detected by gel electrophoresis was established through extensive validation and is proposed as an international standard. This study addresses the increasing demand of quality assurance laboratories for standard diagnostic methods and presents findings that can facilitate the international comparison and exchange of epidemiological data.
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Affiliation(s)
- Burkhard Malorny
- Federal Institute for Health Protection of Consumers and Veterinary Medicine, D-12277 Berlin, Germany
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