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1.
AIMS Microbiol ; 7(4): 399-414, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-35071939

RESUMEN

Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives. This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 106 CFU/mL of both Salmonella and Campylobacter strains stored at -20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.

2.
Appl Environ Microbiol ; 83(5)2017 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-27986726

RESUMEN

Salmonella is recognized as one of the most important foodborne bacteria and has wide health and socioeconomic impacts worldwide. Fresh pork meat is one of the main sources of Salmonella, and efficient and fast methods for detection are therefore necessary. Current methods for Salmonella detection in fresh meat usually include >16 h of culture enrichment, in a few cases <12 h, thus requiring at least two working shifts. Here, we report a rapid (<5 h) and high-throughput method for screening of Salmonella in samples from fresh pork meat, consisting of a 3-h enrichment in standard buffered peptone water and a real-time PCR-compatible sample preparation method based on filtration, centrifugation, and enzymatic digestion, followed by fast-cycling real-time PCR detection. The method was validated in an unpaired comparative study against the Nordic Committee on Food Analysis (NMKL) reference culture method 187. Pork meat samples (n = 140) were either artificially contaminated with Salmonella at 0, 1 to 10, or 10 to 100 CFU/25 g of meat or naturally contaminated. Cohen's kappa for the degree of agreement between the rapid method and the reference was 0.64, and the relative accuracy, sensitivity, and specificity for the rapid method were 81.4, 95.1, and 97.9%, respectively. The 50% limit of detections (LOD50s) were 8.8 CFU/25 g for the rapid method and 7.7 CFU/25 g for the reference method. Implementation of this method will enable faster release of Salmonella low-risk meat, providing savings for meat producers, and it will help contribute to improved food safety.IMPORTANCE While the cost of analysis and hands-on time of the presented rapid method were comparable to those of reference culture methods, the fast product release by this method can provide the meat industry with a competitive advantage. Not only will the abattoirs save costs for work hours and cold storage, but consumers and retailers will also benefit from fresher meat with a longer shelf life. Furthermore, the presented sample preparation might be adjusted for application in the detection of other pathogenic bacteria in different sample types.


Asunto(s)
Técnicas Bacteriológicas/economía , Técnicas Bacteriológicas/métodos , Microbiología de Alimentos , Carne/microbiología , Salmonella enterica/aislamiento & purificación , Animales , Análisis Costo-Beneficio , Medios de Cultivo , ADN Bacteriano/análisis , Contaminación de Alimentos/análisis , Inocuidad de los Alimentos , Enfermedades Transmitidas por los Alimentos/microbiología , Indicadores y Reactivos , Límite de Detección , Reacción en Cadena en Tiempo Real de la Polimerasa/economía , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Carne Roja/microbiología , Sensibilidad y Especificidad , Porcinos , Factores de Tiempo
3.
J Appl Microbiol ; 119(5): 1391-402, 2015 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-26293831

RESUMEN

AIMS: The aim of this study was to cost-effectively improve detection of foodborne pathogens in PCR inhibitory samples through the use of alternative DNA polymerases. METHODS AND RESULTS: Commercially available polymerases (n = 16) and PCR master mixes (n = 4) were screened on DNA purified from bacterial cells in two validated real-time PCR assays for Campylobacter and Salmonella. The five best performing (based on: limit of detection (LOD), maximum fluorescence, shape of amplification curves and amplification efficiency) were subsequently applied to meat and faecal samples. The VeriQuest qPCR master mix performed best for both meat and faecal samples (LODs of 10(2) and 10(4) CFU ml(-1) in the purest and crudest DNA extractions respectively) compared with Tth (LOD = 10(2)-10(3) and 10(5)-10(6) CFU ml(-1)). AmpliTaqGold and HotMasterTaq both performed well (LOD = 10(2)-10(4) CFU ml(-1)) with meat samples and poorly (LOD = 10(3)-10(6) CFU ml(-1)/not detected) with faecal samples. CONCLUSIONS: Applying the VeriQuest qPCR master mix in the two tested real-time PCR assays could allow for simpler sample preparation and thus a reduction in cost. SIGNIFICANCE AND IMPACT OF THE STUDY: This work exemplifies a cost-effective strategy for optimizing real-time PCR-based assays. However, a DNA polymerase suitable for one assay and sample type is not necessarily optimal for other assays or sample types.


Asunto(s)
Campylobacter/aislamiento & purificación , ADN Polimerasa Dirigida por ADN/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Salmonella/aislamiento & purificación , Animales , Campylobacter/genética , ADN Bacteriano/genética , ADN Polimerasa Dirigida por ADN/química , ADN Polimerasa Dirigida por ADN/economía , Heces/microbiología , Límite de Detección , Carne/microbiología , Reacción en Cadena en Tiempo Real de la Polimerasa/economía , Salmonella/genética
4.
Epidemiol Infect ; 143(11): 2381-9, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-25471550

RESUMEN

Consumption of poultry meat is considered as one of the main sources of human campylobacteriosis, and there is clearly a need for new surveillance and control measures based on quantitative data on Campylobacter spp. colonization dynamics in broiler chickens. We conducted four experimental infection trials, using four isolators during each infection trial to evaluate colonization of individual broiler chickens by Campylobacter jejuni over time. Individual and pooled faecal samples were obtained at days 4, 7 and 12 post-inoculation (p.i.) and caecal samples at day 12 p.i. There were large differences between broiler chickens in the number of C. jejuni in caecal and faecal material. Faecal samples of C. jejuni ranged from 4·0 to 9·4 log c.f.u./g and from 4·8 to 9·3 log c.f.u./g in the caeca. Faecal c.f.u./g decreased with time p.i. Most variation in c.f.u. for faecal and caecal samples was attributed to broiler chickens and a minor part to isolators, whereas infection trials did not affect the total variance. The results showed that pooled samples within isolators had lower c.f.u./g compared to the arithmetic mean of the individual samples. There was a significant correlation between faecal c.f.u./g at days 4 and 7 p.i., days 7 and 12 p.i. and for caecal and faecal c.f.u./g at day 12 p.i.


Asunto(s)
Infecciones por Campylobacter/veterinaria , Campylobacter jejuni/aislamiento & purificación , Portador Sano , Ciego/microbiología , Pollos/microbiología , Heces/microbiología , Enfermedades de las Aves de Corral/microbiología , Animales , Campylobacter/aislamiento & purificación , Modelos Lineales , Factores de Tiempo
5.
J Food Prot ; 77(2): 325-30, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24490929

RESUMEN

The present study describes the evaluation of a method for the quantification of Campylobacter by air sampling in poultry houses. Sampling was carried out in conventional chicken houses in Poland, in addition to a preliminary sampling in Denmark. Each measurement consisted of three air samples, two standard boot swab fecal samples, and one airborne particle count. Sampling was conducted over an 8-week period in three flocks, assessing the presence and levels of Campylobacter in boot swabs and air samples using quantitative real-time PCR. The detection limit for air sampling was approximately 100 Campylobacter cell equivalents (CCE)/m3. Airborne particle counts were used to analyze the size distribution of airborne particles (0.3 to 10 µm) in the chicken houses in relation to the level of airborne Campylobacter. No correlation was found. Using air sampling, Campylobacter was detected in the flocks right away, while boot swab samples were positive after 2 weeks. All samples collected were positive for Campylobacter from week 2 through the rest of the rearing period for both sampling techniques, although levels 1- to 2-log CCE higher were found with air sampling. At week 8, the levels were approximately 10(4) and 10(5) CCE per sample for boot swabs and air, respectively. In conclusion, using air samples combined with quantitative real-time PCR, Campylobacter contamination could be detected earlier than by boot swabs and was found to be a more convenient technique for monitoring and/or to obtain enumeration data useful for quantitative risk assessment of Campylobacter.


Asunto(s)
Microbiología del Aire , Campylobacter/aislamiento & purificación , Heces/microbiología , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Animales , Pollos , Costos y Análisis de Costo , Dinamarca , Vivienda para Animales , Humanos , Polonia , Reacción en Cadena en Tiempo Real de la Polimerasa/economía
6.
J Appl Microbiol ; 116(1): 167-78, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23998352

RESUMEN

AIMS: Three pre-PCR processing strategies for the detection and/or quantification of Salmonella in naturally contaminated soya bean meal were evaluated. METHODS AND RESULTS: Methods included: (i) flotation-qPCR [enumeration of intact Salmonella cells prior to quantitative PCR (qPCR)], (ii) MPN-PCR (modified most probable number method combined with qPCR) and (iii) qualitative culture enrichment PCR. The limit of quantification was 1·8 × 10(2) CFU g(-1) (flotation-qPCR) and 0·02 MPN g(-1) (MPN-PCR). Fifteen naturally contaminated Salmonella positive soya bean meal samples from one lot were analysed in parallel with the three methods, using 2·5, 50 and 25 g of feed, respectively, resulting in detection of Salmonella in 6, 15 and 9 bags. Enumeration resulted in 1·8 × 10(2) -7·8 × 10(3) CFU g(-1) (flotation-qPCR) and 0·024 to >5·2 MPN g(-1) (MPN-PCR). CONCLUSIONS: Except for differences in methodology, results obtained with the three techniques could be due to the presence of nonculturable Salmonella and/or a heterogeneous distribution of Salmonella in the material. SIGNIFICANCE AND IMPACT OF THE STUDY: The evaluated methods provide different possibilities to assess the prevalence of Salmonella in feed, together with the numbers of culturable, as well as nonculturable cells, and can be applied to generate data to allow more accurate quantitative microbial risk assessment for Salmonella in the feed chain.

7.
Appl Environ Microbiol ; 77(9): 3160-2, 2011 May.
Artículo en Inglés | MEDLINE | ID: mdl-21378040

RESUMEN

Free-range geese were sampled longitudinally and Salmonella isolates characterized to reveal highly diverging colonization dynamics. One flock was intermittently colonized with one strain of Salmonella enterica serovar Enteritidis from 2 weeks of age, while in another, S. enterica serovar Mbandaka appeared after 9 weeks, without dissemination but with multiple serovars appearing at later stages.


Asunto(s)
Gansos/microbiología , Salmonelosis Animal/epidemiología , Salmonelosis Animal/microbiología , Salmonella enterica/clasificación , Salmonella enterica/aislamiento & purificación , Animales , Técnicas de Tipificación Bacteriana , Biodiversidad , Electroforesis en Gel de Campo Pulsado , Heces/microbiología , Tipificación Molecular , Serotipificación
8.
APMIS Suppl ; (133): 1-24, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22250747

RESUMEN

As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount.


Asunto(s)
Microbiología de Alimentos , Enfermedades Transmitidas por los Alimentos/prevención & control , Técnicas Microbiológicas/métodos , Técnicas de Diagnóstico Molecular/métodos , Animales , Automatización/economía , Automatización/métodos , Humanos , Tamizaje Masivo/economía , Tamizaje Masivo/métodos , Tamizaje Masivo/tendencias , Técnicas Microbiológicas/economía , Técnicas Microbiológicas/tendencias , Técnicas de Diagnóstico Molecular/economía , Técnicas de Diagnóstico Molecular/tendencias , Factores de Tiempo
9.
Appl Environ Microbiol ; 76(15): 5097-104, 2010 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-20562292

RESUMEN

A number of intervention strategies against Campylobacter-contaminated poultry focus on postslaughter reduction of the number of cells, emphasizing the need for rapid and reliable quantitative detection of only viable Campylobacter bacteria. We present a new and rapid quantitative approach to the enumeration of food-borne Campylobacter bacteria that combines real-time quantitative PCR (Q-PCR) with simple propidium monoazide (PMA) sample treatment. In less than 3 h, this method generates a signal from only viable and viable but nonculturable (VBNC) Campylobacter bacteria with an intact membrane. The method's performance was evaluated by assessing the contributions to variability by individual chicken carcass rinse matrices, species of Campylobacter, and differences in efficiency of DNA extraction with differing cell inputs. The method was compared with culture-based enumeration on 50 naturally infected chickens. The cell contents correlated with cycle threshold (C(T)) values (R(2) = 0.993), with a quantification range of 1 x 10(2) to 1 x 10(7) CFU/ml. The correlation between the Campylobacter counts obtained by PMA-PCR and culture on naturally contaminated chickens was high (R(2) = 0.844). The amplification efficiency of the Q-PCR method was not affected by the chicken rinse matrix or by the species of Campylobacter. No Q-PCR signals were obtained from artificially inoculated chicken rinse when PMA sample treatment was applied. In conclusion, this study presents a rapid tool for producing reliable quantitative data on viable Campylobacter bacteria in chicken carcass rinse. The proposed method does not detect DNA from dead Campylobacter bacteria but recognizes the infectious potential of the VBNC state and is thereby able to assess the effect of control strategies and provide trustworthy data for risk assessment.


Asunto(s)
Azidas/metabolismo , Campylobacter/aislamiento & purificación , Pollos/microbiología , Viabilidad Microbiana , Reacción en Cadena de la Polimerasa/métodos , Propidio/análogos & derivados , Animales , Recuento de Colonia Microbiana/métodos , Propidio/metabolismo , Medición de Riesgo/métodos , Factores de Tiempo
10.
Appl Environ Microbiol ; 73(9): 3040-8, 2007 May.
Artículo en Inglés | MEDLINE | ID: mdl-17351094

RESUMEN

We developed a 12-h Salmonella detection method, based on 8 h of preenrichment, followed by automated DNA extraction and a sensitive real-time PCR. The method was optimized to obtain the highest possible yield of cells and DNA. The growth of different Salmonella strains in various preenrichment media and the effects of adding growth-promoting and selective reagents were explored, taking into account their PCR compatibility. The effects of (i) analyzing larger volumes (1 to 5 ml) from preenriched samples and introducing wash steps prior to DNA extraction, (ii) regulating the amount of paramagnetic particles (increasing it from 60 to 90 microl) in the DNA extraction, (iii) eluting the DNA in reduced volumes (25 or 50 microl rather than 100 microl), and (iv) increasing the PCR template volume (from 5 to 20 microl) were investigated. After 8 h of preenrichment, buffered peptone water yielded the highest number of salmonellae. When analyzing minced meat samples, positive effects of increasing the initial sampling volume from 1 to 5 ml and increasing the amount of paramagnetic particles to 90 microl were observed. However, washing the pellet and eluting the DNA in reduced volumes (25 and 50 microl) had no positive effects and resulted in decreased reproducibility. Increasing the amount of PCR template DNA from 5 to 20 mul improved the threshold cycle value by approximately 2. The improved 12-h PCR method was successfully compared to a reference culture method with 100 minced meat and poultry samples, with a relative accuracy of 99%, a relative sensitivity of 98%, and a relative specificity of 100%.


Asunto(s)
Contaminación de Alimentos/análisis , Microbiología de Alimentos , Carne/microbiología , Reacción en Cadena de la Polimerasa/métodos , Salmonella , Colorantes Fluorescentes
11.
Appl Environ Microbiol ; 72(8): 5463-8, 2006 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-16885299

RESUMEN

Certified Campylobacter-free poultry products have been produced in Denmark since 2002, the first example of fresh (unprocessed and nonfrozen) chickens labeled "Campylobacter free." This success occurred partly through use of a 4-hour gel-based PCR testing scheme on fecal swabs. In this study, a faster, real-time PCR approach was validated in comparative and collaborative trials, based on recommendations from the Nordic system for validation of alternative microbiological methods (NordVal). The comparative real-time PCR trial was performed in comparison to two reference culture protocols on naturally contaminated samples (99 shoe covers, 101 cloacal swabs, 102 neck skins from abattoirs, and 100 retail neck skins). Culturing included enrichment in both Bolton and Preston broths followed by isolation on Preston agar and mCCDA. In one or both culture protocols, 169 samples were identified as positive. The comparative trial resulted in relative accuracy, sensitivity, and specificity of 98%, 95%, and 97%, respectively. The collaborative trial included nine laboratories testing neck skin, cloacal swab, and shoe cover samples, spiked with low, medium, and high concentrations of Campylobacter jejuni. Valid results were obtained from six of the participating laboratories. Accuracy for high levels was 100% for neck skin and cloacal swab samples. For low levels, accuracy was 100% and 92% for neck skin and cloacal swab samples, respectively; however, detection in shoe cover samples failed. A second collaborative trial, with an optimized DNA extraction procedure, gave 100% accuracy results for all three spiking levels. Finally, on-site validation at the abattoir on a flock basis was performed on 400 samples. Real-time PCR correctly identified 10 of 20 flocks as positive; thus, the method fulfilled the NordVal validation criteria and has since been implemented at a major abattoir.


Asunto(s)
Campylobacter/aislamiento & purificación , Pollos/microbiología , Reacción en Cadena de la Polimerasa/métodos , Productos Avícolas/normas , Animales , Campylobacter/clasificación , Campylobacter/genética , Infecciones por Campylobacter/microbiología , Infecciones por Campylobacter/veterinaria , Contaminación de Alimentos/prevención & control , Enfermedades de las Aves de Corral/microbiología , Productos Avícolas/microbiología , Sensibilidad y Especificidad , Polimerasa Taq
12.
J Microbiol Methods ; 66(2): 206-16, 2006 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-16364478

RESUMEN

A validated PCR-based Salmonella method targeting a 94-bp sequence of the ttr gene was used as a model to compare six different combinations of reporter and quencher dyes of a TaqMan probe, on three different instruments, to improve the detection limit in a real-time PCR assay with the aim of a same-day analysis. The use of locked nucleic acids (LNA) and Scorpion probes were also tested. The combination FAM-BHQ1 or Cy5-BHQ3, both dark quenchers, gave the best results (Cycle threshold (Ct) of 25.42+/-0.65 and 24.47+/-0.18 at 10(3) DNA copies). When comparing different probe technologies, the LNA probe (FAM-BHQ1) was the most sensitive with the strongest fluorescence signal (dR last 48066), resulting in 0.6 to 1.1 lower Ct values than a DNA TaqMan probe, and 1.9 to 4.0 lower Ct than the Scorpion system (FAM-BHQ1). The RotorGene real-time PCR instrument gave 0.4-1.0 lower Ct values (more sensitive) than the Mx3005p, and 1.5-3.0 lower than the ABI 7700. Using the LNA in a RotorGene instrument, we detected the following Salmonella DNA copies in 1-ml pre-enriched samples: fishmeal (100 copies), chicken rinse (100 copies) and pig feces (10 copies). The detection probability of the final assay on inoculated fecal samples was 100% at 2x10(4) copies per ml. In conclusion, the LNA probe with annealing temperature of 65 degrees C could be useful for more sensitive detection limits.


Asunto(s)
Cartilla de ADN/genética , Sondas de ADN/genética , Microbiología de Alimentos , Reacción en Cadena de la Polimerasa/métodos , Salmonella typhimurium/genética , Animales , Pollos/microbiología , Cartilla de ADN/normas , Sondas de ADN/normas , ADN Bacteriano/análisis , ADN Bacteriano/genética , Heces/microbiología , Productos Pesqueros/microbiología , Colorantes Fluorescentes/química , Reacción en Cadena de la Polimerasa/instrumentación , Sensibilidad y Especificidad , Polimerasa Taq/química
13.
J Microbiol Methods ; 63(2): 151-6, 2005 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-16226639

RESUMEN

A real-time PCR assay was developed based on a 181-bp fragment of the recently cloned per gene, including an internal amplification control (124 bp), for the detection of Yersinia enterocolitica O:9 (Ye O:9). The validation included 48 Ye O:9, 33 Y. enterocolitica non-O:9 and 35 other closely-related bacterial strains, containing per gene homologies. The assay was specific for the Ye O:9 tested, the detection limit was 1-10 genome copies of purified DNA and amplification efficiency was between 90.5-103%, indicating a linear regression throughout the detection window.


Asunto(s)
Carbohidrato Epimerasas/genética , Reacción en Cadena de la Polimerasa/métodos , Transaminasas/genética , Yersinia enterocolitica/clasificación , Animales , Bovinos , ADN Bacteriano/análisis , Humanos , Serotipificación , Especificidad de la Especie , Yersinia enterocolitica/genética
15.
J Clin Microbiol ; 43(6): 2724-8, 2005 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-15956389

RESUMEN

As part of a large international project for validation and standardization of PCR, the influence of thermocyclers on PCR was tested. Six brand-new, Peltier technology-driven 96-well thermocyclers were subjected to a novel and stringent in-tube (not block) physical testing. The temperature was directly monitored in PCR tubes containing 50 microl of distilled water at 13 different block positions. The certified temperature accuracy of the measurement system was +/-0.3 degrees C. Finally, the results of the physical testing were compared to those of an amplification efficiency study running an in-house PCR assay. The cyclers did not perform within the manufacturer's specification. Premature timing, under- and overshooting, and spatial variation of heat transfer were found to be the critical factors. The physical testing allowed us to distinguish accurate from less-accurate (2/6) cyclers. The lack of thermal homogeneities became most evident at the denaturation level during the first 15 s. At the time point zero, the accurate cyclers showed temperature deviations of 0.5 to 1.5 degrees C, whereas less-accurate cyclers failed to reach the set temperature by 13 to 20 degrees C. Consequently, the two less-accurate cyclers could not gain positive PCR results by running an in-house PCR assay. However, by modifying the original temperature protocol by increasing the denaturation temperature and time, the amplification efficiency of these two cyclers could be improved significantly. The results have implication for laboratories using diagnostic PCR testing.


Asunto(s)
Reacción en Cadena de la Polimerasa/instrumentación , ADN Bacteriano/análisis , ADN Bacteriano/genética , Calor , Listeria/genética , Desnaturalización de Ácido Nucleico , Reacción en Cadena de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa/normas , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Temperatura
16.
J Food Prot ; 67(8): 1646-55, 2004 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-15330529

RESUMEN

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.


Asunto(s)
Microbiología de Alimentos , Listeria monocytogenes/aislamiento & purificación , Leche/microbiología , Reacción en Cadena de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa/normas , Animales , Reacciones Falso Negativas , Reacciones Falso Positivas , Cooperación Internacional , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Especificidad de la Especie
17.
Appl Environ Microbiol ; 70(7): 4379-83, 2004 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-15240324

RESUMEN

A PCR-based method for rapid detection of food-borne thermotolerant campylobacters was evaluated through a collaborative trial with 12 laboratories testing spiked carcass rinse samples. The method showed an interlaboratory diagnostic sensitivity of 96.7% and a diagnostic specificity of 100% for chicken samples, while these values were 94.2 and 83.3%, respectively, for pig samples.


Asunto(s)
Campylobacter/aislamiento & purificación , Carne/microbiología , Reacción en Cadena de la Polimerasa/métodos , Animales , Pollos , Sensibilidad y Especificidad , Porcinos
18.
Appl Environ Microbiol ; 70(6): 3588-92, 2004 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-15184161

RESUMEN

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.


Asunto(s)
Campylobacter/aislamiento & purificación , Pollos/microbiología , Reacción en Cadena de la Polimerasa/métodos , Animales , Campylobacter/genética , Recuento de Colonia Microbiana , Medios de Cultivo , ADN Bacteriano/análisis , Contaminación de Alimentos , Microbiología de Alimentos/normas , Calor , Medición de Riesgo , Factores de Tiempo , Microbiología del Agua
19.
J Microbiol Methods ; 58(1): 39-48, 2004 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-15177902

RESUMEN

As part of a large EU project for standardisation of polymerase chain reaction (PCR), a systematic evaluation of the interaction of enrichment media, type of DNA polymerase and pre-PCR sample treatment for a PCR detecting thermotolerant campylobacters was carried out. The growth-supporting capacity and PCR compatibility of enrichment in Preston, Mueller-Hinton and Bolton broth (blood-containing and blood-free) were evaluated. The effect of resin-based DNA extraction and DNA extraction by boiling on the final PCR assay was investigated. The time-course studies indicated that a 20-h sample enrichment in blood-containing Bolton broth, followed by a simple resin-based extraction of DNA and a PCR amplification using Tth polymerase, resulted in strong and clear PCR amplicons for target (287 bp) and internal amplification control (IAC, 124 bp). The enrichment PCR-based method, tested on 68 presumably naturally contaminated poultry-rinse samples, showed a diagnostic sensitivity of 97.5% (39 PCR-positive/40 total positive samples) and a diagnostic specificity of 100% (28 PCR-negative/28 total negative samples; P=0.32) when compared to a standard bacteriological method (ISO 10272).


Asunto(s)
Campylobacter/crecimiento & desarrollo , Microbiología de Alimentos , Carne/microbiología , Reacción en Cadena de la Polimerasa/normas , Animales , Campylobacter/genética , Infecciones por Campylobacter/prevención & control , Pollos/microbiología , Medios de Cultivo/normas , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Polimerasa Dirigida por ADN/normas , Patos/microbiología , Carne/normas , Reacción en Cadena de la Polimerasa/métodos , Sensibilidad y Especificidad
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