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Wang J, Li R, Hu L, Sun X, Wang J, Li J. Development of a quantitative fluorescence single primer isothermal amplification-based method for the detection of Salmonella. Int J Food Microbiol 2015; 219:22-7. [PMID: 26704066 DOI: 10.1016/j.ijfoodmicro.2015.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/14/2015] [Accepted: 12/11/2015] [Indexed: 11/24/2022]
Abstract
Food-borne disease caused by Salmonella has long been, and continues to be, an important global public health problem, necessitating rapid and accurate detection of Salmonella in food. Real time PCR is the most recently developed approach for Salmonella detection. Single primer isothermal amplification (SPIA), a novel gene amplification technique, has emerged as an attractive microbiological testing method. SPIA is performed under a constant temperature, eliminating the need for an expensive thermo-cycler. In addition, SPIA reactions can be accomplished in 30 min, faster than real time PCR that usually takes over 2h. We developed a quantitative fluorescence SPIA-based method for the detection of Salmonella. Using Salmonella Typhimurium genomic DNA as template and a primer targeting Salmonella invA gene, we showed the detection limit of SPIA was 2.0 × 10(1)fg DNA. Its successful amplification of different serotypic Salmonella genomic DNA but not non-Salmonella bacterial DNA demonstrated the specificity of SPIA. Furthermore, this method was validated with artificially contaminated beef. In conclusion, we showed high sensitivity and specificity of SPIA in the detection of Salmonella, comparable to real time PCR. In addition, SPIA is faster and more cost-effective (non-use of expensive cyclers), making it a potential alternative for field detection of Salmonella in resource-limited settings that are commonly encountered in developing countries.
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Affiliation(s)
- Jianchang Wang
- The Technical Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd, Xinhua District, Shijiazhuang 050050, China
| | - Rui Li
- College of Food Science and Technology, Agricultural University of Hebei, No.38 Lingyusi Street, Baoding 071001, China
| | - Lianxia Hu
- The Technical Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd, Xinhua District, Shijiazhuang 050050, China
| | - Xiaoxia Sun
- The Technical Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd, Xinhua District, Shijiazhuang 050050, China
| | - Jinfeng Wang
- The Technical Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd, Xinhua District, Shijiazhuang 050050, China
| | - Jing Li
- The Technical Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd, Xinhua District, Shijiazhuang 050050, China.
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Xiao L, Zhang Z, Sun X, Pan Y, Zhao Y. Development of a quantitative real-time PCR assay for viable Salmonella spp. without enrichment. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.03.050] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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53
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Bell RL, Zheng J, Burrows E, Allard S, Wang CY, Keys CE, Melka DC, Strain E, Luo Y, Allard MW, Rideout S, Brown EW. Ecological prevalence, genetic diversity, and epidemiological aspects of Salmonella isolated from tomato agricultural regions of the Virginia Eastern Shore. Front Microbiol 2015; 6:415. [PMID: 25999938 PMCID: PMC4423467 DOI: 10.3389/fmicb.2015.00415] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/20/2015] [Indexed: 11/13/2022] Open
Abstract
Virginia is the third largest producer of fresh-market tomatoes in the United States. Tomatoes grown along the eastern shore of Virginia are implicated almost yearly in Salmonella illnesses. Traceback implicates contamination occurring in the pre-harvest environment. To get a better understanding of the ecological niches of Salmonella in the tomato agricultural environment, a 2-year study was undertaken at a regional agricultural research farm in Virginia. Environmental samples, including tomato (fruit, blossoms, and leaves), irrigation water, surface water and sediment, were collected over the growing season. These samples were analyzed for the presence of Salmonella using modified FDA-BAM methods. Molecular assays were used to screen the samples. Over 1500 samples were tested. Seventy-five samples tested positive for Salmonella yielding over 230 isolates. The most commonly isolated serovars were S. Newport and S. Javiana with pulsed-field gel electrophoresis yielding 39 different patterns. Genetic diversity was further underscored among many other serotypes, which showed multiple PFGE subtypes. Whole genome sequencing (WGS) of several S. Newport isolates collected in 2010 compared to clinical isolates associated with tomato consumption showed very few single nucleotide differences between environmental isolates and clinical isolates suggesting a source link to Salmonella contaminated tomatoes. Nearly all isolates collected during two growing seasons of surveillance were obtained from surface water and sediment sources pointing to these sites as long-term reservoirs for persistent and endemic contamination of this environment.
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Affiliation(s)
- Rebecca L. Bell
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Jie Zheng
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Erik Burrows
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Sarah Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Charles Y. Wang
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Christine E. Keys
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - David C. Melka
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Errol Strain
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Yan Luo
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Steven Rideout
- Eastern Shore Agricultural Research and Extension Center, Virginia TechPainter, VA, USA
| | - Eric W. Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
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Wang H, Gill VS, Cheng CM, Gonzalez-Escalona N, Irvin KA, Zheng J, Bell RL, Jacobson AP, Hammack TS. Evaluation and comparison of rapid methods for the detection of Salmonella in naturally contaminated pine nuts using different pre enrichment media. Food Microbiol 2015; 46:58-65. [DOI: 10.1016/j.fm.2014.06.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 06/18/2014] [Accepted: 06/20/2014] [Indexed: 11/30/2022]
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Yang Q, Wang F, Jones KL, Meng J, Prinyawiwatkul W, Ge B. Evaluation of loop-mediated isothermal amplification for the rapid, reliable, and robust detection of Salmonella in produce. Food Microbiol 2015; 46:485-493. [DOI: 10.1016/j.fm.2014.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 11/16/2022]
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Mourembou G, Fenollar F, Socolovschi C, Lemamy GJ, Nzoughe H, Kouna LC, Toure-Ndouo F, Million M, Mbiguino AN, Lekana-Douki JB, Raoult D. Molecular Detection of Fastidious and Common Bacteria as Well as Plasmodium spp. in Febrile and Afebrile Children in Franceville, Gabon. Am J Trop Med Hyg 2015; 92:926-32. [PMID: 25802432 DOI: 10.4269/ajtmh.14-0699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/07/2015] [Indexed: 01/19/2023] Open
Abstract
Malaria was considered as the main cause of fever in Africa. However, with the roll back malaria initiative, the causes of fever in Africa may change. This study aimed to evaluate the prevalence of bacteria and Plasmodium spp. in febrile and afebrile (controls) children from Franceville, Gabon. About 793 blood samples from febrile children and 100 from controls were analyzed using polymerase chain reaction (PCR) coupled with sequencing. Plasmodium spp. was the microorganism most detected in febrile (74.5%, 591/793) and controls (13%, 13/100), P < 0.0001. Its coinfection with bacteria was found only in febrile children (P = 0.0001). Staphylococcus aureus was the most prevalent bacterium in febrile children (2.8%, 22/793) and controls (3%, 3/100). Eight cases of Salmonella spp. (including two Salmonella enterica serovar Paratyphi) and two of Streptococcus pneumoniae were found only among febrile children. Borrelia spp. was found in 2 controls while Rickettsia felis was detected in 10 children (in 8 febriles and 2 afebriles). No DNA of other targeted microorganisms was detected. Plasmodium spp. remains prevalent while Salmonella spp., Staphylococcus aureus, and Streptococcus pneumoniae were common bacteria in Gabon. Two fastidious bacteria, Rickettsia felis and Borrelia spp., were found. Inclusion of controls should improve the understanding of the causes of fever in sub-Saharan Africa.
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Affiliation(s)
- Gaël Mourembou
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Florence Fenollar
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Cristina Socolovschi
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Guy Joseph Lemamy
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Hermann Nzoughe
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Lady Charlene Kouna
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Fousseyni Toure-Ndouo
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Matthieu Million
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Angelique Ndjoyi Mbiguino
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Jean Bernard Lekana-Douki
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - Didier Raoult
- URMITE, Aix Marseille Université, Marseille, France; Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon; Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon; Département de Biologie Cellulaire et Génétique, Université des Science de la Santé, Libreville, Gabon; Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Science de la Santé, Libreville, Gabon; Département de Microbiologie, Laboratoire National de Référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
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Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR. PLoS One 2015; 10:e0118668. [PMID: 25774907 PMCID: PMC4361174 DOI: 10.1371/journal.pone.0118668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/22/2015] [Indexed: 01/03/2023] Open
Abstract
Salmonellosis, a communicable disease caused by members of the Salmonella species, transmitted to humans through contaminated food or water. It is of paramount importance, to generate accurate detection methods for discriminating the various Salmonella species that cause severe infection in humans, including S. Typhi and S. Paratyphi A. Here, we formulated a strategy of detection and differentiation of salmonellosis by a multiplex polymerase chain reaction assay using S. Typhi non-protein coding RNA (sRNA) genes. With the designed sequences that specifically detect sRNA genes from S. Typhi and S. Paratyphi A, a detection limit of up to 10 pg was achieved. Moreover, in a stool-seeding experiment with S. Typhi and S. Paratyphi A, we have attained a respective detection limit of 15 and 1.5 CFU/mL. The designed strategy using sRNA genes shown here is comparatively sensitive and specific, suitable for clinical diagnosis and disease surveillance, and sRNAs represent an excellent molecular target for infectious disease.
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58
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Gopinath SC, Tang TH, Chen Y, Citartan M, Lakshmipriya T. Bacterial detection: From microscope to smartphone. Biosens Bioelectron 2014; 60:332-42. [DOI: 10.1016/j.bios.2014.04.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/13/2014] [Accepted: 04/07/2014] [Indexed: 01/15/2023]
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59
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Barbau-Piednoir E, Mahillon J, Pillyser J, Coucke W, Roosens NH, Botteldoorn N. Evaluation of viability-qPCR detection system on viable and dead Salmonella serovar Enteritidis. J Microbiol Methods 2014; 103:131-7. [DOI: 10.1016/j.mimet.2014.06.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/02/2014] [Accepted: 06/02/2014] [Indexed: 11/25/2022]
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60
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Rapid Methods for Quality Assurance of Foods: the Next Decade with Polymerase Chain Reaction (PCR)-Based Food Monitoring. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9915-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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61
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Fusco V, Quero GM. Culture-Dependent and Culture-Independent Nucleic-Acid-Based Methods Used in the Microbial Safety Assessment of Milk and Dairy Products. Compr Rev Food Sci Food Saf 2014; 13:493-537. [DOI: 10.1111/1541-4337.12074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Vincenzina Fusco
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
| | - Grazia Marina Quero
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
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62
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Zheng Q, Mikš-Krajnik M, Yang Y, Xu W, Yuk HG. Real-time PCR method combined with immunomagnetic separation for detecting healthy and heat-injured Salmonella Typhimurium on raw duck wings. Int J Food Microbiol 2014; 186:6-13. [PMID: 24974274 DOI: 10.1016/j.ijfoodmicro.2014.06.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/23/2014] [Accepted: 06/08/2014] [Indexed: 11/16/2022]
Abstract
Conventional culture detection methods are time consuming and labor-intensive. For this reason, an alternative rapid method combining real-time PCR and immunomagnetic separation (IMS) was investigated in this study to detect both healthy and heat-injured Salmonella Typhimurium on raw duck wings. Firstly, the IMS method was optimized by determining the capture efficiency of Dynabeads(®) on Salmonella cells on raw duck wings with different bead incubation (10, 30 and 60 min) and magnetic separation (3, 10 and 30 min) times. Secondly, three Taqman primer sets, Sal, invA and ttr, were evaluated to optimize the real-time PCR protocol by comparing five parameters: inclusivity, exclusivity, PCR efficiency, detection probability and limit of detection (LOD). Thirdly, the optimized real-time PCR, in combination with IMS (PCR-IMS) assay, was compared with a standard ISO and a real-time PCR (PCR) method by analyzing artificially inoculated raw duck wings with healthy and heat-injured Salmonella cells at 10(1) and 10(0) CFU/25 g. Finally, the optimized PCR-IMS assay was validated for Salmonella detection in naturally contaminated raw duck wing samples. Under optimal IMS conditions (30 min bead incubation and 3 min magnetic separation times), approximately 85 and 64% of S. Typhimurium cells were captured by Dynabeads® from pure culture and inoculated raw duck wings, respectively. Although Sal and ttr primers exhibited 100% inclusivity and exclusivity for 16 Salmonella spp. and 36 non-Salmonella strains, the Sal primer showed lower LOD (10(3) CFU/ml) and higher PCR efficiency (94.1%) than the invA and ttr primers. Moreover, for Sal and invA primers, 100% detection probability on raw duck wings suspension was observed at 10(3) and 10(4) CFU/ml with and without IMS, respectively. Thus, the Sal primer was chosen for further experiments. The optimized PCR-IMS method was significantly (P=0.0011) better at detecting healthy Salmonella cells after 7-h enrichment than traditional PCR method. However there was no significant difference between the two methods with longer enrichment time (14 h). The diagnostic accuracy of PCR-IMS was shown to be 98.3% through the validation study. These results indicate that the optimized PCR-IMS method in this study could provide a sensitive, specific and rapid detection method for Salmonella on raw duck wings, enabling 10-h detection. However, a longer enrichment time could be needed for resuscitation and reliable detection of heat-injured cells.
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Affiliation(s)
- Qianwang Zheng
- Food Science & Technology Programme, Department of Chemistry, National University of Singapore, Science Drive 4, 117543, Singapore
| | - Marta Mikš-Krajnik
- Food Science & Technology Programme, Department of Chemistry, National University of Singapore, Science Drive 4, 117543, Singapore; Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10-726 Olsztyn, Poland
| | - Yishan Yang
- Food Science & Technology Programme, Department of Chemistry, National University of Singapore, Science Drive 4, 117543, Singapore
| | - Wang Xu
- Department of Chemistry, National University of Singapore, Science Drive 4, 117543, Singapore
| | - Hyun-Gyun Yuk
- Food Science & Technology Programme, Department of Chemistry, National University of Singapore, Science Drive 4, 117543, Singapore; National University of Singapore (Suzhou) Research Institute, No. 377 Linquan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China.
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63
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Yeni F, Acar S, Polat Ö, Soyer Y, Alpas H. Rapid and standardized methods for detection of foodborne pathogens and mycotoxins on fresh produce. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.12.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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64
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Enumeration of salmonellae in table eggs, pasteurized egg products, and egg-containing dishes by using quantitative real-time PCR. Appl Environ Microbiol 2013; 80:1616-22. [PMID: 24362433 DOI: 10.1128/aem.03360-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Salmonellae are a major cause of food-borne outbreaks in Europe, with eggs and egg products being identified as major sources. Due to the low levels of salmonellae in eggs and egg products, direct quantification is difficult. In the present study, enrichment quantitative real-time PCR (qPCR) was employed for enumeration of salmonellae in different matrices: table eggs, pasteurized egg products, and egg-containing dishes. Salmonella enterica serovar Enteritidis and S. enterica serovar Tennessee were used to artificially contaminate these matrices. The results showed a linear regression between the numbers of salmonellae and the quantification cycle (Cq) values for all matrices used, with the exception of pasteurized egg white. Standard curves were constructed by using both stationary-phase cells and heat-stressed cells, with similar results. Finally, this method was used to evaluate the fate of salmonellae in two egg-containing dishes, long egg and tiramisu, at abused refrigeration temperatures, and results indicated the growth of bacteria over a 1-week period. In conclusion, enrichment qPCR was shown to be reliable for enumeration of salmonellae in different egg products.
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65
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Barbau-Piednoir E, Bertrand S, Mahillon J, Roosens NH, Botteldoorn N. SYBR®Green qPCR Salmonella detection system allowing discrimination at the genus, species and subspecies levels. Appl Microbiol Biotechnol 2013; 97:9811-24. [PMID: 24113820 PMCID: PMC3825158 DOI: 10.1007/s00253-013-5234-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 01/25/2023]
Abstract
In this work, a three-level Salmonella detection system based on a combination of seven SYBR®Green qPCR was developed. This detection system discriminates Salmonella at the genus, species and subspecies levels using a single 96-well plate. The SYBR®Green qPCR assays target the invA, rpoD, iroB and safC genes, as well as the STM0296 locus, putatively coding for a cytoplasmic protein. This study includes the design of primer pairs, in silico and in situ selectivity, sensitivity, repeatability and reproducibility evaluations of the seven SYBR®Green qPCR assays. Each detection level displayed a selectivity of 100 %. This combinatory SYBR®Green qPCR system was also compared with three commercially available Salmonella qPCR detection kits. This comparison highlighted the importance of using a multi-gene detection system to be able to detect every target strain, even those with deletion or mutation of important genes.
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67
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Babu L, Reddy P, Murali HS, Batra HV. Optimization and evaluation of a multiplex PCR for simultaneous detection of prominent foodborne pathogens of Enterobacteriaceae. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0622-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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68
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Gadkar VJ, Filion M. Development of a versatile TaqMan™ real-time quantitative PCR (RT-qPCR) compliant anchor sequence to quantify bacterial gene transcripts from RNA samples containing carryover genomic DNA. BMC Biotechnol 2013; 13:7. [PMID: 23369378 PMCID: PMC3689636 DOI: 10.1186/1472-6750-13-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/22/2013] [Indexed: 12/23/2022] Open
Abstract
Background In bacterial systems, the sequence congruence of genomic DNA (gDNA) and cDNA obtained following reverse transcription of RNA, makes gDNA an automatic target for qPCR primers. This could lead to aberrant gene expression quantification. This is why a rigorous treatment of bacterial RNA with DNase I is usually required to remove any traces of carryover gDNA. As bacterial RNA is known to be extremely labile, any procedure that affects RNA yield, such as DNase I treatment, can be logically assumed to also influence detection and quantification of gene transcripts, leading to either an underestimation or no detection at all. To address such problems, we have developed a novel and versatile TaqMan RT-qPCR compliant anchor sequence (MYT4) for quantifying bacterial gene transcripts without the need for DNase I treatment. Results A non-genomic anchor sequence, henceforth referred to as MYT4 was designed using a synthetic DNA sequence called myIC, previously shown to share no significant homology to any known accession in the GenBank database. The sequence characteristic of MYT4 was kept within the design parameters required for the TaqMan RT-qPCR platform. The specificity and robustness of the novel MYT4 sequence was validated on RNA extracted from the bacterium Pseudomonas sp. LBUM300, grown under liquid culture and spiked soil conditions. Two transcripts, namely hcnC and phlD, were quantified from these two experimental systems. Using the MYT4 anchor, no RT-qPCR signal was detected from non-DNase I treated RNA, while strong signals were obtained using conventional reverse primers and RT-qPCR, indicating the presence of carryover gDNA in the RNA, extracted from either liquid culture or soil. Serial treatment of the RNA samples with DNase I (required to achieve absolute gDNA elimination) resulted in 50-70% loss of RNA which, when submitted to conventional RT-qPCR, significantly altered the transcript numbers detected when compared to the MYT4-based approach. Conclusions Implementation of the versatile approach described in this study, which can be “retrofitted” to any existing TaqMan RT-qPCR system, should contribute to reducing the time and lowering the costs required to perform adequate bacterial RNA purification for downstream quantification of gene transcripts.
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Affiliation(s)
- Vijay J Gadkar
- Department of Biology, Université de Moncton, 18 Antonine-Maillet, Moncton, NB E1A 3E9, Canada
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69
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Weigel KM, Jones KL, Do JS, Melton Witt J, Chung JH, Valcke C, Cangelosi GA. Molecular viability testing of bacterial pathogens from a complex human sample matrix. PLoS One 2013; 8:e54886. [PMID: 23365682 PMCID: PMC3554692 DOI: 10.1371/journal.pone.0054886] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/17/2012] [Indexed: 11/30/2022] Open
Abstract
Assays for bacterial ribosomal RNA precursors (pre-rRNA) have been shown to distinguish viable from inactivated bacterial cells in drinking water samples. Because the synthesis of pre-rRNA is rapidly induced by nutritional stimulation, viable bacteria can be distinguished from inactivated cells and free nucleic acids by measuring the production of species-specific pre-rRNA in samples that have been briefly stimulated with nutrients. Here, pre-rRNA analysis was applied to bacteria from serum, a human sample matrix. In contrast to drinking water, serum is rich in nutrients that might be expected to mask the effects of nutritional stimulation. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays were used to detect pre-rRNA of four bacterial species: Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, and the Mycobacterium tuberculosis complex. These species were chosen for their clinical significance and phylogenetic diversity (Proteobacteria, Firmicutes, and Actinobacteria). To maximize resolving power, pre-rRNA was normalized to genomic DNA of each pathogen. When viable cells were shifted from serum to bacteriological culture medium, rapid replenishment of pre-rRNA was always observed. Cells of P. aeruginosa that were inactivated in the presence of serum exhibited no pre-rRNA response to nutritional stimulation, despite strong genomic DNA signals in these samples. When semi-automated methods were used, pre-rRNA analysis detected viable A. baumannii cells in serum at densities of ≤100 CFU/mL in <5.5 hours. Originally developed for rapid microbiological analysis of drinking water, ratiometric pre-rRNA analysis can also assess the viability of bacterial cells derived from human specimens, without requiring bacteriological culture.
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Affiliation(s)
- Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kelly L. Jones
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Julie S. Do
- AttoDx, Inc., Seattle, Washington, United States of America
| | - Jody Melton Witt
- Novartis Diagnostics, Emeryville, California, United States of America
| | - Jae-Hyun Chung
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Christian Valcke
- Novartis Diagnostics, Emeryville, California, United States of America
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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70
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González-Escalona N, Brown EW, Zhang G. Development and evaluation of a multiplex real-time PCR (qPCR) assay targeting ttrRSBCA locus and invA gene for accurate detection of Salmonella spp. in fresh produce and eggs. Food Res Int 2012. [DOI: 10.1016/j.foodres.2012.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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71
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72
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Xiao L, Zhang L, Wang HH. Critical issues in detecting viable Listeria monocytogenes cells by real-time reverse transcriptase PCR. J Food Prot 2012; 75:512-7. [PMID: 22410225 DOI: 10.4315/0362-028x.jfp-11-346] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rapid and specific detection of viable Listeria monocytogenes cells, particularly in processed foods, is a major challenge in the food industry. To assess the suitability of using RNA-based detection methods to detect viable cells, several sets of PCR primers and florescent probes were designed targeting the 16S rRNA, internalin A, and ribosomal protein L4 genes. One-step real-time reverse transcriptase (RT) PCR assays were conducted using RNAs extracted from control and heat-treated L. monocytogenes samples. The cycle threshold values were significantly higher in heat-treated cells than in controls. However, real-time RT-PCR amplification signals were still detected even in samples stored at room temperature for 24 h after lethal treatments, and the intensity of the signals was correlated with the cell population. The 16S rRNA molecules were the most stable of the three targets evaluated, and the impact on detection efficacy of the relative positions of the PCR primers within the target genes was limited under the experimental conditions. These results suggest that real-time RT-PCR assays have advantages over conventional PCR assays for assessing viable L. monocytogenes cells, but the results are affected by the stability of the RNA molecules targeted. These findings could have a major impact on interpretation of RNA-based detection data and gene expression studies.
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Affiliation(s)
- Linlin Xiao
- Department of Food Science, The Ohio State University, 2015 Fyffe Court, Columbus, Ohio 43210, USA
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73
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Cheung PY, Kam KM. Salmonella in food surveillance: PCR, immunoassays, and other rapid detection and quantification methods. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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74
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Techathuvanan C, D'Souza DH. Reverse-Transcriptase Loop-Mediated Isothermal Amplification as a Rapid Screening/Monitoring Tool for Salmonella Enterica Detection in Liquid Whole Eggs. J Food Sci 2012; 77:M200-5. [DOI: 10.1111/j.1750-3841.2011.02601.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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75
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Marathe SA, Chowdhury R, Bhattacharya R, Nagarajan AG, Chakravortty D. Direct detection of Salmonella without pre-enrichment in milk, ice-cream and fruit juice by PCR against hilA gene. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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76
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Kisluk G, Hoover DG, Kneil KE, Yaron S. Quantification of low and high levels of Salmonella enterica serovar Typhimurium on leaves. Lebensm Wiss Technol 2012. [DOI: 10.1016/j.lwt.2011.07.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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77
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Aw TG, Rose JB. Detection of pathogens in water: from phylochips to qPCR to pyrosequencing. Curr Opin Biotechnol 2011; 23:422-30. [PMID: 22153035 PMCID: PMC7126744 DOI: 10.1016/j.copbio.2011.11.016] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 10/30/2011] [Accepted: 11/11/2011] [Indexed: 12/24/2022]
Abstract
Waterborne pathogens pose a significant threat to human health and a proper assessment of microbial water quality is important for decision making regarding water infrastructure and treatment investments and eventually to provide early warning of disease, particularly given increasing global disasters associated with severe public health risks. Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. Future challenges lie in integrating these molecular tools with concentration techniques and bioinformatics platforms for unbiased guide of pathogen surveillance in water and developing standardized protocols.
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Affiliation(s)
- Tiong Gim Aw
- Department of Fisheries and Wildlife, 13 Natural Resources, Michigan State University, East Lansing, MI 48824, United States.
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78
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Comparison of real-time PCR, reverse transcriptase real-time PCR, loop-mediated isothermal amplification, and the FDA conventional microbiological method for the detection of Salmonella spp. in produce. Appl Environ Microbiol 2011; 77:6495-501. [PMID: 21803916 DOI: 10.1128/aem.00520-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Contamination of foods, especially produce, with Salmonella spp. is a major concern for public health. Several methods are available for the detection of Salmonella in produce, but their relative efficiency for detecting Salmonella in commonly consumed vegetables, often associated with outbreaks of food poisoning, needs to be confirmed. In this study, the effectiveness of three molecular methods for detection of Salmonella in six produce matrices was evaluated and compared to the FDA microbiological detection method. Samples of cilantro (coriander leaves), lettuce, parsley, spinach, tomato, and jalapeno pepper were inoculated with Salmonella serovars at two different levels (10(5) and <10(1) CFU/25 g of produce). The inoculated produce was assayed by the FDA Salmonella culture method (Bacteriological Analytical Manual) and by three molecular methods: quantitative real-time PCR (qPCR), quantitative reverse transcriptase real-time PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP). Comparable results were obtained by these four methods, which all detected as little as 2 CFU of Salmonella cells/25 g of produce. All control samples (not inoculated) were negative by the four methods. RT-qPCR detects only live Salmonella cells, obviating the danger of false-positive results from nonviable cells. False negatives (inhibition of either qPCR or RT-qPCR) were avoided by the use of either a DNA or an RNA amplification internal control (IAC). Compared to the conventional culture method, the qPCR, RT-qPCR, and LAMP assays allowed faster and equally accurate detection of Salmonella spp. in six high-risk produce commodities.
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79
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Chen Y, Kumar N, Siddique N. Development and evaluation of a real-time polymerase chain reaction assay targeting iap for the detection of Listeria monocytogenes in select food matrices. Foodborne Pathog Dis 2011; 8:1063-9. [PMID: 21612427 DOI: 10.1089/fpd.2010.0820] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Listeria monocytogenes is an intracellular foodborne pathogen that has been associated with severe human illnesses. Various rapid detection methods have been developed for the specific detection of this pathogen. In the present study, a real-time quantitative polymerase chain reaction (PCR) assay targeting iap, a gene encoding extracellular protein p60, was developed for L. monocytogenes. The PCR efficiency is above 85% and the limit of detection (LOD) is 30 copies of genome per reaction for all strains tested. The assay exhibited 100% inclusivity and exclusivity rates. The detection of L. monocytogenes in five food matrices, whole milk, soft cheese, turkey deli meat, smoked salmon, and alfalfa sprouts, was evaluated with and without enrichment. Without enrichment, the LOD for all food matrices were 4×10(3) CFU/mL food enrichment mix for whole milk and 4×10(4) CFU/mL for all other foods. With 24 h incubation in Buffered Listeria Enrichment Broth, the LOD was 3 CFU/25 g food for whole milk, turkey deli meat, and smoked salmon and 9 CFU/25 g food for soft cheese and alfalfa sprouts. With 48 h incubation, the LOD was 3 CFU/25 g food for all matrices. This quantitative PCR appears to be a promising alternative for rapid detection of L. monocytogenes in select foods.
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Affiliation(s)
- Yi Chen
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA.
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80
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Miller ND, Davidson P, D’Souza DH. Real-time reverse-transcriptase PCR for Salmonella Typhimurium detection from lettuce and tomatoes. Lebensm Wiss Technol 2011. [DOI: 10.1016/j.lwt.2010.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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81
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Rapid detection of viable salmonellae in produce by coupling propidium monoazide with loop-mediated isothermal amplification. Appl Environ Microbiol 2011; 77:4008-16. [PMID: 21498750 DOI: 10.1128/aem.00354-11] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent outbreaks linked to Salmonella-contaminated produce heightened the need to develop simple, rapid, and accurate detection methods, particularly those capable of determining cell viability. In this study, we examined a novel strategy for the rapid detection and quantification of viable salmonellae in produce by coupling a simple propidium monoazide sample treatment with loop-mediated isothermal amplification (PMA-LAMP). We first designed and optimized a LAMP assay targeting Salmonella. Second, the performance of PMA-LAMP for detecting and quantifying viable salmonellae was determined. Finally, the assay was evaluated in experimentally contaminated produce items (cantaloupe, spinach, and tomato). Under the optimized condition, PMA-LAMP consistently gave negative results for heat-killed Salmonella cells with concentrations up to 10(8) CFU/ml (or CFU/g in produce). The detection limits of PMA-LAMP were 3.4 to 34 viable Salmonella cells in pure culture and 6.1 × 10(3) to 6.1 × 10(4) CFU/g in spiked produce samples. In comparison, PMA-PCR was up to 100-fold less sensitive. The correlation between LAMP time threshold (T(T)) values and viable Salmonella cell numbers was high (R(2) = 0.949 to 0.993), with a quantification range (10(2) to 10(5) CFU/reaction in pure culture and 10(4) to 10(7) CFU/g in produce) comparable to that of PMA in combination with quantitative real-time PCR (PMA-qPCR). The complete PMA-LAMP assay took about 3 h to complete when testing produce samples. In conclusion, this rapid, accurate, and simple method to detect and quantify viable Salmonella cells in produce may present a useful tool for the produce industry to better control potential microbial hazards in produce.
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82
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Affiliation(s)
- John J. Maurer
- Department of Population Health, The University of Georgia, Athens, Georgia 30602
- Center for Food Safety, The University of Georgia, Griffin, Georgia 30223;
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83
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Techathuvanan C, D'Souza DH. Optimization of Rapid Salmonella enterica Detection in Liquid Whole Eggs by SYBR Green I–Based Real-Time Reverse Transcriptase–Polymerase Chain Reaction. Foodborne Pathog Dis 2011; 8:527-34. [DOI: 10.1089/fpd.2010.0721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chayapa Techathuvanan
- Department of Food Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Doris Helen D'Souza
- Department of Food Science and Technology, University of Tennessee, Knoxville, Tennessee
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84
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Carraro L, Maifreni M, Bartolomeoli I, Martino ME, Novelli E, Frigo F, Marino M, Cardazzo B. Comparison of culture-dependent and -independent methods for bacterial community monitoring during Montasio cheese manufacturing. Res Microbiol 2011; 162:231-9. [DOI: 10.1016/j.resmic.2011.01.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 01/01/2011] [Indexed: 11/24/2022]
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85
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86
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DeCoste NJ, Gadkar VJ, Filion M. Relative and absolute quantitative real-time PCR-based quantifications of hcnC and phlD gene transcripts in natural soil spiked with Pseudomonas sp. strain LBUM300. Appl Environ Microbiol 2011; 77:41-7. [PMID: 21075889 PMCID: PMC3019740 DOI: 10.1128/aem.01387-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 11/01/2010] [Indexed: 11/20/2022] Open
Abstract
Transcriptional analysis of microbial gene expression using relative quantitative real-time PCR (qRT-PCR) has been hampered by various technical problems. One such problem is the unavailability of an exogenous standard robust enough for use in a complex matrix like soil. To circumvent this technical issue, we made use of a recently developed artificial RNA (myIC) as an exogenous "spike-in" control. Nonsterile field soil was inoculated with various concentrations of the test bacterium Pseudomonas sp. strain LBUM300, ranging from 4.3- to 8.3-log bacterial cells per gram of soil. Total soil RNA was extracted at days 0, 7, and 14 postinoculation, and using two-step TaqMan assays, phlD (encoding the production of 2,4-diacetylphloroglucinol) and hcnC (encoding the production of hydrogen cyanide) gene expression was monitored. For relative quantification, a defined quantity of in vitro-synthesized myIC RNA was spiked during the RNA extraction procedure. Absolute qRT-PCR was also performed in parallel. Both the absolute and relative quantifications showed similar transcriptional trends. Overall, the transcriptional activity of phlD and hcnC changed over time and with respect to the bacterial concentrations used. Transcripts of the phlD and hcnC genes were detected for all five bacterial concentrations, but the phlD transcript copy numbers detected were lower than those detected for hcnC, regardless of the initial bacterial concentration or sampling date. For quantifying a low number of transcripts, the relative method was more reliable than the absolute method. This study demonstrates for the first time the use of a relative quantification approach to quantifying microbial gene transcripts from field soil using an exogenous spike-in control.
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Affiliation(s)
- Nadine J. DeCoste
- Université de Moncton, Department of Biology, 18 Antonine-Maillet, Moncton, NB E1A 3E9, Canada
| | - Vijay J. Gadkar
- Université de Moncton, Department of Biology, 18 Antonine-Maillet, Moncton, NB E1A 3E9, Canada
| | - Martin Filion
- Université de Moncton, Department of Biology, 18 Antonine-Maillet, Moncton, NB E1A 3E9, Canada
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87
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Gou J, Lee HY, Ahn J. Inactivation kinetics and virulence potential of Salmonella Typhimurium and Listeria monocytogenes treated by combined high pressure and nisin. J Food Prot 2010; 73:2203-10. [PMID: 21219737 DOI: 10.4315/0362-028x-73.12.2203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of this study was to characterize the physiological and molecular changes of Salmonella Typhimurium and Listeria monocytogenes in deionized water (DIW) and nisin solutions (100 IU/g) during high pressure processing (HPP). Strains of Salmonella Typhimurium and L. monocytogenes in DIW or nisin solutions were subjected to 200, 300, and 400 MPa for 20 min. The Weibull model adequately described the HPP inactivation of Salmonella Typhimurium and L. monocytogenes. Salmonella Typhimurium and L. monocytogenes populations were reduced to less than 1 CFU/ml in DIW and nisin solutions under 400 MPa. The highest b value was 5.75 for Salmonella Typhimurium in nisin solution under 400 MPa. L. monocytogenes was more sensitive to pressure change when suspended in DIW than when suspended in nisin. The pressure sensitivity of both Salmonella Typhimurium and L. monocytogenes was higher in DIW solution (141 to 243 MPa) than in nisin solution (608 to 872 MPa). No recovery of HPP-injured cells in DIW and nisin solutions treated at 400 MPa was observed after 7 days of refrigerated storage. The heterogeneity of HPP-treated cells was revealed in flow cytometry dot plots. The transcripts of stn, invA, prfA, and inlA were relatively down-regulated in HPP-treated nisin solution. The combination of high pressure and nisin could noticeably suppress the expression of virulence-associated genes. These results provide useful information for understanding the physiological and molecular characteristics of foodborne pathogens under high-pressure stress.
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Affiliation(s)
- Jingyu Gou
- Medical and Bio-material Research Center and Division of Biomaterials Engineering, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
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88
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Dwivedi HP, Jaykus LA. Detection of pathogens in foods: the current state-of-the-art and future directions. Crit Rev Microbiol 2010; 37:40-63. [PMID: 20925593 DOI: 10.3109/1040841x.2010.506430] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Over the last fifty years, microbiologists have developed reliable culture-based techniques to detect food borne pathogens. Although these are considered to be the "gold-standard," they remain cumbersome and time consuming. Despite the advent of rapid detection methods such as ELISA and PCR, it is clear that reduction and/or elimination of cultural enrichment will be essential in the quest for truly real-time detection methods. As such, there is an important role for bacterial concentration and purification from the sample matrix as a step preceding detection, so-called pre-analytical sample processing. This article reviews recent advancements in food borne pathogen detection and discusses future methods with a focus on pre-analytical sample processing, culture independent methods, and biosensors.
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Affiliation(s)
- Hari P Dwivedi
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC-27695-7624, USA.
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89
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García R, Bælum J, Fredslund L, Santorum P, Jacobsen CS. Influence of temperature and predation on survival of Salmonella enterica serovar Typhimurium and expression of invA in soil and manure-amended soil. Appl Environ Microbiol 2010; 76:5025-31. [PMID: 20562283 PMCID: PMC2916483 DOI: 10.1128/aem.00628-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/07/2010] [Indexed: 11/20/2022] Open
Abstract
The effects of three temperatures (5, 15, and 25 degrees C) on the survival of Salmonella enterica serovar Typhimurium in topsoil were investigated in small microcosms by three different techniques: plate counting, invA gene quantification, and invA mRNA quantification. Differences in survival were related to the effect of protozoan predation. Tetracycline-resistant Salmonella serovar Typhimurium was inoculated into soil and manure-amended soil at 1.5 x 10(8) cells g soil(-1). Population densities were determined by plate counting and by molecular methods and monitored for 42 days. Simultaneous extraction of RNA and DNA, followed by quantitative PCR, was used to investigate invA gene levels and expression. Analysis by these three techniques showed that Salmonella serovar Typhimurium survived better at 5 degrees C. Comparing DNA and CFU levels, significantly higher values were determined by DNA-based techniques. invA mRNA levels showed a fast decrease in activity, with no detectable mRNA after an incubation period of less than 4 days in any of the soil scenarios. A negative correlation was found between Salmonella serovar Typhimurium CFU levels and protozoan most probable numbers, and we propose the role of the predator-prey interaction as a factor to explain the die-off of the introduced strain by both culture- and DNA quantification-based methods. The results indicate that temperature, manure, and protozoan predation are important factors influencing the survival of Salmonella serovar Typhimurium in soil.
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Affiliation(s)
- R. García
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - J. Bælum
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - L. Fredslund
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - P. Santorum
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - C. S. Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
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90
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Rump LV, Asamoah B, Gonzalez-Escalona N. Comparison of commercial RNA extraction kits for preparation of DNA-free total RNA from Salmonella cells. BMC Res Notes 2010; 3:211. [PMID: 20663210 PMCID: PMC3161365 DOI: 10.1186/1756-0500-3-211] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/27/2010] [Indexed: 12/23/2022] Open
Abstract
Background The isolation of DNA-free RNA is a crucial step in the reverse transcription PCR (RT-PCR). Every RNA extraction procedure results in RNA samples contaminated with genomic DNA, which can cause false-positive outcomes in highly sensitive applications, including a recently developed quantitative real-time PCR (RT-qPCR) assay that targets invA mRNA for the detection of live Salmonella cells. The assay of this specific mRNA can be used to indicate the presence of live, as opposed to dead, cells of Salmonella enterica in a food matrix. Findings We evaluated the ability of five RNA extraction kits to produce RNA preparations from exponentially growing Salmonella cells. The acceptability of the preparations for use in downstream applications such as RT-qPCR was judged in terms of the total amount of RNA recovered, the integrity of the RNA molecules, and minimal content of DNA. The five kits produced RNA preparations that differed markedly in yield, integrity of the Salmonella RNA and the amount of contaminant DNA. The greatest RNA recovery was achieved with the MasterPure kit; however, the preparation contained high levels of genomic DNA. The UltraClean extraction kit gave a low level of RNA recovery with a poor level of integrity. The RNeasy Mini, RiboPure and PureLink extraction kits produced high-quality, DNA-free RNA suitable for Salmonella detection by RT-qPCR. Conclusions We showed that the RNeasy Mini and PureLink RNA extraction kits were the most suitable for the detection of Salmonella invA mRNA by RT-qPCR. The use of these two kits will greatly reduce the frequency of false-positive results and might allow fast RT-qPCR determination of invA mRNA produced by viable Salmonella in food samples.
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Affiliation(s)
- Lydia V Rump
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA.
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91
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Miller ND, Draughon FA, D'Souza DH. Real-time reverse-transcriptase--polymerase chain reaction for Salmonella enterica detection from jalapeño and serrano peppers. Foodborne Pathog Dis 2010; 7:367-73. [PMID: 19911882 DOI: 10.1089/fpd.2009.0398] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Outbreaks of Salmonella linked to fresh produce emphasize the need for rapid detection methods to curb the spread of foodborne pathogens. Reverse-transcriptase-polymerase chain reaction (RT-PCR) detects the presence of mRNA (shorter half-life than DNA), with greater potential of detecting viable pathogens. Real-time RT-PCR eliminates the need for gel electrophoresis and significantly enhances the speed of detection (<1 day) compared with traditional methods (>5 days). The objectives of this research were to apply real-time SYBR Green I-based RT-PCR to detect Salmonella from jalapeño and serrano peppers spiked with low and high inocula of Salmonella. Inoculated and uninoculated peppers were rinsed with water and dried under ultraviolet light for 10 min. Approximately 25 g peppers was inoculated with 10(8) to 10(1) colony forming units (CFU) of Salmonella enterica serovar Typhimurium in a stomacher bag and hand massaged in sterile 0.05 M glycine-0.14 M saline buffer (0.05% Tween, 3% beef extract) for optimal recovery of bacteria. A short preenrichment step of 6 h in buffered peptone water was needed for the detection of low inocula (10(4) CFU/25 g). One-milliliter portions of the extracts were serially diluted, plated on XLT4 agar, and used for RNA extraction with the Qiagen RNeasy Mini Kit. RT-PCR was carried out using SYBR Green I one-step RT-PCR with previously described invA gene primers and an internal amplification control. Detection limits were 10(4) CFU/25 g (approximately 10(2) CFU/g) and 10(7) CFU/25 g (approximately 10(5) CFU/g) Salmonella from enriched and unenriched inoculated peppers, respectively. Even though this method included a 6-h incubation period, the results were still obtainable in 1 day. This method shows promise for applications in routine surveillance and during outbreaks.
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Affiliation(s)
- Nathan D Miller
- Department of Food Science and Technology, The University of Tennessee, Knoxville, Tennessee, USA
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92
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Deer D, Lampel K, González-Escalona N. A versatile internal control for use as DNA in real-time PCR and as RNA in real-time reverse transcription PCR assays. Lett Appl Microbiol 2010; 50:366-72. [DOI: 10.1111/j.1472-765x.2010.02804.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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93
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Techathuvanan C, Draughon FA, D'Souza DH. Loop-Mediated Isothermal Amplification (LAMP) for the Rapid and Sensitive Detection ofSalmonella Typhimurium from Pork. J Food Sci 2010; 75:M165-72. [DOI: 10.1111/j.1750-3841.2010.01554.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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94
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TECHATHUVANAN CHAYAPA, DRAUGHON FRANCESANN, D'SOUZA DORISHELEN. Real-Time Reverse Transcriptase PCR for the Rapid and Sensitive Detection of Salmonella Typhimurium from Pork. J Food Prot 2010; 73:507-14. [DOI: 10.4315/0362-028x-73.3.507] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Reverse transcriptase PCR (RT-PCR) detects the presence of mRNA and has a greater potential for detecting viable pathogens than do DNA-based PCR assays, with improved speed and sensitivity compared with traditional methods. Our objective was to rapidly and sensitively detect Salmonella Typhimurium from pork within two 8-h work shifts using a SYBR Green I real-time RT-PCR (rt-RT-PCR) assay. Pork chop and sausage samples (25 g) were inoculated with 108 to 100 CFU of Salmonella Typhimurium and stomached in 225 ml of tetrathionate broth. Serial dilutions were spread plated on xylose lysine Tergitol 4 agar either immediately or after 10 h of selective preenrichment or preenrichment followed by 12 h of selective enrichment (for stressed cells) at 37°C for standard cultural enumeration. RNA was extracted using the TRIzol method. The rt-RT-PCR assay was carried out in a Bio-Rad iCycler using a SYBR Green I one-step RT-PCR kit and Salmonella specific invA gene primers with an internal amplification control (IAC). The PCR was followed by melting temperature (Tm) analysis to determine specific Salmonella invA (Tm = 87.5°C) and IAC (Tm = 82°C) products. Improved Salmonella detection up to 101 CFU/25 g of pork and 100 CFU/25 g of sausages was obtained after 10 h of enrichment within approximately 24 h. Even without enrichment, Salmonella could be detected from both pork chop and sausage at 106 CFU/25 g within 1 day. This robust rt-RT-PCR detects and confirms Salmonella in pork within approximately 24 h and thus is significantly faster than traditional methods that take ≥1 week. This assay shows promise for routine testing and monitoring of Salmonella by the pork industry.
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Affiliation(s)
- CHAYAPA TECHATHUVANAN
- Department of Food Science and Technology, University of Tennessee, 2605 River Drive, Knoxville, Tennessee 37996-4591, USA
| | - FRANCES ANN DRAUGHON
- Department of Food Science and Technology, University of Tennessee, 2605 River Drive, Knoxville, Tennessee 37996-4591, USA
| | - DORIS HELEN D'SOUZA
- Department of Food Science and Technology, University of Tennessee, 2605 River Drive, Knoxville, Tennessee 37996-4591, USA
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95
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Reimann S, Grattepanche F, Rezzonico E, Lacroix C. Development of a real-time RT-PCR method for enumeration of viable Bifidobacterium longum cells in different morphologies. Food Microbiol 2009; 27:236-42. [PMID: 20141941 DOI: 10.1016/j.fm.2009.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 10/08/2009] [Accepted: 10/14/2009] [Indexed: 11/27/2022]
Abstract
Viability of probiotic bacteria is traditionally assessed by plate counting which has several limitations, including underestimation of cells in aggregates or chains morphology. We describe a quantitative PCR (qPCR)-based method for an accurate enumeration of viable cells of Bifidobacterium longum NCC2705 exhibiting different morphologies by measuring the mRNA levels of cysB and purB, two constitutively expressed housekeeping genes. Three primer-sets targeting short fragments of 57-bp of cysS and purB and one 400-bp fragment of purB were used. Cell quantification of serially diluted samples showed a good correlation coefficient of R(2) 0.984 +/- 0.003 between plate counts and qRT-PCR for all tested primer sets. Loss of viable cells exposed to a lethal heat stress (56 degrees C, 10, 20 and 30 min) was estimated by qRT-PCR and plate counts. No significant difference was observed using qRT-PCR targeting the 400-bp fragment of purB compared to plate counts indicating that this fragment is a suitable marker of cell viability. In contrast, the use of the 57-bp fragments led to a significant overestimation of viable cell counts (18 +/- 3 and 7 +/- 2 fold for cysB and purB, respectively). Decay of the mRNA fragments was studied by treatment of growing cells with rifampicin prior qRT-PCR. The 400-bp fragment of purB was faster degraded than the 57-bp fragments of cysB and purB. The 400-bp fragment of purB was further used to enumerate viable cells in aggregate state. Cell counts were more than 2 log(10) higher using the qRT-PCR method compared to plate counts. Growing interest in probiotic characteristics of aggregating bacteria cells make this technique a valuable tool to accurately quantify viable probiotic bacteria exhibiting heterogeneous morphology.
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Affiliation(s)
- Sebastian Reimann
- Laboratory of Food Biotechnology, Institute of Food Science and Nutrition, Swiss Federal Institute of Technology, Schmelzbergstrasse. 7 8092 Zurich, Switzerland
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