1
|
Johnson TJ, Flores-Figueroa C, Munoz-Aguayo J, Pinho G, Miller E. Persistence of vaccine origin Salmonella Typhimurium through the poultry production continuum, and development of a rapid typing scheme for their differentiation from wild type field isolates. Poult Sci 2024; 103:103707. [PMID: 38608390 PMCID: PMC11017335 DOI: 10.1016/j.psj.2024.103707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Salmonella enterica serovar Typhimurium is one of the top Salmonella serovars annually linked to poultry production and corresponding human illnesses. Because of this, vaccination of commercial poultry against Salmonella Typhimurium has been a focal point in recent years. There are several commercially available Salmonella Typhimurium vaccines available for use in poultry production. Among these are modified live vaccines, including Poulvac ST (Zoetis), Megan Egg (AviPro), and Megan Vac 1 (AviPro). In this study, analyses of 27 field isolates of Salmonella Typhimurium from poultry sources indicated evidence for the persistence of some vaccine-origin strains through the commercial production cycle. Further analyses of 26,812 database isolates indicated vaccine-origin isolates are persisting frequently through processing, are present on retail meat products, and are even occasionally found in human patients. A novel polymerase chain reaction (PCR) was created and validated which enables simultaneous identification of Salmonella enterica sp., the Salmonella Typhimurium serovar, and differentiation of wild type Salmonella Typhimurium from live attenuated vaccines involving mutations in the cya/crp or aroA genes. The PCR was developed considering whole genome differences between the vaccines and wild type field isolates and was validated using different field isolates and recovered vaccine strains. This method enables poultry producers to rapidly determine if recovered field isolates have a vaccine origin.
Collapse
Affiliation(s)
- Timothy J Johnson
- University of Minnesota, Department of Veterinary and Biomedical Sciences, Saint Paul, MN 55108, USA; University of Minnesota, Mid-Central Research and Outreach Center, Willmar, MN 56201, USA.
| | - Cristian Flores-Figueroa
- University of Minnesota, Department of Veterinary and Biomedical Sciences, Saint Paul, MN 55108, USA; University of Minnesota, Mid-Central Research and Outreach Center, Willmar, MN 56201, USA
| | - Jeannette Munoz-Aguayo
- University of Minnesota, Department of Veterinary and Biomedical Sciences, Saint Paul, MN 55108, USA; University of Minnesota, Mid-Central Research and Outreach Center, Willmar, MN 56201, USA
| | - Glenda Pinho
- University of Minnesota, Department of Veterinary and Biomedical Sciences, Saint Paul, MN 55108, USA
| | - Elizabeth Miller
- University of Minnesota, Department of Veterinary and Biomedical Sciences, Saint Paul, MN 55108, USA
| |
Collapse
|
2
|
Liao C, Pan L, Tan M, Zhou Z, Long S, Yi X, Li X, Wei G, Liang L. A dual RPA-LFD assay for the simultaneous detection of Salmonella typhimurium and Salmonella enteritidis. Front Bioeng Biotechnol 2024; 12:1379939. [PMID: 38524195 PMCID: PMC10958489 DOI: 10.3389/fbioe.2024.1379939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction: Salmonella was one of the most common bacteria that caused foodborne illness, with S. typhimurium (Salmonella typhimurium) and S. enteritidis (Salmonella enteritidis) infections accounting for more than 75% of human salmonella infections. Methods: In this study, we developed a method of dual recombinase polymerase amplification (RPA) combined with a lateral flow dipstick for the rapid detection of S. typhimurium and S. enteritidis in clinical specimens (stool). Results: The entire reaction process, including amplification and result reading, could be completed within 65 min. The detection limits of S. typhimurium and S. enteritidis in pure culture samples were 5.23 × 101 CFU/mL and 3.59 × 101 CFU/mL, respectively. The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were 8.30 × 101 CFU/mL and 2.70 × 102 CFU/mL, respectively. In addition, the method had no cross-reaction with other pathogenic microorganisms. The results in clinical samples were fully consistent with those obtained using Bacterial Analysis Manual, with sensitivity and specificity were 100% (8/8) and 100% (17/17) for S. typhimurium and 100% (4/4) and 100% (21/21) for S. enteritidis, respectively. Discussion: The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were higher than those in pure culture samples, which might be attributed to the inherent complex composition of artificially contaminated samples. In addition, the detection limits of S. typhimurium and S. enteritidis in the same sample were also different, which might be attributed to different amplification efficiency of two target genes in the same reaction system. Conclusion: This assay had potential application outdoors, as it could be performed within 1 h at 38°C without a complex instrument, and the results could be observed with the naked eye. In conclusion, the dual RPA-LFD assay established in this study had practical significance for the rapid detection of S. typhimurium and S. enteritidis in the future.
Collapse
Affiliation(s)
- Chuan Liao
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Lele Pan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Meiying Tan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Zihan Zhou
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Shaoping Long
- Department of Clinical Laboratory, Baise People’s Hospital, Baise, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Xuebin Li
- Department of Neurology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Lina Liang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| |
Collapse
|
3
|
Mok K, Honwichit O, Funnuam T, Charoensiddhi S, Nitisinprasert S, Nielsen DS, Nakphaichit M. Synergistic activity of Limosilactobacillus reuteri KUB-AC5 and water-based plants against Salmonella challenge in a human in vitro gut model. Sci Rep 2024; 14:4730. [PMID: 38413615 PMCID: PMC10899581 DOI: 10.1038/s41598-024-53912-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
A synbiotic is a combination of live microorganisms and specific substrates that are selectively utilized by host microorganisms, resulting in health benefits for the host. Previous studies have demonstrated the protective effects of L. reuteri KUB-AC5 against Salmonella infection in chicken and mouse models. The probiotic activity of L. reuteri KUB-AC5 in these hosts was influenced by nutritional supplements. Water-based plants contain significant amounts of carbohydrates, particularly dietary fiber and proteins, making them potential prebiotic substrates. In this study, four water-based plants (Ulva rigida, Caulerpa lentillifera, Wolffia globosa, and Gracillaria fisheri) were screened for their ability to support the growth of L. reuteri KUB-AC5. Under monoculture testing, U. rigida exhibited the highest capacity to support the growth of L. reuteri KUB-AC5 and the production of organic acids, including acetic acid, lactic acid, and propionic acid (p ≤ 0.05). In co-culture experiments, the synbiotic combination of U. rigida and L. reuteri KUB-AC5 demonstrated the potential to eliminate Salmonella Typhimurium DMST 48437 when inoculated at 104 CFU/mL within 9 h. The synbiotic activities of U. rigida and L. reuteri KUB-AC5 were further investigated using an in vitro human gut model. Compared to the probiotic treatment, the synbiotic combination of L. reuteri KUB-AC5 and U. rigida showed significantly higher levels of L. reuteri KUB-AC5 (5.1 log copies/mL) and a reduction of S. Typhimurium by 0.8 log (CFU/ml) after 24 h (p ≤ 0.05). Synbiotic treatment also significantly promoted the production of short-chain fatty acids (SCFAs), including butyric acid, propionic acid, and acetic acid, compared to prebiotic and probiotic treatments alone (p ≤ 0.05). Furthermore, the synbiotic formulation modulated the in vitro simulated gut microbiome, enhancing putatively beneficial gut microbes, including lactobacilli, Faecalibacterium, and Blautia. Our findings demonstrated that L. reuteri KUB-AC5, in combination with U. rigida, exhibited synergistic activity, as indicated by increased viability, higher anti-pathogenicity toward Salmonella, and the ability to modulate the gut microbiome.
Collapse
Affiliation(s)
- Kevin Mok
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Orranich Honwichit
- Department of Food Science and Technology, Faculty of Agro‑Industry, Kasetsart University, Bangkok, Thailand
| | - Thanyakan Funnuam
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Suvimol Charoensiddhi
- Department of Food Science and Technology, Faculty of Agro‑Industry, Kasetsart University, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | | | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand.
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand.
| |
Collapse
|
4
|
Weller DL, Murphy CM, Love TMT, Danyluk MD, Strawn LK. Methodological differences between studies confound one-size-fits-all approaches to managing surface waterways for food and water safety. Appl Environ Microbiol 2024; 90:e0183523. [PMID: 38214516 PMCID: PMC10880618 DOI: 10.1128/aem.01835-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.
Collapse
Affiliation(s)
- Daniel L. Weller
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Claire M. Murphy
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Tanzy M. T. Love
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Michelle D. Danyluk
- Department of Food Science and Human Nutrition, Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, USA
| | - Laura K. Strawn
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| |
Collapse
|
5
|
Ham H, Park DS. New Insights and Approach Toward the Genetic Diversity and Strain Typing of Erwinia pyrifoliae Based on rsxC, an Electron Transport Gene. PLANT DISEASE 2024; 108:296-301. [PMID: 37669173 DOI: 10.1094/pdis-03-23-0475-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Erwinia pyrifoliae, a causal agent of black shoot blight in apple and pear trees, is a plant pathogenic bacterium first reported in South Korea. The symptoms of black shoot blight are very similar to those of the fire blight disease in apple and pear trees caused by E. amylovora, as E. pyrifoliae has a genetically very close relationship with E. amylovora. Recently, there have been reports that E. pyrifoliae causes disease in European strawberries, resulting in severe fruit loss that aroused great concern about its spread, distribution, and host range. Therefore, it is essential to establish a trustworthy approach to understanding the distribution patterns of E. pyrifoliae based on the genetic background to strengthen the barrier of potential spreading risks, although advanced methods have been provided to accurately detect E. pyrifoliae and E. amylovora. Consequently, this study discovered a noble and noteworthy gene, rsxC, capable of providing the pathogen genotype by comparing E. pyrifoliae genomic sequences in the international representative genome archive. Different numbers of 40-unit amino acid repeats in this gene among the strains induced intraspecific traits in RsxC. By comparing their repeat pattern, E. pyrifoliae isolates were divided into two main groups, branching into several clades via sequence alignment of 35 E. pyrifoliae isolates from various apple orchards from 2020 to 2021 in South Korea. The newly discovered quadraginta amino acid repeat within this gene would be a valuable genetic touchstone for determining the genotype and distribution pattern of E. pyrifoliae strains, ultimately leading to exploring their evolution. The function of amino acid repeats and the biological significance of strains need to be elucidated further.
Collapse
Affiliation(s)
- Hyeonheui Ham
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju-gun 55365, Republic of Korea
| | - Dong Suk Park
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju-gun 55365, Republic of Korea
| |
Collapse
|
6
|
Murphy CM, Weller DL, Strawn LK. Scale and detection method impacted Salmonella prevalence and diversity in ponds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167812. [PMID: 37852489 DOI: 10.1016/j.scitotenv.2023.167812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Site-specific approaches for managing food safety hazards in agricultural water require an understanding of foodborne pathogen ecology. This study identified factors associated with Salmonella contamination in Virginia ponds. Grab samples (250 mL, N = 600) were collected from 30 sites across nine ponds. Culture- and culture-independent (CIDT)-based methods were used to detect Salmonella in each sample. Salmonella isolated by culture-based methods were serotyped by Kauffman-White classification. Environmental data were collected for each sample. McNemar's χ2 was used to determine if Salmonella detection differed by testing method. Separate mixed effect models were used to identify environmental factors associated with culture and CIDT-based Salmonella detection. Separate models were built for each pond, and for all ponds combined. Salmonella detection differed significantly (p < 0.001) between CIDT (31 %; 183/600)- and culture (13 %; 77/600)-based methods. Culture-based methods yielded 11 different serovars. All cultured Salmonella samples were confirmed by CIDT; 42.1 % of CIDT Salmonella-positive samples could be cultured. Associations between environmental factors and Salmonella detection also varied substantially by pond and detection method. In the all-pond model, associations were observed for five factors (total coliforms, Escherichia coli, air temperature, UV, rain) for both culture- and CIDT-based Salmonella detection. Rain prior to sampling (24 h) increased odds of Salmonella detection for culture (OR = 5.09) and CIDT (OR = 3.62) in the all-pond model. When all the pond data were used, models masked associations at the individual pond level, as there were noticeable differences between ponds and the odds of isolating Salmonella by environmental factors. Ponds were within a 187-ha area in this study, emphasizing water management needs to be individualized (i.e., assess hazards/risks by pond). Results also highlight detection methods and scale strongly affect observed water quality and should be considered when developing monitoring programs to develop guidance for growers.
Collapse
Affiliation(s)
- Claire M Murphy
- Department of Food Science and Technology, Virginia Tech, 1230 Washington Street SW, Blacksburg, VA 24061, USA
| | - Daniel L Weller
- Department of Food Science and Technology, Virginia Tech, 1230 Washington Street SW, Blacksburg, VA 24061, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Boulevard, Rochester, NY 14642, USA
| | - Laura K Strawn
- Department of Food Science and Technology, Virginia Tech, 1230 Washington Street SW, Blacksburg, VA 24061, USA.
| |
Collapse
|
7
|
Kim HJ, Jung Y, Kim MJ, Kim HY. Novel Heptaplex PCR-Based Diagnostics for Enteric Fever Caused by Typhoidal Salmonella Serovars and Its Applicability in Clinical Blood Culture. J Microbiol Biotechnol 2023; 33:1457-1466. [PMID: 37674393 DOI: 10.4014/jmb.2307.07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023]
Abstract
Enteric fever is caused by typhoidal Salmonella serovars (Typhi, Paratyphi A, Paratyphi B, and Paratyphi C). Owing to the importance of Salmonella serovars in clinics and public hygiene, reliable diagnostics for typhoidal serovars are crucial. This study aimed to develop a novel diagnostic tool for typhoidal Salmonella serovars and evaluate the use of human blood for clinically diagnosing enteric fever. Five genes were selected to produce specific PCR results against typhoidal Salmonella serovars based on the genes of Salmonella Typhi. Heptaplex PCR, including genetic markers of generic Salmonella, Salmonella enterica subsp. enterica, and typhoidal Salmonella serovars, was developed. Typhoidal Salmonella heptaplex PCR using genomic DNAs from 200 Salmonella strains (112 serovars) provided specifically amplified PCR products for each typhoidal Salmonella serovar. These results suggest that heptaplex PCR can sufficiently discriminate between typhoidal and nontyphoidal Salmonella serovars. Heptaplex PCR was applied to Salmonella-spiked blood cultures directly and provided diagnostic results after 12- or 13.5-h blood culture. Additionally, it demonstrated diagnostic performance with colonies recovered from a 6-h blood culture. This study provides a reliable DNA-based tool for diagnosing typhoidal Salmonella serovars that may be useful in clinical microbiology and epidemiology.
Collapse
Affiliation(s)
- Hyun-Joong Kim
- Department of Food Engineering, Mokpo National University, Muan 58554, Republic of Korea
| | - Younsik Jung
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| | - Mi-Ju Kim
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| |
Collapse
|
8
|
Use of Organic Acid Mixtures Containing 2-Hydroxy-4-(Methylthio) Butanoic Acid (HMTBa) to Mitigate Salmonella enterica, Shiga Toxin-Producing Escherichia coli (STEC) and Aspergillus flavus in Pet Food Kibbles. Animals (Basel) 2023; 13:ani13050877. [PMID: 36899734 PMCID: PMC10000158 DOI: 10.3390/ani13050877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Post-processing operations of extruded pet food kibbles involve coating the product with fats and flavorings. These processes increase the risk for cross-contamination with food-borne pathogens such as Salmonella and Shiga toxin-producing Escherichia coli (STEC), and mycotoxin-producing molds such as Aspergillus spp. after the thermal kill step. In this study, the antimicrobial effects of two types of organic acid mixtures containing 2-hydroxy-4-(methylthio) butanoic acid (HMTBa), Activate DA™ and Activate US WD-MAX™, against Salmonella enterica, STEC and Aspergillus flavus when used as a coating on pet food kibbles were evaluated. Using canola oil and dry dog digest as fat and flavor coatings, the efficacy of Activate DA (HMTBa + fumaric acid + benzoic acid) at 0%, 1% and 2%, and Activate US WD-MAX (HMTBa + lactic acid + phosphoric acid) at 0%, 0.5% and 1% was tested on kibbles inoculated with a cocktail of S. enterica serovars (Enteritidis, Heidelberg and Typhimurium) or Shiga toxin-producing E. coli (STEC) serovars (O121, and O26) at 37 °C for 0, 12, 24, 48, 72 h, 30 and 60 days. Similarly, their efficacy was tested against A. flavus at 25 °C for 0, 3, 7, 14, 21, 28 and 35 days. Activate DA at 2% and Activate US WD-MAX at 1% reduced Salmonella counts by ~3 logs after 12 h and 4-4.6 logs after 24 h. Similarly, STEC counts were reduced by ~2 logs and 3 logs after 12 h and 24 h, respectively. Levels of A. flavus did not vary up to 7 days, and afterwards started to decline by >2 logs in 14 days, and up to 3.8-log reduction in 28 days for Activate DA and Activate US WD-MAX at 2% and 1%, respectively. The results suggest that the use of these organic acid mixtures containing HMTBa during kibble coating may mitigate post-processing enteric pathogen and mold contamination in pet food kibbles, with Activate US WD-MAX being effective at a lower concentration (0.5-1%) compared to Activate DA.
Collapse
|
9
|
Mitigation of Salmonella on Food Contact Surfaces by Using Organic Acid Mixtures Containing 2-Hydroxy-4-(methylthio) Butanoic Acid (HMTBa). Foods 2023; 12:foods12040874. [PMID: 36832949 PMCID: PMC9956140 DOI: 10.3390/foods12040874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Contaminated surfaces can transmit pathogens to food in industrial and domestic food-handling environments. Exposure to pathogens on food contact surfaces may take place via the cross-contamination of pathogens during postprocessing activities. Formaldehyde-based commercial sanitizers in recent years are less commonly being used within food manufacturing facilities due to consumer perception and labeling concerns. There is interest in investigating clean-label, food-safe components for use on food contact surfaces to mitigate contamination from pathogenic bacteria, including Salmonella. In this study, the antimicrobial effects of two types of organic acid mixtures containing 2-hydroxy-4-(methylthio) butanoic acid (HMTBa), Activate DA™ and Activate US WD-MAX™, against Salmonella when applied onto various food contact surfaces were evaluated. The efficacy of Activate DA (HMTBa + fumaric acid + benzoic acid) at 1% and 2% and Activate US WD-MAX (HMTBa + lactic acid + phosphoric acid) at 0.5% and 1% against Salmonella enterica (serovars Enteritidis, Heidelberg, and Typhimurium) were evaluated on six different material surfaces: plastic (bucket elevator and tote bag), rubber (bucket elevator belt and automobile tire), stainless steel, and concrete. There was a significant difference in the Salmonella log reduction on the material surfaces due to the organic acid treatments when compared to the untreated surfaces. The type of material surface also had an effect on the log reductions obtained. Stainless steel and plastic (tote) had the highest Salmonella log reductions (3-3.5 logs), while plastic (bucket elevator) and rubber (tire) had the lowest log reductions (1-1.7 logs) after treatment with Activate US WD-MAX. For Activate DA, the lowest log reductions (~1.6 logs) were observed for plastic (bucket elevator) and rubber (tire), and the highest reductions were observed for plastic (tote), stainless steel, and concrete (2.8-3.2 logs). Overall, the results suggested that Activate DA at 2% and Activate US WD-MAX at 1% are potentially effective at reducing Salmonella counts on food contact surfaces by 1.6-3.5 logs.
Collapse
|
10
|
Lee JI, Kim SS, Park JW, Kang DH. Detection of Salmonella enterica serovar Montevideo in food products using specific PCR primers developed by comparative genomics. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
11
|
Ye Q, Shang Y, Chen M, Pang R, Li F, Wang C, Xiang X, Zhou B, Zhang S, Zhang J, Wu S, Xue L, Ding Y, Wu Q. Identification of new serovar-specific detection targets against salmonella B serogroup using large-scale comparative genomics. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
12
|
Shang Y, Ye Q, Wu Q, Pang R, Xiang X, Wang C, Li F, Zhou B, Xue L, Zhang Y, Sun X, Zhang J. PCR identification of Salmonella serovars for the E serogroup based on novel specific targets obtained by pan-genome analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
13
|
Loop-mediated isothermal amplification (LAMP) for rapid detection of Salmonella in foods based on new molecular targets. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110999] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
14
|
Ye Q, Shang Y, Chen M, Pang R, Li F, Xiang X, Zhou B, Wang C, Zhang S, Zhang J, Wang J, Xue L, Ding Y, Wu Q. Mining and evaluating novel serovar-specific Salmonella C1 serogroup genes by polymerase chain reaction analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
15
|
Ye Q, Shang Y, Chen M, Pang R, Li F, Xiang X, Wang C, Zhou B, Zhang S, Zhang J, Yang X, Xue L, Ding Y, Wu Q. Identification of Novel Sensitive and Reliable Serovar-Specific Targets for PCR Detection of Salmonella Serovars Hadar and Albany by Pan-Genome Analysis. Front Microbiol 2021; 12:605984. [PMID: 33815306 PMCID: PMC8011537 DOI: 10.3389/fmicb.2021.605984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/22/2021] [Indexed: 01/16/2023] Open
Abstract
The accurate and rapid classification of Salmonella serovars is an essential focus for the identification of isolates involved in disease in humans and animals. The purpose of current research was to identify novel sensitive and reliable serovar-specific targets and to develop PCR method for Salmonella C2 serogroups (O:8 epitopes) in food samples to facilitate timely treatment. A total of 575 genomic sequences of 16 target serovars belonging to serogroup C2 and 150 genomic sequences of non-target serovars were analysed by pan-genome analysis. As a result, four and three specific genes were found for serovars Albany and Hadar, respectively. Primer sets for PCR targeting these serovar-specific genes were designed and evaluated based on their specificity; the results showed high specificity (100%). The sensitivity of the specific PCR was 2.8 × 101–103 CFU/mL and 2.3 × 103–104 CFU/mL for serovars Albany and Hadar, respectively, and the detection limits were 1.04 × 103–104 CFU/g and 1.16 × 104–105 CFU/g in artificially contaminated raw pork samples. Furthermore, the potential functions of these serovar-specific genes were analysed; all of the genes were functionally unknown, except for one specific serovar Albany gene known to be a encoded secreted protein and one specific gene for serovars Hadar and Albany that is a encoded membrane protein. Thus, these findings demonstrate that pan-genome analysis is a precious method for mining new high-quality serovar-targets for PCR assays or other molecular methods that are highly sensitive and can be used for rapid detection of Salmonella serovars.
Collapse
Affiliation(s)
- Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuting Shang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinran Xiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chufang Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Baoqing Zhou
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Institute of Food Safety & Nutrition, Jinan University, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| |
Collapse
|
16
|
Kim MJ, Kim HJ, Kim HY. Direct triplex loop-mediated isothermal amplification assay for the point-of-care molecular detection of Salmonella genus, subspecies I, and serovar Typhimurium. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
17
|
Highly Sensitive and Specific Detection and Serotyping of Five Prevalent Salmonella Serovars by Multiple Cross-Displacement Amplification. J Mol Diagn 2020; 22:708-719. [PMID: 32359725 DOI: 10.1016/j.jmoldx.2020.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 12/16/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
Salmonella is a common cause of foodborne disease worldwide, including Australia. More than 85% of outbreaks of human salmonellosis in Australia were caused by five Salmonella serovars. Rapid, accurate, and sensitive identification of Salmonella serovars is vital for diagnosis and public health surveillance. Recently, an isothermal amplification technique, termed multiple cross-displacement amplification (MCDA), has been employed to detect Salmonella at the species level. Herein, seven MCDA assays were developed and evaluated for rapid detection and differentiation of the five most common Salmonella serovars in Australia: Typhimurium, Enteritidis, Virchow, Saintpaul, and Infantis. MCDA primer sets were designed by targeting seven serovar/lineage-specific gene markers identified through genomic comparisons. The sensitivity and specificity of the seven MCDA assays were evaluated using 79 target strains and 32 nontarget strains. The assays were all highly sensitive and specific to target serovars, with the sensitivity ranging from 92.9% to 100% and the specificity from 93.3% to 100%. The limit of detection of the seven MCDA assays was 50 fg per reaction (10 copies) from pure DNA, and positive results were detected in as little as 8 minutes. These seven MCDA assays offer a rapid, accurate, and sensitive serotyping method. With further validation in clinically relevant conditions, these assays could be used for culture-independent serotyping of common Salmonella serovars directly from clinical samples.
Collapse
|
18
|
Ren J, Man Y, Li A, Liang G, Jin X, Pan L. Detection of
Salmonella enteritidis
and
Salmonella typhimurium
in foods using a rapid, multiplex real‐time recombinase polymerase amplification assay. J Food Saf 2020. [DOI: 10.1111/jfs.12784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Junan Ren
- Beijing Food & Wine Inspection and Testing Station Beijing China
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Risk Assessment Lab for Agro‐ products (Beijing), Ministry of Agriculture Beijing China
| | - Yan Man
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Risk Assessment Lab for Agro‐ products (Beijing), Ministry of Agriculture Beijing China
| | - An Li
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Risk Assessment Lab for Agro‐ products (Beijing), Ministry of Agriculture Beijing China
| | - Gang Liang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Risk Assessment Lab for Agro‐ products (Beijing), Ministry of Agriculture Beijing China
| | - Xinxin Jin
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Risk Assessment Lab for Agro‐ products (Beijing), Ministry of Agriculture Beijing China
| | - Ligang Pan
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Risk Assessment Lab for Agro‐ products (Beijing), Ministry of Agriculture Beijing China
| |
Collapse
|
19
|
Kaprou GD, Papadopoulos V, Loukas CM, Kokkoris G, Tserepi A. Towards PCB-Based Miniaturized Thermocyclers for DNA Amplification. MICROMACHINES 2020; 11:mi11030258. [PMID: 32121172 PMCID: PMC7143664 DOI: 10.3390/mi11030258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
Abstract
In recent years, printed circuit board (PCB)-based microfluidics have been explored as a means to achieve standardization, seamless integration, and large-scale manufacturing of microfluidics, thus paving the way for widespread commercialization of developed prototypes. In this work, static micro polymerase chain reaction (microPCR) devices comprising resistive microheaters integrated on PCBs are introduced as miniaturized thermocyclers for efficient DNA amplification. Their performance is compared to that of conventional thermocyclers, in terms of amplification efficiency, power consumption and duration. Exhibiting similar efficiency to conventional thermocyclers, PCB-based miniaturized thermocycling achieves faster DNA amplification, with significantly smaller power consumption. Simulations guide the design of such devices and propose means for further improvement of their performance.
Collapse
Affiliation(s)
| | | | | | - George Kokkoris
- Correspondence: (G.K.); (A.T.); Tel.: +30-210-650-3238 (G.K.); +30-210-650-3264 (A.T.)
| | - Angeliki Tserepi
- Correspondence: (G.K.); (A.T.); Tel.: +30-210-650-3238 (G.K.); +30-210-650-3264 (A.T.)
| |
Collapse
|
20
|
Xu J, Zhang P, Zhuang L, Zhang D, Qi K, Dou X, Wang C, Gong J. Multiplex polymerase chain reaction to detectSalmonellaserovars Indiana, Enteritidis, and Typhimurium in raw meat. J Food Saf 2019. [DOI: 10.1111/jfs.12674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jingxiao Xu
- Poultry InstituteChinese Academy of Agricultural Sciences Yangzhou Jiangsu China
| | - Ping Zhang
- Poultry InstituteChinese Academy of Agricultural Sciences Yangzhou Jiangsu China
| | - Linlin Zhuang
- Poultry InstituteChinese Academy of Agricultural Sciences Yangzhou Jiangsu China
| | - Di Zhang
- Poultry InstituteChinese Academy of Agricultural Sciences Yangzhou Jiangsu China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease ControlAnhui Agricultural University Hefei Anhui China
| | - Xinhong Dou
- Poultry InstituteChinese Academy of Agricultural Sciences Yangzhou Jiangsu China
| | - Chengming Wang
- Department of PathobiologyAuburn University College of Veterinary Medicine Auburn Alabama
| | - Jiansen Gong
- Poultry InstituteChinese Academy of Agricultural Sciences Yangzhou Jiangsu China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonoseYangzhou University Yangzhou Jiangsu China
| |
Collapse
|
21
|
Savas S, Ersoy A, Gulmez Y, Kilic S, Levent B, Altintas Z. Nanoparticle Enhanced Antibody and DNA Biosensors for Sensitive Detection of Salmonella. MATERIALS 2018; 11:ma11091541. [PMID: 30150524 PMCID: PMC6163637 DOI: 10.3390/ma11091541] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022]
Abstract
Bacteria-related pathogenic diseases are one of the major health problems throughout the world. Salmonella is a genus of rod-shaped Gram-negative enterobacteria of which more than 2600 serotypes have been identified. Infection with Salmonella can cause salmonellosis, a serious bacterial toxi-infection syndrome associated with gastroenteritis, and paralyphoid and typhoid fevers. Its rapid and sensitive detection is a key to the prevention of problems related to health. This paper describes the development of antibody and DNA sensors for Salmonella detection using a microfluidic-based electrochemical system. Commercial Salmonella typhimurium and Salmonella typhimurium from human stool samples were investigated using standard and nanomaterial-amplified antibody sensors. S. typhimurium could be detected down to 1 cfu mL-1. The specificity of immunoassay was tested by studying with non-specific bacteria including E. coli and S. aureus that revealed only 2.01% and 2.66% binding when compared to the target bacterium. On the other hand, the quantification of Salmonella DNA was investigated in a concentration range of 0.002⁻200 µM using the developed DNA biosensor that demonstrated very high specificity and sensitivity with a detection limit of 0.94 nM. Our custom-designed microfluidic sensor offers rapid, highly sensitive, and specific diagnostic assay approaches for pathogen detection.
Collapse
Affiliation(s)
- Sumeyra Savas
- National Research Institute of Electronics and Cryptology, The Scientific and Technological Research Council of Turkey (TUBITAK), Kocaeli 41470, Turkey.
| | - Aylin Ersoy
- National Research Institute of Electronics and Cryptology, The Scientific and Technological Research Council of Turkey (TUBITAK), Kocaeli 41470, Turkey.
| | - Yakup Gulmez
- National Research Institute of Electronics and Cryptology, The Scientific and Technological Research Council of Turkey (TUBITAK), Kocaeli 41470, Turkey.
| | - Selcuk Kilic
- Turkey Public Health General Headquarter, Ankara 06100, Turkey.
| | - Belkis Levent
- Turkey Public Health General Headquarter, Ankara 06100, Turkey.
| | - Zeynep Altintas
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 124, Berlin 10623, Germany.
| |
Collapse
|
22
|
Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Evaluation of Different Genetic Targets for Salmonella enterica Serovar Enteriditis and Typhimurium, Using Loop-Mediated Isothermal AMPlification for Detection in Food Samples. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
|
23
|
Afroj S, Aldahami K, Reddy G, Guard J, Adesiyun A, Samuel T, Abdela W. Simultaneous Detection of Multiple Salmonella Serovars from Milk and Chicken Meat by Real-Time PCR Using Unique Genomic Target Regions. J Food Prot 2017; 80:1944-1957. [PMID: 29058479 DOI: 10.4315/0362-028x.jfp-17-133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/19/2017] [Indexed: 12/29/2022]
Abstract
A novel genomic and plasmid target-based PCR platform was developed for the detection of Salmonella serovars Heidelberg, Dublin, Hadar, Kentucky, and Enteritidis. Unique genome loci were obtained through extensive genome mining of protein databases and comparative genomic analysis of these serovars. Assays targeting Salmonella serovars Hadar, Heidelberg, Kentucky, and Dublin had 100% specificity and sensitivity, whereas those for Salmonella Enteritidis had 97% specificity and 88% sensitivity. The limits of detection for Salmonella serovars Heidelberg, Kentucky, Hadar, Enteritidis, and Dublin were 12, 9, 40, 13, and 5,280 CFU, respectively. A sensitivity assay was also performed by using milk artificially inoculated with pooled Salmonella serovars, yielding a detection limit of 1 to10 CFU/25 mL of milk samples after enrichment. The minimum DNA detected using the multiplexed TaqMan assay was 75.8 fg (1.53 × 101 genomic equivalents [GE]) for Salmonella Heidelberg, 140.8 fg (2.8 × 101 GE) for Salmonella Enteritidis, and 3.48 pg (6.96 × 102 GE) for Salmonella Dublin. PCR efficiencies were 89.8% for Salmonella Heidelberg, 94.5% for Salmonella Enteritidis, and 75.5% for Salmonella Dublin. Four types of 30 pasteurized milk samples were tested negative by culture techniques and with a genus-specific Salmonella invA gene PCR assay. Among 30 chicken samples similarly tested, 12 (40%) were positive by both culture and the invA PCR. Testing of these 12 samples with the serovar-specific PCR assay detected single and mixed contamination with Salmonella Kentucky, Salmonella Enteritidis, and Salmonella Heidelberg. Five unique primers were designed and tested by multiplex conventional PCR in conjunction with the use of the multiplex TaqMan assay with three of the primers. The diagnostic assays developed in this study could be used as tools for routine detection of these five Salmonella serovars and for epidemiological investigations of foodborne disease outbreaks.
Collapse
Affiliation(s)
- Sayma Afroj
- Department of Biology and.,Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.]).,Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama 36849, USA
| | - Khaled Aldahami
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Gopal Reddy
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Jean Guard
- U.S. Department of Agriculture, Agricultural Research Service, Athens, Georgia 30602, USA
| | - Abiodun Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Woubit Abdela
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| |
Collapse
|
24
|
Garrido-Maestu A, Fuciños P, Azinheiro S, Carvalho J, Prado M. Systematic loop-mediated isothermal amplification assays for rapid detection and characterization of Salmonella spp., Enteritidis and Typhimurium in food samples. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
25
|
Kim TH, Hwang HJ, Kim JH. Development of a Novel, Rapid Multiplex Polymerase Chain Reaction Assay for the Detection and Differentiation of Salmonella enterica Serovars Enteritidis and Typhimurium Using Ultra-Fast Convection Polymerase Chain Reaction. Foodborne Pathog Dis 2017; 14:580-586. [PMID: 28696782 DOI: 10.1089/fpd.2017.2290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella enterica serovars Enteritidis and Typhimurium are the most common causative agents of human nontyphoidal salmonellosis. The rapid detection and timely treatment of salmonellosis are important to increase the curative ratio and prevent spreading of the disease. In this study, we developed a rapid multiplex convection polymerase chain reaction (PCR) method to detect Salmonella spp. and differentiate Salmonella Enteritidis and Salmonella Typhimurium. We used the invA gene for Salmonella spp. detection. Salmonella Enteritidis-specific primers and Salmonella Typhimurium-specific primers were designed using the insertion element (IE) and spy genes, respectively. The primer set for Salmonella spp. detection clearly detected both Salmonella Enteritidis and Salmonella Typhimurium after a 21-min amplification reaction. Serovar-specific primer sets for Salmonella Enteritidis and Salmonella Typhimurium specifically detected each target species in a 21-min amplification reaction. We were able to detect Salmonella spp. at a single copy level in the singleplex mode. The limits of detection for Salmonella Enteritidis and Salmonella Typhimurium were 30 copies in both the singleplex and multiplex modes. The PCR run time could be reduced to 10.5 min/15 cycles. The multiplex convection PCR method developed in this study could detect the Salmonella spp. Salmonella Enteritidis and Salmonella Typhimurium in artificially contaminated milk with as few as 100 colony-forming unit/mL after 4-h enrichment. The PCR assay developed in this study provides a rapid, specific, and sensitive method for the detection of Salmonella spp. and the differentiation of Salmonella Enteritidis and Salmonella Typhimurium.
Collapse
Affiliation(s)
- Tae-Hoon Kim
- 1 Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University , Seoul, Korea
| | | | - Jeong Hee Kim
- 1 Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University , Seoul, Korea.,3 Department of Oral Biochemistry and Molecular Biology, School of Dentistry, Kyung Hee University , Seoul, Korea
| |
Collapse
|
26
|
Kim HJ, Ryu JO, Song JY, Kim HY. Multiplex Polymerase Chain Reaction for Identification of Shigellae and Four Shigella Species Using Novel Genetic Markers Screened by Comparative Genomics. Foodborne Pathog Dis 2017; 14:400-406. [PMID: 28402677 DOI: 10.1089/fpd.2016.2221] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the detection of Shigella species using molecular biological methods, previously known genetic markers for Shigella species were not sufficient to discriminate between Shigella species and diarrheagenic Escherichia coli. The purposes of this study were to screen for genetic markers of the Shigella genus and four Shigella species through comparative genomics and develop a multiplex polymerase chain reaction (PCR) for the detection of shigellae and Shigella species. A total of seven genomic DNA sequences from Shigella species were subjected to comparative genomics for the screening of genetic markers of shigellae and each Shigella species. The primer sets were designed from the screened genetic markers and evaluated using PCR with genomic DNAs from Shigella and other bacterial strains in Enterobacteriaceae. A novel Shigella quintuplex PCR, designed for the detection of Shigella genus, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, was developed from the evaluated primer sets, and its performance was demonstrated with specifically amplified results from each Shigella species. This Shigella multiplex PCR is the first to be reported with novel genetic markers developed through comparative genomics and may be a useful tool for the accurate detection of the Shigella genus and species from closely related bacteria in clinical microbiology and food safety.
Collapse
Affiliation(s)
- Hyun-Joong Kim
- Department of Food Science and Biotechnology, Kyung Hee University , Yongin, Republic of Korea
| | - Ji-Oh Ryu
- Department of Food Science and Biotechnology, Kyung Hee University , Yongin, Republic of Korea
| | - Ji-Yeon Song
- Department of Food Science and Biotechnology, Kyung Hee University , Yongin, Republic of Korea
| | - Hae-Yeong Kim
- Department of Food Science and Biotechnology, Kyung Hee University , Yongin, Republic of Korea
| |
Collapse
|
27
|
Ren D, Chen P, Wang Y, Wang J, Liu H, Liu H. Phenotypes and antimicrobial resistance genes in Salmonella
isolated from retail chicken and pork in Changchun, China. J Food Saf 2016. [DOI: 10.1111/jfs.12314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dayong Ren
- Food Safety Department, College of Food Science and Engineering; Jilin Agriculture University; Changchun 130118 PR China
| | - Ping Chen
- Food Safety Department, College of Food Science and Engineering; Jilin Agriculture University; Changchun 130118 PR China
| | - Ying Wang
- Food Safety Department, College of Food Science and Engineering; Jilin Agriculture University; Changchun 130118 PR China
| | - Jianan Wang
- Food Safety Department, College of Food Science and Engineering; Jilin Agriculture University; Changchun 130118 PR China
| | - Hongyan Liu
- Food Safety Department, College of Food Science and Engineering; Jilin Agriculture University; Changchun 130118 PR China
| | - Hongfeng Liu
- Veterinary Science Department, College of Veterinary Medicine; Jilin University; Changchun 130062 PR China
| |
Collapse
|
28
|
Kim HJ, Ryu JO, Lee SY, Kim ES, Kim HY. Multiplex PCR for detection of the Vibrio genus and five pathogenic Vibrio species with primer sets designed using comparative genomics. BMC Microbiol 2015; 15:239. [PMID: 26502878 PMCID: PMC4624192 DOI: 10.1186/s12866-015-0577-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/19/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The genus Vibrio is clinically significant and major pathogenic Vibrio species causing human Vibrio infections are V. cholerae, V. parahaemolyticus, V. vulnificus, V. alginolyticus and V. mimicus. In this study, we screened for novel genetic markers using comparative genomics and developed a Vibrio multiplex PCR for the reliable diagnosis of the Vibrio genus and the associated major pathogenic Vibrio species. METHODS A total of 30 Vibrio genome sequences were subjected to comparative genomics, and specific genes of the Vibrio genus and five major pathogenic Vibrio species were screened. The designed primer sets from the screened genes were evaluated by single PCR using DNAs from various Vibrio spp. and other non-Vibrio bacterial strains. A sextuplet multiplex PCR using six primer sets was developed to enable detection of the Vibrio genus and five pathogenic Vibrio species. RESULTS The designed primer sets from the screened genes yielded specific diagnostic results for target the Vibrio genus and Vibrio species. The specificity of the developed multiplex PCR was confirmed with various Vibrio and non-Vibrio strains. This Vibrio multiplex PCR was evaluated using 117 Vibrio strains isolated from the south seashore areas in Korea and Vibrio isolates were identified as Vibrio spp., V. parahaemolyticus, V. vulnificus and V. alginolyticus, demonstrating the specificity and discriminative ability of the assay towards Vibrio species. CONCLUSIONS This novel multiplex PCR method could provide reliable and informative identification of the Vibrio genus and major pathogenic Vibrio species in the food safety industry and in early clinical treatment, thereby protecting humans against Vibrio infection.
Collapse
Affiliation(s)
- Hyun-Joong Kim
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Ji-Oh Ryu
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Shin-Young Lee
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Ei-Seul Kim
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| |
Collapse
|
29
|
Chen W, Yu S, Ren J, Shi C, Hang F, Guo B. Development of a PCR Assay for Rapid Detection of C
ronobacter sakazakii
from Powdered Infant Formula Using a Target Sequence Identified by Comparative Genomic Analysis. J Food Saf 2015. [DOI: 10.1111/jfs.12185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Wanyi Chen
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Shuijing Yu
- School of Resources and Environment; Jiangxi University of Science and Technology; Ganzhou Jiangxi China
| | - Jing Ren
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety; School of Agriculture & Biology; State Key Lab of Microbial Metabolism; Shanghai Jiao Tong University; Shanghai China
| | - Feng Hang
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Benheng Guo
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| |
Collapse
|
30
|
Handley JA, Shi Z, Park SH, Dawoud TM, Kwon YM, Ricke SC. Salmonella and the Potential Role for Methods to Develop Microbial Process Indicators on Chicken Carcasses. Food Saf (Tokyo) 2015. [DOI: 10.1016/b978-0-12-800245-2.00006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
31
|
Cho MS, Joh K, Ahn TY, Park DS. Improved PCR assay for the specific detection and quantitation of Escherichia coli serotype O157 in water. Appl Microbiol Biotechnol 2014; 98:7869-77. [PMID: 24903818 DOI: 10.1007/s00253-014-5855-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/11/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
Escherichia coli serotype O157 is still a major global healthcare problem. However, only limited information is now available on the molecular and serological detection of pathogenic bacteria. Therefore, the development of appropriate strategies for their rapid identification and monitoring is still needed. In general, the sequence analysis based on stx, slt, eae, hlyA, rfb, and fliCh7 genes is widely employed for the identification of E. coli serotype O157; but there have been critical defects in the diagnosis and identification of E. coli serotype O157, in that they are also present in other E. coli serogroups. In this study, NCBI-BLAST searches using the nucleotide sequences of the putative regulatory protein gene from E. coli O157:H7 str. Sakai found sequence difference at the serotype level. The specific primers from the putative regulatory protein gene were designed and investigated for their sensitivity and specificity for detecting the pathogen in environment water samples. The specificity of the primer set was evaluated using genomic DNA from 8 isolates of E. coli serotype O157 and 32 other reference strains. In addition, the sensitivity and specificity of this assay were confirmed by successful identification of E. coli serotype O157 in environmental water samples. In conclusion, this study showed that the newly developed quantitative serotype-specific PCR method is a highly specific and efficient tool for the surveillance and rapid detection of high-risk E. coli serotype O157.
Collapse
Affiliation(s)
- Min Seok Cho
- National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Republic of Korea
| | | | | | | |
Collapse
|
32
|
Improved PCR for identification of Pseudomonas aeruginosa. Appl Microbiol Biotechnol 2013; 97:3643-51. [PMID: 23504075 DOI: 10.1007/s00253-013-4709-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
Abstract
The aim of the present study was to develop a noble and specific marker for a quantitative polymerase chain reaction (PCR) assay for the species-specific detection of Pseudomonas aeruginosa based on the O-antigen acetylase gene. It is an important challenge to characterize populations of the bacterium P. aeruginosa, an opportunist by virtue of its physiological and genetic adaptability. However, molecular and serological methods currently available for sensitive and specific detection of P. aeruginosa are by no means satisfactory because there have been critical defects in the diagnosis and identification of P. aeruginosa strains in that these assays also detect other Pseudomonas species, or do not obtain amplified products from P. aeruginosa strains. Therefore, a primer set was designed based on the O-antigen acetylase gene of P. aeruginosa PA01 because it has been known that this gene is structurally diverse among species. The specificity of the primer set was evaluated using genomic DNA from six isolates of P. aeruginosa, 18 different species of Pseudomonas, and 23 other reference pathogenic bacteria. The primer set used in the PCR assay amplified a 232-bp amplicon for only six P. aeruginosa strains. The assay was also able to detect at least 1.41 × 10(3) copies/μl of cloned amplified target DNA using purified DNA, or 2.7 × 10(2) colony-forming unit per reaction when using calibrated cell suspension. In conclusion, this assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of water with a low level or latent infection of P. aeruginosa.
Collapse
|
33
|
Park S, Hanning I, Perrota A, Bench B, Alm E, Ricke S. Modifying the gastrointestinal ecology in alternatively raised poultry and the potential for molecular and metabolomic assessment. Poult Sci 2013; 92:546-61. [DOI: 10.3382/ps.2012-02734] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
34
|
Liu B, Zhou X, Zhang L, Liu W, Dan X, Shi C, Shi X. Development of a novel multiplex PCR assay for the identification of Salmonella enterica Typhimurium and Enteritidis. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.01.062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
35
|
Akiba M, Kusumoto M, Iwata T. Rapid identification of Salmonella enterica serovars, Typhimurium, Choleraesuis, Infantis, Hadar, Enteritidis, Dublin and Gallinarum, by multiplex PCR. J Microbiol Methods 2011; 85:9-15. [PMID: 21329737 DOI: 10.1016/j.mimet.2011.02.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/28/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
Abstract
Salmonella enterica subsp. enterica poses a threat to both human and animal health, with more than 2500 serovars having been reported to date. Salmonella serovars are identified by slide and tube agglutination tests using O and H antigen-specific anti-sera, although this procedure is both labor intensive and time consuming. Establishment of a method for rapid screening of the major Salmonella serovars is therefore required. We have established multiplex polymerase chain reaction (m-PCR) assays for identification of seven serovars of Salmonella, i.e., Typhimurium, Choleraesuis, Infantis, Hadar, Enteritidis, Dublin and Gallinarum. Three serovar-specific genomic regions (SSGRs) of each serovar were selected using an approach in comparative genomics. The Salmonella-specific invA gene was used to confirm the genetic background of the organisms. The isolates tested were identified as a target serovar when the three selected SSGRs and invA were all positive for amplification. The specificity of each m-PCR assay was investigated using 118 serovars of Salmonella and 12 species of non-Salmonella strains. Although a small number of false-positive results were observed in the m-PCR assays used to identify Typhimurium, Choleraesuis, Enteritidis and Dublin for closely related serovars, false-negative results were not observed in any assays. These assays had sufficient specificity to identify the seven Salmonella serovars, and therefore, have the potential for use as rapid screening methods.
Collapse
Affiliation(s)
- Masato Akiba
- Safety Research Team, National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba 305-0856, Japan.
| | | | | |
Collapse
|
36
|
Development of a single base extension-tag microarray for the detection of pathogenic Vibrio species in seafood. Appl Microbiol Biotechnol 2010; 89:1979-90. [DOI: 10.1007/s00253-010-2959-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/20/2010] [Accepted: 10/18/2010] [Indexed: 10/18/2022]
|
37
|
ZHANG DANDAN, ZHANG LIDA, WANG DAPENG, SUO BIAO, SHI XIANMING. A PCR METHOD FOR THE DETECTION OF LISTERIA MONOCYTOGENES BASED ON A NOVEL TARGET SEQUENCE IDENTIFIED BY COMPARATIVE GENOMIC ANALYSIS. J Food Saf 2010. [DOI: 10.1111/j.1745-4565.2010.00245.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
38
|
Yu S, Chen W, Wang D, He X, Zhu X, Shi X. Species-specific PCR detection of the food-borne pathogen Vibrio parahaemolyticus using the irgB gene identified by comparative genomic analysis. FEMS Microbiol Lett 2010; 307:65-71. [PMID: 20402781 DOI: 10.1111/j.1574-6968.2010.01952.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Vibrio parahaemolyticus is an enteric pathogen, which can cause acute gastroenteritis in humans after consumption of raw or partially cooked seafood, and specific molecular markers are necessary for its accurate identification by PCR methods. In the present study, 23 protein-coding sequences were identified by the comparative genomics method as V. parahaemolyticus-specific candidate markers. We targeted the irgB gene (vp2603), coding for iron-regulated virulence regulatory protein IrgB, in order to develop a PCR method for the detection of V. parahaemolyticus. PCR specificity was identified by amplification of 293 V. parahaemolyticus templates and by the loss of a PCR product with 11 strains from other Vibrio species and 35 non-Vibrio bacterial strains. The PCR assay had the 369-bp fragment and the sensitivity of 0.17 pg purified genomic DNA from V. parahaemolyticus. Furthermore, a multiplex PCR assay for the detection of total and virulent strains of V. parahaemolyticus was developed by targeting irgB, tdh and trh genes. These data indicated that the irgB gene is a new and effective marker for the detection of V. parahaemolyticus. In addition, this study demonstrates that genome sequence comparison has a powerful application in identifying specific markers for the detection and identification of bacterial pathogens.
Collapse
Affiliation(s)
- Shuijing Yu
- Department of Food Science and Technology, Joint Sino-US Food Safety Research Center & Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | | | | | | | | |
Collapse
|
39
|
A real-time PCR method for the detection of Salmonella enterica from food using a target sequence identified by comparative genomic analysis. Int J Food Microbiol 2010; 137:168-74. [PMID: 20060189 DOI: 10.1016/j.ijfoodmicro.2009.12.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 11/04/2009] [Accepted: 12/03/2009] [Indexed: 12/25/2022]
Abstract
A 5'-nuclease real-time PCR assay using a minor groove binding probe was developed for the detection of Salmonella enterica from artificially contaminated foods. S. enterica-specific sequences were identified by a comparative genomic approach. Several species-specific target sequences were evaluated for specificity. A real-time PCR assay was developed targeting a nucleotide sequence within the putative type III secretion ATP synthase gene (ssaN). An internal amplification control (IAC) probe was designed by randomly shuffling the target probe sequence and a single-stranded oligonucleotide was synthesized to serve as an IAC. The assay demonstrated 100% inclusivity for the 40 Salmonella strains tested and 100% exclusivity for 24 non-Salmonella strains. The detection limit of the real-time PCR assay was 41.2 fg/PCR with Salmonella Typhimurium genomic DNA and 18.6 fg/PCR using Salmonella Enteritidis genomic DNA; 8 and 4 genome equivalents, respectively. In the presence of a natural background flora derived from chicken meat enrichment cultures, the sample preparation and PCR method were capable of detecting as few as 130 Salmonella cfu/mL. Using the developed real-time PCR method to detect Salmonella in artificially contaminated chicken, liquid egg and peanut butter samples, as few as 1 cfu/10 g of sample was detectable after a brief (6h) non-selective culture enrichment.
Collapse
|
40
|
McCarthy N, Reen FJ, Buckley JF, Frye JG, Boyd EF, Gilroy D. Sensitive and rapid molecular detection assays for Salmonella enterica serovars Typhimurium and Heidelberg. J Food Prot 2009; 72:2350-7. [PMID: 19903399 DOI: 10.4315/0362-028x-72.11.2350] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Salmonella enterica is a significant cause of gastroenteritis worldwide, with serovars Typhimurium and Heidelberg being particularly prevalent, which have broad host ranges infecting poultry, dairy animals, and humans. Traditional methods used for the detection of Salmonella from contaminated food products are time-consuming and labor-intensive. The aim of this study was to develop a sensitive and rapid PCR-based detection method with optimized specificity for high-throughput screening of food and clinical samples. We used bioinformatics to identify potential serovar-specific regions from the available S. enterica sequenced genomes. We designed primer pairs to targeted regions unique to Typhimurium and Heidelberg. A primer pair targeting a putative cytoplasmic protein STM4492 amplified a 759-bp product specific to Typhimurium, and a primer pair targeting a putative inner membrane protein STM2745 amplified a 199-bp product from both Typhimurium and Heidelberg. A primer pair for the oriC locus was used to identify all Salmonella. We screened 217 isolates including the Salmonella reference collections A and B, validating the specificity of each primer set. Next, a multiplex PCR (mPCR) assay and quantitative real-time PCR assay were optimized for identification and differentiation of Typhimurium and Heidelberg. An mPCR assay was developed and successfully detected S. enterica isolates from inoculated Cheddar cheese, raw turkey, and cooked turkey at concentrations as low as 1 CFU/g of food. The reaction conditions for this mPCR have significantly reduced the time needed to identify S. enterica Typhimurium and Heidelberg, making this a rapid selective tool.
Collapse
Affiliation(s)
- Noelle McCarthy
- Department of Microbiology, University College, Cork, National University of Ireland, Cork, Ireland
| | | | | | | | | | | |
Collapse
|
41
|
Park SH, Kim HJ, Cho WH, Kim JH, Oh MH, Kim SH, Lee BK, Ricke SC, Kim HY. Identification of Salmonella enterica subspecies I, Salmonella enterica serovars Typhimurium, Enteritidis and Typhi using multiplex PCR. FEMS Microbiol Lett 2009; 301:137-46. [PMID: 19843307 DOI: 10.1111/j.1574-6968.2009.01809.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This study was designed to develop a multiplex PCR method with five specific primer pairs for the detection of Salmonella spp., Salmonella subspecies I, Salmonella enterica serovars Typhimurium, Typhi and Enteritidis. A multiplex PCR was constructed with five primer pairs for the detection of Salmonella and pathogenic Salmonella serovars, including a specific primer pair for Salmonella Typhi, based on the sequence comparison between genomic DNA sequences of 12 Salmonella strains. Each primer pair was specifically targeted to Salmonella spp., Salmonella subspecies I, Salmonella Typhimurium, Typhi and Enteritidis. This multiplex PCR was evaluated with various DNAs of Salmonella serovars that yielded high specificity for amplifying the expected PCR products of Salmonella serovars. Using this primer pair, a set of multiplex PCR was performed for the rapid identification of salmonellae and major pathogenic Salmonella serovars. Although this multiplex PCR method will need to be evaluated for a wide range of Salmonella serovars among multilaboratories, it should be useful for identifying clinically significant strains of Salmonella serovars rapidly and accurately without the need for serological testing.
Collapse
Affiliation(s)
- Si Hong Park
- Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Shanmugasundaram M, Radhika M, Murali HS, Batra HV. Detection of Salmonella enterica serovar Typhimurium by selective amplification of fliC, fljB, iroB, invA, rfbJ, STM2755, STM4497 genes by polymerase chain reaction in a monoplex and multiplex format. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0025-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
43
|
Lomonaco S, Decastelli L, Bianchi DM, Nucera D, Grassi MA, Sperone V, Civera T. Detection ofSalmonellain Finishing Pigs on Farm and at Slaughter in Piedmont, Italy. Zoonoses Public Health 2009; 56:137-44. [DOI: 10.1111/j.1863-2378.2008.01192.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
44
|
Joshi R, Janagama H, Dwivedi HP, Senthil Kumar TMA, Jaykus LA, Schefers J, Sreevatsan S. Selection, characterization, and application of DNA aptamers for the capture and detection of Salmonella enterica serovars. Mol Cell Probes 2008; 23:20-8. [PMID: 19049862 DOI: 10.1016/j.mcp.2008.10.006] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 09/27/2008] [Accepted: 10/20/2008] [Indexed: 02/07/2023]
Abstract
Sensitive and specific pre-analytical sample processing methods are needed to enhance our ability to detect and quantify food borne pathogens from complex food and environmental samples. In this study, DNA aptamers were selected and evaluated for the capture and detection of Salmonella enterica serovar. Typhimurium. A total of 66 candidate sequences were enriched against S. Typhimurium outer membrane proteins (OMPs) with counter-selection against Escherichia coli OMPs and lipopolysaccharides (LPS). Specificity of the selected aptamers was evaluated by gel-shift analysis against S. Typhimurium OMP. Five Salmonella-specific aptamer candidates were selected for further characterization. A dilution-to-extinction capture protocol using pure cultures of S. Typhimurium further narrowed the field to two candidates (aptamers 33 and 45) which showed low-end detection limits of 10-40CFU. DNase protection assays applied to these aptamers confirmed sequence-specific binding to S. Typhimurium OMP preparations, while South-Western blot analysis combined with mass spectrometry identified putative membrane proteins as targets for aptamer binding. Aptamer 33 was bound to magnetic beads and used for the capture of S. Typhimurium seeded into whole carcass chicken rinse samples, followed by detection using quantitative real-time RT-PCR. In a pull-down assay format, detection limits were 10(1)-10(2)CFU S. Typhimurium/9mL rinsate, while in a recirculation format, detection limits were 10(2)-10(3)CFU/25mL rinsate. Reproducible detection at <10(1)S. typhimurium CFU/g was also achieved in spike-and-recovery experiments using bovine feces. The pull-down analysis using aptamer 33 was validated on 3 naturally infected chicken litter samples confirming their applicability in the field. This study demonstrates the applicability of Salmonella specific aptamers for pre-analytical sample processing as applied to food and environmental sample matrices.
Collapse
Affiliation(s)
- Raghavendra Joshi
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, United States
| | | | | | | | | | | | | |
Collapse
|
45
|
Polymerase Chain Reaction for the Rapid Detection and Serovar Identification of Salmonella in Food and Feeding Stuff. FOOD ANAL METHOD 2008. [DOI: 10.1007/s12161-008-9057-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
46
|
Kim HJ, Park SH, Lee TH, Nahm BH, Kim YR, Kim HY. Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics. Biosens Bioelectron 2008; 24:238-46. [DOI: 10.1016/j.bios.2008.03.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 03/05/2008] [Accepted: 03/25/2008] [Indexed: 10/22/2022]
|