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Quinn MW, Linton NF, Leon-Velarde CG, Chen S. Application of a CRISPR Sequence-Based Method for a Large-Scale Assessment of Salmonella Serovars in Ontario Poultry Production Environments. Appl Environ Microbiol 2023; 89:e0192322. [PMID: 36853053 PMCID: PMC10057875 DOI: 10.1128/aem.01923-22] [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: 11/16/2022] [Accepted: 01/17/2023] [Indexed: 03/01/2023] Open
Abstract
Accurate detection of all Salmonella serovars present in a sample is important in surveillance programs. Current detection protocols are limited to detection of a predominant serovar, missing identification of less abundant serovars in a sample. An alternative method, called CRISPR-SeroSeq, serotyping by sequencing of amplified CRISPR spacers, was employed to detect multiple serovars in a sample without the need of culture isolation. The CRISPR-SeroSeq method successfully detected 34 most frequently reported Salmonella serovars in pure cultures and target serovars at 104 CFU/mL in 27 Salmonella-negative environmental enrichment samples post-spiked with one of 15 different serovars, plus 2 additional serovars at 1 log CFU/mL higher abundance. When the method was applied to 442 naturally contaminated environmental samples collected from 192 poultry farms, 25 different serovars were detected from 430 of the samples. In 73.1% of the samples, 2 to 7 serovars were detected, with Salmonella Kiambu (55.7%), Salmonella Infantis (48.4%), Salmonella Kentucky (27.1%), Salmonella Livingstone (26.6%), and Salmonella Mbandaka/Montevideo (23.4%) being the most prevalent on the farms. Single isolates from 384 samples were also analyzed using a traditional serotyping method, and the same serovar identified by culture was detected by CRISPR-SeroSeq in 96.1% (369/384) of samples, with the former missing detection of additional and sometimes critical serovars. The surveillance data obtained via CRISPR-SeroSeq revealed a significant emergence of Salmonella Kiambu and Salmonella Rissen on poultry farms in Ontario. The results highlight the effectiveness of the CRISPR-SeroSeq approach in detecting multiple Salmonella serovars in poultry environmental samples under applied conditions, providing updated surveillance information on Salmonella serovars on poultry farms in Ontario. IMPORTANCE The CRISPR-SeroSeq method represents an alternative molecular tool to the traditional culture-based serotyping method that can detect multiple Salmonella serovars in a sample and provide rapid serovar results without the need of selective enrichment and culture isolation. The evaluation results can facilitate implementation of the method in routine Salmonella surveillance on poultry farms and in outbreak investigations. The application of the method can increase the accuracy of current serovar prevalence information. The results highlight the effectiveness of the validated method and the need for monitoring Salmonella serovars in poultry environments to improve current surveillance programs. The updated surveillance data provide timely information on emergence of different Salmonella serovars on poultry farms in Ontario and support on-farm risk assessment and risk management of Salmonella.
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Affiliation(s)
- Matthew W. Quinn
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - Nicola F. Linton
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | | | - Shu Chen
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
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Elbehiry A, Abalkhail A, Marzouk E, Elmanssury AE, Almuzaini AM, Alfheeaid H, Alshahrani MT, Huraysh N, Ibrahem M, Alzaben F, Alanazi F, Alzaben M, Anagreyyah SA, Bayameen AM, Draz A, Abu-Okail A. An Overview of the Public Health Challenges in Diagnosing and Controlling Human Foodborne Pathogens. Vaccines (Basel) 2023; 11:vaccines11040725. [PMID: 37112637 PMCID: PMC10143666 DOI: 10.3390/vaccines11040725] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
- Correspondence:
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
| | - Ahmed Elnadif Elmanssury
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia (E.M.)
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Hani Alfheeaid
- Department of Food Science and Human Nutrition, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 51452, Saudi Arabia
- Human Nutrition, School of Medicine, Nursing and Dentistry, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G31 2ER, UK
| | - Mohammed T. Alshahrani
- Department of Neurology, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Nasser Huraysh
- Department of Family Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia;
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Farhan Alanazi
- Supply Administration, Armed Forces Hospital, King Abdul Aziz Naval Base in Jubail, Jubail 35517, Saudi Arabia
| | - Mohammed Alzaben
- Department of Food Factories Inspection, Operation Sector, Saudi Food and Drug Authority, Riyadh 13513, Saudi Arabia
| | | | | | - Abdelmaged Draz
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
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3
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Molecular Methods for Identification and Quantification of Foodborne Pathogens. Molecules 2022; 27:molecules27238262. [PMID: 36500353 PMCID: PMC9737419 DOI: 10.3390/molecules27238262] [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: 10/24/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Foodborne pathogens that enter the human food chain are a significant threat worldwide to human health. Timely and cost-effective detection of them became challenging for many countries that want to improve their detection and control of foodborne illness. We summarize simple, rapid, specific, and highly effective molecular technology that is used to detect and identify foodborne pathogens, including polymerase chain reaction, isothermal amplification, loop-mediated isothermal amplification, nucleic acid sequence-based amplification, as well as gene chip and gene probe technology. The principles of their operation, the research supporting their application, and the advantages and disadvantages of each technology are summarized.
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Detection by real-time PCR and conventional culture of Salmonella Typhimurium and Listeria monocytogenes adhered to stainless steel surfaces under dry conditions. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Guard J. Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica. Pathogens 2022; 11:pathogens11050581. [PMID: 35631102 PMCID: PMC9144603 DOI: 10.3390/pathogens11050581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
This review revisits previous concepts on biological phenomenon contributing to the success of the Salmonella enterica subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, the impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.
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Affiliation(s)
- Jean Guard
- U. S. Department of Agriculture, Agricultural Research Service, U. S. National Poultry Research Center, 950 College Station Road, Athens, GA 30605, USA
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Yang X, Zhong Y, Wang D, Lu Z. A simple colorimetric method for viable bacteria detection based on cell counting Kit-8. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5211-5215. [PMID: 34694314 DOI: 10.1039/d1ay01624e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this study, Cell Counting Kit-8 (CCK-8) was introduced to detect the concentration of live bacteria for the first time depending on the redox reaction between CCK-8 solution and dehydrogenase. CCK-8 solution can be reduced to form water soluble orange-yellow formazan by the dehydrogenase present in bacterial cells, and the concentration of live bacteria is proportional to the absorbance value of formazan at 450 nm. Based on this principle, Staphylococcus aureus and Escherichia coli were chosen as the model bacteria. The optimal detection conditions were investigated and a good linear relationship was obtained in the concentration range from 2.600 × 102 to 1.160 × 109 CFU mL-1 with a linear equation of Y = 0.06305 log10 X-0.1153 (X in CFU mL-1, R2 = 0.9747) for S. aureus and 9.750 × 102 to 6.000 × 108 CFU mL-1 with a linear equation of Y = 0.06122 log10 X-0.1358 (X in CFU mL-1, R2 = 0.9958) for E. coli. The CCK-8 based viable bacteria detection method can be completed within 2 h with a wide bacterial detection concentration range. Satisfactory results were obtained when applied to an actual sample analysis and there is a good consistency between the proposed CCK-8 based method and the traditional plate counting method. More importantly, this method can realize the one-time detection of a large number of samples with high sensitivity, which suggests its great potential in high-throughput bacterial detection.
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Affiliation(s)
- Xianhong Yang
- Key Laboratory of Textile Fiber and Products, Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan 430200, China.
| | - Yaping Zhong
- Key Laboratory of Textile Fiber and Products, Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan 430200, China.
| | - Dong Wang
- Key Laboratory of Textile Fiber and Products, Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan 430200, China.
| | - Zhentan Lu
- Key Laboratory of Textile Fiber and Products, Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan 430200, China.
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Yin Q, Nie M, Diwu Z, Zhang Y, Wang L, Yin D, Li L. Establishment and application of a novel fluorescence-based analytical method for the rapid detection of viable bacteria in different samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3933-3943. [PMID: 32724967 DOI: 10.1039/d0ay01247e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A rapid method for readily detecting the total numbers of viable bacterial cells in numerous samples (including surface water, solid inoculants, and soil samples) is reported using a newly developed hand-held fluorometer and a fluorescent dye Calcein UltraGreen™ AM. Compared to the traditional plate counting method that requires 48 hours of cultivation, the newly established method does not require any incubation time, making the detection method faster and more convenient. The portable rapid detection fluorometer has a wide dynamic range of relative fluorescence intensity from 45 to 30 133. It can detect bacterial concentration ranging from 105 to 1010 cells per mL. This newly established method has good applicability for accurately and quickly detecting the cell number of viable bacteria in various samples. The results of the fluorescence-based method were compared with those of the traditional plate counting method, and it was found that the relative standard deviation was less than 6%. This new rapid measurement system provides a robust method for the rapid on-site detection of viable bacteria.
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Affiliation(s)
- Qiuyue Yin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, Shanxi Province, People's Republic of China.
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Nadin-Davis S, Pope L, Chmara J, Duceppe MO, Burke T, Devenish J, Andrievskaia O, Allain R, Ogunremi D. An Unusual Salmonella Enteritidis Strain Carrying a Modified Virulence Plasmid Lacking the prot6e Gene Represents a Geographically Widely Distributed Lineage. Front Microbiol 2020; 11:1322. [PMID: 32625191 PMCID: PMC7311658 DOI: 10.3389/fmicb.2020.01322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/25/2020] [Indexed: 12/02/2022] Open
Abstract
This study identifies a strain of Salmonella enterica subspecies enterica serovar Enteritidis that harbors a highly unusual virulence plasmid. During the characterisation of a group of S. Enteritidis isolates, 10 isolates recovered from Canadian duck production facilities, of which seven were phage type 9b and three were closely related atypical phage types, failed detection by a PCR targeting the prot6e gene, a marker located on the virulence plasmid often employed for identification of this serovar. Comparison to prot6e+ isolates by several standard genetic typing tools, further revealed their distinctive genomic makeup. Both short read and long read whole genome sequencing were completed on six of these isolates. In addition to loss of the prot6e gene, the virulence plasmid of each isolate was found to be exceptionally large (86.5 Kb) due to a 28 Kb insertion of S. Typhimurium plasmid sequence that encodes multiple genes of the incF operon. Interrogation of the chromosome sequence data of these isolates using a SNP-based typing tool and MLST both indicated their close genetic relatedness. One additional isolate carrying this plasmid was identified in an in-house collection of S. Enteritidis isolates. Finally, the identification of this unusual plasmid sequence in additional isolates submitted to public repositories of Salmonella sequence data was explored. All these analyses indicated that a very distinctive but rarely reported strain of S. Enteritidis was widely distributed across North America and the United Kingdom with one additional report involving a case from Brazil. With increased use of genetic methods for Salmonella identification, the loss of the prot6e sequence may confound correct identification of this serovar while also potentially altering the mode of transmission to humans given the gene’s role in facilitating propagation of this bacterium in eggs. Accordingly, this strain may present certain challenges with respect to public health investigations. Our studies also suggest this strain is often associated with duck hosts thereby providing a possible mechanism by which this strain has spread over an extensive geographical area.
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Affiliation(s)
- Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Louise Pope
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Chmara
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Teresa Burke
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Devenish
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Olga Andrievskaia
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Ray Allain
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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Ogunremi D, Dupras AA, Naushad S, Gao R, Duceppe MO, Omidi K, Márquez IG, Huang H, Goodridge L, Lévesque RC, Hasan NA, Dadlani M, Dixon B, Magierowski S, Masson L. A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce. Front Microbiol 2020; 11:602. [PMID: 32362880 PMCID: PMC7181323 DOI: 10.3389/fmicb.2020.00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/18/2020] [Indexed: 11/13/2022] Open
Abstract
The rapid detection of foodborne microbial pathogens contaminating fresh fruits and vegetables during the intervening period between harvest and consumption could revolutionize microbial quality assurance of food usually consumed raw and those with a limited shelf life. We have developed a sensitive, shotgun whole genome sequencing protocol capable of detecting as few as 1 colony forming unit (cfu) of Salmonella enterica serovar Typhimurium spiked on 25 g of lettuce. The Ion Torrent sequencing platform was used to generate reads of globally amplified DNA from microbes recovered from the surface of lettuce followed by bioinformatic analyses of the nucleotide sequences to detect the presence of Salmonella. The test is rapid and sensitive, and appropriate for testing perishable foods, and those consumed raw, for Salmonella contamination. The test has the potential to be universally applicable to any microbial contaminant on lettuce as long as a suitable bioinformatics pipeline is available and validated. A universal test is expected to pave the way for preventive and precision food safety and the re-shaping of the entire spectrum of food safety investigations from the current disease-limiting, reactive procedure to a proactive, disease prevention process.
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Affiliation(s)
- Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Andrée Ann Dupras
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Sohail Naushad
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Ruimin Gao
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Katayoun Omidi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | | | - Hongsheng Huang
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Roger C Lévesque
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
| | | | | | - Brent Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Sebastian Magierowski
- Department of Electrical Engineering and Computer Science, York University, Toronto, ON, Canada
| | - Luke Masson
- National Research Council of Canada, Montreal, QC, Canada
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