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Hirose S, Ohya K, Yoshinari T, Ohnishi T, Mizukami K, Suzuki T, Takinami K, Suzuki T, Lee K, Iyoda S, Akeda Y, Yahata Y, Tsuchihashi Y, Sunagawa T, Hara-Kudo Y. Atypical diarrhoeagenic Escherichia coli in milk related to a large foodborne outbreak. Epidemiol Infect 2023; 151:e150. [PMID: 37694773 PMCID: PMC10540162 DOI: 10.1017/s0950268823001395] [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] [Indexed: 09/12/2023] Open
Abstract
A foodborne outbreak related to milk cartons served in school lunches occurred in June 2021, which involved more than 1,800 cases from 25 schools. The major symptoms were abdominal pain, diarrhoea, vomiting, and fever. Although major foodborne toxins and pathogens were not detected, a specific Escherichia coli strain, serotype OUT (OgGp9):H18, was predominantly isolated from milk samples related to the outbreak and most patients tested. The strains from milk and patient stool samples were identified as the same clone by core genome multilocus sequence typing and single-nucleotide polymorphism analysis. The strain was detected in milk samples served for two days related to the foodborne outbreak at a rate of 69.6% and levels of less than ten most probable number/100 mL but not on days unrelated to the outbreak. The acid tolerance of the strain for survival in the stomach was similar to that of enterohaemorrhagic E. coli O157:H7, and the same inserts in the chu gene cluster in the acid fitness island were genetically revealed. The pathogenicity of the strain was not clear; however, it was indicated that the causative pathogen was atypical diarrhoeagenic E. coli OUT (OgGp9):H18.
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Affiliation(s)
- Shouhei Hirose
- Division of Microbiology, National Institute of Health Sciences, Kanagawa, Japan
| | - Kenji Ohya
- Division of Microbiology, National Institute of Health Sciences, Kanagawa, Japan
| | - Tomoya Yoshinari
- Division of Microbiology, National Institute of Health Sciences, Kanagawa, Japan
| | - Takahiro Ohnishi
- Division of Microbiology, National Institute of Health Sciences, Kanagawa, Japan
| | | | | | | | - Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuichiro Yahata
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuuki Tsuchihashi
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukiko Hara-Kudo
- Division of Microbiology, National Institute of Health Sciences, Kanagawa, Japan
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Cao Y, Fang T, Shen J, Zhang G, Guo D, Zhao L, Jiang Y, Zhi S, Zheng L, Lv X, Yao Z, Yu D. Development of Recombinase Aided Amplification (RAA)-Exo-Probe Assay for the Rapid Detection of Shiga Toxin-Producing Escherichia coli. J AOAC Int 2023; 106:1246-1253. [PMID: 37252814 DOI: 10.1093/jaoacint/qsad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Shiga toxin-producing Escherichia coli (STEC) is a significant cause of foodborne illness causing various gastrointestinal diseases including hemolytic uremic syndrome (HUS), the most severe form, which can lead to kidney failure or even death. OBJECTIVE Here, we report the development of recombinase aided amplification (RAA)-exo-probe assays targeting the stx1 and stx2 genes for the rapid detection of STEC in food samples. METHODS Primers and exo-probes were designed and optimized for the detection of stx1 and stx2 using RAA technology. The optimal STEC RAA-exo-probe assays were then tested for specificity and sensitivity, and validated in both spiked and real food samples. RESULTS These assays were found to be 100% specific to STEC strains and were also highly sensitive with a detection limit of 1.6 × 103 CFU/mL or 32 copies/reaction. Importantly, the assays were able to successfully detect STEC in spiked and real food samples (beef, mutton, and pork), with a detection limit as low as 0.35 CFU/25g in beef samples after an overnight enrichment step. CONCLUSIONS Overall, the RAA assay reactions completed within ∼20 min and were less dependent on expensive equipment, suggesting they can be easily adopted for in-field testing requiring only a fluorescent reader. HIGHLIGHTS As such, we have developed two rapid, sensitive, and specific assays that can be used for the routine monitoring of STEC contamination in food samples, particularly in the field or in poorly equipped labs.
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Affiliation(s)
- Yuhao Cao
- Ningbo University, Health Science Center, 818 Fenghua Road, Jiangbei District, Ningbo 315211, China
| | - Taisong Fang
- Zhejiang University, College of Biosystems Engineering and Food Science, 866 Yuhangtang Road, Xihu District, Hangzhou 310058, China
| | - Jinling Shen
- Shanghai Customs, Technology Center for Animal Plant and Food Inspection and Quarantine, 299 Mianbei Road, Pudong New District, Shanghai 201210, China
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740, USA
| | - Dehua Guo
- Shanghai Customs, Technology Center for Animal Plant and Food Inspection and Quarantine, 299 Mianbei Road, Pudong New District, Shanghai 201210, China
| | - Lina Zhao
- Shanghai Customs, Technology Center for Animal Plant and Food Inspection and Quarantine, 299 Mianbei Road, Pudong New District, Shanghai 201210, China
| | - Yuan Jiang
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, 1 Weigang, Nanjing 210095, China
| | - Shuai Zhi
- Ningbo University, Health Science Center, 818 Fenghua Road, Jiangbei District, Ningbo 315211, China
| | - Lin Zheng
- Ningbo University, The First Affiliated Hospital of Ningbo University, 59 Liuting Street, Haishu District, Ningbo 315211, China
| | - Xiaofei Lv
- China Jiliang University, Department of Environmental Engineering, 258 Xueyuan Street, Qiantang District, Hangzhou 310018, China
| | - Zhiyuan Yao
- Ningbo University, School of Civil and Environmental Engineering, 818 Fenghua Road, Jiangbei District, Ningbo 315211, China
| | - Daniel Yu
- University of Alberta, School of Public Health, 116 Street and 85 Avenue, Edmonton, AB, Canada
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Auvray F, Bièche-Terrier C, Um MM, Dupouy V, Nzuzi N, David L, Allais L, Drouet M, Oswald E, Bibbal D, Brugère H. Prevalence and characterization of the seven major serotypes of Shiga toxin-producing Escherichia coli (STEC) in veal calves slaughtered in France. Vet Microbiol 2023; 282:109754. [PMID: 37116423 DOI: 10.1016/j.vetmic.2023.109754] [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: 10/22/2022] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 04/30/2023]
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) belonging to the "top 7″ serotypes (i.e. O157:H7, O26:H11, O45:H2, O103:H2, O111:H8, O121:H19 and O145:H28) are considered as the main pathogenic enterohemorrhagic E. coli (EHEC). As ruminants, including calves, are a reservoir of pathogenic STEC, we investigated the prevalence, major virulence genes and genetic relatedness of top7 STEC in veal calves slaughtered in France, through the analysis of 500 fecal samples collected over one year. Thirty top7 STEC isolates were recovered from 28 calves. The two serotypes O103:H2 and O26:H11 accounted for 73% of STEC strains, followed by O145:H28 and O157:H7. STEC super-shedding levels were identified for two calves carrying STEC O103:H2 and O157:H7, respectively. Thirty-nine atypical enteropathogenic E. coli (aEPEC) were also recovered from calves. Overall, a prevalence of 5.6% top7 STEC-positive calves was found, thus higher than that previously determined for the French slaughtered adult cattle (1.8%), confirming the impact of animals age on STEC carriage. Most top7 STEC strains carried the stx1a subtype suggesting a low pathogenicity for humans. Seasonal variation in STEC carriage was also observed, with two peaks of higher prevalence during spring and fall. Genetic similarity of top7 STEC isolates was found for calves originating from the same fattening facilities, reflecting STEC circulation between animals kept in groups. This study indicates that veal calves grown for meat production are at higher risk of shedding top7 STEC compared to adult cattle. They thus represent ideal targets for the implementation of farm interventions aimed at reducing STEC burden in cattle and the food chain.
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Affiliation(s)
- Frédéric Auvray
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France.
| | | | - Maryse Michèle Um
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | | | - Nathalie Nzuzi
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Laure David
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Laurent Allais
- Institut de l'Elevage, Laboratoire Analyse et Technologie des Produits, Villers Bocage, France
| | - Marie Drouet
- Institut de l'Elevage, Service Qualité des Viandes, Villers Bocage, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Delphine Bibbal
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France; InTheRes, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Hubert Brugère
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
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Ikeda R, Nakamura K, Saulmont M, Habets A, Duprez JN, Korsak N, Hayashi T, Thiry D, Mainil JG. Escherichia coli O80 in Healthy Cattle: Absence of Shigatoxigenic and Enteropathogenic E. coli O80:H2 and (Phylo) Genomics of Non-Clonal Complex 165 E. coli O80. Microorganisms 2023; 11:microorganisms11020230. [PMID: 36838195 PMCID: PMC9962692 DOI: 10.3390/microorganisms11020230] [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: 12/21/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The origin of human and calf infections by Shigatoxigenic (STEC) and enteropathogenic (EPEC) Escherichia coli O80:H2 is still unknown. The aim of this study was to identify E. coli O80 in healthy cattle with an emphasis on melibiose non-fermenting E. coli O80:H2. Faecal materials collected from 149 bulls at 1 slaughterhouse and 194 cows on 9 farms were tested with O80 antigen-encoding gene PCR after overnight growth in enrichment broths. The 53 O80 PCR-positive broths were streaked on different (semi-)selective agar plates. Five E. coli colonies from 3 bulls and 11 from 2 cows tested positive with the O80 PCR, but no melibiose non-fermenting E. coli was isolated. However, these 16 E. coli O80 were negative with PCR targeting the fliCH2, eae, stx1, stx2 and hlyF genes and were identified by WGS to serotypes and sequence types O80:H6/ST8619 and O80:H45/ST4175. They were phylogenetically related to E. coli O80:H6 and O80:H45 isolated from different animal species in different countries, respectively, but neither to STEC and EPEC O80:H2/ST301, nor to other serotypes of the clonal complex 165. As a conclusion, healthy adult cattle were not identified as a source of contamination of humans and calves by STEC or EPEC O80:H2.
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Affiliation(s)
- Rie Ikeda
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, B-4000 Liège, Belgium
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Marc Saulmont
- Association Régionale de Santé et d’Identification Animale (ARSIA), B-5590 Ciney, Belgium
| | - Audrey Habets
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, B-4000 Liège, Belgium
| | - Jean-Noël Duprez
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, B-4000 Liège, Belgium
| | - Nicolas Korsak
- Food Inspection, Department of Food Science, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, B-4000 Liège, Belgium
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Damien Thiry
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, B-4000 Liège, Belgium
- Correspondence:
| | - Jacques G. Mainil
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, B-4000 Liège, Belgium
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Alharbi MG, Al-Hindi RR, Esmael A, Alotibi IA, Azhari SA, Alseghayer MS, Teklemariam AD. The "Big Six": Hidden Emerging Foodborne Bacterial Pathogens. Trop Med Infect Dis 2022; 7:356. [PMID: 36355898 PMCID: PMC9693546 DOI: 10.3390/tropicalmed7110356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 04/20/2024] Open
Abstract
Non-O157 Shiga toxin-producing Escherichia coli (STEC) are emerging serogroups that often result in diseases ranging from diarrhea to severe hemorrhagic colitis in humans. The most common non-O157 STEC are O26, O45, O103, O111, O121, and O145. These serogroups are known by the name "big six" because they cause severe illness and death in humans and the United States Department of Agriculture declared these serogroups as food contaminants. The lack of fast and efficient diagnostic methods exacerbates the public impact of the disease caused by these serogroups. Numerous outbreaks have been reported globally and most of these outbreaks were caused by ingestion of contaminated food or water as well as direct contact with reservoirs. Livestock harbor a variety of non-O157 STEC serovars that can contaminate meat and dairy products, or water sources when used for irrigation. Hence, effective control and prevention approaches are required to safeguard the public from infections. This review addresses the disease characteristics, reservoirs, the source of infections, the transmission of the disease, and major outbreaks associated with the six serogroups ("big six") of non-O157 STEC encountered all over the globe.
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Affiliation(s)
- Mona G. Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rashad R. Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Esmael
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Ibrahim A. Alotibi
- Health Information Technology Department, Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sheren A. Azhari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mazen S. Alseghayer
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Monitoring and Risk Assessment Department, Saudi Food and Drug Authority, Riyadh 13513, Saudi Arabia
| | - Addisu D. Teklemariam
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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6
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Antimicrobial Resistance, Pathogenic, and Molecular Characterization of Escherichia coli from Diarrheal Patients in South Korea. Pathogens 2022; 11:pathogens11040385. [PMID: 35456060 PMCID: PMC9030120 DOI: 10.3390/pathogens11040385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
Diarrheal diseases due to foodborne Escherichia coli are the leading cause of illness in humans. Here, we performed pathogenic typing, molecular typing, and antimicrobial susceptibility tests on seventy-five isolates of E. coli isolated from stool samples of patients suffering from foodborne diseases in Busan, South Korea. All the isolates were identified as E. coli by both biochemical analysis (API 20E system) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The bacteria displayed entero-pathogenic E. coli (EPEC) (47.0%), entero-aggregative E. coli (EAEC) (33.3%), entero-toxigenic E. coli (ETEC) (6.6%), ETEC and EPEC (6.6%), EPEC and EAEC (4%), and ETEC and EAEC (2.7%) characteristics. The E. coli isolates were highly resistant to nalidixic acid (44.0%), tetracycline (41.3%), ampicillin (40%), ticarcillin (38.7%), and trimethoprim/sulfamethoxazole (34.7%); however, they were highly susceptible to imipenem (98.6%), cefotetan (98.6%), cefepime (94.6%), and chloramphenicol (94.6%). Although 52 strains (69.3%) showed resistance against at least 1 of the 16 antibiotics tested, 23 strains (30.7%) were susceptible to all the antibiotics. Nine different serotypes (O166, O8, O20, O25, O119, O159, O28ac, O127a, and O18), five genotypes (I to V, random-amplified polymorphic DNA), and four phenotypes (A to D, MALDI-TOF MS) were identified, showing the high level of heterogeneity between the E. coli isolates recovered from diarrheal patients in South Korea.
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Mostafa A, Ganguli A, Berger J, Rayabharam A, Saavedra C, Aluru NR, Bashir R. Culture-free biphasic approach for sensitive detection of Escherichia coli O157:H7 from beef samples. Biotechnol Bioeng 2021; 118:4516-4529. [PMID: 34415570 DOI: 10.1002/bit.27920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022]
Abstract
Foodborne illnesses are a major threat to public health also leading to significant mortality and financial and reputational damage to industry. It is very important to detect pathogen presence in food products early, rapidly, and accurately to avoid potential outbreaks and economic loss. However, "gold standard" culture methods, including enrichment of pathogens, can take up to several days. Moreover, the food matrix often interferes with nucleic acid amplification methods of detection, requiring DNA extraction from the sample for successful molecular detection of pathogens. Here, we introduce a "biphasic" amplification method that can achieve high sensitivity detection with background noise from ground beef food samples without culture or other extraction methods in 2.5 h. Homogenized ground beef is dried resulting in an increase in porosity of the dried food matrix to allowing amplification enzymes and primers to access the target DNA and initiate the reaction within the dried food matrix. Using Loop Mediated Isothermal Amplification, we demonstrate the detection of 1-3 cfu of Escherichia coli bacteria in 30 mg of dried food matrix. Our approach significantly lowers the time to result to less than a few hours and have a pronounced impact on reduction of instrumentation complexity and costs.
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Affiliation(s)
- Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Archith Rayabharam
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Carlos Saavedra
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Narayana R Aluru
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Carle Illinois College of Medicine, Urbana, Illinois, USA
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Glaize A, Young M, Harden L, Gutierrez-Rodriguez E, Thakur S. The effect of vegetation barriers at reducing the transmission of Salmonella and Escherichia coli from animal operations to fresh produce. Int J Food Microbiol 2021; 347:109196. [PMID: 33906045 DOI: 10.1016/j.ijfoodmicro.2021.109196] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 02/08/2023]
Abstract
Due to the recent outbreaks of Salmonella and Escherichia coli in fresh produce in the United States, the transfer of foodborne pathogens between animal feeding operations and fresh produce continues to be a considerable risk. The purpose of this study was to determine if the establishment of a vegetation barrier (VB) on small-scale sustainable farms could prevent the transmission of Salmonella and E. coli to nearby fresh produce fields. A 5-layer VB (31 × 49 m) was constructed between a dairy farm, a poultry farm, and a nearby produce field. Fresh produce (i.e., romaine lettuce and tomato), animal feces, and environmental (i.e., air, soil, and barrier) samples were collected for 15 months from 2018 to 2019. Four replicates of soil and fresh produce samples were taken from three plots located 10 m, 61 m, and 122 m away from the respective animal locations and processed for Salmonella and E. coli. Air and vegetative strip samples were sampled at 15-day intervals. Multiple colonies were processed from each positive sample, and a total of 143 positive Salmonella (n = 15) and E. coli (n = 128) isolates were retrieved from the soil, produce, air, and fecal samples. Interestingly, 18.2% of the Salmonella and E. coli isolates (n = 26) were recovered from fresh produce (n = 9) samples. Surprisingly, Salmonella isolates (n = 9) were only found in fecal (n = 3) samples collected from the dairy pasture. Data analysis suggests that the VB is an effective tool at reducing the transmission of E. coli and Salmonella from animal farms to fresh produce fields. However, based on phenotypic and genotypic testing, it is clear that fecal samples from animal farms are not the only source of pathogen contamination. This indicates that the environment (e.g., soil and wind), as well as the initial setup of the farm (e.g., proximity to service roads and produce plot placement), can contribute to the contamination of fresh produce. Our study recommends the need for more effective bioremediation and prevention control measures to use in conjunction with VBs to reduce pathogen transmission.
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Affiliation(s)
- Ayanna Glaize
- Department of Population Health & Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Morgan Young
- Department of Population Health & Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Lyndy Harden
- Department of Population Health & Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Eduardo Gutierrez-Rodriguez
- Department of Horticulture and Landscape Architecture College of Agricultural Sciences, Colorado State University, USA
| | - Siddhartha Thakur
- Department of Population Health & Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
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Identification, Shiga toxin subtypes and prevalence of minor serogroups of Shiga toxin-producing Escherichia coli in feedlot cattle feces. Sci Rep 2021; 11:8601. [PMID: 33883564 PMCID: PMC8060326 DOI: 10.1038/s41598-021-87544-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/23/2021] [Indexed: 01/12/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that cause illnesses in humans ranging from mild to hemorrhagic enteritis with complications of hemolytic uremic syndrome and even death. Cattle are a major reservoir of STEC, which reside in the hindgut and are shed in the feces, a major source of food and water contaminations. Seven serogroups, O26, O45, O103, O111, O121, O145 and O157, called ‘top-7’, are responsible for the majority of human STEC infections in North America. Additionally, 151 serogroups of E. coli are known to carry Shiga toxin genes (stx). Not much is known about fecal shedding and prevalence and virulence potential of STEC other than the top-7. Our primary objectives were to identify serogroups of STEC strains, other than the top-7, isolated from cattle feces and subtype stx genes to assess their virulence potential. Additional objective was to develop and validate a novel multiplex PCR assay to detect and determine prevalence of six serogroups, O2, O74, O109, O131, O168, and O171, in cattle feces. A total of 351 strains, positive for stx gene and negative for the top-7 serogroups, isolated from feedlot cattle feces were used in the study. Of the 351 strains, 291 belonged to 16 serogroups and 60 could not be serogrouped. Among the 351 strains, 63 (17.9%) carried stx1 gene and 300 (82.1%) carried stx2, including 12 strains positive for both. The majority of the stx1 and stx2 were of stx1a (47/63; 74.6%) and stx2a subtypes (234/300; 78%), respectively, which are often associated with human infections. A novel multiplex PCR assay developed and validated to detect six serogroups, O2, O74, O109, O131, O168, and O171, which accounted for 86.9% of the STEC strains identified, was utilized to determine their prevalence in fecal samples (n = 576) collected from a commercial feedlot. Four serogroups, O2, O109, O168, and O171 were identified as the dominant serogroups prevalent in cattle feces. In conclusion, cattle shed in the feces a number of STEC serogroups, other than the top-7, and the majority of the strains isolated possessed stx2, particularly of the subtype 2a, suggesting their potential risk to cause human infections.
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Das A, Wang Y, Babiuk S, Bai J, Dodd K, Jia W. Development of multiplex real-time PCR assays for differential detection of capripoxvirus, parapoxvirus and foot-and-mouth disease virus. Transbound Emerg Dis 2021; 69:1326-1337. [PMID: 33837669 DOI: 10.1111/tbed.14099] [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: 09/15/2020] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
This study reports the development of multiplex real-time PCR assays for differential detection of capripoxvirus (CaPV), parapoxvirus (PaPV) and foot-and-mouth disease virus (FMDV) in sheep, goats and cattle. Three multiplex assays were developed, a capripox (CaP) rule-out assay for simultaneous detection and differentiation of CaPV and PaPV, a FMD rule-out assay for simultaneous detection and differentiation of FMDV and PaPV, and a FMD/CaP rule-out assay for simultaneous detection and differentiation of CaPV, PaPV and FMDV. All multiplex assays included β-actin gene ACTB as an internal positive control to monitor PCR inhibition and accuracy of nucleic acid extractions. The optimized assays were highly specific to the target viruses (CaPV, PaPV and FMDV) with no cross-reactivity against other viruses that cause similar clinical signs. Using positive control plasmids as template, the limit of detection (LOD) of the multiplex assays were estimated as 2 CaPV, 7 PaPV and 15 FMDV copies per assay. The amplification efficiency (AE) and correlation coefficient (R2 ), estimated from the standard curves (Ct vs. log10 template dilution), were 94%-106% and >0.99, respectively, for CaP and FMD rule-out assays, 96%-116% (AE) and >0.98 (R2 ), respectively, for CaP/FMD rule-out assays and 91%-102% and >0.99, respectively, for the corresponding singleplex assays. The diagnostic sensitivity (DSe) of the multiplex assays was assessed on 35 CaPV and 39 FMDV clinical specimens from experimentally infected (CS-E) animals, and 29 CaPV (LSDV), 28 FMDV and 36 PaPV clinical specimens from naturally infected (CS-N) animals; all tested positive (DSe 100%) except two CS-E FMDV specimens that were tested negative by FMD rule-out and the corresponding singleplex (FMDV) assays (37/39; DSe 95%). The newly developed multiplex assays offer a valuable tool for differential detection of clinically indistinguishable CaPV, PaPV and FMDV in suspected animals and animals with mixed infections.
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Affiliation(s)
- Amaresh Das
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Kimberly Dodd
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Wei Jia
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
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Elabbasy MT, Hussein MA, Algahtani FD, Abd El-Rahman GI, Morshdy AE, Elkafrawy IA, Adeboye AA. MALDI-TOF MS Based Typing for Rapid Screening of Multiple Antibiotic Resistance E. coli and Virulent Non-O157 Shiga Toxin-Producing E. coli Isolated from the Slaughterhouse Settings and Beef Carcasses. Foods 2021; 10:foods10040820. [PMID: 33920071 PMCID: PMC8069270 DOI: 10.3390/foods10040820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/26/2021] [Accepted: 04/07/2021] [Indexed: 11/23/2022] Open
Abstract
Background: The emergence of multiple antibiotic resistance (MAR) Escherichia coli (E. coli) and virulent non-O157 Shiga toxin-producing Escherichia coli (STEC) poses a growing concern to the meat industry. Non-O157 STEC strains including O26, O45, O103, O111, O121, and O145 have been implicated in the occurrence of bloody diarrhea and hemolytic uremic syndrome in humans. This research assessed prevalence, matrix-assisted laser desorption/ionization-time of flight mass-spectrometry (MALDI-TOF MS) protein mass-spectra profiles, multidrug-resistance traits, polymerase chain reaction detection of virulence, and antibiotic-resistance genes of E. coli isolated from beef carcasses and slaughterhouse environments. Methods: A total of 180 convenience sponge samples were collected from two different sources-specific parts of beef carcasses and surfaces of the processing environment at the slaughterhouse of Ha′il, Saudi Arabia between September and November 2020. MALDI BioTyper and phylotype-based identification methods accurately identified and classified the samples as belonging to the genus belonging to the Escherichia coli domain of bacteria (NCBI txid: 562). Results: Expected changes were seen in the mass peak spectrum defining nine closely related isolates and four unrelated E. coli isolates. Serological typing of E. coli revealed enterotoxigenic E. coli O166 (19.10%); enteropathogenic E. coli O146 (16.36%) and O44 (18.18%); enterohemorrhagic E. coli O111 (31.18%) and O26 (14.54%). Forty-five percent of examined E. coli were resistant to seven antimicrobials; 75% of 20 selected isolates were resistant to three or more antimicrobials. phoA and blaTEM genes were detected in all selected E. coli isolates. Conclusion: This study confirmed the efficiency and validity of Matrix-assisted laser desorption/ionization time of flight mass-spectrometry in screening for multi-drug resistant E. coli isolated from slaughterhouse derived beef carcasses in Ha’il, Saudi Arabia. We contributed by revealing the distinction between related and non-related strains of E.coli in livestock. The findings in this study can inform improved policy development decision making and resource allocation related to livestock processing regarding antimicrobial use in food animals and rapid screening for effective multiple antibiotic resistance E. coli and virulent non-O157 STEC control in the slaughterhouses.
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Affiliation(s)
- Mohamed Tharwat Elabbasy
- Public Health Department, College of Public Health and Health Informatics, Ha’il University, Ha’il 2440, Saudi Arabia; (F.D.A.); (A.A.A.)
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt; (M.A.H.); (A.E.M.)
- Correspondence: ; Tel.: +9-665-4689-7569
| | - Mohamed A. Hussein
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt; (M.A.H.); (A.E.M.)
| | - Fahad Dhafer Algahtani
- Public Health Department, College of Public Health and Health Informatics, Ha’il University, Ha’il 2440, Saudi Arabia; (F.D.A.); (A.A.A.)
| | - Ghada I. Abd El-Rahman
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Alaa Eldin Morshdy
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt; (M.A.H.); (A.E.M.)
| | - Ibrahim A. Elkafrawy
- Department of Psychological Sciences, Faculty of Early Childhood Education, University of Sadat City, Sadat City 32897, Egypt;
| | - Adeniyi A. Adeboye
- Public Health Department, College of Public Health and Health Informatics, Ha’il University, Ha’il 2440, Saudi Arabia; (F.D.A.); (A.A.A.)
- Department of Public Health, University of Texas Health Sciences at Houston, Houston, TX 77030, USA
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Evaluation of Cattle for Naturally Colonized Shiga Toxin-Producing Escherichia coli Requires Combinatorial Strategies. Int J Microbiol 2021; 2021:6673202. [PMID: 33868404 PMCID: PMC8032530 DOI: 10.1155/2021/6673202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/06/2021] [Accepted: 03/21/2021] [Indexed: 01/01/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) serogroups O157, O26, O103, O111, O121, O145, and O45 are designated as food adulterants by the U.S. Department of Agriculture-Food Safety and Inspection Service. Cattle are the primary reservoir of these human pathogens. In this study, 59 Angus crossbred heifers were tested specifically for these seven STEC serogroups using a combination of standard culture, serological, PCR, and cell cytotoxicity methods to determine if comparable results would be obtained. At the time of fecal sampling, the animals were approximately 2 years old and weighed 1000–1200 lbs. The diet comprised of 37% ground alfalfa hay, 25% ground Sudan hay, and 38% ground corn supplemented with trace minerals and rumensin with ad libitum access to water. Non-O157 STEC were isolated from 25% (15/59) of the animals tested using a combination of EC broth, CHROMagar STECTM, and Rainbow Agar O157. Interestingly, the O157 serogroup was not isolated from any of the animals. Non-O157 STEC isolates were confirmed to be one of the six adulterant serogroups by serology and/or colony PCR in 10/15 animals with the predominant viable, serogroup being O103. PCR using DNA extracted from feces verified most of the colony PCR results but also identified additional virulence and O-antigen genes from samples with no correlating culture results. Shiga toxin- (Stx-) related cytopathic effects on Vero cells with fecal extracts from 55/59 animals could only be associated with the Stx gene profiles obtained by fecal DNA PCR and not culture results. The differences between culture versus fecal DNA PCR and cytotoxicity assay results suggest that the latter two assays reflect the presence of nonviable STEC or infection with STEC not belonging to the seven adulterant serogroups. This study further supports the use of combinatorial culture, serology, and PCR methods to isolate viable STEC that pose a greater food safety threat.
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Kim JH, Oh SW. Rapid detection for low numbers of Escherichia coli O157:H7 by real-time PCR in cabbage using a combination of filtration, short microbial enrichment, and DNA concentration within 4 h. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Singh P, Cubillos G, Kirshteyn G, Bosilevac JM. High-resolution melting real-time PCR assays for detection of Escherichia coli O26 and O111 strains possessing Shiga toxin genes. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Ludwig JB, Shi X, Shridhar PB, Roberts EL, DebRoy C, Phebus RK, Bai J, Nagaraja TG. Multiplex PCR Assays for the Detection of One Hundred and Thirty Seven Serogroups of Shiga Toxin-Producing Escherichia coli Associated With Cattle. Front Cell Infect Microbiol 2020; 10:378. [PMID: 32850480 PMCID: PMC7403468 DOI: 10.3389/fcimb.2020.00378] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli carrying prophage with genes that encode for Shiga toxins are categorized as Shiga toxin-producing E. coli (STEC) pathotype. Illnesses caused by STEC in humans, which are often foodborne, range from mild to bloody diarrhea with life-threatening complications of renal failure and hemolytic uremic syndrome and even death, particularly in children. As many as 158 of the total 187 serogroups of E. coli are known to carry Shiga toxin genes, which makes STEC a major pathotype of E. coli. Seven STEC serogroups, called top-7, which include O26, O45, O103, O111, O121, O145, and O157, are responsible for the majority of the STEC-associated human illnesses. The STEC serogroups, other than the top-7, called “non-top-7” have also been associated with human illnesses, more often as sporadic infections. Ruminants, particularly cattle, are principal reservoirs of STEC and harbor the organisms in the hindgut and shed in the feces, which serves as a major source of food and water contaminations. A number of studies have reported on the fecal prevalence of top-7 STEC in cattle feces. However, there is paucity of data on the prevalence of non-top-7 STEC serogroups in cattle feces, generally because of lack of validated detection methods. The objective of our study was to develop and validate 14 sets of multiplex PCR (mPCR) assays targeting serogroup-specific genes to detect 137 non-top-7 STEC serogroups previously reported to be present in cattle feces. Each assay included 7–12 serogroups and primers were designed to amplify the target genes with distinct amplicon sizes for each serogroup that can be readily identified within each assay. The assays were validated with 460 strains of known serogroups. The multiplex PCR assays designed in our study can be readily adapted by most laboratories for rapid identification of strains belonging to the non-top-7 STEC serogroups associated with cattle.
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Affiliation(s)
- Justin B Ludwig
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Xiaorong Shi
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Pragathi B Shridhar
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Elisabeth L Roberts
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Chitrita DebRoy
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Randy K Phebus
- Department of Animal Sciences and Industry/Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Jianfa Bai
- Veterinary Diagnostic Laboratory, Industry/Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
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Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes. J Clin Microbiol 2020; 58:JCM.01684-19. [PMID: 31896667 DOI: 10.1128/jcm.01684-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/13/2019] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx 1 and stx 2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the "top 7" Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E. coli strains, regular PCR cannot confirm whether the virulence genes are carried by adulterant or nonadulterant E. coli serogroups. Thus, traditional gold-standard STEC detection requires bacterial isolation and characterization, which are not compatible with high-throughput settings and often take a week to obtain a definitive result. In this study, we demonstrated that the partition-based multichannel digital PCR (dPCR) system can be used to detect and associate the E. coli serogroup-specific gene with major virulence genes and developed a single-cell-based dPCR approach for rapid (within 1 day) and accurate detection and confirmation of major STEC serogroups in high-throughput settings. Major virulence genes carried by each of the top 7 STEC serogroups were detected by dPCR with appropriately diluted intact bacterial cells from pure cultures, culture-spiked cattle feces, and culture-spiked ground beef. Furthermore, from 100 randomly collected, naturally shed cattle fecal samples, 3 O103 strains carrying eae and 2 O45 strains carrying stx 1 were identified by this dPCR assay and verified by the traditional isolation method. This novel and rapid dPCR assay is a culture-independent, high-throughput, accurate, and sensitive method for STEC detection and confirmation.
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Mori T, Nagao-Sato S, Kishino K, Namba T, Hara-Kudo Y. [DNA Extraction for Sensitive Detection of Shiga Toxin-Producing Escherichia coli in Food by Real-Time PCR Assays]. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2020; 60:183-186. [PMID: 31969538 DOI: 10.3358/shokueishi.60.183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Alkali-heat DNA extraction, a rapid and economical method, was evaluated for use in the detection of Shiga toxin-producing Escherichia coli in food using real-time PCR assays. Alkali-heat DNA extracts led to highly sensitive detection (102-104 CFU/mL) of stx and O-antigen genes in beef liver, ground beef, sliced pork, cheese, lettuce, radish sprouts, tomato, and spinach, equivalent to the sensitivity obtained using a commercial DNA extraction kit that utilizes proteinase K lysis, and silica membrane purification. Although there were differences in DNA concentration and purity between DNA extraction methods, the sensitivity of real-time PCR assays was similar. These results indicate that alkali-heat DNA extraction is a viable method when testing food products with real-time PCR assays for the presence of stx and O-antigen genes.
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Affiliation(s)
- Tetsuya Mori
- Institute for Food and Environment Sciences Tokyo Kenbikyo-in Foundation
| | | | - Kanae Kishino
- Institute for Food and Environment Sciences Tokyo Kenbikyo-in Foundation
| | - Toyohiko Namba
- Institute for Food and Environment Sciences Tokyo Kenbikyo-in Foundation
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Kang R, Park B, Chen K. Identifying non-O157 Shiga toxin-producing Escherichia coli (STEC) using deep learning methods with hyperspectral microscope images. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117386. [PMID: 31336320 DOI: 10.1016/j.saa.2019.117386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
Non-O157 Shiga toxin-producing Escherichia coli (STEC) serogroups such as O26, O45, O103, O111, O121 and O145 often cause illness to people in the United States and the conventional identification of these "Big-Six" are complex. The label-free hyperspectral microscope imaging (HMI) method, which provides spectral "fingerprints" information of bacterial cells, was employed to classify serogroups at the cellular level. In spectral analysis, principal component analysis (PCA) method and stacked auto-encoder (SAE) method were conducted to extract principal spectral features for classification task. Based on these features, multiple classifiers including linear discriminant analysis (LDA), support vector machine (SVM) and soft-max regression (SR) methods were evaluated. Different sizes of datasets were also tested in search for the suitable classification models. Among the results, SAE-based classification models performed better than PCA-based models, achieving classification accuracy of SAE-LDA (93.5%), SAE-SVM (94.9%) and SAE-SR (94.6%), respectively. In contrast, classification results of PCA-based methods such as PCA-LDA, PCA-SVM and PCA-SR were only 75.5%, 85.7% and 77.1%, respectively. The results also suggested the increasing number of training samples have positive effects on classification models. Taking advantage of increasing dataset, the SAE-SR classification model finally performed better than others with average accuracy of 94.9% in classifying STEC serogroups. Specifically, O103 serogroup was classified with the highest accuracy of 97.4%, followed by O111 (96.5%), O26 (95.3%), O121 (95%), O145 (92.9%) and O45 (92.4%), respectively. Thus, the HMI technology coupled with SAE-SR classification model has the potential for "Big-Six" identification.
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Affiliation(s)
- Rui Kang
- College of Engineering, Nanjing Agricultural University, Nanjing, Jiangsu 210031, China; United States Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA 30605, USA
| | - Bosoon Park
- United States Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA 30605, USA.
| | - Kunjie Chen
- College of Engineering, Nanjing Agricultural University, Nanjing, Jiangsu 210031, China.
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Manage DP, Lauzon J, Jones CM, Ward PJ, Pilarski LM, Pilarski PM, McMullen LM. Detection of pathogenic Escherichia coli on potentially contaminated beef carcasses using cassette PCR and conventional PCR. BMC Microbiol 2019; 19:175. [PMID: 31362696 PMCID: PMC6668150 DOI: 10.1186/s12866-019-1541-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over a one year period, swabs of 820 beef carcasses were tested for the presence of Shiga toxin-producing Escherichia coli by performing Polymerase Chain Reaction (PCR) in a novel technology termed "cassette PCR", in comparison to conventional liquid PCR. Cassette PCR is inexpensive and ready-to-use. The operator need only add the sample and press "go". Cassette PCR can simultaneously test multiple samples for multiple targets. Carcass swab samples were first tested for the presence of STEC genes (O157, eae, stx1 and stx2). Samples were considered to be pathogenic if positive for eae plus stx1 and/or stx2. For samples scored as pathogenic, further testing screened for 6 additional high frequency O-antigens (O26, O45, O103, O111, O121, and O145). RESULTS Of the 820 samples, 41% were pathogenic and 30% were O157 positive. Of these, 19% of samples were positive for O157 and carried potentially pathogenic E. coli (eae plus stx1 and/or stx2). Of all samples identified as carrying pathogenic E. coli, 18.9, 38.8, 41.4, 0, 36.1, and 4.1% respectively were positive for O26, O45, O103, O111, O121, and O145. To validate cassette PCR testing, conventional PCR using STEC primers was performed on each of the 820 samples. Only 148 of 3280 cassette PCR tests were discordant with conventional PCR results. However, further fractional testing showed that 110 of these 148 PCRs reflected low numbers of E. coli in the enrichment broth and could be explained as due to Poisson limiting dilution of the template, affecting both cassette PCR and conventional PCR. Of the remaining 38 discordant tests, 27 initial capillary PCRs and 10 initial conventional tests were nominally discordant between cassette and conventional PCR, perhaps reflecting human/technical error on both sides of the comparison. CONCLUSIONS Contaminated beef carcass swabs were often complex, likely harboring more than one strain of pathogenic E. coli. Cassette PCR had 98.8% concordance with parallel conventional PCR for detection of STEC genes. This indicates that cassette PCR is highly reliable for detecting multiple pathogens in beef carcass swabs from processing plants.
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Affiliation(s)
- Dammika P Manage
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Jana Lauzon
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Christina M Jones
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Patrick J Ward
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
| | - Patrick M Pilarski
- Division of Physical Medicine & Rehabilitation, Department of Medicine, University of Alberta, 5-005 Katz Group Centre for Pharmacy and Health Research, Edmonton, AB, T6G 2E1, Canada
| | - Lynn M McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
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Manage DP, Lauzon J, McMullen LM, Pilarski LM. Application of lab-on-a-chip multiplex cassette PCR for the detection of enterohemorrhagic Escherichia coli. BMC Microbiol 2019; 19:93. [PMID: 31088365 PMCID: PMC6515682 DOI: 10.1186/s12866-019-1463-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/23/2019] [Indexed: 11/20/2022] Open
Abstract
Background Fast molecular detection methods benefit from ready-to-run lab-on-a-chip molecular assays with minimum preparation time. Detection efficiency of such methods can improve if multiple targets are detected simultaneously per given reaction. Detection of food pathogens, i.e. Escherichia coli (E. coli), is generally performed in two stages with the detection of multiple targets in each stage.With simultaneous testing, screening for pathogens is fast and efficient. Results In this study, we show the application of multiplex PCR performed on a ready-made cassette to detect 10 targets each for eight samples known to harbor E. coli. In cassette PCR, the aluminum cassette (38.6 mm × 31.4 mm) contains 10 trenches having a total of 50 capillaries with microliter volumes of desiccated acrylamide gels holding all reagents required for the PCR including internal positive and negative controls. The gel contains LCGreen dye to detect double stranded DNA. Fluorescence monitoring allows the detection of the amplified products by melt curve analysis. In this application, each of the five capillaries in a given trench contains two of the primer sets for the detection of 10 targets in pathogenic E. coli, namely, O157, Eae, Stx1, Stx2 and six O-antigen genes. Primer specificity was confirmed. Each trench tests one sample. Eight minimally processed enriched beef carcass swab samples were analyzed for parallel detection of 10 targets within 1 h and 15 min. Samples were delivered to the capillaries by capillary forces thereby hydrating the gels. Multiplex cassette PCR results were confirmed with conventional multiplex PCRs performed in a commercial real-time PCR system. Conclusions Cassette PCR technology is ideally suited to multi-target detection of pathogens in food products. The cassette performs multiple PCR reactions in parallel, with multiplex detection of targets within each reaction unit. Cassette PCR/ melt curve analysis results for the simultaneous detection of 10 targets of pathogenic E.coli in beef carcass swab samples were confirmed with a conventional real-time PCR/ melt curve analysis as well as with agarose gel electrophoresis. Although designed for the detection of E. coli, this multiplex cassette PCR technique can be applied to any other assay where the fast detection of multiple targets is required.
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Affiliation(s)
- Dammika P Manage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Jana Lauzon
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Lynn M McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
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Uddin J, Hossain K, Hossain S, Saha K, Jubyda FT, Haque R, Billah B, Talukder AA, Parvez AK, Dey SK. Bacteriological assessments of foodborne pathogens in poultry meat at different super shops in Dhaka, Bangladesh. Ital J Food Saf 2019; 8:6720. [PMID: 31008079 PMCID: PMC6452097 DOI: 10.4081/ijfs.2019.6720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 01/17/2018] [Indexed: 11/22/2022] Open
Abstract
Poultry is now considered as a major fast-growing source of meat in the world. The consumers demand safe and hygienic products without contamination with pathogenic microorganisms when the production and consumption of poultry meat is gradually increasing. The present study was conducted to assess the bacterial contamination of dressed chicken collected from different supershops in Dhaka, Bangladesh. The chicken samples from S1, S2, M1, M2 and A supershops were analyzed to determine the enteropathogenic bacteria in poultry meat. Three genera of bacteria were isolated from all of the chicken meat samples. These enteropathogens from various organs of dressing chickens were also enumerated. The isolates were presumptively identified as E. coli, Salmonella spp., and Shigella spp. by conventional culture method. The three enteropathogens were subjected to PCR assay for their confirmation as virulent enteropathogens. Only E. coli isolates were confirmed as pathogenic E. coli (Enterotoxigenic), other isolates were not confirmed as virulent Salmonella spp., Shigella spp.. Results of this study demonstrated that more cautions are recommended for personnel hygiene in processing and handling of poultry and poultry products to prevent occurrence of enterotoxigenic E. coli in dressed poultry meat sold by the supershops in Bangladesh.
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Affiliation(s)
| | | | | | | | | | | | - Baki Billah
- Department of Zoology, Jahangirnagar University, Dhaka, Bangladesh
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Vidic J, Vizzini P, Manzano M, Kavanaugh D, Ramarao N, Zivkovic M, Radonic V, Knezevic N, Giouroudi I, Gadjanski I. Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1100. [PMID: 30836707 PMCID: PMC6427207 DOI: 10.3390/s19051100] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.
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Affiliation(s)
- Jasmina Vidic
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Priya Vizzini
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Devon Kavanaugh
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nalini Ramarao
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Milica Zivkovic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, 11000 Belgrade, Serbia.
| | - Vasa Radonic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Nikola Knezevic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ioanna Giouroudi
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ivana Gadjanski
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
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Detection of Shiga toxin-producing Escherichia coli, stx1, stx2 and Salmonella by two high resolution melt curve multiplex real-time PCR. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.09.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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25
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Rotundo L, Amagliani G, Carloni E, Omiccioli E, Magnani M, Paoli G. Evaluation of PCR-based methods for the identification of enteroaggregative hemorrhagic Escherichia coli in sprouts. Int J Food Microbiol 2019; 291:59-64. [DOI: 10.1016/j.ijfoodmicro.2018.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 11/27/2022]
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Varcasia BM, Tomassetti F, De Santis L, Di Giamberardino F, Lovari S, Bilei S, De Santis P. Presence of Shiga Toxin-Producing Escherichia coli (STEC) in Fresh Beef Marketed in 13 Regions of ITALY (2017). Microorganisms 2018; 6:E126. [PMID: 30563244 PMCID: PMC6313577 DOI: 10.3390/microorganisms6040126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/02/2023] Open
Abstract
The aim of this study was to determine the prevalence of Shiga toxin-producing Escherichia coli in fresh beef marketed in 2017 in 13 regions of Italy, to evaluate the potential risk to human health. According to the ISO/TS 13136:2012 standard, 239 samples were analysed and nine were STEC positive, from which 20 strains were isolated. The STEC-positive samples were obtained from Calabria (n = 1), Campania (n = 1), Lazio (n = 2), Liguria (n = 1), Lombardia (n = 1) and Veneto (n = 3). All STEC strains were analysed for serogroups O26, O45, O55, O91, O103, O104, O111, O113, O121, O128, O145, O146 and O157, using Real-Time PCR. Three serogroups were identified amongst the 20 strains: O91 (n = 5), O113 (n = 2), and O157 (n = 1); the O-group for each of the 12 remaining STEC strains was not identified. Six stx subtypes were detected: stx1a, stx1c, stx2a, stx2b, stx2c and stx2d. Subtype stx2c was the most common, followed by stx2d and stx2b. Subtype stx2a was identified in only one eae-negative strain and occurred in combination with stx1a, stx1c and stx2b. The presence in meat of STEC strains being potentially harmful to human health shows the importance, during harvest, of implementing additional measures to reduce contamination risk.
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Affiliation(s)
- Bianca Maria Varcasia
- Istituto Zooprofilattico Sperimentale Lazio e Toscana, "M. Aleandri", 00178 Rome, Italy.
| | - Francesco Tomassetti
- Istituto Zooprofilattico Sperimentale Lazio e Toscana, "M. Aleandri", 00178 Rome, Italy.
| | - Laura De Santis
- Istituto Zooprofilattico Sperimentale Lazio e Toscana, "M. Aleandri", 00178 Rome, Italy.
| | | | - Sarah Lovari
- Istituto Zooprofilattico Sperimentale Lazio e Toscana, "M. Aleandri", 00178 Rome, Italy.
| | - Stefano Bilei
- Istituto Zooprofilattico Sperimentale Lazio e Toscana, "M. Aleandri", 00178 Rome, Italy.
| | - Paola De Santis
- Istituto Zooprofilattico Sperimentale Lazio e Toscana, "M. Aleandri", 00178 Rome, Italy.
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Amézquita-López BA, Soto-Beltrán M, Lee BG, Yambao JC, Quiñones B. Isolation, genotyping and antimicrobial resistance of Shiga toxin-producing Escherichia coli. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 51:425-434. [DOI: 10.1016/j.jmii.2017.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 06/28/2017] [Accepted: 07/12/2017] [Indexed: 12/27/2022]
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28
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Comparison of the Diatheva STEC FLUO with BAX System Kits for Detection of O157:H7 and Non-O157 Shiga Toxin-Producing Escherichia coli (STEC) in Ground Beef and Bean Sprout Samples Using Different Enrichment Protocols. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1269-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Abstract
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.
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30
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Zulkifli SN, Rahim HA, Lau WJ. Detection of contaminants in water supply: A review on state-of-the-art monitoring technologies and their applications. SENSORS AND ACTUATORS. B, CHEMICAL 2018; 255:2657-2689. [PMID: 32288249 PMCID: PMC7126548 DOI: 10.1016/j.snb.2017.09.078] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 05/12/2023]
Abstract
Water monitoring technologies are widely used for contaminants detection in wide variety of water ecology applications such as water treatment plant and water distribution system. A tremendous amount of research has been conducted over the past decades to develop robust and efficient techniques of contaminants detection with minimum operating cost and energy. Recent developments in spectroscopic techniques and biosensor approach have improved the detection sensitivities, quantitatively and qualitatively. The availability of in-situ measurements and multiple detection analyses has expanded the water monitoring applications in various advanced techniques including successful establishment in hand-held sensing devices which improves portability in real-time basis for the detection of contaminant, such as microorganisms, pesticides, heavy metal ions, inorganic and organic components. This paper intends to review the developments in water quality monitoring technologies for the detection of biological and chemical contaminants in accordance with instrumental limitations. Particularly, this review focuses on the most recently developed techniques for water contaminant detection applications. Several recommendations and prospective views on the developments in water quality assessments will also be included.
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Affiliation(s)
| | - Herlina Abdul Rahim
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Woei-Jye Lau
- Advanced Membrane Technology Research Centre (AMTEC), Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
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31
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Amagliani G, Rotundo L, Carloni E, Omiccioli E, Magnani M, Brandi G, Fratamico P. Detection of Shiga toxin-producing Escherichia coli (STEC) in ground beef and bean sprouts: Evaluation of culture enrichment conditions. Food Res Int 2018; 103:398-405. [DOI: 10.1016/j.foodres.2017.10.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/17/2017] [Accepted: 10/28/2017] [Indexed: 11/26/2022]
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32
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Kraft AL, Lacher DW, Shelver WL, Sherwood JS, Bergholz TM. Comparison of immunomagnetic separation beads for detection of six non-O157 Shiga toxin-producing Escherichia coli serogroups in different matrices. Lett Appl Microbiol 2017; 65:213-219. [PMID: 28656639 DOI: 10.1111/lam.12771] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
Immunomagnetic separation used with culture based methods has been a useful technique in the detection of pathogens. However, previous studies have not answered many of the necessary questions for real world applications. The objective of this study was to assess the efficacy of different immunomagnetic separation (IMS) bead types in recovery of the correct serogroup from a mixture of big six non-O157 Shiga toxin-producing Escherichia coli strains. To determine the impact of different matrices on recovery, samples of sterile phosphate buffered saline (PBS), sterile and non-sterile cattle faeces, ground beef and lettuce were inoculated with 10 CFU per ml mixture of isolates representing the six serogroups. After a 6 h incubation at 37°C, samples were mixed with IMS beads from three different commercial sources and plated on eosin methylene blue agar (EMB). Three suspect E. coli colonies were selected from each EMB plate and multiplex polymerase chain reaction was used to determine the serogroup. The rate of correct identification varied with the serogroup, IMS bead manufacturer and matrix. Overall, recovery of the correct serogroup became less likely with increase in matrix complexity, with enrichments containing lettuce having the greatest number of bead types with significantly lower likelihood of correct recovery compared to recovery in PBS. SIGNIFICANCE AND IMPACT OF THE STUDY The need to accurately and efficiently detect Shiga toxin-producing Escherichia coli (STEC) O26, O45, O103, O111, O121 and O145, which have caused outbreaks on numerous occasions, is a major public health and food safety concern in the United States. Detecting these STEC serogroups can be challenging because methods to detect non-O157 serogroups have not been refined as compared to those for O157. Immunomagnetic separation (IMS) has the potential to isolate STEC from a mixture in complex matrices. Our results highlight the need for optimization of IMS-based detection of STEC to effectively recover the targeted serogroup from a variety of sample matrices.
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Affiliation(s)
- A L Kraft
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - D W Lacher
- Division of Molecular Biology, United States Food and Drug Administration, Laurel, MD, USA
| | - W L Shelver
- Biosciences Research Laboratory, United States Department of Agriculture - Red River Valley Agricultural Research Service, Fargo, ND, USA
| | - J S Sherwood
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - T M Bergholz
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
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34
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Yoo BB, Liu Y, Juneja V, Huang L, Hwang CA. Effect of environmental stresses on the survival and cytotoxicity of Shiga toxin-producing Escherichia coli†. FOOD QUALITY AND SAFETY 2017. [DOI: 10.1093/fqsafe/fyx010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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35
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Evaluating the efficacy of beef slaughter line interventions by quantifying the six major non-O157 Shiga toxin producing Escherichia coli serogroups using real-time multiplex PCR. Food Microbiol 2017; 63:228-238. [DOI: 10.1016/j.fm.2016.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
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36
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Hallewell J, Alexander T, Reuter T, Stanford K. Limitations of Immunomagnetic Separation for Detection of the Top Seven Serogroups of Shiga Toxin-Producing Escherichia coli. J Food Prot 2017; 80:598-603. [PMID: 28334549 DOI: 10.4315/0362-028x.jfp-16-427] [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] [Indexed: 11/11/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) strains are foodborne pathogens that negatively impact human health and compromise food safety. Serogroup O157 is the most frequently isolated and studied STEC serogroup, but six others (O26, O45, O103, O111, O121, and O145) have also been identified as significant sources of human disease and collectively have been referred to as the "top six" pathogenic serogroups. Because detection methods for non-O157 serogroups are not yet refined, the objective of this study was to compare the effectiveness of immunomagnetic separation (IMS) for recovery of serogroup O157 isolates with that for each of the top six E. coli serogroups in pure and mixed cultures of STEC at 103 to 107 CFU/mL. After serogroup-specific IMS, DNA was extracted from cultured isolates to analyze the specificity of each IMS assay using conventional and quantitative PCR. In pure cultures, DNA copy number obtained after IMS was lower for O111 and O157 (P < 0.01) than for other serogroups. Based on quantitative PCR (qPCR) analyses, specificity was reduced for all IMS assays when STEC isolates were mixed at 7 log CFU/mL, although the O157 IMS assays recovered only O157 over a wider range of concentrations than did assays for non-O157 serogroups. At the lowest dilution tested, conventional PCR was specific for all serogroups except O121 and O145. For these two serogroups, no dilution tested recovered only O121 or O145 when evaluated with conventional PCR. Refinements to IMS assays, development of selective media, and determination of optimal enrichment times to reduce background microflora or competition among serogroups would be especially beneficial for recovery of O111, O121, and O145 serogroups to improve STEC detection and isolation.
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Affiliation(s)
- J Hallewell
- Agriculture and Agri-food Canada, Lethbridge Research Center, Lethbridge, Alberta, Canada T1J 4P4
| | - T Alexander
- Agriculture and Agri-food Canada, Lethbridge Research Center, Lethbridge, Alberta, Canada T1J 4P4
| | - T Reuter
- Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, Alberta, Canada T1J 4V6 (ORCID: http://orcid.org/0000-0001-8784-0042 [K.S.])
| | - K Stanford
- Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, Alberta, Canada T1J 4V6 (ORCID: http://orcid.org/0000-0001-8784-0042 [K.S.])
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37
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Mondani L, Delannoy S, Mathey R, Piat F, Mercey T, Slimani S, Fach P, Livache T, Roupioz Y. Fast detection of both O157 and non-O157 shiga-toxin producing Escherichia coli by real-time optical immunoassay. Lett Appl Microbiol 2016; 62:39-46. [PMID: 26432989 DOI: 10.1111/lam.12503] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/04/2015] [Accepted: 09/24/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Among bacterial pathogens involved in food-illnesses, seven serogroups (O26, O45, O103, O111, O121, O145 and O157) of Shiga-toxin producing Escherichia coli (STEC), are frequently identified. During such outbreak, and due to the perishable property of most foodstuff, the time laps for the identification of contaminated products and pathogens is thus critical to better circumvent their spread. Traditional detection methods using PCR or culture plating are time consuming and may present some limitations. In this study, we present a multiplexed immunoassay for the optical detection of most commonly enterohemorrhagic E. coli serogroups: O26, O45, O103, O111, O121, O145 and O157:H7 in a single device. The use of Surface Plasmon Resonance imaging not only enabled the label-free analysis of the samples but gave results in a real-time manner. A dedicated protocol was set up for the detection of both low contaminating bacterial concentrations of food samples (5 CFU per 25 g) and postenrichment aliquots. By combining one single device for the detection of O157 and non-O157 STEC in a label-free manner, this rapid approach may have an important economic and societal impact. SIGNIFICANCE AND IMPACT OF THE STUDY This article presents a simple-to-operate immunoassay for the specific detection of Shiga-toxin producing Escherichia coli (STEC). This approach consists in the on-chip assay detection of viable cells on a specifically designed antibody microarray. By skipping any enrichment step and avoiding the use of labelling agent, this approach based on the Surface Plasmon Resonance imaging of the microarrays turns out to be much faster and more cost effective by comparison with standardized methods.
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Affiliation(s)
- L Mondani
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
| | - S Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - R Mathey
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
| | - F Piat
- Prestodiag, Villejuif, France
| | | | | | - P Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - T Livache
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
| | - Y Roupioz
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
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Morris D, Kavanagh S, Carney K, MacDomhnaill B, Cormican M. CapE (capture, amplify, extract): A rapid method for detection of low level contamination of water with Verocytotoxigenic Escherichia coli (VTEC). THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 563-564:267-272. [PMID: 27135590 DOI: 10.1016/j.scitotenv.2016.04.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/10/2016] [Accepted: 04/10/2016] [Indexed: 06/05/2023]
Abstract
Verocytotoxigenic Escherichia coli (VTEC) is associated with a wide spectrum of disease from mild self-limiting diarrhoea to haemolytic uremic syndrome. Contaminated drinking water is accepted as an important route of transmission in Ireland as elsewhere however established methods for detection of VTEC in drinking water have limitations. We describe a sensitive and rapid method for detection of VTEC from large volumes (20 to 30L) of drinking water based on filtration, enrichment culture of filters and real-time PCR detection of VTEC virulence and O antigen determinants from enrichments. The method has potential applications for other waterborne pathogens.
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Affiliation(s)
- Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland.
| | - Siobhán Kavanagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Karen Carney
- National Federation of Group Water Schemes, Monaghan, Ireland
| | | | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland
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Baker CA, Park SH, Kim SA, Rubinelli PM, Roto SM, Lee SI, Ramsaroop S, Miller M, Ricke SC. Formalin-fixed cells as an internal standard approach for the detection and quantitative assessment of Shiga toxin-producing Escherichia coli (STEC). Food Control 2016. [DOI: 10.1016/j.foodcont.2015.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Hara-Kudo Y, Konishi N, Ohtsuka K, Iwabuchi K, Kikuchi R, Isobe J, Yamazaki T, Suzuki F, Nagai Y, Yamada H, Tanouchi A, Mori T, Nakagawa H, Ueda Y, Terajima J. An interlaboratory study on efficient detection of Shiga toxin-producing Escherichia coli O26, O103, O111, O121, O145, and O157 in food using real-time PCR assay and chromogenic agar. Int J Food Microbiol 2016; 230:81-8. [PMID: 27153219 DOI: 10.1016/j.ijfoodmicro.2016.03.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 03/21/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Abstract
To establish an efficient detection method for Shiga toxin (Stx)-producing Escherichia coli (STEC) O26, O103, O111, O121, O145, and O157 in food, an interlaboratory study using all the serogroups of detection targets was firstly conducted. We employed a series of tests including enrichment, real-time PCR assays, and concentration by immunomagnetic separation, followed by plating onto selective agar media (IMS-plating methods). This study was particularly focused on the efficiencies of real-time PCR assays in detecting stx and O-antigen genes of the six serogroups and of IMS-plating methods onto selective agar media including chromogenic agar. Ground beef and radish sprouts samples were inoculated with the six STEC serogroups either at 4-6CFU/25g (low levels) or at 22-29CFU/25g (high levels). The sensitivity of stx detection in ground beef at both levels of inoculation with all six STEC serogroups was 100%. The sensitivity of stx detection was also 100% in radish sprouts at high levels of inoculation with all six STEC serogroups, and 66.7%-91.7% at low levels of inoculation. The sensitivity of detection of O-antigen genes was 100% in both ground beef and radish sprouts at high inoculation levels, while at low inoculation levels, it was 95.8%-100% in ground beef and 66.7%-91.7% in radish sprouts. The sensitivity of detection with IMS-plating was either the same or lower than those of the real-time PCR assays targeting stx and O-antigen genes. The relationship between the results of IMS-plating methods and Ct values of real-time PCR assays were firstly analyzed in detail. Ct values in most samples that tested negative in the IMS-plating method were higher than the maximum Ct values in samples that tested positive in the IMS-plating method. This study indicates that all six STEC serogroups in food contaminated with more than 29CFU/25g were detected by real-time PCR assays targeting stx and O-antigen genes and IMS-plating onto selective agar media. Therefore, screening of stx and O-antigen genes followed by isolation of STECs by IMS-plating methods may be an efficient method to detect the six STEC serogroups.
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Affiliation(s)
- Yukiko Hara-Kudo
- Division of Microbiology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya, Tokyo 158-8501, Japan.
| | - Noriko Konishi
- Tokyo Metropolitan Institute of Public Health, 3-24-1, Hyakunin-cho, Shinjuku, Tokyo 169-0073, Japan
| | - Kayoko Ohtsuka
- Saitama Institute of Public Health, 410-1, Ewai, Yoshimi-machi, Hiki-gun, Saitama 355-0133, Japan
| | - Kaori Iwabuchi
- Research Institute for Environmental Sciences and Public Health of Iwate Prefecture, 1-11-16, Kitaiioka, Morioka 020-0857, Japan
| | - Rie Kikuchi
- Fukushima Institute for Public Health, 16-6, Mitouchi, Houkida, Fukushima 960-8560, Japan
| | - Junko Isobe
- Toyama Institute of Health, 17-1, Nakataikouyama, Imizu 939-0363, Japan
| | - Takumiko Yamazaki
- Suginami City Institute of the Public Health, 3-20-3, Takaidohigashi, Suginami, Tokyo 168-0072, Japan
| | - Fumie Suzuki
- Shizuoka City Institute of Environmental Sciences and Public Health, 1-4-7, Oguro, Suruga, Shizuoka 422-8072, Japan
| | - Yuhki Nagai
- Mie Prefecture Health and Environment Research Institute, 3684-11, Sakura-cho, Yokkaichi 512-1211, Japan
| | - Hiroko Yamada
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, 1-6-29, Minami-machi, Minami, Hiroshima 734-0007, Japan
| | - Atsuko Tanouchi
- Hiroshima City Institute of Public Health, 4-1-2, Shoko-Center, Nishi, Hiroshima 733-8650, Japan
| | - Tetsuya Mori
- Institute for Food and Environment Sciences Tokyo Kenbikyo-in Foundation, 4F, 5-1, Toyomi-cho, Chuo, Tokyo 104-0055, Japan
| | - Hiroshi Nakagawa
- BML Food Science Solutions, Inc., 1491, Matoba, Kawagoe 350-1101, Japan
| | - Yasufumi Ueda
- Center of Inspection of Imported Foods and Infectious Diseases, Kobe Quarantine Station, 1-1, Toyahama-cho, Hyogo, Kobe 652-0866, Japan
| | - Jun Terajima
- Division of Microbiology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya, Tokyo 158-8501, Japan
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Souii A, M’hadheb-Gharbi MB, Gharbi J. Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics. Food Sci Biotechnol 2016; 25:11-20. [PMID: 30263230 PMCID: PMC6049363 DOI: 10.1007/s10068-016-0002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/23/2023] Open
Abstract
Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.
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Affiliation(s)
- Amira Souii
- The Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El manar-Tunis, Rommana, 1068 Tunisia
- The Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, 5000 Tunisia
| | | | - Jawhar Gharbi
- The Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, 5000 Tunisia
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Beutin L, Delannoy S, Fach P. Genetic Analysis and Detection of fliC H1 and fliC H12 Genes Coding for Serologically Closely Related Flagellar Antigens in Human and Animal Pathogenic Escherichia coli. Front Microbiol 2016; 7:135. [PMID: 26913025 PMCID: PMC4753304 DOI: 10.3389/fmicb.2016.00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/25/2016] [Indexed: 01/29/2023] Open
Abstract
The E. coli flagellar types H1 and H12 show a high serological cross-reactivity and molecular serotyping appears an advantageous method to establish a clear discrimination between these flagellar types. Analysis of fliCH1 and fliCH12 gene sequences showed that they were 97.5% identical at the nucleotide level. Because of this high degree of homology we developed a two-step real-time PCR detection procedure for reliable discrimination of H1 and H12 flagellar types in E. coli. In the first step, a real-time PCR assay for common detection of both fliCH1 and fliCH12 genes is used, followed in a second step by real-time PCR assays for specific detection of fliCH1 and fliCH12, respectively. The real-time PCR for common detection of fliCH1 and fliCH12 demonstrated 100% sensitivity and specificity as it reacted with all tested E. coli H1 and H12 strains and not with any of the reference strains encoding all the other 51 flagellar antigens. The fliCH1 and fliCH12 gene specific assays detected all E. coli H1 and all E. coli H12 strains, respectively (100% sensitivity). However, both assays showed cross-reactions with some flagellar type reference strains different from H1 and H12. The real-time PCR assays developed in this study can be used in combination for the detection and identification of E. coli H1 and H12 strains isolated from different sources.
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Affiliation(s)
- Lothar Beutin
- Department of Biology, Chemistry, Pharmacy, Institute for Biology - Microbiology, Freie Universität Berlin Berlin, Germany
| | - Sabine Delannoy
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Maisons-Alfort, France
| | - Patrick Fach
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Maisons-Alfort, France
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43
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Abstract
Shiga toxin-producing Escherichia coli (STEC) strains are commonly found in the intestine of ruminant species of wild and domestic animals. Excretion of STEC with animal feces results in a broad contamination of food and the environment. Humans get infected with STEC through ingestion of contaminated food, by contact with the environment, and from STEC-excreting animals and humans. STEC strains can behave as human pathogens, and some of them, called enterohemorrhagic E. coli (EHEC), may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS). Because of the diversity of STEC types, detection strategies for STEC and EHEC are based on the identification of Shiga toxins or the underlying genes. Cultural enrichment of STEC from test samples is needed for identification, and different protocols were developed for this purpose. Multiplex real-time PCR protocols (ISO/CEN TS13136 and USDA/FSIS MLG5B.01) have been developed to specifically identify EHEC by targeting the LEE (locus of enterocyte effacement)-encoded eae gene and genes for EHEC-associated O groups. The employment of more genetic markers (nle and CRISPR) is a future challenge for better identification of EHEC from any kinds of samples. The isolation of STEC or EHEC from a sample is required for confirmation, and different cultivation protocols and media for this purpose have been developed. Most STEC strains present in food, animals, and the environment are eae negative, but some of these strains can cause HC and HUS in humans as well. Phenotypic assays and molecular tools for typing EHEC and STEC strains are used to detect and characterize human pathogenic strains among members of the STEC group.
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Shridhar PB, Noll LW, Shi X, An B, Cernicchiaro N, Renter DG, Nagaraja TG, Bai J. Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces. J Food Prot 2016; 79:66-74. [PMID: 26735031 DOI: 10.4315/0362-028x.jfp-15-319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture-spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P > 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.
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Affiliation(s)
- P B Shridhar
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - L W Noll
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - X Shi
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - B An
- Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas 66506, USA
| | - N Cernicchiaro
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - D G Renter
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA.
| | - J Bai
- Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas 66506, USA.
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45
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Harada T, Iguchi A, Iyoda S, Seto K, Taguchi M, Kumeda Y. Multiplex Real-Time PCR Assays for Screening of Shiga Toxin 1 and 2 Genes, Including All Known Subtypes, and Escherichia coli O26-, O111-, and O157-Specific Genes in Beef and Sprout Enrichment Cultures. J Food Prot 2015; 78:1800-11. [PMID: 26408128 DOI: 10.4315/0362-028x.jfp-15-050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shiga toxin family members have recently been classified using a new nomenclature into three Stx1 subtypes (Stx1a, Stx1c, and Stx1d) and seven Stx2 subtypes (Stx2a, Stx2b, Stx2c, Stx2d, Stx2e, Stx2f, and Stx2g). To develop screening methods for Stx genes, including all of these subtype genes, and Escherichia coli O26-, O111-, and O157-specific genes in laboratory investigations of Shiga toxin-producing E. coli (STEC) foodborne cases, we developed multiplex real-time PCR assays and evaluated their specificity and quantitative accuracy using STEC and non-STEC isolates, recombinant plasmids, and food enrichment cultures and by performing STEC spiking experiments with beef and sprout enrichment cultures. In addition, we evaluated the relationship between the recovery rates of the target strains by direct plating and immunomagnetic separation and the cycle threshold (CT) values of the real-time PCR assays for the Stx subtypes and STEC O26, O111, and O157 serogroups. All three stx1- and seven stx2-subtype genes were detected by real-time PCR with high sensitivity and specificity, and the quantitative accuracy of this assay was confirmed using control plasmids and STEC spiking experiments. The results of the STEC spiking experiments suggest that it is not routinely possible to isolate STEC from enrichment cultures with real-time PCR CT values greater than 30 by direct plating on MacConkey agar, although highly selective media and immunomagnetic beads were able to isolate the inoculated strains from the enrichment cultures. These data suggest that CT values obtained from the highly quantitative real-time PCR assays developed in this study provide useful information to develop effective isolation strategies for STEC from food samples. The real-time PCR assays developed here are expected to aid in investigations of infections or outbreaks caused by STEC harboring any of the stx-subtype genes in the new Stx nomenclature, as well as STEC O26, O111, and O157.
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Affiliation(s)
- Tetsuya Harada
- Division of Bacteriology, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan.
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kazuko Seto
- Division of Bacteriology, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Masumi Taguchi
- Division of Bacteriology, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Yuko Kumeda
- Division of Bacteriology, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
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Singh P, Mustapha A. Multiplex real-time PCR assays for detection of eight Shiga toxin-producing Escherichia coli in food samples by melting curve analysis. Int J Food Microbiol 2015; 215:101-8. [PMID: 26355415 DOI: 10.1016/j.ijfoodmicro.2015.08.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 11/18/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are pathogenic strains of E. coli that can cause bloody diarrhea and kidney failure. Seven STEC serogroups, O157, O26, O45, O103, O111, O121 and O145 are responsible for more than 71% of the total infections caused by this group of pathogens. All seven serogroups are currently considered as adulterants in non-intact beef products in the U.S. In this study, two multiplex melt curve real-time PCR assays with internal amplification controls (IACs) were standardized for the detection of eight STEC serogroups. The first multiplex assay targeted E. coli serogroups O145, O121, O104, and O157; while the second set detected E. coli serogroups O26, O45, O103 and O111. The applicability of the assays was tested using 11 different meat and produce samples. For food samples spiked with a cocktail of four STEC serogroups with a combined count of 10 CFU/25 g food, all targets of the multiplex assays were detected after an enrichment period of 6h. The assays also worked efficiently when 325 g of food samples were spiked with 10 CFU of STECs. The assays are not dependent on fluorescent-labeled probes or immunomagnetic beads, and can be used for the detection of eight STEC serogroups in less than 11h. Routine preliminary screening of STECs in food samples is performed by testing for the presence of STEC virulence genes. The assays developed in this study can be useful as a first- or second-tier test for the identification of the eight O serogroup-specific genes in suspected food samples.
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Affiliation(s)
- Prashant Singh
- Food Science Program, University of Missouri, Columbia, USA
| | - Azlin Mustapha
- Food Science Program, University of Missouri, Columbia, USA.
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47
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Noll LW, Shridhar PB, Dewsbury DM, Shi X, Cernicchiaro N, Renter DG, Nagaraja TG. A Comparison of Culture- and PCR-Based Methods to Detect Six Major Non-O157 Serogroups of Shiga Toxin-Producing Escherichia coli in Cattle Feces. PLoS One 2015; 10:e0135446. [PMID: 26270482 PMCID: PMC4536017 DOI: 10.1371/journal.pone.0135446] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 07/23/2015] [Indexed: 11/20/2022] Open
Abstract
Culture-based methods to detect the six major non-O157 (O26, O45, O103, O111, O121 and O145) Shiga toxin-producing E. coli (STEC) are not well established. Our objectives of this study were to develop a culture-based method to detect the six non-O157 serogroups in cattle feces and compare the detection with a PCR method. Fecal samples (n = 576) were collected in a feedlot from 24 pens during a 12-week period and enriched in E. coli broth at 40° C for 6 h. Enriched samples were subjected to immunomagnetic separation, spread-plated onto a selective chromogenic medium, and initially pooled colonies, and subsequently, single colonies were tested by a multiplex PCR targeting six serogroups and four virulence genes, stx1, stx2, eae, and ehxA (culture method). Fecal suspensions, before and after enrichment, were also tested by a multiplex PCR targeting six serogroups and four virulence genes (PCR method). There was no difference in the proportions of fecal samples that tested positive (74.3 vs. 77.4%) for one or more of the six serogroups by either culture or the PCR method. However, each method detected one or more of the six serogroups in samples that were negative by the other method. Both culture method and PCR indicated that O26, O45, and O103 were the dominant serogroups. Higher proportions (P < 0.05) of fecal samples were positive for O26 (44.4 vs. 22.7%) and O121 (22.9 vs. 2.3%) serogroups by PCR than by the culture method. None of the fecal samples contained more than four serogroups. Only a small proportion of the six serogroups (23/640; 3.6%) isolated carried Shiga toxin genes. The culture method and the PCR method detected all six serogroups in samples negative by the other method, highlighting the importance of subjecting fecal samples to both methods for accurate detection of the six non-O157 STEC in cattle feces.
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Affiliation(s)
- Lance W. Noll
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Pragathi B. Shridhar
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Diana M. Dewsbury
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Xiaorong Shi
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Natalia Cernicchiaro
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - David G. Renter
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - T. G. Nagaraja
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
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48
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Automatic Counting and Classification of Bacterial Colonies Using Hyperspectral Imaging. FOOD BIOPROCESS TECH 2015. [DOI: 10.1007/s11947-015-1555-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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49
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Beutin L, Delannoy S, Fach P. Sequence Variations in the Flagellar Antigen Genes fliCH25 and fliCH28 of Escherichia coli and Their Use in Identification and Characterization of Enterohemorrhagic E. coli (EHEC) O145:H25 and O145:H28. PLoS One 2015; 10:e0126749. [PMID: 26000885 PMCID: PMC4441469 DOI: 10.1371/journal.pone.0126749] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/07/2015] [Indexed: 11/19/2022] Open
Abstract
Enterohemorrhagic E. coli (EHEC) serogroup O145 is regarded as one of the major EHEC serogroups involved in severe infections in humans. EHEC O145 encompasses motile and non-motile strains of serotypes O145:H25 and O145:H28. Sequencing the fliC-genes associated with the flagellar antigens H25 and H28 revealed the genetic diversity of the fliCH25 and fliCH28 gene sequences in E. coli. Based on allele discrimination of these fliC-genes real-time PCR tests were designed for identification of EHEC O145:H25 and O145:H28. The fliCH25 genes present in O145:H25 were found to be very similar to those present in E. coli serogroups O2, O100, O165, O172 and O177 pointing to their common evolution but were different from fliCH25 genes of a multiple number of other E. coli serotypes. In a similar way, EHEC O145:H28 harbor a characteristic fliCH28 allele which, apart from EHEC O145:H28, was only found in enteropathogenic (EPEC) O28:H28 strains that shared some common traits with EHEC O145:H28. The real time PCR-assays targeting these fliCH25[O145] and fliCH28[O145] alleles allow better characterization of EHEC O145:H25 and EHEC O145:H28. Evaluation of these PCR assays in spiked ready-to eat salad samples resulted in specific detection of both types of EHEC O145 strains even when low spiking levels of 1-10 cfu/g were used. Furthermore these PCR assays allowed identification of non-motile E. coli strains which are serologically not typable for their H-antigens. The combined use of O-antigen genotyping (O145wzy) and detection of the respective fliCH25[O145] and fliCH28[O145] allele types contributes to improve identification and molecular serotyping of E. coli O145 isolates.
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Affiliation(s)
- Lothar Beutin
- National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277, Berlin, Germany
| | - Sabine Delannoy
- Université Paris-Est, Anses (French Agency for Food, Environmental and Occupational Health and Safety), Food Safety Laboratory, IdentyPath platform, 14 rue Pierre et Marie Curie, Fr-94700, Maisons-Alfort, France
| | - Patrick Fach
- Université Paris-Est, Anses (French Agency for Food, Environmental and Occupational Health and Safety), Food Safety Laboratory, IdentyPath platform, 14 rue Pierre et Marie Curie, Fr-94700, Maisons-Alfort, France
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50
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Paoli GC, Wijey C, Uhlich GA. Genetically Marked Strains of Shiga Toxin-Producing O157:H7 and Non-O157 Escherichia coli: Tools for Detection and Modeling. J Food Prot 2015; 78:888-901. [PMID: 25951382 DOI: 10.4315/0362-028x.jfp-14-472] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shiga toxin-producing E. coli (STEC) is an important group of foodborne pathogens in the United States and worldwide. Nearly half of STEC-induced diarrheal disease in the United States is caused by serotype O157:H7, while non-O157 STEC account for the remaining illnesses. Thus, the U.S. Department of Agriculture (USDA) Food Safety and Inspection Service has instituted regulatory testing of beef products and has a zero-tolerance policy for regulatory samples that test positive for STEC O157:H7 and six other non-O157 STEC (serogroups O26, O45, O103, O111, O121, and O145). In this study, positive control (PC) strains for the detection of STEC O157:H7 and the six USDA-regulated non-O157 STEC were constructed. To ensure that the food testing samples are not cross-contaminated by the PC sample, it is important that the STEC-PC strains are distinguishable from STEC isolated from test samples. The PC strains were constructed by integrating a unique DNA target sequence and a gene for spectinomycin (Sp) resistance into the chromosomes of the seven STEC strains. End-point and real-time PCR assays were developed for the specific detection of the PC strains and were tested using 93 strains of E. coli (38 STEC O157:H7, at least 6 strains of each of the USDA-regulated non-O157 STEC, and 2 commensal E. coli) and 51 strains of other bacteria (30 species from 20 genera). The PCR assays demonstrated high specificity for the unique target sequence. The target sequence was detectable by PCR after 10 culture passages (∼100 generations), demonstrating the stability of the integrated target sequence. In addition, the strains were tested for their potential use in modeling the growth of STEC. Plating the PC strains mixed with ground beef flora on modified rainbow agar containing Sp eliminated the growth of the background flora that grew on modified rainbow agar without Sp. Thus, these strains could be used to enumerate and model the growth of STEC in the presence of foodborne background flora.
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Affiliation(s)
- George C Paoli
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA.
| | - Chandi Wijey
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
| | - Gaylen A Uhlich
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
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