1
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Dutta B, Lahiri D, Nag M, Abukhader R, Sarkar T, Pati S, Upadhye V, Pandit S, Amin MFM, Al Tawaha ARMS, Kumar M, Ray RR. Multi-Omics Approach in Amelioration of Food Products. Front Microbiol 2022; 13:955683. [PMID: 35903478 PMCID: PMC9315205 DOI: 10.3389/fmicb.2022.955683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Determination of the quality of food products is an essential key factor needed for safe-guarding the quality of food for the interest of the consumers, along with the nutritional and sensory improvements that are necessary for delivering better quality products. Bacteriocins are a group of ribosomally synthesized antimicrobial peptides that help in maintaining the quality of food. The implementation of multi-omics approach has been important for the overall enhancement of the quality of the food. This review uses various recent technologies like proteomics, transcriptomics, and metabolomics for the overall enhancement of the quality of food products. The matrix associated with the food products requires the use of sophisticated technologies that help in the extraction of a large amount of information necessary for the amelioration of the food products. This review would provide a wholesome view of how various recent technologies can be used for improving the quality food products and for enhancing their shelf-life.
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Affiliation(s)
- Bandita Dutta
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Dibyajit Lahiri
- Department of Biotechnology, University of Engineering & Management, Kolkata, India
| | - Moupriya Nag
- Department of Biotechnology, University of Engineering & Management, Kolkata, India
| | - Rose Abukhader
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
- *Correspondence: Rose Abukhader,
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, India
- Tanmay Sarkar,
| | - Siddhartha Pati
- NatNov Bioscience Private Limited, Balasore, India
- Skills Innovation & Academic Network (SIAN) Institute, Association for Biodiversity Conservation & Research (ABC), Balasore, India
| | - Vijay Upadhye
- Center of Research for Development (CR4D), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, India
| | - Soumya Pandit
- Department of Life Sciences, Sharda University, Noida, India
| | | | | | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, India
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India
- Rina Rani Ray,
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2
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Microbial risk assessment of Escherichia coli shiga-toxin producers (STEC) in raw sheep's milk cheeses in Italy. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Tao D, Zhang D, Hu R, Rundensteiner E, Feng H. Crowdsourcing and machine learning approaches for extracting entities indicating potential foodborne outbreaks from social media. Sci Rep 2021; 11:21678. [PMID: 34737325 PMCID: PMC8568976 DOI: 10.1038/s41598-021-00766-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Foodborne outbreaks are a serious but preventable threat to public health that often lead to illness, loss of life, significant economic loss, and the erosion of consumer confidence. Understanding how consumers respond when interacting with foods, as well as extracting information from posts on social media may provide new means of reducing the risks and curtailing the outbreaks. In recent years, Twitter has been employed as a new tool for identifying unreported foodborne illnesses. However, there is a huge gap between the identification of sporadic illnesses and the early detection of a potential outbreak. In this work, the dual-task BERTweet model was developed to identify unreported foodborne illnesses and extract foodborne-illness-related entities from Twitter. Unlike previous methods, our model leveraged the mutually beneficial relationships between the two tasks. The results showed that the F1-score of relevance prediction was 0.87, and the F1-score of entity extraction was 0.61. Key elements such as time, location, and food detected from sentences indicating foodborne illnesses were used to analyze potential foodborne outbreaks in massive historical tweets. A case study on tweets indicating foodborne illnesses showed that the discovered trend is consistent with the true outbreaks that occurred during the same period.
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Affiliation(s)
- Dandan Tao
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, 382F Agricultural Engineering Sciences Building, 1304 W. Pennsylvania Ave., Urbana, IL, 61801, USA
| | - Dongyu Zhang
- Data Science Program, Worcester Polytechnic Institute, Fuller Labs 135, 100 Institute Road, Worcester, MA, 01609, USA
| | - Ruofan Hu
- Data Science Program, Worcester Polytechnic Institute, Fuller Labs 135, 100 Institute Road, Worcester, MA, 01609, USA
| | - Elke Rundensteiner
- Data Science Program, Worcester Polytechnic Institute, Fuller Labs 135, 100 Institute Road, Worcester, MA, 01609, USA.
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, USA.
| | - Hao Feng
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, 382F Agricultural Engineering Sciences Building, 1304 W. Pennsylvania Ave., Urbana, IL, 61801, USA.
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4
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Hajia M, Sohrabi A. In silico characteristics for re-emerging possibility of Vibrio cholerae genotypes in Iran. New Microbes New Infect 2019; 31:100577. [PMID: 31360526 PMCID: PMC6637262 DOI: 10.1016/j.nmni.2019.100577] [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: 11/14/2018] [Revised: 05/07/2019] [Accepted: 06/07/2019] [Indexed: 11/29/2022] Open
Abstract
Epidemic cholera has been registered several times within recent years in Iran. The dominant genotype was Ogawa until 2011, but this gradually changed to Inaba. However, in 2015, the re-appearance of a previous Ogawa genotype was detected by the Iranian CDC. This raised worries because no evidence was found for its origin abroad. The aim of the present study was to identify clearly the source of this outbreak. Pulsed field gel electrophoresis (PFGE) was used to compare the recently detected Vibrio cholerae strains with those isolated from 2011 to 2015. We selected one strain per PFGE pattern, and compared the distinct patterns. BioNumerics software was applied, which enables interpretation of phenotypic and genotypic differences. In total, we studied 33 V. cholerae Ogawa strains. Analysis showed that strains could be discriminated on the basis of annual clusters but with a similarity of more than 80%. The highest homology was observed among those isolated each year from 2011 to 2014. In contrast, strains isolated in 2015 also exhibited close correlation with each other but were located in distinct clusters. The analysis also proved genetic variations among some strains. All 2015 strains showed differences with regard to previous genotypes despite some similarities. The new genotypes were probably imported into Iran from neighbouring countries such as Iraq by travellers or contaminated food sources since 2015. However, more investigations are required to identify the exact source of the 2015 outbreak.
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Affiliation(s)
- M Hajia
- Department of Molecular Biology, Research Center of Health Reference Laboratory, Ministry of Health and Medical Education, Tehran, Iran
| | - Amir Sohrabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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5
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Marus JR, Magee MJ, Manikonda K, Nichols MC. Outbreaks of Salmonella enterica infections linked to animal contact: Demographic and outbreak characteristics and comparison to foodborne outbreaks-United States, 2009-2014. Zoonoses Public Health 2019; 66:370-376. [PMID: 30821071 DOI: 10.1111/zph.12569] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/28/2018] [Accepted: 01/20/2019] [Indexed: 11/29/2022]
Abstract
In the United States, multistate Salmonella outbreaks are most commonly linked to a food source; however, contact with live animals can also result in outbreaks of human illness. To characterize Salmonella outbreaks linked to animal contact and examine differences compared to foodborne outbreaks, we analysed data reported to the Centers for Disease Control and Prevention through the National Outbreak Reporting System (NORS) from 2009 to 2014 with a primary mode of transmission listed as "animal contact" or "food." Four hundred and eighty-four outbreaks with animal contact or foodborne transmission were reported through NORS; of these outbreaks, 99 (20.5%) resulted from Salmonella transmission through animal contact and 385 (79.5%) resulted from foodborne transmission, which resulted in 3,604 (19.8%) and 13,568 (80.2%) illnesses, respectively. A higher proportion of illnesses among children aged <1 year and children aged 1-4 years were linked to animal contact outbreaks compared to foodborne outbreaks (15.2% vs. 1.4%, p < 0.01 and 24.5% vs. 5.6%, p < 0.01, respectively). Illnesses resulting in hospitalizations (OR: 1.81, 95% CI: 1.62, 2.02) were more likely to be associated with animal contact compared to food. Animal contact outbreaks reported to NORS were more likely to be multistate compared to foodborne outbreaks (OR: 5.43, 95% CI: 3.37, 8.76) and had a longer median duration (99.0 days vs. 9.0 days, p < 0.01). Characterizing the differences between outbreaks of illness linked to animal contact and outbreaks linked to food provides useful information to investigators to improve public health response.
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Affiliation(s)
- Jessica Rae Marus
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Matthew James Magee
- Division of Epidemiology and Biostatistics, School of Public Health, Georgia State University, Atlanta, Georgia
| | - Karunya Manikonda
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Megin C Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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6
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Hajia M. Barriers of molecular epidemiology in Iran:Action plan and necessary steps. CASPIAN JOURNAL OF INTERNAL MEDICINE 2019; 10:356-358. [PMID: 31559002 PMCID: PMC6729163 DOI: 10.22088/cjim.10.3.356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/03/2019] [Accepted: 02/10/2019] [Indexed: 11/01/2022]
Affiliation(s)
- Massoud Hajia
- Department of Molecular biology, Research center of Health Reference Laboratories, Ministry of Health and Medical Education, Tehran, Iran
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7
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Weinroth MD, Britton BC, Belk KE. Genetics and microbiology of meat. Meat Sci 2018; 144:15-21. [DOI: 10.1016/j.meatsci.2018.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
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8
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Treatment of Enteropathogenic Escherichia coli Diarrhea in Cancer Patients: A Series of Three Cases. Case Rep Infect Dis 2018; 2018:8438701. [PMID: 29850308 PMCID: PMC5933037 DOI: 10.1155/2018/8438701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/03/2018] [Indexed: 11/25/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a common cause of watery diarrhea in children in the developing world and an infrequent cause of significant diarrhea in adult patients. EPEC diarrhea, while not commonly seen in cancer patients, can cause significant distress to patients, and antimicrobial choice for this condition in this patient population is not clearly delineated in the literature. We report 3 cases of EPEC diarrhea in cancer patients and discuss the use of azithromycin for successful treatment of these patients. Positive outcomes were seen while using azithromycin in our first two patients and ciprofloxacin in our third patient.
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9
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Li W, Wu S, Fu P, Liu J, Han H, Bai L, Pei X, Li N, Liu X, Guo Y. National molecular tracing network for foodborne disease surveillance in China. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.12.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Shane AL, Mody RK, Crump JA, Tarr PI, Steiner TS, Kotloff K, Langley JM, Wanke C, Warren CA, Cheng AC, Cantey J, Pickering LK. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clin Infect Dis 2017; 65:e45-e80. [PMID: 29053792 PMCID: PMC5850553 DOI: 10.1093/cid/cix669] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 12/11/2022] Open
Abstract
These guidelines are intended for use by healthcare professionals who care for children and adults with suspected or confirmed infectious diarrhea. They are not intended to replace physician judgement regarding specific patients or clinical or public health situations. This document does not provide detailed recommendations on infection prevention and control aspects related to infectious diarrhea.
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Affiliation(s)
- Andi L Shane
- Division of Infectious Diseases, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - Rajal K Mody
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John A Crump
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina; Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Theodore S Steiner
- Nutrition, Washington University in St. Louis School of Medicine, St. Louis, MO; 5Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Karen Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, and the Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD
| | | | - Christine Wanke
- Division of Nutrition and Infection, Tufts University, Boston, Massachusetts,Cirle Alcantara Warren, MD
| | - Cirle Alcantara Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Joseph Cantey
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Larry K Pickering
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, Georgia
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11
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Zolfaghari Emameh R, Purmonen S, Sukura A, Parkkila S. Surveillance and diagnosis of zoonotic foodborne parasites. Food Sci Nutr 2017; 6:3-17. [PMID: 29387356 PMCID: PMC5778216 DOI: 10.1002/fsn3.530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 12/16/2022] Open
Abstract
Foodborne parasites are a source of human parasitic infection. Zoonotic infections of humans arise from a variety of domestic and wild animals, including sheep, goats, cattle, camels, horses, pigs, boars, bears, felines, canids, amphibians, reptiles, poultry, and aquatic animals such as fishes and shrimp. Therefore, the implementation of efficient, accessible, and controllable inspection policies for livestock, fisheries, slaughterhouses, and meat processing and packaging companies is highly recommended. In addition, more attention should be paid to the education of auditors from the quality control (QC) and assurance sectors, livestock breeders, the fishery sector, and meat inspection veterinarians in developing countries with high incidence of zoonotic parasitic infections. Furthermore, both the diagnosis of zoonotic parasitic infections by inexpensive, accessible, and reliable identification methods and the organization of effective control systems with sufficient supervision of product quality are other areas to which more attention should be paid. In this review, we present some examples of successful inspection policies and recent updates on present conventional, serologic, and molecular diagnostic methods for zoonotic foodborne parasites from both human infection and animal‐derived foods.
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Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology Division of Industrial & Environmental Biotechnology National Institute of Genetic Engineering and Biotechnology (NIGEB) Tehran Iran
| | - Sami Purmonen
- Faculty of Medicine and Life Sciences University of Tampere Tampere Finland
| | - Antti Sukura
- Department of Veterinary Biosciences Faculty of Veterinary Medicine University of Helsinki Helsinki Finland
| | - Seppo Parkkila
- Faculty of Medicine and Life Sciences University of Tampere Tampere Finland.,Fimlab Laboratories Ltd and Tampere University Hospital Tampere Finland
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12
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Priyanka B, Patil RK, Dwarakanath S. A review on detection methods used for foodborne pathogens. Indian J Med Res 2017; 144:327-338. [PMID: 28139531 PMCID: PMC5320838 DOI: 10.4103/0971-5916.198677] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Foodborne pathogens have been a cause of a large number of diseases worldwide and more so in developing countries. This has a major economic impact. It is important to contain them, and to do so, early detection is very crucial. Detection and diagnostics relied on culture-based methods to begin with and have developed in the recent past parallel to the developments towards immunological methods such as enzyme-linked immunosorbent assays (ELISA) and molecular biology-based methods such as polymerase chain reaction (PCR). The aim has always been to find a rapid, sensitive, specific and cost-effective method. Ranging from culturing of microbes to the futuristic biosensor technology, the methods have had this common goal. This review summarizes the recent trends and brings together methods that have been developed over the years.
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Affiliation(s)
- B Priyanka
- Department of Applied Zoology, Mangalore University, Mangaluru, India
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13
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Taboada EN, Graham MR, Carriço JA, Van Domselaar G. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol 2017; 8:909. [PMID: 28588568 PMCID: PMC5440521 DOI: 10.3389/fmicb.2017.00909] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/04/2017] [Indexed: 11/24/2022] Open
Abstract
Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.
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Affiliation(s)
- Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Biological Sciences, University of Lethbridge, LethbridgeAB, Canada
| | - Morag R Graham
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
| | - João A Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
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14
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Jones TF, Sashti N, Ingram A, Phan Q, Booth H, Rounds J, Nicholson CS, Cosgrove S, Crocker K, Gould LH. Characteristics of Clusters of Salmonella and Escherichia coli O157 Detected by Pulsed-Field Gel Electrophoresis that Predict Identification of Outbreaks. Foodborne Pathog Dis 2016; 13:674-678. [DOI: 10.1089/fpd.2016.2171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Nupur Sashti
- Tennessee Department of Health, Nashville, Tennessee
| | - Amanda Ingram
- Tennessee Department of Health, Nashville, Tennessee
| | - Quyen Phan
- Connecticut Department of Public Health, Hartford, Connecticut
| | | | | | | | - Shaun Cosgrove
- Colorado Department of Public Health and Environment, Denver, Colorado
| | - Kia Crocker
- Maryland Department of Health and Mental Hygiene, Baltimore, Maryland
| | - L. Hannah Gould
- Centers for Disease Control and Prevention, Atlanta, Georgia
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15
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Wang S, Weller D, Falardeau J, Strawn LK, Mardones FO, Adell AD, Moreno Switt AI. Food safety trends: From globalization of whole genome sequencing to application of new tools to prevent foodborne diseases. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Abstract
Foodborne diseases represent a significant public health burden to the United States, considering that they cause illness in 1 in 6 people annually, which amounts to ∼48 million people (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson, S. L. Roy, J. L. Jones, and P. M. Griffin, Emerg Infect Dis 17:7-15, 2011). The average national cost of illness associated with 30 foodborne pathogens is estimated to be $55.5 to $93.2 billion based on two cost-of-illness models (R.L. Scharff, J Food Prot 78:1064-1071, 2015). Predominately, foodborne illnesses are the result of accidental contamination or unintentional mishandling of food materials during the farm-to-table continuum. Nevertheless, principles and methodologies derived from microbial forensics are applied in foodborne outbreaks investigation to determine the source of the pathogen. Drawing from multiple real-life examples and case studies, this review discusses how the current food industry practice, demography, and consumer preference are shaping the landscape of food safety. The approaches to source tracking, or traceback, are described, with a focus on bacterial pathogens associated with food-producing animals. Current challenges and opportunities in microbial forensics in food safety are also addressed.
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17
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Yeni F, Acar S, Soyer Y, Alpas H. How can we improve foodborne disease surveillance systems: A comparison through EU and US systems. FOOD REVIEWS INTERNATIONAL 2016. [DOI: 10.1080/87559129.2016.1175018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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The Impact of Molecular Diagnostics on Surveillance of Foodborne Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Affiliation(s)
- Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC , Changping District, Beijing 102206, China
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20
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Abstract
BACKGROUND Antibiotic resistance continues to rise due to the increased number of antibiotic prescriptions and is now a major threat to public health. In particular, there is an increase in antibiotic resistance to Escherichia coli according to the latest reports. TRIAL DESIGN This article examines, retrospectively, antibiotic resistance in patients with community- and nosocomial-acquired pneumonia caused by E coli. METHODS The data of all patients with community- and nosocomial-acquired pneumonia caused by E coli were collected from the hospital charts at the HELIOS Clinic, Witten/Herdecke University, Wuppertal, Germany, within the study period 2004 to 2014. An antibiogram was performed for the study patients with pneumonia caused by E coli. Antimicrobial susceptibility testing was performed for the different antibiotics that have been consistently used in the treatment of patients with pneumonia caused by E coli. All demographic, clinical, and laboratory data of all of the patients with pneumonia caused by E coli were collected from the patients' records. RESULTS During the study period of January 1, 2004 to August 12, 2014, 135 patients were identified with community- and nosocomial-acquired pneumonia affected by E coli. These patients had a mean age of 72.5 ± 11.6 (92 [68.1%, 95% CI 60.2%-76.0%] males and 43 [31.9%, 95% CI 24.0%-39.8%] females). E coli had a high resistance rate to ampicillin (60.7%), piperacillin (56.3%), ampicillin-sulbactam (44.4%), and co-trimoxazole (25.9%). No patients with pneumonia caused by E coli showed resistance to imipenem (P < 0.0001). CONCLUSION E coli was resistant to many of the typically used antibiotics. No resistance was detected toward imipenem in patients with pneumonia caused by E coli.
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Affiliation(s)
- Josef Yayan
- From the Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, HELIOS Clinic Wuppertal, Witten/Herdecke University, Wuppertal (JY, KR); Institute for Medical Laboratory Diagnostics, Center for Clinical and Translational Research Wuppertal, Witten/Herdecke University, Witten (BG), Germany
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21
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Resilient information networks for coordination of foodborne disease outbreaks. Disaster Med Public Health Prep 2015; 9:186-98. [PMID: 25882125 DOI: 10.1017/dmp.2014.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Foodborne disease outbreaks are increasingly being seen as a greater concern by public health authorities. It has also become a global research agenda to identify improved pathways to coordinating outbreak detection. Furthermore, a significant need exists for timely coordination of the detection of potential foodborne disease outbreaks to reduce the number of infected individuals and the overall impact on public health security. This study aimed to offer an effective approach for coordinating foodborne disease outbreaks. First, we identify current coordination processes, complexities, and challenges. We then explore social media surveillance strategies, usage, and the power of these strategies to influence decision-making. Finally, based on informal (social media) and formal (organizational) surveillance approaches, we propose a hybrid information network model for improving the coordination of outbreak detection.
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22
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Amani J, Mirhosseini SA, Imani Fooladi AA. A review approaches to identify enteric bacterial pathogens. Jundishapur J Microbiol 2015; 8:e17473. [PMID: 25793091 PMCID: PMC4353029 DOI: 10.5812/jjm.17473] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/10/2014] [Accepted: 04/05/2014] [Indexed: 12/15/2022] Open
Abstract
CONTEXT Diarrhea is a common disease across the world. According to WHO, every year about two billion cases of diarrhea are reported in the world. It occurs mainly in the tropical regions and is a main cause of morbidity and mortality, particularly in young children and adults. EVIDENCE ACQUISITION One of the major causes of diarrheal diseases is bacteria; detection of pathogenic bacteria is a global key to the prevention and identification of food-borne diseases and enteric infections (like diarrhea). CONCLUSIONS Therefore, development of rapid diagnostic methods with suitable sensitivity and specificity is very important about this infectious disease. In this review, we will discuss some of the important diagnostic methods.
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Affiliation(s)
- Jafar Amani
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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Osterholm MT, Hedberg CW. Epidemiologic Principles. MANDELL, DOUGLAS, AND BENNETT'S PRINCIPLES AND PRACTICE OF INFECTIOUS DISEASES 2015. [PMCID: PMC7152219 DOI: 10.1016/b978-1-4557-4801-3.00013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Chui L, Li V. Technical and Software Advances in Bacterial Pathogen Typing. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bergholz TM, Moreno Switt AI, Wiedmann M. Omics approaches in food safety: fulfilling the promise? Trends Microbiol 2014; 22:275-81. [PMID: 24572764 DOI: 10.1016/j.tim.2014.01.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/13/2014] [Accepted: 01/22/2014] [Indexed: 12/30/2022]
Abstract
Genomics, transcriptomics, and proteomics are rapidly transforming our approaches to the detection, prevention, and treatment of foodborne pathogens. Microbial genome sequencing in particular has evolved from a research tool into an approach that can be used to characterize foodborne pathogen isolates as part of routine surveillance systems. Genome sequencing efforts will not only improve outbreak detection and source tracking, but will also create large amounts of foodborne pathogen genome sequence data, which will be available for data-mining efforts that could facilitate better source attribution and provide new insights into foodborne pathogen biology and transmission. Although practical uses and application of metagenomics, transcriptomics, and proteomics data and associated tools are less prominent, these tools are also starting to yield practical food safety solutions.
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Affiliation(s)
- Teresa M Bergholz
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | | | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA.
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Outbreak of Salmonella enterica serotype I 4,5,12:i:- infections: the challenges of hypothesis generation and microwave cooking. Epidemiol Infect 2013; 142:1050-60. [PMID: 23916064 DOI: 10.1017/s0950268813001787] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated an outbreak of 396 Salmonella enterica serotype I 4,5,12:i:- infections to determine the source. After 7 weeks of extensive hypothesis-generation interviews, no refined hypothesis was formed. Nevertheless, a case-control study was initiated. Subsequently, an iterative hypothesis-generation approach used by a single interviewing team identified brand A not-ready-to-eat frozen pot pies as a likely vehicle. The case-control study, modified to assess this new hypothesis, along with product testing indicated that the turkey variety of pot pies was responsible. Review of product labels identified inconsistent language regarding preparation, and the cooking instructions included undefined microwave wattage categories. Surveys found that most patients did not follow the product's cooking instructions and did not know their oven's wattage. The manufacturer voluntarily recalled pot pies and improved the product's cooking instructions. This investigation highlights the value of careful hypothesis-generation and the risks posed by frozen not-ready-to-eat microwavable foods.
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Taboada EN, Clark CG, Sproston EL, Carrillo CD. Current methods for molecular typing of Campylobacter species. J Microbiol Methods 2013; 95:24-31. [PMID: 23871858 DOI: 10.1016/j.mimet.2013.07.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 12/11/2022]
Abstract
Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection.
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Affiliation(s)
- Eduardo N Taboada
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, PO Box 640, Township Rd. 9-1, Lethbridge, AB T1J 3Z4, Canada.
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Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification. J Clin Microbiol 2013; 51:2950-8. [PMID: 23824765 PMCID: PMC3754622 DOI: 10.1128/jcm.01010-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Typhi, the causative agent of typhoid fever, is highly clonal and genetically conserved, making isolate subtyping difficult. We describe a standardized multiplex ligation-dependent probe amplification (MLPA) genotyping scheme targeting 11 key phylogenetic markers of the S. Typhi genome. The MLPA method demonstrated 90% concordance with single nucleotide polymorphism (SNP) typing, the gold standard for S. Typhi genotyping, and had the ability to identify isolates of the H58 haplotype, which is associated with resistance to multiple antimicrobials. Additionally, the assay permitted the detection of fluoroquinolone resistance-associated mutations in the DNA gyrase-encoding gene gyrA and the topoisomerase gene parC with a sensitivity of 100%. The MLPA methodology is simple and reliable, providing phylogenetically and phenotypically relevant genotyping information. This MLPA scheme offers a more-sensitive and interpretable alternative to the nonphylogenetic subgrouping methodologies that are currently used in reference and research laboratories in areas where typhoid is endemic.
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Frye JG, Jackson CR. Genetic mechanisms of antimicrobial resistance identified in Salmonella enterica, Escherichia coli, and Enteroccocus spp. isolated from U.S. food animals. Front Microbiol 2013; 4:135. [PMID: 23734150 PMCID: PMC3661942 DOI: 10.3389/fmicb.2013.00135] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 05/07/2013] [Indexed: 01/26/2023] Open
Abstract
The prevalence of antimicrobial resistance (AR) in bacteria isolated from U.S. food animals has increased over the last several decades as have concerns of AR foodborne zoonotic human infections. Resistance mechanisms identified in U.S. animal isolates of Salmonella enterica included resistance to aminoglycosides (e.g., alleles of aacC, aadA, aadB, ant, aphA, and StrAB), β-lactams (e.g., blaCMY−2, TEM−1, PSE−1), chloramphenicol (e.g., floR, cmlA, cat1, cat2), folate pathway inhibitors (e.g., alleles of sul and dfr), and tetracycline [e.g., alleles of tet(A), (B), (C), (D), (G), and tetR]. In the U.S., multi-drug resistance (MDR) mechanisms in Salmonella animal isolates were associated with integrons, or mobile genetic elements (MGEs) such as IncA/C plasmids which can be transferred among bacteria. It is thought that AR Salmonella originates in food animals and is transmitted through food to humans. However, some AR Salmonella isolated from humans in the U.S. have different AR elements than those isolated from food animals, suggesting a different etiology for some AR human infections. The AR mechanisms identified in isolates from outside the U.S. are also predominantly different. For example the extended spectrum β-lactamases (ESBLs) are found in human and animal isolates globally; however, in the U.S., ESBLs thus far have only been found in human and not food animal isolates. Commensal bacteria in animals including Escherichia coli and Enterococcus spp. may be reservoirs for AR mechanisms. Many of the AR genes and MGEs found in E. coli isolated from U.S. animals are similar to those found in Salmonella. Enterococcus spp. isolated from animals frequently carry MGEs with AR genes, including resistances to aminoglycosides (e.g., alleles of aac, ant, and aph), macrolides [e.g., erm(A), erm(B), and msrC], and tetracyclines [e.g., tet(K), (L), (M), (O), (S)]. Continuing investigations are required to help understand and mitigate the impact of AR bacteria on human and animal health.
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Affiliation(s)
- Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Agricultural Research Service, U.S. Department of Agriculture Athens, GA, USA
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Li W, Lu S, Cui Z, Cui J, Zhou H, Wang Y, Shao Z, Ye C, Kan B, Xu J. PulseNet China, a model for future laboratory-based bacterial infectious disease surveillance in China. Front Med 2012; 6:366-75. [DOI: 10.1007/s11684-012-0214-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 06/18/2012] [Indexed: 10/27/2022]
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Abstract
According to the Kauffmann-White scheme, 39 pairs of serovars in Salmonella serogroup C2 differ only by the minor antigen O:6(1). We characterized strains from 10 serovars representing five Salmonella serogroup C2 pairs. All strains demonstrated variable expression of O:6(1). These results indicate that these pairs are not distinct serovars.
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So HC, Pearl DL, von Königslöw T, Louie M, Chui L, Svenson LW. Spatio-Temporal Scan Statistics for the Detection of Outbreaks Involving Common Molecular Subtypes: Using Human Cases ofEscherichia coliO157:H7 Provincial PFGE Pattern 8 (National Designation ECXAI.0001) in Alberta as an Example. Zoonoses Public Health 2012; 60:341-8. [DOI: 10.1111/zph.12012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Brengi SP, O'Brien SB, Pichel M, Iversen C, Arduino M, Binsztein N, Jensen B, Pagotto F, Ribot EM, Stephan R, Cernela N, Cooper K, Fanning S. Development and validation of a PulseNet standardized protocol for subtyping isolates of Cronobacter species. Foodborne Pathog Dis 2012; 9:861-7. [PMID: 22891917 DOI: 10.1089/fpd.2012.1161] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cronobacter (formerly known as Enterobacter sakazakii) is a genus comprising seven species regarded as opportunistic pathogens that can be found in a wide variety of environments and foods, including powdered infant formula (PIF). Cronobacter sakazakii, the major species of this genus, has been epidemiologically linked to cases of bacteremia, meningitis in neonates, and necrotizing enterocolitis, and contaminated PIF has been identified as an important source of infection. Robust and reproducible subtyping methods are required to aid in the detection and investigation, of foodborne outbreaks. In this study, a pulsed-field gel electrophoresis (PFGE) protocol was developed and validated for subtyping Cronobacter species. It was derived from an existing modified PulseNet protocol, wherein XbaI and SpeI were the primary and secondary restriction enzymes used, generating an average of 14.7 and 20.3 bands, respectively. The PFGE method developed was both reproducible and discriminatory for subtyping Cronobacter species.
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Affiliation(s)
- Silvina P Brengi
- Servicio Enterobacterias, Departamento Bacteriología, INEI-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
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Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics 2012; 13:88. [PMID: 22409488 PMCID: PMC3359268 DOI: 10.1186/1471-2164-13-88] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 03/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. RESULTS We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes. CONCLUSIONS Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.
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Campos J, Pichel M, Vaz T, Tavechio A, Fernandes S, Muñoz N, Rodriguez C, Realpe M, Moreno J, Araya P, Fernández J, Fernández A, Campos E, Duarte F, Gustafson NW, Binsztein N, Gutierrez EP. Building PulseNet Latin America and Caribbean Salmonella regional database: First conclusions of genetic subtypes of S. Typhi, S. Typhimurium and S. Enteritidis circulating in six countries of the region. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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