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Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. J Food Prot 2022; 85:755-772. [PMID: 35259246 DOI: 10.4315/jfp-21-437] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety. HIGHLIGHTS
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Affiliation(s)
- Eric L Stevens
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Heather A Carleton
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jennifer Beal
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Glenn E Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - A C Lauer
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Arthur Pightling
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Karen G Jarvis
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Andrea Ottesen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Padmini Ramachandran
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Leslie Hintz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Lee S Katz
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jason P Folster
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jean M Whichard
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eija Trees
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Ruth E Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Patrick McDERMOTT
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Beverly Wolpert
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Michael Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Sabina Lindley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Beau B Bruce
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eric Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Sandra Tallent
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Kari Irvin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Maria Hoffmann
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Matt Wise
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Robert Tauxe
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Mustafa Simmons
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Bonnie Kissler
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | | | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - James Lindsay
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Kimberly Cook
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Suelee Robbe Austerman
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, Iowa 50010, USA
| | - David Goldman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Sherri McGARRY
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Kis Robertson Hale
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Steven M Musser
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Chris Braden
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
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2
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Davedow T, Carleton H, Kubota K, Palm D, Schroeder M, Gerner-Smidt P, Al-Jardani A, Chinen I, Kam KM, Smith AM, Nadon C. PulseNet International Survey on the Implementation of Whole Genome Sequencing in Low and Middle-Income Countries for Foodborne Disease Surveillance. Foodborne Pathog Dis 2022; 19:332-340. [PMID: 35325576 PMCID: PMC10863729 DOI: 10.1089/fpd.2021.0110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS. To broaden the routine use of WGS around the world, challenges and barriers must be overcome. We conducted this study to determine the challenges and barriers countries are encountering in their attempts to implement WGS and to identify how PNI can provide support to improve and become a better integrated system overall. A survey was designed with a set of qualitative questions to capture the status, challenges, barriers, and successes of countries in the implementation of WGS and was administered to laboratories in Africa, Asia-Pacific, Latin America and the Caribbean, and Middle East. One-third of respondents do not use WGS, and only 8% reported using WGS for routine, real-time surveillance. The main barriers for implementation of WGS were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation. Features of an ideal system to facilitate implementation and global surveillance were identified as an all-in-one software that is free, accessible, standardized and validated. This survey highlights the minimal use of WGS for foodborne disease surveillance outside the United States, Canada, and Europe to date. Although funding remains a major barrier to WGS-based surveillance, critical gaps in expertise and availability of tools must be overcome. Opportunities to seek sustainable funding, provide training, and identify solutions for a globally standardized surveillance platform will accelerate implementation of WGS worldwide.
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Affiliation(s)
- Taylor Davedow
- Division of Enteric Diseases, Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Heather Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristy Kubota
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Daniel Palm
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Morgan Schroeder
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Amina Al-Jardani
- Central Public Health Laboratories, Ministry of Health, Muscat, Oman
| | - Isabel Chinen
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Kai Man Kam
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anthony M Smith
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Celine Nadon
- Division of Enteric Diseases, Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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3
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Moura A, Lefrancq N, Wirth T, Leclercq A, Borges V, Gilpin B, Dallman TJ, Frey J, Franz E, Nielsen EM, Thomas J, Pightling A, Howden BP, Tarr CL, Gerner-Smidt P, Cauchemez S, Salje H, Brisse S, Lecuit M. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Sci Adv 2021; 7:eabj9805. [PMID: 34851675 PMCID: PMC8635441 DOI: 10.1126/sciadv.abj9805] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering Lm-CC1 first isolation to present days, to define its evolutionary history and population dynamics. We show that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming and food industrialization in the 20th century. In sharp contrast to its global spread over the past century, transmission chains are now mostly local, with limited inter- and intra-country spread. This study provides an unprecedented insight into L. monocytogenes phylogeography and population dynamics and highlights the importance of genome analyses for a better control of pathogen transmission.
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Affiliation(s)
- Alexandra Moura
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Noémie Lefrancq
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Thierry Wirth
- Institut Systématique Evolution Biodiversité (ISYEB),Museum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, Paris, France
- PSL University, EPHE, Paris, France
| | - Alexandre Leclercq
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Vítor Borges
- Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Brent Gilpin
- Christchurch Science Centre, Institute of Environmental Science and Research Limited, Christchurch, New Zealand
| | | | - Joachim Frey
- Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Juno Thomas
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arthur Pightling
- Biostatistics and Bioinformatics, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia
| | - Cheryl L. Tarr
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Simon Cauchemez
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Henrik Salje
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
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4
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Hernandez SM, Maurer JJ, Yabsley MJ, Peters VE, Presotto A, Murray MH, Curry S, Sanchez S, Gerner-Smidt P, Hise K, Huang J, Johnson K, Kwan T, Lipp EK. Free-Living Aquatic Turtles as Sentinels of Salmonella spp. for Water Bodies. Front Vet Sci 2021; 8:674973. [PMID: 34368271 PMCID: PMC8339271 DOI: 10.3389/fvets.2021.674973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Reptile-associated human salmonellosis cases have increased recently in the United States. It is not uncommon to find healthy chelonians shedding Salmonella enterica. The rate and frequency of bacterial shedding are not fully understood, and most studies have focused on captive vs. free-living chelonians and often in relation to an outbreak. Their ecology and significance as sentinels are important to understanding Salmonella transmission. In 2012-2013, Salmonella prevalence was determined for free-living aquatic turtles in man-made ponds in Clarke and Oconee Counties, in northern Georgia (USA) and the correlation between species, basking ecology, demographics (age/sex), season, or landcover with prevalence was assessed. The genetic relatedness between turtle and archived, human isolates, as well as, other archived animal and water isolates reported from this study area was examined. Salmonella was isolated from 45 of 194 turtles (23.2%, range 14-100%) across six species. Prevalence was higher in juveniles (36%) than adults (20%), higher in females (33%) than males (18%), and higher in bottom-dwelling species (31%; common and loggerhead musk turtles, common snapping turtles) than basking species (15%; sliders, painted turtles). Salmonella prevalence decreased as forest cover, canopy cover, and distance from roads increased. Prevalence was also higher in low-density, residential areas that have 20-49% impervious surface. A total of 9 different serovars of two subspecies were isolated including 3 S. enterica subsp. arizonae and 44 S. enterica subsp. enterica (two turtles had two serotypes isolated from each). Among the S. enterica serovars, Montevideo (n = 13) and Rubislaw (n = 11) were predominant. Salmonella serovars Muenchen, Newport, Mississippi, Inverness, Brazil, and Paratyphi B. var L(+) tartrate positive (Java) were also isolated. Importantly, 85% of the turtle isolates matched pulsed-field gel electrophoresis patterns of human isolates, including those reported from Georgia. Collectively, these results suggest that turtles accumulate Salmonella present in water bodies, and they may be effective sentinels of environmental contamination. Ultimately, the Salmonella prevalence rates in wild aquatic turtles, especially those strains shared with humans, highlight a significant public health concern.
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Affiliation(s)
- Sonia M Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - John J Maurer
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Michael J Yabsley
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Valerie E Peters
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, United States
| | - Andrea Presotto
- Department of Geography, University of Georgia, Athens, GA, United States
| | - Maureen H Murray
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Davee Center for Epidemiology and Endocrinology and the Urban Wildlife Institute, Lincoln Park Zoo, Chicago, IL, United States
| | - Shannon Curry
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kelley Hise
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joyce Huang
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Kasey Johnson
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Tiffany Kwan
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Erin K Lipp
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, United States
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5
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Kubota KA, Wolfgang WJ, Baker DJ, Boxrud D, Turner L, Trees E, Carleton HA, Gerner-Smidt P. PulseNet and the Changing Paradigm of Laboratory-Based Surveillance for Foodborne Diseases. Public Health Rep 2020; 134:22S-28S. [PMID: 31682558 PMCID: PMC6832030 DOI: 10.1177/0033354919881650] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PulseNet, the National Molecular Subtyping Network for Foodborne Disease Surveillance, was established in 1996 through a collaboration with the Centers for Disease Control and Prevention; the US Department of Agriculture, Food Safety and Inspection Service; the US Food and Drug Administration; 4 state public health laboratories; and the Association of Public Health Laboratories. The network has since expanded to include 83 state, local, and food regulatory public health laboratories. In 2016, PulseNet was estimated to be helping prevent an estimated 270 000 foodborne illnesses annually. PulseNet is undergoing a transformation toward whole-genome sequencing (WGS), which provides better discriminatory power and precision than pulsed-field gel electrophoresis (PFGE). WGS improves the detection of outbreak clusters and could replace many traditional reference identification and characterization methods. This article highlights the contributions made by public health laboratories in transforming PulseNet's surveillance and describes how the transformation is changing local and national surveillance practices. Our data show that WGS is better at identifying clusters than PFGE, especially for clonal organisms such as Salmonella Enteritidis. The need to develop prioritization schemes for cluster follow-up and additional resources for both public health laboratory and epidemiology departments will be critical as PulseNet implements WGS for foodborne disease surveillance in the United States.
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Affiliation(s)
- Kristy A Kubota
- Association of Public Health Laboratories, Food Safety Program, Silver Spring, MD, USA
| | - William J Wolfgang
- New York State Department of Health, Bacteriology Laboratory, Albany, NY, USA
- Department of Biomedical Sciences, University of Albany, Rensselaer, NY, USA
| | - Deborah J Baker
- New York State Department of Health, Bacteriology Laboratory, Albany, NY, USA
| | - David Boxrud
- Public Health Laboratory Division, Minnesota Department of Health, St. Paul, MN, USA
| | - Lauren Turner
- Virginia Department of General Services, Division of Consolidated Laboratory Services, Richmond, VA, USA
| | - Eija Trees
- Association of Public Health Laboratories, Food Safety Program, Silver Spring, MD, USA
| | - Heather A Carleton
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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6
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Gerner-Smidt P, Besser J, Concepción-Acevedo J, Folster JP, Huffman J, Joseph LA, Kucerova Z, Nichols MC, Schwensohn CA, Tolar B. Corrigendum: Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases. Front Public Health 2019; 7:365. [PMID: 31867301 PMCID: PMC6908885 DOI: 10.3389/fpubh.2019.00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022] Open
Affiliation(s)
- Peter Gerner-Smidt
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - John Besser
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jeniffer Concepción-Acevedo
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jason P Folster
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jasmine Huffman
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lavin A Joseph
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Zuzana Kucerova
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Megin C Nichols
- The Outbreak Response and Prevention Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Colin A Schwensohn
- The Outbreak Response and Prevention Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Beth Tolar
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
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7
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Messens W, Hugas M, Afonso A, Aguilera J, Berendonk TU, Carattoli A, Dhollander S, Gerner-Smidt P, Kriz N, Liebana E, Medlock J, Robinson T, Stella P, Waltner-Toews D, Catchpole M. Advancing biological hazards risk assessment. EFSA J 2019; 17:e170714. [PMID: 32626451 PMCID: PMC7015523 DOI: 10.2903/j.efsa.2019.e170714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
This paper focusses on biological hazards at the global level and considers the challenges to risk assessment (RA) from a One Health perspective. Two topics – vector‐borne diseases (VBD) and antimicrobial resistance (AMR) – are used to illustrate the challenges ahead and to explore the opportunities that new methodologies such as next‐generation sequencing can offer. Globalisation brings complexity and introduces drivers for infectious diseases. Cooperation and the application of an integrated RA approach – one that takes into consideration food farming and production systems including social and environmental factors – are recommended. Also needed are methodologies to identify emerging risks at a global level and propose prevention strategies. AMR is one of the biggest threats to human health in the infectious disease environment. Whereas new genomic typing techniques such as whole genome sequencing (WGS) provide further insights into the mechanisms of spread of resistance, the role of the environment is not fully elucidated, nor is the role of plants as potential vehicles for spread of resistance. Historical trends and recent experience indicate that (re)‐emergence and/or further spread of VBD within the EU is a matter of when rather than if. Standardised and validated vector monitoring programs are required to be implemented at an international level for continuous surveillance and assessment of potential threats. There are benefits to using WGS – such as a quicker and better response to outbreaks and additional evidence for source attribution. However, significant challenges need to be addressed, including method standardisation and validation to fully realise these benefits; barriers to data sharing; and establishing epidemiological capacity for cluster triage and response.
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Affiliation(s)
| | - Marta Hugas
- European Food Safety Authority (EFSA) Parma IT
| | - Ana Afonso
- European Food Safety Authority (EFSA) Parma IT
| | | | | | | | | | | | | | | | | | | | | | | | - Mike Catchpole
- European Centre for Disease Prevention and Control (ECDC) SE
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8
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Besser JM, Carleton HA, Trees E, Stroika SG, Hise K, Wise M, Gerner-Smidt P. Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation. Foodborne Pathog Dis 2019; 16:504-512. [PMID: 31246502 PMCID: PMC6653782 DOI: 10.1089/fpd.2019.2650] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The routine use of whole-genome sequencing (WGS) as part of enteric disease surveillance is substantially enhancing our ability to detect and investigate outbreaks and to monitor disease trends. At the same time, it is revealing as never before the vast complexity of microbial and human interactions that contribute to outbreak ecology. Since WGS analysis is primarily used to characterize and compare microbial genomes with the goal of addressing epidemiological questions, it must be interpreted in an epidemiological context. In this article, we identify common challenges and pitfalls encountered when interpreting sequence data in an enteric disease surveillance and investigation context, and explain how to address them.
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Affiliation(s)
- John M Besser
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
| | - Heather A Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
| | - Eija Trees
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
| | - Steven G Stroika
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
| | - Kelley Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
| | - Matthew Wise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
| | - Peter Gerner-Smidt
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia
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9
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Gerner-Smidt P, Besser J, Concepción-Acevedo J, Folster JP, Huffman J, Joseph LA, Kucerova Z, Nichols MC, Schwensohn CA, Tolar B. Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases. Front Public Health 2019; 7:172. [PMID: 31316960 PMCID: PMC6610495 DOI: 10.3389/fpubh.2019.00172] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/10/2019] [Indexed: 11/13/2022] Open
Abstract
Infections caused by pathogens commonly acquired from consumption of food are not always transmitted by that route. They may also be transmitted through contact to animals, other humans or the environment. Additionally, many outbreaks are associated with food contaminated from these non-food sources. For this reason, such presumed foodborne outbreaks are best investigated through a One Health approach working across human, animal and environmental sectors and disciplines. Outbreak strains or clones that have propagated and continue to evolve in non-human sources and environments often show more sequence variation than observed in typical monoclonal point-source outbreaks. This represents a challenge when using whole genome sequencing (WGS), the new gold standard for molecular surveillance of foodborne pathogens, for outbreak detection and investigation. In this review, using recent examples from outbreaks investigated in the United States (US) some aspects of One Health approaches that have been used successfully to solve such outbreaks are presented. These include using different combinations of flexible WGS based case definition, efficient epidemiological follow-up, traceback, surveillance, and testing of potential food and environmental sources and animal hosts.
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Affiliation(s)
- Peter Gerner-Smidt
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - John Besser
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jeniffer Concepción-Acevedo
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jason P Folster
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jasmine Huffman
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lavin A Joseph
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Zuzana Kucerova
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Megin C Nichols
- The Outbreak Response and Prevention Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Colin A Schwensohn
- The Outbreak Response and Prevention Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Beth Tolar
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
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10
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Abstract
Since 1996, PulseNet has served as the national laboratory-based surveillance system for the rapid detection of outbreaks caused by foodborne bacterial pathogens in the United States. For the past two decades, pulsed-field gel electrophoresis was the gold standard subtyping method for the pathogens tracked by PulseNet. A new gold standard is now being implemented with the introduction of cost-effective whole genome sequencing (WGS) for analysis of all the organisms tracked by PulseNet. This transformation is a major undertaking that touches every functional aspect of PulseNet, including laboratory workflows, data storage, analysis management and data interpretation, and language used to communicate information (sequence profile nomenclature system). The benefits of implementing WGS go beyond improved discrimination and precision of the data; it provides an opportunity to determine strain characteristics typically obtained through resource-intensive traditional methodologies, for example, species identification, serotyping, virulence, and antimicrobial resistance profiling, all of which can be consolidated into a single WGS workflow. Such a strategy represents a major shift in the workflows currently practiced in most public health laboratories, but one that brings opportunities for streamlining surveillance activities for the network as a whole. In this study, we provide a brief summary of PulseNet's evolution the past decade along with a general description of the challenges and opportunities that lie ahead.
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Affiliation(s)
- Efrain M Ribot
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Molly Freeman
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kelley B Hise
- Centers for Disease Control and Prevention, Atlanta, Georgia
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11
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Abstract
Whole-genome sequencing (WGS) is increasingly used by food regulatory and public health agencies in the United States to facilitate the detection, investigation, and control of foodborne bacterial outbreaks, and food regulatory and other activities in support of food safety. WGS has added a level of precision to the surveillance leading to faster and more efficient decision making in the preparedness and response to foodborne infections. In this review, we report the history of WGS technology at the Centers for Disease Control & Prevention (CDC), the Food and Drug Administration (FDA), and the United States Department of Agriculture's Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety. The basic principle of the method, the analysis, and interpretation of the data are explained as is its major strengths and limitations. We also describe the benefits and possibilities of the WGS technology to the food industry throughout the farm-to-fork continuum and the prospects of metagenomic sequencing applied directly to the sample specimen with or without pre-enrichment culture.
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Affiliation(s)
- Eric Brown
- 1 Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland
| | - Uday Dessai
- 2 Office of Public Health Science, Food Safety and Inspection Service, United States Department of Agriculture, Washington, District of Columbia
| | - Sherri McGarry
- 3 Enteric Diseases Laboratory Branch, Centers for Disease Control & Prevention, Atlanta, Georgia
| | - Peter Gerner-Smidt
- 3 Enteric Diseases Laboratory Branch, Centers for Disease Control & Prevention, Atlanta, Georgia
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12
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Carleton HA, Besser J, Williams-Newkirk AJ, Huang A, Trees E, Gerner-Smidt P. Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges. Foodborne Pathog Dis 2019; 16:474-479. [PMID: 31170005 PMCID: PMC6653786 DOI: 10.1089/fpd.2019.2636] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly identify the bacteria causing illness within hours. CIDTs, unlike previous gold standard methods such as bacterial culture, do not produce an isolate that can be subtyped as part of the national molecular subtyping network for foodborne disease surveillance, PulseNet. Without subtype information, cases can no longer be linked using molecular data to identify potentially related cases that are part of an outbreak. In this review, we discuss the public health needs for a molecular subtyping approach directly from patient specimen and highlight different approaches, including amplicon and shotgun metagenomic sequencing.
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Affiliation(s)
- Heather A Carleton
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Besser
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amanda J Williams-Newkirk
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Andrew Huang
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eija Trees
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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13
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Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol 2019; 79:96-115. [PMID: 30621881 PMCID: PMC6492263 DOI: 10.1016/j.fm.2018.11.005] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 01/06/2023]
Abstract
Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.
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Affiliation(s)
- Balamurugan Jagadeesan
- Nestlé Research, Nestec Ltd, Route du Jorat 57, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland.
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, MS-CO-3, 1600 Clifton Road, 30329-4027, Atlanta, USA
| | - Marc W Allard
- US Food and Drug Administration, 5001 Campus Drive, College Park, MD, 02740, USA
| | - Sébastien Leuillet
- Institut Mérieux, Mérieux NutriSciences, 3 route de la Chatterie, 44800, Saint Herblain, France
| | - Anett Winkler
- Cargill Deutschland GmbH, Cerestarstr. 2, 47809, Krefeld, Germany
| | - Yinghua Xiao
- Arla Innovation Center, Agro Food Park 19, 8200, Aarhus, Denmark
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France
| | - Jos Van Der Vossen
- The Netherlands Organisation for Applied Scientific Research, TNO, Utrechtseweg 48, 3704 HE, Zeist, NL, the Netherlands
| | - Silin Tang
- Mars Global Food Safety Center, Yanqi Economic Development Zone, 101407, Beijing, China
| | - Mitsuru Katase
- Fuji Oil Co., Ltd., Sumiyoshi-cho 1, Izumisano Osaka, 598-8540, Japan
| | - Peter McClure
- Mondelēz International, Linden 3, Bournville Lane, B30 2LU, Birmingham, United Kingdom
| | - Bon Kimura
- Tokyo University of Marine Science & Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Lay Ching Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - John Chapman
- Unilever Research & Development, Postbus, 114, 3130 AC, Vlaardingen, the Netherlands
| | - Kathie Grant
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom.
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14
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Abstract
PulseNet USA is the molecular surveillance network for foodborne disease in the United States. The network consists of state and local public health laboratories, as well as food regulatory agencies, that follow PulseNet's standardized protocols to perform pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) and analyze the results using standardized software. The raw sequences are uploaded to the GenomeTrakr or PulseNet bioprojects at the National Center for Biotechnology Information. The PFGE patterns and analyzed sequence data are uploaded in real time with associated demographic data to the PulseNet national databases managed at the Centers for Disease Control and Prevention. The PulseNet databases are organism specific and provide a central storage location for molecular and demographic data related to an isolate. Sequences are compared in the databases, thereby facilitating the rapid detection of clusters of foodborne diseases that may represent widespread outbreaks. WGS genotyping data, for example, antibiotic resistance and virulence profiles, are also uploaded in real time to the PulseNet databases to improve food safety surveillance activities.
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Affiliation(s)
- Beth Tolar
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lavin A Joseph
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Morgan N Schroeder
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Steven Stroika
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Efrain M Ribot
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kelley B Hise
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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15
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Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. ACTA ACUST UNITED AC 2017; 22:30544. [PMID: 28662764 PMCID: PMC5479977 DOI: 10.2807/1560-7917.es.2017.22.23.30544] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/11/2017] [Indexed: 11/21/2022]
Abstract
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.
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Affiliation(s)
- Celine Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Canada.,These authors contributed equally to this work
| | - Ivo Van Walle
- These authors contributed equally to this work.,European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Josefina Campos
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | - Isabel Chinen
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | | | - Brent Gilpin
- Institute of Environmental Science and Research Limited; Christchurch, New Zealand
| | | | - Kai Man Kam
- Chinese University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - Enrique Perez
- Pan American Health Organization/World Health Organization, Washington, DC, United States
| | - Eija Trees
- Centers for Disease Control and Prevention, United States
| | - Kristy Kubota
- Association of Public Health Laboratories, United States
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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- The members of the FWD-NEXT Expert Panel are listed at the end of the article
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16
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Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E. Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect 2017; 24:335-341. [PMID: 29074157 DOI: 10.1016/j.cmi.2017.10.013] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/05/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND With the efficiency and the decreasing cost of next-generation sequencing, the technology is being rapidly introduced into clinical and public health laboratory practice. AIMS The historical background and principles of first-, second- and third-generation sequencing are described, as are the characteristics of the most commonly used sequencing instruments. SOURCES Peer-reviewed literature, white papers and meeting reports. CONTENT AND IMPLICATIONS Next-generation sequencing is a technology that could potentially replace many traditional microbiological workflows, providing clinicians and public health specialists with more actionable information than hitherto achievable. Examples of the clinical and public health uses of the technology are provided. The challenge of comparability of different sequencing platforms is discussed. Finally, the future directions of the technology integrating it with laboratory management and public health surveillance systems, and moving it towards performing sequencing directly from the clinical specimen (metagenomics), could lead to yet another fundamental transformation of clinical diagnostics and public health surveillance.
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Affiliation(s)
- J Besser
- Enteric Diseases Laboratory Branch, Center for Disease Control & Prevention, Atlanta, GA, USA
| | - H A Carleton
- Enteric Diseases Laboratory Branch, Center for Disease Control & Prevention, Atlanta, GA, USA
| | - P Gerner-Smidt
- Enteric Diseases Laboratory Branch, Center for Disease Control & Prevention, Atlanta, GA, USA.
| | - R L Lindsey
- Enteric Diseases Laboratory Branch, Center for Disease Control & Prevention, Atlanta, GA, USA
| | - E Trees
- Enteric Diseases Laboratory Branch, Center for Disease Control & Prevention, Atlanta, GA, USA
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17
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Sharapov UM, Wendel AM, Davis JP, Keene WE, Farrar J, Sodha S, Hyytia-Trees E, Leeper M, Gerner-Smidt P, Griffin PM, Braden C. Multistate Outbreak of Escherichia coli O157:H7 Infections Associated with Consumption of Fresh Spinach: United States, 2006. J Food Prot 2016; 79:2024-2030. [PMID: 28221950 DOI: 10.4315/0362-028x.jfp-15-556] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During September to October, 2006, state and local health departments and the Centers for Disease Control and Prevention investigated a large, multistate outbreak of Escherichia coli O157:H7 infections. Case patients were interviewed regarding specific foods consumed and other possible exposures. E. coli O157:H7 strains isolated from human and food specimens were subtyped using pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analyses (MLVA). Two hundred twenty-five cases (191 confirmed and 34 probable) were identified in 27 states; 116 (56%) case patients were hospitalized, 39 (19%) developed hemolytic uremic syndrome, and 5 (2%) died. Among 176 case patients from whom E. coli O157:H7 with the outbreak genotype (MLVA outbreak strain) was isolated and who provided details regarding spinach exposure, 161 (91%) reported fresh spinach consumption during the 10 days before illness began. Among 116 patients who provided spinach brand information, 106 (91%) consumed bagged brand A. E. coli O157:H7 strains were isolated from 13 bags of brand A spinach collected from patients' homes; isolates from 12 bags had the same MLVA pattern. Comprehensive epidemiologic and laboratory investigations associated this large multistate outbreak of E. coli O157:H7 infections with consumption of fresh bagged spinach. MLVA, as a supplement to pulsed-field gel electrophoresis genotyping of case patient isolates, was important to discern outbreak-related cases. This outbreak resulted in enhanced federal and industry guidance to improve the safety of leafy green vegetables and launched an independent collaborative approach to produce safety research in 2007.
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Affiliation(s)
- Umid M Sharapov
- Epidemic Intelligence Service, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329.,Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
| | - Arthur M Wendel
- Epidemic Intelligence Service, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329.,Wisconsin Division of Public Health, 1 West Wilson Street, P.O. Box 2659, Madison, Wisconsin 53703
| | - Jeffrey P Davis
- Wisconsin Division of Public Health, 1 West Wilson Street, P.O. Box 2659, Madison, Wisconsin 53703
| | - William E Keene
- Oregon Public Health Division, 800 N.E. Oregon Street, Portland, Oregon 97232
| | - Jeffrey Farrar
- California Department of Health Services, P.O. Box 997377, MS 0500, Sacramento, California 95899, USA
| | - Samir Sodha
- Epidemic Intelligence Service, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329.,Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
| | - Eija Hyytia-Trees
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
| | - Molly Leeper
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
| | - Chris Braden
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329
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18
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Hernandez SM, Welch CN, Peters VE, Lipp EK, Curry S, Yabsley MJ, Sanchez S, Presotto A, Gerner-Smidt P, Hise KB, Hammond E, Kistler WM, Madden M, Conway AL, Kwan T, Maurer JJ. Urbanized White Ibises (Eudocimus albus) as Carriers of Salmonella enterica of Significance to Public Health and Wildlife. PLoS One 2016; 11:e0164402. [PMID: 27768705 PMCID: PMC5074519 DOI: 10.1371/journal.pone.0164402] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
Worldwide, Salmonella spp. is a significant cause of disease for both humans and wildlife, with wild birds adapted to urban environments having different opportunities for pathogen exposure, infection, and transmission compared to their natural conspecifics. Food provisioning by people may influence these factors, especially when high-density mixed species flocks aggregate. White Ibises (Eudocimus albus), an iconic Everglades species in decline in Florida, are becoming increasingly common in urbanized areas of south Florida where most are hand-fed. We examined the prevalence of Salmonella shedding by ibises to determine the role of landscape characteristics where ibis forage and their behavior, on shedding rates. We also compared Salmonella isolated from ibises to human isolates to better understand non-foodborne human salmonellosis. From 2010-2013, 13% (n = 261) adult/subadult ibises and 35% (n = 72) nestlings sampled were shedding Salmonella. The prevalence of Salmonella shedding by ibises significantly decreased as the percent of Palustrine emergent wetlands and herbaceous grasslands increased, and increased as the proportion of open-developed land types (e.g. parks, lawns, golf courses) increased, suggesting that natural ecosystem land cover types supported birds with a lower prevalence of infection. A high diversity of Salmonella serotypes (n = 24) and strain types (43 PFGE types) were shed by ibises, of which 33% of the serotypes ranked in the top 20 of high significance for people in the years of the study. Importantly, 44% of the Salmonella Pulsed-Field Gel Electrophoresis patterns for ibis isolates (n = 43) matched profiles in the CDC PulseNet USA database. Of these, 20% came from Florida in the same three years we sampled ibis. Importantly, there was a negative relationship between the amount of Palustrine emergent wetland and the number of Salmonella isolates from ibises that matched human cases in the PulseNet database (p = 0.056). Together, our results indicate that ibises are good indicators of salmonellae strains circulating in their environment and they have both the potential and opportunity to transmit salmonellae to people. Finally, they may act as salmonellae carriers to natural environments where other more highly-susceptible groups (nestlings) may be detrimentally affected.
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Affiliation(s)
- Sonia M. Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Catharine N. Welch
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Valerie E. Peters
- Institute for Environment and Sustainability, Department of Zoology, Miami University, Columbia, Ohio, United States of America
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Shannon Curry
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Michael J. Yabsley
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Andrea Presotto
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, United States of America
| | - Kelley B. Hise
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, United States of America
| | - Elizabeth Hammond
- Lion Country Safari Park, Loxahatchee, Florida, United States of America
| | - Whitney M. Kistler
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Marguerite Madden
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - April L. Conway
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Tiffany Kwan
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - John J. Maurer
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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19
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Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal-Francisque V, Kucerova Z, Rocha EPC, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol 2016; 2:16185. [PMID: 27723724 DOI: 10.1038/nmicrobiol.2016.185] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 08/30/2016] [Indexed: 01/31/2023]
Abstract
Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.
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Affiliation(s)
- Alexandra Moura
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.,Inserm U1117, 75015 Paris, France.,Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| | - Alexis Criscuolo
- Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France
| | | | - Mylène M Maury
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.,Inserm U1117, 75015 Paris, France.,Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France.,Sorbonne Paris Cité, Cellule Pasteur, Paris Diderot University, 75013 Paris, France
| | - Alexandre Leclercq
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France
| | - Cheryl Tarr
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | | | | | - Aleisha Reimer
- Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Vincent Enouf
- Pasteur International Bioresources network (PIBnet), Mutualized Microbiology Platform (P2M), Institut Pasteur, 75724 Paris, France
| | - Elise Larsonneur
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France.,CNRS, UMS 3601 IFB-Core, 91198 Gif-sur-Yvette, France
| | - Heather Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Hélène Bracq-Dieye
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France
| | - Lee S Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Louis Jones
- Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| | | | - Matthew Walker
- Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Steven Stroika
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Thomas Cantinelli
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France
| | - Viviane Chenal-Francisque
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France
| | - Zuzana Kucerova
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
| | - Celine Nadon
- Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | | | | | - Bruno Pot
- Applied-Maths, 9830 Sint-Martens-Latem, Belgium
| | | | - Marc Lecuit
- National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.,Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.,Inserm U1117, 75015 Paris, France.,Sorbonne Paris Cité, Institut Imagine, 75006 Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Paris Descartes University, 75015 Paris, France
| | - Sylvain Brisse
- Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.,CNRS, UMR 3525, 75015 Paris, France
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20
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Timmons C, Trees E, Ribot EM, Gerner-Smidt P, LaFon P, Im S, Ma LM. Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli. J Microbiol Methods 2016; 125:70-80. [PMID: 27071532 PMCID: PMC6553613 DOI: 10.1016/j.mimet.2016.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 11/21/2022]
Abstract
Non-O157 Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of growing concern worldwide that have been associated with several recent multistate and multinational outbreaks of foodborne illness. Rapid and sensitive molecular-based bacterial strain discrimination methods are critical for timely outbreak identification and contaminated food source traceback. One such method, multiple-locus variable-number tandem repeat analysis (MLVA), is being used with increasing frequency in foodborne illness outbreak investigations to augment the current gold standard bacterial subtyping technique, pulsed-field gel electrophoresis (PFGE). The objective of this study was to develop a MLVA assay for intra- and inter-serogroup discrimination of six major non-O157 STEC serogroups-O26, O111, O103, O121, O45, and O145-and perform a preliminary internal validation of the method on a limited number of clinical isolates. The resultant MLVA scheme consists of ten variable number tandem repeat (VNTR) loci amplified in three multiplex PCR reactions. Sixty-five unique MLVA types were obtained among 84 clinical non-O157 STEC strains comprised of geographically diverse sporadic and outbreak related isolates. Compared to PFGE, the developed MLVA scheme allowed similar discrimination among serogroups O26, O111, O103, and O121 but not among O145 and O45. To more fully compare the discriminatory power of this preliminary MLVA method to PFGE and to determine its epidemiological congruence, a thorough internal and external validation needs to be performed on a carefully selected large panel of strains, including multiple isolates from single outbreaks.
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Affiliation(s)
- Chris Timmons
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater OK 74078, United States
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, GA 30329, United States
| | - Efrain M Ribot
- Centers for Disease Control and Prevention, Atlanta, GA 30329, United States
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Atlanta, GA 30329, United States
| | - Patti LaFon
- Centers for Disease Control and Prevention, Atlanta, GA 30329, United States
| | - Sung Im
- Centers for Disease Control and Prevention, Atlanta, GA 30329, United States
| | - Li Maria Ma
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater OK 74078, United States.
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21
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Jackson BR, Tarr C, Strain E, Jackson KA, Conrad A, Carleton H, Katz LS, Stroika S, Gould LH, Mody RK, Silk BJ, Beal J, Chen Y, Timme R, Doyle M, Fields A, Wise M, Tillman G, Defibaugh-Chavez S, Kucerova Z, Sabol A, Roache K, Trees E, Simmons M, Wasilenko J, Kubota K, Pouseele H, Klimke W, Besser J, Brown E, Allard M, Gerner-Smidt P. Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation. Clin Infect Dis 2016; 63:380-6. [PMID: 27090985 DOI: 10.1093/cid/ciw242] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/07/2016] [Indexed: 12/15/2022] Open
Abstract
Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.
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Affiliation(s)
| | - Cheryl Tarr
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Errol Strain
- Food and Drug Administration, College Park, Maryland
| | - Kelly A Jackson
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amanda Conrad
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Lee S Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Steven Stroika
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - L Hannah Gould
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Rajal K Mody
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Benjamin J Silk
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer Beal
- Food and Drug Administration, College Park, Maryland
| | - Yi Chen
- Food and Drug Administration, College Park, Maryland
| | - Ruth Timme
- Food and Drug Administration, College Park, Maryland
| | - Matthew Doyle
- Food and Drug Administration, College Park, Maryland
| | - Angela Fields
- Food and Drug Administration, College Park, Maryland
| | - Matthew Wise
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Glenn Tillman
- US Department of Agriculture, Food Safety and Inspection Service, Athens, Georgia
| | | | - Zuzana Kucerova
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ashley Sabol
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Katie Roache
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mustafa Simmons
- US Department of Agriculture, Food Safety and Inspection Service, Athens, Georgia
| | - Jamie Wasilenko
- US Department of Agriculture, Food Safety and Inspection Service, Athens, Georgia
| | - Kristy Kubota
- Association of Public Health Laboratories, Silver Spring, Maryland
| | | | - William Klimke
- National Institute for Biotechnology Information, National Institutes of Health, Bethesda, Maryland
| | - John Besser
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eric Brown
- Food and Drug Administration, College Park, Maryland
| | - Marc Allard
- Food and Drug Administration, College Park, Maryland
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22
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Maurer JJ, Martin G, Hernandez S, Cheng Y, Gerner-Smidt P, Hise KB, Tobin D’Angelo M, Cole D, Sanchez S, Madden M, Valeika S, Presotto A, Lipp EK. Diversity and Persistence of Salmonella enterica Strains in Rural Landscapes in the Southeastern United States. PLoS One 2015; 10:e0128937. [PMID: 26131552 PMCID: PMC4489491 DOI: 10.1371/journal.pone.0128937] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/01/2015] [Indexed: 11/22/2022] Open
Abstract
Salmonellosis cases in the in the United States show distinct geographical trends, with the southeast reporting among the highest rates of illness. In the state of Georgia, USA, non-outbreak associated salmonellosis is especially high in the southern low-lying coastal plain. Here we examined the distribution of Salmonella enterica in environmental waters and associated wildlife in two distinct watersheds, one in the Atlantic Coastal Plain (a high case rate rural area) physiographic province and one in the Piedmont (a lower case rate rural area). Salmonella were isolated from the two regions and compared for serovar and strain diversity, as well as distribution, between the two study areas, using both a retrospective and prospective design. Thirty-seven unique serovars and 204 unique strain types were identified by pulsed-field gel electrophoresis (PFGE). Salmonella serovars Braenderup, Give, Hartford, and Muenchen were dominant in both watersheds. Two serovars, specifically S. Muenchen and S. Rubislaw, were consistently isolated from both systems, including water and small mammals. Conversely, 24 serovars tended to be site-specific (64.8%, n = 37). Compared to the other Salmonella serovars isolated from these sites, S. Muenchen and S. Rubislaw exhibited significant genetic diversity. Among a subset of PFGE patterns, approximately half of the environmental strain types matched entries in the USA PulseNet database of human cases. Ninety percent of S. Muenchen strains from the Little River basin (the high case rate area) matched PFGE entries in PulseNet compared to 33.33% of S. Muenchen strains from the North Oconee River region (the lower case rate area). Underlying the diversity and turnover of Salmonella strains observed for these two watersheds is the persistence of specific Salmonella serovars and strain types that may be adapted to these watersheds and landscapes.
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Affiliation(s)
- John J. Maurer
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Gordon Martin
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Sonia Hernandez
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Peter Gerner-Smidt
- Centers for Disease and Control and Prevention, Atlanta, Georgia, United States of America
| | - Kelley B. Hise
- Centers for Disease and Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Dana Cole
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- Centers for Disease and Control and Prevention, Atlanta, Georgia, United States of America
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Marguerite Madden
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - Steven Valeika
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Andrea Presotto
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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23
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Griffing SM, MacCannell DR, Schmidtke AJ, Freeman MM, Hyytiä-Trees E, Gerner-Smidt P, Ribot EM, Bono JL. Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7. PLoS One 2015; 10:e0131967. [PMID: 26132731 PMCID: PMC4488506 DOI: 10.1371/journal.pone.0131967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023] Open
Abstract
The objective of this study was to develop a canonical, parsimoniously-informative SNP panel for subtyping Shiga-toxin producing Escherichia coli (STEC) O157:H7 that would be consistent with epidemiological, PFGE, and MLVA clustering of human specimens. Our group had previously identified 906 putative discriminatory SNPs, which were pared down to 391 SNPs based on their prevalence in a test set. The 391 SNPs were screened using a high-throughput form of TaqMan PCR against a set of clinical isolates that represent the most diverse collection of O157:H7 isolates from outbreaks and sporadic cases examined to date. Another 30 SNPs identified by others were also screened using the same method. Two additional targets were tested using standard TaqMan PCR endpoint analysis. These 423 SNPs were reduced to a 32 SNP panel with the almost the same discriminatory value. While the panel partitioned our diverse set of isolates in a manner that was consistent with epidemiological data and PFGE and MLVA phylogenies, it resulted in fewer subtypes than either existing method and insufficient epidemiological resolution in 10 of 47 clusters. Therefore, another round of SNP discovery was undertaken using comparative genomic resequencing of pooled DNA from the 10 clusters with insufficient resolution. This process identified 4,040 potential SNPs and suggested one of the ten clusters was incorrectly grouped. After its removal, there were 2,878 SNPs, of which only 63 were previously identified and 438 occurred across multiple clusters. Among highly clonal bacteria like STEC O157:H7, linkage disequilibrium greatly limits the number of parsimoniously informative SNPs. Therefore, it is perhaps unsurprising that our panel accounted for the potential discriminatory value of numerous other SNPs reported in the literature. We concluded published O157:H7 SNPs are insufficient for effective epidemiological subtyping. However, the 438 multi-cluster SNPs we identified may provide the additional information required.
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Affiliation(s)
- Sean M. Griffing
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Duncan R. MacCannell
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amber J. Schmidtke
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Molly M. Freeman
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Eija Hyytiä-Trees
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Peter Gerner-Smidt
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Efrain M. Ribot
- PulseNet Next Generation Subtyping Methods Unit, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James L. Bono
- United States Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Service, Clay Center, Nevada, United States of America
- * E-mail:
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24
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Jackson B, Jackson K, Tarr C, Evans P, Klimke W, Kubota K, Kucerova Z, Katz L, Trees E, Carleton H, Stroika S, Conrad A, Besser J, Gerner-Smidt P, Mody R. 1338Improving Detection and Investigation of Listeriosis Outbreaks Using Real-Time Whole-Genome Sequencing. Open Forum Infect Dis 2014. [DOI: 10.1093/ofid/ofu051.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Kelly Jackson
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Cheryl Tarr
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Peter Evans
- Food and Drug Administration, College Park, MD
| | | | - Kristy Kubota
- Association of Public Health Laboratories, Silver Spring, MD
| | | | - Lee Katz
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | - Amanda Conrad
- Centers for Disease Control and Prevention, Atlanta, GA
| | - John Besser
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Rajal Mody
- Centers for Disease Control and Prevention, Atlanta, GA
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25
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Affiliation(s)
- Thomas J Sandora
- Division of Infectious Diseases, Departments of Medicine and Laboratory Medicine, Boston Children's Hospital, Boston MA
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26
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Jackson BR, Talkington DF, Pruckler JM, Fouché MDB, Lafosse E, Nygren B, Gómez GA, Dahourou GA, Archer WR, Payne AB, Hooper WC, Tappero JW, Derado G, Magloire R, Gerner-Smidt P, Freeman N, Boncy J, Mintz ED. Seroepidemiologic survey of epidemic cholera in Haiti to assess spectrum of illness and risk factors for severe disease. Am J Trop Med Hyg 2013; 89:654-664. [PMID: 24106192 PMCID: PMC3795095 DOI: 10.4269/ajtmh.13-0208] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To assess the spectrum of illness from toxigenic Vibrio cholerae O1 and risk factors for severe cholera in Haiti, we conducted a cross-sectional survey in a rural commune with more than 21,000 residents. During March 22–April 6, 2011, we interviewed 2,622 residents ≥ 2 years of age and tested serum specimens from 2,527 (96%) participants for vibriocidal and antibodies against cholera toxin; 18% of participants reported a cholera diagnosis, 39% had vibriocidal titers ≥ 320, and 64% had vibriocidal titers ≥ 80, suggesting widespread infection. Among seropositive participants (vibriocidal titers ≥ 320), 74.5% reported no diarrhea and 9.0% had severe cholera (reported receiving intravenous fluids and overnight hospitalization). This high burden of severe cholera is likely explained by the lack of pre-existing immunity in this population, although the virulence of the atypical El Tor strain causing the epidemic and other factors might also play a role.
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Affiliation(s)
- Brendan R. Jackson
- *Address correspondence to Brendan R. Jackson, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop A38, Atlanta, GA 30333. E-mail:
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27
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Nadon CA, Trees E, Ng LK, Møller Nielsen E, Reimer A, Maxwell N, Kubota KA, Gerner-Smidt P. Development and application of MLVA methods as a tool for inter-laboratory surveillance. ACTA ACUST UNITED AC 2013; 18:20565. [PMID: 24008231 DOI: 10.2807/1560-7917.es2013.18.35.20565] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Multiple-locus variable-number of tandem-repeats analysis (MLVA) has emerged as a valuable method for subtyping bacterial pathogens and has been adopted in many countries as a critical component of their laboratory-based surveillance. Lack of harmonisation and standardisation of the method, however, has made comparison of results generated in different laboratories difficult, if not impossible, and has therefore hampered its use in international surveillance. This paper proposes an international consensus on the development, validation, nomenclature and quality control for MLVA used for molecular surveillance and outbreak detection based on a review of the current state of knowledge.
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Affiliation(s)
- C A Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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28
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Silk BJ, Mahon BE, Griffin PM, Gould LH, Tauxe RV, Crim SM, Jackson KA, Gerner-Smidt P, Herman KM, Henao OL. Vital signs: Listeria illnesses, deaths, and outbreaks--United States, 2009-2011. MMWR Morb Mortal Wkly Rep 2013; 62:448-52. [PMID: 23739339 PMCID: PMC4604984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Older adults, pregnant women, and persons with immunocompromising conditions are at higher risk than others for invasive Listeria monocytogenes infection (listeriosis), a rare and preventable foodborne illness that can cause bacteremia, meningitis, fetal loss, and death. METHODS This report summarizes data on 2009-2011 listeriosis cases and outbreaks reported to U.S. surveillance systems. The Listeria Initiative and PulseNet conduct nationwide surveillance to rapidly detect and respond to outbreaks, the Foodborne Diseases Active Surveillance Network (FoodNet) conducts active, sentinel population-based surveillance to track incidence trends, and the Foodborne Disease Outbreak Surveillance System (FDOSS) receives reports of investigated outbreaks to track foods and settings associated with outbreaks. RESULTS Nationwide, 1,651 cases of listeriosis occurring during 2009-2011 were reported. The case-fatality rate was 21%. Most cases occurred among adults aged ≥65 years (950 [58%]), and 14% (227) were pregnancy-associated. At least 74% of nonpregnant patients aged <65 years had an immunocompromising condition, most commonly immunosuppressive therapy or malignancy. The average annual incidence was 0.29 cases per 100,000 population. Compared with the overall population, incidence was markedly higher among adults aged ≥65 years (1.3; relative rate [RR]: 4.4) and pregnant women (3.0; RR: 10.1). Twelve reported outbreaks affected 224 patients in 38 states. Five outbreak investigations implicated soft cheeses made from pasteurized milk that were likely contaminated during cheese-making (four implicated Mexican-style cheese, and one implicated two other types of cheese). Two outbreaks were linked to raw produce. CONCLUSIONS Almost all listeriosis occurs in persons in higher-risk groups. Soft cheeses were prominent vehicles, but other foods also caused recent outbreaks. Prevention targeting higher-risk groups and control of Listeria monocytogenes contamination in foods implicated by outbreak investigations will have the greatest impact on reducing the burden of listeriosis. IMPLICATIONS FOR PUBLIC HEALTH PRACTICE Careful attention to food safety is especially important to protect vulnerable populations. Surveillance for foodborne infections like listeriosis identifies food safety gaps that can be addressed by industry, regulatory authorities, food preparers, and consumers.
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Lomonaco S, Verghese B, Gerner-Smidt P, Tarr C, Gladney L, Joseph L, Katz L, Turnsek M, Frace M, Chen Y, Brown E, Meinersmann R, Berrang M, Knabel S. Novel epidemic clones of Listeria monocytogenes, United States, 2011. Emerg Infect Dis 2013; 19:147-50. [PMID: 23260778 PMCID: PMC3558006 DOI: 10.3201/eid1901.121167] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We identified a novel serotype 1/2a outbreak strain and 2 novel epidemic clones of Listeria monocytogenes while investigating a foodborne outbreak of listeriosis associated with consumption of cantaloupe during 2011 in the United States. Comparative analyses of strains worldwide are essential to identification of novel outbreak strains and epidemic clones.
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Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J. Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg Infect Dis 2013; 18:e1. [PMID: 23092707 PMCID: PMC3559169 DOI: 10.3201/eid/1811.120453] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients. Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases of pathogen genomes that would ensure more efficient detection, prevention, and control of endemic, emerging, and other infectious disease outbreaks worldwide.
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Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Wong DLF, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J. Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response. Emerg Infect Dis 2012. [DOI: 10.3201/eid1811.120453] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Laksanalamai P, Joseph LA, Silk BJ, Burall LS, L. Tarr C, Gerner-Smidt P, Datta AR. Genomic characterization of Listeria monocytogenes strains involved in a multistate listeriosis outbreak associated with cantaloupe in US. PLoS One 2012; 7:e42448. [PMID: 22860127 PMCID: PMC3409164 DOI: 10.1371/journal.pone.0042448] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/06/2012] [Indexed: 12/29/2022] Open
Abstract
A multistate listeriosis outbreak associated with cantaloupe consumption was reported in the United States in September, 2011. The outbreak investigation recorded a total of 146 invasive illnesses, 30 deaths and one miscarriage. Subtyping of the outbreak associated clinical, food and environmental isolates revealed two serotypes (1/2a and 1/2b) and four pulsed-field gel electrophoresis two-enzyme pattern combinations I, II, III, and IV, including one rarely seen before this outbreak. A DNA-microarray, Listeria GeneChip®, developed by FDA from 24 Listeria monocytogenes genome sequences, was used to further characterize a representative sample of the outbreak isolates. The microarray data (in the form of present or absent calls of specific DNA sequences) separated the isolates into two distinct groups as per their serotypes. The gene content of the outbreak-associated isolates was distinct from that of the previously-reported outbreak strains belonging to the same serotypes. Although the 1/2b outbreak associated isolates are closely related to each other, the 1/2a isolates could be further divided into two distinct genomic groups, one represented by pattern combination I strains and the other represented by highly similar pattern combinations III and IV strains. Gene content analysis of these groups revealed unique genomic sequences associated with these two 1/2a genovars. This work underscores the utility of multiple approaches, such as serotyping, PFGE and DNA microarray analysis to characterize the composition of complex polyclonal listeriosis outbreaks.
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Affiliation(s)
- Pongpan Laksanalamai
- Center for Food Safety and Applied Nutrition, FDA, Laurel, Maryland, United States of America
| | - Lavin A. Joseph
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Benjamin J. Silk
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Laurel S. Burall
- Center for Food Safety and Applied Nutrition, FDA, Laurel, Maryland, United States of America
| | - Cheryl L. Tarr
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Peter Gerner-Smidt
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Atin R. Datta
- Center for Food Safety and Applied Nutrition, FDA, Laurel, Maryland, United States of America
- * E-mail:
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Abstract
The diagnosis of acute gastroenteritis (AGE) has traditionally been based on culture results of feces from patients with diarrhea. Virtually everything we know about disease and the epidemiology of enteric pathogens, such as Salmonella spp., Shiga toxin-producing Escherichia coli (STEC), e.g., O157, and Campylobacter spp., has been generated from the study of patients with culture-confirmed infections. However, this pattern may be changing because AGE diagnostics are moving away from culture toward rapid nonculture methods. These infections are mainly foodborne and therefore preventable, and it is of paramount importance that public health surveillance for these infections is consistent and reliable.
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Gaffga NH, Barton Behravesh C, Ettestad PJ, Smelser CB, Rhorer AR, Cronquist AB, Comstock NA, Bidol SA, Patel NJ, Gerner-Smidt P, Keene WE, Gomez TM, Hopkins BA, Sotir MJ, Angulo FJ. Outbreak of salmonellosis linked to live poultry from a mail-order hatchery. N Engl J Med 2012; 366:2065-73. [PMID: 22646629 DOI: 10.1056/nejmoa1111818] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Outbreaks of human salmonella infections are increasingly associated with contact with live poultry, but effective control measures are elusive. In 2005, a cluster of human salmonella Montevideo infections with a rare pattern on pulsed-field gel electrophoresis (the outbreak strain) was identified by PulseNet, a national subtyping network. METHODS In cooperation with public health and animal health agencies, we conducted multistate investigations involving patient interviews, trace-back investigations, and environmental testing at a mail-order hatchery linked to the outbreak in order to identify the source of infections and prevent additional illnesses. A case was defined as an infection with the outbreak strain between 2004 and 2011. RESULTS From 2004 through 2011, we identified 316 cases in 43 states. The median age of the patient was 4 years. Interviews were completed with 156 patients (or their caretakers) (49%), and 36 of these patients (23%) were hospitalized. Among the 145 patients for whom information was available, 80 (55%) had bloody diarrhea. Information on contact with live young poultry was available for 159 patients, and 122 of these patients (77%) reported having such contact. A mail-order hatchery in the western United States was identified in 81% of the trace-back investigations, and the outbreak strain was isolated from samples collected at the hatchery. After interventions at the hatchery, the number of human infections declined, but transmission continued. CONCLUSIONS We identified a prolonged multistate outbreak of salmonellosis, predominantly affecting young children and associated with contact with live young poultry from a mail-order hatchery. Interventions performed at the hatchery reduced, but did not eliminate, associated human infections, demonstrating the difficulty of eliminating salmonella transmission from live poultry.
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Affiliation(s)
- Nicholas H Gaffga
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Talkington D, Bopp C, Tarr C, Parsons MB, Dahourou G, Freeman M, Joyce K, Turnsek M, Garrett N, Humphrys M, Gomez G, Stroika S, Boncy J, Ochieng B, Oundo J, Klena J, Smith A, Keddy K, Gerner-Smidt P. Characterization of toxigenic Vibrio cholerae from Haiti, 2010-2011. Emerg Infect Dis 2012; 17:2122-9. [PMID: 22099116 PMCID: PMC3310580 DOI: 10.3201/eid1711.110805] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In October 2010, the US Centers for Disease Control and Prevention received reports of cases of severe watery diarrhea in Haiti. The cause was confirmed to be toxigenic Vibrio cholerae, serogroup O1, serotype Ogawa, biotype El Tor. We characterized 122 isolates from Haiti and compared them with isolates from other countries. Antimicrobial drug susceptibility was tested by disk diffusion and broth microdilution. Analyses included identification of rstR and VC2346 genes, sequencing of ctxAB and tcpA genes, and pulsed-field gel electrophoresis with SfiI and NotI enzymes. All isolates were susceptible to doxycycline and azithromycin. One pulsed-field gel electrophoresis pattern predominated, and ctxB sequence of all isolates matched the B-7 allele. We identified the tcpETCIRS allele, which is also present in Bangladesh strain CIRS 101. These data show that the isolates from Haiti are clonally and genetically similar to isolates originating in Africa and southern Asia and that ctxB-7 and tcpET(CIRS) alleles are undergoing global dissemination.
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Affiliation(s)
- Deborah Talkington
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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Reimer AR, Van Domselaar G, Stroika S, Walker M, Kent H, Tarr C, Talkington D, Rowe L, Olsen-Rasmussen M, Frace M, Sammons S, Dahourou GA, Boncy J, Smith AM, Mabon P, Petkau A, Graham M, Gilmour MW, Gerner-Smidt P. Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa. Emerg Infect Dis 2012; 17:2113-21. [PMID: 22099115 PMCID: PMC3310578 DOI: 10.3201/eid1711.110794] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A strain from Haiti shares genetic ancestry with those from Asia and Africa. Cholera was absent from the island of Hispaniola at least a century before an outbreak that began in Haiti in the fall of 2010. Pulsed-field gel electrophoresis (PFGE) analysis of clinical isolates from the Haiti outbreak and recent global travelers returning to the United States showed indistinguishable PFGE fingerprints. To better explore the genetic ancestry of the Haiti outbreak strain, we acquired 23 whole-genome Vibriocholerae sequences: 9 isolates obtained in Haiti or the Dominican Republic, 12 PFGE pattern-matched isolates linked to Asia or Africa, and 2 nonmatched outliers from the Western Hemisphere. Phylogenies for whole-genome sequences and core genome single-nucleotide polymorphisms showed that the Haiti outbreak strain is genetically related to strains originating in India and Cameroon. However, because no identical genetic match was found among sequenced contemporary isolates, a definitive genetic origin for the outbreak in Haiti remains speculative.
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Pichel M, Brengi SP, Cooper KLF, Ribot EM, Al-Busaidy S, Araya P, Fernández J, Vaz TI, Kam KM, Morcos M, Nielsen EM, Nadon C, Pimentel G, Pérez-Gutiérrez E, Gerner-Smidt P, Binsztein N. Standardization and international multicenter validation of a PulseNet pulsed-field gel electrophoresis protocol for subtyping Shigella flexneri isolates. Foodborne Pathog Dis 2012; 9:418-24. [PMID: 22506731 DOI: 10.1089/fpd.2011.1067] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Shigella flexneri is one of the agents most frequently linked to diarrheal illness in developing countries and often causes outbreaks in settings with poor hygiene or sanitary conditions. Travel is one of the means by which S. flexneri can be imported into developed countries, where this pathogen is not commonly seen. A robust and discriminatory subtyping method is needed for the surveillance of S. flexneri locally and regionally, and to aid in the detection and investigation of outbreaks. The PulseNet International network utilizes standardized pulsed-field gel electrophoresis (PFGE) protocols to carry out laboratory-based surveillance of foodborne pathogens in combination with epidemiologic data. A multicenter validation was carried out in nine PulseNet laboratories located in North and South America, Europe, and Asia, and it demonstrated that a new protocol is highly robust and reproducible for subtyping of S. flexneri. This protocol, already approved for PulseNet laboratories, applies NotI and XbaI as primary and secondary restriction enzymes, respectively, under electrophoresis conditions of initial switch time of 5 s to final switch time of 35 s, at 6 volts/cm.
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Affiliation(s)
- Mariana Pichel
- Instituto Nacional de Enfermedades Infecciosas, ANLIS "Carlos G. Malbrán," Buenos Aires, Argentina.
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Bono JL, Smith TPL, Keen JE, Harhay GP, McDaneld TG, Mandrell RE, Jung WK, Besser TE, Gerner-Smidt P, Bielaszewska M, Karch H, Clawson ML. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Mol Biol Evol 2012; 29:2047-62. [PMID: 22355013 PMCID: PMC3408066 DOI: 10.1093/molbev/mss072] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cattle are a major reservoir for Shiga toxin-producing Escherichia coli O157 (STEC O157) and harbor multiple genetic subtypes that do not all associate with human disease. STEC O157 evolved from an E. coli O55:H7 progenitor; however, a lack of genome sequence has hindered investigations on the divergence of human- and/or cattle-associated subtypes. Our goals were to 1) identify nucleotide polymorphisms for STEC O157 genetic subtype detection, 2) determine the phylogeny of STEC O157 genetic subtypes using polymorphism-derived genotypes and a phage insertion typing system, and 3) compare polymorphism-derived genotypes identified in this study with pulsed field gel electrophoresis (PFGE), the current gold standard for evaluating STEC O157 diversity. Using 762 nucleotide polymorphisms that were originally identified through whole-genome sequencing of 189 STEC O157 human- and cattle-isolated strains, we genotyped a collection of 426 STEC O157 strains. Concatenated polymorphism alleles defined 175 genotypes that were tagged by a minimal set of 138 polymorphisms. Eight major lineages of STEC O157 were identified, of which cattle are a reservoir for seven. Two lineages regularly harbored by cattle accounted for the majority of human disease in this study, whereas another was rarely represented in humans and may have evolved toward reduced human virulence. Notably, cattle are not a known reservoir for E. coli O55:H7 or STEC O157:H− (the first lineage to diverge within the STEC O157 serogroup), which both cause human disease. This result calls into question how cattle may have originally acquired STEC O157. The polymorphism-derived genotypes identified in this study did not surpass PFGE diversity assessed by BlnI and XbaI digestions in a subset of 93 strains. However, our results show that they are highly effective in assessing the evolutionary relatedness of epidemiologically unrelated STEC O157 genetic subtypes, including those associated with the cattle reservoir and human disease.
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Affiliation(s)
- James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
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Filliol-Toutain I, Chiou CS, Mammina C, Gerner-Smidt P, Thong KL, Phung DC, Pichel M, Ranjbar R, Sow AG, Cooper K, Ribot E, Binsztein N, Liang SY. Global Distribution of Shigella sonnei Clones. Emerg Infect Dis 2012; 17:1910-2. [PMID: 22000369 PMCID: PMC3310650 DOI: 10.3201/eid1710.101486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To investigate global epidemiology of Shigella sonnei, we performed multilocus variable number tandem repeat analysis of 1,672 isolates obtained since 1943 from 50 countries on 5 continents and the Pacific region. Three major clonal groups were identified; 2 were globally spread. Type 18 and its derivatives have circulated worldwide in recent decades.
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Filliol-Toutain I, Chiou CS, Mammina C, Gerner-Smidt P, Thong KL, Phung D, Pichel M, Ranjbar R, Gassama Sow A, Cooper K, Ribot E, Binsztein N, Liang SY. Global Distribution of Shigella sonnei Clones. Emerg Infect Dis 2011. [DOI: 10.3201/eid1710.101486_article.htm] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Cavallaro E, Date K, Medus C, Meyer S, Miller B, Kim C, Nowicki S, Cosgrove S, Sweat D, Phan Q, Flint J, Daly ER, Adams J, Hyytia-Trees E, Gerner-Smidt P, Hoekstra RM, Schwensohn C, Langer A, Sodha SV, Rogers MC, Angulo FJ, Tauxe RV, Williams IT, Behravesh CB. Salmonella typhimurium infections associated with peanut products. N Engl J Med 2011; 365:601-10. [PMID: 21848461 DOI: 10.1056/nejmoa1011208] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Contaminated food ingredients can affect multiple products, each distributed through various channels and consumed in multiple settings. Beginning in November 2008, we investigated a nationwide outbreak of salmonella infections. METHODS A case was defined as laboratory-confirmed infection with the outbreak strain of Salmonella Typhimurium occurring between September 1, 2008, and April 20, 2009. We conducted two case-control studies, product "trace-back," and environmental investigations. RESULTS Among 714 case patients identified in 46 states, 166 (23%) were hospitalized and 9 (1%) died. In study 1, illness was associated with eating any peanut butter (matched odds ratio, 2.5; 95% confidence interval [CI], 1.3 to 5.3), peanut butter-containing products (matched odds ratio, 2.2; 95% CI, 1.1 to 4.7), and frozen chicken products (matched odds ratio, 4.6; 95% CI, 1.7 to 14.7). Investigations of focal clusters and single cases associated with nine institutions identified a single institutional brand of peanut butter (here called brand X) distributed to all facilities. In study 2, illness was associated with eating peanut butter outside the home (matched odds ratio, 3.9; 95% CI, 1.6 to 10.0) and two brands of peanut butter crackers (brand A: matched odds ratio, 17.2; 95% CI, 6.9 to 51.5; brand B: matched odds ratio, 3.6; 95% CI, 1.3 to 9.8). Both cracker brands were made from brand X peanut paste. The outbreak strain was isolated from brand X peanut butter, brand A crackers, and 15 other products. A total of 3918 peanut butter-containing products were recalled between January 10 and April 29, 2009. CONCLUSIONS Contaminated peanut butter and peanut products caused a nationwide salmonellosis outbreak. Ingredient-driven outbreaks are challenging to detect and may lead to widespread contamination of numerous food products.
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Affiliation(s)
- Elizabeth Cavallaro
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Foodborne, Waterborne and Environmental Diseases, Program Office for Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, USA.
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Barton Behravesh C, Mody RK, Jungk J, Gaul L, Redd JT, Chen S, Cosgrove S, Hedican E, Sweat D, Chávez-Hauser L, Snow SL, Hanson H, Nguyen TA, Sodha SV, Boore AL, Russo E, Mikoleit M, Theobald L, Gerner-Smidt P, Hoekstra RM, Angulo FJ, Swerdlow DL, Tauxe RV, Griffin PM, Williams IT. 2008 outbreak of Salmonella Saintpaul infections associated with raw produce. N Engl J Med 2011; 364:918-27. [PMID: 21345092 DOI: 10.1056/nejmoa1005741] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Raw produce is an increasingly recognized vehicle for salmonellosis. We investigated a nationwide outbreak that occurred in the United States in 2008. METHODS We defined a case as diarrhea in a person with laboratory-confirmed infection with the outbreak strain of Salmonella enterica serotype Saintpaul. Epidemiologic, traceback, and environmental studies were conducted. RESULTS Among the 1500 case subjects, 21% were hospitalized, and 2 died. In three case-control studies of cases not linked to restaurant clusters, illness was significantly associated with eating raw tomatoes (matched odds ratio, 5.6; 95% confidence interval [CI], 1.6 to 30.3); eating at a Mexican-style restaurant (matched odds ratio, 4.6; 95% CI, 2.1 to ∞) and eating pico de gallo salsa (matched odds ratio, 4.0; 95% CI, 1.5 to 17.8), corn tortillas (matched odds ratio, 2.3; 95% CI, 1.2 to 5.0), or salsa (matched odds ratio, 2.1; 95% CI, 1.1 to 3.9); and having a raw jalapeño pepper in the household (matched odds ratio, 2.9; 95% CI, 1.2 to 7.6). In nine analyses of clusters associated with restaurants or events, jalapeño peppers were implicated in all three clusters with implicated ingredients, and jalapeño or serrano peppers were an ingredient in an implicated item in the other three clusters. Raw tomatoes were an ingredient in an implicated item in three clusters. The outbreak strain was identified in jalapeño peppers collected in Texas and in agricultural water and serrano peppers on a Mexican farm. Tomato tracebacks did not converge on a source. CONCLUSIONS Although an epidemiologic association with raw tomatoes was identified early in this investigation, subsequent epidemiologic and microbiologic evidence implicated jalapeño and serrano peppers. This outbreak highlights the importance of preventing raw-produce contamination.
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Affiliation(s)
- Casey Barton Behravesh
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Abstract
A large outbreak of Salmonella Saintpaul associated with raw jalapeño peppers, serrano peppers, and possibly tomatoes was reported in the United States in 2008. During the outbreak, two clusters of illness investigated among restaurant patrons were significantly associated with eating salsa. Experiments were performed to determine the survival and growth characteristics of Salmonella in salsa and related major ingredients, i.e., tomatoes, jalapeño peppers, and cilantro. Intact and chopped vegetables and different formulations of salsas were inoculated with a five-strain mixture of Salmonella and then stored at 4, 12, and 21 degrees C for up to 7 days. Salmonella populations were monitored during storage. Salmonella did not grow, but survived on intact tomatoes and jalapeño peppers, whereas significant growth at 12 and 21 degrees C was observed on intact cilantro. In general, growth of Salmonella occurred in all chopped vegetables when stored at 12 and 21 degrees C, with chopped jalapeño peppers being the most supportive of Salmonella growth. Regardless of differences in salsa formulation, no growth of Salmonella (initial inoculation ca. 3 log CFU/g) was observed in salsa held at 4 degrees C; however, rapid or gradual decreases in Salmonella populations were only observed in formulations that contained both fresh garlic and lime juice. Salmonella grew at 12 and 21 degrees C in salsas, except for those formulations that contained both fresh garlic and lime juice, in which salmonellae were rapidly or gradually inactivated, depending on salsa formulation. These results highlight the importance of preharvest pathogen contamination control of fresh produce and proper formulation and storage of salsa.
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Affiliation(s)
- Li Ma
- Center for Food Safety, University of Georgia, Griffin, Georgia 30223-1797, USA
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Lanier WA, Leeper MM, Smith KE, Tillman GE, Holt KG, Gerner-Smidt P. Pulsed-Field Gel Electrophoresis Subtypes of Shiga Toxin–ProducingEscherichia coliO157 Isolated from Ground Beef and Humans, United States, 2001–2006. Foodborne Pathog Dis 2009; 6:1075-82. [DOI: 10.1089/fpd.2009.0269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- William A. Lanier
- Office of Field Operations, Food Safety and Inspection Service, U.S. Department of Agriculture, Canby, Oregon
- Public Health Service, U.S. Department of Health and Human Services, Rockville, Maryland
| | - Molly M. Leeper
- Enteric Diseases Laboratory Branch, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kirk E. Smith
- Acute Disease Investigation and Control Section, Minnesota Department of Health, St. Paul, Minnesota
| | - Glenn E. Tillman
- Office of Public Health Science, Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, Georgia
| | - Kristin G. Holt
- Office of Public Health Science, Food Safety and Inspection Service, U.S. Department of Agriculture, Atlanta, Georgia
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia
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Gould LH, Bopp C, Strockbine N, Atkinson R, Baselski V, Body B, Carey R, Crandall C, Hurd S, Kaplan R, Neill M, Shea S, Somsel P, Tobin-D'Angelo M, Griffin PM, Gerner-Smidt P. Recommendations for diagnosis of shiga toxin--producing Escherichia coli infections by clinical laboratories. MMWR Recomm Rep 2009; 58:1-14. [PMID: 19834454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Shiga toxin--producing Escherichia coli (STEC) are a leading cause of bacterial enteric infections in the United States. Prompt, accurate diagnosis of STEC infection is important because appropriate treatment early in the course of infection might decrease the risk for serious complications such as renal damage and improve overall patient outcome. In addition, prompt laboratory identification of STEC strains is essential for detecting new and emerging serotypes, for effective and timely outbreak responses and control measures, and for monitoring trends in disease epidemiology. Guidelines for laboratory identification of STEC infections by clinical laboratories were published in 2006. This report provides comprehensive and detailed recommendations for STEC testing by clinical laboratories, including the recommendation that all stools submitted for routine testing from patients with acute community-acquired diarrhea (regardless of patient age, season of the year, or presence or absence of blood in the stool) be simultaneously cultured for E. coli O157:H7 (O157 STEC) and tested with an assay that detects Shiga toxins to detect non-O157 STEC. The report also includes detailed procedures for specimen selection, handling, and transport; a review of culture and nonculture tests for STEC detection; and clinical considerations and recommendations for management of patients with STEC infection. Improving the diagnostic accuracy of STEC infection by clinical laboratories should ensure prompt diagnosis and treatment of these infections in patients and increase detection of STEC outbreaks in the community.
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Affiliation(s)
- L Hannah Gould
- Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-Borne, and Enteric Diseases, CDC, Atlanta, Georgia 30333, USA.
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Abstract
The objective of this study was to determine the rates of thermal inactivation of three Salmonella Tennessee strains in peanut butter associated with an outbreak and to compare them to the rates of inactivation of Salmonella strains of other serotypes (Enteritidis, Typhimurium, and Heidelberg) (SSOS) and of clinical isolates of Salmonella Tennessee from sporadic cases (STSC). Commercial peanut butter was inoculated with Salmonella isolates and heated at 71, 77, 83, and 90 degrees C. The thermal inactivation curves were upwardly concave, indicating rapid death at the beginning (20 min) of heating followed by lower death rates thereafter. The first-order kinetics approach and nonlinear Weibull model were used to fit the inactivation curves and describe the rates of thermal inactivation of Salmonella in peanut butter. The calculated minimum times needed to obtain a 7-log reduction at 90 degrees C for the composited three outbreak-associated strains were significantly greater (P < 0.05) than those of SSOS and STSC. Approximately 120 min were needed to reduce the outbreak strains of Salmonella Tennessee by 7 log, whereas 86 and 55 min were needed for SSOS and STSC, respectively. These results indicate that the outbreak-associated Salmonella strains were more thermotolerant than the other Salmonella strains tested, and this greater thermal resistance was not serotype specific. Thermal treatments of peanut butter at 90 degrees C for less than 30 min are not sufficient to kill large populations (5 log CFU/g) of Salmonella in highly contaminated peanut butter.
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Affiliation(s)
- Li Ma
- Center for Food Safety, University of Georgia, Griffin, Georgia 30223-1797, USA
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Gerner-Smidt P, Whichard JM. Sources of Outbreaks of Foodborne Infections in Different Regions of the World. Foodborne Pathog Dis 2009; 6:523-4. [DOI: 10.1089/fpd.2009.9998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Gerner-Smidt P, Whichard JM. Foodborne Disease Trends and Reports. Foodborne Pathog Dis 2009; 6:261-4. [DOI: 10.1089/fpd.2009.9999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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