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Timme RE, Pfefer T, Bias CH, Allard MW, Huang X, Strain E, Balkey M. A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens. Methods Mol Biol 2025; 2852:199-209. [PMID: 39235746 DOI: 10.1007/978-1-0716-4100-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens collected for different purposes. There are five protocols included in this chapter: (1) quality control (QC) assessment for the genome sequence data, (2) validation for the contextual data, (3) data submission for the standard pathogen package or Pathogen Data Object Model (DOM) to the public repository, (4) viewing and querying data at NCBI, and (5) data curation for maintaining relevance of public data. The data are available through one of the International Nucleotide Sequence Database Consortium (INSDC) members, with the National Center for Biotechnology Information (NCBI) being the primary focus of this document. NCBI Pathogen Detection is a custom dashboard at NCBI that provides easy access to pathogen data plus results for a standard suite of automated cluster and genotyping analyses important for informing public health and regulatory decision-making.
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Affiliation(s)
- Ruth E Timme
- Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA.
| | - Tina Pfefer
- Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA
| | - C Hope Bias
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, TN, USA
| | - Marc W Allard
- Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA
| | - Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland - College Park, College Park, MD, USA
| | - Errol Strain
- Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA
| | - Maria Balkey
- Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA
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2
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Jenkins E, Cripe J, Whitney BM, Greenlee T, Schneider B, Nguyen TA, Pightling A, Manetas J, Abraham A, Fox T, Mickelsen N, Priddy C, McMullen S, Crosby A, Viazis S. An Outbreak Investigation of Salmonella Weltevreden Illnesses in the United States Linked to Frozen Precooked Shrimp Imported from India - 2021. J Food Prot 2024; 87:100360. [PMID: 39284384 DOI: 10.1016/j.jfp.2024.100360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024]
Abstract
In 2021, the U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and state partners investigated a multistate sample-initiated retrospective outbreak investigation (SIROI) consisting of a cluster of nine Salmonella Weltevreden illnesses associated with frozen, precooked shrimp imported from India. Import surveillance testing identified Salmonella Weltevreden recovered from a cooked shrimp sample from Supplier B. In total, nine patients with clinical isolates highly related via whole genome sequencing were reported in four states with illness onset dates between February 26 and July 17, 2021. Epidemiologic data were gathered by state partners for seven patients, who all reported exposure to shrimp. Five patients reported consuming shrimp cocktail from the same retailer. A traceback investigation for five of the six patients converged on Supplier B. This evidence demonstrated that the outbreak of Salmonella Weltevreden illnesses was caused by the consumption of cooked, ready-to-eat shrimp manufactured by Supplier B. At the time of the investigation, outbreak and recall information was shared with Indian competent authorities. In March 2022, a follow-up inspection of Supplier B's facility in India was conducted, and insanitary conditions and practices were observed. This outbreak investigation highlighted the importance of multidisciplinary national and international public health partnerships. The lessons learned from this investigation should continue to inform investigational activities and food safety guidance for the industry.
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Affiliation(s)
- Erin Jenkins
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA.
| | - Jennifer Cripe
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Brooke M Whitney
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Tiffany Greenlee
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | | | - Thai-An Nguyen
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Julia Manetas
- Office of Regulatory Science, Immediate Office, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Ashley Abraham
- Office of Import Operations, Division of Import Operations, Food and Drug Administration, Silver Spring, MD, USA
| | - Teresa Fox
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Natalie Mickelsen
- Office of Global Policy and Strategy, Food and Drug Administration, New Delhi, India
| | - Christopher Priddy
- Office of Global Policy and Strategy, Food and Drug Administration, New Delhi, India
| | - Sarah McMullen
- Office of Global Policy and Strategy, Food and Drug Administration, New Delhi, India
| | - Alvin Crosby
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Stelios Viazis
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
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3
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Ikhimiukor OO, Mingle L, Wirth SE, Mendez-Vallellanes DV, Hoyt H, Musser KA, Wolfgang WJ, Andam CP. Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes. Genome Med 2024; 16:109. [PMID: 39232757 PMCID: PMC11373459 DOI: 10.1186/s13073-024-01379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/29/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND The foodborne bacterium Listeria monocytogenes (Lm) causes a range of diseases, from mild gastroenteritis to invasive infections that have high fatality rate in vulnerable individuals. Understanding the population genomic structure of invasive Lm is critical to informing public health interventions and infection control policies that will be most effective especially in local and regional communities. METHODS We sequenced the whole draft genomes of 936 Lm isolates from human clinical samples obtained in a two-decade active surveillance program across 58 counties in New York State, USA. Samples came mostly from blood and cerebrospinal fluid. We characterized the phylogenetic relationships, population structure, antimicrobial resistance genes, virulence genes, and mobile genetic elements. RESULTS The population is genetically heterogenous, consisting of lineages I-IV, 89 clonal complexes, 200 sequence types, and six known serogroups. In addition to intrinsic antimicrobial resistance genes (fosX, lin, norB, and sul), other resistance genes tetM, tetS, ermG, msrD, and mefA were sparsely distributed in the population. Within each lineage, we identified clusters of isolates with ≤ 20 single nucleotide polymorphisms in the core genome alignment. These clusters may represent isolates that share a most recent common ancestor, e.g., they are derived from the same contamination source or demonstrate evidence of transmission or outbreak. We identified 38 epidemiologically linked clusters of isolates, confirming eight previously reported disease outbreaks and the discovery of cryptic outbreaks and undetected chains of transmission, even in the rarely reported Lm lineage III (ST3171). The presence of animal-associated lineages III and IV may suggest a possible spillover of animal-restricted strains to humans. Many transmissible clones persisted over several years and traversed distant sites across the state. CONCLUSIONS Our findings revealed the bacterial determinants of invasive listeriosis, driven mainly by the diversity of locally circulating lineages, intrinsic and mobile antimicrobial resistance and virulence genes, and persistence across geographical and temporal scales. Our findings will inform public health efforts to reduce the burden of invasive listeriosis, including the design of food safety measures, source traceback, and outbreak detection.
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Affiliation(s)
| | - Lisa Mingle
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Samantha E Wirth
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | | | - Hannah Hoyt
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | | | | | - Cheryl P Andam
- University at Albany, State University of New York, Albany, NY, USA.
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4
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Stapleton GS, Habrun C, Nemechek K, Gollarza L, Ellison Z, Tolar B, Koski L, Brandenburg JM, Salah Z, Palacios A, Basler C, Varela K, Nichols M, Benedict K. Multistate outbreaks of salmonellosis linked to contact with backyard poultry-United States, 2015-2022. Zoonoses Public Health 2024; 71:708-722. [PMID: 38686950 PMCID: PMC11368616 DOI: 10.1111/zph.13134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/05/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024]
Abstract
AIMS Contact with backyard poultry (i.e., privately-owned, non-commercial poultry) was first associated with a multistate outbreak of salmonellosis in 1955. In recent years, backyard poultry-associated salmonellosis outbreaks have caused more illnesses in the United States than salmonellosis outbreaks linked to any other type of animal. Here, we describe the epidemiology of outbreaks from 2015-2022 to inform prevention efforts. METHODS AND RESULTS During 2015-2022, there were 88 multistate backyard poultry-associated salmonellosis outbreaks and 7866 outbreak-associated illnesses caused by 21 different Salmonella serotypes. Salmonella Enteritidis accounted for the most outbreaks (n = 21) and illnesses (n = 2400) of any serotype. Twenty-four percent (1840/7727) of patients with available information were <5 years of age. In total, 30% (1710/5644) of patients were hospitalized, and nine deaths were attributed to Salmonella infection. Throughout this period, patients reported behaviours that have a higher risk of Salmonella transmission, including kissing or snuggling poultry or allowing poultry inside their home. CONCLUSIONS Despite ongoing efforts to reduce the burden of salmonellosis associated with backyard poultry, outbreak-associated illnesses have nearly tripled and hospitalizations more than quadrupled compared with those in 1990-2014. Because this public health problem is largely preventable, government officials, human and veterinary healthcare providers, hatcheries, and retailers might improve the prevention of illnesses by widely disseminating health and safety recommendations to the public and by continuing to develop and implement prevention measures to reduce zoonotic transmission of Salmonella by backyard poultry.
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Affiliation(s)
- G. Sean Stapleton
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Caroline Habrun
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaylea Nemechek
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Lauren Gollarza
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zachary Ellison
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- ASRT, Inc., Smyrna, Georgia, USA
| | - Beth Tolar
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lia Koski
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joshua M. Brandenburg
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zainab Salah
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alexandra Palacios
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Colin Basler
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kate Varela
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Megin Nichols
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katharine Benedict
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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5
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Nichols M, Stapleton GS, Rotstein DS, Gollarza L, Adams J, Caidi H, Chen J, Hodges A, Glover M, Peloquin S, Payne L, Norris A, DeLancey S, Donovan D, Dietrich S, Glaspie S, McWilliams K, Burgess E, Holben B, Pietrzen K, Benko S, Feldpausch E, Orel S, Neises D, Kline KE, Tobin B, Caron G, Viveiros B, Miller A, Turner C, Holmes-Talbot K, Mank L, Nishimura C, Nguyen TN, Hale S, Francois Watkins LK. Outbreak of multidrug-resistant Salmonella infections in people linked to pig ear pet treats, United States, 2015-2019: results of a multistate investigation. LANCET REGIONAL HEALTH. AMERICAS 2024; 34:100769. [PMID: 38817954 PMCID: PMC11137515 DOI: 10.1016/j.lana.2024.100769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/17/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
Background International distribution of contaminated foods can be a source of Salmonella infections in people and can contribute to the spread of antimicrobial-resistant bacteria across countries. We report an investigation led by the United States Centers for Disease Control and Prevention, the Food and Drug Administration (FDA), and state governmental officials into a multistate outbreak of salmonellosis linked to pig ear pet treats. Methods Pig ear treats and companion dogs were tested for Salmonella by state officials and the FDA. Products were traced back to the country of origin when possible. Cases were defined as outbreak illnesses in people associated with one of seven Salmonella serotypes genetically related to samples from pig ear pet treats, with isolation dates from June 2015 to September 2019. Whole genome sequencing (WGS) of isolates was used to predict antimicrobial resistance. Findings The outbreak included 154 human cases in 34 states. Of these, 107 of 122 (88%) patients reported dog contact, and 65 of 97 (67%) reported contact with pig ear pet treats. Salmonella was isolated from 137 pig ear treats, including some imported from Argentina, Brazil, and Colombia, and from four dogs. WGS predicted 77% (105/137) of human and 43% (58/135) of pig ear treat isolates were resistant to ≥3 antimicrobial classes. Interpretation This was the first documented United States multistate outbreak of Salmonella infections linked to pig ear pet treats. This multidrug-resistant outbreak highlights the interconnectedness of human health and companion animal ownership and the need for zoonotic pathogen surveillance to prevent human illness resulting from internationally transported pet food products. Funding Animal Feed Regulatory Program Standards award. Animal and product testing conducted by FDA Vet-LIRN was funded by Vet-LIRN infrastructure grants (PAR-22-063).
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Affiliation(s)
- Megin Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - G. Sean Stapleton
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - David S. Rotstein
- Office of Surveillance and Compliance, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, USA
| | - Lauren Gollarza
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer Adams
- Association of Public Health Laboratories, Silver Spring, MD, USA
| | - Hayat Caidi
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - April Hodges
- Office of Surveillance and Compliance, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, USA
| | - Mark Glover
- Office of Surveillance and Compliance, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, USA
| | - Sarah Peloquin
- Veterinary Laboratory Investigation and Response Network, Office of Applied Science, Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, USA
| | - Lloyd Payne
- Office of Surveillance and Compliance, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, USA
| | - Anne Norris
- Office of the Director, Strategic Communications, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, USA
| | - Siobhan DeLancey
- Office of the Director, Strategic Communications, Center for Veterinary Medicine, United States Food and Drug Administration, Rockville, MD, USA
| | - Danielle Donovan
- Michigan Department of Health & Human Services, Lansing, MI, USA
| | - Steve Dietrich
- Michigan Department of Health & Human Services, Lansing, MI, USA
| | - Stevie Glaspie
- Michigan Department of Agriculture & Rural Development, MI, USA
| | | | | | - Beth Holben
- Michigan Department of Health & Human Services, Lansing, MI, USA
| | - Karen Pietrzen
- Michigan Department of Agriculture & Rural Development, MI, USA
| | - Scott Benko
- Michigan Department of Agriculture & Rural Development, MI, USA
| | | | - Sydney Orel
- Kansas Department of Agriculture Laboratory, Manhattan, KS, USA
| | - Daniel Neises
- Kansas Department of Health and Environment, Topeka, KS, USA
| | | | - Bradley Tobin
- Pennsylvania Department of Agriculture, Harrisburg, PA, USA
| | | | | | - Adam Miller
- Rhode Island Department of Health, Providence, RI, USA
| | | | | | - Laurn Mank
- Connecticut Department of Public Health, Hartford, CT, USA
| | | | - Tu Ngoc Nguyen
- Connecticut Department of Public Health, Hartford, CT, USA
| | - Shelby Hale
- Ohio Department of Health, Columbus, OH, USA
| | - Louise K. Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Brandenburg JM, Stapleton GS, Kline KE, Khoury J, Mallory K, Machesky KD, Ladd-Wilson SG, Scholz R, Freiman J, Schwensohn C, Palacios A, Gieraltowski L, Ellison Z, Tolar B, Webb HE, Tagg KA, Salah Z, Nichols M. Salmonella Hadar linked to two distinct transmission vehicles highlights challenges to enteric disease outbreak investigations. Epidemiol Infect 2024; 152:e86. [PMID: 38736416 PMCID: PMC11384159 DOI: 10.1017/s0950268824000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.
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Affiliation(s)
- Joshua M Brandenburg
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Gregory Sean Stapleton
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Kelly E Kline
- Pennsylvania Department of Health, Harrisburg, PA, USA
| | | | - Krystle Mallory
- New Hampshire Division of Public Health Services, Concord, NH, USA
| | | | | | - Ryan Scholz
- Oregon Department of Agriculture, Salem, OR, USA
| | - Jennifer Freiman
- U.S. Department of Agriculture, Office of Public Health Science, Food Safety and Inspection Service, Washington, DC, USA
| | - Colin Schwensohn
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alexandra Palacios
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Laura Gieraltowski
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Zachary Ellison
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- ASRT, Inc., Suwanee, GA, USA
| | - Beth Tolar
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hattie E Webb
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kaitlin A Tagg
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Zainab Salah
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Megin Nichols
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Powell MR, Williams MS. Trends in Salmonella Infantis human illness incidence and chicken carcass prevalence in the United States; 1996-2019. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2024. [PMID: 38616416 DOI: 10.1111/risa.14311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
The incidence of human illness due to Salmonella Infantis reported to Foodborne Diseases Active Surveillance Network and the prevalence of Infantis on chicken carcasses reported by the United States Department of Agriculture Food Safety and Inspection Service have increased significantly in the past decade. However, the trends do not appear coincident, as would be expected if the increased prevalence in chicken led to the increase in the incidence of human illness. Salmonella Infantis incidence and prevalence trends are analyzed using penalized B-spline methods for generalized additive regression models. The association between the two time series is analyzed using time-lagged rank-order cross-correlation. Geographic variations in reported incidence and trends are also explored. The increase in human incidence of Salmonella Infantis began circa 2011. The increase in chicken carcass prevalence began circa 2015. A 4-year lag on chicken carcass prevalence maximizes the rank-order cross-correlation with the incidence of illness. While chicken consumption undoubtedly contributes to the incidence of human illness due to Salmonella Infantis, the initial increase in reported illness was likely due to one or more other transmission pathways. Other potential transmission pathways include non-chicken foodborne, waterborne, person-to-person, animal contact, and environmental.
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Affiliation(s)
- Mark R Powell
- Office of Risk Assessment and Cost Benefit Analysis, US Department of Agriculture, Washington, DC, USA
| | - Michael S Williams
- Food Safety and Inspection Service, US Department of Agriculture, Fort Collins, Colorado, USA
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8
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Dickinson MC, Wirth SE, Baker D, Kidney AM, Mitchell KK, Nazarian EJ, Shudt M, Thompson LM, Gubbala Venkata SL, Musser KA, Mingle L. Implementation of a high-throughput whole genome sequencing approach with the goal of maximizing efficiency and cost effectiveness to improve public health. Microbiol Spectr 2024; 12:e0388523. [PMID: 38451098 PMCID: PMC10986607 DOI: 10.1128/spectrum.03885-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
This manuscript describes the development of a streamlined, cost-effective laboratory workflow to meet the demands of increased whole genome sequence (WGS) capacity while achieving mandated quality metrics. From 2020 to 2021, the Wadsworth Center Bacteriology Laboratory (WCBL) used a streamlined workflow to sequence 5,743 genomes that contributed sequence data to nine different projects. The combined use of the QIAcube HT, Illumina DNA Prep using quarter volume reactions, and the NextSeq allowed the WCBL to process all samples that required WGS while also achieving a median turn-around time of 7 days (range 4 to 10 days) and meeting minimum sequence quality requirements. Public Health Laboratories should consider implementing these methods to aid in meeting testing requirements within budgetary restrictions. IMPORTANCE Public Health Laboratories that implement whole genome sequencing (WGS) technologies may struggle to find the balance between sample volume and cost effectiveness. We present a method that allows for sequencing of a variety of bacterial isolates in a cost-effective manner. This report provides specific strategies to implement high-volume WGS, including an innovative, low-cost solution utilizing a novel quarter volume sequencing library preparation. The methods described support the use of high-throughput DNA extraction and WGS within budgetary constraints, strengthening public health responses to outbreaks and disease surveillance.
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Affiliation(s)
- Michelle C. Dickinson
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Samantha E. Wirth
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Deborah Baker
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Anna M. Kidney
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Kara K. Mitchell
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Elizabeth J. Nazarian
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health (NYSDOH), Advanced Genomic Technologies Cluster, Albany, New York, USA
| | - Lisa M. Thompson
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Sai Laxmi Gubbala Venkata
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
| | - Lisa Mingle
- Wadsworth Center, New York State Department of Health (NYSDOH), Division of Infectious Diseases Bacteriology Laboratory, Albany, New York, USA
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9
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Francois Watkins LK, Luna S, Bruce BB, Medalla F, Reynolds JL, Ray LC, Wilson EL, Caidi H, Griffin PM. Clinical Outcomes of Patients With Nontyphoidal Salmonella Infections by Isolate Resistance-Foodborne Diseases Active Surveillance Network, 10 US Sites, 2004-2018. Clin Infect Dis 2024; 78:535-543. [PMID: 37823421 PMCID: PMC10954391 DOI: 10.1093/cid/ciad631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Nontyphoidal Salmonella causes an estimated 1.35 million US infections annually. Antimicrobial-resistant strains are a serious public health threat. We examined the association between resistance and the clinical outcomes of hospitalization, length-of-stay ≥3 days, and death. METHODS We linked epidemiologic data from the Foodborne Diseases Active Surveillance Network with antimicrobial resistance data from the National Antimicrobial Resistance Monitoring System (NARMS) for nontyphoidal Salmonella infections from 2004 to 2018. We defined any resistance as resistance to ≥1 antimicrobial and clinical resistance as resistance to ampicillin, azithromycin, ceftriaxone, ciprofloxacin, or trimethoprim-sulfamethoxazole (for the subset of isolates tested for all 5 agents). We compared outcomes before and after adjusting for age, state, race/ethnicity, international travel, outbreak association, and isolate serotype and source. RESULTS Twenty percent of isolates (1105/5549) had any resistance, and 16% (469/2969) had clinical resistance. Persons whose isolates had any resistance were more likely to be hospitalized (31% vs 28%, P = .01) or have length-of-stay ≥3 days (20% vs 16%, P = .01). Deaths were rare but more common among those with any than no resistance (1.0% vs 0.4%, P = .01). Outcomes for patients whose isolates had clinical resistance did not differ significantly from those with no resistance. After adjustment, any resistance (adjusted odds ratio 1.23, 95% confidence interval 1.04-1.46) remained significantly associated with hospitalization. CONCLUSIONS We observed a significant association between nontyphoidal Salmonella infections caused by resistant pathogens and likelihood of hospitalization. Clinical resistance was not associated with poorer outcomes, suggesting that factors other than treatment failure (eg, strain virulence, strain source, host factors) may be important.
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Affiliation(s)
- Louise K Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah Luna
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Beau B Bruce
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Felicita Medalla
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jared L Reynolds
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Logan C Ray
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elisha L Wilson
- Colorado Department of Public Health & Environment, Denver, Colorado, USA
| | - Hayat Caidi
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Patricia M Griffin
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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10
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Kim TN, Edmundson AR, Hedberg CW. Foodborne Illness Complaint Systems Detect, and Restaurant Inspection Programs Prevent Restaurant-Associated Foodborne Illness Outbreaks. Foodborne Pathog Dis 2024; 21:92-98. [PMID: 38010953 PMCID: PMC10877379 DOI: 10.1089/fpd.2023.0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Restaurants are important settings for foodborne illness transmission. Environmental health agencies routinely inspect restaurants to assess compliance with food safety regulations. They also evaluate foodborne illness complaints from consumers to detect potential outbreaks of foodborne illness. Local environmental health agencies were surveyed to identify methods used to conduct surveillance for consumer complaints of foodborne illness, link them to inspection grading and disclosure practices, and evaluate the association between these practices and the number of foodborne illness outbreaks in restaurant settings reported to the Centers for Disease Control and Prevention. We developed a novel framework for assessing the effectiveness of restaurant inspection grading and disclosure of inspection results while accounting for any biases introduced by surveillance factors that affect outbreak detection. Our findings showed the importance of routine restaurant inspection grading and disclosure practices as prevention measures and having a centralized database to manage consumer complaints as a useful surveillance tool for detecting outbreaks. Improving consumer complaint system structure and management can bolster outbreak detection and maximize limited public health resources while increasing the efficiency of complaint-based surveillance.
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Affiliation(s)
- Thuy N. Kim
- Division of Environmental Health Sciences, University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
| | - Alexandra R. Edmundson
- Division of Environmental Health Sciences, University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
| | - Craig W. Hedberg
- Division of Environmental Health Sciences, University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
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11
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Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023; 21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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12
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Ahart L, Jacobson D, Rice M, Richins T, Peterson A, Zheng Y, Barratt J, Cama V, Qvarnstrom Y, Montgomery S, Straily A. Retrospective evaluation of an integrated molecular-epidemiological approach to cyclosporiasis outbreak investigations - United States, 2021. Epidemiol Infect 2023; 151:e131. [PMID: 37466070 PMCID: PMC10540164 DOI: 10.1017/s0950268823001176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Cyclosporiasis results from an infection of the small intestine by Cyclospora parasites after ingestion of contaminated food or water, often leading to gastrointestinal distress. Recent developments in temporally linking genetically related Cyclospora isolates demonstrated effectiveness in supporting epidemiological investigations. We used 'temporal-genetic clusters' (TGCs) to investigate reported cyclosporiasis cases in the United States during the 2021 peak-period (1 May - 31 August 2021). Our approach split 655 genotyped isolates into 55 genetic clusters and 31 TGCs. We linked two large multi-state epidemiological clusters (Epidemiologic Cluster 1 [n = 136 cases, 54 genotyped] and Epidemiologic Cluster 2 [n = 42 cases, 15 genotyped]) to consumption of lettuce varieties; however, product traceback did not identify a specific product for either cluster due to the lack of detailed product information. To evaluate the utility of TGCs, we performed a retrospective case study comparing investigation outcomes of outbreaks first detected using epidemiological methods with those of the same outbreaks had TGCs been used to first detect them. Our study results indicate that adjustments to routine epidemiological approaches could link additional cases to epidemiological clusters of cyclosporiasis. Overall, we show that CDC's integrated genotyping and epidemiological investigations provide valuable insights into cyclosporiasis outbreaks in the United States.
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Affiliation(s)
- Lauren Ahart
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David Jacobson
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Marion Rice
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Travis Richins
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Anna Peterson
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Yueli Zheng
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Eagle Global Scientific, San Antonio, TX, USA
| | - Joel Barratt
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vitaliano Cama
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan Montgomery
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anne Straily
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
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13
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Trees E, Poates A, Sabol A, LaFon P, Truong J, Lindsey R. Evaluation of the Illumina iSeq whole genome sequencing system for enteric disease surveillance and outbreak detection. J Microbiol Methods 2023; 211:106784. [PMID: 37451348 DOI: 10.1016/j.mimet.2023.106784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
The Illumina iSeq low-capacity sequencing platform was evaluated for use in foodborne disease surveillance and outbreak detection. The platform produced high quality sequence data comparable to that of the Illumina MiSeq and was cost-effective with fast turn-around time in low sample volume environments.
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Affiliation(s)
- Eija Trees
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA.
| | - Angela Poates
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Ashley Sabol
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Patricia LaFon
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Jenny Truong
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Rebecca Lindsey
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
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14
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Lu D, Liu J, Liu H, Guo Y, Dai Y, Liang J, Chen L, Xu L, Fu P, Li N. Epidemiological Features of Foodborne Disease Outbreaks in Catering Service Facilities - China, 2010-2020. China CDC Wkly 2023; 5:479-484. [PMID: 37408617 PMCID: PMC10318556 DOI: 10.46234/ccdcw2023.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/29/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction In terms of food preparation settings, catering service facilities have been identified as locations with the highest incidence of foodborne disease outbreaks in China. Since 2010, the China National Center for Food Safety Risk Assessment has established the Foodborne Disease Outbreak Surveillance System (FDOSS) to monitor foodborne disease outbreaks. Consequently, data from the FDOSS has provided a more accurate depiction of the epidemic characteristics of outbreaks within these facilities. Methods From 2010 to 2020, the FDOSS gathered data related to the prevalence of outbreaks, cases, hospitalizations, and deaths linked to foodborne disease outbreaks in catering service facilities. This study examined the temporal and geographical distribution, pathogenic factors, and contributing variables of these outbreaks over the course of the decade. Results From 2010 to 2020, China's catering service facilities reported 18,331 outbreaks, which resulted in 206,718 illnesses, 68,561 hospitalizations, and 201 deaths. The second and third quarters of the year accounted for 76.12% of the outbreaks and 72.93% of the cases. The primary pathogenic factors were pathogenic organisms, which caused 4,883 (26.64%) outbreaks, 94,047 (45.50%) cases, 32,170 (46.92%) hospitalizations, and 21 (10.45%) deaths. There were 5,607 (30.59%) outbreaks in restaurants, 2,876 (15.69%) outbreaks from street vendors, and 2,560 (13.97%) outbreaks in employee canteens in China. Conclusions The implementation of relevant control methods, including health education and promotion, is critical for addressing foodborne diseases in catering service facilities. Regular food safety training sessions for restaurant personnel and managers are essential to ensuring the effective management of these health risks.
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Affiliation(s)
- Donglei Lu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jikai Liu
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Hong Liu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yunchang Guo
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yue Dai
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing City, Jiangsu Province, China
| | - Junhua Liang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou City, Guangdong Province, China
| | - Lili Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou City, Zhejiang Province, China
| | - Lizi Xu
- Anhui Provincial Center for Disease Control and Prevention, Hefei City, Anhui Province, China
| | - Ping Fu
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Ning Li
- China National Center for Food Safety Risk Assessment, Beijing, China
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15
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Smith AM, Erasmus LK, Tau NP, Smouse SL, Ngomane HM, Disenyeng B, Whitelaw A, Lawrence CA, Sekwadi P, Thomas J. Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi. Microb Genom 2023; 9. [PMID: 37339282 DOI: 10.1099/mgen.0.001044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi (Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one (n=11 isolates), cluster two (n=13 isolates), and cluster three (n=14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla TEM-1B, catA1, sul1, sul2, dfrA7). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.
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Affiliation(s)
- Anthony Marius Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Linda Kathleen Erasmus
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nomsa Pauline Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon Lucrecia Smouse
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Hlengiwe Mimmy Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Andrew Whitelaw
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charlene Ann Lawrence
- Communicable Disease Control, Service Priorities Coordination, Department of Health, Cape Town, South Africa
| | - Phuti Sekwadi
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
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16
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Baker DJ, Robbins A, Newman J, Anand M, Wolfgang WJ, Mendez-Vallellanes DV, Wirth SE, Mingle LA. Challenges Associated with Investigating Salmonella Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data. Foodborne Pathog Dis 2023; 20:230-236. [PMID: 37335914 PMCID: PMC10282972 DOI: 10.1089/fpd.2022.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Defining investigation-worthy genomic clusters among strains of Salmonella Enteritidis is challenging because of their highly clonal nature. We investigated a cluster identified by core genome multilocus sequence typing (cgMLST) consisting of 265 isolates with isolation dates spanning two and a half years. This cluster experienced chaining, growing to a range of 14 alleles. The volume of isolates and broad allele range of this cluster made it difficult to ascertain whether it represented a common-source outbreak. We explored laboratory-based methods to subdivide and refine this cluster. These methods included using cgMLST with a narrower allele range, whole genome multilocus sequence typing (wgMLST) and high-quality single-nucleotide polymorphism (hqSNP) analysis. At each analysis level, epidemiologists retroactively reviewed exposures, geography, and temporality for potential commonalities. Lowering the threshold to 0 alleles using cgMLST proved an effective method to refine this analysis, resulting in this large cluster being subdivided into 34 smaller clusters. Additional analysis by wgMLST and hqSNP provided enhanced cluster resolution, with the majority of clusters being further refined. These analysis methods combined with more stringent allele thresholds and layering of epidemiologic data proved useful in helping to subdivide this large cluster into actionable subclusters.
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Affiliation(s)
- Deborah J. Baker
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | - Amy Robbins
- New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York, USA
| | - Jennifer Newman
- New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York, USA
| | - Madhu Anand
- New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York, USA
| | - William J. Wolfgang
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | | | - Samantha E. Wirth
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | - Lisa A. Mingle
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
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17
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Wellman A, Bazaco M, Blessington T, Pightling A, Dwarka A, Hintz L, Wise ME, Gieraltowski L, Conrad A, Nguyen TA, Hise K, Viazis S, Beal J. An Overview of Foodborne Sample-Initiated Retrospective Outbreak Investigations and Interagency Collaboration in the United States. J Food Prot 2023; 86:100089. [PMID: 37024093 DOI: 10.1016/j.jfp.2023.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Foodborne outbreak investigations have traditionally included the detection of a cluster of illnesses first, followed by an epidemiologic investigation to identify a food of interest. The increasing use of whole genome sequencing (WGS) subtyping technology for clinical, environmental, and food isolates of foodborne pathogens, and the ability to share and compare the data on public platforms, present new opportunities to identify earlier links between illnesses and their potential sources. We describe a process called sample-initiated retrospective outbreak investigations (SIROI) used by federal public health and regulatory partners in the United States. SIROIs begin with an evaluation of the genomic similarity between bacterial isolates recovered from food or environmental samples and clusters of clinical isolates while subsequent and parallel epidemiologic and traceback investigations are initiated to corroborate their connection. SIROIs allow for earlier hypothesis generation, followed by targeted collection of information about food exposures and the foods and manufacturer of interest, to confirm a link between the illnesses and their source. This often leads to earlier action that could reduce the breadth and burden of foodborne illness outbreaks. We describe two case studies of recent SIROIs and present the benefits and challenges. Benefits include insight into foodborne illness attribution, international collaboration, and opportunities for enhanced food safety efforts in the food industry. Challenges include resource intensiveness, variability of epidemiologic and traceback data, and an increasingly complex food supply chain. SIROIs are valuable in identifying connections among small numbers of illnesses that may span significant time periods; detecting early signals for larger outbreaks or food safety issues associated with manufacturers; improving our understanding of the scope of contamination of foods; and identifying novel pathogen/commodity pairs.
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Affiliation(s)
- Allison Wellman
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland.
| | - Michael Bazaco
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Tyann Blessington
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Asha Dwarka
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Leslie Hintz
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Matthew E Wise
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Amanda Conrad
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thai-An Nguyen
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kelley Hise
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stelios Viazis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Jennifer Beal
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
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18
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Varma JK, Taylor J, Sharfstein JM. Planning For The Next Pandemic: Lab Systems Need Policy Shift To Speed Emerging Infectious Disease Warning And Tracking. Health Aff (Millwood) 2023; 42:366-373. [PMID: 36877905 DOI: 10.1377/hlthaff.2022.01211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Early detection and ongoing monitoring of infectious diseases depends on diagnostic testing. The US has a large, diverse system of public, academic, and private laboratories that develop new diagnostic tests; perform routine testing; and conduct specialized reference testing, such as genomic sequencing. These laboratories operate under a complex mix of laws and regulations at the federal, state, and local levels. The COVID-19 pandemic exposed major weaknesses in the nation's laboratory system, some of which were seen again during the global mpox outbreak in 2022. In this article we review how the US laboratory system has been designed to detect and monitor emerging infections, describe what gaps were revealed during COVID-19, and propose specific steps that policy makers can take both to strengthen the current system and to prepare the US for the next pandemic.
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Affiliation(s)
- Jay K Varma
- Jay K. Varma , Cornell University, New York, New York
| | - Jill Taylor
- Jill Taylor, Association of Public Health Laboratories, Silver Spring, Maryland
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19
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Lakicevic B, Jankovic V, Pietzka A, Ruppitsch W. Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain. J Food Prot 2023; 86:100003. [PMID: 36916580 DOI: 10.1016/j.jfp.2022.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022]
Abstract
Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing (WGS) facilitates foodborne outbreak investigations, pathogen source tracking and tracing geographic distributions of different clonal complexes, routine microbiological/epidemiological surveillance of listeriosis, and quantitative microbial risk assessment. WGS can also be used to predict various genetic traits related to virulence, stress, or antimicrobial resistance, which can be of great benefit for improving food safety management as well as public health.
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Affiliation(s)
- Brankica Lakicevic
- Department for Microbiological and Molecular-biological Testing, Institute of Meat Hygiene and Technology, Belgrade, Serbia.
| | - Vesna Jankovic
- Department for Microbiological and Molecular-biological Testing, Institute of Meat Hygiene and Technology, Belgrade, Serbia
| | - Ariane Pietzka
- Institute of Medical Microbiology and Hygiene/National Reference Laboratory for Listeria Division for Public Health, Austrian Agency for Health and Food Safety, Graz, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene Division for Public Health, Austrian Agency for Health and Food Safety, Vienna, Austria
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20
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Nadon C, Croxen M, Knox N, Tanner J, Zetner A, Yoshida C, Van Domselaar G. Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories. BMC Public Health 2022; 22:1817. [PMID: 36153510 PMCID: PMC9508744 DOI: 10.1186/s12889-022-14210-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada’s public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. Methods We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. Results We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. Conclusions These findings enable the strategic prioritization and deployment of resources to increase Canada’s ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-14210-9.
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Sweet R, Kroon PA, Webber MA. Activity of antibacterial phytochemicals and their potential use as natural food preservatives. Crit Rev Food Sci Nutr 2022; 64:2076-2087. [PMID: 36121430 DOI: 10.1080/10408398.2022.2121255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The risk to human health from bacterial foodborne infection is presently controlled by the addition of antimicrobial preservatives to food. However, the use of chemical preservatives such as sodium nitrite poses a health risk in themselves with concerns around carcinogenic effects. This makes the development of improved preservatives a priority for the food industry. One promising source of novel antimicrobial compounds can be found in nature; phytochemicals, in particular polyphenols are secondary metabolites produced by plants for numerous purposes including antimicrobial defence. There has been significant study of phytochemicals; including quantifying their antimicrobial activity, potential to synergise with current antibiotics and the feasibility of their application as natural food preservatives. However, there remains significant uncertainty about the relative antimicrobial efficacy of different phytochemicals, their mechanisms of action (MOA) and the potential for emergence of bacterial resistance to their effects. This review summarizes recent work relevant to the potential development of phytochemicals as antimicrobial agents.
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Affiliation(s)
- Ryan Sweet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Paul A Kroon
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, Norwich Research Park, Norwich, UK
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22
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Ray LC, Griffin PM, Wymore K, Wilson E, Hurd S, LaClair B, Wozny S, Eikmeier D, Nicholson C, Burzlaff K, Hatch J, Fankhauser M, Kubota K, Huang JY, Geissler A, Payne DC, Tack DM. Changing Diagnostic Testing Practices for Foodborne Pathogens, Foodborne Diseases Active Surveillance Network, 2012-2019. Open Forum Infect Dis 2022; 9:ofac344. [PMID: 35928506 PMCID: PMC9345410 DOI: 10.1093/ofid/ofac344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Pathogen detection has changed with increased use of culture-independent diagnostic tests (CIDTs). CIDTs do not yield isolates, which are necessary to detect outbreaks using whole-genome sequencing. The Foodborne Diseases Active Surveillance Network (FoodNet) monitors clinical laboratory testing practices to improve interpretation of surveillance data and assess availability of isolates. We describe changes in practices over 8 years. METHODS During 2012-2019, 10 FoodNet sites collected standardized data about practices in clinical laboratories (range, 664-723 laboratories) for select enteric pathogens. We assessed changes in practices. RESULTS During 2012-2019, the percentage of laboratories that used only culture methods decreased, with the largest declines for Vibrio (99%-57%) and Yersinia (99%-60%). During 2019, the percentage of laboratories using only CIDTs was highest for Shiga toxin-producing Escherichia coli (43%), Campylobacter (34%), and Vibrio (34%). From 2015 to 2019, the percentage of laboratories that performed reflex culture after a positive CIDT decreased, with the largest declines for Shigella (75%-42%) and Salmonella (70%-38%). The percentage of laboratories that routinely submitted isolates to a public health laboratory decreased for all bacterial pathogens examined from 2015 to 2019. CONCLUSIONS By increasing use of CIDTs and decreasing reflex culture, clinical laboratories have transferred the burden of isolate recovery to public health laboratories. Until technologies allow for molecular subtyping directly from a patient specimen, state public health laboratories should consider updating enteric disease reporting requirements to include submission of isolates or specimens. Public health laboratories need resources for isolate recovery.
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Affiliation(s)
- Logan C Ray
- Correspondence: Logan C. Ray, 1600 Clifton Road NE, Atlanta, GA 30333 ()
| | - Patricia M Griffin
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katie Wymore
- California Department of Public Health,Sacramento, California, USA
| | - Elisha Wilson
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Sharon Hurd
- Connecticut Emerging Infections Program, New Haven, Connecticut, USA
| | | | - Sophia Wozny
- Maryland Department of Health, Baltimore, Maryland, USA
| | - Dana Eikmeier
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Cyndy Nicholson
- New Mexico Emerging Infections Program, Albuquerque, New Mexico, USA
| | - Kari Burzlaff
- New York State Department of Health, Buffalo, New York, USA
| | | | | | - Kristy Kubota
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Jennifer Y Huang
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aimee Geissler
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Daniel C Payne
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Danielle M Tack
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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23
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Poates A, Truong J, Lindsey R, Griswold T, Williams-Newkirk AJ, Carleton H, Trees E. Sequencing of Enteric Bacteria: Library Preparation Procedure Matters for Accurate Identification and Characterization. Foodborne Pathog Dis 2022; 19:569-578. [PMID: 35861967 DOI: 10.1089/fpd.2022.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Enzymatic library preparation kits are increasingly used for bacterial whole genome sequencing. While they offer a rapid workflow, the transposases used in the kits are recognized to be somewhat biased. The aim of this study was to optimize and validate a protocol for the Illumina DNA Prep kit (formerly Nextera DNA Flex) for sequencing enteric pathogens and compare its performance against the Nextera XT kit. One hundred forty-three strains of Campylobacter, Escherichia, Listeria, Salmonella, Shigella, and Vibrio were prepared with both methods and sequenced on the Illumina MiSeq using 300 and/or 500 cycle chemistries. Sequences were compared using core genome multilocus sequence typing (cgMLST), 7-gene multilocus sequence typing (MLST), and detection of markers encoding serotype, virulence, and antimicrobial resistance. Sequences for one Escherichia strain were downsampled to determine the minimum coverage required for the analyses. While organism-specific differences were observed, the Prep libraries generated longer average read lengths and less fragmented assemblies compared to the XT libraries. In downstream analysis, the most notable difference between the kits was observed for Escherichia, particularly for the 300 cycle sequences. The O group was not predicted in 32% and 4% of XT sequences when using blast and kmer algorithms, respectively, while the O group was predicted from all Prep sequences regardless of the algorithm. In addition, the ehxA gene was not detected in 6% of XT sequences and 34% were missing one or more of the type III secretion systems and/or plasmid-associated genes, which were detected in the Prep sequences. The coverage downsampling revealed that acceptable assembly quality and allele detection was achieved at 30 × coverage with the Prep libraries, whereas 40-50 × coverage was required for the XT libraries. The better performance of the Prep libraries was attributed to more even coverage, particularly in genome regions low in GC content.
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Affiliation(s)
- Angela Poates
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jenny Truong
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Rebecca Lindsey
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taylor Griswold
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Heather Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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24
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Zhang L, Qin K, Li Y, Wu L. Public-Public Collaboration for Food Safety Risk Management: Essence, Modes, and Identification of Key Influencing Factors Using DANP. Front Public Health 2022; 10:944090. [PMID: 35910862 PMCID: PMC9326024 DOI: 10.3389/fpubh.2022.944090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Food safety risk management is an important cross-boundary issue from both theoretical and practical standpoints. Because food safety has the social attributes of public goods, public-public collaboration can be considered a particularly important mode of cross-boundary governance. The study aims to provide a theoretical basis for the Chinese government to promote public-public collaboration for food safety risk management by identifying key factors. Methods Based on a review of literature across diverse fields, such as political science, sociology, and new public governance, this study discusses the essence, modes, and dilemma of public-public collaboration for food safety risk management using practical explorations in various countries as the main thread and taking into account the actual situation in China. Moreover, this study quantitatively analyzes the relationships between the dimensions and factors affecting public-public collaboration and identifies key dimensions and factors using the Decision-making Trial and Evaluation Laboratory-based Analytic Network Process (DANP). Results Among the 20 factors in the calculation results of DANP, Lawmaking has the highest value of (fi +ei ) (7.022) and ranks sixth in terms of influence weight. The (fi +ei )value of Professionalism (6.993) ranks second and its influence weight ranks fourth. The (fi +ei ) value of Administrative enforcement (6.722) ranks fifth, and its influence weight ranks seventh. The (fi +ei ) value of Improvement of the social environment (6.699) ranks sixth, and its influence weight ranks fifth. The (fi +ei ) value of Legal authorization (6.614) ranks seventh, and its influence weight ranks tenth. Data analysis indicated that these are the five key factors affecting the governance capacity in public-public collaboration for food safety risk management. Conclusion The legal basis is the most important dimension affecting public-public collaboration. Legislation-based governance, administrative law enforcement-based governance, and social environment improvement-based governance in the behavior and capabilities dimension, professionalism in the basic characteristics dimension, and laws and regulations in the legal basis dimension are the five key factors.
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Affiliation(s)
- Liwei Zhang
- College of Economics and Management, Shanghai Ocean University, Shanghai, China
| | - Ke Qin
- School of Business, Jiangnan University, Wuxi, China
| | - Yufeng Li
- College of Economics and Management, Shanghai Ocean University, Shanghai, China
| | - Linhai Wu
- School of Business, Jiangnan University, Wuxi, China
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25
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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] [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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26
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Hoff C, Nichols M, Gollarza L, Scheftel J, Adams J, Tagg KA, Francois Watkins L, Poissant T, Stapleton GS, Morningstar-Shaw B, Signs K, Bidol S, Donovan D, Basler C. Multistate outbreak of Salmonella Typhimurium linked to pet hedgehogs, United States, 2018-2019. Zoonoses Public Health 2022; 69:167-174. [PMID: 35048538 PMCID: PMC11325814 DOI: 10.1111/zph.12904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/19/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]
Abstract
In December 2018, PulseNet, the national laboratory network for enteric disease surveillance, identified an increase in Salmonella Typhimurium isolates with an uncommon pulsed-field gel electrophoresis pattern which was previously isolated from hedgehogs. CDC, state, and local health partners interviewed patients with a questionnaire that focused on hedgehog exposures, conducted traceback of patients' hedgehog purchases, and collected hedgehog faecal pellets and environmental samples. Isolates in this outbreak were analysed using core-genome multi-locus sequence typing (cgMLST) and compared to sequence data from historic clinical isolates from a 2011-2013 outbreak of Salmonella Typhimurium illnesses linked to pet hedgehogs. Fifty-four illnesses in 23 states were identified between October 2018 and September 2019. Patients ranged from <1 to 95 years, and 65% were female. Eight patients were hospitalized. Eighty-one per cent (29/36) of patients interviewed reported contact with a hedgehog before becoming ill; of these, 21 (72%) reported owning a hedgehog. Analysis of 53 clinical, 11 hedgehog, and two hedgehog bedding isolates from this outbreak, seven hedgehog isolates obtained prior to this outbreak, and two clinical isolates from the 2011-2013 outbreak fell into three distinct groupings (37 isolates in Clade 1 [0-10 alleles], 28 isolates in Clade 2 [0-7 alleles], and eight isolates in Clade 3 [0-12 alleles]) and were collectively related within 0-31 alleles by cgMLST. Purchase information available from 20 patients showed hedgehogs were purchased from multiple breeders across nine states, a pet store, and through an online social media website; a single source of hedgehogs was not identified. This outbreak highlights the ability of genetic sequencing analysis to link historic and ongoing Salmonella illness outbreaks and demonstrates the strain of Salmonella linked to hedgehogs might continue to be a health risk to hedgehog owners unless measures are taken to prevent transmission.
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Affiliation(s)
- Connor Hoff
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Megin Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Gollarza
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joni Scheftel
- Minnesota Department of Health, Saint Paul, Minnesota, USA
| | - Jennifer Adams
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Kaitlin A Tagg
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Weems Design Studio Inc., Decatur, Georgia, USA
| | - Louise Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - G Sean Stapleton
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Brenda Morningstar-Shaw
- Diagnostic Bacteriology and Pathobiology Laboratory, National Veterinary Services Laboratories, United States Department of Agriculture, Ames, Iowa, USA
| | - Kim Signs
- Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Sally Bidol
- Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Danielle Donovan
- Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Colin Basler
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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27
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Nichols M, Gollarza L, Sockett D, Aulik N, Patton E, Watkins LKF, Gambino-Shirley KJ, Folster JP, Chen JC, Tagg KA, Stapleton GS, Trees E, Ellison Z, Lombard J, Morningstar-Shaw B, Schlater L, Elbadawi L, Klos R. Outbreak of Multidrug-Resistant Salmonella Heidelberg Infections Linked to Dairy Calf Exposure, United States, 2015-2018. Foodborne Pathog Dis 2022; 19:199-208. [PMID: 34989634 PMCID: PMC9524362 DOI: 10.1089/fpd.2021.0077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In August 2016, the Wisconsin Department of Health Services notified the U.S. Centers for Disease Control and Prevention of multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg infections in people who reported contact with dairy calves. Federal and state partners investigated this to identify the source and scope of the outbreak and to prevent further illnesses. Cases were defined as human Salmonella Heidelberg infection caused by a strain that had one of seven pulsed-field gel electrophoresis (PFGE) patterns or was related by whole genome sequencing (WGS), with illness onset from January 1, 2015, through July 2, 2018. Patient exposure and calf purchase information was collected and analyzed; calves were traced back from the point of purchase. Isolates obtained from animal and environmental samples collected on-farm were supplied by veterinary diagnostic laboratories and compared with patient isolates using PFGE and WGS. Antimicrobial susceptibility testing by standardized broth microdilution was performed. Sixty-eight patients from 17 states were identified. Forty (63%) of 64 patients noted cattle contact before illness. Thirteen (33%) of 40 patients with exposure to calves reported that calves were sick or had died. Seven individuals purchased calves from a single Wisconsin livestock market. One hundred forty cattle from 14 states were infected with the outbreak strain. WGS indicated that human, cattle, and environmental isolates from the livestock market were genetically closely related. Most isolates (88%) had resistance or reduced susceptibility to antibiotics of ≥5 antibiotic classes. This resistance profile included first-line antibiotic treatments for patients with severe salmonellosis, including ampicillin, ceftriaxone, and ciprofloxacin. In this outbreak, MDR Salmonella Heidelberg likely spread from sick calves to humans, emphasizing the importance of illness surveillance in animal populations to prevent future spillover of this zoonotic disease.
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Affiliation(s)
- Megin Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Gollarza
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Donald Sockett
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin, USA
| | - Nicole Aulik
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin, USA
| | - Elisabeth Patton
- Wisconsin Department of Agriculture, Trade and Consumer Protection, Madison, Wisconsin, USA
| | - Louise K. Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelly J. Gambino-Shirley
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jason P. Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica C. Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaitlin A. Tagg
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Weems Design Studio, Inc., Suwanee, Georgia, USA
| | - Gregory Sean Stapleton
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Eija Trees
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Zachary Ellison
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jason Lombard
- Animal and Plant Health Inspection Service, Veterinary Services, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Brenda Morningstar-Shaw
- Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Linda Schlater
- Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Lina Elbadawi
- Wisconsin Department of Health Services, Madison, Wisconsin, USA
| | - Rachel Klos
- Wisconsin Department of Health Services, Madison, Wisconsin, USA
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28
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Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 2022; 11:giac003. [PMID: 35169842 PMCID: PMC8847733 DOI: 10.1093/gigascience/giac003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. RESULTS As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. CONCLUSIONS Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI's BioSample database.
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Affiliation(s)
- Emma J Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Catarina Inês Mendes
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Andrew J Page
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Nabil-Fareed Alikhan
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Dan Fornika
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5, Canada
| | - Josefina Campos
- INEI-ANLIS “Dr Carlos G. Malbrán,” Buenos Aires C1282AFF, Argentina
| | - Daniel Park
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Idowu B Olawoye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Dominique Anderson
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Rhiannon Cameron
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Lee S Katz
- Center for Food Safety, University of Georgia, Atlanta, GA 30333, USA
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
| | - Allison Black
- Department of Epidemiology, University of Washington, WA 98109, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tanya Barrett
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | | | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin 12277, Germany
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian Alcock
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Emma Hodcroft
- Biozentrum, University of Basel, Basel 3012, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William W L Hsiao
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7 V6T 1Z7, Canada
| | - Ana Tereza R Vasconcelos
- Bioinformatics Laboratory National Laboratory of Scientific Computation LNCC/MCTI, Petrópolis 25651-075, Brazil
| | - Duncan R MacCannell
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
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Sabol A, Joung YJ, VanTubbergen C, Ale J, Ribot EM, Trees E. Assessment of Genetic Stability During Serial In Vitro Passage and In Vivo Carriage. Foodborne Pathog Dis 2021; 18:894-901. [PMID: 34520233 DOI: 10.1089/fpd.2021.0029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, our objective was to evaluate the genetic stability of foodborne bacterial pathogens during serial passage in vitro and persistent in vivo carriage. Six strains of Listeria, Campylobacter, Escherichia, Salmonella, and Vibrio were serially passaged 20 times. Three colonies were picked for whole-genome sequencing (WGS) from passes P0, P5, P10, P15, and P20. In addition, isolates of Salmonella and Escherichia from three patients with persistent infections were sequenced. Genetic stability was evaluated in terms of variations detected in high-quality single-nucleotide polymorphism (hqSNP), core genome multilocus sequence typing (cgMLST), seven-gene MLST, and determinants encoding serotype, antimicrobial resistance (AMR), and virulence. During serial passage, increasing diversity was observed in Listeria, Salmonella, and Vibrio as measured by hqSNPs (from median of 0 SNPs to median of 3-5 SNPs, depending on the organism) and to a lesser extent with cgMLST (from median of 0 alleles to median of 0-5 alleles), while Escherichia and Campylobacter genomes showed minimal variation. The serotype, AMR, and virulence markers remained stable in all organisms. Isolates from persistent infections lasting up to 10 weeks remained genetically stable. However, isolates from a persistent Salmonella enterica ser. Montevideo infection spanning 9 years showed early heterogeneity leading to the emergence of one predominant genotype that continued to evolve over the years, including gains and losses of AMR markers. While the hqSNP and cgMLST variation observed during the serial passage was minimal, culture passages should be limited to as few times as possible before WGS. Our WGS data show that in vivo carriage lasting for a few weeks did not appear to alter the genotype. Longer persistent infections spanning for years, particularly in the presence of selective pressure, may cause changes in the genotype making it challenging to differentiate persistent infections from reinfections.
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Affiliation(s)
- Ashley Sabol
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yoo Jin Joung
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Jerdie Ale
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Efrain M Ribot
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Wakabayashi Y, Harada T, Kawai T, Takahashi Y, Umekawa N, Izumiya H, Kawatsu K. Multilocus Variable-Number Tandem-Repeat Analysis of Enterohemorrhagic Escherichia coli Serogroups O157, O26, and O111 Based on a De Novo Look-Up Table Constructed by Regression Analysis. Foodborne Pathog Dis 2021; 18:647-654. [PMID: 34191598 DOI: 10.1089/fpd.2020.2921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multilocus variable-number tandem-repeat analysis (MLVA) is a widely accepted molecular typing tool for enterohemorrhagic Escherichia coli (EHEC). However, ensuring the accuracy of MLVA data among multiple laboratories remains difficult. We developed a method of constructing adjusted look-up tables, which are necessary for MLVA profiling, at each laboratory using a regression analysis based on electrophoresis data from 24 in-house reference strains. On performing MLVA against 51 EHEC O157 isolates, the repeat numbers of 46 isolates were determined accurately using the look-up table with a 99% prediction interval, an outcome superior to that when using a 95% prediction interval. For the remaining five isolates, although the electrophoresis size fell outside the look-up table, we were able to predict the repeat number accurately by extrapolation or the nearest values of the look-up table. Our approach provides more accurate results than a nonadjusted conventional look-up table for calibrating MLVA profiles.
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Affiliation(s)
- Yuki Wakabayashi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Tetsuya Harada
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Takao Kawai
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yusuke Takahashi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Nao Umekawa
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Hidemasa Izumiya
- Department of Bacteriology 1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Kawatsu
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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31
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Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal Salmonella in London and South East of England, 2016-17. Epidemiol Infect 2021; 149:e164. [PMID: 34196266 PMCID: PMC8314958 DOI: 10.1017/s0950268821001400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
An outbreak surveillance system for Salmonella integrating whole genome sequencing (WGS) and epidemiological data was developed in South East and London in 2016–17 to assess local WGS clusters for triage and investigation. Cases genetically linked within a 5 single-nucleotide polymorphism (SNP) single linkage cluster were assessed using a set of locally agreed thresholds based on time, person and place, for reporting to local health protection teams (HPTs). Between September 2016 and September 2017, 230 unique 5-SNP clusters (442 weekly reports) of non-typhoidal Salmonella 5-SNP WGS clusters were identified, of which 208 unique 5-SNP clusters (316 weekly reports) were not reported to the HPTs. In the remaining 22 unique clusters (126 weekly clusters) reported to HPTs, nine were known active outbreak investigations, seven were below locally agreed thresholds and six exceeded local thresholds. A common source or vehicle was identified in four of six clusters that exceeded locally agreed thresholds. This work demonstrates that a threshold-based surveillance system, taking into account time, place and genetic relatedness, is feasible and effective in directing the use of local public health resources for risk assessment and investigation of non-typhoidal Salmonella clusters.
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Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr. J Clin Microbiol 2021; 59:JCM.02200-20. [PMID: 33177125 DOI: 10.1128/jcm.02200-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022] Open
Abstract
Clostridium perfringens is the second leading cause of bacterial foodborne illness in the United States. The Wadsworth Center (WC) at the New York State Department of Health enumerates infectious dose from primary patient and food samples and, until recently, identified C. perfringens to the species level only. We investigated whether whole-genome sequence-based subtyping could benefit epidemiological investigations of this pathogen, as it has with other enteric organisms. We retrospectively sequenced 76 patient and food samples received between May 2010 and February 2020, including 52 samples linked epidemiologically to 13 outbreaks and 24 sporadic samples not linked to other samples. Phylogenetic trees were built using two Web-based platforms: National Centers for Biotechnology Information Pathogen Detection (NCBI-PD) and GalaxyTrakr (a Galaxy instance supported by the GenomeTrakr initiative). For GalaxyTrakr analyses, single nucleotide polymorphism (SNP) matrices and maximum-likelihood (ML) trees were generated using 3 different reference genomes. Across the four separate analyses, phylogenetic clustering was generally concordant with epidemiologically identified outbreaks. SNP diversity among phylogenetically linked samples from an outbreak ranged from 0 to 20 SNPs, excepting one outbreak ranging from 4 to 62 SNPs. Importantly, four of the 13 outbreak isolates harbored one or more samples that were phylogenetic outliers, and for two outbreaks, no samples were closely related. Two specimens were found harboring two distinct genotypes. For samples below CDC enumeration dose threshold, phylogenetic clustering was robust and linked patient and/or food samples. We concluded that WGS phylogenetic clusters (i) are largely concordant with epidemiologically defined outbreaks, irrespective of analysis platform or reference genome we employed; (ii) have limited pairwise SNP diversity, allowing phylogenetic clusters to be distinguished from sporadic cases; and (iii) can aid in epidemiological investigations by identifying outlier and polyclonal samples.
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Allard MW, Zheng J, Cao G, Timme R, Stevens E, Brown EW. Food Safety Genomics and Connections to One Health and the Clinical Microbiology Laboratory. Clin Lab Med 2020; 40:553-563. [PMID: 33121622 DOI: 10.1016/j.cll.2020.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This article describes the potential for one health surveillance of foodborne pathogens and disease using the revolutionary methodologies of whole genome sequencing. Whole genome sequencing of viral and bacterial pathogens is a natural fit to a one health perspective because these pathogens reside and are shared by humans, animals, and the environment and their genomes are compared easily regardless of where or from what host the pathogen was isolated. A genome provides a huge amount of data that can be analyzed for numerous applications. Sharing data coordinates surveillance efforts across the various disciplines.
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Affiliation(s)
- Marc W Allard
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA.
| | - Jie Zheng
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Guojie Cao
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Ruth Timme
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Eric Stevens
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Eric W Brown
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
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Rokney A, Valinsky L, Vranckx K, Feldman N, Agmon V, Moran-Gilad J, Weinberger M. WGS-Based Prediction and Analysis of Antimicrobial Resistance in Campylobacter jejuni Isolates From Israel. Front Cell Infect Microbiol 2020; 10:365. [PMID: 32903472 PMCID: PMC7438411 DOI: 10.3389/fcimb.2020.00365] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/15/2020] [Indexed: 12/03/2022] Open
Abstract
Rapid developments in the field of whole genome sequencing (WGS) make in silico antimicrobial resistance (AMR) a target within reach. Campylobacter jejuni is a leading cause of foodborne infections in Israel with increasing rates of resistance. We applied WGS analysis to study the prevalence and genetic basis of AMR in 263 C. jejuni human and veterinary representative isolates retrieved from a national collection during 2003–2012. We evaluated the prediction of phenotypic AMR from genomic data. Genomes were screened by the NCBI AMRFinderPlus and the BioNumerics tools for acquired AMR genes and point mutations. The results were compared to phenotypic resistance determined by broth microdilution. The most prevalent resistant determinants were the multi-drug efflux transporter gene cmeABC (100%), the tetracycline resistance tet(O) gene (82.1%), the quinolone resistance gyrA T861 point mutation (75.7%), and the aadE streptomycin resistance gene. A variety of 12 known β lactam resistance genes (blaOXA variants) were detected in 241 (92%) isolates, the most prevalent being blaOXA−193, blaOXA−461, and blaOXA−580 (56, 16, and 7%, respectively). Other aminoglycoside resistance genes and the macrolide resistance point mutation were rare (<1%). The overall correlation rate between WGS-based genotypic prediction and phenotypic resistance was 98.8%, sensitivity, specificity, positive, and negative predictive values being 98.0, 99.3, 99.1, and 98.5%, respectively. wgMLST-based phylogeny indicated a high level of clonality and clustering among the studied isolates. Closely related isolates that were part of a genetic cluster (single linkage distance ≤ 15 alleles) based on wgMLST phylogeny mostly shared a homogenous AMR determinant profile. This was observed in 18 of 20 (90.0%) clusters within clonal complex-21, suggesting clonal expansion of resistant isolates. Strong association to lineage was noted for the aadE gene and the various blaOXA genes. High resistance rates to tetracycline and quinolones and a low resistance rate to macrolides were detected among the Israeli C. jejuni isolates. While a high genotypic-phenotypic correlation was found, some resistance phenotypes could not be predicted by the presence of AMR determinants, and particularly not the level of resistance. WGS-based prediction of antimicrobial resistance in C. jejuni requires further optimization in order to integrate this approach in the routine workflow of public health laboratories for foodborne surveillance.
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Affiliation(s)
- Assaf Rokney
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Lea Valinsky
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | | | - Noa Feldman
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Vered Agmon
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Jacob Moran-Gilad
- Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Miriam Weinberger
- Infectious Diseases Unit, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Egli A, Schrenzel J, Greub G. Digital microbiology. Clin Microbiol Infect 2020; 26:1324-1331. [PMID: 32603804 PMCID: PMC7320868 DOI: 10.1016/j.cmi.2020.06.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Digitalization and artificial intelligence have an important impact on the way microbiology laboratories will work in the near future. Opportunities and challenges lie ahead to digitalize the microbiological workflows. Making efficient use of big data, machine learning, and artificial intelligence in clinical microbiology requires a profound understanding of data handling aspects. OBJECTIVE This review article summarizes the most important concepts of digital microbiology. The article gives microbiologists, clinicians and data scientists a viewpoint and practical examples along the diagnostic process. SOURCES We used peer-reviewed literature identified by a PubMed search for digitalization, machine learning, artificial intelligence and microbiology. CONTENT We describe the opportunities and challenges of digitalization in microbiological diagnostic processes with various examples. We also provide in this context key aspects of data structure and interoperability, as well as legal aspects. Finally, we outline the way for applications in a modern microbiology laboratory. IMPLICATIONS We predict that digitalization and the usage of machine learning will have a profound impact on the daily routine of laboratory staff. Along the analytical process, the most important steps should be identified, where digital technologies can be applied and provide a benefit. The education of all staff involved should be adapted to prepare for the advances in digital microbiology.
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Affiliation(s)
- A Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - J Schrenzel
- Laboratory of Bacteriology, University Hospitals of Geneva, Geneva, Switzerland
| | - G Greub
- Institute of Medical Microbiology, University Hospital Lausanne, Lausanne, Switzerland
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St George K, Ned-Sykes R, Salerno R, Pentella MA. Advancing the Public Health Laboratory System Through Partnerships. Public Health Rep 2020; 134:3S-5S. [PMID: 31682554 PMCID: PMC6832028 DOI: 10.1177/0033354919882704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Renée Ned-Sykes
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Reynolds Salerno
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, USA
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