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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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Peng S, Xiong H, Lu J, Luo F, Liu C, Zhou H, Tong W, Xia Z, Liu D. Epidemiological and Whole Genome Sequencing Analysis of Restaurant Salmonella Enteritidis Outbreak Associated with an Infected Food Handler in Jiangxi Province, China, 2023. Foodborne Pathog Dis 2024; 21:316-322. [PMID: 38354216 DOI: 10.1089/fpd.2023.0123] [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: 02/16/2024] Open
Abstract
In China, Salmonella is one of the most frequent causes of bacterial gastroenteritis, and food handlers in restaurants as an important contaminated source were rarely reported. In May 2023, an outbreak of Salmonella enterica serovar Enteritidis infection in a restaurant in Jiangxi Province, China, was investigated. Cases were interviewed. Stool samples from cases, anal swabs from restaurant employees, suspicious raw food materials, and semifinished food were collected and examined. Pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed to determine the relatedness of the pathogen isolates. Antimicrobial resistance genes and virulence genes of isolates were analyzed by WGS. The antimicrobial profile of the isolates was detected by broth microdilution, which involved 20 different antibiotics. Among the 31 patrons, 26 showed gastrointestinal symptoms. Five Salmonella Enteritidis strains were isolated from patients (2), semifinished food (2), and food handler (1). The results of PFGE and single-nucleotide polymorphism showed that these five isolates were identical clones. These findings demonstrated that this outbreak was a restaurant Salmonella Enteritidis outbreak associated with an infected food handler. The rates of resistance to nalidixic acid and colistin and intermediate resistance to ciprofloxacin were 100%, 80%, and 100%, respectively. These outbreak isolates harbored point mutation gyrA p.D87G. The cause of inconsistency between the genotype and phenotype of resistance was deeply discussed. A total of 107 virulence genes were found in each isolate, with many being associated with Salmonella pathogenicity island (SPI)-1 and SPI-2. As an overlooked contamination source, infected food handlers can easily cause large-scale outbreaks. This outbreak highlighted that the government should enhance the training and supervision of food hygiene and safety for food handlers to prevent foodborne outbreaks.
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Affiliation(s)
- Silu Peng
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Huomei Xiong
- Jiujiang Center for Disease Control and Prevention, Jiujiang, China
| | - Jun Lu
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Fei Luo
- Jiujiang Center for Disease Control and Prevention, Jiujiang, China
| | - Chengwei Liu
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Houde Zhou
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Wei Tong
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Zhilu Xia
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Daofeng Liu
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
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3
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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. [PMID: 38686950 DOI: 10.1111/zph.13134] [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: 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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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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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a one health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 DOI: 10.1016/j.anaerobe.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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6
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Strakova N, Michova H, Shagieva E, Ovesna P, Karpiskova R, Demnerova K. Genotyping of Campylobacter jejuni and prediction tools of its antimicrobial resistance. Folia Microbiol (Praha) 2024; 69:207-219. [PMID: 37816942 PMCID: PMC10876727 DOI: 10.1007/s12223-023-01093-5] [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: 03/24/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
Although Campylobacter jejuni is the pathogen responsible for the most common foodborne illness, tracing of the infection source remains challenging due to its highly variable genome. Therefore, one of the aim of the study was to compare three genotyping methods (MLST, PFGE, and mP-BIT) to determine the most effective genotyping tool. C. jejuni strains were divided into 4 clusters based on strain similarity in the cgMLST dendrogram. Subsequently, the dendrograms of the 3 tested methods were compared to determine the accuracy of each method compared to the reference cgMLST method. Moreover, a cost-benefit analysis has showed that MLST had the highest inverse discrimination index (97%) and required less workflow, time, fewer consumables, and low bacterial sample quantity. PFGE was shown to be obsolete both because of its low discriminatory power and the complexity of the procedure. Similarly, mP‑BIT showed low separation results, which was compensated by its high availability. Therefore, our data showed that MLST is the optimal tool for genotyping C. jejuni. Another aim was to compare the antimicrobial resistance to ciprofloxacin, erythromycin, and tetracycline in C. jejuni strains isolated from human, water, air, food, and animal samples by two gene sequence-based prediction methods and to compare them with the actual susceptibility of C. jejuni strains using the disc diffusion method. Both tools, ResFinder and RGI, synchronously predict the antimicrobial susceptibility of C. jejuni and either can be used.
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Affiliation(s)
- Nicol Strakova
- Veterinary Research Institute, Hudcova 296/70, Brno, Czech Republic.
| | - Hana Michova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Ekaterina Shagieva
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Petra Ovesna
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Renata Karpiskova
- Department of Public Health, Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Katerina Demnerova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
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7
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Paphitis K, Habrun CA, Stapleton GS, Reid A, Lee C, Majury A, Murphy A, McClinchey H, Corbeil A, Kearney A, Benedict K, Tolar B, Forrest RO. Salmonella Vitkin Outbreak Associated with Bearded Dragons, Canada and United States, 2020-2022. Emerg Infect Dis 2024; 30:225-233. [PMID: 38270159 PMCID: PMC10826748 DOI: 10.3201/eid3002.230963] [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: 01/26/2024] Open
Abstract
We identified 2 cases of Salmonella enterica serovar Vitkin infection linked by whole-genome sequencing in infants in Ontario, Canada, during 2022. Both households of the infants reported having bearded dragons as pets. The outbreak strain was also isolated from an environmental sample collected from a patient's bearded dragon enclosure. Twelve cases were detected in the United States, and onset dates occurred during March 2021-September 2022 (isolates related to isolates from Canada within 0-9 allele differences by core-genome multilocus sequence typing). Most US patients (66.7%) were <1 year of age, and most (72.7%) had reported bearded dragon exposure. Hospitalization was reported for 5 (38.5%) of 13 patients. Traceback of bearded dragons identified at least 1 potential common supplier in Southeast Asia. Sharing rare serovar information and whole-genome sequencing data between Canada and the United States can assist in timely identification of outbreaks, including those that might not be detected through routine surveillance.
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Frey E, Stapleton GS, Nichols MC, Gollarza LM, Birhane M, Chen JC, McCullough A, Carleton HA, Trees E, Hise KB, Tolar B, Francois Watkins L. Antimicrobial resistance in multistate outbreaks of nontyphoidal Salmonella infections linked to animal contact-United States, 2015-2018. J Clin Microbiol 2024; 62:e0098123. [PMID: 38084949 PMCID: PMC10793259 DOI: 10.1128/jcm.00981-23] [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: 07/28/2023] [Accepted: 11/01/2023] [Indexed: 01/18/2024] Open
Abstract
Animal contact is an established risk factor for nontyphoidal Salmonella infections and outbreaks. During 2015-2018, the U.S. Centers for Disease Control and Prevention (CDC) and other U.S. public health laboratories began implementing whole-genome sequencing (WGS) of Salmonella isolates. WGS was used to supplement the traditional methods of pulsed-field gel electrophoresis for isolate subtyping, outbreak detection, and antimicrobial susceptibility testing (AST) for the detection of resistance. We characterized the epidemiology and antimicrobial resistance (AMR) of multistate salmonellosis outbreaks linked to animal contact during this time period. An isolate was considered resistant if AST yielded a resistant (or intermediate, for ciprofloxacin) interpretation to any antimicrobial tested by the CDC or if WGS showed a resistance determinant in its genome for one of these agents. We identified 31 outbreaks linked to contact with poultry (n = 23), reptiles (n = 6), dairy calves (n = 1), and guinea pigs (n = 1). Of the 26 outbreaks with resistance data available, we identified antimicrobial resistance in at least one isolate from 20 outbreaks (77%). Of 1,309 isolates with resistance information, 247 (19%) were resistant to ≥1 antimicrobial, and 134 (10%) were multidrug-resistant to antimicrobials from ≥3 antimicrobial classes. The use of resistance data predicted from WGS increased the number of isolates with resistance information available fivefold compared with AST, and 28 of 43 total resistance patterns were identified exclusively by WGS; concordance was high (>99%) for resistance determined by AST and WGS. The use of predicted resistance from WGS enhanced the characterization of the resistance profiles of outbreaks linked to animal contact by providing resistance information for more isolates.
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Affiliation(s)
- Erin Frey
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - G. Sean Stapleton
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Megin C. Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren M. Gollarza
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Meseret Birhane
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica C. Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andre McCullough
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC Inc., Atlanta, Georgia, USA
| | - Heather A. Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eija Trees
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelley B. Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Beth Tolar
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Louise Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Habrun CA, Birhane MG, François Watkins LK, Benedict K, Bottichio L, Nemechek K, Tolar B, Schroeder MN, Chen JC, Caidi H, Robyn M, Nichols M. Multistate nontyphoidal Salmonella and Shiga toxin-producing Escherichia coli outbreaks linked to international travel-United States, 2017-2020. Epidemiol Infect 2024; 152:e17. [PMID: 38204341 PMCID: PMC10894901 DOI: 10.1017/s0950268823002017] [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: 06/23/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Enteric bacterial infections are common among people who travel internationally. During 2017-2020, the Centers for Disease Control and Prevention investigated 41 multistate outbreaks of nontyphoidal Salmonella and Shiga toxin-producing Escherichia coli linked to international travel. Resistance to one or more antimicrobial agents was detected in at least 10% of isolates in 16 of 30 (53%) nontyphoidal Salmonella outbreaks and 8 of 11 (73%) Shiga toxin-producing E. coli outbreaks evaluated by the National Antimicrobial Resistance Monitoring System. At least 10% of the isolates in 14 nontyphoidal Salmonella outbreaks conferred resistance to one or more of the clinically significant antimicrobials used in human medicine. This report describes the epidemiology and antimicrobial resistance patterns of these travel-associated multistate outbreaks. Investigating illnesses among returned travellers and collaboration with international partners could result in the implementation of public health interventions to improve hygiene practices and food safety standards and to prevent illness and spread of multidrug-resistant organisms domestically and internationally.
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Affiliation(s)
- Caroline A. Habrun
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Centers for Disease Control and Prevention, Epidemic Intelligence Service Program, Atlanta, GA, USA
| | - Meseret G. Birhane
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Louise K. François 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
| | - Katharine Benedict
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lyndsay Bottichio
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kaylea Nemechek
- 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
| | - Beth Tolar
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Morgan N. Schroeder
- 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 C. 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
| | - 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
| | - Misha Robyn
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 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, GA, USA
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10
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Cersosimo LM, Worley JN, Bry L. Approaching pathogenic Clostridia from a One Health perspective. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574718. [PMID: 38260382 PMCID: PMC10802438 DOI: 10.1101/2024.01.08.574718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M. Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
| | - Jay N. Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- National Center for Biotechnology Information, NIH, Bethesda, MD
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- Clinical Microbiology Laboratory, Dept. Pathology, Brigham & Women's Hospital, Boston, MA
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11
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Lindsey RL, Gladney LM, Huang AD, Griswold T, Katz LS, Dinsmore BA, Im MS, Kucerova Z, Smith PA, Lane C, Carleton HA. Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics. Front Microbiol 2023; 14:1225207. [PMID: 38156000 PMCID: PMC10752928 DOI: 10.3389/fmicb.2023.1225207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023] Open
Abstract
Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.
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Affiliation(s)
- Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, United States
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12
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Yan R, M'ikanatha NM, Nachamkin I, Hudson LK, Denes TG, Kovac J. Prevalence of ciprofloxacin resistance and associated genetic determinants differed among Campylobacter isolated from human and poultry meat sources in Pennsylvania. Food Microbiol 2023; 116:104349. [PMID: 37689423 DOI: 10.1016/j.fm.2023.104349] [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: 07/08/2022] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 09/11/2023]
Abstract
Poultry is the primary source of Campylobacter infections and severe campylobacteriosis cases are treated with macrolides and fluoroquinolones. However, these drugs are less effective against antimicrobial-resistant strains. Here, we investigated the prevalence of phenotypic antimicrobial resistance and associated resistance genetic determinants in Campylobacter isolates collected from human clinical (N = 123) and meat (N = 80) sources in Pennsylvania in 2017 and 2018. Our goal was to assess potential differences in the prevalence of antimicrobial resistance in Campylobacter isolated from human and poultry meat sources in Pennsylvania and to assess the accuracy of predicting antimicrobial resistance phenotypes based on resistance genotypes. We whole genome sequenced isolates and identified genetic resistance determinants using the National Antimicrobial Resistance Monitoring System Campylobacter AMR workflow v2.0 in GalaxyTrakr. Phenotypic antimicrobial susceptibility testing was carried out using the E-Test and Sensititre CAMPYCMV methods for human clinical and poultry meat isolates, respectively, and the results were interpreted using the EUCAST epidemiological cutoff values. The 193 isolates were represented by 85 MLST sequence types and 23 clonal complexes, suggesting high genetic diversity. Resistance to erythromycin was confirmed in 6% human and 4% meat isolates. Prevalence of ciprofloxacin resistance was significantly higher in human isolates as compared to meat isolates. A good concordance was observed between phenotypic resistance and the presence of the corresponding known resistance genetic determinants.
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Affiliation(s)
- Runan Yan
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Irving Nachamkin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauren K Hudson
- Department of Food Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas G Denes
- Department of Food Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
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13
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Gu W, Cui Z, Stroika S, Carleton HA, Conrad A, Katz LS, Richardson LC, Hunter J, Click ES, Bruce BB. Predicting Food Sources of Listeria monocytogenes Based on Genomic Profiling Using Random Forest Model. Foodborne Pathog Dis 2023; 20:579-586. [PMID: 37699246 DOI: 10.1089/fpd.2023.0046] [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: 09/14/2023] Open
Abstract
Listeria monocytogenes can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of L. monocytogenes illness occur, it may be possible to determine the food source of the outbreak. However, most reported L. monocytogenes illnesses do not occur as part of a recognized outbreak and most of the time the food source of sporadic L. monocytogenes illness in people cannot be determined. In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. We investigated whether machine learning approaches applied to wgMLST allele call data could assist in attribution analysis of food source of L. monocytogenes isolates. We compiled isolates with a known source from five food categories (dairy, fruit, meat, seafood, and vegetable) using the metadata of L. monocytogenes isolates in PulseNet, deduplicated closely genetically related isolates, and developed random forest models to predict the food sources of isolates. Prediction accuracy of the final model varied across the food categories; it was highest for meat (65%), followed by fruit (45%), vegetable (45%), dairy (44%), and seafood (37%); overall accuracy was 49%, compared with the naive prediction accuracy of 28%. Our results show that random forest can be used to capture genetically complex features of high-resolution wgMLST for attribution of isolates to their sources.
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Affiliation(s)
- Weidong Gu
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zhaohui Cui
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Steven Stroika
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather A Carleton
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amanda Conrad
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lee S Katz
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - LaTonia C Richardson
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer Hunter
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eleanor S Click
- Division of Foodborne, Waterborne and Environmental Diseases, 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
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14
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Lindsey RL, Prasad A, Feldgarden M, Gonzalez-Escalona N, Kapsak C, Klimke W, Melton-Celsa A, Smith P, Souvorov A, Truong J, Scheutz F. Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States. Microorganisms 2023; 11:2561. [PMID: 37894219 PMCID: PMC10608928 DOI: 10.3390/microorganisms11102561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.
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Affiliation(s)
- Rebecca L. Lindsey
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (C.K.); (P.S.)
| | - Arjun Prasad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA;
| | - Curtis Kapsak
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (C.K.); (P.S.)
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Angela Melton-Celsa
- Department of Microbiology and Immunology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20184, USA;
| | - Peyton Smith
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (C.K.); (P.S.)
| | - Alexandre Souvorov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Jenny Truong
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA;
| | - Flemming Scheutz
- The International Escherichia and Klebsiella Centre, Statens Serum Institut, 2300 Copenhagen, Denmark;
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15
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Leeper MM, Tolar BM, Griswold T, Vidyaprakash E, Hise KB, Williams GM, Im SB, Chen JC, Pouseele H, Carleton HA. Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA. Front Microbiol 2023; 14:1254777. [PMID: 37808298 PMCID: PMC10558246 DOI: 10.3389/fmicb.2023.1254777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Salmonella enterica is a leading cause of bacterial foodborne and zoonotic illnesses in the United States. For this study, we applied four different whole genome sequencing (WGS)-based subtyping methods: high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multilocus sequence typing using either all loci [wgMLST (all loci)] and only chromosome-associated loci [wgMLST (chrom)], and core genome multilocus sequence typing (cgMLST) to a dataset of isolate sequences from 9 well-characterized Salmonella outbreaks. For each outbreak, we evaluated the genomic and epidemiologic concordance between hqSNP and allele-based methods. We first compared pairwise genomic differences using all four methods. We observed discrepancies in allele difference ranges when using wgMLST (all loci), likely caused by inflated genetic variation due to loci found on plasmids and/or other mobile genetic elements in the accessory genome. Therefore, we excluded wgMLST (all loci) results from any further comparisons in the study. Then, we created linear regression models and phylogenetic tanglegrams using the remaining three methods. K-means analysis using the silhouette method was applied to compare the ability of the three methods to partition outbreak and sporadic isolate sequences. Our results showed that pairwise hqSNP differences had high concordance with cgMLST and wgMLST (chrom) allele differences. The slopes of the regressions for hqSNP vs. allele pairwise differences were 0.58 (cgMLST) and 0.74 [wgMLST (chrom)], and the slope of the regression was 0.77 for cgMLST vs. wgMLST (chrom) pairwise differences. Tanglegrams showed high clustering concordance between methods using two statistical measures, the Baker's gamma index (BGI) and cophenetic correlation coefficient (CCC), where 9/9 (100%) of outbreaks yielded BGI values ≥ 0.60 and CCCs were ≥ 0.97 across all nine outbreaks and all three methods. K-means analysis showed separation of outbreak and sporadic isolate groups with average silhouette widths ≥ 0.87 for outbreak groups and ≥ 0.16 for sporadic groups. This study demonstrates that Salmonella isolates clustered in concordance with epidemiologic data using three WGS-based subtyping methods and supports using cgMLST as the primary method for national surveillance of Salmonella outbreak clusters.
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Affiliation(s)
- Molly M. Leeper
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Beth M. Tolar
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Taylor Griswold
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Eshaw Vidyaprakash
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kelley B. Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Grant M. Williams
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sung B. Im
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica C. Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Heather A. Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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16
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Khan MA, Bruce BB, Bottichio L, Wise M. A Bayesian Method for Exposure Prevalence Comparison During Foodborne Disease Outbreak Investigations. Foodborne Pathog Dis 2023; 20:414-418. [PMID: 37578455 DOI: 10.1089/fpd.2023.0059] [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: 08/15/2023] Open
Abstract
CDC and health departments investigate foodborne disease outbreaks to identify a source. To generate and test hypotheses about vehicles, investigators typically compare exposure prevalence among case-patients with the general population using a one-sample binomial test. We propose a Bayesian alternative that also accounts for uncertainty in the estimate of exposure prevalence in the reference population. We compared exposure prevalence in a 2020 outbreak of Escherichia coli O157:H7 illnesses linked to leafy greens with 2018-2019 FoodNet Population Survey estimates. We ran prospective simulations using our Bayesian approach at three time points during the investigation. The posterior probability that leafy green consumption prevalence was higher than the general population prevalence increased as additional case-patients were interviewed. Probabilities were >0.70 for multiple leafy green items 2 weeks before the exact binomial p-value was statistically significant. A Bayesian approach to assessing exposure prevalence among cases could be superior to the one-sample binomial test typically used during foodborne outbreak investigations.
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Affiliation(s)
- Mohammed A Khan
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious 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, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lyndsay Bottichio
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Matthew Wise
- 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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17
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Chen JC, Patel K, Smith PA, Vidyaprakash E, Snyder C, Tagg KA, Webb HE, Schroeder MN, Katz LS, Rowe LA, Howard D, Griswold T, Lindsey RL, Carleton HA. Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens-Associated Outbreaks, 2016-2019. Emerg Infect Dis 2023; 29:1895-1899. [PMID: 37610207 PMCID: PMC10461648 DOI: 10.3201/eid2909.230069] [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: 08/24/2023] Open
Abstract
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.
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Affiliation(s)
| | | | - Peyton A. Smith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Eshaw Vidyaprakash
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Caroline Snyder
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Kaitlin A. Tagg
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Hattie E. Webb
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Morgan N. Schroeder
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Lee S. Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | | | - Dakota Howard
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Taylor Griswold
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Heather A. Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
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18
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Ford L, Shah HJ, Eikmeier D, Hanna S, Chen J, Tagg KA, Langley G, Payne DC, Plumb ID. Antimicrobial-Resistant Nontyphoidal Salmonella Infection Following International Travel-United States, 2018-2019. J Infect Dis 2023; 228:533-541. [PMID: 37129066 PMCID: PMC10839744 DOI: 10.1093/infdis/jiad128] [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: 02/01/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Antimicrobial resistance in nontyphoidal Salmonella (NTS) can limit treatment options. We assessed the contribution of international travel to antimicrobial-resistant NTS infections. METHODS We describe NTS infections that were reported to the Foodborne Diseases Active Surveillance Network during 2018-2019 and screened for genetic resistance determinants, including those conferring decreased susceptibility to first-line agents (ciprofloxacin, ceftriaxone, or azithromycin). We used multivariable logistic regression to assess the association between resistance and international travel during the 7 days before illness began. We estimated the contribution of international travel to resistance using population-attributable fractions, and we examined reported antimicrobial use. RESULTS Among 9301 NTS infections, 1159 (12%) occurred after recent international travel. Predicted resistance to first-line antimicrobials was more likely following travel; the adjusted odds ratio varied by travel region and was highest after travel to Asia (adjusted odds ratio, 7.2 [95% confidence interval, 5.5-9.5]). Overall, 19% (95% confidence interval, 17%-22%) of predicted resistance to first-line antimicrobials was attributable to international travel. More travelers than nontravelers receiving ciprofloxacin or other fluoroquinolones had isolates with predicted resistance to fluoroquinolones (29% vs 9%, respectively; P < .01). CONCLUSIONS International travel is a substantial risk factor for antimicrobial-resistant NTS infections. Understanding risks of resistant infection could help target prevention efforts.
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Affiliation(s)
- Laura Ford
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hazel J. Shah
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dana Eikmeier
- Minnesota Department of Health, St Paul, Minnesota, USA
| | - Samir Hanna
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Jessica Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaitlin A. Tagg
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- ASRT, Inc., Smyrna Georgia, USA
| | - Gayle Langley
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Daniel C. Payne
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ian D. Plumb
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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19
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Shi ZJ, Nayfach S, Pollard KS. Maast: genotyping thousands of microbial strains efficiently. Genome Biol 2023; 24:186. [PMID: 37563669 PMCID: PMC10416524 DOI: 10.1186/s13059-023-03030-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatics tool, Maast, which empowers population genetic meta-analysis of microbes at an unrivaled scale. Maast implements a novel algorithm to heuristically identify a minimal set of diverse conspecific genomes, then constructs a reliable SNP panel for each species, and enables rapid and accurate genotyping using a hybrid of whole-genome alignment and k-mer exact matching. We demonstrate Maast's utility by genotyping thousands of Helicobacter pylori strains and tracking SARS-CoV-2 diversification.
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Affiliation(s)
- Zhou Jason Shi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, USA
| | - Stephen Nayfach
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine S Pollard
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
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20
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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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21
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Townsend A, den Bakker HC, Mann A, Murphy CM, Strawn LK, Dunn LL. 16S microbiome analysis of microbial communities in distribution centers handling fresh produce. Front Microbiol 2023; 14:1041936. [PMID: 37502401 PMCID: PMC10369000 DOI: 10.3389/fmicb.2023.1041936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 05/18/2023] [Indexed: 07/29/2023] Open
Abstract
Little is known about the microbial communities found in distribution centers (DCs), especially in those storing and handling food. As many foodborne bacteria are known to establish residence in food facilities, it is reasonable to assume that DCs handling foods are also susceptible to pathogen colonization. To investigate the microbial communities within DCs, 16S amplicon sequencing was completed on 317 environmental surface sponge swabs collected in DCs (n = 18) across the United States. An additional 317 swabs were collected in parallel to determine if any viable Listeria species were also present at each sampling site. There were significant differences in median diversity measures (observed, Shannon, and Chao1) across individual DCs, and top genera across all reads were Carnobacterium_A, Psychrobacter, Pseudomonas_E, Leaf454, and Staphylococcus based on taxonomic classifications using the Genome Taxonomy Database. Of the 39 16S samples containing Listeria ASVs, four of these samples had corresponding Listeria positive microbiological samples. Data indicated a predominance of ASVs identified as cold-tolerant bacteria in environmental samples collected in DCs. Differential abundance analysis identified Carnobacterium_A, Psychrobacter, and Pseudomonas_E present at a significantly greater abundance in Listeria positive microbiological compared to those negative for Listeria. Additionally, microbiome composition varied significantly across groupings within variables (e.g., DC, season, general sampling location).
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Affiliation(s)
- Anna Townsend
- Department of Food Science and Technology, University of Georgia, Athens, GA, United States
| | - Hendrik C. den Bakker
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, United States
| | - Amy Mann
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, United States
| | - Claire M. Murphy
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Laura K. Strawn
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Laurel L. Dunn
- Department of Food Science and Technology, University of Georgia, Athens, GA, United States
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22
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Pereira E, Conrad A, Tesfai A, Palacios A, Kandar R, Kearney A, Locas A, Jamieson F, Elliot E, Otto M, Kurdilla K, Tijerina M, Son I, Pettengill JB, Chen Y, Fox T, Lane C, Aguillon R, Huffman J, Sheau Fong Low M, Wise M, Edwards L, Bidol S, Blankenship HM, Rosen HE, Leclercq A, Lecuit M, Tourdjman M, Herber H, Singleton LS, Viazis S, Bazaco MC. Multinational Outbreak of Listeria monocytogenes Infections Linked to Enoki Mushrooms Imported from the Republic of Korea 2016-2020. J Food Prot 2023; 86:100101. [PMID: 37169291 PMCID: PMC10947956 DOI: 10.1016/j.jfp.2023.100101] [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: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Keeping the global food supply safe necessitates international collaborations between countries. Health and regulatory agencies routinely communicate during foodborne illness outbreaks, allowing partners to share investigational evidence. A 2016-2020 outbreak of Listeria monocytogenes infections linked to imported enoki mushrooms required a multinational collaborative investigation among the United States, Canada, Australia, and France. Ultimately, this outbreak included 48 ill people, 36 in the United States and 12 in Canada, and was linked to enoki mushrooms sourced from one manufacturer located in the Republic of Korea. Epidemiologic, laboratory, and traceback evidence led to multiple regulatory actions, including extensive voluntary recalls by three firms in the United States and one firm in Canada. In the United States and Canada, the Korean manufacturer was placed on import alert while other international partners provided information about their respective investigations and advised the public not to eat the recalled enoki mushrooms. The breadth of the geographic distribution of this outbreak emphasizes the global reach of the food industry. This investigation provides a powerful example of the impact of national and international coordination of efforts to respond to foodborne illness outbreaks and protect consumers. It also demonstrates the importance of fast international data sharing and collaboration in identifying and stopping foodborne outbreaks in the global community. Additionally, it is a meaningful example of the importance of food sampling, testing, and integration of sequencing results into surveillance databases.
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Affiliation(s)
- Evelyn Pereira
- Food and Drug Administration, College Park, Maryland, USA.
| | - Amanda Conrad
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
| | - Adiam Tesfai
- Food and Drug Administration, College Park, Maryland, USA
| | | | - Rima Kandar
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Ashley Kearney
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Annie Locas
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Fred Jamieson
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Elisa Elliot
- Food and Drug Administration, College Park, Maryland, USA
| | - Mark Otto
- Food and Drug Administration, College Park, Maryland, USA; Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kerry Kurdilla
- Food and Drug Administration, College Park, Maryland, USA
| | - Mary Tijerina
- Food and Drug Administration, College Park, Maryland, USA
| | - Insook Son
- Food and Drug Administration, College Park, Maryland, USA
| | | | - Yi Chen
- Food and Drug Administration, College Park, Maryland, USA
| | - Teresa Fox
- Food and Drug Administration, College Park, Maryland, USA
| | - Chris Lane
- Food and Drug Administration, College Park, Maryland, USA
| | - Ryan Aguillon
- Food and Drug Administration, College Park, Maryland, USA
| | - Jasmine Huffman
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Matthew Wise
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Edwards
- Michigan Department of Agriculture and Rural Development, USA
| | - Sally Bidol
- Michigan Department of Health and Human Services, USA
| | | | | | - Alexandre Leclercq
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, Paris-F, France; Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, Paris-F, France
| | - Marc Lecuit
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, Paris-F, France; Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, Paris-F, France; Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris-F, France
| | | | - Hubert Herber
- Alert Unit, General Directorate for Competition Policy, Consumer Affairs and Fraud Control, French Ministry for the Economy and Finance, France
| | | | - Stelios Viazis
- Food and Drug Administration, College Park, Maryland, USA
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23
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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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24
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Blankenship HM, Dietrich SE, Burgess E, Wholehan J, Soehnlen M, Manning SD. Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation. Microorganisms 2023; 11:1298. [PMID: 37317272 DOI: 10.3390/microorganisms11051298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes high frequencies of foodborne infections worldwide and has been linked to numerous outbreaks each year. Pulsed-field gel electrophoresis (PFGE) has been the gold standard for surveillance until the recent transition to whole-genome sequencing (WGS). To further understand the genetic diversity and relatedness of outbreak isolates, a retrospective analysis of 510 clinical STEC isolates was conducted. Among the 34 STEC serogroups represented, most (59.6%) belonged to the predominant six non-O157 serogroups. Core genome single nucleotide polymorphism (SNP) analysis differentiated clusters of isolates with similar PFGE patterns and multilocus sequence types (STs). One serogroup O26 outbreak strain and another non-typeable (NT) strain, for instance, were identical by PFGE and clustered together by MLST; however, both were distantly related in the SNP analysis. In contrast, six outbreak-associated serogroup O5 strains clustered with five ST-175 serogroup O5 isolates, which were not part of the same outbreak as determined by PFGE. The use of high-quality SNP analyses enhanced the discrimination of these O5 outbreak strains into a single cluster. In all, this study demonstrates how public health laboratories can more rapidly use WGS and phylogenetics to identify related strains during outbreak investigations while simultaneously uncovering important genetic attributes that can inform treatment practices.
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Affiliation(s)
- Heather M Blankenship
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Stephen E Dietrich
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Elizabeth Burgess
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Jason Wholehan
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Marty Soehnlen
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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25
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Joseph LA, Griswold T, Vidyaprakash E, Im SB, Williams GM, Pouseele HA, Hise KB, Carleton HA. Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA. Microb Genom 2023; 9. [PMID: 37133905 DOI: 10.1099/mgen.0.001012] [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: 05/04/2023] Open
Abstract
Campylobacter is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Pulsed-field gene electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST) have been historically used to differentiate sporadic from outbreak Campylobacter isolates. Whole genome sequencing (WGS) has been shown to provide superior resolution and concordance with epidemiological data when compared with PFGE and 7-gene MLST during outbreak investigations. In this study, we evaluated epidemiological concordance for high-quality SNP (hqSNP), core genome (cg)MLST and whole genome (wg)MLST to cluster or differentiate outbreak-associated and sporadic Campylobacter jejuni and Campylobacter coli isolates. Phylogenetic hqSNP, cgMLST and wgMLST analyses were also compared using Baker's gamma index (BGI) and cophenetic correlation coefficients. Pairwise distances comparing all three analysis methods were compared using linear regression models. Our results showed that 68/73 sporadic C. jejuni and C. coli isolates were differentiated from outbreak-associated isolates using all three methods. There was a high correlation between cgMLST and wgMLST analyses of the isolates; the BGI, cophenetic correlation coefficient, linear regression model R 2 and Pearson correlation coefficients were >0.90. The correlation was sometimes lower comparing hqSNP analysis to the MLST-based methods; the linear regression model R 2 and Pearson correlation coefficients were between 0.60 and 0.86, and the BGI and cophenetic correlation coefficient were between 0.63 and 0.86 for some outbreak isolates. We demonstrated that C. jejuni and C. coli isolates clustered in concordance with epidemiological data using WGS-based analysis methods. Discrepancies between allele and SNP-based approaches may reflect the differences between how genomic variation (SNPs and indels) are captured between the two methods. Since cgMLST examines allele differences in genes that are common in most isolates being compared, it is well suited to surveillance: searching large genomic databases for similar isolates is easily and efficiently done using allelic profiles. On the other hand, use of an hqSNP approach is much more computer intensive and not scalable to large sets of genomes. If further resolution between potential outbreak isolates is needed, wgMLST or hqSNP analysis can be used.
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Affiliation(s)
- Lavin A Joseph
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Taylor Griswold
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eshaw Vidyaprakash
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sung B Im
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Grant M Williams
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Kelley B Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Heather A Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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26
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Plumb ID, Brown AC, Stokes EK, Chen JC, Carleton H, Tolar B, Sundararaman P, Saupe A, Payne DC, Shah HJ, Folster JP, Friedman CR. Increased Multidrug-Resistant Salmonella enterica I Serotype 4,[5],12:i:- Infections Associated with Pork, United States, 2009-2018. Emerg Infect Dis 2023; 29. [PMID: 36692335 PMCID: PMC9881761 DOI: 10.3201/eid2902.220950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Reports of Salmonella enterica I serotype 4,[5],12:i:- infections resistant to ampicillin, streptomycin, sulphamethoxazole, and tetracycline (ASSuT) have been increasing. We analyzed data from 5 national surveillance systems to describe the epidemiology, resistance traits, and genetics of infections with this Salmonella strain in the United States. We found ASSuT-resistant Salmonella 4,[5],12:i:- increased from 1.1% of Salmonella infections during 2009-2013 to 2.6% during 2014-2018; the proportion of Salmonella 4,[5],12:i:- isolates without this resistance pattern declined from 3.1% to 2.4% during the same timeframe. Among isolates sequenced during 2015-2018, a total of 69% were in the same phylogenetic clade. Within that clade, 77% of isolates had genetic determinants of ASSuT resistance, and 16% had genetic determinants of decreased susceptibility to ciprofloxacin, ceftriaxone, or azithromycin. Among outbreaks related to the multidrug-resistant clade, 63% were associated with pork consumption or contact with swine. Preventing Salmonella 4,[5],12:i:- carriage in swine would likely avert human infections with this strain.
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27
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Turcotte MR, Smith JT, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020. BMC Genomics 2022; 23:537. [PMID: 35870884 PMCID: PMC9308939 DOI: 10.1186/s12864-022-08769-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/15/2022] [Indexed: 12/27/2022] Open
Abstract
Abstract
Background
The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire’s initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020.
Results
The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927–1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination.
Conclusions
WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.
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28
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Souza SSR, Turcotte MR, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States. Front Microbiol 2022; 13:983083. [PMID: 36338064 PMCID: PMC9626534 DOI: 10.3389/fmicb.2022.983083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Microbes frequently encounter heavy metals and other toxic compounds generated from natural biogeochemical processes and anthropogenic activities. Here, we analyzed the prevalence and association of genes conferring resistance to heavy metals, biocides, and antimicrobial compounds in 394 genome sequences of clinical human-derived S. enterica from New Hampshire, USA. The most prevalent was the gold operon (gesABC-golTSB), which was present in 99.2% of the genomes. In contrast, the other five heavy metal operons (arsenic, copper, mercury, silver, tellurite) were present in 0.76% (3/394)–5.58% (22/394) of the total population. The heavy metal operons and three biocide resistance genes were differentially distributed across 15 sequence types (STs) and 16 serotypes. The number of heavy metal operons and biocide resistance genes per genome was significantly associated with high number of antimicrobial resistance (AMR) genes per genome. Notable is the mercury operon which exhibited significant association with genes conferring resistance to aminoglycosides, cephalosporins, diaminopyrimidine, sulfonamide, and fosfomycin. The mercury operon was co-located with the AMR genes aac(3)-IV, ant(3”)-IIa, aph(3’)-Ia, and aph(4)-Ia, CTX-M-65, dfrA14, sul1, and fosA3 genes within the same plasmid types. Lastly, we found evidence for negative selection of individual genes of each heavy metal operon and the biocide resistance genes (dN/dS < 1). Our study highlights the need for continued surveillance of S. enterica serotypes that carry those genes that confer resistance to heavy metals and biocides that are often associated with mobile AMR genes. The selective pressures imposed by heavy metals and biocides on S. enterica may contribute to the co-selection and spread of AMR in human infections.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- *Correspondence: Stephanie S. R. Souza, ; orcid.org/0000-0002-4207-8231
| | - Madison R. Turcotte
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Kristin L. Wolfe
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | | | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- Cheryl P. Andam, ; orcid.org/0000-0003-4428-0924
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Genome Sequences of 18 Salmonella enterica Serotype Hadar Strains Collected from Patients in the United States. Microbiol Resour Announc 2022; 11:e0052222. [PMID: 36036604 PMCID: PMC9583786 DOI: 10.1128/mra.00522-22] [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] [Indexed: 11/29/2022] Open
Abstract
Despite being linked to a number of recent poultry-associated outbreaks in the United States, few reference genomes are available for Salmonella enterica serotype Hadar. Here, we address this need by reporting 18 Salmonella Hadar genomes from samples collected from patients in the United States between 2014 and 2020.
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30
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Ochieng C, Chen JC, Osita MP, Katz LS, Griswold T, Omballa V, Ng’eno E, Ouma A, Wamola N, Opiyo C, Achieng L, Munywoki PK, Hendriksen RS, Freeman M, Mikoleit M, Juma B, Bigogo G, Mintz E, Verani JR, Hunsperger E, Carleton HA. Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya. PLoS Negl Trop Dis 2022; 16:e0010704. [PMID: 36007074 PMCID: PMC9451065 DOI: 10.1371/journal.pntd.0010704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/07/2022] [Accepted: 07/28/2022] [Indexed: 11/18/2022] Open
Abstract
A high burden of Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) bacteremia has been reported from urban informal settlements in sub-Saharan Africa, yet little is known about the introduction of these strains to the region. Understanding regional differences in the predominant strains of S. Typhi can provide insight into the genomic epidemiology. We genetically characterized 310 S. Typhi isolates from typhoid fever surveillance conducted over a 12-year period (2007–2019) in Kibera, an urban informal settlement in Nairobi, Kenya, to assess the circulating strains, their antimicrobial resistance attributes, and how they relate to global S. Typhi isolates. Whole genome multi-locus sequence typing (wgMLST) identified 4 clades, with up to 303 pairwise allelic differences. The identified genotypes correlated with wgMLST clades. The predominant clade contained 290 (93.5%) isolates with a median of 14 allele differences (range 0–52) and consisted entirely of genotypes 4.3.1.1 and 4.3.1.2. Resistance determinants were identified exclusively in the predominant clade. Determinants associated with resistance to aminoglycosides were observed in 245 isolates (79.0%), sulphonamide in 243 isolates (78.4%), trimethoprim in 247 isolates (79.7%), tetracycline in 224 isolates (72.3%), chloramphenicol in 247 isolates (79.6%), β-lactams in 239 isolates (77.1%) and quinolones in 62 isolates (20.0%). Multidrug resistance (MDR) determinants (defined as determinants conferring resistance to ampicillin, chloramphenicol and cotrimoxazole) were found in 235 (75.8%) isolates. The prevalence of MDR associated genes was similar throughout the study period (2007–2012: 203, 76.3% vs 2013–2019: 32, 72.7%; Fisher’s Exact Test: P = 0.5478, while the proportion of isolates harboring quinolone resistance determinants increased (2007–2012: 42, 15.8% and 2013–2019: 20, 45.5%; Fisher’s Exact Test: P<0.0001) following a decline in S. Typhi in Kibera. Some isolates (49, 15.8%) harbored both MDR and quinolone resistance determinants. There were no determinants associated with resistance to cephalosporins or azithromycin detected among the isolates sequenced in this study. Plasmid markers were only identified in the main clade including IncHI1A and IncHI1B(R27) in 226 (72.9%) isolates, and IncQ1 in 238 (76.8%) isolates. Molecular clock analysis of global typhoid isolates and isolates from Kibera suggests that genotype 4.3.1 has been introduced multiple times in Kibera. Several genomes from Kibera formed a clade with genomes from Kenya, Malawi, South Africa, and Tanzania. The most recent common ancestor (MRCA) for these isolates was from around 1997. Another isolate from Kibera grouped with several isolates from Uganda, sharing a common ancestor from around 2009. In summary, S. Typhi in Kibera belong to four wgMLST clades one of which is frequently associated with MDR genes and this poses a challenge in treatment and control. Typhoid fever is a major public health concern in endemic regions. Understanding the circulating strains of S. Typhi, could provide insight into the genomic epidemiology and guide in the choice of appropriate antibiotics. In this paper, our aim was to characterize S. Typhi strains causing invasive disease in Kibera, where a high typhoid burden has been described. We also aim to understand the evolutionary history of these strains and how antimicrobial resistance determinants have changed over time. We found that there was low diversity of S. Typhi observed in Kibera isolates with isolates grouping into 4 wgMLST clades and five genotypes. The majority (93.5%) of the isolates belonged to genotype 4.3.1; phylodynamic analysis suggest isolates of this genotype from Kibera are related to other 4.3.1 isolates from Africa and this genotype has been introduced multiple times in Kibera. This genotype in particular warrants close monitoring to inform antibiotic strategy in this population. Furthermore, concurrent detection of gene markers for MDR and quinolone resistance in some isolates raise concern about the potential emergence of extensive drug resistant (XDR) strains. Additional surveillance is needed in Kibera to monitor changing trends in resistance that may require altering clinical treatment, and to inform other preventive measures such as typhoid-conjugate vaccine introduction.
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Affiliation(s)
- Caroline Ochieng
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Jessica C. Chen
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mike Powel Osita
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Lee S. Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Taylor Griswold
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victor Omballa
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Eric. Ng’eno
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Alice Ouma
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Newton Wamola
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Christine Opiyo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Loicer Achieng
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Patrick K. Munywoki
- Centers for Disease Control and Prevention-Kenya, Division of Global Health Protection, Nairobi, Kenya
| | - Rene S. Hendriksen
- Technical University of Denmark, National Food Institute, DTU-Food. Kemitorvet, Denmark
| | - Molly Freeman
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Matthew Mikoleit
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bonventure Juma
- Centers for Disease Control and Prevention-Kenya, Division of Global Health Protection, Nairobi, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Eric Mintz
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jennifer R. Verani
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Centers for Disease Control and Prevention-Kenya, Division of Global Health Protection, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Centers for Disease Control and Prevention-Kenya, Division of Global Health Protection, Nairobi, Kenya
| | - Heather A. Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems. NPJ Sci Food 2022; 6:35. [PMID: 35974024 PMCID: PMC9381742 DOI: 10.1038/s41538-022-00150-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.
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32
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Five Complete
Salmonella enterica
Serotype Reading Genomes Recovered from Patients in the United States. Microbiol Resour Announc 2022; 11:e0038822. [PMID: 35727013 PMCID: PMC9302092 DOI: 10.1128/mra.00388-22] [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] [Indexed: 11/20/2022] Open
Abstract
Between 2018 and 2019,
Salmonella enterica
serotype Reading caused a large, multistate outbreak linked to contact with raw turkey products in the United States. Here, we provide five
Salmonella
Reading reference genomes collected from US patients between 2016 and 2018.
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33
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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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34
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Application of Electrolyzed Water in the Food Industry: A Review. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Electrolyzed water is a novel disinfectant and cleaner that has been widely utilized in the food sector for several years to ensure that surfaces are sterilized, and that food is safe. It is produced by the electrolysis of a dilute salt solution, and the reaction products include sodium hydroxide (NaOH) and hypochlorous acid. In comparison to conventional cleaning agents, electrolyzed water is economical and eco-friendly, easy to use, and strongly effective. Electrolyzed water is also used in its acidic form, but it is non-corrosive to the human epithelium and other organic matter. The electrolyzed water can be utilized in a diverse range of foods; thus, it is an appropriate choice for synergistic microbial control in the food industry to ensure food safety and quality without damaging the organoleptic parameters of the food. The present review article highlights the latest information on the factors responsible for food spoilage and the antimicrobial potential of electrolyzed water in fresh or processed plant and animal products.
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35
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Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. J Food Prot 2022; 85:755-772. [PMID: 35259246 DOI: 10.4315/jfp-21-437] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety. HIGHLIGHTS
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Affiliation(s)
- Eric L Stevens
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Heather A Carleton
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jennifer Beal
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Glenn E Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - A C Lauer
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Arthur Pightling
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Karen G Jarvis
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Andrea Ottesen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Padmini Ramachandran
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Leslie Hintz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Lee S Katz
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jason P Folster
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jean M Whichard
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eija Trees
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Ruth E Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Patrick McDERMOTT
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Beverly Wolpert
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Michael Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Sabina Lindley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Beau B Bruce
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eric Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Sandra Tallent
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Kari Irvin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Maria Hoffmann
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Matt Wise
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Robert Tauxe
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Mustafa Simmons
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Bonnie Kissler
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | | | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - James Lindsay
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Kimberly Cook
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Suelee Robbe Austerman
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, Iowa 50010, USA
| | - David Goldman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Sherri McGARRY
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Kis Robertson Hale
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Steven M Musser
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Chris Braden
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
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36
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Whitehill FM, Stapleton GS, Koski L, Sievert D, Nichols M. Risk factors for hospitalization among adults aged ≥65 years with non-typhoidal Salmonella infection linked to backyard poultry contact. Zoonoses Public Health 2022; 69:215-223. [PMID: 35060679 PMCID: PMC10866372 DOI: 10.1111/zph.12911] [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: 05/13/2021] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE We describe the epidemiology of live poultry-associated salmonellosis (LPAS) and investigate potential risk factors associated with hospitalization among adults aged ≥65 years in the United States during 2008-2017. LPAS is a public health concern in the United States, especially among people with increased risk for hospitalization, such as older adults. SAMPLE We analysed data from people aged ≥65 years with non-typhoidal salmonellosis who reported live poultry contact within seven days prior to illness onset. PROCEDURE We used logistic regression to estimate the odds of hospitalization associated with several risk factors including types of live poultry contact exposures. RESULTS LPAS among older adults in this analysis resulted in high hospitalization rates. Salmonella Hadar infection was associated with increased hospitalization. Among older adults with LPAS, 109 individuals of 127 (86%) reported contact with live poultry at their or someone else's residence, and 85 of 105 with available information (81%) reported owning poultry. CONCLUSIONS AND CLINICAL RELEVANCE Additional infection prevention information and education targeted at poultry-owning older adults are needed to prevent illness and hospitalization.
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Affiliation(s)
- Florence M. Whitehill
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Emory University Rollins School of Public Health, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - G. Sean Stapleton
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Lia Koski
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- CAITTA Inc., Herndon, VA, USA
| | - Dawn Sievert
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Megin Nichols
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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37
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Vogt NA, Hetman BM, Vogt AA, Pearl DL, Reid-Smith RJ, Parmley EJ, Kadykalo S, Ziebell K, Bharat A, Mulvey MR, Janecko N, Ricker N, Allen SE, Bondo KJ, Jardine CM. Using whole-genome sequence data to examine the epidemiology of antimicrobial resistance in Escherichia coli from wild meso-mammals and environmental sources on swine farms, conservation areas, and the Grand River watershed in southern Ontario, Canada. PLoS One 2022; 17:e0266829. [PMID: 35395054 PMCID: PMC8993012 DOI: 10.1371/journal.pone.0266829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) threatens the health of humans and animals and has repeatedly been detected in wild animal species across the world. This cross-sectional study integrates whole-genome sequence data from Escherichia coli isolates with demonstrated phenotypic resistance that originated from a previous longitudinal wildlife study in southern Ontario, as well as phenotypically resistant E. coli water isolates previously collected as part of a public health surveillance program. The objective of this work was to assess for evidence of possible transmission of antimicrobial resistance determinants between wild meso-mammals, swine manure pits, and environmental sources on a broad scale in the Grand River watershed, and at a local scale—for the subset of samples collected on both swine farms and conservation areas in the previous wildlife study. Logistic regression models were used to assess potential associations between sampling source, location type (swine farm vs. conservation area), and the occurrence of select resistance genes and predicted plasmids. In total, 200 isolates from the following sources were included: water (n = 20), wildlife (n = 73), swine manure pit (n = 31), soil (n = 73), and dumpsters (n = 3). Several genes and plasmid incompatibility types were significantly more likely to be identified on swine farms compared to conservation areas. Conversely, internationally distributed sequence types (e.g., ST131), extended-spectrum beta-lactamase- and AmpC-producing E. coli were isolated in lower prevalences (<10%) and were almost exclusively identified in water sources, or in raccoon and soil isolates obtained from conservation areas. Differences in the odds of detecting resistance genes and predicted plasmids among various sources and location types suggest different primary sources for individual AMR determinants, but, broadly, our findings suggest that raccoons, skunks and opossums in this region may be exposed to AMR pollution via water and agricultural sources, as well as anthropogenic sources in conservation areas.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Adam A. Vogt
- Independent Researcher, Mississauga, Ontario, Canada
| | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Stefanie Kadykalo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, Ontario, Canada
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Sun Y, Li J, Zhu L, Jiang L. Cooperation and competition between CRISPR- and omics-based technologies in foodborne pathogens detection: a state of the art review. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100813] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Vogt NA, Hetman BM, Vogt AA, Pearl DL, Reid-Smith RJ, Parmley EJ, Kadykalo S, Janecko N, Bharat A, Mulvey MR, Ziebell K, Robertson J, Nash J, Allen V, Majury A, Ricker N, Bondo KJ, Allen SE, Jardine CM. Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data. Front Vet Sci 2022; 9:840416. [PMID: 35280127 PMCID: PMC8914089 DOI: 10.3389/fvets.2022.840416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Non-typhoidal Salmonella infections represent a substantial burden of illness in humans, and the increasing prevalence of antimicrobial resistance among these infections is a growing concern. Using a combination of Salmonella isolate short-read whole-genome sequence data from select human cases, raccoons, livestock and environmental sources, and an epidemiological framework, our objective was to determine if there was evidence for potential transmission of Salmonella and associated antimicrobial resistance determinants between these different sources in the Grand River watershed in Ontario, Canada. Logistic regression models were used to assess the potential associations between source type and the presence of select resistance genes and plasmid incompatibility types. A total of 608 isolates were obtained from the following sources: humans (n = 58), raccoons (n = 92), livestock (n = 329), and environmental samples (n = 129). Resistance genes of public health importance, including blaCMY−2, were identified in humans, livestock, and environmental sources, but not in raccoons. Most resistance genes analyzed were significantly more likely to be identified in livestock and/or human isolates than in raccoon isolates. Based on a 3,002-loci core genome multi-locus sequence typing (cgMLST) scheme, human Salmonella isolates were often more similar to isolates from livestock and environmental sources, than with those from raccoons. Rare instances of serovars S. Heidelberg and S. Enteritidis in raccoons likely represent incidental infections and highlight possible acquisition and dissemination of predominantly poultry-associated Salmonella by raccoons within these ecosystems. Raccoon-predominant serovars were either not identified among human isolates (S. Agona, S. Thompson) or differed by more than 350 cgMLST loci (S. Newport). Collectively, our findings suggest that the rural population of raccoons on swine farms in the Grand River watershed are unlikely to be major contributors to antimicrobial resistant human Salmonella cases in this region.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- *Correspondence: Nadine A. Vogt
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
| | | | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Stefanie Kadykalo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | | | - Anna Majury
- Public Health Ontario, Kingston, ON, Canada
- Department of Biomedical and Molecular Science, Queen's University, Kingston, ON, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Laramie, WY, United States
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, United States
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, ON, Canada
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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 DOI: 10.1111/zph.12904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [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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41
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Waltenburg MA, Schwensohn C, Madad A, Seelman SL, Peralta V, Koske SE, Boyle MM, Arends K, Patel K, Mattioli M, Gieraltowski L, Neil KP. Two multistate outbreaks of a reoccurring Shiga toxin-producing Escherichia coli strain associated with romaine lettuce: USA, 2018-2019. Epidemiol Infect 2021; 150:e16. [PMID: 35060456 PMCID: PMC8796143 DOI: 10.1017/s0950268821002703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/10/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022] Open
Abstract
Leafy green vegetables are a common source of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) foodborne illness outbreaks. Ruminant animals, primarily cattle, are the major reservoir of STEC O157. Epidemiological, traceback and field investigations were conducted to identify potential outbreak sources. Product and environmental samples were tested for STEC. A reoccurring strain of STEC O157 caused two multistate outbreaks linked to romaine lettuce in 2018 and 2019, resulting in 234 illnesses in 33 states. Over 80% of patients interviewed consumed romaine lettuce before illness. The romaine lettuce was sourced from two California growing regions: Santa Maria and Salinas Valley in 2018 and Salinas Valley in 2019. The outbreak strain was isolated from environmental samples collected at sites >90 miles apart across growing regions, as well as from romaine-containing products in 2019. Although the definitive route of romaine contamination was undetermined, use of a contaminated agricultural water reservoir in 2018 and contamination from cattle grazing on adjacent land in 2019 were suspected as possible factors. Preventing lettuce contamination from growth to consumption is imperative to preventing illness. These outbreaks highlight the need to further understand mechanisms of romaine contamination, including the role of environmental or animal reservoirs for STEC O157.
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Affiliation(s)
- Michelle A. Waltenburg
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
- Epidemic Intelligence Service, CDC, Atlanta, Georgia, USA
| | - Colin Schwensohn
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Asma Madad
- United States Food and Drug Administration, College Park, Maryland, USA
| | - Sharon L. Seelman
- United States Food and Drug Administration, College Park, Maryland, USA
| | - Vi Peralta
- California Department of Public Health, Richmond, California, USA
| | - Sarah E. Koske
- Wisconsin Department of Health Services, Madison, Wisconsin, USA
| | | | - Katherine Arends
- Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Kane Patel
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Mia Mattioli
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | - Karen P. Neil
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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42
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Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada. PLoS One 2021; 16:e0260234. [PMID: 34793571 PMCID: PMC8601536 DOI: 10.1371/journal.pone.0260234] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022] Open
Abstract
To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.
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Hudson LK, Andershock WE, Yan R, Golwalkar M, M’ikanatha NM, Nachamkin I, Thomas LS, Moore C, Qian X, Steece R, Garman KN, Dunn JR, Kovac J, Denes TG. Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania. Microorganisms 2021; 9:microorganisms9112300. [PMID: 34835426 PMCID: PMC8625337 DOI: 10.3390/microorganisms9112300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022] Open
Abstract
Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.
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Affiliation(s)
- Lauren K. Hudson
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA;
| | | | - Runan Yan
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA; (R.Y.); (J.K.)
| | - Mugdha Golwalkar
- Tennessee Department of Health, Nashville, TN 37243, USA; (M.G.); (K.N.G.); (J.R.D.)
| | | | - Irving Nachamkin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Linda S. Thomas
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Christina Moore
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Xiaorong Qian
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Richard Steece
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN 37216, USA; (L.S.T.); (C.M.); (X.Q.); (R.S.)
| | - Katie N. Garman
- Tennessee Department of Health, Nashville, TN 37243, USA; (M.G.); (K.N.G.); (J.R.D.)
| | - John R. Dunn
- Tennessee Department of Health, Nashville, TN 37243, USA; (M.G.); (K.N.G.); (J.R.D.)
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA; (R.Y.); (J.K.)
| | - Thomas G. Denes
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA;
- Correspondence:
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Dewart CM, Waltenburg MA, Dietrich S, Machesky K, Singh A, Brandt E, de Fijter S. Cluster of human Salmonella Guinea infections: Reported reptile exposures and associated opportunities for infection prevention - Ohio, 2019-2020. Prev Vet Med 2021; 198:105530. [PMID: 34798304 DOI: 10.1016/j.prevetmed.2021.105530] [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] [Received: 08/23/2021] [Revised: 10/26/2021] [Accepted: 10/31/2021] [Indexed: 11/29/2022]
Abstract
A cluster of five human Salmonella Guinea cases was identified among Ohio residents through core genome multilocus sequence typing of clinical isolates. An investigation was conducted to characterize illnesses and identify common exposures. Four patients were aged ≤5 years and three of four patients with information available regarding exposure to animals reported prior exposure to bearded dragons. Practices that potentially increased the risk for Salmonella transmission from reptiles to humans included allowing pet reptiles to roam freely in the home, cleaning reptile habitats indoors, and kissing reptiles. These findings prompted a multistate investigation that resulted in the identification of additional closely related Salmonella Guinea isolates from patients across multiple states. The investigation of cases in Ohio and information shared by other states indicated the potential association between human Salmonella Guinea infections and reptiles, particularly bearded dragons. To prevent Salmonella transmission from reptiles, continued educational efforts should address pet owners and focus on specific reptile ownership practices.
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Affiliation(s)
- Courtney M Dewart
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA; Ohio Department of Health, Columbus, OH, USA.
| | - Michelle A Waltenburg
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA; Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Atlanta, GA, USA
| | - Stephen Dietrich
- Michigan Department of Health and Human Services, Lansing, MI, USA
| | | | - Amber Singh
- Ohio Department of Health, Columbus, OH, USA
| | - Eric Brandt
- Ohio Department of Health, Columbus, OH, USA
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Salmonella illness outbreaks linked to backyard poultry purchasing during the COVID-19 pandemic: United States, 2020. Epidemiol Infect 2021; 149:e234. [PMID: 34702393 PMCID: PMC8576122 DOI: 10.1017/s0950268821002132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Poultry contact is a risk factor for zoonotic transmission of non-typhoidal Salmonella spp. Salmonella illness outbreaks in the United States are identified by PulseNet, the national laboratory network for enteric disease surveillance. During 2020, PulseNet observed a 25% decline in the number of Salmonella clinical isolates uploaded by state and local health departments. However, 1722 outbreak-associated Salmonella illnesses resulting from 12 Salmonella serotypes were linked to contact with privately owned poultry, an increase from all previous years. This report highlights the need for continued efforts to prevent backyard poultry-associated outbreaks of Salmonella as ownership increases in the United States.
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46
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Bourdichon F, Betts R, Dufour C, Fanning S, Farber J, McClure P, Stavropoulou DA, Wemmenhove E, Zwietering MH, Winkler A. Processing environment monitoring in low moisture food production facilities: Are we looking for the right microorganisms? Int J Food Microbiol 2021; 356:109351. [PMID: 34500287 DOI: 10.1016/j.ijfoodmicro.2021.109351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 11/27/2022]
Abstract
Processing environment monitoring is gaining increasing importance in the context of food safety management plans/HACCP programs, since past outbreaks have shown the relevance of the environment as contamination pathway, therefore requiring to ensure the safety of products. However, there are still many open questions and a lack of clarity on how to set up a meaningful program, which would provide early warnings of potential product contamination. Therefore, the current paper aims to summarize and evaluate existing scientific information on outbreaks, relevant pathogens in low moisture foods, and knowledge on indicators, including their contribution to a "clean" environment capable of limiting the spread of pathogens in dry production environments. This paper also outlines the essential elements of a processing environment monitoring program thereby supporting the design and implementation of better programs focusing on the relevant microorganisms. This guidance document is intended to help industry and regulators focus and set up targeted processing environment monitoring programs depending on their purpose, and therefore provide the essential elements needed to improve food safety.
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Affiliation(s)
- François Bourdichon
- Food Safety, Microbiology, Hygiene, 16 Rue Gaston de Caillavet, 75015 Paris, France; Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy.
| | - Roy Betts
- Campden BRI, Chipping Campden, Gloucestershire, United Kingdom
| | - Christophe Dufour
- Mérieux NutriSciences, 25 Boulevard de la Paix, 95891 Cergy Pontoise, France
| | - Séamus Fanning
- UCD - Centre for Food Safety, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Jeffrey Farber
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Peter McClure
- Mondelēz International, Bournville Lane, Birmingham B30 2LU, United Kingdom
| | | | | | - Marcel H Zwietering
- Food Microbiology, Wageningen University, PO Box 17, 6700AA, Wageningen, The Netherlands
| | - Anett Winkler
- Cargill Germany GmbH, Cerestar str. 2, D-47809 Krefeld, Germany
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Im SB, Gupta S, Jain M, Chande AT, Carleton HA, Jordan IK, Rishishwar L. Genome-Enabled Molecular Subtyping and Serotyping for Shiga Toxin-Producing Escherichia coli. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.752873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Foodborne pathogens are a major public health burden in the United States, leading to 9.4 million illnesses annually. Since 1996, a national laboratory-based surveillance program, PulseNet, has used molecular subtyping and serotyping methods with the aim to reduce the burden of foodborne illness through early detection of emerging outbreaks. PulseNet affiliated laboratories have used pulsed-field gel electrophoresis (PFGE) and immunoassays to subtype and serotype bacterial isolates. Widespread use of serotyping and PFGE for foodborne illness surveillance over the years has resulted in the accumulation of a wealth of routine surveillance and outbreak epidemiological data. This valuable source of data has been used to understand seasonal frequency, geographic distribution, demographic information, exposure information, disease severity, and source of foodborne isolates. In 2019, PulseNet adopted whole genome sequencing (WGS) at a national scale to replace PFGE with higher-resolution methods such as the core genome multilocus sequence typing. Consequently, PulseNet's recent shift to genome-based subtyping methods has rendered the vast collection of historic surveillance data associated with serogroups and PFGE patterns potentially unusable. The goal of this study was to develop a bioinformatics method to associate the WGS data that are currently used by PulseNet for bacterial pathogen subtyping to previously characterized serogroup and PFGE patterns. Previous efforts to associate WGS to PFGE patterns relied on predicting DNA molecular weight based on restriction site analysis. However, these approaches failed owing to the non-uniform usage of genomic restriction sites by PFGE restriction enzymes. We developed a machine learning approach to classify isolates to their most probable serogroup and PFGE pattern, based on comparisons of genomic k-mer signatures. We applied our WGS classification method to 5,970 Shiga toxin-producing Escherichia coli (STEC) isolates collected as part of PulseNet's routine foodborne surveillance activities between 2003 and 2018. Our machine learning classifier is able to associate STEC WGS to higher-level serogroups with very high accuracy and lower-level PFGE patterns with somewhat lower accuracy. Taken together, these classifications support the ability of public health investigators to associate currently generated WGS data with historical epidemiological knowledge linked to serogroups and PFGE patterns in support of outbreak surveillance for food safety and public health.
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48
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Comparison of Conventional Molecular and Whole-Genome Sequencing Methods for Differentiating Salmonella enterica Serovar Schwarzengrund Isolates Obtained from Food and Animal Sources. Microorganisms 2021; 9:microorganisms9102046. [PMID: 34683367 PMCID: PMC8540620 DOI: 10.3390/microorganisms9102046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 11/16/2022] Open
Abstract
Over the last decade, Salmonella enterica serovar Schwarzengrund has become more prevalent in Asia, Europe, and the US with the simultaneous emergence of multidrug-resistant isolates. As these pathogens are responsible for many sporadic illnesses and chronic complications, as well as outbreaks over many countries, improved surveillance is urgently needed. For 20 years, pulsed-field gel electrophoresis (PFGE) has been the gold standard for determining bacterial relatedness by targeting genome-wide restriction enzyme polymorphisms. Despite its utility, recent studies have reported that PFGE results correlate poorly with that of closely related outbreak strains and clonally dominant endemic strains. Due to these concerns, alternative amplification-based molecular methods for bacterial strain typing have been developed, including clustered regular interspaced short palindromic repeats (CRISPR) and multilocus sequence typing (MLST). Furthermore, as the cost of sequencing continues to decrease, whole genome sequencing (WGS) is poised to replace other molecular strain typing methods. In this study, we assessed the discriminatory power of PFGE, CRISPR, MLST, and WGS methods to differentiate between 23 epidemiologically unrelated S. enterica serovar Schwarzengrund isolates collected over an 18-year period from distinct locations in Taiwan. The discriminatory index (DI) of each method for different isolates was calculated, resulting in values between 0 (not discriminatory) and 1 (highly discriminatory). Our results showed that WGS has the greatest resolution (DI = 0.982) compared to PFGE (DI = 0.938), CRISPR (DI = 0.906), and MLST (DI = 0.463) methods. In conclusion, the WGS typing approach was shown to be the most sensitive for S. enterica serovar Schwarzengrund fingerprinting.
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Truong J, Poates A, Joung YJ, Sabol A, Griswold T, Williams-Newkirk AJ, Lindsey R, Trees E. Comparison of four enzymatic library preparation kits for sequencing Shiga toxin-producing Escherichia coli for surveillance and outbreak detection. J Microbiol Methods 2021; 190:106329. [PMID: 34560162 DOI: 10.1016/j.mimet.2021.106329] [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: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022]
Abstract
Four enzymatic DNA library preparation kits were compared for sequencing Shiga toxin-producing E. coli. All kits produced high quality sequence data which performed equally well in the downstream analyses for surveillance and outbreak detection. Important differences were noted in the workflow user-friendliness and per sample cost.
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Affiliation(s)
- Jenny Truong
- 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
| | - Yoo Jin Joung
- 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
| | - Taylor Griswold
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Amanda J Williams-Newkirk
- 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
| | - Eija Trees
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, 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: 3] [Impact Index Per Article: 1.0] [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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