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Hathcock T, Raiford D, Conley A, Barua S, Murillo DFB, Prarat M, Kaur P, Scaria J, Wang C. Antimicrobial-Resistant Escherichia coli, Enterobacter cloacae, Enterococcus faecium, and Salmonella Kentucky Harboring Aminoglycoside and Beta-Lactam Resistance Genes in Raw Meat-Based Dog Diets, USA. Foodborne Pathog Dis 2023; 20:477-483. [PMID: 37615516 DOI: 10.1089/fpd.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
The practice of feeding raw meat-based diets to dogs has grown in popularity worldwide in recent years. However, there are public health risks in handling and feeding raw meat-based dog diets (RMDDs) to dogs since there are no pathogen reduction steps to reduce the microbial load, which may include antimicrobial-resistant pathogenic bacteria. A total of 100 RMDDs from 63 suppliers were sampled, and selective media were used to isolate bacteria from the diets. Bacterial identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) were conducted to identify antimicrobial resistance (AMR). The primary meat sources for RMDDs included in this study were poultry (37%) and beef (24%). Frozen-dry was the main method of product production (68%). In total, 52 true and opportunistic pathogens, including Enterobacterales (mainly Escherichia coli, Enterobacter cloacae) and Enterococcus faecium, were obtained from 30 RMDDs. Resistance was identified to 19 of 28 antimicrobials tested, including amoxicillin/clavulanic acid (23/52, 44%), ampicillin (19/52, 37%), cephalexin (16/52, 31%), tetracycline (7/52, 13%), marbofloxacin (7/52, 13%), and cefazolin (6/52, 12%). All 19 bacterial isolates submitted for WGS harbored at least one type of AMR gene. The identified AMR genes were found to mediate resistance to aminoglycoside (gentamicin, streptomycin, amikacin/kanamycin, gentamicin/kanamycin/tobramycin), macrolide, beta-lactam (carbapenem, cephalosporin), tetracycline, fosfomycin, quinolone, phenicol/quinolone, and sulfonamide. In conclusion, the results of this study suggest that feeding and handling RMDDs may pose a significant public health risk due to the presence of antimicrobial-resistant pathogens, and further research and intervention may be necessary to minimize these risks.
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Affiliation(s)
- Terri Hathcock
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Donna Raiford
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Austin Conley
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Subarna Barua
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | | | - Melanie Prarat
- Ohio Department of Agriculture, Virology, and Molecular Diagnostics, Reynoldsburg, Ohio, USA
| | - Prabhjot Kaur
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Joy Scaria
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
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Mitchell PK, Wang L, Stanhope BJ, Cronk BD, Anderson R, Mohan S, Zhou L, Sanchez S, Bartlett P, Maddox C, DeShambo V, Mani R, Hengesbach LM, Gresch S, Wright K, Mor S, Zhang S, Shen Z, Yan L, Mackey R, Franklin-Guild R, Zhang Y, Prarat M, Shiplett K, Ramachandran A, Narayanan S, Sanders J, Hunkapiller AA, Lahmers K, Carbonello AA, Aulik N, Lim A, Cooper J, Jones A, Guag J, Nemser SM, Tyson GH, Timme R, Strain E, Reimschuessel R, Ceric O, Goodman LB. Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria. Microb Genom 2022; 8:000717. [PMID: 35113783 PMCID: PMC8942033 DOI: 10.1099/mgen.0.000717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-defined bioinformatic protocols, the technological capability to incorporate this technique for real-time surveillance and genomic epidemiology has greatly expanded. There is a need, however, to ensure that data are of high quality. The goal of this study was to assess the utility of a small benchtop sequencing platform using a multi-laboratory verification approach. Thirteen laboratories were provided the same equipment, reagents, protocols and bacterial reference strains. The Illumina DNA Prep and Nextera XT library preparation kits were compared, and 2×150 bp iSeq i100 chemistry was used for sequencing. Analyses comparing the sequences produced from this study with closed genomes from the provided strains were performed using open-source programs. A detailed, step-by-step protocol is publicly available via protocols.io (https://www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw). The throughput for this method is approximately 4-6 bacterial isolates per sequencing run (20-26 Mb total load). The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations. The Prep method produced more consistent coverage compared to XT, and when coverage benchmarks were met, nearly all AMR, virulence and subtyping gene targets were correctly identified. Because it reduces the technical and financial barriers to generating WGS data, the iSeq platform is a viable option for small laboratories interested in genomic surveillance of microbial pathogens.
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Affiliation(s)
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
- *Correspondence: Leyi Wang,
| | | | | | - Renee Anderson
- Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
| | - Shipra Mohan
- Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Lijuan Zhou
- Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA
| | - Paula Bartlett
- Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA
| | - Carol Maddox
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Vanessa DeShambo
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Rinosh Mani
- Michigan State University, Veterinary Diagnostic Laboratory, Lansing, MI, USA
| | | | - Sarah Gresch
- University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA
| | - Katie Wright
- University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA
| | - Sunil Mor
- University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA
| | - Shuping Zhang
- University of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA
| | - Zhenyu Shen
- University of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA
| | - Lifang Yan
- Mississippi State University, Veterinary Diagnostic Laboratory, MS, USA
| | - Rebecca Mackey
- Mississippi State University, Veterinary Diagnostic Laboratory, MS, USA
| | | | - Yan Zhang
- Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Melanie Prarat
- Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Katherine Shiplett
- Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA
| | - Sai Narayanan
- Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA
| | - Justin Sanders
- Oregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA
| | - Andree A. Hunkapiller
- Oregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA
| | - Kevin Lahmers
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | | | - Nicole Aulik
- University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA
| | - Ailam Lim
- University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA
| | - Jennifer Cooper
- University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA
| | - Angelica Jones
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Jake Guag
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Sarah M. Nemser
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Gregory H. Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Ruth Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Silver Spring, MD, USA
| | - Errol Strain
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Renate Reimschuessel
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Olgica Ceric
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Laura B. Goodman
- Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
- *Correspondence: Laura B. Goodman,
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3
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Tyson GH, Ceric O, Guag J, Nemser S, Borenstein S, Slavic D, Lippert S, McDowell R, Krishnamurthy A, Korosec S, Friday C, Pople N, Saab ME, Fairbrother JH, Janelle I, McMillan D, Bommineni YR, Simon D, Mohan S, Sanchez S, Phillips A, Bartlett P, Naikare H, Watson C, Sahin O, Stinman C, Wang L, Maddox C, DeShambo V, Hendrix K, Lubelski D, Burklund A, Lubbers B, Reed D, Jenkins T, Erol E, Patel M, Locke S, Fortner J, Peak L, Balasuriya U, Mani R, Kettler N, Olsen K, Zhang S, Shen Z, Landinez MP, Thornton JK, Thachil A, Byrd M, Jacob M, Krogh D, Webb B, Schaan L, Patil A, Dasgupta S, Mann S, Goodman LB, Franklin-Guild RJ, Anderson RR, Mitchell PK, Cronk BD, Aprea M, Cui J, Jurkovic D, Prarat M, Zhang Y, Shiplett K, Campos DD, Rubio JVB, Ramanchandran A, Talent S, Tewari D, Thirumalapura N, Kelly D, Barnhart D, Hall L, Rankin S, Dietrich J, Cole S, Scaria J, Antony L, Lawhon SD, Wu J, McCoy C, Dietz K, Wolking R, Alexander T, Burbick C, Reimschuessel R. Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring. Vet Microbiol 2021; 254:109006. [PMID: 33581494 DOI: 10.1016/j.vetmic.2021.109006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/28/2021] [Indexed: 02/07/2023]
Abstract
Whole-genome sequencing (WGS) has changed our understanding of bacterial pathogens, aiding outbreak investigations and advancing our knowledge of their genetic features. However, there has been limited use of genomics to understand antimicrobial resistance of veterinary pathogens, which would help identify emerging resistance mechanisms and track their spread. The objectives of this study were to evaluate the correlation between resistance genotypes and phenotypes for Staphylococcus pseudintermedius, a major pathogen of companion animals, by comparing broth microdilution antimicrobial susceptibility testing and WGS. From 2017-2019, we conducted antimicrobial susceptibility testing and WGS on S. pseudintermedius isolates collected from dogs in the United States as a part of the Veterinary Laboratory Investigation and Response Network (Vet-LIRN) antimicrobial resistance monitoring program. Across thirteen antimicrobials in nine classes, resistance genotypes correlated with clinical resistance phenotypes 98.4 % of the time among a collection of 592 isolates. Our findings represent isolates from diverse lineages based on phylogenetic analyses, and these strong correlations are comparable to those from studies of several human pathogens such as Staphylococcus aureus and Salmonella enterica. We uncovered some important findings, including that 32.3 % of isolates had the mecA gene, which correlated with oxacillin resistance 97.0 % of the time. We also identified a novel rpoB mutation likely encoding rifampin resistance. These results show the value in using WGS to assess antimicrobial resistance in veterinary pathogens and to reveal putative new mechanisms of resistance.
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Affiliation(s)
- Gregory H Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States.
| | - Olgica Ceric
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Jake Guag
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Sarah Nemser
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Stacey Borenstein
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Durda Slavic
- University of Guelph - Animal Health Laboratory, Canada
| | - Sarah Lippert
- University of Guelph - Animal Health Laboratory, Canada
| | | | | | - Shannon Korosec
- Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada
| | - Cheryl Friday
- Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada
| | - Neil Pople
- Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada
| | - Matthew E Saab
- Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Canada
| | | | - Isabelle Janelle
- Complexe de diagnostic et d'épidémiosurveillance vétérinaires du Québec, Canada
| | - Deanna McMillan
- University of Saskatchewan - Prairie Diagnostic Services Inc, Canada
| | | | - David Simon
- Bronson Animal Disease Diagnostic Laboratory, United States
| | - Shipra Mohan
- Bronson Animal Disease Diagnostic Laboratory, United States
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States
| | - Ashley Phillips
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States
| | - Paula Bartlett
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States
| | - Hemant Naikare
- University of Georgia - Tifton Veterinary Diagnostic & Investigational Laboratory, United States
| | - Cynthia Watson
- University of Georgia - Tifton Veterinary Diagnostic & Investigational Laboratory, United States
| | | | | | - Leyi Wang
- University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States
| | - Carol Maddox
- University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States
| | - Vanessa DeShambo
- University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States
| | | | - Debra Lubelski
- Indiana Animal Disease Diagnostic Laboratory, United States
| | | | | | - Debbie Reed
- Murray State University Breathitt Veterinary Center, United States
| | - Tracie Jenkins
- Murray State University Breathitt Veterinary Center, United States
| | | | | | | | | | - Laura Peak
- Louisiana State University, United States
| | | | | | | | - Karen Olsen
- University of Minnesota Veterinary Diagnostic Lab, United States
| | - Shuping Zhang
- University of Missouri Veterinary Medical Diagnostic Laboratory, United States
| | - Zhenyu Shen
- University of Missouri Veterinary Medical Diagnostic Laboratory, United States
| | - Martha Pulido Landinez
- Mississippi State University, Veterinary Research and Diagnostic Lab System, United States
| | - Jay Kay Thornton
- Mississippi State University, Veterinary Research and Diagnostic Lab System, United States
| | - Anil Thachil
- North Carolina Veterinary Diagnostic Lab System, United States
| | | | - Megan Jacob
- North Carolina State University, United States
| | - Darlene Krogh
- North Dakota State University Veterinary Diagnostic Laboratory, United States
| | - Brett Webb
- North Dakota State University Veterinary Diagnostic Laboratory, United States
| | - Lynn Schaan
- North Dakota State University Veterinary Diagnostic Laboratory, United States
| | - Amar Patil
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, United States
| | - Sarmila Dasgupta
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, United States
| | - Shannon Mann
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, United States
| | - Laura B Goodman
- Cornell University, College of Veterinary Medicine, United States
| | | | - Renee R Anderson
- Cornell University, College of Veterinary Medicine, United States
| | | | - Brittany D Cronk
- Cornell University, College of Veterinary Medicine, United States
| | - Missy Aprea
- Cornell University, College of Veterinary Medicine, United States
| | - Jing Cui
- Ohio Animal Disease Diagnostic Lab, United States
| | | | | | - Yan Zhang
- Ohio Animal Disease Diagnostic Lab, United States
| | | | - Dubra Diaz Campos
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, United States
| | - Joany Van Balen Rubio
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, United States
| | - Akhilesh Ramanchandran
- Oklahoma Animal Disease Diagnostic Laboraotry, College of Veterinary Medicine, Oklahoma State University, United States
| | - Scott Talent
- Oklahoma Animal Disease Diagnostic Laboraotry, College of Veterinary Medicine, Oklahoma State University, United States
| | - Deepanker Tewari
- PA Veterinary Laboratory, Pennsylvania Department of Agriculture, United States
| | | | - Donna Kelly
- University of Pennsylvania, New Bolton Center, United States
| | - Denise Barnhart
- University of Pennsylvania, New Bolton Center, United States
| | - Lacey Hall
- University of Pennsylvania, New Bolton Center, United States
| | - Shelley Rankin
- University of Pennsylvania, Ryan Veterinary Hospital, United States
| | - Jaclyn Dietrich
- University of Pennsylvania, Ryan Veterinary Hospital, United States
| | - Stephen Cole
- University of Pennsylvania, Ryan Veterinary Hospital, United States
| | - Joy Scaria
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, United States
| | - Linto Antony
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, United States
| | - Sara D Lawhon
- Texas A&M University, College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Pathobiology, United States
| | - Jing Wu
- Texas A&M University, College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Pathobiology, United States
| | - Christine McCoy
- Virginia Department of Agriculture and Consumer Services- Lynchburg Regional Animal Health Laboratory, United States
| | - Kelly Dietz
- Virginia Department of Agriculture and Consumer Services- Lynchburg Regional Animal Health Laboratory, United States
| | | | | | | | - Renate Reimschuessel
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
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4
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Gangiredla J, Rand H, Benisatto D, Payne J, Strittmatter C, Sanders J, Wolfgang WJ, Libuit K, Herrick JB, Prarat M, Toro M, Farrell T, Strain E. GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians. BMC Genomics 2021; 22:114. [PMID: 33568057 PMCID: PMC7877046 DOI: 10.1186/s12864-021-07405-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background Processing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstacles for smaller laboratories, or laboratories not affiliated with larger projects, which may not have dedicated bioinformatics staff or computing power to effectively use genomic data to protect public health. Building on the success of the cloud-based Galaxy bioinformatics platform (http://galaxyproject.org), already known for its user-friendliness and powerful WGS analytical tools, the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration (FDA) created a customized ‘instance’ of the Galaxy environment, called GalaxyTrakr (https://www.galaxytrakr.org), for use by laboratory scientists performing food-safety regulatory research. The goal was to enable laboratories outside of the FDA internal network to (1) perform quality assessments of sequence data, (2) identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive (https://www.ncbi.nlm.nih.gov/sra/), and (3) explore new methodologies such as metagenomics. GalaxyTrakr hosts a variety of free and adaptable tools and provides the data storage and computing power to run the tools. These tools support coordinated analytic methods and consistent interpretation of results across laboratories. Users can create and share tools for their specific needs and use sequence data generated locally and elsewhere. Results In its first full year (2018), GalaxyTrakr processed over 85,000 jobs and went from 25 to 250 users, representing 53 different public and state health laboratories, academic institutions, international health laboratories, and federal organizations. By mid-2020, it has grown to 600 registered users and processed over 450,000 analytical jobs. To illustrate how laboratories are making use of this resource, we describe how six institutions use GalaxyTrakr to quickly analyze and review their data. Instructions for participating in GalaxyTrakr are provided. Conclusions GalaxyTrakr advances food safety by providing reliable and harmonized WGS analyses for public health laboratories and promoting collaboration across laboratories with differing resources. Anticipated enhancements to this resource will include workflows for additional foodborne pathogens, viruses, and parasites, as well as new tools and services.
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Affiliation(s)
- Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20708, Laurel, MD, USA.
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20740, College Park, MD, USA
| | | | - Justin Payne
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20740, College Park, MD, USA
| | - Charles Strittmatter
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20740, College Park, MD, USA
| | | | - William J Wolfgang
- Wadsworth Center, New York State Department of Health, NY, 12201, Albany, USA
| | - Kevin Libuit
- Division of Consolidated Laboratory Services, Department of General Services, VA, 23219, Richmond, USA.,Libuit Scientific LLC, 23219, Richmond, VA, USA
| | - James B Herrick
- Center for Genome and Metagenome Studies, James Madison University, 22807, Harrisonburg, VA, USA
| | - Melanie Prarat
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 43068, Reynoldsburg, Ohio, USA
| | - Magaly Toro
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Thomas Farrell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 20740, College Park, MD, USA
| | - Errol Strain
- Center for Veterinary Medicine, U.S. Food and Drug Administration, MD, 20708, Laurel, USA
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5
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Harris B, Hicks J, Prarat M, Sanchez S, Crossley B. Next-generation sequencing capacity and capabilities within the National Animal Health Laboratory Network. J Vet Diagn Invest 2020; 33:248-252. [PMID: 32608345 PMCID: PMC7953108 DOI: 10.1177/1040638720937015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
With the cost of next-generation sequencing (NGS) decreasing, this technology is rapidly being integrated into the workflows of veterinary clinical and diagnostic laboratories nationwide. The mission of the U.S. Department of Agriculture-National Animal Health Laboratory Network (NAHLN) is in part to evaluate new technologies and develop standardized processes for deploying these technologies to network laboratories for improving detection and response to emerging and foreign animal diseases. Thus, in 2018, the NAHLN identified the integration of NGS into the network as a top priority. In order to assess the current state of preparedness across NAHLN laboratories and to identify which have the capability for performing NGS, a questionnaire was developed by the NAHLN Methods Technical Working Group and submitted to all NAHLN laboratories in December 2018. Thirty of 59 laboratories completed the questionnaire, of which 18 (60%) reported having some sequencing capability. Multiple sequencing platforms and reagents were identified, and limited standardized quality control parameters were reported. Our results confirm that NGS capacity is available within the NAHLN, but several gaps remain. Gaps include not having sufficient personnel trained in bioinformatics and data interpretation, lack of standardized methods and equipment, and maintenance of sufficient computing capacity to meet the growing demand for this technology.
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Affiliation(s)
- Beth Harris
- USDA-APHIS-VS-DB National Animal Health Laboratory Network, Ames, IA
| | - Jessica Hicks
- USDA-APHIS-VS-DB National Veterinary Services Laboratories, Ames, IA
| | - Melanie Prarat
- Ohio Department of Agriculture Animal Disease Diagnostic Laboratory, Reynoldsburg, OH
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA
| | - Beate Crossley
- California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA
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6
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Ceric O, Tyson GH, Goodman LB, Mitchell PK, Zhang Y, Prarat M, Cui J, Peak L, Scaria J, Antony L, Thomas M, Nemser SM, Anderson R, Thachil AJ, Franklin-Guild RJ, Slavic D, Bommineni YR, Mohan S, Sanchez S, Wilkes R, Sahin O, Hendrix GK, Lubbers B, Reed D, Jenkins T, Roy A, Paulsen D, Mani R, Olsen K, Pace L, Pulido M, Jacob M, Webb BT, Dasgupta S, Patil A, Ramachandran A, Tewari D, Thirumalapura N, Kelly DJ, Rankin SC, Lawhon SD, Wu J, Burbick CR, Reimschuessel R. Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada. BMC Vet Res 2019; 15:130. [PMID: 31060608 PMCID: PMC6501310 DOI: 10.1186/s12917-019-1864-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/05/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) of bacterial pathogens is an emerging public health threat. This threat extends to pets as it also compromises our ability to treat their infections. Surveillance programs in the United States have traditionally focused on collecting data from food animals, foods, and people. The Veterinary Laboratory Investigation and Response Network (Vet-LIRN), a national network of 45 veterinary diagnostic laboratories, tested the antimicrobial susceptibility of clinically relevant bacterial isolates from animals, with companion animal species represented for the first time in a monitoring program. During 2017, we systematically collected and tested 1968 isolates. To identify genetic determinants associated with AMR and the potential genetic relatedness of animal and human strains, whole genome sequencing (WGS) was performed on 192 isolates: 69 Salmonella enterica (all animal sources), 63 Escherichia coli (dogs), and 60 Staphylococcus pseudintermedius (dogs). RESULTS We found that most Salmonella isolates (46/69, 67%) had no known resistance genes. Several isolates from both food and companion animals, however, showed genetic relatedness to isolates from humans. For pathogenic E. coli, no resistance genes were identified in 60% (38/63) of the isolates. Diverse resistance patterns were observed, and one of the isolates had predicted resistance to fluoroquinolones and cephalosporins, important antibiotics in human and veterinary medicine. For S. pseudintermedius, we observed a bimodal distribution of resistance genes, with some isolates having a diverse array of resistance mechanisms, including the mecA gene (19/60, 32%). CONCLUSION The findings from this study highlight the critical importance of veterinary diagnostic laboratory data as part of any national antimicrobial resistance surveillance program. The finding of some highly resistant bacteria from companion animals, and the observation of isolates related to those isolated from humans demonstrates the public health significance of incorporating companion animal data into surveillance systems. Vet-LIRN will continue to build the infrastructure to collect the data necessary to perform surveillance of resistant bacteria as part of fulfilling its mission to advance human and animal health. A One Health approach to AMR surveillance programs is crucial and must include data from humans, animals, and environmental sources to be effective.
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Affiliation(s)
- Olgica Ceric
- Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, United States Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, 20708, USA.
| | - Gregory H Tyson
- Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, United States Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, 20708, USA
| | - Laura B Goodman
- Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | - Patrick K Mitchell
- Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | - Yan Zhang
- Ohio Department of Agriculture, Ohio Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Melanie Prarat
- Ohio Department of Agriculture, Ohio Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Jing Cui
- Ohio Department of Agriculture, Ohio Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Laura Peak
- School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Joy Scaria
- Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Linto Antony
- Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Milton Thomas
- Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Sarah M Nemser
- Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, United States Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, 20708, USA
| | - Renee Anderson
- Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | - Anil J Thachil
- Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | | | - Durda Slavic
- Animal Health Laboratory, University of Guelph, Guelph, Canada
| | - Yugendar R Bommineni
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Shipra Mohan
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Rebecca Wilkes
- Tifton Veterinary Diagnostic and Investigational Laboratory, The University of Georgia, Tifton, GA, USA
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - G Kenitra Hendrix
- Animal Disease Diagnostic Laboratory, Purdue University, West Lafayette, IN, USA
| | - Brian Lubbers
- Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Deborah Reed
- Breathitt Veterinary Center, Murray State University, Murray, KY, USA
| | - Tracie Jenkins
- Breathitt Veterinary Center, Murray State University, Murray, KY, USA
| | - Alma Roy
- School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Daniel Paulsen
- School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Rinosh Mani
- Veterinary Diagnostic Laboratory, Michigan State University, East Lansing, MI, USA
| | - Karen Olsen
- Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN, USA
| | - Lanny Pace
- Veterinary Research and Diagnostic Lab System, Mississippi State University, Starkville, MS, USA
| | - Martha Pulido
- Veterinary Research and Diagnostic Lab System, Mississippi State University, Starkville, MS, USA
| | - Megan Jacob
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Brett T Webb
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, USA
| | - Sarmila Dasgupta
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, Ewing Township, NJ, USA
| | - Amar Patil
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, Ewing Township, NJ, USA
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA
| | - Deepanker Tewari
- Pennsylvania Department of Agriculture, Pennsylvania Veterinary Laboratory, Harrisburg, PA, USA
| | - Nagaraja Thirumalapura
- Pennsylvania Department of Agriculture, Pennsylvania Veterinary Laboratory, Harrisburg, PA, USA
| | - Donna J Kelly
- Pennsylvania Animal Diagnostic Laboratory, New Bolton Center, University of Pennsylvania, Kenneth Square, PA, USA
| | - Shelley C Rankin
- School of Veterinary Medicine, The Ryan Veterinary Hospital Clinical Microbiology Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jing Wu
- Texas A&M University, College Station, TX, USA
| | - Claire R Burbick
- College of Veterinary Medicine, Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Renate Reimschuessel
- Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, United States Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, 20708, USA
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Montgomery MP, Robertson S, Koski L, Salehi E, Stevenson LM, Silver R, Sundararaman P, Singh A, Joseph LA, Weisner MB, Brandt E, Prarat M, Bokanyi R, Chen JC, Folster JP, Bennett CT, Francois Watkins LK, Aubert RD, Chu A, Jackson J, Blanton J, Ginn A, Ramadugu K, Stanek D, DeMent J, Cui J, Zhang Y, Basler C, Friedman CR, Geissler AL, Crowe SJ, Dowell N, Dixon S, Whitlock L, Williams I, Jhung MA, Nichols MC, de Fijter S, Laughlin ME. Multidrug-Resistant Campylobacter jejuni Outbreak Linked to Puppy Exposure - United States, 2016-2018. MMWR Morb Mortal Wkly Rep 2018; 67:1032-1035. [PMID: 30235182 PMCID: PMC6147421 DOI: 10.15585/mmwr.mm6737a3] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Campylobacter causes an estimated 1.3 million diarrheal illnesses in the United States annually (1). In August 2017, the Florida Department of Health notified CDC of six Campylobacter jejuni infections linked to company A, a national pet store chain based in Ohio. CDC examined whole-genome sequencing (WGS) data and identified six isolates from company A puppies in Florida that were highly related to an isolate from a company A customer in Ohio. This information prompted a multistate investigation by local and state health and agriculture departments and CDC to identify the outbreak source and prevent additional illness. Health officials from six states visited pet stores to collect puppy fecal samples, antibiotic records, and traceback information. Nationally, 118 persons, including 29 pet store employees, in 18 states were identified with illness onset during January 5, 2016-February 4, 2018. In total, six pet store companies were linked to the outbreak. Outbreak isolates were resistant by antibiotic susceptibility testing to all antibiotics commonly used to treat Campylobacter infections, including macrolides and quinolones. Store record reviews revealed that among 149 investigated puppies, 142 (95%) received one or more courses of antibiotics, raising concern that antibiotic use might have led to development of resistance. Public health authorities issued infection prevention recommendations to affected pet stores and recommendations for testing puppies to veterinarians. This outbreak demonstrates that puppies can be a source of multidrug-resistant Campylobacter infections in humans, warranting a closer look at antimicrobial use in the commercial dog industry.
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Metwally S, Mohamed F, Faaberg K, Burrage T, Prarat M, Moran K, Bracht A, Mayr G, Berninger M, Koster L, To TL, Nguyen VL, Reising M, Landgraf J, Cox L, Lubroth J, Carrillo C. Pathogenicity and molecular characterization of emerging porcine reproductive and respiratory syndrome virus in Vietnam in 2007. Transbound Emerg Dis 2010; 57:315-29. [PMID: 20629970 DOI: 10.1111/j.1865-1682.2010.01152.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In 2007, Vietnam experienced swine disease outbreaks causing clinical signs similar to the 'porcine high fever disease' that occurred in China during 2006. Analysis of diagnostic samples from the disease outbreaks in Vietnam identified porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV-2). Additionally, Escherichia coli and Streptococcus equi subspecies zooepidemicus were cultured from lung and spleen, and Streptococcus suis from one spleen sample. Genetic characterization of the Vietnamese PRRSV isolates revealed that this virus belongs to the North American genotype (type 2) with a high nucleotide identity to the recently reported Chinese strains. Amino acid sequence in the nsp2 region revealed 95.7-99.4% identity to Chinese strain HUN4, 68-69% identity to strain VR-2332 and 58-59% identity to strain MN184. A partial deletion in the nsp2 gene was detected; however, this deletion did not appear to enhance the virus pathogenicity in the inoculated pigs. Animal inoculation studies were conducted to determine the pathogenicity of PRRSV and to identify other possible agents present in the original specimens. Pigs inoculated with PRRSV alone and their contacts showed persistent fever, and two of five pigs developed cough, neurological signs and swollen joints. Necropsy examination showed mild to moderate bronchopneumonia, enlarged lymph nodes, fibrinous pericarditis and polyarthritis. PRRSV was re-isolated from blood and tissues of the inoculated and contact pigs. Pigs inoculated with lung and spleen tissue homogenates from sick pigs from Vietnam developed high fever, septicaemia, and died acutely within 72 h, while their contact pigs showed no clinical signs throughout the experiment. Streptococcus equi subspecies zooepidemicus was cultured, and PRRSV was re-isolated only from the inoculated pigs. Results suggest that the cause of the swine deaths in Vietnam is a multifactorial syndrome with PRRSV as a major factor.
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Affiliation(s)
- S Metwally
- FAO Reference Center for Vesicular Diseases, USDA, APHIS, Foreign Animal Disease Diagnostic Laboratory, National Veterinary Service Laboratories (NVSL), Plum Island Animal Disease Center (PIADC), Greenport, NY, USA.
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