1
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Eckstrand CD, Torrevillas BK, Wolking RM, Francis M, Goodman LB, Ceric O, Alexander TL, Snekvik KR, Burbick CR. Genomic characterization of antimicrobial resistance in 61 aquatic bacterial isolates. J Vet Diagn Invest 2024:10406387241241042. [PMID: 38566327 DOI: 10.1177/10406387241241042] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial resistance (AMR) in pathogens important to aquatic animal health is of increasing concern but vastly understudied. Antimicrobial therapy is used to both treat and prevent bacterial disease in fish and is critical for a viable aquaculture industry and for maintenance of wild fish populations. Unfortunately, phenotypic antimicrobial susceptibility testing is technically difficult for bacteria recovered from aquatic animal hosts resulting in challenges in resistance monitoring using traditional methods. Whole-genome sequencing provides an appealing methodology for investigation of putative resistance. As part of the ongoing efforts of the FDA CVM Vet-LIRN to monitor AMR, source laboratories cultured and preliminarily identified pathogenic bacteria isolated from various fish species collected in 2019 from across the United States. Sixty-one bacterial isolates were evaluated using whole-genome sequencing. We present here the assembled draft genomes, AMR genes, predicted resistance phenotypes, and virulence factors of the 61 isolates and discuss concurrence of the identifications made by source laboratories using matrix-assisted laser desorption/time-of-flight mass spectrometry.
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Affiliation(s)
- Chrissy D Eckstrand
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Brandi K Torrevillas
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Rebecca M Wolking
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Marla Francis
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Olgica Ceric
- Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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2
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Maddock KJ, Burbick CR, Cole SD, Daniels JB, LeCuyer TE, Li XZ, Loy JD, Sanchez S, Stenger BLS, Diaz-Campos D. A One Health perspective on the use of genotypic methods for antimicrobial resistance prediction. J Am Vet Med Assoc 2024; 262:303-312. [PMID: 38295518 DOI: 10.2460/javma.23.12.0687] [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] [Received: 12/15/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024]
Abstract
Antimicrobial resistance is a global One Health concern with critical implications for the health of humans, animals, and the environment. Phenotypic methods of bacterial culture and antimicrobial susceptibility testing remain the gold standards for the detection of antimicrobial resistance and appropriate patient care; however, genotypic-based methods, such as PCR, whole genome sequencing, and metagenomic sequencing, for detection of genes conferring antimicrobial resistance are increasingly available without inclusion of appropriate standards for quality or interpretation. Misleading test results may lead to inappropriate antimicrobial treatment and, in turn, poor patient outcomes and the potential for increased incidence of antimicrobial resistance. This article explores the current landscape of clinical and methodological aspects of antimicrobial susceptibility testing and genotypic antimicrobial resistance test methods. Additionally, it describes the limitations associated with employing genotypic-based test methods in the management of veterinary patients from a One Health perspective. The companion Currents in One Health by Maddock et al, AJVR, March 2024, addresses current and future needs for veterinary antimicrobial resistance research.
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Affiliation(s)
- Kelli J Maddock
- 1Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND
| | - Claire R Burbick
- 2Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA
| | - Stephen D Cole
- 3School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Joshua B Daniels
- 4College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tessa E LeCuyer
- 5School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Xian-Zhi Li
- 6Veterinary Drugs Directorate, Health Canada, Ottawa, ON, Canada
| | - John Dustin Loy
- 7Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Susan Sanchez
- 8Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
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Maddock KJ, Bowden R, Cole SD, Diaz-Campos D, Daniels JB, LeCuyer TE, Li XZ, Loy JD, Sanchez S, Stenger BLS, Burbick CR. Current state and future directions for veterinary antimicrobial resistance research. Am J Vet Res 2024:1-8. [PMID: 38262139 DOI: 10.2460/ajvr.23.12.0294] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
Antimicrobial resistance (AMR) is a critical One Health concern with implications for human, animal, plant, and environmental health. Antimicrobial susceptibility testing (AST), antimicrobial resistance testing (ART), and surveillance practices must be harmonized across One Health sectors to ensure consistent detection and reporting practices. Veterinary diagnostic laboratory stewardship, clinical outcomes studies, and training for current and future generations of veterinarians and laboratorians are necessary to minimize the spread of AMR and move veterinary medicine forward into an age of better antimicrobial use practices. The purpose of this article is to describe current knowledge gaps present in the literature surrounding ART, AST, and clinical or surveillance applications of these methods and to suggest areas where AMR research can fill these knowledge gaps. The related Currents in One Health by Maddock et al, JAVMA, March 2024, addresses current limitations to the use of genotypic ART methods in clinical veterinary practice.
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Affiliation(s)
- Kelli J Maddock
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND
| | | | - Stephen D Cole
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Joshua B Daniels
- Veterinary Diagnostic Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tessa E LeCuyer
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Canada, Ottawa, ON, Canada
| | - John Dustin Loy
- Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
| | | | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA
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4
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LeCuyer TE, Sellon RK, Byrne BA, Daniels JB, Diaz-Campos DV, Hendrix GK, Burbick CR, Besser TE, Davis MA. Multicenter molecular investigation of recurrent Escherichia coli bacteriuria in dogs. Vet Microbiol 2024; 288:109914. [PMID: 38113575 DOI: 10.1016/j.vetmic.2023.109914] [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] [Received: 05/19/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023]
Abstract
Escherichia coli is the most common cause of recurrent urinary tract infection (UTI) in dogs. UTI recurrence comprises of persistent, unresolved E. coli infection or reinfection with a different strain of E. coli. Differentiating between these processes is clinically important but is often impossible with routine diagnostics. We tested the hypothesis that most recurrent canine E. coli bacteriuria is due to recurrence of the same E. coli strain involved in the initial infection. Molecular typing was performed on 98 urinary E. coli isolated from dogs with recurrent bacteriuria from five veterinary diagnostic laboratories in the United States. Of the 42 dogs in this study with multiple E. coli bacteriuria observations, a single strain of E. coli caused recurrent bacteriuria in 26 (62 %) dogs, in some cases on multiple occasions for prolonged periods of time (up to eight months). A single E. coli strain was detected during both subclinical bacteriuria and clinically-apparent UTI in three dogs. Isolates with the P-fimbrial adhesin genes papA and papC were associated with recurrence by the same strain of E. coli. Multiple isolations of a single strain of E. coli associated with recurrent bacteriuria suggests that E. coli may be maintained within the urinary tract of some dogs for prolonged periods of time. In some patients, the same strain can cause both clinical UTI and subclinical bacteriuria. This indicates that in dogs, the urinary bladder may serve as a subclinical, long-term reservoir of E. coli that may cause clinical UTI in the future.
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Affiliation(s)
- Tessa E LeCuyer
- Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA; Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA.
| | - Rance K Sellon
- Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Barbara A Byrne
- Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Joshua B Daniels
- Veterinary Clinical Sciences, College of Veterinary Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Dubraska V Diaz-Campos
- Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA; Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - G Kenitra Hendrix
- Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Indiana Animal Disease Diagnostic Laboratory, West Lafayette, IN, USA
| | - Claire R Burbick
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, USA
| | - Thomas E Besser
- Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Margaret A Davis
- Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA; Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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5
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Lawhon SD, Burbick CR, Munson E, Thelen E, Zapp A, Wilson A. Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022. J Clin Microbiol 2023; 61:e0083923. [PMID: 37889054 PMCID: PMC10729710 DOI: 10.1128/jcm.00839-23] [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: 10/28/2023] Open
Abstract
Expansion of our knowledge of the microbial world continues to progress at a rapid rate and carries with it an associated need for recognizing and understanding the implications of those changes. Here, we describe additions of novel taxa from domestic animals published in 2022 that are validly published per the International Code of Nomenclature of Prokaryotes. These included new members of Staphylococcaceae, Moraxella nasovis sp. nov. in sheep with respiratory disease, three additions to Campylobacteraceae (including one from chickens with spotty liver disease), and multiple additions of organisms from the microbiota of dogs, pigs, and especially honeybees and other important pollinators. Noteworthy additions were associated with diseases of cattle, including mastitis, endocarditis, orchitis, and endometritis. Also described in 2022 was Pseudochrobactrum algeriense sp. nov., a member of the Brucellaceae family, isolated from the mammary lymph nodes of cows.
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Affiliation(s)
- Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Anastasia Wilson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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Burbick CR, Lawhon SD, Munson E, Thelen E, Zapp A, Wilson A. An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022. J Clin Microbiol 2023; 61:e0084023. [PMID: 37888990 PMCID: PMC10741638 DOI: 10.1128/jcm.00840-23] [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: 10/28/2023] Open
Abstract
Numbers of new and revised microbial taxa are continuously expanding, and the rapid accumulation of novel bacterial species is challenging to keep up with in the best of circumstances. With that in mind, following the template of reports on prokaryotic species isolated from humans, this is now the second publication summarizing new and revised taxa in non-domestic animal species in the Journal of Clinical Microbiology. The majority of new taxa were obtained as part of programs to identify bacteria from mucosal surfaces and the gastrointestinal tract from healthy wildlife. A few notable bacteria included new Erysipelothrix spp. from mammalian and aquatic sources and a novel Bartonella spp. isolated from a rodent, both of which could be considered members of emerging and re-emerging genera with pathogenic potential in humans and animals.
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Affiliation(s)
- Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Anastasia Wilson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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Burbick CR, Fajt VR, Frey E, Fritz H, Goodman LB, Lorenz C, Lubbers BV, Marshall E, Rankin SC, Silva M. Benefits and challenges of creating veterinary antibiograms for empiric antimicrobial selection in support of antimicrobial stewardship and advancement of one-health goals. Am J Vet Res 2023; 84:ajvr.23.05.0086. [PMID: 37315936 DOI: 10.2460/ajvr.23.05.0086] [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] [Received: 05/02/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Antibiograms are important tools for antimicrobial stewardship that are often underutilized in veterinary medicine. Antibiograms summarize cumulative antimicrobial susceptibility testing (AST) data for specific pathogens over a defined time period; in veterinary medicine, they are often stratified by host species and site of infection. They can aid practitioners with empiric therapy choices and assessment of antimicrobial resistance trends within a population in support of one-health goals for antimicrobial stewardship. For optimal application, consideration must be given to the number of isolates used, the timeframe of sample collection, laboratory analytical methodology, and the patient population contributing to the data (eg, treatment history, geographic region, and production type). There are several limitations to veterinary antibiograms, including a lack of breakpoint availability for bacterial species, a lack of standardization of laboratory methodology and technology for culture and AST, and a lack of funding to staff veterinary diagnostic laboratories at a level that supports antibiogram development and education. It is vital that veterinarians who use antibiograms understand how to apply them in practice and receive relevant information pertaining to the data to utilize the most appropriate antibiogram for their patients. This paper explores the benefits and challenges of developing and using veterinary antibiograms and proposes strategies to enhance their applicability and accuracy. Further detail regarding the application of veterinary antibiograms by privately practicing clinicians is addressed in the companion Currents in One Health article by Lorenz et al (JAVMA, September 2023).
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Affiliation(s)
- Claire R Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA
| | - Virginia R Fajt
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine, Texas A&M University, College Station, TX
| | - Erin Frey
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC
| | - Heather Fritz
- California Animal Health and Food Safety Laboratory System, University of California, Davis, CA
| | - Laura B Goodman
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY
| | | | - Brian V Lubbers
- Department of Clinical Sciences, Kansas State University, Manhattan, KS
| | - Edith Marshall
- California Department of Food and Agriculture, Sacramento, CA
| | | | - Marissa Silva
- California Department of Food and Agriculture, Sacramento, CA
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Maddock KJ, Gefroh SJ, Burbick CR. β-Lactam resistance in veterinary β-hemolytic Streptococcus species: Are we experiencing a public health or test method crisis? J Am Vet Med Assoc 2023; 261:1403-1406. [PMID: 37225158 DOI: 10.2460/javma.23.03.0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023]
Abstract
β-Hemolytic Streptococcus (BHS) species are important pathogens with both human and veterinary significance. In human medicine, BHS are considered universally susceptible to β-lactams while BHS of veterinary origin have been reported with up to 8% β-lactam resistance. Recently, veterinary diagnostic laboratories were made aware of significant variability of test method performance for BHS among laboratories. This article explores potential sources of error in antimicrobial susceptibility test performance and result interpretation that may have contributed to the unusual rates of resistance to β-lactams observed in this bacterial species. In addition, potential impacts to research, clinical practice, surveillance, and public health will be discussed.
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Affiliation(s)
- Kelli J Maddock
- 1North Dakota State University Veterinary Diagnostic Laboratory, Fargo, ND
| | - Sarah J Gefroh
- 1North Dakota State University Veterinary Diagnostic Laboratory, Fargo, ND
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9
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Witherell K, White L, Shaw L, Tomassini L, Eckstrand C, Nelson D, McConnel CS, Burbick CR. Utility of postmortem bacterial culture of abdominal organs at autopsy of young calves. J Vet Diagn Invest 2023; 35:182-186. [PMID: 36772787 PMCID: PMC9999389 DOI: 10.1177/10406387231152576] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Postmortem bacterial culture is controversial in human medicine, and veterinary-specific research in this area is lacking. To address this knowledge gap, we cultured liver, kidney, and spleen individually from on-farm calf mortalities to determine the number of bacterial species present, concordance between organ cultures, and agreement with gross and histologic findings. We hypothesized that the spleen, a filtering organ, would be the most useful organ with the least amount of postmortem contamination given that it does not have a direct conduit to a bacterial population. Fresh liver, kidney, and spleen were collected for culture from 30 calves 5-28-d-old with various causes of mortality. Bacterial growth of ≥2 species was observed in ~48% of cultures, with Escherichia coli and Streptococcus spp. being most frequent. One bacterial species was present in 20% of cultures, with E. coli predominating. No growth was observed in ~32% of cultures. In 43% of cases, there was agreement in the culture results for all 3 organs; however, the majority were mixed bacterial growth. The best agreement was observed when there were no gross and/or histologic septic lesions in target organs and no bacterial growth on culture. The spleen was not helpful in determining bacterial significance in comparison to kidney or liver.
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Affiliation(s)
- Kaitlin Witherell
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Laura White
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Departments of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Lisa Shaw
- Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Letizia Tomassini
- Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Chrissy Eckstrand
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Departments of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Danielle Nelson
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Departments of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Craig S. McConnel
- Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Claire R. Burbick
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Departments of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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10
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Burbick CR, Alexander TL, Wolking R, Gull T, Ceric O, Reimschuessel R. Non-carbapenemase producing carbapenem-resistant Klebsiella pneumoniae isolated from the urinary tract of a dog. Can Vet J 2022; 63:740-744. [PMID: 35784769 PMCID: PMC9207975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Objective Carbapenems are broad-spectrum β-lactams with excellent activity against multidrug-resistant (MDR) Enterobacterales. Unfortunately, resistance to carbapenems within this bacterial family, known as carbapenem-resistant Enterobacterales (CRE), occurs and challenges the ability to treat difficult MDR infections. Although the impact of carbapenem-resistance has been greatest in human medicine, reports in the veterinary literature are increasing especially as national veterinary antimicrobial resistance surveillance programs are now in place. In this brief communication, we report the isolation of a non-carbapenemase-producing, carbapenem-resistant Klebsiella pneumoniae from the urine of a dog, discuss the likely mechanism of resistance, and wider implications. Animal Canine. Procedure Whole genome sequencing and phenotypic antimicrobial susceptibility testing was performed on a K. pneumoniae isolated from the urine of a dog. Results Antimicrobial susceptibility testing identified phenotypic resistance to imipenem and meropenem. Phenotypic detection of carbapenemase production was negative. Whole genome sequencing identified efflux pump genes associated with carbapenem resistance and point mutations in membrane porin genes. No carbapenemase gene was identified. Conclusion Phenotypic antimicrobial susceptibility testing identified the K. pneumoniae as a non-carbapenemase producing carbapenem-resistant organism with the proposed genotypic mechanism including alteration of efflux pumps and membrane porin activity and/or expression. Clinical significance Currently, there is limited use of carbapenem antimicrobial drugs in veterinary medicine, and practitioners may be unfamiliar or unaware of this type of resistance, its significance on routine antimicrobial susceptibility test reports, and implications for antimicrobial therapy and public health. Carbapenem-resistant Enterobacterales are infrequently isolated from companion animals; however, due to increasing adoption of advanced medical and surgical interventions, they may become more prevalent.
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Affiliation(s)
- Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Rebecca Wolking
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Tamara Gull
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Olgica Ceric
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Renate Reimschuessel
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
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11
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LaFrentz BR, Králová S, Burbick CR, Alexander TL, Phillips CW, Griffin MJ, Waldbieser GC, García JC, de Alexandre Sebastião F, Soto E, Loch TP, Liles MR, Snekvik KR. The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare. Syst Appl Microbiol 2021; 45:126293. [PMID: 35026686 DOI: 10.1016/j.syapm.2021.126293] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023]
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36T), F. davisii sp. nov. (90-106T), and F. oreochromis sp. nov. (Costa Rica 04-02-TNT) are proposed to represent genetic groups 2, 3, and 4, respectively.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States.
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Conner W Phillips
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS, United States
| | - Geoffrey C Waldbieser
- Warmwater Aquaculture Research Unit, USDA-ARS, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, United States
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States
| | | | - Esteban Soto
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
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12
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Berreta A, Kopper JJ, Alexander TL, Kogan CJ, Burbick CR. Effect of an In Vitro Proximal Gastrointestinal Tract on Viability of Commercially Available Equine Probiotics. J Equine Vet Sci 2021; 104:103671. [PMID: 34416988 DOI: 10.1016/j.jevs.2021.103671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/19/2022]
Abstract
Probiotics, by definition, are live micro-organisms and should remain viable when they reach the intended site of action which is typically the cecum and/or colon. In humans, probiotics often need enteric protection to survive transit through the proximal gastrointestinal (GI) tract. Typically, equine probiotics do not advertise enteric protection and to the author's knowledge the viability of equine probiotics after exposure to the proximal GI tract has not been evaluated. The objective of this study was to evaluate the effect of an in vitro simulation of the equine proximal GI tract on probiotic viability. We hypothesized that the simulated proximal GI tract would adversely effect microbial viability and that the adverse effects would be partially ameliorated by increasing the gastric pH to 4. A total of 11 products were evaluated of which six had at least one micro-organism that was adversely effected by exposure to the proximal GI tract and four of which had at least one micro-organism that was adversely affected when the gastric pH was increased to 4.0. Results from this study indicate that some micro-organisms in equine probiotics do not appear to be adversely affected by exposure to the equine proximal GI tract.
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Affiliation(s)
- Ana Berreta
- Department of Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA
| | - Jamie J Kopper
- Department of Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA.
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA
| | - Clark J Kogan
- Center for Interdisciplinary Statistical Education and Research, Washington State University, Pullman, WA
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA
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13
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Kopper JJ, Alexander TL, Kogan CJ, Berreta AR, Burbick CR. In Vitro Evaluation of the Effect of Storage at -20°C and Proximal Gastrointestinal Conditions on Viability of Equine Fecal Microbiota Transplant. J Equine Vet Sci 2020; 98:103360. [PMID: 33663713 DOI: 10.1016/j.jevs.2020.103360] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/18/2022]
Abstract
Fecal microbiota transplant (FMT), a technique used to restore normal intestinal microbial communities, has been successful in treating humans with Clostridioides difficile colitis. Subsequently, FMT is being used in veterinary patients with suspected intestinal dysbiosis. Unfortunately, little data are available regarding best practices for FMT in horses. The objective of this study was to evaluate the effects of storing manure prepared for equine FMT (MP-FMT) at -20°C for up to 4 weeks and passage through a simulated proximal gastrointestinal (GI) tract on the viability of MP-FMT. The results of this study indicate that storage at -20°C for greater than 1 week and exposure to conditions consistent with the proximal GI tract significantly decreased viability of the microbial population, with gram-negative enteric bacteria most significantly impacted. This preliminary evaluation indicates that further work is necessary to determine best practices to preserve the viability MP-FMT in horses.
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Affiliation(s)
- Jamie J Kopper
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA.
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA
| | - Clark J Kogan
- Center for Interdisciplinary Statistical Education and Research, Washington State University, Pullman, WA
| | - Ana R Berreta
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA
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14
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Oliveira RD, Wolking RM, Bradway DS, Alexander TL, Burbick CR, Cerchiaro I, Eckstrand CD. Algal Lymphadenitis in a Dog Caused by Scenedesmus Species. Vet Pathol 2020; 57:821-824. [PMID: 32783503 DOI: 10.1177/0300985820948819] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A 6-year-old, spayed female Labrador/Weimaraner cross-breed dog that had previously lived in Arizona presented in Montana for an annual examination with an incidentally enlarged popliteal lymph node, which was subsequently biopsied. Histologically, the lymph node was expanded by eosinophil-rich granulomas with both extracellular and intrahistiocytic green algae. These algae had intracytoplasmic, birefringent, and refractile granules; readily formed 2 to 3 mm green colonies on Columbia blood agar medium; and ultrastructurally had a multilayered cell wall and intracytoplasmic chloroplasts. Amplified product from the internal transcribed spacer and D1/D2 regions of the 28S ribosomal RNA gene had high sequence identity to Scenedesmus sp. Despite similar infection in the retropharyngeal lymph node 1 year later, the animal remained otherwise healthy with no clinical signs. To the authors' knowledge, this is the first case of Scenedesmus species infection in a dog and is a differential diagnosis for Coccidioides immitis.
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15
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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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McConnel CS, Nelson DD, Burbick CR, Buhrig SM, Wilson EA, Klatt CT, Moore DA. Clarifying dairy calf mortality phenotypes through postmortem analysis. J Dairy Sci 2019; 102:4415-4426. [PMID: 30879809 PMCID: PMC7094407 DOI: 10.3168/jds.2018-15527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/14/2019] [Indexed: 12/27/2022]
Abstract
Health problems can be thought of as phenotypic expressions of the complex relationships between genes, environments, and phenomes as a whole. Detailed evaluations of phenotypic expressions of illness are required to characterize important biological outcomes. We hypothesized that classifying dairy calf mortality phenotypes via a systematic postmortem analysis would identify different cause-of-death diagnoses than those derived from treatments alone. This cross-sectional study was carried out on a dairy calf ranch in the northwestern United States from June to September 2017 and focused on calves ≤90 d of age. Comparisons were made between causes of death based on 3 levels of information: on-farm treatment records alone, necropsy-based postmortem analyses in addition to treatment records, and Washington Animal Disease Diagnostic Laboratory (WADDL) results in addition to all other information. A total of 210 dairy calves were necropsied during this study, of which 122 cases were submitted to WADDL. Necropsy- and WADDL-derived mortality phenotypes were in almost perfect agreement (Cohen's κ = 0.86) when broadly categorized as diarrhea, respiratory, diarrhea and respiratory combined, or other causes. The level of agreement between on-farm treatment records and postmortem-derived results was low and varied by the level of diagnostic detail provided. There was just fair agreement (κ = 0.22) between treatment-based and necropsy-based phenotypes without WADDL input and only slight agreement (κ = 0.13) between treatment-based and corresponding necropsy-based phenotypes with WADDL input. Even for those cases in which causes of death aligned along a comparable pathologic spectrum, the lack of detail inherent to standard treatment-based causes of death failed to identify meaningful target areas for intervention. This was especially apparent for numerous cases of necrotizing enteritis and typhlitis (cecal inflammation) that were variously categorized as diarrhea and pneumonia by treatment-based diagnoses. The specificity of these lesions stood in stark contrast to the otherwise generic cause of death diagnoses derived from treatments. The findings from this study supported the hypothesis and highlighted the value of on-farm necropsies and laboratory-based diagnostics to (1) detect antemortem disease misclassifications, (2) provide detail regarding disease processes and mortality phenotypes, and (3) direct disease mitigation strategies.
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Affiliation(s)
- C S McConnel
- Department of Veterinary Clinical Sciences, Washington State University, Pullman 99164.
| | - D D Nelson
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman 99164
| | - C R Burbick
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman 99164
| | - S M Buhrig
- Agricultural and Natural Resource Program, Eastern Oregon University, La Grande 97850
| | - E A Wilson
- Animal Science Program, College of Southern Idaho, Twin Falls 83301
| | - C T Klatt
- Laramie Peak Veterinary Associates, Wheatland, WY 82201
| | - D A Moore
- Department of Veterinary Clinical Sciences, Washington State University, Pullman 99164
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17
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Burbick CR, Nydam SD, Hendrix GK, Besser TE, Diaz D, Snekvik K. Use of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for the Identification of Pathogenic Vibrio in Fish. J Aquat Anim Health 2018; 30:332-338. [PMID: 30352480 DOI: 10.1002/aah.10044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, cost-effective method for identification of a broad range of bacterial taxa, but its accuracy for Vibrio spp. from samples of aquatic animal origin is unknown. We used DNA sequence analysis targeting two conserved genes, rpoB and rpoD, as the identification standard for 5 reference strains and 35 Vibrio spp. field isolates obtained from diagnostic aquaculture samples. Overall, MALDI-TOF MS correctly identified 100% of the five reference strains to the genus level and 80% (4 of 5) to the species level. For field isolates, 83% (29 of 35) were correctly identified to the genus level, and 49% (17 of 35) were correctly identified to the species level. Eight (23%) field isolates were incorrectly identified at the species level. The MALDI-TOF MS method produced no identification for 17% (6 of 35) of the field isolates. Using traditional culture identification, 100% of the five reference strains were correctly identified to the species level. All 35 field isolates were correctly identified to the genus level; 51% (18 of 35) of the isolates were identified correctly to the species level, while 29% (10 of 35) were misidentified at the species level. Overall, MALDI-TOF MS was comparable to phenotypic identification, and accuracy will likely improve with enhancement of MALDI-TOF MS database robustness.
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Affiliation(s)
- Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Post Office Box 647034, Pullman, Washington, 99164, USA
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, 99164, USA
| | - Seth D Nydam
- Department of Animal Care and Technologies, Arizona State University, Tempe, Arizona, 85287, USA
| | - G Kenitra Hendrix
- Indiana Animal Disease Diagnostic Laboratory, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Thomas E Besser
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, 99164, USA
| | - Dubraska Diaz
- Department of Veterinary Clinical Sciences, Ohio State University, Columbus, Ohio, 43210, USA
| | - Kevin Snekvik
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Post Office Box 647034, Pullman, Washington, 99164, USA
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, 99164, USA
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