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Runtuvuori-Salmela A, Kunttu H, Laanto E, Almeida G, Mäkelä K, Middelboe M, Sundberg LR. Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control. Environ Microbiol 2022; 24:2404-2420. [PMID: 35049114 PMCID: PMC9304149 DOI: 10.1111/1462-2920.15901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Intensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage‐based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 phages against F. columnare from Finland and Sweden in 2017. Bacterial isolates were virulent on rainbow trout (Oncorhynchus mykiss) and fell into four previously described genetic groups A, C, E and G, with genetic groups C and E being the most virulent. Phage host range studied against a collection of 227 bacterial isolates (from 2013 to 2017) demonstrated modular infection patterns based on host genetic group. Phages infected contemporary and previously isolated bacterial hosts, but bacteria isolated most recently were generally resistant to previously isolated phages. Despite large differences in geographical origin, isolation year or host range of the phages, whole‐genome sequencing of 56 phages showed high level of genetic similarity to previously isolated F. columnare phages (Ficleduovirus, Myoviridae). Altogether, this phage collection demonstrates a potential for use in phage therapy.
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Affiliation(s)
- A Runtuvuori-Salmela
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Hmt Kunttu
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - E Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.,Department Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Gmf Almeida
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.,Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - K Mäkelä
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - M Middelboe
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - L-R Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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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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Thunes NC, Conrad RA, Mohammed HH, Zhu Y, Barbier P, Evenhuis JP, Perez-Pascual D, Ghigo JM, Lipscomb RS, Schneider JR, Li N, Erbes DH, Birkett C, LaFrentz BR, Welch TJ, McBride MJ. Type IX secretion system effectors and virulence of the model Flavobacterium columnare strain MS-FC-4. Appl Environ Microbiol 2021;:AEM0170521. [PMID: 34818105 DOI: 10.1128/AEM.01705-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flavobacterium columnare causes columnaris disease in wild and cultured freshwater fish and is a major problem for sustainable aquaculture worldwide. The F. columnare type IX secretion system (T9SS) secretes many proteins and is required for virulence. The T9SS component GldN is required for secretion and for gliding motility over surfaces. Genetic manipulation of F. columnare is inefficient, which has impeded identification of secreted proteins that are critical for virulence. Here we identified a virulent wild-type F. columnare strain (MS-FC-4) that is highly amenable to genetic manipulation. This facilitated isolation and characterization of two deletion mutants lacking core components of the T9SS. Deletion of gldN disrupted protein secretion and gliding motility and eliminated virulence in zebrafish and rainbow trout. Deletion of porV disrupted secretion and virulence but not motility. Both mutants exhibited decreased extracellular proteolytic, hemolytic, and chondroitin sulfate lyase activities. They also exhibited decreased biofilm formation and decreased attachment to fish fins and to other surfaces. Using genomic and proteomic approaches, we identified proteins secreted by the T9SS. We deleted ten genes encoding secreted proteins and characterized the virulence of mutants lacking individual or multiple secreted proteins. A mutant lacking two genes encoding predicted peptidases exhibited reduced virulence in rainbow trout, and mutants lacking a predicted cytolysin showed reduced virulence in zebrafish and rainbow trout. The results establish F. columnare strain MS-FC-4 as a genetically amenable model to identify virulence factors. This may aid development of measures to control columnaris disease and impact fish health and sustainable aquaculture. IMPORTANCE: Flavobacterium columnare causes columnaris disease in wild and aquaculture-reared freshwater fish and is a major problem for aquaculture. Little is known regarding the virulence factors involved in this disease and control measures are inadequate. The type IX secretion system (T9SS) secretes many proteins and is required for virulence, but the secreted virulence factors are not known. We identified a strain of F. columnare (MS-FC-4) that is well suited for genetic manipulation. The components of the T9SS and the proteins secreted by this system were identified. Deletion of core T9SS genes eliminated virulence. Genes encoding ten secreted proteins were deleted. Deletion of two peptidase-encoding genes resulted in decreased virulence in rainbow trout, and deletion of a cytolysin-encoding gene resulted in decreased virulence in rainbow trout and zebrafish. Secreted peptidases and cytolysins are likely virulence factors and are targets for the development of control measures.
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Kayansamruaj P, Areechon N, Unajak S. Development of fish vaccine in Southeast Asia: A challenge for the sustainability of SE Asia aquaculture. Fish Shellfish Immunol 2020; 103:73-87. [PMID: 32335313 DOI: 10.1016/j.fsi.2020.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/23/2020] [Accepted: 04/15/2020] [Indexed: 05/08/2023]
Abstract
Southeast (SE) Asia plays an important role in global food security as this region has been regarded as one of the major producers of aquaculture product and, to date, freshwater fish accounted for one-third of the total aquaculture in SE Asia. The intensification of freshwater farming corresponding to increase of consumer demands has inevitably led to the emergence and re-emergence of diseases causing tremendous economic loss in the region. Nile tilapia (Oreochromis niloticus) and striped catfish (Pangasianodon hypophthalmus), the major freshwater fish species of SE Asia, have been reported susceptible to several bacterial pathogens, e.g. Streptococcus agalactiae, Edwardsiella ictalurid and Flavobacterium columnare. Since only a limited number of vaccines being registered and marketed, these pathogenic organisms still represent a severe threat to aquaculture industry in SE Asia. However, there is profound advancement in the understanding of disease epidemiology, pathogenic mechanisms, teleost mucosal immunity and vaccine delivery system over the last few years. This review aimed to summarize those recent findings which hopefully can provide novel insight into the future development of suitable vaccine and vaccination regime against bacterial infection in SE Asia region.
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Affiliation(s)
- Pattanapon Kayansamruaj
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.
| | - Nontawith Areechon
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.
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LaFrentz BR, García JC, Shelley JP. Multiplex PCR for genotyping Flavobacterium columnare. J Fish Dis 2019; 42:1531-1542. [PMID: 31469439 DOI: 10.1111/jfd.13068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Recent research has identified four distinct genetic groups among isolates of Flavobacterium columnare through multilocus phylogenetic analyses; however, there are no quick methods to determine the genotype of an isolate. The objective of this research was to develop a multiplex PCR to rapidly genotype F. columnare to genetic group. Comparative bacterial genomics was used to identify regions in the genomes unique to each genetic group, and primers were designed to specifically amplify different sized amplicons for each genetic group. The optimized assay was demonstrated to be specific for each genetic group and F. columnare, and no specific amplicons were generated using gDNA from a panel of other Flavobacterium spp. and bacterial fish pathogens. The analytical sensitivity of the assay ranged from 209 to 883 genome equivalents depending on the genetic group. The multiplex PCR was evaluated by genotyping a panel of 22 unknown F. columnare isolates and performing DNA sequencing of the dnaK gene in parallel. The results demonstrated 100% accordance between multiplex PCR results and assignment to genetic group via phylogenetic analysis. The multiplex PCR provides a useful tool for assigning an unknown isolate to genetic group and may be used to determine which genetic groups of F. columnare are circulating and most predominant in different aquaculture industries.
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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, USA
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - John P Shelley
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
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García JC, LaFrentz BR, Waldbieser GC, Wong FS, Chang SF. Characterization of atypical Flavobacterium columnare and identification of a new genomovar. J Fish Dis 2018; 41:1159-1164. [PMID: 29697149 DOI: 10.1111/jfd.12778] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/17/2017] [Accepted: 12/05/2017] [Indexed: 06/08/2023]
Affiliation(s)
- J C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - B R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - G C Waldbieser
- USDA-ARS, Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, USA
| | - F S Wong
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore City, Singapore
| | - S F Chang
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore City, Singapore
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Bartelme RP, Barbier P, Lipscomb RS, LaPatra SE, Newton RJ, Evenhuis JP, McBride MJ. Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain MS-FC-4. Genome Announc 2018; 6:e00429-18. [PMID: 29773635 DOI: 10.1128/genomeA.00429-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Flavobacterium columnare MS-FC-4 is a highly virulent genetic group 1 (formerly genomovar I) strain isolated from rainbow trout (Oncorhynchus mykiss). The draft genome consists of three contigs totaling 3,449,277 bp with 2,811 predicted open reading frames. F. columnare MS-FC-4 is a model strain for functional genomic analyses.
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LaFrentz BR, García JC, Waldbieser GC, Evenhuis JP, Loch TP, Liles MR, Wong FS, Chang SF. Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations. Front Microbiol 2018; 9:452. [PMID: 29593693 PMCID: PMC5859164 DOI: 10.3389/fmicb.2018.00452] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 11/28/2017] [Accepted: 02/27/2018] [Indexed: 12/04/2022] Open
Abstract
Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, whereby six established genomovars have been described to date. However, little has been done to quantify or characterize this diversity further in a systematic fashion. The objective of this research was to perform phylogenetic analyses of 16S rRNA and housekeeping gene sequences to decipher the genetic diversity of F. columnare. Fifty isolates and/or genomes of F. columnare, originating from diverse years, geographic locations, fish hosts, and representative of the six genomovars were analyzed in this study. A multilocus phylogenetic analysis (MLPA) of the 16S rRNA and six housekeeping genes supported four distinct F. columnare genetic groups. There were associations between genomovar and genetic group, but these relationships were imperfect indicating that genomovar assignment does not accurately reflect F. columnare genetic diversity. To expand the dataset, an additional 90 16S rRNA gene sequences were retrieved from GenBank and a phylogenetic analysis of this larger dataset also supported the establishment of four genetic groups. Examination of isolate historical data indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from specific fish species or families. It is proposed that F. columnare isolates be assigned to the four genetic groups defined in this study rather than genomovar in order to facilitate a standard nomenclature across the scientific community. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries may allow for the development of improved targeted control and treatment measures for columnaris disease.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service, Auburn, AL, United States
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service, Auburn, AL, United States
| | - Geoffrey C Waldbieser
- Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, United States Department of Agriculture - Agricultural Research Service, Stoneville, MS, United States
| | - Jason P Evenhuis
- National Center for Cool and Cold Water Aquaculture, United States Department of Agriculture - Agricultural Research Service, Kearneysville, WV, United States
| | - Thomas P Loch
- 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
| | - Fong S Wong
- MSD Animal Health Innovation Pte. Ltd., Singapore, Singapore
| | - Siow F Chang
- MSD Animal Health Innovation Pte. Ltd., Singapore, Singapore
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Tekedar HC, Karsi A, Reddy JS, Nho SW, Kalindamar S, Lawrence ML. Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. Front Microbiol 2017; 8:588. [PMID: 28469601 PMCID: PMC5395568 DOI: 10.3389/fmicb.2017.00588] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/21/2017] [Indexed: 12/28/2022] Open
Abstract
Flavobacterium columnare is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of F. columnare and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of F. columnare strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other Flavobacterium genomes. In this analysis, we identified predicted proteins whose functions indicate F. columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of F. columnare ATCC 49512 with nitrate supplementation was detected experimentally. F. columnare ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other Flavobacterium species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in F. columnare along with F. johnsoniae and F. branchiophilum. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of F. columnare ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.
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Affiliation(s)
- Hasan C Tekedar
- College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, USA
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, USA
| | - Joseph S Reddy
- Mayo Clinic, Department of Health Sciences ResearchJacksonville, FL, USA
| | - Seong W Nho
- College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, USA
| | - Safak Kalindamar
- College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, USA
| | - Mark L Lawrence
- College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, USA
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