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Infections caused by antimicrobial-resistant Escherichia coli are the leading cause of death attributed to antimicrobial resistance (AMR) worldwide, and the known AMR mechanisms involve a range of functional proteins. Here, we employed a pan-genome wide association study (GWAS) approach on over 1,000 E. coli isolates from sick dogs collected across the US and Canada and identified a strong statistical association (empirical P < 0.01) of AMR, involving a range of antibiotics to a group 1 capsular (CPS) gene cluster. This cluster included genes under relaxed selection pressure, had several loci missing, and had pseudogenes for other key loci. Furthermore, this cluster is widespread in E. coli and Klebsiella clinical isolates across multiple host species. Earlier studies demonstrated that the octameric CPS polysaccharide export protein Wza can transmit macrolide antibiotics into the E. coli periplasm. We suggest that the CPS in question, and its highly divergent Wza, functions as an antibiotic trap, preventing antimicrobial penetration. We also highlight the high diversity of lineages circulating in dogs across all regions studied, the overlap with human lineages, and regional prevalence of resistance to multiple antimicrobial classes., Importance: Much of the human genomic epidemiology data available for E. coli mechanism discovery studies has been heavily biased toward shiga-toxin producing strains from humans and livestock. E. coli occupies many niches and produces a wide variety of other significant pathotypes, including some implicated in chronic disease. We hypothesized that since dogs tend to share similar strains with their owners and are treated with similar antibiotics, their pathogenic isolates will harbor unexplored AMR mechanisms of importance to humans as well as animals. By comparing over 1,000 genomes with in vitro antimicrobial susceptibility data from sick dogs across the US and Canada, we identified a strong multidrug resistance association with an operon that appears to have once conferred a type 1 capsule production system., Competing Interests: The authors declare no conflict of interest.

Aims: To estimate the prevalence of carbapenemase-producing Enterobacterales (CPE) carriage among pets using faecal specimens submitted to veterinary diagnostic laboratories throughout the US. A secondary aim was to employ whole-genome sequencing (WGS) to characterize isolates of CPE from companion animals and compare them to publicly available CPE genomes., Methods and Results: To estimate the prevalence of CPE in companion animals in the USA, a multicenter surveillance study including 8 different veterinary diagnostic laboratories from across the USA was conducted. Briefly, remnant faecal specimens from dogs and cats were screened using two selective agar plates (CHROMID Carba and MacConkey with 1 mg/L cefotaxime and 0.125 mg/L meropenem) and presumptive CPE isolates screened by the modified carbapenemase inactivation method for carbapenemase production. A total of 2393 specimens were screened and yielded 196 isolates for carbapenemase screening. A total of 5 isolates from 4 dogs and 1 cat at 3 different veterinary diagnostic laboratories were confirmed to produce a carbapenemase (0.21%). Whole-genome sequencing (WGS) revealed two E. coli (ST167) isolates that both produced an NDM-5 carbapenemase, two Enterobacter hormaechei (ST171) isolates that produced an NDM-5 carbapenemase and a KPC-4 carbapenemase respectively and one Klebsiella oxytoca (ST199) that produced an Oxa-48-type carbapenemase. Both E. coli isolates were found to be within at least 22 SNPs of previously characterized canine and human CPE isolates., Conclusions: This study demonstrates that the prevalence of CPE among companion animals is relatively low (0.21%) but that given the genetic relatedness of animal isolates to human isolates, additional surveillance is needed., (© 2024 The Author(s). Zoonoses and Public Health published by Wiley‐VCH GmbH. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Salmonella enterica serovar Dublin (S. Dublin) is an important enteric pathogen affecting cattle and poses increasing public health risks. Understanding the pathophysiology and host-pathogen interactions of S. Dublin infection are critical for developing effective control strategies, yet studies are hindered by the lack of physiologically relevant in vitro models. This study aimed to generate a robust ileal monolayer derived from adult bovine organoids, validate its feasibility as an in vitro infection model with S. Dublin, and evaluate the epithelial response to infection. A stable, confluent monolayer with a functional epithelial barrier was established under optimized culture conditions. The model's applicability for studying S. Dublin infection was confirmed by documenting intracellular bacterial invasion and replication, impacts on epithelial integrity, and a specific inflammatory response, providing insights into the pathogen-epithelium interactions. The study underscores the utility of organoid-derived monolayers in advancing our understanding of enteric infections in livestock and highlights implications for therapeutic strategy development and preventive measures, with potential applications extending to both veterinary and human medicine. The established bovine ileal monolayer offers a novel and physiologically relevant in vitro platform for investigating enteric pathogen-host interactions, particularly for pathogens like S. Dublin., (© 2024. The Author(s).)

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., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to research, authorship, and/or publication of this article. The views expressed in this manuscript are those of the authors and may not reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration, or the U.S. Government.

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.

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.

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., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

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., Competing Interests: The authors declare no conflict of interest.

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., Competing Interests: The authors declare no conflict of interest.

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).

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.

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.

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae , Staphylococcaceae , and Actinomycetaceae ; bovine reproductive tract pathogens in Corynebacteriaceae ; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma .

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota ) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum , Flavobacterium , and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix , and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Recent progress in bovine intestinal organoid research has expanded opportunities for creating improved in vitro models to study intestinal physiology and pathology. However, the establishment of a culture condition capable of generating organoids from all segments of the cattle intestine has remained elusive. Although previous research has described the development of bovine jejunal, ileal, and colonic organoids, this study marks the first report of successful bovine duodenal and rectal organoid development. Maintenance of these organoids through serial passages and cryopreservation was achieved, with higher success rates observed in large intestinal organoids compared to their small intestinal counterparts. A novel approach involving the use of biopsy forceps during initial tissue sampling streamlined the subsequent tissue processing, simplifying the procedure compared to previously established protocols in cattle. Additionally, our study introduced a more cost-effective culture medium based on Advanced DMEM/F12, diverging from frequently used commercially available organoid culture media. This enhancement improves accessibility to organoid technology by reducing culture costs. Crucially, the derived organoids from jejunum, ileum, colon and rectum faithfully preserved the structural, cellular, and genetic characteristics of in vivo intestinal tissue. This research underscores the significant potential of adult bovine intestinal organoids as a physiologically and morphologically relevant in vitro model. Such organoids provide a renewable and sustainable resource for a broad spectrum of studies, encompassing investigations into normal intestinal physiology in cattle and the intricate host-pathogen interactions of clinically and economically significant enteric pathogens., Competing Interests: Conflict of Interest Statement The authors have no conflicts of interest to declare.

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., (Copyright and/or publishing rights held by the Canadian Veterinary Medical Association.)

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 23463 T ; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36 T , genetic group 3 isolate 90-106 T , and genetic group 4 isolate Costa Rica 04-02-TN T shared less than <98.8 % sequence identity to F. columnare ATCC 23463 T . 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 23463 T , genetic group 2 isolate AL-02-36 T , genetic group 3 isolate 90-106 T , and genetic group 4 isolate Costa Rica 04-02-TN T 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-02-36 T ), F. davisii sp. nov. (90-106 T ), and F. oreochromis sp. nov. (Costa Rica 04-02-TN T ) are proposed to represent genetic groups 2, 3, and 4, respectively., (Published by Elsevier GmbH.)

Probiotics are defined as live microorganisms that confer a health benefit to the host when administered in adequate amounts, therefore the presence of viable microorganisms is essential. Previous studies reported inconsistencies when comparing contents of probiotics marketed for use in animals with label claims. However, to the author's knowledge the variability of the same product between different lots has yet to be evaluated. The objective of this observational study was to evaluate the content and inter-lot variability of commercial equine probiotic products using culture dependent and independent techniques. Eleven probiotics marketed for use in horses were evaluated for microbial content using culture-dependent and independent techniques. The content was then compared to microorganisms listed and quantities on the label of the probiotic. Statistical analyses were performed using a Kruskal-Wallis test. None of the 11 probiotics met their label claim. Nine of the 11 did not have statistically significant inter-lot variability. Several products lacked microorganisms listed on the label based on both culture and polymerase chain reaction (PCR) analyses., (Copyright © 2021 Elsevier Inc. All rights reserved.)

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., (Copyright © 2021 Elsevier Inc. All rights reserved.)

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., (Copyright © 2020 Elsevier Inc. All rights reserved.)

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 .

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.

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., (Copyright © 2019 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

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., (© 2018 American Fisheries Society.)