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Continued investigation into the bacteria associated with non-domestic animals provides important information for recognizing normal flora, assessing the health status of these unique species of animals, and identifying new or emerging pathogens of concern. In this summary of novel taxa and taxonomic revisions, considerable additions have been made toward understanding fecal and mucosal flora in multiple wild animal species. In addition, novel pathogenic bacteria are discussed, including multiple Chlamydia spp. causing disease in a hawk and crocodile, two Corynebacterium spp. causing oral lesions in penguins and a lesser-known genus, Mergibacter within Family Pasteurellaceae , causing disease in multiple wild bird species. Finally, a few revisions to bacteria isolated from normal non-domestic animal body sites are mentioned.

Rhodococcus equi causes pyogranulomatous pneumonia in foals and immunocompromised people. Despite decades of research efforts, no vaccine is available against this common cause of disease and death in foals. The purpose of this narrative review is to summarise the current understanding of interactions between R. equi and the host innate immune system, to describe features of the immune response that are associated with resistance or susceptibility to R. equi infection, and help guide strategies for developing novel approaches for preventing R. equi infections. Virulence of R. equi in foals has been attributed to the virulence associated protein A which allows intracellular survival in macrophages by preventing acidification of R. equi-containing vacuole. Additionally, foal susceptibility to R. equi infection is associated with immaturity and naivety of innate and adaptive immune systems, while adult horses with fully functional immune system are resistant to pneumonia. Specific interaction between R. equi and innate immune cells can result in bacterial survival or death; learning how to manipulate these responses to control infection is critical to prevent pneumonia in foals. Administration of live vaccines and stimulation of innate immune responses appears to improve foals' immune response and has the potential to overcome the challenges of foal active vaccination and elicit protection against pneumonia., (© 2024 The Author(s). Equine Veterinary Journal published by John Wiley & Sons Ltd on behalf of EVJ Ltd.)

Validated glass bead sterilization protocols to effectively sterilize rodent surgical instruments after bacterial exposure (for example, cecal contamination) are lacking. To refine current approaches, we added either a multienzyme detergent, neutral pH detergent, or chlorhexidine scrub step before glass bead sterilization of forceps or needle drivers exposed to cecal contents. We exposed sets of forceps and needle drivers to cecal contents, which were then air dried for 3 min. Immediately after, the instruments were wiped several times with a clean, dry paper towel. The contaminated tips were soaked in either a multienzyme or neutral pH detergent ( t = 5 min), chlorhexidine scrub ( t = 2 min), or no pretreatment solution. To further increase debris removal, instruments (from all groups) were brushed using a clean toothbrush. The nonpretreatment instruments were briefly soaked in saline before brushing. After being rinsed with sterile water, all instruments were exposed to a glass bead sterilizer for 60 s at 500 °F (260 °C). Sets were then swabbed for bacterial culturing. Swabs were plated onto either sheep blood agar ( n = 23) or chocolate agar ( n = 20) for aerobic culturing or Brucella agar ( n = 20) for anaerobic culturing. A subset of instruments was sampled to determine organic material presence after treatment using an ATP luminometer ( n = 21). Multiple agar types and bioluminescence were used to more deeply evaluate tool sterility and to differentiate the relative effectiveness of each protocol. From the saline group, only one pair of forceps yielded growth on Brucella agar, and 2 pairs yielded growth on chocolate agar. No other bacterial growth was observed. The use of a pretreatment agent also lowered overall organic contamination levels in needle drivers compared with using only saline. These results indicate that brushing instruments to mechanically remove debris from instruments is paramount to ensure sterility. However, a best practice would be to also use one of the pretreatment options used in this study.

Discospondylitis is a well-recognized disease in dogs, but the relative prevalence of causal infectious agents and efficiency of relevant diagnostic tests are not well-established. Medical record review identified 117 dogs diagnosed with discospondylitis in our clinic over a 5-year period. In 32 dogs, discospondylitis was diagnosed as an incidental imaging finding; 24 of these dogs had concomitant neoplasia. A likely causal infection was identified in 45 of the remaining 85 dogs in which blood and urine cultures, serology for Brucella spp., and galactomannan fungal antigen testing were recommended. Ten dogs were diagnosed with Brucella canis , and ten were diagnosed with suspected fungal infection. Brucella suis serology was negative in all 35 dogs that were tested. Blood cultures were positive in 28 of 71 (39%) tested dogs, and urine culture was positive in 12 of 79 (15%). Cultures were positive from the lesion site of four of eight dogs that underwent surgery and one of the five dogs that underwent image-guided lesion sample collection. Subluxation secondary to discospondylitis was stabilized with metallic implants in four dogs. A similar proportion of known satisfactory treatment outcomes at last follow-up were recorded in dogs that had suspected fungal disease, other bacterial infections, or were Brucella -positive and in those dogs with imaging diagnosis only, although some individuals continued to receive anti-microbial agents or showed recurrent signs. These data support the value of blood culture in discospondylitis and suggest a relatively high prevalence of infection with Brucella spp. and suspected fungal infection.

Campylobacter jejuni or Campylobacter coli infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques ( Macaca mulatta ). We report the complete genomes of 8 C . jejuni isolates and 103 C . coli isolates obtained from rhesus macaques with and without intestinal disease., Competing Interests: The authors declare no conflict of interest.

Staphylococcus pseudintermedius is a frequent cause of infections in dogs. Infectious isolates of this coagulase-positive staphylococcal species are often methicillin- and multidrug-resistant, which complicates therapy. In staphylococci, methicillin resistance is encoded by determinants found on mobile genetic elements called Staphylococcal Chromosome Cassette mec (SCC mec ), which, in addition to methicillin resistance factors, sometimes encode additional genes, such as further resistance factors and, rarely, virulence determinants. In this study, we analyzed SCC mec in a collection of infectious methicillin-resistant S. pseudintermedius (MRSP) isolates from predominant lineages in the United States. We found that several lineages characteristically have specific types of SCC mec elements and Agr types and harbor additional factors in their SCC mec elements that may promote virulence or affect DNA uptake. All isolates had SCC mec -encoded restriction-modification (R-M) systems of types I or II, and sequence types (STs) ST84 and ST64 had one type II and one type I R-M system, although the latter lacked a complete methylation enzyme gene. ST68 isolates also had an SCC mec -encoded CRISPR system. ST71 isolates had a psm-mec gene, which, in all but apparently Agr-dysfunctional isolates, produced a PSM-mec peptide toxin, albeit at relatively small amounts. This study gives detailed insight into the composition of SCC mec elements in infectious isolates of S. pseudintermedius and lays the genetic foundation for further efforts directed at elucidating the contribution of identified accessory SCC mec factors in impacting SCC mec -encoded and thus methicillin resistance-associated virulence and resistance to DNA uptake in this leading canine pathogen.

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.

Background: Dilute sodium hypochlorite (bleach) baths at 0.005% concentration twice weekly have been shown to markedly reduce the severity of atopic dermatitis in children, yet no tolerability and efficacy data are available for this treatment in dogs., Objectives: To determine the local tolerability and the longitudinal effect on the density of Staphylococcus pseudintermedius of repeated diluted bleach baths on healthy dog skin., Animals: Four healthy hound cross-bred dogs., Methods: Bleach baths (0.005%; twice weekly for 15 min) were applied to four healthy hound cross-bred dogs over four weeks (eight baths). Local tolerability was assessed for axillae, abdomen and legs by an investigator before, immediately after and 24 h after each bath. The longitudinal effect on density of S. pseudintermedius from axillae and groin was analysed through quantitative PCR before treatment [at Day (D)-7 and -3], during treatment on D4, D11 and D25, and on D30., Results: There was no erythema or scaling after the baths in any dog. Copy numbers of S. pseudintermedius in axillae, groin and both (axillae and groin together) were not significantly different at any time point during the study., Conclusions and Clinical Relevance: Repeated 0.005% hypochlorite bleach baths over four weeks were safe and well-tolerated in healthy dogs without significant changes in the density of S. pseudintermedius., (© 2023 ESVD and ACVD.)

Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 ( n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: bla CMY-2 , bla CTX-M , mphA , qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, bla CMY-2 gene copies per gram of feces increased significantly ( p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, bla CTX-M , mphA, and qnrB19 gene quantities did not differ significantly ( p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater ( p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.

Strangles is a contagious bacterial disease of horses caused by Streptococcus equi subspecies equi (SEE) that occurs globally. Rapid and accurate identification of infected horses is essential for controlling strangles. Because of limitations of existing PCR assays for SEE, we sought to identify novel primers and probes that enable simultaneous detection and differentiation of infection with SEE and S. equi subsp. zooepidemicus (SEZ). Comparative genomics of U.S. strains of SEE and SEZ (n = 50 each) identified SE00768 from SEE and comB from SEZ as target genes. Primers and probes for real-time PCR (rtPCR) were designed for these genes and then aligned in silico with the genomes of strains of SEE (n = 725) and SEZ (n = 343). Additionally, the sensitivity and specificity relative to microbiologic culture were compared between 85 samples submitted to an accredited veterinary medical diagnostic laboratory. The respective primer and probe sets aligned with 99.7 % (723/725) isolates of SEE and 97.1 % (333/343) of SEZ. Of 85 diagnostic samples, 20 of 21 (95.2 %) SEE and 22 of 23 SEZ (95.6 %) culture-positive samples were positive by rtPCR for SEE and SEZ, respectively. Both SEE (n = 2) and SEZ (n = 3) were identified by rtPCR among 32 culture-negative samples. Results were rtPCR-positive for both SEE and SEZ in 21 of 44 (47.7 %) samples that were culture-positive for SEE or SEZ. The primers and probe sets reported here reliably detect SEE and SEZ from Europe and the U.S., and permit detection of concurrent infection with both subspecies., 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 Elsevier B.V. All rights reserved.)

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.

Objective: To compare: (1) the load and diversity of cultivatable bacterial species isolated from tissue biopsies with cultures from surface swabs, and (2) the ability of each technique to detect methicillin-resistant Staphylococcus aureus (MRSA) in a model of MRSA-infected equine wounds., Study Design: Experimental in vivo study., Animals: Three light-breed adult horses., Methods: Four 2.5 × 2.5 cm full-thickness skin wounds were created on the dorsolateral aspect of each forelimb. Five days later, each wound was inoculated with a pure culture of MRSA (ATCC 43300). One hundred microlitres of 0, 5 × 10 8 , 5 × 10 9 or 5 × 10 10 colony forming units (CFU)/ml was used to inoculate each wound. Surface swabs (Levine technique) and tissue biopsy samples (3 mm punch biopsy) were obtained at 2, 7, 14, and 21 days after inoculation. Quantitative aerobic culture was performed using routine clinical techniques., Results: A similar bacterial profile was identified from the culture of each wound-sampling technique and there was moderate correlation (R = 0.49, P < .001) between the bacterial bioburdens. Agreement was fair (κ = 0.31; 95% CI, 0.129-0.505) between the sampling techniques in identification of MRSA. Methicillin-resistant Staphylococcus aureus was isolated more frequently (P = .016) from cultures of tissue biopsies (79%; 76/96) than from surface swabs (62%; 60/96)., Conclusion: Bacterial load and diversity did not differ between sampling techniques but MRSA was detected more often from the cultures of tissue biopsies., Clinical Significance: Tissue biopsy should be preferred to culture swab in wounds where MRSA is suspected., (© 2022 American College of Veterinary Surgeons.)

Extended-spectrum-β-lactamase (ESBL) and AmpC-lactamase-producing Enterobacteriaceae are serious public health threats. Due to an increasing number of reports of ESBL and AmpC producing Escherichia coli in agricultural settings, it is critical to understand the relationship between the use of two of the highest priority critically important human antibiotics (e.g., third generation cephalosporins [3GC] and macrolides) in food animals and their potential contribution to the selection of ESBL/AmpC E. coli. The objective of our randomized controlled feedlot trial was to measure the effects of ceftiofur crystalline-free acid and tulathromycin on 3GC resistant fecal E. coli populations in cattle before and at various time points after treatment up to and including at slaughter. Multi-level mixed-effects linear regression showed no effect of ceftiofur and tulathromycin on 3GC E. coli CFU counts at slaughter (Day 99); however, a significant (p < 0.05) population shift was observed from susceptible to 3GC resistant E. coli immediately after ceftiofur administration (Day 7). Among 799 fecal samples screened using selective media, 17.7% were ESBL/AmpC E. coli positive, which were further tested for phenotypic antibiotic susceptibility. The majority of the isolates from these plates were multidrug-resistant (94.3%) and expressed either AmpC (78.1%) or ESBL (28.1%) phenotype. A subset of isolates was whole-genome sequenced (n = 20) and identified to harbor chromosomal and/or plasmidal bla genes such as CMY-2, CTX-M, and TEM. Our findings show a time-dependent selection of antibiotics on 3GC-resistant E. coli. High prevalence of multidrug-resistant ESBL/AmpC E. coli found in cattle feces highlights the importance of prudent use of antibiotics in livestock.

Streptococcus equi subsp. equi (SEE) is a host-restricted equine pathogen considered to have evolved from Streptococcus equi subsp. zooepidemicus (SEZ). SEZ is promiscuous in host range and is commonly recovered from horses as a commensal. Comparison of a single strain each of SEE and SEZ using whole-genome sequencing, supplemented by PCR of selected genes in additional SEE and SEZ strains, was used to characterize the evolution of SEE. But the known genetic variability of SEZ warrants comparison of the whole genomes of multiple SEE and SEZ strains. To fill this knowledge gap, we utilized whole-genome sequencing to characterize the accessory genome elements (AGEs; i.e., elements present in some SEE strains but absent in SEZ or vice versa) and methylomes of 50 SEE and 50 SEZ isolates from Texas. Consistent with previous findings, AGEs consistently found in all SEE isolates were primarily from mobile genetic elements that might contribute to host restriction or pathogenesis of SEE. Fewer AGEs were identified in SEZ because of the greater genomic variability among these isolates. The global methylation patterns of SEE isolates were more consistent than those of the SEZ isolates. Among homologous genes of SEE and SEZ, differential methylation was identified only in genes of SEE encoding proteins with functions of quorum sensing, exopeptidase activity, and transitional metal ion binding. Our results indicate that effects of genetic mobile elements in SEE and differential methylation of genes shared by SEE and SEZ might contribute to the host specificity of SEE. IMPORTANCE Strangles, caused by the host-specific bacterium Streptococcus equi subsp. equi (SEE), is the most commonly diagnosed infectious disease of horses worldwide. Its ancestor, Streptococcus equi subsp. zooepidemicus (SEZ), is frequently isolated from a wide array of hosts, including horses and humans. A comparison of the genomes of a single strain of SEE and SEZ has been reported, but sequencing of further isolates has revealed variability among SEZ strains. Thus, the importance of this study is that it characterizes genomic and methylomic differences of multiple SEE and SEZ isolates from a common geographic region ( viz. , Texas). Our results affirm many of the previously described differences between the genomes of SEE and SEZ, including the role of mobile genetic elements in contributing to host restriction. We also provide the first characterization of the global methylome of Streptococcus equi and evidence that differential methylation might contribute to the host restriction of SEE.

Dermatophytosis, also known as ringworm, is a contagious fungal skin disease affecting humans and animals worldwide. Persian cats exhibit severe forms of the disease more commonly than other breeds of cat, including other long-haired breeds. Certain types of severe dermatophytosis in humans are reportedly caused by monogenic inborn errors of immunity. The goal of this study was to identify genetic variants in Persian cats contributing to the phenotype of severe dermatophytosis. Whole-genome sequencing of case and control Persian cats followed by a genome-wide association study identified a highly divergent, disease-associated haplotype on chromosome F1 containing the S100 family of genes. S100 calcium binding protein A9 (S100A9), which encodes a subunit of the antimicrobial heterodimer known as calprotectin, contained 13 nonsynonymous variants between cases and controls. Evolutionary analysis of S100A9 haplotypes comparing cases, controls, and wild felids suggested the divergent disease-associated haplotype was likely introgressed into the domestic cat lineage and maintained via balancing selection. We demonstrated marked upregulation of calprotectin expression in the feline epidermis during dermatophytosis, suggesting involvement in disease pathogenesis. Given this divergent allele has been maintained in domestic cat and wildcat populations, this haplotype may have beneficial effects against other pathogens. The pathogen specificity of this altered protein should be investigated before attempting to reduce the allele frequency in the Persian cat breed. Further work is needed to clarify if severe Persian dermatophytosis is a monogenic disease or if hidden disease-susceptibility loci remain to be discovered. Consideration should be given to engineering antimicrobial peptides such as calprotectin for topical treatment of dermatophytosis in humans and animals., Competing Interests: The authors have declared that no competing interests exist.

In two sequential replicates ( n = 90 and n = 96 feedlot finisher cattle, respectively) we measured the impact of an Enterococcus faecium -based probiotic (DFM) and an altered feedlot pen environment on antimicrobial resistance among fecal enterococci in cattle fed (or, not fed) the macrolide tylosin. Diluted fecal samples were spiral-plated on plain and antibiotic-supplemented m- Enterococcus agar. In the first replicate, tylosin significantly ( p < 0.05) increased the relative quantity of erythromycin-resistant enterococci. This effect was diminished in cattle fed the DFM in conjunction with tylosin, indicating a macrolide susceptible probiotic may help mitigate resistance. A similar observed effect was not statistically significant ( p > 0.05) in the second replicate. Isolates were speciated and resistance phenotypes were obtained for E. faecium and E. hirae . Susceptible strains of bacteria fed as DFM may prove useful for mitigating the selective effects of antibiotic use; however, the longer-term sustainability of such an approach remains unclear.

The objective of this experiment was to determine if statistical process control (SPC) procedures coupled with remote continuous data collection could accurately differentiate between animals experimentally inoculated with a viral-bacterial (VB) challenge or phosphate buffer solution (PBS). Crossbred heifers (N = 38; BW = 230 ± 16.4 kg) were randomly assigned to treatments by initial weight, average daily gain (ADG), bovine herpes virus 1, and Mannheimia haemolytica serum titers. Feeding behavior, dry matter intake (DMI), animal activity, and rumen temperature were continuously monitored remotely prior to and following VB challenge. VB-challenged heifers exhibited decreased (P < 0.01) ADG and DMI, as well as increased (P < 0.01) neutrophils and rumen temperature consistent with a bovine respiratory disease (BRD) infection. However, none of the heifers displayed overt clinical signs of disease. Shewhart and cumulative summation (CUSUM) charts were evaluated, with sensitivity and specificity computed on the VB-challenged heifers (n = 19) and PBS-challenged heifers (n = 19), respectively, and the accuracy was determined as the average of sensitivity and specificity. To address the diurnal nature of rumen temperature responses, summary statistics (mean, minimum, and maximum) were computed for daily quartiles (6-h intervals), and these quartile temperature models were evaluated separately. In the Shewhart analysis, DMI was the most accurate (95%) at deciphering between PBS- and VB-challenged heifers, followed by rumen temperature (94%) collected in the 2nd and 3rd quartiles. Rest was most the accurate accelerometer-based traits (89%), and meal duration (87%) and bunk visit (BV) frequency (82%) were the most accurate feeding behavior traits. Rumen temperature collected in the 3rd quartile signaled the earliest (2.5 d) of all the variables monitored with the Shewhart, followed by BV frequency (2.8 d), meal duration (2.8 d), DMI (3.0 d), and rest (4.0 d). Rumen temperature and DMI remained the most accurate variables in the CUSUM at 80% and 79%, respectively. Meal duration (58%), BV frequency (71%), and rest (74%) were less accurate when monitored with the CUSUM analysis. Furthermore, signal day was greater for DMI, rumen temperature, and meal duration (4.4, 5.0, and 3.7 d, respectively) in the CUSUM compared to Shewhart analysis. These results indicate that Shewhart and CUSUM charts can effectively identify deviations in feeding behavior, activity, and rumen temperature patterns for the purpose of detecting sub-clinical BRD in beef cattle., (Published by Oxford University Press on behalf of the American Society of Animal Science 2021.)

Background: The fecal microbiome of healthy horses may be influenced by signalment, diet, environmental factors, and disease., Objectives: To assess the effects of age, breed, sex, geographic location, season, diet, and colitis caused by antibiotic use (antimicrobial-associated diarrhea [AAD]) and Salmonella infection on fecal microbiota., Animals: Healthy horses (n = 80) were sampled from nonhospital environments across multiple geographical locations in the United States. Horses with AAD (n = 14) were defined as those that developed diarrhea secondary to antimicrobial use. Horses with Salmonella infection (n = 12) were presented with spontaneous onset of colitis and subsequently tested positive on Salmonella quantitative polymerase chain reaction. All horses were >1 year of age and stratified by a dietary scale that included forages (pasture and hay) and concentrates grouped by percentage of fiber and amount., Methods: Illumina sequencing of 16S rRNA genes was performed on fecal DNA., Results: Healthy horses fed higher amounts of grain clustered separately from those fed lower amounts of grain (analysis of similarities [ANOSIM], R = 0.356-0.385, Q = 0.002). Horses with AAD and Salmonella had decreased richness and evenness compared to healthy horses (P < .05). Univariable analysis of the 3 groups identified increases in Bacteroidetes (Q = 0.002) and Protebacteria (Q = 0.001) and decreases in Verrucomicrobia (Q = 0.001) in AAD horses whereas Salmonella horses had less Firmicutes (Q = 0.001) when compared to healthy horses., Conclusions and Clinical Importance: Although the amount of grain in the diet had some impact on the fecal microbiome, colitis had a significantly larger influence. Horses with ADD have a more severe dysbiosis than do horses with Salmonella., (© 2021 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC on behalf of American College of Veterinary Internal Medicine.)

While Staphylococcus aureus is associated with significant morbidity and mortality in equids (horses, donkeys, and mules), few studies have performed whole-genome sequencing to fully categorize large collections of equine isolates. Such sequencing allows for a comprehensive analysis of the genetic lineage and relationships of isolates, as well as the virulence genes present in each, which can be important for understanding the epidemiology of strains and their range of infections. Seventy-two clinical Staphylococcus aureus isolates from equids were collected at the Texas A&M University Veterinary Medical Teaching Hospital between 2007 and 2017. Whole-genome sequencing was performed to characterize the isolates according to sequence typing, biofilm association, antimicrobial resistance, and toxin gene carriage. Of the 72 isolates, 19% were methicillin resistant, of which the majority belonged to clonal complex 8. Eighteen distinct sequence types (STs) were represented, with the most common being ST1, ST133, ST8, and ST97. Most isolates had weak or negative overall biofilm production. Toxin and antimicrobial resistance gene carriage was varied; of note, this study revealed that a large proportion of North American equine isolates carry the leucocidin PQ toxin (66% of isolates). One isolate (17-021) carried genes imparting lincosamide and high-level mupirocin resistance, a combination not previously reported in equine-derived S. aureus isolates. IMPORTANCE This is one of the first studies to perform whole-genome sequencing (WGS) of a large collection of Staphylococcus aureus isolates, both methicillin resistant and susceptible, collected from horses. A large proportion of the isolates carry leucocidin PQ (LukPQ), making this one of the first reports of such carriage in the United States. The presence of lincosamide and high-level mupirocin resistance in a methicillin-susceptible S. aureus (MSSA) isolate highlights the importance of MSSA as a reservoir of important antimicrobial resistance genes. As microbial resistance genes on mobile genetic elements can pass between S. aureus strains and livestock-associated strains can be transferred to humans, these findings have important public health implications.

Background: Persian cats are predisposed to chronic and severe dermatophytosis. Alterations to the cutaneous microbiota are one potential contributor to this predisposition., Objectives: To characterise the cutaneous and environmental fungal microbiota of Persian cats with chronic, severe dermatophytosis, and to compare the fungal microbiota of cats with and without dermatophytosis., Animals: Thirty-six client-owned cats, including 26 Persian cats and 10 domestic long hair (DLH) cats., Methods and Materials: Skin and home environment swabs were collected from Persian cats with severe, chronic dermatophytosis as well as groups of healthy control cats (Persian and DLH). Sequencing of the internal transcribed spacer 1 (ITS1) region was performed in addition to ITS1 quantitative PCR and fungal culture., Results: Next-generation sequencing (NGS) targeting the fungal ITS region detected Microsporum sp. DNA from all Persian cats diagnosed with dermatophytosis and from environmental samples of their homes. A significant difference in community structure was identified between cases and controls, largely resulting from the Microsporum spp. DNA in samples from affected cats. Persian cats with dermatophytosis do not exhibit decreased fungal diversity. NGS failed to identify dermatophyte DNA on two culture-positive asymptomatic Persian controls and identified Trichophyton rubrum DNA from a culture-negative asymptomatic Persian control., Conclusions: Aside from M. canis, our results indicate that an underlying fungal dysbiosis is not likely to play a role in development of dermatophytosis in Persian cats. Other explanations for predisposition to this disease, such as a primary immunodeficiency, ineffective grooming or unique features of Persian cat hair should be investigated., (© 2021 ESVD and ACVD, Veterinary Dermatology.)

Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as one of the primary sources of Salmonella -related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype and subpopulation specific, which makes it essential to understand high-resolution Salmonella population dynamics in cattle. Time of year, source of cattle, pen, and sample type (i.e., feces, hide, or lymph nodes) have previously been identified as important factors influencing the serotype distribution of Salmonella (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism-based maximum-likelihood phylogeny and hierarchical clustering of core-genome multilocus sequence typing. The importance of the aforementioned features in clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each subpopulation. Our findings indicate that clonal expansion of Salmonella strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle, i.e., regardless of sampling time and sample type (i.e., feces, lymph node, or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carryover contributions of existing strains of Salmonella and their bacteriophages. IMPORTANCE Salmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella , and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of Salmonella in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within Salmonella serotypes in feedlot cattle from the beginning of feeding up until slaughter. Here, we explore Salmonella population dynamics within each serotype using core-genome phylogeny and hierarchical classifications. We used machine learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that Salmonella populations in cattle are highly clonal over a 6-month study period and that clonal dissemination of Salmonella in cattle is mainly influenced spatially by experimental block and pen, as well by the geographical origin of the cattle.

Molecular techniques are increasingly being applied to stained cytology slides for the diagnosis of neoplastic and infectious diseases. Such techniques for the identification of fungi from stained cytology slides have not yet been evaluated. This study aimed to assess the diagnostic accuracy of direct (without nucleic acid isolation) panfungal polymerase chain reaction (PCR) followed by sequencing for identification of fungi and oomycetes on stained cytology slides from dogs, cats, horses, and other species. Thirty-six cases were identified with cytologically identifiable fungi/oomycetes and concurrent identification via fungal culture or immunoassay. Twenty-nine controls were identified with no cytologically or histologically visible organisms and a concurrent negative fungal culture. Direct PCR targeting the internal transcribed spacer region followed by sequencing was performed on one cytology slide from each case and control, and the sensitivity and specificity of the assay were calculated. The sensitivity of the panfungal PCR assay performed on stained cytology slides was 67% overall, 73% excluding cases with oomycetes, and 86% when considering only slides with abundant fungi. The specificity was 62%, which was attributed to amplification of fungal DNA from control slides with no visible fungus and negative culture results. Direct panfungal PCR is capable of providing genus- or species-level identification of fungi from stained cytology slides. Given the potential of panfungal PCR to amplify contaminant fungal DNA, this assay should be performed on slides with visible fungi and interpreted in conjunction with morphologic assessment by a clinical pathologist.

Background: Combatting antimicrobial resistance requires a One Health approach to antimicrobial stewardship including antimicrobial drug (AMD) use evaluation. Current veterinary AMD prescribing data are limited., Objectives: To quantify companion animal AMD prescribing in primary care and specialty practice across 3 academic veterinary hospitals with particular focus on third-generation cephalosporins, fluoroquinolones, and carbapenems., Animals: Dogs and cats presented to 3 academic veterinary hospitals from 2012 to 2017., Methods: In this retrospective study, AMD prescribing data from 2012 to 2017 were extracted from electronic medical records at each hospital and prescriptions classified by service type: primary care, specialty practice or Emergency/Critical Care (ECC). Hospital-level AMD prescribing data were summarized by species, service type, AMD class, and drug. Multivariable logistic full-factorial regression models were used to estimate hospital, year, species, and service-type effects on AMD prescribing. Estimated marginal means and confidence intervals were plotted over time., Results: The probability of systemic AMD prescribing for any indication ranged between 0.15 and 0.28 and was higher for dogs than cats (P < .05) apart from 2017 at hospital 1. Animals presented to primary care were least likely to receive AMDs (dogs 0.03-0.15, cats 0.03-0.18). The most commonly prescribed AMD classes were aminopenicillins/β-lactamase inhibitors (0.02-0.15), first-generation cephalosporins (0.00-0.09), fluoroquinolones (0.00-0.04), nitroimidazoles (0.01-0.06), and tetracyclines (0.00-0.03). Among the highest priority classes, fluoroquinolones (dogs 0.00-0.09, cats 0.00-0.08) and third-generation cephalosporins (dogs 0.00-0.04, cats 0.00-0.05) were most frequently prescribed., Conclusions and Clinical Importance: Antimicrobial drug prescribing frequencies were comparable to previous studies. Additional stewardship efforts might focus on fluoroquinolones and third-generation cephalosporins., (© 2021 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC on behalf of American College of Veterinary Internal Medicine.)

Background: Salmonella spp. represent a significant zoonotic concern to pregnant owners as infection can cause septic abortions and post-partum illness. Enteric salmonellosis is well documented in canines however urinary salmonellosis is rarely described and Salmonella prostatitis has never been described in dogs., Case Presentation: This case report describes the diagnosis and management of a five-year-old, intact male Labrador Retriever mix dog that was diagnosed with Salmonella prostatitis among other comorbidities including heartworm infestation. Additionally, mitigation of zoonotic spread is emphasized as one of the owners was six months pregnant at the time of diagnosis., Discussion: The pathogenesis of Salmonella prostatitis is unknown but explanations pertaining to enteric salmonellosis, such as the lifestyle and stress of living as a stray may have contributed and contamination from an enteric infection may have also been possible. Several recommendations were made to reduce the likelihood of zoonotic transmission including frequent hand washing, avoidance of the patient's mouth, change in location of where the patient was fed, the use of an isolated area outside for urination and defecation, and the use of dilute bleach to clean areas soiled by the patient's bodily fluids. Monitoring of the prostatic infection was facilitated with prostatic wash instead of urine culture. This decision was made as prostatic infections have been shown to intermittently shed bacteria into the urine, leading to possible false negative urine cultures and potential catastrophic zoonotic infection.

Whole-genome sequencing (WGS) has changed our understanding of bacterial pathogens, aiding outbreak investigations and advancing our knowledge of their genetic features. However, there has been limited use of genomics to understand antimicrobial resistance of veterinary pathogens, which would help identify emerging resistance mechanisms and track their spread. The objectives of this study were to evaluate the correlation between resistance genotypes and phenotypes for Staphylococcus pseudintermedius, a major pathogen of companion animals, by comparing broth microdilution antimicrobial susceptibility testing and WGS. From 2017-2019, we conducted antimicrobial susceptibility testing and WGS on S. pseudintermedius isolates collected from dogs in the United States as a part of the Veterinary Laboratory Investigation and Response Network (Vet-LIRN) antimicrobial resistance monitoring program. Across thirteen antimicrobials in nine classes, resistance genotypes correlated with clinical resistance phenotypes 98.4 % of the time among a collection of 592 isolates. Our findings represent isolates from diverse lineages based on phylogenetic analyses, and these strong correlations are comparable to those from studies of several human pathogens such as Staphylococcus aureus and Salmonella enterica. We uncovered some important findings, including that 32.3 % of isolates had the mecA gene, which correlated with oxacillin resistance 97.0 % of the time. We also identified a novel rpoB mutation likely encoding rifampin resistance. These results show the value in using WGS to assess antimicrobial resistance in veterinary pathogens and to reveal putative new mechanisms of resistance., (Published by Elsevier B.V.)

Background: Various Staphylococcus species have been demonstrated to play important roles on the skin, including causing disease and protecting the host from pathogens. Although culture-based studies have isolated various Staphylococcus spp. from feline skin, very little is known regarding the species-level communities on the host., Hypothesis/objectives: To describe the species-level staphylococcal communities inhabiting the skin of healthy cats and cats with allergic dermatitis., Animals: Skin swabs from the ear canal and groin of 11 healthy and 10 allergic (nonlesional) cats were obtained., Methods and Materials: DNA was extracted from the skin swabs and used for next-generation sequencing targeting the V1-3 region of the 16S rRNA gene. Following a standard microbiota analysis of the sequencing data, species-level assignment for the staphylococcal sequences were obtained using a staphylococci-specific database., Results: Staphylococcus spp. had similar relative abundance in healthy and allergic samples. The most abundant staphylococcal species were S. epidermidis in healthy samples, and S. felis and S. capitis in allergic samples. The composition of staphylococcal communities, as well as relative abundance of Staphylococcus spp., was variable between body sites and individual cats sampled., Conclusions and Clinical Relevance: These results demonstrate that diverse staphylococcal communities inhabit the skin of healthy and allergic cats, and provide a starting point for further research into the importance of Staphylococcus spp. in feline allergic skin disease., (© 2020 ESVD and ACVD.)

Antibiotic resistance represents a growing crisis in both human and veterinary medicine. We evaluated the use of antibiotic alternatives-heavy metals and essential oils-in beef cattle feeding, and their effects on Gram-negative and Gram-positive bacteria. In this randomized controlled field trial, we measured the impact of supplemental zinc and menthol on antibiotic resistance among commensal enteric bacteria of feeder cattle. Fecal suspensions were plated onto plain- and antibiotic-supplemented MacConkey and m- Enterococcus agar for quantification of total and antibiotic-resistant Escherichia coli and Enterococcus spp., respectively. Temporal effects on overall E. coli growth were significant ( p < 0.05), and menthol was associated with decreased growth on tetracycline-supplemented agar. Zinc was associated with significant increases in growth on erythromycin-supplemented m- Enterococcus agar. Cattle fed zinc exhibited significantly higher levels of macrolide resistance among fecal enterococci isolates.

In the enteric pathogen Salmonella enterica serovar Typhimurium, invasion and motility are coordinated by the master regulator HilD, which induces expression of the type III secretion system 1 (T3SS1) and motility genes. Methyl-accepting chemotaxis proteins (MCPs) detect specific ligands and control the direction of the flagellar motor, promoting tumbling and changes in direction (if a repellent is detected) or smooth swimming (in the presence of an attractant). Here, we show that HilD induces smooth swimming by upregulating an uncharacterized MCP (McpC), and this is important for invasion of epithelial cells. Remarkably, in vitro assays show that McpC can suppress tumbling and increase smooth swimming in the absence of exogenous ligands. Expression of mcpC is repressed by the universal regulator H-NS, which can be displaced by HilD. Our results highlight the importance of smooth swimming for Salmonella Typhimurium invasiveness and indicate that McpC can act via a ligand-independent mechanism when incorporated into the chemotactic receptor array.

Though carbapenems are not licensed for use in food animals in the U.S., carbapenem resistance among Enterobacteriaceae has been identified in farm animals and their environments. The objective of our study was to determine the extent to which older-generation β-lactam antibiotics approved for use in food animals in the U.S. might differentially select for resistance to antibiotics of critical importance to human health, such as carbapenems. Escherichia coli (E. coli) strains from humans, food animals, or the environment bearing a single β-lactamase gene (n = 20 each) for blaTEM-1, blaCMY-2, and blaCTX-M-* or else blaKPC/IMP/NDM (due to limited availability, often in combination with other bla genes), were identified, along with 20 E. coli strains lacking any known beta-lactamase genes. Baseline estimates of intrinsic bacterial fitness were derived from the population growth curves. Effects of ampicillin (32 μg/mL), ceftriaxone (4 μg/mL) and meropenem (4 μg/mL) on each strain and resistance-group also were assessed. Further, in vitro batch cultures were prepared by mixing equal concentrations of 10 representative E. coli strains (two from each resistance gene group), and each mixture was incubated at 37°C for 24 hours in non-antibiotic cation-adjusted Mueller-Hinton II (CAMH-2) broth, ampicillin + CAMH-2 broth (at 2, 4, 8, 16, and 32 μg/mL) and ceftiofur + CAMH-2 broth (at 0.5, 1, 2, 4, and 8μg/mL). Relative and absolute abundance of resistance-groups were estimated phenotypically. Line plots of the raw data were generated, and non-linear Gompertz models and multilevel mixed-effect linear regression models were fitted to the data. The observed strain growth rate distributions were significantly different across the groups. AmpC strains (i.e., blaCMY-2) had distinctly less robust (p < 0.05) growth in ceftriaxone (4 μg/mL) compared to extended-spectrum beta-lactamase (ESBL) producers harboring blaCTX-M-*variants. With increasing beta-lactam antibiotic concentrations, relative proportions of ESBLs and CREs were over-represented in the mixed bacterial communities; importantly, this was more pronounced with ceftiofur than with ampicillin. These results indicate that aminopenicillins and extended-spectrum cephalosporins would be expected to propagate carbapenemase-producing Enterobacteriaceae in food animals if and when Enterobacteriaceae from human health care settings enter the food animal environment., Competing Interests: The authors have declared that no competing interests exist.

Background: We report the first case of canine Salmonella meningoencephalomyelitis and second case of canine Salmonella bacteriuria, as well as the first reported case of Salmonella enterica subspecies houtenae in a dog., Case Presentation: Immunosuppressive treatment in a dog for a relapse of steroid-responsive meningitis and arteritis (SRMA) allowed for the opportunistic establishment of a bacteremia with Salmonella enterica subsp. houtenae, ultimately causing meningoencephalomyelitis and subclinical bacteriuria. The bacterial infections were treated with a four-month course of amoxicillin; clinical treatment success was determined by serial negative urine cultures and lack of clinical signs correlated to the meningoencephalomyelitis., Conclusions: Both the bacteriuria and meningoencephalomyelitis represented opportunistic infections in a dog immunosuppressed for SRMA. The clinical course of this infectious meningoencephalitis emphasizes the importance of differentiating relapse of initial disease from opportunistic infection occurring in a compromised central nervous system. The novel Salmonella species identified in this case acts as a reminder that infectious disease diagnostics should not be curbed by anecdotal prediction of routine pathogenic suspects.

The genomes of three clinical isolates of Salmonella enterica subsp. houtenae were sequenced using an Illumina MiSeq instrument. These isolates came from the urine and cerebrospinal fluid of a dog treated for hind-limb paresis with immunosuppressive drugs. S. enterica subsp. houtenae has also been implicated in brain infections in humans., (Copyright © 2020 Krath et al.)

This is a draft genome of an orf virus (ORFV) vaccine strain assembled via long- and short-read hybrid assembly. ORFV is a zoonotic pathogen that affects sheep and goats. The genome of the virus contained in the vaccine was found to have high similarity (98%) to those of other published strains., (Copyright © 2020 Heare et al.)

To evaluate the effects of a patented Bacillus subtilis probiotic, weaned Holstein steers, not shedding Salmonella ( n  = 40; ∼90 kg), were supplemented (CLO) or not (CON) with CLOSTAT ® (13 g/hd per day; Kemin Industries, Des Moines, IA) in a starter ration for 35 d. The calves were assigned to one of four treatments in a 2 × 2 factorial design with CLO and CON calves that were orally administered Salmonella (STM) or not (NoSTM). Calves were challenged with 1.6 × 10 6 colony-forming unit (CFU) Salmonella Typhimurium (resistant to 50 μg/mL nalidixic acid) in 1 L of milk replacer on day 0. Blood samples were collected through jugular catheters every 6 h for 96 h, and body temperature was measured every 5 min through indwelling rectal temperature recording devices. Five calves from each treatment were harvested 48 h postchallenge, and the remaining calves were harvested 96 h postchallenge. During necropsy, tissues were collected for the isolation and quantification of the inoculated STM from various tissues. The CLOSTM group had reduced STM concentrations in the jejunum, ileum, and transverse colon 48 h after the challenge ( p  ≤ 0.03), but were not different 96 h postchallenge ( p  > 0.05). Decreased ( p  < 0.01) pyrexia was observed after the challenge in CLOSTM calves when compared with CONSTM calves. White blood cells and lymphocyte counts were increased ( p  ≤ 0.05) in CLOSTM calves after the challenge in comparison with other treatments. In calves given STM, the CLO group had greater feed intake before and after the challenge ( p  < 0.01) compared with the CON group. Increased serum IL-6 and IFN-γ concentrations were observed in the CONSTM group compared with other treatments. Overall, CLO reduced Salmonella presence and concentrations in gastrointestinal tissues while simultaneously reducing the severity of the challenge as indicated by blood parameters and the reduced febrile response.

Malassezia dermatitis and otitis are recurrent features of canine atopic dermatitis, increasing the cost of care, and contributing to a reduced quality of life for the pet. The exact pathogenesis of secondary yeast infections in allergic dogs remains unclear, but some have proposed an overgrowth of M. pachydermatis to be one of the flare factors. The distribution of Malassezia populations on healthy and allergic canine skin has not been previously investigated using culture-independent methods. Skin swabs were collected from healthy, naturally affected allergic, and experimentally sensitized atopic dogs. From the extracted DNA, fungal next-generations sequencing (NGS) targeting the ITS region with phylogenetic analysis of sequences for species level classification, and Malassezia species-specific quantitative real-time polymerase chain reaction (qPCR) were performed. M. globosa was significantly more abundant on healthy canine skin by both methods (NGS P < .0001, qPCR P < .0001). M. restricta was significantly more abundant on healthy skin by NGS (P = .0023), and M. pachydermatis was significantly more abundant on naturally-affected allergic skin by NGS (P < .0001) and on allergen-induced atopic skin lesions by qPCR (P = .0015). Shifts in Malassezia populations were not observed in correlation with the development of allergen-induced skin lesions. Differences in the lipid dependency of predominant Malassezia commensals between groups suggests a role of the skin lipid content in driving community composition and raises questions of whether targeting skin lipids with therapeutics could promote healthy Malassezia populations on canine skin., (© The Author(s) 2019. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

Objective: To determine the ability of cell salvage washing and leukoreduction filtration to remove bacterial contamination from canine whole blood., Study Design: Ex vivo nested cohort study., Sample Population: Commercially purchased fresh canine whole blood (n = 33 units)., Methods: Commercially obtained canine whole blood was inoculated with known concentrations of one of three species of bacteria, Escherichia coli (ATCC 25922), Staphylococcus pseudintermedius (quality control strain; Texas A&M University), or Pseudomonas aeruginosa (ATCC 27853). Negative controls were inoculated with sterile saline. The inoculated blood was processed through a cell salvage system and filtered through a series of two leukocyte reduction filters. Samples were aseptically collected at five points during processing (inoculum, prewash, postwash, post-first filtration, and post-second filtration) for bacterial enumeration., Results: Bacterial concentrations were reduced by 85.2%, 91.5%, and 93.9% for E coli, S pseudintermedius, and P aeruginosa, respectively, after washing (P < .0001), and bacterial concentrations were reduced by 99.9%, 100%, and 100%, respectively, after the first filtration (P < .0001). After the second filtration, none of the three species of bacteria could be isolated (100% reduction). No bacterial growth was obtained from negative controls throughout the study. The type of bacteria (P = .29) did not allow prediction of bacterial reduction., Conclusion: Cell salvage washing combined with leukoreduction filtration eliminated bacterial contamination of whole dog blood (P < .0001)., Clinical Significance: Cell salvage washing and leukoreduction filtration could be applied to intraoperative autotransfusion in clinical animals, especially those treated for trauma or hemorrhage with concurrent bacterial contamination., (© 2020 The American College of Veterinary Surgeons.)

[This corrects the article DOI: 10.1371/journal.pone.0190829.].

This is the draft genome of an Erysipelothrix rhusiopathiae strain isolated from the blood of a canine. Initial 16S ribosomal DNA amplification identified the isolate as belonging to the Erysipelothrix genus but could not elucidate the species due to previous misidentification of E. rhusiopathiae and E. tonsillarum The species identification was confirmed by whole-genome sequencing., (Copyright © 2020 Little et al.)

Distal limb wounds are common injuries sustained by horses and their healing is fraught with complications due to equine anatomy, prevalence of infection, and challenges associated with wound management. Gallium is a semi-metallic element that has been shown to possess antimicrobial properties and aid in wound healing in various preclinical models. The effects of Gallium have not been studied in equine wound healing. Therefore, the objective of this study was to compare healing rates between gallium-treated and untreated wounds of equine distal limbs and to demonstrate the antimicrobial effects of gallium on wounds inoculated with S. aureus. Using an established model of equine wound healing we demonstrated beneficial effects of 0.5% topical gallium maltolate on equine wound healing. Specifically we documented reduced healing times, reduced bioburden, and reduced formation of exuberant granulation tissue in wounds treated with gallium maltolate as compared with untreated wounds. Gallium appeared to exert its beneficial effects via its well-described antimicrobial actions as well as by altering the expression of specific genes known to be involved in wound healing of horses and other animals. Specifically, gallium maltolate appeared to increase expression of transforming growth factor-β in both infected and un-infected wounds. Further work is needed to document the effects of gallium on naturally occurring equine wounds and to compare the effects of gallium with other wound treatment options. These data, however, suggest that gallium may be an attractive and novel means of improving equine distal limb wound healing., Competing Interests: The authors have declared that no competing interests exist.

Antibiotic administration can be a cause of gastrointestinal disease in horses, creating a disruption in the normal population and function of bacteria found in the hindgut. The objective of this study was to describe the changes in the cecal and fecal microbiomes and metabolomes of clinically healthy horses before and after metronidazole administration. Metronidazole (15 mg/kg BID PO) was given to five horses with cecal cannulas. The study was suspended on Day 3 due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before (Days minus52, m28, m14, and 0) and after (Days 7, 14, 28, and 52) metronidazole administration. DNA was extracted from the cecal and fecal samples, and 16S rRNA genes were sequenced. Richness and evenness indices were significantly decreased by metronidazole administration in both cecal and fecal samples, but the overall composition was only significantly changed in fecal samples on Day 3 (ANOSIM, p = 0.008). The most dominant phyla were Bacteroidetes and Firmicutes in all groups examined. In fecal samples, significant changes of the phyla Actinobacteria, Spirochaetes, Lentisphaerae, and Verrucomicrobia occurred on Day 3, which correlated with clinical signs of gastrointestinal disease. The metabolome was characterized by mass spectrometry-based methods and only named metabolites were included in the analysis. Fecal, but not cecal, metabolites were significantly affected by metronidazole. The fecal metabolites affected represent diverse metabolic pathways, such as the metabolism of amino acids, carbohydrates, lipids, nucleic acids and cofactors and vitamins. Metronidazole administration has potential to cause adverse effects in horses, alters the bacterial composition of the horse's cecal and fecal content, and the metabolome of fecal samples., Competing Interests: The authors have declared that no competing interests exist.

This is a report of two Bacillus safensis genomes sequenced from separate cultures isolated from the uterus of a 16-year-old Westphalian mare that aborted a dead fetus. This strain represents the first case of a B. safensis -associated equine abortion and the first case of infection caused by this bacterium., (Copyright © 2020 Little et al.)

Strangles, caused by Streptococcus equi subspecies equi (S. equi) is an infectious disease of horses with worldwide distribution, but there are limited data available regarding strain variation using whole genome sequencing among and within outbreaks in the United States (US), and how US isolates compare with S. equi isolated globally. To address this knowledge-gap, we compared the whole genomes of 54 S. equi isolates from Texas and Kentucky and those of 230 publicly available sequences of S. equi isolates collected from other countries. Our results show that despite minimal variation among isolates within an outbreak some mutations do occur among individual outbreak isolates. Some S. equi strains from the US are closely related to S. equi isolates from other countries, likely reflecting international dissemination of isolates. Collectively, these data improve our understanding of phenotypic and genotypic variation of isolates within an outbreak, and the international distribution of S. equi. We also identify a novel variant of the S. equi M-protein, and observed cases of strangles that were caused by the modified-live vaccine but that were not recognized as vaccine-associated at the time of clinical sample submission., (Copyright © 2020 Elsevier B.V. All rights reserved.)

This is an announcement for the genome sequence of a clinical isolate of Salmonella enterica subsp. arizonae isolated from the urine and prostate of a 6-year-old male Labrador retriever. This is one of the few reports of a Salmonella enterica subsp. arizonae isolate cultured from canine urine., (Copyright © 2020 Krath et al.)

Background: Urine cultures are frequently recommended to rule out infection as a postrenal cause of proteinuria., Objective: Identify characteristics associated with bacterial growth in urine in proteinuric dogs., Animals: Four hundred and fifty-one dogs admitted to a teaching hospital between January 2008 and January 2018 with urine protein-to-creatinine ratios (UPCs) >0.5., Methods: Retrospective study included dogs with a UPC, urinalysis, and quantitative urine culture (QUC) performed within a 72-hour period by searching electronic records. Dogs with recent antimicrobial therapy, urine collected by methods other than cystocentesis, or UPC ≤0.5 were excluded. Signalment, comorbidities, serum BUN and creatinine concentrations, urinalysis findings, and QUC results were recorded. The association between these characteristics and presence of bacterial growth in urine was assessed by univariable and multivariable analysis., Results: Thirty of four hundred fifty-one dogs (6.7%) had bacterial growth in urine. Of these, 18 (60.0%) had active urine sediment. Bacterial growth in urine was associated with pyuria (odd ratio [OR] 25.1, 95% confidence interval [CI] 7.9-79.6, P < .001), bacteriuria (OR 11.1, 95% CI 3.2-39.1, P < .001), and lower urinary tract disease (OR 6.7, 95% CI 1.9-23.0; P = .0028). If QUC was prompted based on these criteria, 8/451 (1.8%) of proteinuric dogs would have had undetected bacterial growth., Conclusions and Clinical Importance: The proportion of proteinuric dogs with both inactive urine sediment and bacterial growth in urine was low, suggesting that QUC might not be necessary in the evaluation of all proteinuric dogs. An active urine sediment or lower urinary tract disease should prompt QUC for proteinuric dogs., (© 2020 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.)

The genome of a Weissella confusa strain isolated from a foal with sepsis is reported. Weissella confusa inhabits feces and causes disease in immunocompromised humans and animals. It is important for veterinarians to be aware of the pathogenic ability of these bacteria due to the unknown potential for zoonotic transmission., (Copyright © 2020 Little et al.)

Staphylococcus epidermidis is a leading cause of nosocomial infections in patients with a compromised immune system and/or an implanted medical device. Seventy to 90% of S. epidermidis clinical isolates are methicillin resistant and carry the mecA gene, present in a mobile genetic element (MGE) called the staphylococcal cassette chromosome mec (SCC mec ) element. Along with the presence of antibiotic and heavy metal resistance genes, MGEs can also contain genes encoding secreted or cell wall-anchored virulence factors. In our earlier studies of S. epidermidis clinical isolates, we discovered S. epidermidis surface protein J (SesJ), a prototype of a recently discovered subfamily of the microbial surface component recognizing adhesive matrix molecule (MSCRAMM) group. MSCRAMMs are major virulence factors of pathogenic Gram-positive bacteria. Here, we report that the sesJ gene is always accompanied by two glycosyltransferase genes, gtfA and gtfB , and is present in two MGEs, called the arginine catabolic mobile element (ACME) and the staphylococcal cassette chromosome (SCC) element. The presence of the sesJ gene was associated with the left-hand direct repeat DR&#95;B or DR&#95;E. When inserted via DR&#95;E, the sesJ gene was encoded in the SCC element. When inserted via DR&#95;B, the sesJ gene was accompanied by the genes for the type 1 restriction modification system and was encoded in the ACME. Additionally, the SCC element and ACME carry different isoforms of the SesJ protein. To date, the genes encoding MSCRAMMs have been seen to be located in the bacterial core genome. Here, we report the presence of an MSCRAMM in an MGE in S. epidermidis clinical isolates. IMPORTANCE S. epidermidis is an opportunistic bacterium that has established itself as a successful nosocomial pathogen. The modern era of novel therapeutics and medical devices has extended the longevity of human life, but at the same time, we also witness the evolution of pathogens to adapt to newly available niches in the host. Increasing antibiotic resistance among pathogens provides an example of such pathogen adaptation. With limited opportunities to modify the core genome, most of the adaptation occurs by acquiring new genes, such as virulence factors and antibiotic resistance determinants present in MGEs. In this study, we describe that the sesJ gene, encoding a recently discovered cell wall-anchored protein in S. epidermidis , is present in both ACME and the SCC element. The presence of virulence factors in MGEs can influence the virulence potential of a specific strain. Therefore, it is critical to study the virulence factors found in MGEs in emerging pathogenic bacteria or strains to understand the mechanisms used by these bacteria to cause infections., (Copyright © 2020 Arora et al.)

The objective of this experiment was to determine if statistical process control (SPC) procedures coupled with the remote continuous collection of feeding behavior patterns, accelerometer-based behaviors, and rumen temperature can accurately differentiate between animals experimentally inoculated with Mannheimia haemolytica (MH) or PBS. Thirty-six crossbred steers (BW = 352 ± 23 kg) seronegative for MH were randomly assigned to bronchoselective endoscopic inoculation with MH (n = 18) or PBS (n = 18). Electronic feed bunks were used to measure DMI and feeding behavior traits, accelerometer-based neck collars measured feeding- and activity-behavior traits, and ruminal thermo-boluses measured rumen temperature. Data were collected for 28 d prior to and following inoculation. Steers inoculated with MH exhibited elevated (P < 0.02) levels of neutrophils and rumen temperature indicating that MH challenge effectively stimulated immunologic responses. However, only nine of the MH steers exhibited increased serum haptoglobin concentrations indicative of an acute-phase protein response and one displayed clinical signs of disease. Shewhart charts (SPC procedure) were used for two analyses, and sensitivity was computed using all MH-challenged steers (n = 18), and a subset that included only MH-challenged haptoglobin-responsive steers (n = 9). Specificity was calculated using all PBS steers in both analyses. In the haptoglobin-responsive only analysis, DMI and bunk visit (BV) duration had the greatest accuracy (89%), with accuracies for head-down (HD) duration, BV frequency, time to bunk, and eating rate being less (83%, 69%, 53%, and 61%, respectively). To address the diurnal nature of rumen temperature, data were averaged over 6-h intervals, and quarterly temperature models were evaluated separately. Accuracy for the fourth quarter rumen temperature was higher (78%) than the other quarterly temperature periods (first = 56%, second = 50%, and third = 67%). In general, the accelerometer-based behavior traits were highly specific ranging from 82% for ingestion to 100% for rest, rumination, and standing. However, the sensitivity of these traits was low (0% to 50%), such that the accuracies were moderate compared with feeding behavior and rumen temperature response variables. These results indicate that Shewhart procedures can effectively identify deviations in feeding behavior and rumen temperature patterns to enable subclinical detection of BRD in beef cattle., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Antibiotic use in beef cattle is a risk factor for the expansion of antimicrobial-resistant Salmonella populations. However, actual changes in the quantity of Salmonella in cattle feces following antibiotic use have not been investigated. Previously, we observed an overall reduction in Salmonella prevalence in cattle feces associated with both ceftiofur crystalline-free acid (CCFA) and chlortetracycline (CTC) use; however, during the same time frame the prevalence of multidrug-resistant Salmonella increased. The purpose of this analysis was to quantify the dynamics of Salmonella using colony counting (via a spiral-plating method) and hydrolysis probe-based qPCR (TaqMan® qPCR). Additionally, we quantified antibiotic-resistant Salmonella by plating to agar containing antibiotics at Clinical & Laboratory Standards Institute breakpoint concentrations. Cattle were randomly assigned to 4 treatment groups across 16 pens in 2 replicates consisting of 88 cattle each. Fecal samples from Days 0, 4, 8, 14, 20, and 26 were subjected to quantification assays. Duplicate qPCR assays targeting the Salmonella invA gene were performed on total community DNA for 1,040 samples. Diluted fecal samples were spiral plated on plain Brilliant Green Agar (BGA) and BGA with ceftriaxone (4 μg/ml) or tetracycline (16 μg/ml). For comparison purposes, indicator non-type-specific (NTS) E. coli were also quantified by direct spiral plating. Quantity of NTS E. coli and Salmonella significantly decreased immediately following CCFA treatment. CTC treatment further decreased the quantity of Salmonella but not NTS E. coli. Effects of antibiotics on the imputed log10 quantity of Salmonella were analyzed via a multi-level mixed linear regression model. The invA gene copies decreased with CCFA treatment by approximately 2 log10 gene copies/g feces and remained low following additional CTC treatment. The quantities of tetracycline or ceftriaxone-resistant Salmonella were approximately 4 log10 CFU/g feces; however, most of the samples were under the quantification limit. The results of this study demonstrate that antibiotic use decreases the overall quantity of Salmonella in cattle feces in the short term; however, the overall quantities of antimicrobial-resistant NTS E. coli and Salmonella tend to remain at a constant level throughout., Competing Interests: Dr. Guy H. Loneragan has provided scientific consulting services to Zoetis Inc. (manufacturer of the CCFA product). This does not alter the authors’ adherence to all the journal policies on sharing data and materials.