Redefining piscine lactococcosis.

Piscine lactococcosis is a significant threat to cultured and wild fish populations worldwide. The disease typically presents as a per-acute to acute hemorrhagic septicemia causing high morbidity and mortality, recalcitrant to antimicrobial treatment or management interventions. Historically, the disease was attributed to the gram-positive pathogen Lactococcus garvieae. However, recent work has revealed three distinct lactococcosis-causing bacteria (LCB)-L. garvieae, L. petauri, and L. formosensis-which are phenotypically and genetically similar, leading to widespread misidentification. An update on our understanding of lactococcosis and improved methods for identification are urgently needed. To this end, we used representative isolates from each of the three LCB species to compare currently available and recently developed molecular and phenotypic typing assays, including whole-genome sequencing (WGS), end-point and quantitative PCR (qPCR) assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), API 20 Strep and Biolog systems, fatty acid methyl ester analysis (FAME), and Sensititre antimicrobial profiling. Apart from WGS, sequencing of the gyrB gene was the only method capable of consistent and accurate identification to the species and strain level. A qPCR assay based on a putative glycosyltransferase gene was also able to distinguish L. petauri from L. garvieae/formosensis. Biochemical tests and MALDI-TOF MS showed some species-specific patterns in sugar and fatty acid metabolism or protein profiles but should be complemented by additional analyses. The LCB demonstrated overlap in host and geographic range, but there were relevant differences in host specificity, regional prevalence, and antimicrobial susceptibility impacting disease treatment and prevention. IMPORTANCE: Lactococcosis affects a broad range of host species, including fish from cold, temperate, and warm freshwater or marine environments, as well as several terrestrial animals, including humans. As such, lactococcosis is a disease of concern for animal and ecosystem health. The disease is endemic in European and Asian aquaculture but is rapidly encroaching on ecologically and economically important fish populations across the Americas. Piscine lactococcosis is difficult to manage, with issues of vaccine escape, ineffective antimicrobial treatment, and the development of carrier fish or biofilms leading to recurrent outbreaks. Our understanding of the disease is also widely outdated. The accepted etiologic agent of lactococcosis is Lactococcus garvieae. However, historical misidentification has masked contributions from two additional species, L. petauri and L. formosensis, which are indistinguishable from L. garvieae by common diagnostic methods. This work is the first comprehensive characterization of all three agents and provides direct recommendations for species-specific diagnosis and management.

Lactococcus lactis MA5 is a potential autochthonous probiotic for nutrient digestibility enhancement and bacterial pathogen inhibition in hybrid catfish (Ictalurus punctatus × I. furcatus).

With the emergence of diseases, the U.S. catfish industry is under challenge. Current trends prefer autochthonous bacteria as potential probiotic candidates owing to their adaptability and capacity to effectively colonize the host's intestine, which can enhance production performance and bolster disease resistance. The objective of this study was to isolate an autochthonous bacterium as probiotic for hybrid catfish. Initially, an analysis of the intestinal microbiota of hybrid catfish reared in earthen ponds was conducted for subsequent probiotic development. Twenty lactic acid bacteria were isolated from the digesta of overperforming catfish, and most of the candidates demonstrated probiotic traits, including proteolytic and lipolytic abilities; antagonistic inhibition of catfish enteric bacterial pathogens, negative haemolytic activity and antibiotic susceptibility. Subsequent to this screening process, an isolate of Lactococcus lactis (MA5) was deemed the most promising probiotic candidate. In silico analyses were conducted, and several potential probiotic functions were predicted, including essential amino acids and vitamin synthesis. Moreover, genes for three bacteriocins, lactococcin A, enterolysin A and sactipeptide BmbF, were identified. Lastly, various protectant media for lyophilization of MA5 were assessed. These findings suggest that Lactococcus lactis MA5 can be an autochthonous probiotic from hybrid catfish, holding promise to be further tested in feeding trials.

Influence of probiotic and prebiotic supplementation on intestinal microbiota and resistance to Edwardsiella ictaluri infection in channel catfish (Ictalurus punctatus) following florfenicol administration.

Enteric septicemia of catfish (ESC), caused by the gram-negative enteric bacteria Edwardsiella ictaluri, is a significant threat to catfish aquaculture in the southeastern United States. Antibiotic intervention can reduce mortality; however, antibiotic use results in an imbalance, or dysbiosis, of the gut microbiota, which may increase susceptibility of otherwise healthy fish to enteric infections. Herein, recovery of the intestinal microbiota and survivability of channel catfish in response to ESC challenge was evaluated following a 10-day course of florfenicol and subsequent probiotic or prebiotic supplementation. Following completion of florfenicol therapy, fish were transitioned to a basal diet or diets supplemented with a probiotic or prebiotic for the remainder of the study. Digesta was collected on Days 0, 4, 8 and 12, beginning on the first day after cessation of antibiotic treatment, and gut microbiota was characterized by Illumina sequencing of the 16S rRNA gene (V4 region). Remaining fish were challenged with E. ictaluri and monitored for 32 days post-challenge. Florfenicol administration resulted in dysbiosis characterized by inflated microbial diversity, which began to recover in terms of diversity and composition 4 days after cessation of florfenicol administration. Fish fed the probiotic diet had higher survival in response to ESC challenge than the prebiotic (p = .019) and negative control (p = .029) groups.

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions.

BACKGROUND: Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences. RESULTS: We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F1 hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species. CONCLUSIONS: We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.

Considerations for performing companion animal skin microbiome studies.

The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.

Le domaine du microbiome s'est considérablement développé au cours de la dernière décennie, et les études publiées fournisse une vue d'ensemble des micro­organismes présents sur la peau des animaux de compagnie. Avec la croissance continue et l'intérêt concernant ce domaine, des interrogations ont été soulevées concernant les méthodes de collecte des échantillons, la contamination des réactifs, le traitement des données et les facteurs environnementaux qui peuvent nuire à l'interprétation des données (en particulier en ce qui concerne les échantillons de peau à faible biomasse). Dans un souci de transparence, il est important de rendre compte de toutes les étapes, de la collecte des échantillons à l'analyse des données, y compris l'utilisation de contrôles appropriés, et de rendre les données séquentielles et les métadonnées des échantillons accessibles au public. Même s'il y existe toujours des variations entre les études, les efforts de normalisation des méthodes réduiront les variables confusionnelles et permettront la reproductibilité et la comparabilité des résultats entre les études. Les études sur le microbiome des animaux de compagnie incluent souvent des cas cliniques, et la petite taille des échantillons peut entraîner un manque de signification statistique dans les petits ensembles de données. La possibilité de combiner les résultats d'études standardisées par le biais de méta­analyses atténuerait les limites de ces petites études et permettrait une interprétation plus solide des résultats, qui pourrait alors éclairer les décisions cliniques. Dans cette revue narrative, nous visons à présenter les considérations relatives à la conception d'une étude destinée à évaluer le microbiome cutané des animaux de compagnie, depuis la conception jusqu'à l'analyse des données.

A área dos estudos do microbioma cresceu significativamente na última década e trabalhos publicados forneceram uma visão geral dos microrganismos que habitam a pele de animais de companhia. Com crescimento do interesse neste campo, surgiram preocupações em relação aos métodos de coleta de amostras, contaminação de reagentes, processamento de dados e fatores ambientais que podem prejudicar a interpretação dos dados (especialmente no que diz respeito a amostras de pele com baixa biomassa). Para garantir a transparência, é importante relatar todas as etapas desde a coleta da amostra até a análise dos dados, incluindo o uso de controles adequados, e disponibilizar publicamente os dados da sequência e os metadados da amostra. Embora a variação entre estudos continue a existir, os esforços para padronizar os métodos reduzirão as variáveis de confusão e permitirão a reprodutibilidade e a comparabilidade dos resultados entre os estudos. Os estudos de microbioma de animais de companhia geralmente incluem casos clínicos, e amostras pequenas podem resultar na ausência de significância estatística em bases de dados pequenas. A capacidade de combinar resultados de estudos padronizados através de meta­análises reduziria as limitações destes estudos menores, proporcionando uma interpretação mais robusta dos resultados que poderiam então influenciar as condutas clínicas. Nesta revisão narrativa, pretendemos apresentar considerações para o delineamento de estudos de microbioma cutâneo de animais de companhia, desde a concepção até a análise dos dados.

El campo del microbioma ha crecido significativamente en la última década y los estudios publicados han proporcionado una visión general de los microorganismos que habitan en la piel de los animales de compañía. Con el continuo crecimiento e interés en este campo, han surgido preocupaciones con respecto a los métodos de recolección de muestras, la contaminación de los reactivos, el procesamiento de datos y los factores ambientales que pueden afectar la interpretación de los datos (especialmente en relación con las muestras de piel de baja biomasa). Para garantizar la transparencia, es importante informar todos los pasos desde la recolección de muestras hasta el análisis de datos, incluido el uso de controles adecuados, y hacer que los datos de secuencia y los metadatos de muestras estén disponibles públicamente. Si bien seguirá existiendo variación entre estudios, los esfuerzos para estandarizar los métodos reducirán las variables de confusión y permitirán la reproducibilidad y comparabilidad de los resultados entre los estudios. Los estudios del microbioma de animales de compañía a menudo incluyen casos clínicos, y los tamaños de muestra pequeños pueden resultar en una falta de significancia estadística dentro de conjuntos de datos pequeños. La capacidad de combinar resultados de estudios estandarizados a través de metanálisis mitigaría las limitaciones de estos estudios más pequeños, proporcionando una interpretación más sólida de los resultados que luego podría informar las decisiones clínicas. En esta revisión narrativa, nuestro objetivo es presentar consideraciones para diseñar un estudio para evaluar el microbioma de la piel de animales de compañía, desde la concepción hasta el análisis de los datos.

Characterization of staphylococcal communities on healthy and allergic feline skin.

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.

Characterization of the cutaneous mycobiota in Persian cats with severe dermatophytosis.

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.

Cytokine expression in feline allergic dermatitis and feline asthma.

BACKGROUND: The pathogenesis of feline allergic dermatitis (FAD) is unclear, with several differences from allergic dermatitis in dogs and humans. HYPOTHESIS/OBJECTIVES: To survey cytokine expression levels in healthy cats and cats affected with allergic dermatitis or asthma. ANIMALS: Formalin-fixed, paraffin-embedded skin biopsies from 22 cats with allergic dermatitis and 21 cats without allergic dermatitis were used for cutaneous assays. Serum was obtained from 17 healthy cats, 18 cats with allergic dermatitis, and 18 cats with a presumptive diagnosis of asthma. METHODS AND MATERIALS: Cutaneous mRNA expression was evaluated with quantitative PCR [interleukin (IL)-31 and IL-31 Receptor A] and RNA in situ hybridisation (ISH) [IL-5, IL-31, IL-31RA, IL-33 and Oncostatin M receptor (OSMR)-ß]. IL-31 protein concentrations were evaluated in serum with an enzyme-linked immunosorbent assay. Serum levels of 19 additional cytokines were evaluated using a Luminex panel. RESULTS: IL-31, IL-31RA, IL-5 and IL-33 mRNA expression were either expressed in low quantities or undetectable in most samples. By contrast, OSMR-ß expression was significantly higher in the skin of allergic versus healthy cats (P < 0.0001). Although serum IL-31 was detected in a larger number of cats with allergic dermatitis than healthy cats, and concentrations appeared to be higher in cats with allergies, this difference was not statistically significant. Cats affected by asthma also exhibited insignificantly higher concentrations of IL-31 in the serum. CONCLUSIONS AND CLINICAL RELEVANCE: Our results suggest that feline allergic diseases may exhibit different pathomechanisms from allergic diseases affecting other species. These findings are useful in guiding further therapeutic development toward targets that may have a role in the pathogenesis of feline allergic skin disease.

Analysis of Bacterial and Fungal Nucleic Acid in Canine Sterile Granulomatous and Pyogranulomatous Dermatitis and Panniculitis.

Next generation sequencing (NGS) studies are revealing a diverse microbiota on the skin of dogs. The skin microbiota of canine sterile granulomatous and pyogranulomatous dermatitis (SGPD) has yet to be investigated using NGS techniques. NGS targeting the 16S rRNA and ITS-1 region of bacterial and fungal DNA, respectively, were used to investigate if bacterial and fungal DNA were associated with skin lesions in cases of canine SGPD. The study included 20 formalin-fixed paraffin-embedded (FFPE) skin samples and 12 fresh samples from SGPD-affected dogs, and 10 FFPE and 10 fresh samples from healthy dogs. DNA was extracted from deep dermis and panniculus, and microbial DNA was amplified using primers targeting the bacterial 16S rRNA V1-V3 and fungal ITS-1 regions. The amplified DNA was utilized for NGS on an Illumina MiSeq instrument. The sequences were processed using QIIME. No differences in fungal or bacterial alpha diversity were observed between the SGPD and control samples. Beta diversity analysis demonstrated differences in the bacterial communities between SGPD and control, but not in the fungal communities. Compared to controls, the family Erysipelotrichaceae and genus Staphylococcus were significantly more abundant in the SGPD FFPE samples, and genus Corynebacterium were more abundant in fresh samples. The bacteria found to be more abundant in SGPD are common inhabitants of skin surfaces, and likely secondary contaminants in SGPD cases. This study provides additional evidence that SGPD lesions are likely sterile.

Novel association of Psychrobacter and Pseudomonas with malodour in bloodhound dogs, and the effects of a topical product composed of essential oils and plant-derived essential fatty acids in a randomized, blinded, placebo-controlled study.

BACKGROUND: The pathogenesis and treatment of cutaneous malodour in dogs have not been investigated previously. Staphylococcus and Corynebacterium spp. are associated with human axillary malodour. HYPOTHESIS: Staphylococcus and Corynebacterium spp. are associated with cutaneous malodour in dogs, and treatment with a topical essential oil-based product will improve malodour and reduce the abundance of odour-causing bacteria. ANIMALS: Twenty seven bloodhound dogs from a south Texas boarding facility were enrolled in this study. METHODS AND MATERIALS: Skin swabs were taken from the axilla and dorsum of 27 dogs at initiation of the study. Mean malodour scores were used to assign dogs to control or malodour groups. The malodourous dogs were randomly assigned to a treatment or placebo group, received four weekly topical applications of the spot-on or placebo, and samples were recollected. Next-generation sequencing (NGS) and real-time quantitative PCR (qPCR) were performed on all swabs. RESULTS: Psychrobacter and Pseudomonas spp. were significantly more abundant (P < 0.001, P = 0.006; respectively), and overall bacterial diversity was reduced (P = 0.0384) on the skin of malodourous dogs. Staphylococcus and Corynebacterium spp. were not associated with malodour. The topical essential oil-based product significantly (P = 0.0078) improved malodour in the treatment group and shifted their bacterial community structure. CONCLUSIONS AND CLINICAL IMPORTANCE: A novel association of bacterial genera with malodour in bloodhound dogs, identified by NGS, highlights future targets for odour control. The topical treatment significantly reduced malodour. The interaction between the topical treatment and cutaneous microbiota should be further investigated and may be useful in other dermatological conditions involving microbiota.

Panfungal Polymerase Chain Reaction for Identification of Fungal Pathogens in Formalin-Fixed Animal Tissues.

Identification of fungal organisms often poses a problem for pathologists because the histomorphology of some fungal organisms is not specific, fresh tissues may not be available, and isolation and identification in culture may take a long time. The purpose of this study was to validate the use of panfungal polymerase chain reaction (PCR) to identify fungal organisms from formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed paraffin-embedded curls were tested from 128 blocks containing canine, feline, equine, and bovine tissues with cutaneous, nasal, pulmonary, and systemic fungal infections, identified by the presence of fungi in histologic sections. Quantitative scoring of histologic sections identified rare (11.9%), occasional (17.5%), moderate (17.5%), or abundant (53.1%) fungal organisms. DNA was isolated from FFPE tissues and PCR was performed targeting the internal transcribed spacer 2 (ITS-2) region, a segment of noncoding DNA found in all eukaryotes. Polymerase chain reaction products were sequenced and identified at ≥97% identity match using the Basic Local Alignment Search Tool and the NCBI database of ITS sequences. Of the 128 blocks, 117 (91.4%) yielded PCR products and high-quality sequences were derived from 89 (69.5%). Sequence and histologic identifications matched in 79 blocks (61.7%). This assay was capable of providing genus- and species-level identification when histopathology could not and, thus, is a beneficial complementary tool for diagnosis of fungal diseases.

Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing.

BACKGROUND: Next generation sequencing (NGS) studies have demonstrated a diverse skin-associated microbiota and microbial dysbiosis associated with atopic dermatitis in people and in dogs. The skin of cats has yet to be investigated using NGS techniques. HYPOTHESIS/OBJECTIVES: We hypothesized that the fungal microbiota of healthy feline skin would be similar to that of dogs, with a predominance of environmental fungi, and that fungal dysbiosis would be present on the skin of allergic cats. ANIMALS: Eleven healthy cats and nine cats diagnosed with one or more cutaneous hypersensitivity disorders, including flea bite, food-induced and nonflea nonfood-induced hypersensitivity. METHODS: Healthy cats were sampled at twelve body sites and allergic cats at six sites. DNA was isolated and Illumina sequencing was performed targeting the internal transcribed spacer region of fungi. Sequences were processed using the bioinformatics software QIIME. RESULTS: The most abundant fungal sequences from the skin of all cats were classified as Cladosporium and Alternaria. The mucosal sites, including nostril, conjunctiva and reproductive tracts, had the fewest number of fungi, whereas the pre-aural space had the most. Allergic feline skin had significantly greater amounts of Agaricomycetes and Sordariomycetes, and significantly less Epicoccum compared to healthy feline skin. CONCLUSIONS: The skin of healthy cats appears to have a more diverse fungal microbiota compared to previous studies, and a fungal dysbiosis is noted in the skin of allergic cats. Future studies assessing the temporal stability of the skin microbiota in cats will be useful in determining whether the microbiota sequenced using NGS are colonizers or transient microbes.

The feline skin microbiome: interrelationship between health and disease.

PRACTICAL RELEVANCE: As with other species, the skin microbiome of cats has been assessed over the past few years utilizing modern technologies. This has resulted in the identification of many more bacterial and fungal organisms compared with what had been recorded historically on the skin in various states of health and disease using culture-based studies. This information is expanding the knowledge of how microbial communities are impacted by various changes in the skin health of cats. More specifically, how these microbial communities change in the face of health and disease, and how various therapeutic interventions affect the cutaneous microbiome, lends a greater understanding of disease pathogenesis and provides a growing area of research for correcting dysbiosis and improving feline skin health. EVIDENCE BASE: Most studies on the feline skin microbiome thus far have been descriptive in nature. These provide a framework for the next level of investigations on how various states of health and disease impact the products produced by the cutaneous microbiome (ie, the cutaneous metabolome), as well as how targeted interventions may promote the restoration of balance. AIMS: This review aims to summarize what is currently known about the feline cutaneous microbiome and its clinical implications. The role of the skin microbiome in health and disease, the current state of research in this area and the potential for future studies to produce targeted interventions for cats are a particular focus.

Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis).

Erysipelothrix spp., including E. rhusiopathiae, are zoonotic bacterial pathogens that can cause morbidity and mortality in mammals, fish, reptiles, birds, and humans. The southern sea otter (SSO; Enhydra lutris nereis) is a federally-listed threatened species for which infectious disease is a major cause of mortality. We estimated the frequency of detection of these opportunistic pathogens in dead SSOs, described pathology associated with Erysipelothrix infections in SSOs, characterized the genetic diversity and antimicrobial susceptibility of SSO isolates, and evaluated the virulence of two novel Erysipelothrix isolates from SSOs using an in vivo fish model. From 1998 to 2021 Erysipelothrix spp. were isolated from six of >500 necropsied SSOs. Erysipelothrix spp. were isolated in pure culture from three cases, while the other three were mixed cultures. Bacterial septicemia was a primary or contributing cause of death in five of the six cases. Other pathology observed included suppurative lymphadenopathy, fibrinosuppurative arteritis with thrombosis and infarction, bilateral uveitis and endophthalmitis, hypopyon, petechia and ecchymoses, mucosal infarction, and suppurative meningoencephalitis and ventriculitis. Short to long slender Gram-positive or Gram-variable bacterial rods were identified within lesions, alone or with other opportunistic bacteria. All six SSO isolates had the spaA genotype-four isolates clustered with spaA E. rhusiopathiae strains from various terrestrial and marine animal hosts. Two isolates did not cluster with any known Erysipelothrix spp.; whole genome sequencing revealed a novel Erysipelothrix species and a novel E. rhusiopathiae subspecies. We propose the names Erysipelothrix enhydrae sp. nov. and Erysipelothrix rhusiopathiae ohloneorum ssp. nov. respectively. The type strains are E. enhydrae UCD-4322-04 and E. rhusiopathiae ohloneorum UCD-4724-06, respectively. Experimental injection of tiger barbs (Puntigrus tetrazona) resulted in infection and mortality from the two novel Erysipelothrix spp. Antimicrobial susceptibility testing of Erysipelothrix isolates from SSOs shows similar susceptibility profiles to isolates from other terrestrial and aquatic animals. This is the first description of the pathology, microbial characteristics, and genetic diversity of Erysipelothrix isolates recovered from diseased SSOs. Methods presented here can facilitate case recognition, aid characterization of Erysipelothrix isolates, and illustrate assessment of virulence using fish models.

Dietary Supplementation of a Commercial Prebiotic, Probiotic and Their Combination Affected Growth Performance and Transient Intestinal Microbiota of Red Drum (Sciaenops ocellatus L.).

In the present study, the potential synergism between beneficial lactic acid bacteria (Pediococcus acidilactici) contained in a probiotic and a mixture of fermentable complex carbohydrates and autolyzed brewer's yeast (or prebiotic) were explored in red drum. Four experimental diets were formulated from practical ingredients, and the basal diet was supplemented with either probiotic, prebiotic, or both supplements. Red drum juveniles (~5.5 g) were offered the four experimental diets for 56 days, and at the end of the feeding trial fish fed diets supplemented with probiotic had significantly better weight gain than those fed the non-supplemented diets, and higher protein content in their whole-body composition. Transient intestinal microbiome alpha and beta diversity were significantly affected by the dietary treatments. Interestingly, a higher relative abundance of the lactic acid genus Pediococcus was observed for fish fed diets supplemented with the prebiotic. A higher relative abundance was also observed for the predicted functions of the microbial metagenome, and many of these pathways involved the biosynthesis of essential amino acids, vitamins, and nucleotides. Even though no potential synergistic effect was observed, the individual inclusion of these prebiotic and probiotic supplements positively affected the intestinal health and growth performance of red drum, respectively.

Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs.

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

Influence of the FIV Status and Chronic Gingivitis on Feline Oral Microbiota.

Feline chronic gingivostomatitis (FCGS) has an unclear pathogenesis with the oral microbiome and viral infections, such as feline immunodeficiency virus (FIV), thought to contribute. Although the relationship between the FIV status and FCGS is not clear, one theory is FIV-induced immune dysregulation could contribute to oral dysbiosis, promoting FCGS development. To further understand the relationship between FCGS, FIV infection, and the oral microbiome, oral cavities of forty cats fitting within 4 groups (FIV- without gingivitis, FIV+ without gingivitis, FIV- with gingivitis, FIV+ with gingivitis) were swabbed. Next generation sequencing targeting the V4 region of the 16s rRNA gene was performed for bacterial community profiling. No differences in diversity were observed, however, analysis of the data in terms of gingivitis revealed differences in the relative abundance of taxa and predicted functional output. Odoribacter spp., a bacteria associated with oral disease, was found in higher relative abundances in cats with the highest gingivitis grade. Cats with gingivitis were also found to harbor communities more involved in production of short-chain fatty acids, which have been connected with oral disease. Significant findings associated with the FIV status were few and of low impact, suggesting any connection between the FIV status and FCGS is likely not related to the oral microbiota.

The feline cutaneous and oral microbiota are influenced by breed and environment.

Previous research revealed the feline skin bacterial microbiota to be site-specific and the fungal microbiota to be individual-specific. The effect of other factors, such as genotype and environment, have not yet been studied in cats, but have been shown to be potentially important in shaping the cutaneous microbiota of other animals. Therefore, the objectives of this study were to evaluate the effect of these factors on the bacterial and fungal microbiota of feline skin and oral cavity. The influence of genotype was assessed through the analysis of different cat breeds, and the influence of environment through comparison of indoor and outdoor cats. DNA was extracted from skin and oral swabs, and bacterial and fungal next-generation sequencing were performed. Analysis of the skin microbiota of different cat breeds revealed significant differences in alpha diversity, with Sphynx and Bengal cats having the most diverse communities. Many taxa were found to be differentially abundant between cat breeds, including Veillonellaceae and Malassezia spp. Outdoor environment exposure had considerable influence on beta diversity, especially in the oral cavity, and resulted in numerous differentially abundant taxa. Our findings indicate that the oral bacterial microbiota and both fungal and bacterial microbiota of feline skin are influenced by breed, and to a lesser degree, environment.

Histoplasmosis and multicentric lymphoma in a Nubian goat.

Following treatment for pneumonia, a 1-y-old female Nubian goat was presented because of a persistent fever for 3 mo and peripheral lymphadenopathy for 1 mo. Cytology and histology of the superficial cervical and prefemoral lymph nodes demonstrated a moderate-to-marked "left-shifted" lymphoid population, suggestive of lymphoma, and extremely rare extracellular, 2-4 µm, oval, basophilic yeast, consistent with Histoplasma capsulatum. On immunohistochemistry, >95% of the lymphocytes demonstrated positive cytoplasmic and membranous immunoreactivity for CD3. Histoplasma spp. urine antigen and serum antibody testing were positive and negative, respectively. Panfungal PCR and sequencing of DNA extracted from scrolls of formalin-fixed, paraffin-embedded tissue yielded matches to H. capsulatum with 99-100% identity. Given the poor prognosis and persistent pyrexia, the animal was euthanized. Postmortem examination confirmed concurrent multicentric, intermediate-size, T-cell, lymphoblastic lymphoma and histoplasmosis; lesions consistent with intestinal coccidiosis and suspected pulmonary Rhodococcus equi were also noted. Although dimorphic fungi have been described previously in goats, lesions of Histoplasma spp. had not been documented in this species, to our knowledge. Given the low disease burden, it is suspected that the lymphoma was primary, leading to an immunocompromised state and development of secondary, opportunistic infections.

The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats.

BACKGROUND: The skin is inhabited by a multitude of microorganisms. An imbalance of these microorganisms is associated with disease, however, the causal relationship between skin microbiota and disease remains unknown. To describe the cutaneous bacterial microbiota of cats and determine whether bacterial dysbiosis occurs on the skin of allergic cats, the skin surfaces on various regions of 11 healthy cats and 10 allergic cats were sampled. METHODOLOGY/PRINCIPAL FINDINGS: Genomic DNA was extracted from skin swabs and sequenced using primers that target the V4 region of the bacterial 16S rRNA. The bacterial sequences from healthy cats revealed that there are differences in species diversity and richness between body sites and different epithelial surfaces. Bacterial communities preferred body site niches in the healthy cats, however, the bacterial communities on allergic cat skin tended to be more unique to the individual cat. Overall, the number of bacterial species was not significantly different between the two health status groups, however, the abundances of these bacterial species were different between healthy and allergic skin. Staphylococcus, in addition to other taxa, was more abundant on allergic skin. CONCLUSIONS/SIGNIFICANCE: This study reveals that there are more bacterial species inhabiting the skin of cats than previously thought and provide some evidence of an association between dysbiosis and skin disease.