Using natural language processing and patient journey clustering for temporal phenotyping of antimicrobial therapies for cat bite abscesses.

BACKGROUND: Temporal phenotyping of patient journeys, which capture the common sequence patterns of interventions in the treatment of a specific condition, is useful to support understanding of antimicrobial usage in veterinary patients. Identifying and describing these phenotypes can inform antimicrobial stewardship programs designed to fight antimicrobial resistance, a major health crisis affecting both humans and animals, in which veterinarians have an important role to play. OBJECTIVE: This research proposes a framework for extracting temporal phenotypes of patient journeys from clinical practice data through the application of natural language processing (NLP) and unsupervised machine learning (ML) techniques, using cat bite abscesses as a model condition. By constructing temporal phenotypes from key events, the relationship between antimicrobial administration and surgical interventions can be described, and similar treatment patterns can be grouped together to describe outcomes associated with specific antimicrobial selection. METHODS: Cases identified as having a cat bite abscess as a diagnosis were extracted from VetCompass Australia, a database of veterinary clinical records. A classifier was trained and used to label the most clinically relevant event features in each record as chosen by a group of veterinarians. The labeled records were processed into coded character strings, where each letter represents a summary of specific types of treatments performed at a given visit. The sequences of letters representing the cases were clustered based on weighted Levenshtein edit distances with KMeans+ + to identify the main variations of the patient treatment journeys, including the antimicrobials used and their duration of administration. RESULTS: A total of 13,744 records that met the selection criteria was extracted and grouped into 8436 cases. There were 9 clinically distinct event sequence patterns (temporal phenotypes) of patient journeys identified, representing the main sequences in which surgery and antimicrobial interventions are performed. Patients receiving amoxicillin and surgery had the shortest duration of antimicrobial administration (median of 3.4 days) and patients receiving cefovecin with no surgical intervention had the longest antimicrobial treatment duration (median of 27 days). CONCLUSION: Our study demonstrates methods to extract and provide an overview of temporal phenotypes of patient journeys, which can be applied to text-based clinical records for multiple species or clinical conditions. We demonstrate the effectiveness of this approach to derive real-world evidence of treatment impacts using cat bite abscesses as a model condition to describe patterns of antimicrobial therapy prescriptions and their outcomes.

Cross-sectional evaluation of a large-scale antimicrobial stewardship trial in Australian companion animal practices.

BACKGROUND: Antimicrobial stewardship programmes (ASPs) are critically important for improving the appropriate use of antimicrobial agents in veterinary practice. METHODS: One of three ASPs was implemented in 135 Australian general veterinary practices in 2018-2020. The ASP interventions and the perceived impact they had on antimicrobial prescribing were assessed by the veterinarians working in these veterinary practices. An online survey was distributed to all 520 veterinarians working in the trial practices and 267 responses were analysed. RESULTS: Most veterinarians (174/267, 65%) thought they had an ASP at their clinic and most respondents who said that they were aware that they had an ASP at their clinic indicated that they had changed the way they prescribed antimicrobials because of the trial (125/170, 74%). Antimicrobial prescribing guidelines, the traffic light system for indicating antimicrobial importance, delayed prescribing and antimicrobial stewardship champions were reported to have had the biggest impact. LIMITATIONS: All practices in the trial belong to a single corporate group, which may impact the external validity of these results when applied to general small animal practice. CONCLUSION: Antimicrobial stewardship has a positive impact on antimicrobial prescribing in veterinary medicine and future interventions should focus on the implementation of the effective interventions identified in this study.

Antimicrobial Consumption in the Livestock Sector in Bhutan: Volumes, Values, Rates, and Trends for the Period 2017-2021.

Data on the use of antimicrobials in humans and livestock may provide evidence to guide policy changes to mitigate the risk of antimicrobial resistance (AMR). However, there is limited information available about antimicrobial use in livestock in low- and middle-income countries, even though these nations are most vulnerable to the impact of AMR. This study aimed to assess the consumption of veterinary antimicrobials in Bhutan and identify areas for improvement to reduce the use of antimicrobials in livestock. National data on livestock numbers and annual procurement of veterinary antimicrobials over five years (2017-2021) were used to calculate rates of antimicrobial consumption and annual national expenditure on veterinary antimicrobials in Bhutan. The rate of antimicrobial consumption in Bhutan was 3.83 mg per population correction unit, which is lower than most countries in Europe, comparable with the rates of consumption in Iceland and Norway, and approximately 120-fold lower than published rates of antimicrobial consumption in South Asian countries, including Nepal and Pakistan. The low rates of antimicrobial consumption by the animal health sector in Bhutan could be attributable to stronger governance of antimicrobial use in Bhutan, higher levels of compliance with regulation, and better adherence to standard guidelines for antimicrobial treatment of livestock.

Attitudes towards Use of High-Importance Antimicrobials-A Cross-Sectional Study of Australian Veterinarians.

The timely implementation of antimicrobial stewardship interventions could delay or prevent the development of higher levels of antimicrobial resistance in the future. In food-producing animals in Australia, high-importance antimicrobials, as rated by the Australian Strategic and Technical Advisory Group (ASTAG), include virginiamycin and third-generation cephalosporins (in individual pigs or cattle). The use of high-importance antimicrobials in companion animals is more widespread and less regulated. There is no national antimicrobial use surveillance system for animals in Australia. Consequently, there is a gap in the knowledge about reasonable use across all sectors of veterinary practice. This study explored attitudes towards the use in veterinary medicine of antimicrobials with high importance to human health, and determined levels of agreement about the introduction of restrictions or other conditions on this use. An online survey was distributed via social media and email from June to December 2020 to veterinarians working in Australia. Of the 278 respondents working in clinical practice, 49% had heard of the ASTAG rating system, and 22% used a traffic light system for antimicrobial importance in their practice. Overall, 61% of participants disagreed that veterinarians should be able to prescribe high-importance antimicrobials without restrictions. If there were to be restrictions, there was most agreement amongst all respondents for only restricting high-importance antimicrobials (73%). There is a need for education, guidance, and practical support for veterinarians for prescribing high-importance antimicrobials alongside any restrictions.

Evaluating the dose, indication and agreement with guidelines of antimicrobial use in companion animal practice with natural language processing.

BACKGROUND: As antimicrobial prescribers, veterinarians contribute to the emergence of MDR pathogens. Antimicrobial stewardship programmes are an effective means of reducing the rate of development of antimicrobial resistance. A key component of antimicrobial stewardship programmes is selecting an appropriate antimicrobial agent for the presenting complaint and using an appropriate dose rate for an appropriate duration. OBJECTIVES: To describe antimicrobial usage, including dose, for common indications for antimicrobial use in companion animal practice. METHODS: Natural language processing (NLP) techniques were applied to extract and analyse clinical records. RESULTS: A total of 343 668 records for dogs and 109 719 records for cats administered systemic antimicrobials from 1 January 2013 to 31 December 2017 were extracted from the database. The NLP algorithms extracted dose, duration of therapy and diagnosis completely for 133 046 (39%) of the records for dogs and 40 841 records for cats (37%). The remaining records were missing one or more of these elements in the clinical data. The most common reason for antimicrobial administration was skin disorders (n = 66 198, 25%) and traumatic injuries (n = 15 932, 19%) in dogs and cats, respectively. Dose was consistent with guideline recommendations in 73% of cases where complete clinical data were available. CONCLUSIONS: Automated extraction using NLP methods is a powerful tool to evaluate large datasets and to enable veterinarians to describe the reasons that antimicrobials are administered. However, this can only be determined when the data presented in the clinical record are complete, which was not the case in most instances in this dataset. Most importantly, the dose administered varied and was often not consistent with guideline recommendations.

Antimicrobial stewardship in Australia: the role of qualitative research in programme development.

Antimicrobial stewardship (AMS) in Australia is supported by a number of factors, including enabling national policies, sectoral clinical governance frameworks and surveillance programmes, clinician-led educational initiatives and health services research. A One Health research programme undertaken by the National Centre for Antimicrobial Stewardship (NCAS) in Australia has combined antimicrobial prescribing surveillance with qualitative research focused on developing antimicrobial use-related situational analyses and scoping AMS implementation options across healthcare settings, including metropolitan hospitals, regional and rural hospitals, aged care homes, general practice clinics and companion animal and agricultural veterinary practices. Qualitative research involving clinicians across these diverse settings in Australia has contributed to improved understanding of contextual factors that influence antimicrobial prescribing, and barriers and facilitators of AMS implementation. This body of research has been underpinned by a commitment to supplementing 'big data' on antimicrobial prescribing practices, where available, with knowledge of the sociocultural, technical, environmental and other factors that shape prescribing behaviours. NCAS provided a unique opportunity for exchange and cross-pollination across the human and animal health programme domains. It has facilitated synergistic approaches to AMS research and education, and implementation of resources and stewardship activities. The NCAS programme aimed to synergistically combine quantitative and qualitative approaches to AMS research. In this article, we describe the qualitative findings of the first 5 years.

Drivers of exit and outcomes for Thoroughbred racehorses participating in the 2017-2018 Australian racing season.

The destinations of Thoroughbred (TB) racehorses exiting the racing industry is a high-profile issue with ethical and welfare implications of interest to both animal welfare groups and racing regulators. This cross-sectional study investigated the reasons that TBs temporarily or permanently exited racing and training in Australia in the 2017-2018 racing season and the outcomes for these horses post-racing. An online questionnaire was sent to the last registered trainers of a representative sample of 2,509 'inactive' TBs. Inactive horses were defined as those horses that were recorded as 'active' but had not trialled or raced in the last 6 months of the racing season or had an inactive status recorded in the Racing Australia database. Of the 1,750 responses received, the largest group of inactive TBs had permanently exited the racing industry (45% retired, 5.3% deceased). A relatively large group exited racing temporarily (43%) but participated in the racing industry in the following season. The reasons for retirement were predominantly voluntary, such as poor performance or owner's request. Almost one third of retirements were due to injuries with tendon or ligament problems the most frequently conditions listed. The median age at retirement was five (Q1 4; Q3 7) years. Extrapolation of the survey results to the population of horses racing or training in Australia in 2017-2018 (n = 37,750) show that that 17% of the population retire each year and 2.1% die. These estimates provide benchmarks for industry and animal welfare organisations to resource and measure the effectiveness of interventions.

Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses.

The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi, establishes a persistent infection in approximately 10 % of animals that recover from the acute disease. Such 'carrier' animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact.

Faecal microbiota and antimicrobial resistance gene profiles of healthy foals.

BACKGROUND: The human and domestic animal faecal microbiota can carry various antimicrobial resistance genes (ARGs), especially if they have been exposed to antimicrobials. However, little is known about the ARG profile of the faecal microbiota of healthy foals. A high-throughput qPCR array was used to detect ARGs in the faecal microbiota of healthy foals. OBJECTIVES: To characterise the faecal microbiota and ARG profiles in healthy Australian foals aged less than 1 month. STUDY DESIGN: Observational study. METHODS: The faecal microbiota and ARG profiles of 37 Thoroughbred foals with no known gastrointestinal disease or antimicrobial treatment were determined using 16S rRNA gene sequencing and a high-throughput ARG qPCR array. Each foal was sampled on one occasion. RESULTS: Firmicutes and Bacteroidetes were dominant in the faecal microbiota. Foals aged 1-2 weeks had significantly lower microbiota richness than older foals. Tetracycline resistance genes were the most common ARGs in the majority of foals, regardless of age. ARGs of high clinical concern were rarely detected in the faeces. The presence of ARGs was associated with the presence of class I integron genes. MAIN LIMITATIONS: Samples were collected for a case-control study so foals were not sampled longitudinally, and thus the development of the microbiota as individual foals aged could not be proven. The history of antimicrobial treatment of the dams was not collected and may have affected the microbiota of the foals. CONCLUSION: The ARGs in foal faeces varied concomitantly with age-related microbiota shifts. The high abundance of tetracycline resistance genes was likely due to the dominance of Bacteroides spp.

A 25-year retrospective study of Chlamydia psittaci in association with equine reproductive loss in Australia.

Introduction. Chlamydia psittaci is primarily a pathogen of birds but can also cause disease in other species. Equine reproductive loss caused by C. psittaci has recently been identified in Australia where cases of human disease were also reported in individuals exposed to foetal membranes from an ill neonatal foal in New South Wales.Hypothesis/Gap Statement. The prevalence of C. psittaci in association with equine reproductive over time and in different regions of Australia is not known.Aim. This study was conducted to detect C. psittaci in equine abortion cases in Australia using archived samples spanning 25 years.Methodology. We tested for C. psittaci in 600 equine abortion cases reported in Australia between 1994 to 2019 using a Chlamydiaceae real-time quantitative PCR assay targeting the 16S rRNA gene followed by high-resolution melt curve analysis. Genotyping and phylogenetic analysis was performed on positive samples.Results. The overall prevalence of C. psittaci in material from equine abortion cases was 6.5 %. C. psittaci-positive cases were detected in most years that were represented in this study and occurred in Victoria (prevalence of 7.6 %), New South Wales (prevalence of 3.9 %) and South Australia (prevalence of 15.4 %). Genotyping and phylogenetic analysis showed that the C. psittaci detected in the equine abortion cases clustered with the parrot-associated 6BC clade (genotype A/ST24), indicating that infection of horses may be due to spillover from native Australian parrots.Conclusion. This work suggests that C. psittaci has been a significant agent of equine abortion in Australia for several decades and underscores the importance of taking appropriate protective measures to avoid infection when handling equine aborted material.

Descriptive analysis of Thoroughbred horses born in Victoria, Australia, in 2010; barriers to entering training and outcomes on exiting training and racing.

The reasons for Thoroughbred (TB) horses not entering training or exiting the racing industry, are of interest to regulators, welfare groups and the broader community. Speculation about the outcomes of these horses threatens the community acceptance, or social license, of the TB breeding and racing industries. A representative survey of the 2010 Victorian born TB foal crop was used to determine the outcomes and reasons for exit for horses that had not entered training, or had exited training and racing by eight years of age. Horses exported for racing or breeding (4%), or that were still actively racing (7%) at the start of the follow up period were excluded from the study. An online questionnaire was sent to breeders or trainers of 3,176 TB horses eligible for enrolment in the study. Of the 2,005 (63%) responses received, the two most frequent outcomes were that the horse had either been retired or rehomed (65%), or deceased (16%). For the 1,637 TB horses that had entered training, the majority of retirements were voluntary (59%), followed by involuntary retirements due to health disorders (28%). For TBs that did not have an industry record of entering training (n = 368), death (34%), or retirement or being rehomed (27%), were the most frequent barriers to entering training. The median age of retirement for TBs that raced was five (Q1 4; Q3 6) years regardless of sex, or whether their first race start was at two, three or four years of age. Relatively large numbers of horses voluntarily retiring at five-years of age suggests that industry-level, rather than individual horse-level factors are the predominant influences on racing career duration.

Ross River Virus Infection of Horses: Appraisal of Ecological and Clinical Consequences.

Ross River virus (RRV) is a mosquito-borne arbovirus of the genus Alphavirus that causes disease in humans and horses in Australia. A temporal association of RRV infection in horses with clinical signs including pyrexia, malaise, and polyarthralgia has been reported, along with reduced athletic performance, often for extended periods. Despite these reports, disease due to RRV remains somewhat controversial as experimental infection of horses has resulted in obvious viraemia yet minimal signs of clinical disease. The relatively high viraemia demonstrated by horses infected with RRV has led to speculation that they could act as an important reservoir host of the virus, although this remains unclear. This review sought to appraise the existing literature relating to RRV infection of horses and to summarize the ecological and clinical consequences of RRV of relevance to the equine industry and to public health more broadly.

Barriers to entering race training before 4 years of age for Thoroughbred horses born in the 2014 Australian foal crop.

Currently, there is a paucity of data on the barriers for Australian Thoroughbred horses transitioning from stud farm to racetrack. This paper reports the reasons why horses failed to enter race training and documents their exit destinations. Biographical records of Australian Thoroughbred horses born in 2014 were investigated to determine the number of horses that had not officially entered race training by the start of the 4-year old racing season (1 August 2018). Of the 13,677 foals born in 2014, 66% had commenced training and 51% had raced before the beginning of their 4-year-old season in Australia. A sampling frame based on the post code of the premises where foals were born and records from Racing Australia were used to select a geographically representative sample of the 2014 Australian Thoroughbred foal crop (n = 4,124). From the population eligible for sampling 1,275 horses that had not entered training were enrolled in the survey and their breeders were sent an online questionnaire with follow-up phone calls for those who had not responded. Of the 633 responses (50% of 1275) the most frequent outcomes for horses were: death (38%, n = 239), participation in the racing industry in their 4-year old racing season (24%, n = 154) and retirement (16%, n = 100) either as Australian Stud Book (ASB) bloodstock (n = 17), or as horses rehomed outside the Thoroughbred industry (n = 83). Illness or injury was the most frequent reason for horses not entering race training that were ASB bloodstock, rehomed or deceased. There was a loss of traceability at the point of sale with most horses sold at 1 year of age. This study provides important information on the reasons, alternative outcomes and gaps in traceability for horses not entering training prior to the 4-year-old racing season.

Detection of Coxiella burnetii and equine herpesvirus 1, but not Leptospira spp. or Toxoplasma gondii, in cases of equine abortion in Australia - a 25 year retrospective study.

Equine abortion is a cause of severe economic loss to the equine industry. Equine herpesvirus 1 is considered a primary cause of infectious abortion in horses, however other infectious agents can also cause abortion. Abortions due to zoonotic pathogens have implications for both human and animal health. We determined the prevalence of Coxiella burnetii, Leptospira spp. and Toxoplasma gondii in 600 aborted equine foetal tissues that were submitted to our diagnostic laboratories at the University of Melbourne from 1994 to 2019. Using qPCR we found that the prevalence of C. burnetii was 4%. The highest annual incidence of C. burnetii was observed between 1997-2003 and 2016-2018. The prevalence of C. burnetii in Victoria and New South Wales was 3% and 6% respectively. All the samples tested negative for Leptospira spp. and Toxoplasma gondii DNA. Equine herpesvirus 1 DNA was detected at a prevalence of 3%. This study has provided evidence for the presence of C. burnetii in equine aborted foetal tissues in Australia, but the role of C. burnetii as potential cause of abortion in Australia requires further investigation. C. burnetii is a zoonotic disease agent that causes the disease 'Q fever' in humans. We recommend that appropriate protective measures should be considered when handling material associated with equine abortions to reduce the risk of becoming infected with C. burnetii.

Describing the antimicrobial usage patterns of companion animal veterinary practices; free text analysis of more than 4.4 million consultation records.

Antimicrobial Resistance is a global crisis that veterinarians contribute to through their use of antimicrobials in animals. Antimicrobial stewardship has been shown to be an effective means to reduce antimicrobial resistance in hospital environments. Effective monitoring of antimicrobial usage patterns is an essential part of antimicrobial stewardship and is critical in reducing the development of antimicrobial resistance. The aim of this study is to describe how frequently antimicrobials were used in veterinary consultations and identify the most frequently used antimicrobials. Using VetCompass Australia, Natural Language Processing techniques, and the Australian Strategic Technical Advisory Group's (ASTAG) Rating system to classify the importance of antimicrobials, descriptive analysis was performed on the antimicrobials prescribed in consultations from 137 companion animal veterinary clinics in Australia between 2013 and 2017 (inclusive). Of the 4,400,519 consultations downloaded there were 595,089 consultations where antimicrobials were prescribed to dogs or cats. Antimicrobials were dispensed in 145 of every 1000 canine consultations; and 38 per 1000 consultations involved high importance rated antimicrobials. Similarly with cats, 108 per 1000 consultations had antimicrobials dispensed, and in 47 per 1000 consultations an antimicrobial of high importance rating was administered. The most common antimicrobials given to cats and dogs were cefovecin and amoxycillin clavulanate, respectively. The most common topical antimicrobial and high-rated topical antimicrobial given to dogs and cats was polymyxin B. This study provides a descriptive analysis of the antimicrobial usage patterns in Australia using methods that can be automated to inform antimicrobial use surveillance programs and promote antimicrobial stewardship.

Effects of nebulized dexamethasone on the respiratory microbiota and mycobiota and relative equine herpesvirus-1, 2, 4, 5 in an equine model of asthma.

BACKGROUND: Prolonged exposure to environmental antigens or allergens elicits an immune response in both healthy horses and those with mild asthma. Corticosteroids often are used to treat lower airway inflammation. OBJECTIVE: To investigate the changes in equine herpesvirus (EHV)-1,2,4,5 glycoprotein B gene expression and changes in respiratory bacterial and fungal communities after nebulized dexamethasone treatment of horses with asthma. ANIMALS: Horses with naturally occurring mild asthma (n = 16) and healthy control horses (n = 4). METHODS: Prospective, randomized, controlled, blinded clinical trial. Polymerase chain reaction amplification of EHV-1,2,4,5 in bronchoalveolar lavage fluid, and 16S (microbiome) and ITS2 (mycobiome) genes with subsequent sequencing was performed on DNA extracted from nasal swabs and transendoscopic tracheal aspirates before and after 13 days treatment with nebulized dexamethasone (15 mg q24h) and saline (control). RESULTS: Nebulized dexamethasone treatment decreased microbial diversity; relative abundance of 8 genera in the upper respiratory tract were altered. For both the microbiota and the mycobiota, environment had a dominant effect over treatment. Alternaria, an opportunistic pathogen and allergen in humans recognized as a risk factor for asthma, asthma severity, and exacerbations, was increased with treatment. Treatment affected relative quantification of the equine gamma herpesviruses (EHV-2 and -5); EHV-2 DNA levels increased and those of EHV-5 decreased. CONCLUSIONS: Nebulized dexamethasone treatment affected the upper respiratory tract microbiota, but not the mycobiota, which was overwhelmed by the effect of a sustained dusty environment.

Equine Transport and Changes in Equid Herpesvirus' Status.

The risk of respiratory disease in the transported horse can increase as a consequence of immunosuppression and stress associated primarily with opportunistic bacterial proliferation and viral reactivation. This study examines the ecology of equid herpesviruses (EHV) in these horses, exploring reactivation and changes in infection and shedding associated with transport, and any potential contributions to transport-related respiratory disease. Twelve horses were subjected to an 8-h road-transport event. Antibodies to EHV-1 and EHV-4 were detected by ELISA in serum collected prior to, immediately after and 2 weeks post transport. Respiratory tract endoscopy and tracheal washes were collected prior to and 5 days after transportation. Nasal swabs collected prior to, immediately after, 1 and 5 days following transport were screened for EHV-1,-2,-4,-5 using qPCR. Six horses had persistent neutrophilic airway infiltrates post transportation, indicative of subclinical respiratory disease. No horses were qPCR positive for either of the alphaherpesviruses (i.e., EHV-1/-4) nor did any seroconvert to either virus. Four out of nine horses positive for either EHV-2 or EHV-5 on qPCR prior to transport developed neutrophilic airway inflammation. Five horses showed increasingly positive readings on qPCR (i.e., reduced Cq) for EHV-2 after transportation and seven out of eleven horses positive for EHV-2 after transport shared strains of high sequence similarity with other horses in the study. One EHV-2 virus detected in one horse after transport was genetically different which may be due to reactivation. The clinical significance of EHV-2 and EHV-5 remains in question. However these results indicate that transportation may lead to increased shedding, transmission and reactivation of EHV-2 and EHV-5 but not EHV-1/-4. Unlike previous work focusing on the role of alphaherpesviruses, this research suggests that investigation of the gammaherpesviruses (i.e., EHV-2/-5) in transport-related disease should not be dismissed, particularly given that these viruses can encode suppressive immunomodulators that may affect host health.

Characterization of the fecal virome in dogs with chronic enteropathy.

The fecal virome has been investigated in humans and various animal species using next generation sequencing. However, limited information is available about the fecal virome of dogs with chronic enteropathy (CE). We aimed to characterize the canine fecal virome of dogs with CE and compare it with the virome of previously analyzed healthy dogs.A total of 16 adult dogs; 8 healthy dogs (data from a parallel study) and 8 dogs with CE had fecal samples assessed by viral shotgun sequencing. Fecal samples were subjected to enrichment of viral nucleic acids prior to sequencing and metagenomic analyses. Characterization of the complete genome of a canine kobuvirus was performed by Sanger sequencing. An additional 21 healthy dogs and 14 dogs with CE were further analyzed for the prevalence of canine kobuvirus.Three fecal samples from dogs with CE contained in total 3 eukaryotic viral families. In contrast, 4/8 fecal samples previously identified from healthy dogs, contained 5 eukaryotic viral families with 2 families exclusive to this group. Bacteriophages were identified in all fecal samples from CE and healthy dogs. Canine kobuvirus was identified in one dog with CE, by shotgun sequencing, and the complete genome was then characterized. This kobuvirus was classified within canine kobuvirus group, being similar to strains from Korea and China. The larger prevalence study did not detect additional samples positive for canine kobuvirus. The fecal virome of dogs with CE differs in number and type of viral families from healthy dogs. The first Australian canine kobuvirus sequence was identified and characterized from a dog with CE.

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without 'wet bottom'.

Koalas (Phascolarctos cinereus) are iconic Australian marsupials currently threatened by several processes, including infectious diseases and ecological disruption. Infection with Chlamydia pecorum, is considered a key driver of population decline. The clinical sign of 'wet bottom', a staining of the rump associated with urinary incontinence, is often caused by chlamydial urinary tract infections. However, wet bottom has been recorded in koalas free of C. pecorum, suggesting other causative agents in those individuals. We used 16S rRNA diversity profiling to investigate the microbiome of the urogenital tract of ten female koalas in order to identify potential causative agents of wet bottom, other than C. pecorum. Five urogenital samples were processed from koalas presenting with wet bottom and five were clinically normal. All koalas were negative for C. pecorum infection. We detected thirteen phyla across the ten samples, with Firmicutes occurring at the highest relative abundance (77.6%). The order Lactobacillales, within the Firmicutes, comprised 70.3% of the reads from all samples. After normalising reads using DESeq2 and testing for significant differences (P < 0.05), there were 25 operational taxonomic units (OTUs) more commonly found in one group over the other. The families Aerococcaceae and Tissierellaceae both had four significantly differentially abundant OTUs. These four Tissierellaceae OTUs were all significantly more abundant in koalas with wet bottom. This study provides the foundation for future investigations of causes of koala wet bottom, other than C. pecorum infection. This is of clinical relevance as wet bottom is often assumed to be caused by C. pecorum and treated accordingly. Our research highlights that other organisms may be causing wet bottom, and these potential aetiological agents need to be further investigated to fully address the problems this species faces.

Infectious Laryngotracheitis Virus Viral Chemokine-Binding Protein Glycoprotein G Alters Transcription of Key Inflammatory Mediators In Vitro and In Vivo.

Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that infects chickens, causing upper respiratory tract disease and significant losses to poultry industries worldwide. Glycoprotein G (gG) is a broad-range viral chemokine-binding protein conserved among most alphaherpesviruses, including ILTV. A number of studies comparing the immunological parameters between infection with gG-expressing and gG-deficient ILTV strains have demonstrated that expression of gG is associated with increased virulence, modification of the amount and the composition of the inflammatory response, and modulation of the immune responses toward antibody production and away from cell-mediated immune responses. The aims of the current study were to examine the establishment of infection and inflammation by ILTV and determine how gG influences that response to infection. In vitro infection studies using tracheal organ tissue specimen cultures and blood-derived monocytes and in vivo infection studies in specific-pathogen-free chickens showed that leukocyte recruitment to the site of infection is an important component of the induced pathology and that this is influenced by the expression of ILTV gG and changes in the transcription of the chicken orthologues of mammalian CXC chemokine ligand 8 (CXCL8), chicken CXCLi1 and chicken CXCLi2, among other cytokines and chemokines. The results from this study demonstrate that ILTV gG interferes with chemokine and cytokine transcription at different steps of the inflammatory cascade, thus altering inflammation, virulence, and the balance of the immune response to infection.IMPORTANCE Infectious laryngotracheitis virus is an alphaherpesvirus that expresses gG, a conserved broad-range viral chemokine-binding protein known to interfere with host immune responses. However, little is known about how gG modifies virulence and influences the inflammatory signaling cascade associated with infection. Here, data from in vitro and in vivo infection studies are presented. These data show that gG has a direct impact on the transcription of cytokines and chemokine ligands in vitro (such as chicken CXCL8 orthologues, among others), which explains the altered balance of the inflammatory response that is associated with gG during ILTV infection of the upper respiratory tract of chickens. This is the first report to associate gG with the dysregulation of cytokine transcription at different stages of the inflammatory cascade triggered by ILTV infection of the natural host.