Department of Pathology, Microbiology, and Immunology

American black bears (Ursus americanus) can be considered vertebrate pests when they come in conflict with humans and create potential public safety situations that require intervention by local wildlife or animal control departments. Black bears are both omnivorous and highly intelligent, and this combination of characteristics make these animals prone to human habituation and developing an association between humans and easy sources of food. Foraging behaviors can put black bears in undesired or unsafe contact with humans when bears root through garbage on private and public lands, consume crops, prey upon small livestock or pets, cause significant property damage, and wander onto roadways leading to traffic accidents. An increasingly recognized cause of bear-human conflict is neurologic disease, such as that caused by infectious pathogens or toxicity, leading to cognitive or behavioral changes. A unique neurologic disease affecting black bears was first observed in 2014 near Lake Tahoe on the border between California and Nevada. Since then, it has been reported in eight counties in California and two counties in Nevada. Affected bears exhibit a range of neurologic symptoms including tremors, seizures, head tilts, and loss of fear of humans (i.e., “dog-like” behavior). Affected animals are typically young (<3 years old), underweight, and most often present in the spring after early emergence from hibernation. Histopathologic examination of brain tissue from these bears revealed varying degrees of inflammation in the brain (encephalitis), but the cause of this encephalitis was not apparent. Testing for common infectious causes of encephalitis (e.g., rabies, canine distemper virus, canine adenovirus, West Nile virus) and common neurotoxins did not identify a cause of the inflammation. A novel gammaherpesvirus, circovirus, parvovirus, and anellovirus were isolated from subsets of affected bears; however, a direct correlation between viral infection and encephalitis has not been established to date. The goal of this study is to investigate the potential role of protozoal parasites in this encephalitis of unknown origin, as members of this group of pathogens are known causes of encephalitis in humans and animals. Brain tissue from bears with encephalitis (n = 21) and unaffected bears (n = 15) from California and Nevada was screened via PCR targeting two loci commonly used to identify protozoal parasites (ITS1 and 18S). Protozoal parasite DNA was detected in 47.6% of bears with encephalitis (10/21) and 26.7% of unaffected bears (4/15). Parasites detected in bears with encephalitis included Sarcocystis neurona (4/21), S. canis (1/21), S. felis (1/21), an uncharacterized Sarcocystis sp. (1/21), Toxoplasma gondii (1/21), and an uncharacterized Cystoisospora-like species (2/21). Sarcocystis neurona, S. canis, and T. gondii are known to cause encephalitis in humans and animals. Sarcocystis canis is an increasingly recognized pathogen of bears and has been reported to cause inflammation in the brain, liver, and muscle in other geographical regions. The clinical significance of the poorly characterized protozoal species is uncertain. Parasites detected in unaffected bears included T. gondii (1/15), an uncharacterized Sarcocystis species (1/15) and an uncharacterized Cystoisospora-like species (2/15). These results suggest that protozoal parasites, particularly Sarcocystis species, may contribute to encephalitis in juvenile black bears, creating a public safety hazard at the human-wildlife interface.

Wide-ranging large carnivores pose myriad challenges for conservation, especially in highly fragmented landscapes. Over a 13-year period, we combined monitoring of radio collared pumas with complementary multi-generational genetic analyses to inform puma conservation in southern California. Our goals were to generate survivorship estimates, determine causes of mortality, identify barriers to movement, and determine the genetic and demographic challenges to puma persistence among >20,000,000 people and extensive urban, suburban, and exurban development. Despite protection from hunting, annual survival for radio collared pumas was surprisingly low (55.8%), and humans caused the majority of puma deaths. The most common sources of mortality were vehicle collisions (28% of deaths), and mortalities resulting from depredation permits issued after pumas killed domestic animals (17% of deaths). Other human-caused mortalities included illegal shootings, public safety removals, and human-caused wildfire. An interstate highway (I-15) bisecting this study area, and associated development, have created a nearly impermeable barrier to puma movements, resulting in severe genetic restriction and demographic isolation of the small puma population (~17-27 adults) in the Santa Ana Mountains west of I-15. Highways that bisect habitat or divide remaining “conserved” habitat, and associated ongoing development, threaten to further subdivide this already fragmented puma population and increase threats to survival. This study highlights the importance of combining demographic and genetic analyses, and illustrates that in the absence of effective measures to reduce mortality and enhance safe movement across highways, translocation of pumas, such as was done with the endangered Florida panther, may ultimately be necessary to prevent further genetic decline and ensure persistence of the Santa Ana Mountains population.

Foothill abortion, also known as epizootic bovine abortion (EBA), has been a long-standing problem for California beef cattle producers. It is a major source of economic loss for California cow and calf producers, and in the 1990s it was estimated that 5% to 10% (45,000 to 90,000 calves) of the California beef calf crop may be lost each year ( Bushnell et al. 1991 ). UC Cooperative Extension (UCCE) farm advisors, specialists and UC Davis School of Veterinary Medicine (SVM) faculty have worked on this disease for nearly 50 years. This long research process finally moved forward in 2005, when the causative agent was identified.

Equine squamous cell carcinomas (eSCCs) are common, and a proportion are likely induced by Equus caballus papillomavirus 2 (EcPV-2). Accurate prediction of clinical outcomes is challenging with no recognized prognostic criteria or consistent histopathological classification scheme for eSCC. The aims of this study were to histopathologically subtype a large case series of eSCCs (genital and ocular) and correlate them with p16 and HER-2 expression, equine papillomavirus infection status, and various clinical and histopathological parameters to predict tumour behavior and prognosis. One hundred and eighty-five samples were examined and subtyped histologically. HER-2 and p16 immunohistochemistry (IHC) and in situ hybridization (ISH) for the EcPV-2 E6/E7 oncogenes were performed on a subset of cases, and follow-up survival data were analyzed. The results were compared and correlated with published guidelines on the categorization of human SCC. Six histopathological subtypes of SCC, according to the WHO, were identified for the first time in horses: usual/invasive (most common), verrucous, pseudoglandular, papillary, warty, and basaloid, with different histological subtypes demonstrating prognostic significance. HER-2 and EcPV-2 statuses were not associated with prognosis in horses with SCC. p16 expression is not associated with EcPV-2 status but could be a potential prognostic factor. ISH demonstrated EcPV-2 genetic material in the majority of eSCCs, except for the papillary subtype, which includes mature, not just pre-cancerous, eSCCs. Widespread HER-2 expression in eSCCs could suggest a role for this cell receptor as a potential therapeutic target.

A six-banded armadillo (Euphractus sexcinctus) from a zoo collection in central California developed acute neurologic signs followed by death. Postmortem examination revealed multisystemic bacterial disease (fibrinosuppurative meningoencephalomyelitis, splenitis, and endocarditis) with fibrinous necrotizing vasculitis and thrombosis. Streptococcus gallinaceus was isolated from the heart, lung, and meninges. To our knowledge, this microorganism has not been reported previously in association with systemic disease in an armadillo. Although the source of infection remains unknown, the animal was housed in the same building as chickens, a species that historically is associated with outbreaks of this bacterial infection. This case further broadens our understanding of the possible host range of S. gallinaceus and emphasizes the risk of interspecies pathogen transmission in captive environments.

Urinary tract infections (UTIs) are diagnosed based on symptoms and confirmed by urine culture, despite its limitations in sensitivity. False-negative cultures can lead to inappropriate antimicrobial use or urosepsis in high-risk patients. Next-generation sequencing (NGS)-based metagenomics offers a comprehensive and precise alternative but is rarely applied clinically. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for pathogen detection in urine. Remnant clinical and spiked urine samples underwent extraction, metagenomic library preparation, and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning to identify pathogens and resistance markers. BIOTIA-DX was intentionally designed and trained to increase stringency and reduce false positive detection of urogenital commensals or opportunistic microbes present at colonization levels. Internal controls ensured standardized, high-stringency results. The assay was validated on 1,470 urine specimens evaluating over 14.5k analytes. The clinical validation achieved a 97.2% sensitivity and 99.6% specificity with a limit of detection (LoD) of <15,000 CFU/mL for most bacterial species and <5,000 CFU/mL for fungal species. Discordant results were reconciled by target-specific qPCR or 16S Sanger sequencing, and 87% of the NGS results were concordant with the comparator. A subset of 332 clinical specimens was tested and validated for antimicrobial resistance (AMR). sul and blaSHV genes were commonly associated with Escherichia coli and Klebsiella pneumoniae, while cfxA was found in Prevotella and Pseudomonas spp. detected by BIOTIA-ID. Overall, these data demonstrate that BIOTIA-ID is a comprehensive, highly accurate end-to-end diagnostic assay with notable advantages over current culture-based diagnostics.IMPORTANCEUrinary tract infections (UTIs) are among the most common infections, yet current diagnostic methods, including urine culture, often fail to detect pathogens accurately, leading to delayed treatment and inappropriate antimicrobial use. Clinical metagenomics offers a powerful alternative, especially in complicated cases. BIOTIA-ID is a validated, clinical-grade next-generation sequencing (NGS)-based assay that provides highly accurate pathogen identification and antimicrobial resistance profiling. By incorporating machine learning and stringent quality controls, BIOTIA-ID minimizes false positives and enhances diagnostic precision. Our study demonstrates its superior performance over culture, with potential to improve UTI diagnostics, guide targeted therapy, and support antimicrobial stewardship. The implementation of urine metagenomic diagnostics could support recurrent and complicated UTI patient management, providing a more reliable alternative to traditional methods.

We investigated a case of severe Serratia odorifera infection in a racehorse. The horse had developed progressive lameness associated with swelling of the left tarsal region, which progressed to ulcerative dermatitis, tendinitis, tenosynovitis, and desmitis. The plantar side of the superficial digital flexor (SDF) tendon was visible through the skin ulcer, and coalescing nodules were present in the dermis. The horse was euthanized and an autopsy was performed. Grossly, in addition to the changes described above, severe edema of the soft tissues was associated with the ulcer. Microscopically, necrotizing and ulcerative, chronic-active dermatitis with granulation tissue was noted, along with lymphoplasmacytic and suppurative tendinitis (SDF), tenosynovitis (SDF and lateral digital flexor), and desmitis (long plantar ligament and flexor retinaculum [FR]), with collagen degradation and intralesional gram-negative bacteria. Serratia odorifera was isolated in pure culture from the ulcerated skin, SDF tendon, FR, and synovial fluid of the tarsus joint. To our knowledge, soft-tissue inflammation caused by S. odorifera has not been described in horses previously.

The temporomandibular joint (TMJ) is a synovial joint that consists of two articulating surfaces, the mandibular head on the condylar process ventrally and the mandibular fossa of the squamous temporal bone dorsally, with a thin fibrocartilage disc that separates the joint into two non-communicating compartments. Degenerative joint disease (DJD) of the TMJ has been evaluated in other carnivorous species; however, it has not previously been described in the lion (Panthera leo). This study characterized the histological, biomechanical and biochemical properties of the TMJ in health and disease in a lioness. The components of the articulating surface and general features of the disc of the TMJ were comparable to other carnivorous species described previously. Spontaneous DJD was observed unilaterally, revealing comparable features with other carnivores. Tensile strength and stiffness differed substantially between the diseased and healthy disc, with the diseased disc having altered direction-dependent mechanical properties. Biochemically, the disc exhibited a similar pattern of collagen and glycosaminoglycan composition to other carnivores. The role of DJD of the TMJ in potential pain or disability is not well understood in these species, and this report offers a glimpse into these disorders.

Here, we detail the pathology findings in a hooded pitta ( Pitta sordida ), a beautiful fruit dove ( Ptilinopus pulchellus ), and a golden-crested myna ( Ampeliceps coronatus ), all housed together in a mixed-species aviary at a zoo in central California that experienced mortalities over 3 mo. Yersinia pseudotuberculosis was identified as the primary pathogen, responsible for necrotizing heterophilic and histiocytic hepatitis, splenitis, pneumonia, nephritis, myositis, myocarditis, and enteritis. We also share the results of a field investigation to identify the source(s) of Y. pseudotuberculosis infection in the aviary; no bacteria were detected in samples of water, soil, feces, earthworms, earwigs, or organs from mice and fox squirrels, leading to the suspicion that the hooded pitta was a carrier. The zoo’s veterinary team implemented control measures, including an 11-mo quarantine and the acquisition of birds before the cold, rainy season, allowing them to acclimate safely. No new cases of yersiniosis occurred at the aviary in the year following the outbreak.