Feline upper respiratory tract infections (URI) are of concern, especially in animal shelters. This scoping review identifies epidemiological literature on URI as caused by feline herpesvirus (FHV), feline calicivirus (FCV), Chlamydia felis, Mycoplasma felis and Bordetella bronchiseptica. Four databases were searched, studies were screened, and data were extracted on a standardised template. We described patterns in spatial locations of the studies, the range of pathogens and diagnostic tests, cohort characteristics and the findings of risk factor analyses. A total of 90 articles were selected for final data extraction. There was diversity in sampling methods, precluding quantitative meta-analysis of prevalence reports. FHV was most frequently studied (n = 57/90). The most popular sampling site was conjunctival swabbing (n = 43). Most studies (n = 57) used polymerase chain reaction (PCR) to confirm diagnosis. Approximately one-third (n = 32/90) of the studies included sheltered felines. This review explores the current state of knowledge on the epidemiology and risk factors of feline URI. Assessing the impact of risk factors has the potential to alleviate the severity of disease, especially in shelters; however, the results were not easily pooled as the studies used inconsistent approaches. We present recommendations for ongoing epidemiological research on feline URI to provide a more structured framework and define research questions for future systematic reviews.

Urban stray cats are cats without owners that survive in the wild for extended periods of time. They are one of the most common stray animals in cities, and as such, monitoring the pathogens carried by urban stray cats is an important component of urban epidemiological surveillance. In order to understand the prevalence of respiratory diseases in urban stray cats in Shanghai and provide scientific evidence for the development of targeted prevention and control strategies for respiratory diseases in stray cats, we collected 374 ocular, nasal, and oropharyngeal swabs from urban stray cats in Shanghai from January 2022 to December 2022. After RNA extraction, we used real-time PCR to detect six respiratory pathogens, including influenza A virus, feline calicivirus, feline herpesvirus type 1, Mycoplasma, Chlamydia, and Bordetella bronchiseptica. The results showed that among the 374 samples, 146 tested positive, with a positivity rate of 39.04%. The highest positivity rate was observed for Mycoplasma felis at 18.72% (70/374), followed by Chlamydia felis at 11.76% (44/374), feline calicivirus at 3.74% (14/374), feline herpesvirus 1 at 3.48% (13/374), Bordetella bronchiseptica at 1.34% (5/374), and influenza A virus was not detected. The highest positivity rate for Mycoplasma felis was in Minhang District at 31.94% (23/72), while Chlamydia felis and Bordetella bronchiseptica had the highest positivity rates in Jiading District at 23.53% (8/34) and 5.88% (2/34), respectively. The highest positivity rates for feline calicivirus and feline herpesvirus 1 were both observed in Qingpu District, at 14.46% (12/83) and 9.64% (8/83), respectively. A total of 36 samples showed mixed infections with two or more pathogens, with Mycoplasma felis being involved in 32 of these mixed infections, with the highest number of mixed infections being with Chlamydia felis at 25 samples. Respiratory pathogen positivity was detected throughout the year, with peak detection rates in summer and winter. The positivity rates of cat respiratory pathogens in different seasons showed statistical differences (χ2 = 27.73, p < 0.01). There was no statistical difference in the positivity rates of respiratory pathogens between cats of different genders (χ2 = 0.92, p > 0.05). The positivity rates of respiratory pathogens in cats of different age groups showed statistical differences (χ2 = 44.41, p < 0.01). Mycoplasma felis and Chlamydia felis were the main pathogens causing respiratory infections in stray cats, with Mycoplasma felis showing a much higher positivity rate than other respiratory pathogens and often co-infecting with Chlamydia felis and feline calicivirus. The positivity rate of Mycoplasma felis was high in summer, autumn, and winter, with no statistical difference between seasons. These results indicate a serious overall prevalence of respiratory pathogens in urban stray cats in the Shanghai area, showing seasonal trends and mixed infections with other pathogens. These findings suggest the need for comprehensive prevention and control measures to address respiratory pathogen infections in urban stray cats in the Shanghai area.

Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.

Mycoplasma cynos is a primary agent of pneumonia in dogs, and Mycoplasma felis is associated with upper respiratory tract disease in cats. We present complete genome sequences of 26 isolates from clinically affected dogs and cats. These genome sequences will facilitate new molecular and epidemiological analyses.

A total of 1158 cats with feline upper respiratory tract infection were incorporated from twenty animal hospitals in Wuhan, China, from April 2019 to April 2022 to investigate the epidemiology of feline calicivirus (FCV), herpesvirus-1 (FHV-1), Mycoplasma felis (M. felis) and Chlamydia felis (C. felis) for the development of a geographically-specific FCV vaccine with reference to prevalence and risk factors for infection. The 871 samples (75.2%) of kittens were younger than 12 months, of which 693 were males, and 456 were females. Among the samples, 443 were British shorthair cats, accounting for 38.3%, and 252 were Chinese rural cats, accounting for 21.8%. PCR/RT-PCR detection of the above four viruses (FCV, FHV-1, M. felis, and C. felis) in the upper respiratory tract of cats showed that the total positive samples were 744 (64.3%), including 465 positive samples of feline calicivirus, accounting for 40.2% of the total 1158 samples. There were 311 positive samples of M. felis, accounting for 26.9% of the total samples, ranked second in clinical practice. The 180 positive samples of feline herpesvirus accounted for 15.5%, and 85 positive samples of Chlamydia felis accounted for 7.3%. Among them, the number of positive samples of single pathogenic infections was 493, accounting for 66.3% of the total 744 positive samples. Double, triple, and quadruple infections accounted for 28.2%, 5.0%, and 0.5%, respectively, with the highest proportion of single infections. The molecular biological characteristics of the 17 isolated FCVd strains in Wuhan were further analyzed. It was found that the F9 vaccine strain and the antigenic epitopes in the 5\'HVR of the E region were collated with the F9 vaccine strain. Moreover, phylogenetic tree analysis showed that the strains related to the F9 and 255 vaccines were distantly related, leading to the failure of the vaccine. In addition, the strains associated with the F9 and 255 vaccines were distant, which might lead to vaccine failure in anticipation of the development of a more phylogenetically close FCV vaccine in China and may require the development of a vaccine for a locally related FCV strain.

Case ascertainment for prevalence and incidence studies from veterinary clinical data poses a major challenge because medical notes are not consistently structured or complete. Using natural language processing (NLP) and machine learning, this study aimed to obtain accurate case recognition for feline upper respiratory tract infections (primarily caused by viruses such as feline herpes virus (FHV-1) and feline calici virus (FCV), and bacteria such as Chlamydophila felis, Mycoplasma felis and Bordetella bronchiseptica using retrospective electronic veterinary records from the Royal Society for Prevention of Cruelty to Animals, Queensland (RSPCA Qld). Data cleaning and NLP on eight years of free-text veterinary records from RSPCA Queensland was carried out to derive text-based predictors. The NLP steps included sorting records by length of stay, vectorising, tokenising and spell checking against a bespoke veterinary database. A gradient boosted model (GBM) was trained to predict the probability of each animal having a diagnosis of upper respiratory infection. A manually annotated dataset was used for training the algorithm to learn dominant patterns between predictors (frequencies of n-grams) and responses (manual binary case classification). The GBM\'s performance was tested against an out of sample validation dataset, and model agnostics were used to interrogate the model\'s learning process. The GBM used patient-level frequencies of 1250 unique n-grams as predictor variables and was able to predict the probability of cases in the validation dataset with an accuracy of 0.95 (95% CI 0.92, 0.97) and F1 score of 0.96. Predictors that exerted the highest influence on the model included frequencies of \"doxycycline\", \"flu\", \"sneezing\", \"doxybrom\" and \"ocular\". The trained GBM was deployed on the full dataset spanning eight years, comprising 60,258 clinical entries. The prevalence in the full dataset was predicted to be 23.59%, which is in line with domain expertise from practicing veterinarians at the shelter. Case ascertainment is a crucial step for further epidemiological study of cat flu. Ultimately, this tool can be extended to other clinical procedures, conditions, and diseases such as intensive care treatment due to snake bites and tick paralysis, physical injuries such as orthopaedic fractures or chest injuries and labour-intensive infectious diseases like parvovirus, canine cough, and ringworm, all of which require prolonged quarantine and care.

Mycoplasma cynos and Mycoplasma felis are often associated with canine and feline infectious respiratory disease in dogs and cats, respectively. Mycoplasmas have a reduced genome and dearth of many biosynthetic pathways, making them dependent on rich medium for growth. Due to this fastidious nature, mycoplasmas have been historically underdiagnosed. The aim of this study was to develop a cost-effective and accurate sequencing workflow for genotypic characterization of clinical isolates of M. cynos and M. felis using a rapid long-read sequencing platform. We explored the following critical aspects of bacterial whole genome sequencing, including: (i) five solid and liquid-based culture approaches based on a specialized media formulation for Mycoplasma culture, (ii) three DNA extraction methods modified for long-read sequencing purposes, and (iii) two de novo assembly platforms, Flye and Canu, as key components of a bioinformatics pipeline. DNA extraction method 1, a solid-phase and column-based kit with enzymatic lysis, provided the best DNA quality and concentration followed by high coverage and sequencing contiguity. This was obtained with a culture volume of 45 ml in modified Hayflick\'s broth incubated for 48 h. DNA extracted directly from colonies on agar or from small broth volumes (6 ml) did not meet the criteria required for long-read sequencing. Overall, Flye generated more contiguous assemblies than the Canu assembler and was more time efficient. This 4-5 day sample-to-sequence workflow provides the scientific and clinical communities with a more comprehensive tool than laborious conventional methods for complete genomic characterization of M. cynos and M. felis clinical isolates.

UNASSIGNED: Upper respiratory tract disease (URTD) is prevalent in cats, and diagnosis can be challenging. This study aimed to determine the most common causes of cat URTD in Latvia and describe computed tomography (CT) and laboratory diagnostic findings.
UNASSIGNED: The present retrospective study included a total of 94 cats who were diagnosed with URTD. All cats underwent CT, and 50 of them had additional diagnostic tests, such as histology and respiratory infection polymerase chain reaction (PCR) testing.
UNASSIGNED: The most common CT finding was rhinosinusitis (55.32%) followed by nasal neoplasia (26.6%) and nasopharyngeal polyp (14.89%), but in three cats, a cause of respiratory symptoms was larynx neoplasia, nasal dermoid cyst, and an oronasal fistula. PCR test showed that the most cause of rhinosinusitis was Mycoplasma felis. Nasopharyngeal polyp as the primary diagnosis was identified in 14 cats from 3 months to 6 years, with an average age of 1.85 ± 1.915 years, and 54% of cats were female. Nasal neoplasia as a primary CT diagnosis was determined in 25 cats at the age of 5-18 years, with an average age of 10.56 ± 3.416 years. Histology diagnosis included four types of neoplasia - squamous cell carcinoma, sarcoma, adenocarcinoma, and aplastic carcinoma.
UNASSIGNED: This study describes the most common CT and laboratory findings in cats with URTD. Included information will be helpful for general veterinary practitioners and researchers and will update their knowledge on feline URTD.

The causative role of some infectious agents found in cases of feline pneumonia is under debate, because they are also part of the physiological microbiota of the respiratory tract of healthy animals. In this retrospective study, archived formalin-fixed and paraffin-wax-embedded lung samples of 69 severe and lethal cases of pneumonia in cats were examined by immunohistochemistry (IHC) for the detection of nine selected infectious agents: Pasteurella multocida, Bordetella bronchiseptica, Mycoplasma felis, M. gateae, Chlamydia felis, feline herpesvirus type 1, feline coronavirus, canine distemper virus, and Toxoplasma gondii. The intention was to elucidate their immediate involvement in pneumonia formation. Due to the cross-reactivity of the applied antibodies, a species-specific polymerase chain reaction (PCR) for both targeted Mycoplasma species was applied additionally. In the 42 cases (60.9%) positive for at least one pathogen, several agents were present in a high proportion of the samples (P. multocida - 34.8%, B. bronchiseptica - 29.0%), while others were present in a moderate (feline herpesvirus type 1 - 18.8%, M. gateae - 13.0%, M. felis - 10.1%) or low percentage (T. gondii - 1.4%). All samples were negative for C. felis, feline coronavirus and canine distemper virus. Mixed infections of up to four pathogens were more frequent than single infections. Mycoplasma preferably colonised lung tissue damaged by other pathogens because they never occurred as single infections. Pasteurella multocida, B. bronchiseptica, M. felis, feline herpesvirus type 1 and T. gondii showed abundant replication within lung lesions, thus suggesting a prominent role in pneumonia formation.

The aim of this study was to conduct a comprehensive assessment of feline infectious upper respiratory tract infection (URTI) and disease (URTD) in Australian cats.
Laboratory data demonstrating URTI from feline URTD multiplex PCR panel (feline herpesvirus 1 [FHV-1], feline calicivirus [FCV], Bordetella bronchiseptica, Chlamydophila felis, Mycoplasma felis and H1N1 influenza) submissions in Australia (2013-2015) were obtained. For comparison, reports of feline URTD during the same time period were sourced from a voluntary companion animal disease surveillance system.
A total of 3126 samples were submitted for testing; 1533 (49%) were positive. Of these, the most commonly detected agents were M felis (21.5%) and FCV (16.0%) alone, followed by FCV and M felis (13.4%) together as a respiratory infection complex, then FHV-1 (7.0%) alone. During the study period, there were 262 reports of 320 clinical feline URTD cases. Most cases (69%) were reported from New South Wales, <1 year of age (41%) and equally distributed between the sexes. Infection was more common in entire cats (69%) and most cases (55%) involved domestic shorthair cats. Of the 90 reports that had a known vaccination status, 63 had a vaccination history, 40 of which were recently vaccinated. Most (72%) feline URTD cases recovered from clinical disease. Both feline URTI and URTD were more common during winter months.
Feline URTI and URTD cause substantial impact in Australia, being most commonly associated with M felis and FCV infection. This information can be used by veterinarians to educate clients about prevention and management of this important infectious disease of cats.