Common cold viruses circulating in children threaten wild chimpanzees through asymptomatic adult carriers.

Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as "common cold" paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3-11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020-2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

Effect of carbohydrates on the adhesion of Bordetella bronchiseptica to the respiratory epithelium in rabbits.

This study proposes an ecological approach for preventing respiratory tract infections caused by Bordetella bronchiseptica in mammals using a mixture of carbohydrates. In an in vivo study, 51-day-old New Zealand rabbits were treated with a solution containing 1 × 107 CFUs of B. bronchiseptica and 250 µg of one of the following carbohydrates: N acetylglucosamine (GlcNAc), N acetylgalactosamine (GalNAc), alpha methyl mannose (AmeMan), alpha methyl glucose (AmeGlc) and sialic acid (Neu5AC). Positive (B. bronchiseptica) and negative (Physiological Saline Solution (PSS)) controls were included. Animals treated with GlcNAc or AmeGlc showed no clinical signs of infection and exhibited a significant reduction (p < 0.05) in the severity of microscopic lesions evaluated in the nasal cavity and lung compared with the positive controls. Additionally, the presence of bacteria was not detected through microbiological isolation or PCR in the lungs of animals treated with these sugars. Use of a mixture of GlcNAc and AmeGlc resulted in greater inhibition of microscopic lesions, with a significant reduction (p < 0.05) in the severity of these lesions compared to the results obtained using individual sugars. Furthermore, the bacterium was not detected through microbiological isolation, Polymerase Chain Reaction (PCR) or indirect immunoperoxidase (IIP) in this group.

Epidemiologic investigation and genetic characterization of canine respiratory coronavirus in the Southeastern United States.

Canine respiratory coronavirus (CRCoV) is one of the main causative agents of canine infectious respiratory disease (CIRD), an illness whose epidemiology is poorly understood. We assessed the prevalence, risk factors, and genetic characterization of CRCoV in privately owned dogs in the Southeastern United States. We PCR-screened 189 nasal swabs from dogs with and without CIRD clinical signs for 9 CIRD-related pathogens, including CRCoV; 14% of dogs, all diagnosed with CIRD, were positive for CRCoV, with a significantly higher rate of cases in younger dogs and during warmer weather. Notably, the presence of CRCoV, alone or in coinfection with other CIRD pathogens, was statistically associated with a worse prognosis. We estimated a CRCoV seroprevalence of 23.7% retrospectively from 540 serum samples, with no statistical association to dog age, sex, or season, but with a significantly higher presence in urban counties. Additionally, the genomes of 6 CRCoVs were obtained from positive samples using an in-house developed targeted amplicon-based approach specific to CRCoV. Subsequent phylogeny clustered their genomes in 2 distinct genomic groups, with most isolates sharing a higher similarity with CRCoVs from Sweden and only 1 more closely related to CRCoVs from Asia. We provide new insights into CIRD and CRCoV epidemiology in the Southeastern United States and further support the association of CRCoV with more severe cases of CIRD. Additionally, we developed and successfully tested a new amplicon-based approach for whole-genome sequencing of CRCoV that can be used to further investigate the genetic diversity within CRCoVs.

Epidemiological insights into the burden of feline upper respiratory tract infections in Queensland RSPCA shelters.

INTRODUCTION: Feline upper respiratory tract infection (FURTI) is a severe problem in animal shelters where there is high turnover of populations and compromised immunity. This retrospective cohort study explores associations of potential animal-based and environmental-based factors with the risk of FURTI, where a previously modelled infection classification is used as the outcome of interest. The study type is a retrospective cohort and the measures of association include Odds Ratios and conditional predictions. OBJECTIVES: To gain epidemiological insights into variation in FURTI using retrospective data from one of Australia's leading animal shelters. METHODS: We stratified FURTI by admission and environmental variables. Predicted infection status, obtained using a machine-learning classifier trained on clinical text (accuracy 0.95 [CI 0.92, 0.97]), was used as the outcome of interest. Prior assumptions were represented by a causal framework or a direct acyclic graph (DAG), which informed creation of multiple Bernoulli models with an observational and prior component. RESULTS: We analysed 43,431 feline entries over 8 years. Males were 1.24 (95% CI 1.19 to 1.31) times more likely than females to be classified as positive, while already desexed animals were only 0.68 (95% CI 0.60 to 0.72) as likely to be classified as positive compared to those not desexed on entry. Cats (>4 months) were twice as likely (95% CI 1.91 to 2.09) as kittens (0-4 months) to be classified positive. Animals entering the shelter as seized by the inspectorate (n = 415) were more likely to be classified positive compared to animals from other sources. Predicted infection probability increased in winter and showed a linear pattern with how full the shelter was. CONCLUSION: This study estimates the association between animal and environmental variables of interest and FURTI classification status, thus better interpreting the distribution of disease as predicted by a previously uninterpretable model. This analysis gives much needed insight into the types of changes in an animal's environment that can impact final animal outcomes.

Associations of serostatus upon arrival with clinical respiratory disease, lung consolidation, and growth in veal calves.

Respiratory tract infections remain a major problem during calf rearing, especially among milk (formula)-fed veal. Preconditioning of calves through appropriate colostrum management and vaccination could be helpful to address this issue. The objective of this study was to investigate whether the presence of serum antibodies against major respiratory tract pathogens (bovine respiratory syncytial virus, parainfluenza 3 virus, bovine coronavirus, Mycoplasmopsis bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) and total serum IgG concentration in calves upon arrival at the veal facility were associated with the occurrence of clinical bovine respiratory disease (BRD) or lung consolidation in the first 3 wk, as assessed by both the Wisconsin BRD scorecard (based on 5 clinical signs: cough, rectal temperature, ear position, and nasal and ocular discharge) and by quick thoracic ultrasound scanning. Additionally, the association between calves' serostatus production parameters were explored. A prospective cohort study was conducted among 442 male dairy calves on a large veal calf facility in Belgium. Both clinical scoring and quick thoracic ultrasound scanning were performed on all calves at 4 key moments in the production cycle: arrival at the facility, initiation of first metaphylactic antimicrobial treatment at peak incidence of BRD (wk 1), end of the first metaphylactic treatment (short-term evaluation) and at wk 10 (long-term evaluation). Mixed effects logit regression models were fitted to quantify relationships. The outcomes of interest were clinical respiratory disease (Wisconsin BRD scorecard positive), lung consolidation (≥1 cm or ≥ 3 cm), average daily weight gain, and cold carcass weight. In the first week of production, incidence of lung consolidation (≥1 cm) quickly increased from 14.9% upon arrival to 43.0% at the peak of the BRD incidence, while clinical BRD increased from 3.6% to 16.1%. The main finding of this study was that calves who were seropositive for bovine respiratory syncytial virus and bovine coronavirus at arrival had reduced odds of developing lung consolidation at the peak of the outbreak, 0.58 odds ratio (95% CI: 0.38-0.89) and 0.37 odds ratio (95% CI: 0.20-0.69), respectively. No relationships between serum IgG concentration at arrival and the development of lung consolidations or clinical respiratory disease were found. Nevertheless, on average, throughout the first 10 wk of the fattening cycle, calves with failed transfer of passive immunity (serum IgG < 7.5 g/L) gained 40 g/d (95% CI: 10-70 g/d) less weight (average daily gain). Hence, ensuring that calves have a positive serostatus for these respiratory tract pathogens before entering the facility may help lower the incidence of lung consolidations, subsequently reducing treatment incidence and the adverse effects on primary economic outcomes.

Predominance of low pathogenic avian influenza virus H9N2 in the respiratory co-infections in broilers in Tunisia: a longitudinal field study, 2018-2020.

Respiratory diseases are a health and economic concern for poultry production worldwide. Given global economic exchanges and migratory bird flyways, respiratory viruses are likely to emerge continuously in new territories. The primary aim of this study was to investigate the major pathogens involved in respiratory disease in Tunisian broiler poultry and their epidemiology. Between 2018 and 2020, broilers farms in northeastern Tunisia were monitored, and 39 clinically diseased flocks were sampled. Samples were screened for five viral and three bacterial respiratory pathogens using a panel of real-time PCR assays. The reemergence of H9N2 low pathogenic avian influenza virus (LPAIV) in commercial poultry was reported, and the Northern and Western African GI lineage strain was typed. The infectious bronchitis virus (IBV) GI-23 lineage and the avian metapneumovirus (aMPV) subtype B also were detected for the first time in broilers in Tunisia. H9N2 LPAIV was the most detected pathogen in the flocks tested, but rarely alone, as 15 of the 16 H9N2 positive flocks were co-infected. Except for infectious laryngotracheitis virus (ILTV), all of the targeted pathogens were detected, and in 61% of the respiratory disease cases, a combination of pathogens was identified. The major combinations were H9N2 + aMPV (8/39) and H9N2 + IBV (6/39), showing the high contribution of H9N2 LPAIV to the multifactorial respiratory diseases. This field survey provided evidence of the emergence of new respiratory viruses and the complexity of respiratory disease in Tunisia. A comprehensive and continuous surveillance strategy therefore is needed to better control respiratory pathogens in Tunisia.

Questionnaire study suggests grave consequences of infectious laryngotracheitis, infectious coryza and mycoplasmosis in small chicken flocks.

BACKGROUND: A growing number of people in western countries keep small chicken flocks. In Sweden, respiratory disease is a common necropsy finding in chickens from such flocks. A respiratory real-time polymerase chain reaction (PCR) panel was applied to detect infectious laryngotracheitis virus (ILTV), Avibacterium paragallinarum (A. paragallinarum) and Mycoplasma gallisepticum (M. gallisepticum) in chickens from small flocks which underwent necropsy in 2017-2019 and had respiratory lesions. Owners (N = 100) of PCR-positive flocks were invited to reply to a web-based questionnaire about husbandry, outbreak characteristics and management. RESULTS: Response rate was 61.0%. The flocks were from 18 out of Sweden's 21 counties indicating that respiratory infections in small chicken flocks are geographically widespread in Sweden. Among participating flocks, 77.0% were coinfected by 2-3 pathogens; 91.8% tested positive for A. paragallinarum, 57.4% for M. gallisepticum and 50.8% for ILTV. Larger flock size and mixed-species flock structure were associated with PCR detection of M. gallisepticum (P = 0.00 and P = 0.02, respectively). Up to 50% mortality was reported by 63.9% of respondents. Euthanasia of some chickens was carried out in 86.9% of the flocks as a result of the outbreaks. Full clinical recovery was reported by 39.3% of owners suggesting chronic infection is a major challenge in infected flocks. Live birds had been introduced in many flocks prior to outbreaks, which suggested these as an important source of infection. Following the outbreaks, 36.1% replaced their flocks with new birds and 9.8% ceased keeping chickens. CONCLUSIONS: This study highlights the severity of respiratory outbreaks in small non-commercial chicken flocks and points to the need for more research and veterinary assistance to prevent and manage respiratory infections in small chicken flocks.

Development and Validation of a Panel of One-Step Four-Plex qPCR/RT-qPCR Assays for Simultaneous Detection of SARS-CoV-2 and Other Pathogens Associated with Canine Infectious Respiratory Disease Complex.

Canine infectious respiratory disease complex (CIRDC) is the primary cause of respiratory disease in the canine population and is caused by a wide array of viruses and bacterial pathogens with coinfections being common. Since its recognition in late 2019, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been reported to cause respiratory disease in dogs. Therefore, the rapid detection and differentiation of SARS-CoV-2 from other common viral and bacterial agents is critical from a public health standpoint. Here, we developed and validated a panel of four one-step multiplex qPCR/RT-qPCR assays for the detection and identification of twelve pathogens associated with CIRDC (canine adenovirus-2, canine distemper virus, canine herpesvirus-1, canine influenza A virus, canine parainfluenza virus, canine pneumovirus, canine respiratory coronavirus, SARS-CoV-2, Bordetella bronchiseptica, Streptococcus equi subsp. zooepidemicus, Mycoplasma cynos, and M. canis), as well as the identification of three main CIV subtypes (i.e., H3N2, H3N8, and H1N1). All developed assays demonstrated high specificity and analytical sensitivity. This panel was used to test clinical specimens (n = 76) from CIRDC-suspected dogs. M. canis, M. cynos, and CRCoV were the most frequently identified pathogens (30.3%, 25.0%, and 19.7% of samples, respectively). The newly emerging pathogens CPnV and SARS-CoV-2 were detected in 5.3% of samples and coinfections were identified in 30.3%. This new multiplex qPCR/RT-qPCR panel is the most comprehensive panel developed thus far for identifying CIRDC pathogens, along with SARS-CoV-2.

Mesomycoplasma ovipneumoniae from goats with respiratory infection: pathogenic characteristics, population structure, and genomic features.

BACKGROUND: Mycoplasma ovipneumoniae is a critical pathogen that causes respiratory diseases that threaten Caprini health and cause economic damage. A genome-wide study of M. ovipneumoniae will help understand the pathogenic characteristics of this microorganism. RESULTS: Toxicological pathology and whole-genome sequencing of nine M. ovipneumoniae strains isolated from goats were performed using an epidemiological survey. These strains exhibited anterior ventral lung consolidation, typical of bronchopneumonia in goats. Average nucleotide identity and phylogenetic analysis based on whole-genome sequences showed that all M. ovipneumoniae strains clustered into two clades, largely in accordance with their geographical origins. The pan-genome of the 23 M. ovipneumoniae strains contained 5,596 genes, including 385 core, 210 soft core, and 5,001 accessory genes. Among these genes, two protein-coding genes were annotated as cilium adhesion and eight as paralog surface adhesins when annotated to VFDB, and no antibiotic resistance-related genes were predicted. Additionally, 23 strains carried glucosidase-related genes (ycjT and group_1595) and glucosidase-related genes (atpD_2), indicating that M. ovipneumoniae possesses a wide range of glycoside hydrolase activities. CONCLUSIONS: The population structure and genomic features identified in this study will facilitate further investigations into the pathogenesis of M. ovipneumoniae and lay the foundation for the development of preventive and therapeutic methods.

Antimicrobial susceptibility among respiratory tract pathogens isolated from diseased cattle and pigs from different parts of Europe.

AIMS: To survey antibiotic susceptibility of bacteria causing cattle and pig respiratory infections in 10 European countries. METHODS AND RESULTS: Non-replicate nasopharyngeal/nasal or lung swabs were collected from animals with acute respiratory signs during 2015-2016. Pasteurella multocida, Mannheimia haemolytica, Histophilus somni from cattle (n = 281), and P. multocida, Actinobacillus pleuropneumoniae, Glaesserella parasuis, Bordetella bronchiseptica, and Streptococcus suis from pigs (n = 593) were isolated. MICs were assessed following CLSI standards and interpreted using veterinary breakpoints where available. Histophilus somni isolates were fully antibiotic susceptible. Bovine P. multocida and M. haemolytica were susceptible to all antibiotics, except tetracycline (11.6%-17.6% resistance). Low macrolide and spectinomycin resistance was observed for P. multocida and M. haemolytica (1.3%-8.8%). Similar susceptibility was observed in pigs, where breakpoints are available. Resistance in P. multocida, A. pleuropneumoniae, and S. suis to ceftiofur, enrofloxacin, and florfenicol was absent or <5%. Tetracycline resistance varied from 10.6% to 21.3%, but was 82.4% in S. suis. Overall multidrug-resistance was low. Antibiotic resistance in 2015-2016 remained similar as in 2009-2012. CONCLUSIONS: Low antibiotic resistance was observed among respiratory tract pathogens, except for tetracycline.

Molecular evidence of ß-lactam resistant Staphylococcus aureus in equids with respiratory tract infections: Frequency and resistance modulation strategy.

The emergence of antimicrobial-resistant strains in Staphylococcus aureus (ß-lactam and methicillin-resistant) is an overwhelming issue worldwide. Using the purposive sampling technique, 217 equids samples were collected from district Layyah which were subjected to culturing followed by genotypic identification of mecA and blaZ genes by PCR. This study revealed that by phenotypic methods, a prevalence of 44.24%, 56.25%, and 47.92% was found for S. aureus, MRSA, and ß-lactam resistant S. aureus in equids. While genotypically, MRSA was found in 29.63% and ß-lactam resistant S. aureus in 28.26% of equids. In-vitro antibiotic susceptibility testing against S. aureus isolates harboring both mecA and blaZ genes showed a high resistance against Gentamicin (75%), followed by Amoxicillin (66.67%) and Trimethoprim+sulfamethoxazole (58.34%). In an attempt to re-sensitize the resistant bacteria to antibiotics, a combination of antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) was used which revealed synergistic effect of Gentamicin and Trimethoprim+sulfamethoxazole with Phenylbutazone; and Amoxicillin with Flunixin meglumine. Analysis of risk factors revealed significant association with the S. aureus-associated respiratory infection in equids. Phylogenetic analysis of mecA and blaZ genes showed a high resemblance of study isolate's sequences with each other and variable resemblance with already reported isolates obtained from different samples of neighboring countries. This study reports the first molecular characterization and phylogenetic analysis of ß-lactam and methicillin resistant S. aureus in equids in Pakistan. Moreover, this study will help in the resistance modulation of resistant antibiotics (Gentamicin, Amoxicillin, Trimethoprim+sulfamethoxazole) and provide a good insight into planning an effective therapeutic regime.

Simultaneous and rapid detection of avian respiratory diseases of small poultry using multiplex reverse transcription-Polymerase Chain Reaction assay.

Major viral infections, such as Newcastle disease virus, infectious bronchitis virus, avian influenza virus, and infectious bursal disease virus, inflict significant injury to small poultry and tremendous economic damage to the poultry sector. This research aims to develop a multiplex reverse transcriptase polymerase chain reaction (m-RT-PCR) approach to simultaneously determine these important viral pathogens. The conserved segment of various viral genetic sequences was used to design and synthesize specific primers. Moreover, as positive controls, recombinant vectors were synthesized in this investigation. The d-optimal approach was used to improve PCR conditions in this investigation. Positive controls and clinical samples were used to assess the m-PCR assay's specificity, sensitivity, repeatability, and reproducibility. According to the sensitivity test findings, the m-PCR technique could generate the 8 target genes from viral genomes using 1 × 102. In addition, 8 viral pathogens were detected from the infected samples. The findings also suggest that live animal oral swabs were not significantly different from tissue sampling of a dead animal (P < 0.05), and this kit had a high sensitivity for analyzing both types of samples. The suggested m-PCR test may detect and evaluate viral infection in birds with excellent specificity, sensitivity, and throughput.

Prevalence and risk factors for common respiratory pathogens within a cohort of pet cats in the UK.

OBJECTIVES: Feline herpesvirus (FHV), feline calicivirus (FCV) and Chlamydia felis are common causes of upper respiratory tract disease (URTD) in cats. Their prevalence in the UK pet cat population has not been reported and little is known regarding the risk factors for their oral carriage. METHODS: Total nucleic acid was extracted from owner-collected buccal swabs (n=600) from cats enrolled in a self-selected longitudinal cohort study. Duplex quantitative PCRs for the detection of FHV and C. felis genomic DNA and reverse-transcriptase quantitative PCRs for the detection of FCV genomic RNA were performed. Duplicates, swabs with insufficient host DNA/RNA, and cats with missing data were excluded. Selected epidemiological data were interrogated using univariable and multi-variable logistic regression modelling to identify risk factors. RESULTS: Data from 430 cats were included in the final statistical model. Of these, 2.1% (n=9/430; 95% CI 1.0% to 3.9%) were positive for FHV, 13.3% (n=57/430; 95% CI 10.2% to 16.8%) positive for FCV and 1.2% (n=5/430; 95% CI 0.4% to 2.7%) positive for C. felis. FCV co-infection was present in five (44%) FHV-positive cats and three (60%) C. felis-positive cats. FCV carriage was more frequent in purebred cats (odds ratio 2.48; 95% CI 1.37 to 4.49) and in cats with current or historical clinical signs compatible with URTD (odds ratio 2.98; 95% CI 1.22 to 7.27). CLINICAL SIGNIFICANCE: FCV was the most frequently encountered URTD pathogen in this sample of cats; this should be noted for disinfectant choice. In cats suspected of having FHV or C. felis infection, assessment for co-infection with FCV is recommended.

Neopterin Levels in Bonobos Vary Seasonally and Reflect Symptomatic Respiratory Infections.

As environmental changes exacerbate the threat coming from infectious diseases in wild mammal species, monitoring their health and gaining a better understanding of the immune functioning at the species level have become critically important. Neopterin is a biomarker of cell-mediated immune responses to intracellular infections. We investigated the variation of urinary neopterin (uNeo) levels of wild, habituated bonobos (Pan paniscus) in relation to individual and environmental factors. We used 309 urine samples collected between 2010 and 2018 at the LuiKotale field site, DRC. Based on current knowledge on zoo-housed conspecifics and closely related species, we predicted uNeo levels to increase (1) during infections, (2) with increasing age, (3) over the gestation period and in estrous females; and (4) to vary seasonally. Our results showed uNeo levels varied over a one-year period and increased in individuals showing respiratory symptoms. Contrary to chimpanzees, uNeo levels did not vary with age or female reproductive status, possibly due to our small sample size. Our study provides a baseline for a better understanding of bonobo's immunocompetence in the context of socio-ecological pressures and for monitoring the health of wild populations.

EFFECTS OF MYCOPLASMA GALLISEPTICUM INFECTION ON PREENING BEHAVIORS AND FEATHER QUALITY IN HOUSE FINCHES (HAEMORHOUS MEXICANUS).

Infections can have far-reaching sublethal effects on wildlife, including reduced maintenance of external structures. For many wildlife taxa, daily maintenance of external structures (termed preening in birds) is critical to fitness, but few studies have examined how infections alter such maintenance. Mycoplasma gallisepticum is a common pathogen in free-living House Finches (Haemorhous mexicanus), where it causes mycoplasmal conjunctivitis. Despite documented behavioral changes associated with M. gallisepticum infections in finches, no studies have examined how preening behavior may change with infection and how potential differences in preening may affect feather quality. To test this, we experimentally inoculated captive House Finches with M. gallisepticum or a control treatment, and we collected behavioral and feather quality data to detect potential changes in feather maintenance due to infection. We found that finches infected with M. gallisepticum preened significantly less often, and within the infected treatment, birds with the highest conjunctivitis severity preened the least often. However, there was no difference in the quality scores for secondary flight feathers collected from control versus infected birds. We also assayed feather water retention and found that the degree of water retention correlated with our feather quality scores, such that feathers with poor scores retained more water. However, as with quality scores, feather water retention did not differ with infection; this may be due to the controlled environment that the birds experienced while in captivity. Our data suggest that, in addition to sickness behaviors previously observed in finches, M. gallisepticum infection decreases other behaviors critical to survival, such as preening. While the consequences of reduced preening on feather maintenance were not apparent in captive conditions, further work is needed to determine whether House Finches in the wild that are infected with M. gallisepticum experience a fitness cost, such as increases in ectoparasite loads, due to this reduced feather maintenance.

Common viral and bacterial avian respiratory infections: an updated review.

Many pathogens that cause chronic diseases in birds use the respiratory tract as a primary route of infection, and respiratory disorders are the main leading source of financial losses in the poultry business. Respiratory infections are a serious problem facing the poultry sector, causing severe economic losses. Avian influenza virus, Newcastle disease virus, infectious bronchitis virus, and avian pneumovirus are particularly serious viral respiratory pathogens. Mycoplasma gallisepticum, Staphylococcus, Bordetella avium, Pasteurella multocida, Riemerella anatipestifer, Chlamydophila psittaci, and Escherichia coli have been identified as the most serious bacterial respiratory pathogens in poultry. This review gives an updated summary, incorporating the latest data, about the evidence for the circulation of widespread, economically important poultry respiratory pathogens, with special reference to possible methods for the control and prevention of these pathogens.

Outbreak management of multidrug-resistant Bordetella bronchiseptica in 16 shelter-housed cats.

CASE SERIES SUMMARY: This case series describes an outbreak of multidrug-resistant (MDR) Bordetella bronchiseptica in 16 shelter-housed cats with infectious respiratory disease. Four cats presented with acute dyspnea on the same day, each with a history of previous upper respiratory disease that had resolved with treatment. Early diagnostic testing and culture and sensitivity allowed for targeted antimicrobial therapy and environmental interventions. A case definition based on exposure and clinical signs identified 12 additional presumptive cases, including the likely index case. Comprehensive outbreak management included diagnostic testing, risk assessment, vaccination, use of isolation and quarantine, increased surveillance and review of biosecurity practices. The outbreak resolved in 26 days. RELEVANCE AND NOVEL INFORMATION: Management of an MDR B bronchiseptica outbreak in shelter-housed cats has not been previously described. Along with standard population and environmental measures, early and appropriate use of necropsy, PCR and bacterial culture allowed rapid and appropriate use of effective, second-line antibiotics. Shelters are resource-challenged population centers. Veterinarians working in animal shelters can play an important role in helping to develop cost-efficient and effective antimicrobial stewardship practices for companion animal settings. Outbreak management expertise and funding for diagnostic testing, as well as application of the principles of antimicrobial stewardship, are essential components of shelter medicine practice.

Using a gradient boosted model for case ascertainment from free-text veterinary records.

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.