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Background Videofluoroscopic swallow studies (VFSS) utilizing penetration‐aspiration (P‐A) scoring assesses airway protection in people. On VFSS, penetration (ingesta or secretions immediately cranial to the vocal folds) and aspiration (material caudal to the vocal folds) are associated with increased risk of lung injury in people. Penetration‐aspiration (P‐A) scoring has been validated in animal models, but the incidence of P‐A, clinical signs (CS), and dysphagic disorders associated with P‐A in dogs are unknown. Objectives Using VFSS, identify the incidence of P‐A, compare CS between dogs with and without P‐A, and identify predisposing dysphagic abnormalities for P‐A. Animals One hundred client‐owned dogs. Methods Sequential VFSS and associated medical records from dogs presenting to the veterinary teaching hospitals at Auburn University (n = 53) and the University of Missouri (n = 47) were retrospectively reviewed. Statistical comparisons were made using Mann‐Whitney tests, one‐way analysis of variance (ANOVA) on ranks, multiple linear regression, and Spearman rank order correlation (P < .05). Results On VFSS, the incidence of pathologic P‐A was 39%. No significant differences in CS were found between dogs with or without P‐A (P > .05), with 14/39 dogs with P‐A presenting without respiratory CS. Pharyngeal (P < .001) and esophageal (P = .009), but not oral‐preparatory (P = .2) dysphagia was more common with P‐A. Pharyngeal weakness (P < .001) and esophago‐oropharyngeal reflux (EOR; P = .05) were independent predictors of P‐A and were moderately and weakly positively correlated with P‐A score respectively (P < .001, r = 0.489; P = .04, r = 0.201). Conclusions Penetration‐aspiration occurs in dogs in the absence of respiratory CS (i.e., occult P‐A). Dogs with pharyngeal weakness and EOR should be considered at risk for P‐A.

Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial communities in the feces, and upper and lower airways. In comparison, blood had an apparent compositional similarity with BALF with regard to a few dominant taxa, but shared more OTUs with feces. Samples clustered more by time than by individual, with OP swabs having subjectively greater variation than other samples. In summary, healthy cats have a rich and distinct lower airway microbiome with dynamic bacterial populations. The microbiome is likely to be altered by factors such as age, environmental influences, and disease states. Further data are necessary to determine how the distinct feline microbiomes from the upper and lower airways, feces and blood are established and evolve. These data are relevant for comparisons between healthy cats and cats with respiratory disease.

Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut‐lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut‐lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.

Background Aerodigestive diseases (AeroD) pathologically link respiratory and alimentary tracts. Dogs with respiratory signs lacking dysphagia, vomiting, or regurgitation typically do not undergo diagnostic testing that identifies comorbid alimentary disease. A videofluoroscopic swallow study (VFSS) identifies defects in swallowing, reflux, and aspiration. Objectives/Hypothesis We hypothesized that dogs with respiratory and no alimentary disease (RESP) would have significantly more abnormal VFSS metrics versus controls (CON). We hypothesized RESP dogs with pulmonary parenchymal disease would have more reflux and higher penetration‐aspiration score (PAS) than those with airway disease. Animals Client‐owned dogs: RESP (n = 45) and CON (n = 15) groups. Methods Prospectively, all dogs underwent VFSS. The RESP dogs had advanced respiratory diagnostic testing. Eight subjective and 3 objective VFSS metrics (pharyngeal constriction ratio [PCR], PAS, and esophageal transit time [ETT]) were assessed. Fisher's exact test compared differences between groups (presence or absence of VFSS abnormalities). The Mann‐Whitney rank sum test was used to compare PCR and PAS. Results Subjective VFSS abnormalities were present in 34/45 (75%) RESP and 2/15 (13%) CON dogs, with RESP dogs significantly more likely to have VFSS abnormalities (P = .01). No difference in PCR was found between groups. Pathologic PAS was more common in RESP than CON dogs (P = .03). The RESP dogs with airway disease had higher PAS than CON dogs (P = .01) but not RESP dogs with parenchymal disease (P = .25). Conclusions Most (75%) RESP dogs had VFSS abnormalities, emphasizing that AeroD are common. The VFSS has value in diagnostic evaluation of respiratory disease.

Inflammatory outcomes, including toxic anterior segment syndrome (TASS) and infectious endophthalmitis, are potentially painful, blinding complications following cataract surgery. In an in vitro pilot study, commercially available, sterile foldable intraocular lenses (IOLs) used during routine canine cataract surgery, and their packaging fluid were surveyed for the presence of bacterial DNA and/or viable (cultivable) bacteria. Swabs from IOLs and packaging fluid from three different veterinary manufacturers and three different production lots/manufacturer were collected for 16S ribosomal ribonucleic acid (rRNA) sequencing. Packaging fluid samples were collected for aerobic/capnophilic bacterial culture. Culture yielded one isolate, identified as Staphylococcus epidermidis . 16S rRNA sequencing revealed distinct brand-specific bacterial DNA profiles, conserved between IOLs and packaging fluid of all production lots within each manufacturer. The dominant taxonomy differentiating each manufacturer was annotated as Staphylococcus sp, and was a 100% match to S . epidermidis . Distinct mixtures of bacterial DNA are present and consistent in IOLs and packaging fluid depending on the manufacturer, and Staphylococcus is the dominant contributor to the bacterial DNA detected. Caralens products had a significantly lower amount of Staphylococcus spp . compared to Anvision and Dioptrix products.

The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF), was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt) software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.

Background Reflux and aspiration in people are associated with respiratory disease, whereas approximately 50% of healthy adults microaspirate without apparent consequence. In dogs, analogous information is lacking. Hypothesis Healthy dogs commonly have gastroesophageal reflux and a proportion of these dogs will have laryngopharyngeal reflux with silent aspiration. Animals Twelve healthy, client‐owned dogs. Methods Prospective study: Dogs were free‐fed a meal containing (111 MBq) colloidal 99m‐technetium phytate. Dynamic‐scans were performed 5 and 30 minutes postingestion. Time‐activity curves, reflux margination, volume, frequency, and duration were evaluated over 7 regions of interest in dorsal ± left‐lateral recumbency. Static scans (dorsal recumbency) were performed 2 and 18 hours postfeeding to detect aspiration. Reflux and aspiration were defined as counts ≥200% background activity ± decreased gastric counts. Between‐group comparisons were performed by Wilcoxon rank‐sum test or one‐way ANOVA on ranks with significance of P < .05. Results In this study, reflux of variable magnitude was detected in 12/12 dogs. No significant differences in outcome parameters were detected with recumbency (P > .05). Margination to the pharynx and proximal, middle, and distal esophagus was identified in 5/12, 2/12, 3/12, and 2/12 dogs, respectively. Median (IQR) reflux frequency and duration were 2 events/5 minutes (1‐3.3 events/5 minutes) and 6 seconds (4‐9 seconds) respectively. No dog had detectable aspiration. Conclusions and Clinical Importance Nuclear scintigraphy can document reflux in dogs. Reflux, but not aspiration, is common in healthy dogs and must be considered when interpreting results in clinically affected dogs.

Background In dogs, antimicrobial drugs are widely prescribed for aspiration pneumonia (AP) despite poor documentation of bacterial infection in AP (b‐AP) using bronchoalveolar lavage fluid (BALF) analysis. Interpretating discordant cytology and culture results is challenging, contributing to lack of a criterion standard, and highlighting differences between veterinary and human medical criteria for b‐AP. Objectives Determine how many dogs with AP had BALF collection and differences in diagnosis of b‐AP using veterinary vs human medical criteria. Report findings of noninvasive markers (e.g. fever, band neutrophilia, radiographic severity score) in dogs with and without b‐AP. Animals Retrospective cohort study of client‐owned dogs (n = 429) with AP at 2 university veterinary hospitals. Twenty‐four dogs met enrollment criteria. Methods Inclusion criteria were radiographic diagnosis of AP, ≥1 risk factor, CBC findings, and BALF cytology and culture results. Veterinary medical b‐AP criteria were cytology findings compatible with sepsis with or without positive culture, or cytology findings not consistent with sepsis and positive culture (≥1.7 × 103 cfu/mL). Human medical b‐AP criteria required culture with ≥104 cfu/mL or > 7% cells with intracellular bacteria on cytology. Results Only 24/429 dogs met all enrollment criteria; 379/429 dogs lacked BALF collection. Diagnosis of b‐AP differed using veterinary (79%) vs human (29%) medical criteria. Fever, band neutrophils and high radiographic scores were noted in dogs with and without b‐AP. Conclusions and Clinical Importance Lack of routine BALF collection hampers definitive recognition of bacterial infection in AP. Differences in dogs meeting veterinary vs human medical definitions for b‐AP and usefulness of noninvasive markers warrant further study to improve understanding of the role of bacteria in AP.

This Perspectives in Veterinary Medicine article seeks to define, describe putative causes, and discuss key diagnostic tests for primary and secondary bronchiolar disorders to propose a classification scheme in cats with support from a literature review and case examples. The small airways (bronchioles with inner diameters <2 mm), located at the transitional zone between larger conducting airways and the pulmonary acinus, have been overlooked as major contributors to clinical syndromes of respiratory disease in cats. Because the trigger for many bronchiolar disorders is environmental and humans live in a shared environment with similar susceptibility, understanding these diseases in pet cats has relevance to One Health. Thoracic radiography, the major imaging modality used in the diagnostic evaluation of respiratory disease in cats, has low utility in detection of bronchiolar disease. Computed tomography (CT) with paired inspiratory and expiratory scans can detect pathology centered on small airways. In humans, treatment of bronchiolar disorders is not well established because of heterogeneous presentations and often late definitive diagnosis. A review of the human and veterinary medical literature will serve as the basis for a proposed classification scheme in cats. A case series of cats with CT or histopathologic evidence of bronchiolar lesions or both, either as a primary disorder or secondary to extension from large airway disease or interstitial lung disease, will be presented. Future multi‐institutional and multidisciplinary discussions among clinicians, radiologists, and pathologists will help refine and develop this classification scheme to promote early and specific recognition and optimize treatment.

The lungs of people and companion animals are now recognized to harbor diverse, low biomass bacterial communities. While these communities are difficult to characterize using culture-based approaches, targeted molecular methods such as 16S rRNA amplicon sequencing can do so using DNA extracted from samples such as bronchoalveolar lavage fluid (BALF). Previous studies identified a surprisingly uniform composition of the microbiota in the lungs of healthy research dogs living in a controlled environment, however there are no reports of the lung microbiota of client-owned dogs. Moreover, compositional changes in the lung microbiota depending on disease status have been reported in people, suggesting that similar events may occur in dogs, a species subject to several respiratory disease mechanisms analogous to those seen in people. To address these knowledge gaps, BALF samples from client-owned dogs presenting to the University of Missouri Veterinary Health Center for respiratory signs between 2014 and 2017 were processed for and subjected to 16S rRNA sequencing. Based on specific diagnostic criteria, dogs were categorized as Chronic Bronchitis (CB, n = 53) or non-CB (n = 11). Community structure was compared between groups, as well as to historical data from healthy research dogs (n = 16) of a uniform breed and environment. The lung microbiota detected in all client-owned dogs was markedly different in composition from that previously detected in research dogs and contained increased relative abundance of multiple canine fecal and environmental bacteria, likely due to aspiration associated with their clinical signs. While inter-sample diversity differed significantly between samples from CB and non-CB dogs, the variability within both groups made it difficult to discern reproducible bacterial classifiers of disease. During subsequent analyses to identify other sources of variability within the data however, population-wide temporal dynamics in community structure were observed, with substantial changes occurring in late 2015 and again in early 2017. A review of regional climate data indicated that the first change occurred during a historically warm and wet period, suggesting that changes in environmental conditions may be associated with changes in the respiratory microbiota in the context of respiratory disease. As the lung microbiota in humans and other animals is believed to result from repetitive micro-aspirations during health and in certain disease states associated with dyspnea and laryngeal dysfunction, these data support the increased colonization of the lower airways during compromised airway function, and the potential for temporal effects due to putative factors such as climate.