Characterization of the urinary microbiome in healthy dogs

Urinalysis and culture results of free-catch urine samples in dogs: a randomised controlled trial

OBJECTIVES

To evaluate the prevalence of bacterial presence in free-catch urine samples preceded by either a standardised prepped ("clean-catch") protocol versus unprepped (non-cleaned) voiding.

MATERIALS AND METHODS

The study was a single-centre prospective single-blinded randomised controlled trial. Urine samples were obtained from 100 client-owned dogs presenting for routine evaluation. Dogs were randomly assigned to either the prepped group (preputial or peri-vulvar area cleaned with sterile saline before collection) or the unprepped group (no preliminary cleansing) stratified by sex. Urinalysis and urine culture (blood and MacConkey agar) were performed on all samples. Significant bacterial presence on urine culture was defined as >104 colony forming units (CFU)/mL.

RESULTS

There were no statistically significant associations between prepped versus unprepped collection method or sex with a urinalysis positive for bacteriuria. However, on culture, significant bacterial growth was almost five times more likely to be associated with males relative to females (odds ratio 4.59, 95% confidence interval 1.61 to 13.10). The probability of finding a positive culture was not statistically associated with prep method (odds ratio 1.43, 95% confidence interval 0.50 to 4.08).

CLINICAL SIGNIFICANCE

For the majority of dogs without clinical signs of urinary tract infection, free-catch urine collection does not result in significant bacteriuria found on analysis or culture. The presence of bacteria found in free-catch samples may be secondary to sample contamination or subclinical bacteriuria. Sample contamination or subclinical bacteriuria may be more prevalent in male dogs.

Evaluation of the vaginal and urinary microbiota of healthy cycling bitches

BACKGROUND

While the urogenital microbiota has recently been characterized in healthy male and female dogs, the influence of sex hormones on the urogenital microbiome of bitches is still unknown. A deeper understanding of the cyclic changes in urinary and vaginal microbiota would allow us to compare the bacterial populations in healthy dogs and assess the impact of the microbiome on various urogenital diseases. Therefore, the aim of this study was to characterize and compare the urogenital microbiota during different phases of the estrous cycle in healthy female dogs. DNA extraction, 16 S rDNA library preparation, sequencing and informatic analysis were performed to determine the vaginal and urinary microbiota in 10 healthy beagle dogs at each phase of the estrous cycle.

RESULTS

There were no significant differences in alpha and beta diversity of the urinary microbiota across the different cycle phases. Similarly, alpha diversity, richness and evenness of vaginal bacterial populations were not significantly different across the cycle phases. However, there were significant differences in vaginal beta diversity between the different cycle phases, except for between anestrus and diestrus.

CONCLUSION

This study strongly suggests that estrogen influences the abundance of the vaginal microbiota in healthy female dogs, but does not appear to affect the urinary microbiome. Furthermore, our data facilitate a deeper understanding of the native urinary and vaginal microbiota in healthy female dogs.

Dietary Features Are Associated with Differences in the Urinary Microbiome in Clinically Healthy Adult Dogs

Nutrition plays an important role in shaping the gut microbiome composition, although the impact of diet on the urinary microbiome (i.e., urobiome) remains unknown. The aim of this pilot study was to discover how nutritional features affect the diversity and composition of the urobiome in dogs. Dietary histories were obtained for 15 clinically healthy adult dogs, including limited nutrient (protein, fat, crude fiber), commercial diet brand, and dietary diversity profiles. The urine samples were collected via cystocentesis, followed by sequencing of the bacterial 16S rRNA gene. The data were analyzed to determine associations between major nutrients and dietary sources with the urobiome's composition. The protein, fat, and crude fiber contents had no statistically significant effect on the alpha or beta diversity. However, the beta diversity values differed (PERMANOVA; p = 0.017, R2 = 0.10) between dogs fed one commercial diet brand compared to dogs consuming any other brand. The beta diversity values also differed (p = 0.019, R2 = 0.10) between dogs consuming more diverse daily diets compared to those consuming less diverse diets (≥3 or <3 unique food sources, respectively). Overall, the results of this pilot study suggest that diet might impact the urobiome and support further exploration of the relationship between diet and the urobiome's composition in dogs.

Gut and Urinary Microbiota in Cats with Kidney Stones

Upper urinary tract urolithiasis is an emerging disease in cats, with 98% of kidney stones composed of calcium oxalate. In humans, disturbances in the intestinal and urinary microbiota are suspected to contribute to the formation of calcium oxalate stones. We hypothesized that similar mechanisms may be at play in cats. This study examines the intestinal and urinary microbiota of nine cats with kidney stones compared to nine healthy cats before, during, and after treatment with the antibiotic cefovecin, a cephalosporin. Initially, cats with kidney stones displayed a less diverse intestinal microbiota. Antibiotic treatment reduced microbiota diversity in both groups. The absence of specific intestinal bacteria could lead to a loss of the functions these bacteria perform, such as oxalate degradation, which may contribute to the formation of calcium oxalate stones. This study confirms the presence of a distinct urobiome in cats with kidney stones, characterized by greater richness and diversity compared to healthy cats. These findings highlight the potential of microbiota modulation as a strategy to prevent renal lithiasis in cats.

Association of Mycoplasma canis with Fertility Disorders in Dogs: A Case Study Supported by Clinical Examination, PCR, 16S Microbiota Profiling, and Serology

The role of Mycoplasma canis in canine fertility disorders is still poorly understood. As infection is often asymptomatic, there is an increasing need for appropriate diagnostic methods and treatment plans that would allow the reliable detection of M. canis infection and rapid alleviation of infection symptoms in affected dogs. In this study, we included 14 dogs with fertility problems and 16 dogs without fertility disorder signs. We compared clinical examination data and selected laboratory parameters (hematology and biochemistry) between the groups. We performed PCR-based detection of M. canis and 16S rRNA gene-based microbiota profiling of DNA isolated from vaginal and preputial swabs. Dog sera were tested for the presence of M. canis-specific antibodies. Hematological and selected biochemical parameters showed no differences between groups. PCR-based detection of M. canis in the samples was consistent with the results of 16S microbiota profiling. Several other bacterial taxa were also identified that could potentially be involved in different fertility disorders. Serological methods were not accurate enough since high cross-reactivity rates were observed. In the future, more accurate and efficient methods will be needed to determine the role of M. canis and its true role in the pathogenesis of specific fertility disorders in dogs.

No viable bacterial communities reside in the urinary bladder of cats with feline idiopathic cystitis

Urinary microbial diversities have been reported in humans according to sex, age and clinical status, including painful bladder syndrome/interstitial cystitis (PBS/IC). To date, the role of the urinary microbiome in the pathogenesis of PBS/IC is debated. Feline idiopathic cystitis (FIC) is a chronic lower urinary tract disorder affecting cats with similarities to PBS/IC in women and represents an important problem in veterinary medicine as its aetiology is currently unknown. In this study, the presence of a bacterial community residing in the urinary bladder of cats with a diagnosis of FIC was investigated. Nineteen cats with clinical signs and history of FIC and without growing bacteria in standard urine culture were included and urine collected with ultrasound-guided cystocentesis. Bacterial community was investigated using a culture-dependent approach consisted of expanded quantitative urine culture techniques and a culture-independent approach consisted of 16S rRNA NGS. Several methodological practices were adopted to both avoid and detect any contamination or bias introduced by means of urine collection and processing which could be relevant due to the low microbial biomass environment of the bladder and urinary tract, including negative controls analysis. All the cats included showed no growing bacteria in the urine analysed. Although few reads were originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and negative controls, and no taxa were confidently classified as non-contaminant. The results obtained suggest the absence of viable bacteria and of bacterial DNA of urinary origin in the urinary bladder of cats with FIC.

BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men

Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.

Identification of bacteria associated with canine otitis externa based on 16S rDNA high-throughput sequencing

Bacteria are regarded as predisposing and perpetuating factors causing otitis externa (OE), whereas auricular anatomy is a predisposing factor. This study aims to investigate bacterial populations in the external auditory canals of healthy dogs and dogs with OE. Four categories of ear swabs included healthy erect-ear dogs, erect-ear dogs with OE, healthy pendulous-ear dogs and pendulous-ear dogs with OE. After bacterial DNA extraction, 16S rDNAs were amplified using specific primers within a V3/V4 region. Following DNA library construction, high-throughput sequencing was performed on MiSeq (Illumina). CLC Microbial Genomics Module was used to determine the rarefaction curve, bacterial classification, relative abundance, richness and diversity index. The results demonstrated that healthy dogs had higher bacterial richness and diversity than the dogs with OE. Comparable with culture-dependent methods described previously, this study revealed predominant Corynebacterium spp., Pseudomonas spp., Staphylococcus spp., and Proteus spp. in OE cases. Furthermore, high-throughput sequencing might disclose some potential emerging pathogens including Tissierella spp., Acinetobacter spp., and Achromobacter spp., which have not been reported in previous canine OE cases. Nevertheless, larger sample sizes are further required for an extensive evidence-based investigation.

Longitudinal examination of urine pH, specific gravity, protein, culture, and antimicrobial resistance profiles in healthy dogs

BACKGROUND

Urine is routinely evaluated in dogs to assess health. Reference ranges for many urine properties are well established, but the scope of variation in these properties over time within healthy dogs is not well characterized.

OBJECTIVES

Longitudinally characterize urine properties in healthy dogs over 3 months.

ANIMALS

Fourteen healthy client-owned dogs.

METHODS

In this prospective study, dogs were evaluated for health; then, mid-stream free-catch urine was collected from each dog at 12 timepoints over 3 months. Urine pH, urine specific gravity (USG), protein, cultures, and antimicrobial resistance profiles were assessed at each timepoint.

RESULTS

Urine pH varied within and between dogs over time (Friedman's test: within P = .03; between P < .005). However, USG, protein, and bacterial diversity of urine were consistent within dogs over time, and only varied between dogs (Kruskal-Wallis: between all P < .005). Antimicrobial resistant isolates were identified in 12 out of 14 dogs with 34 of 48 of the isolates demonstrating resistance to amoxicillin.

CONCLUSIONS AND CLINICAL IMPORTANCE

Urine pH should be assessed at multiple timepoints via pH meter before making clinical decisions. Mid-stream free-catch urine with high concentrations of bacteria (>105  CFU/mL) should not be considered the only indicator of urinary tract infection. Bacterial isolates from dogs in this study had widespread resistance to amoxicillin/oxacillin underscoring the need for antimicrobial stewardship.

The impact of urine collection method on canine urinary microbiota detection: a cross-sectional study

BACKGROUND

The urinary tract harbors unique microbial communities that play important roles in urogenital health and disease. Dogs naturally suffer from several of the same urological disorders as humans (e.g., urinary tract infections, neoplasia, urolithiasis) and represent a valuable translational model for studying the role of urinary microbiota in various disease states. Urine collection technique represents a critical component of urinary microbiota research study design. However, the impact of collection method on the characterization of the canine urinary microbiota remains unknown. Therefore, the objective of this study was to determine whether urine collection technique alters the microbial populations detected in canine urine samples. Urine was collected from asymptomatic dogs by both cystocentesis and midstream voiding. Microbial DNA was isolated from each sample and submitted for amplicon sequencing of the V4 region of the bacterial 16 S rRNA gene, followed by analyses to compare microbial diversity and composition between urine collection techniques.

RESULTS

Samples collected via midstream voiding exhibited significantly higher sequence read counts (P = .036) and observed richness (P = .0024) than cystocentesis urine. Bray Curtis and Unweighted UniFrac measures of beta diversity showed distinct differences in microbial composition by collection method (P = .0050, R2 = 0.06 and P = .010, R2 = 0.07, respectively). Seven taxa were identified as differentially abundant between groups. Pasteurellaceae, Haemophilus, Friedmanniella, two variants of Streptococcus, and Fusobacterium were over-represented in voided urine, while a greater abundance of Burkholderia-Caballeronia-Paraburkholderia characterized cystocentesis samples. Analyses were performed at five thresholds for minimum sequence depth and using three data normalization strategies to validate results; patterns of alpha and beta diversity remained consistent regardless of minimum read count requirements or normalization method.

CONCLUSION

Microbial composition differs in canine urine samples collected via cystocentesis as compared to those collected via midstream voiding. Future researchers should select a single urine collection method based on the biological question of interest when designing canine urinary microbiota studies. Additionally, the authors suggest caution when interpreting results across studies that did not utilize identical urine collection methods.

The human and animals' malignant melanoma: comparative tumor models and the role of microbiome in dogs and humans

Currently, the most progressively occurring incident cancer is melanoma. The mouse is the most popular model in human melanoma research given its various benefits as a laboratory animal. Nevertheless, unlike humans, mice do not develop melanoma spontaneously, so they need to be genetically manipulated. In opposition, there are several reports of other animals, ranging from wild to domesticated animals, that spontaneously develop melanoma and that have cancer pathways that are similar to those of humans. The influence of the gut microbiome on health and disease is being the aim of many recent studies. It has been proven that the microbiome is a determinant of the host's immune status and disease prevention. In human medicine, there is increasing evidence that changes in the microbiome influences malignant melanoma progression and response to therapy. There are several similarities between some animals and human melanoma, especially between canine and human oral malignant melanoma as well as between the gut microbiome of both species. However, microbiome studies are scarce in veterinary medicine, especially in the oncology field. Future studies need to address the relevance of gut and tissue microbiome for canine malignant melanoma development, which results will certainly benefit both species in the context of translational medicine.

The impact of urine storage methods on the results of quantitative bacterial culture in dog and cat

Quantitative bacterial culture (QBC) is the gold standard for determining urinary tract infections. However, the majority of urine samples were sent to a lab for further bacterial culture. Therefore, the storage condition was vital to maintain the quality and accuracy of the urine samples. The main objective of our study was to examine the urine QBC outcomes of (1) immediate culture, (2) culture after urine sample storage at ambient temperature for 24 h, and (3) culture after urine sample storage at 4 °C for 24 hours. There were 49 feline samples and 30 canine samples included in this study. All QBC samples kept at ambient temperature and refrigerator were consistent with immediate QBC in cats. Eight positive results from immediate QBC were in accordance with refrigerated results in dogs. There were ten positive results in the room-temperature sample with two false-positive results. Our study showed that storing conditions at room temperature or refrigeration for 24 h does not impact the results of QBC in cat urine samples. For dog samples, chilled samples have a higher accuracy rate than room temperature samples, although the overall agreement was still satisfactory.

Canine Fecal Microbiota Transplantation: Current Application and Possible Mechanisms

Fecal microbiota transplantation (FMT) is an emerging therapeutic option for a variety of diseases, and is characterized as the transfer of fecal microorganisms from a healthy donor into the intestinal tract of a diseased recipient. In human clinics, FMT has been used for treating diseases for decades, with promising results. In recent years, veterinary specialists adapted FMT in canine patients; however, compared to humans, canine FMT is more inclined towards research purposes than practical applications in most cases, due to safety concerns. Therefore, in order to facilitate the application of fecal transplant therapy in dogs, in this paper, we review recent applications of FMT in canine clinical treatments, as well as possible mechanisms that are involved in the process of the therapeutic effect of FMT. More research is needed to explore more effective and safer approaches for conducting FMT in dogs.

Characterization of the urogenital microbiome in Miniature Schnauzers with and without calcium oxalate urolithiasis

Background

Calcium oxalate (CaOx) uroliths are common in dogs. Humans with CaOx urolithiasis exhibit alterations of the urinary and urogenital microbiomes that might mediate urolith formation. Detection of urogenital microbes associated with CaOx in dogs could inform disease pathophysiology.

Objective

To identify compositional differences in the urogenital microbiome of Miniature Schnauzers with and without CaOx uroliths.

Animals

Nineteen midstream, voided urine samples from Miniature Schnauzers with (n = 9) and without (n = 10) a history of CaOx urolithiasis.

Methods

Analytical cross‐sectional study. Microbial DNA was extracted from previously frozen urine samples and sequenced for the bacterial 16S rRNA V3‐V4 hypervariable regions. Diversity and composition of microbial populations were compared between urolith formers and controls.

Results

Alpha and beta diversity measures were similar between groups. Five individual bacterial taxa differed in abundance (indicator values >0.5 and P < .05): Acinetobacter, 2 Geobacillus variants, and Hydrogenophaga were overrepresented in the urine of urolith formers, and Sphingopyxis was overrepresented in controls. Two distinct subtypes of urine microbial composition were observed based on beta diversity measures, independent of urolith status, and other clinical variables.

Conclusions and Clinical Importance

Although we did not detect a difference in the overall urogenital microbial composition between groups, observed differences in individual bacterial taxa might be clinically relevant. For example, Acinetobacter was overrepresented in urolith formers and is associated with CaOx urolithiasis in humans. Two unique clusters of the microbiome were identified, independent of urolith status, which may represent distinct urotypes present in Miniature Schnauzers.

Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens

The study of livestock microbiota has immediate benefits for animal health as well as mitigating food contamination and emerging pathogens. While prior research has indicated the gastrointestinal tract of cattle as the source for many zoonoses, including Shiga-toxin producing Escherichia coli and antibiotic resistant bacteria, the bovine urinary tract microbiota has yet to be thoroughly investigated. Here, we describe 5 E. coli and 4 Pseudomonas aeruginosa strains isolated from urine of dairy Gyr cattle. While both species are typically associated with urinary tract infections and mastitis, all of the animals sampled were healthy. The bovine urinary strains were compared to E. coli and P. aeruginosa isolates from other bovine samples as well as human urinary samples. While the bovine urinary E. coli isolates had genomic similarity to isolates from the gastrointestinal tract of cattle and other agricultural animals, the bovine urinary P. aeruginosa strains were most similar to human isolates suggesting niche adaptation rather than host adaptation. Examination of prophages harbored by these bovine isolates revealed similarity with prophages within distantly related E. coli and P. aeruginosa isolates from the human urinary tract. This suggests that related urinary phages may persist and/or be shared between mammals. Future studies of the bovine urinary microbiota are needed to ascertain if E. coli and P. aeruginosa are resident members of this niche and/or possible sources for emerging pathogens in humans.

Transient chemotherapy-induced alopecia after successful reversal of 5-fluorouracil myelosuppression and neurotoxicosis in a 9-month-old dog

BACKGROUND

5-Fluorouracil (5-FU) cream is a common human topical chemotherapy agent with potentially fatal neurotoxic effects on dogs if accidentally ingested. There are seldom reports in veterinary literature describing the successful outcome of intervention after accidental ingestion of 5-FU cream.

CASE SUMMARY

A 9-month-old spayed female labradoodle presented 14 h after ingesting an unknown amount of 40 g tube of Efudex cream (5% 5-FU). The dog presented in status epilepticus, which was managed with benzodiazepines and levetiracetam in conjunction with induced coma and mechanical ventilation. No further seizure activity occurred throughout the ensuing 5 days of hospitalisation; however, myelosuppression was featured. The dog was discharged home after 5 days of hospitalisation. Three days post discharge, the dog was noted to develop focal alopecia around the eyes and temporal region. 14 days after discharge, the alopecia progressed to a majority of the head and body.

CONCLUSION

To the authors' knowledge, this is the first report that documents the enduring adverse effects of 5-FU cream after survival of the initial episode, including an earlier onset of myelosuppression and diffuse alopecia. Successful treatment of accidental 5-FU ingestion is possible several hours after the initial event with minimal long-term consequences.

A review of the current concepts in canine urinary tract infections

Traditionally, urinary tract infections (UTIs) have been categorised as either uncomplicated or complicated in veterinary medicine, with treatment differing for the two categories. In human medicine, there is an additional category: Asymptomatic bacteriuria, which is the presence of bacteriuria without symptoms of infection. Escherichia coli (E.coli) is the most common bacterial species involved in UTIs in dogs. Clinical signs can be absent in dogs with complicated UTIs, and this has been likened to asymptomatic bacteriuria (ASB) in people and has been termed subclinical bacteriuria (SBU) with the treatment recommendations for SBU in dogs have been adapted from human recommendations. There is a shift in the current treatment of UTIs to help minimise the development of antimicrobial resistance. Routine screening of dogs with conditions that may predispose them to UTIs has been discouraged as has the treatment of SBU. This has been due to the increase in antimicrobial resistance (AMR).

Clinical features, outcome, and illness severity scoring in 32 dogs with urosepsis (2017-2018)

OBJECTIVE

To describe the clinical features, outcome, and utility of illness severity scoring in dogs diagnosed with urosepsis.

DESIGN

Retrospective study (2017-2018).

SETTING

University teaching hospital.

ANIMALS

Thirty-two dogs diagnosed with urosepsis secondary to pyometra, prostatitis, or pyelonephritis.

INTERVENTIONS

 None.

MEASUREMENTS AND MAIN RESULTS

Urosepsis was identified in 32 dogs, consisting of 9 of 32 (28.1%) with pyometra, 7 of 32 (21.8%) with prostatitis, and 16 of 32 (50%) with pyelonephritis. In total, 28 (87.5%) dogs survived to discharge, with the following group-specific survival rates: pyometra, 9 of 9 (100%); prostatitis, 5 of 7 (71.4%); and pyelonephritis, 14 of 16 (87.5%). Positive bacterial cultures were obtained in 27 of 32 (84.1%) dogs. The most commonly implicated pathogens were Escherichia coli (14/37 [37.8%]), Klebsiella pneumoniae (8/37 [21.6%]), and Staphylococcus pseudintermedius (6/37 [16.2%]). Multiple organ dysfunction syndrome (MODS) was identified in 21 of 32 dogs (65.6%). Although the presence of MODS was not different between survivors and nonsurvivors (P = 0.6), nonsurvivors had more dysfunctional organs (P = 0.04). Nonsurvivors also had higher Acute Patient Physiology and Laboratory Evaluation (APPLE_FAST ) scores compared to survivors (P = 0.01).

CONCLUSIONS

Survival of dogs with urosepsis was good and may be higher than for other sources of sepsis. Compared to survivors, nonsurvivors had more dysfunctional organs and higher illness severity scores, which may be helpful in the assessment and management of dogs with urosepsis.

Dogs' Microbiome From Tip to Toe

Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs' microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.

Dysbiosis of the Urinary Bladder Microbiome in Cats with Chronic Kidney Disease

Although feline urinary tract diseases cause high morbidity and mortality rates, and subclinical bacteriuria is not uncommon, the feline urinary microbiome has not been characterized. We conducted a case-control study to identify the feline urinary bladder microbiome and assess its association with chronic kidney disease (CKD), feline idiopathic cystitis (FIC), and positive urine cultures (PUCs). Of 108 feline urine samples subjected to 16S rRNA gene sequencing, 48 (44.4%) samples reached the 500-sequence rarefaction threshold and were selected for further analysis, suggesting that the feline bladder microbiome is typically sparse. Selected samples included 17 CKD, 9 FIC, 8 PUC cases and 14 controls. Among these, 19 phyla, 145 families, and 218 genera were identified. Proteobacteria were the most abundant, followed by Firmicutes. Notably, four major urotypes were identified, including two urotypes predominated by Escherichia-Shigella or Enterococcus and two others characterized by relatively high alpha diversity, Diverse 1 and Diverse 2. Urotype was associated with disease status (P value of 0.040), with the Escherichia-Shigella-predominant urotype being present in 53% of CKD cases and in all of the Escherichia coli PUC cases. Reflecting these patterns, the overall microbial composition of CKD cases was more similar to that of E. coli PUC cases than to that of controls (P value of <0.001). Finally, PUC cases had microbial compositions distinct from those of controls as well as CKD and FIC cases, with significantly lower Shannon diversity and Faith’s phylogenetic diversity values.

IMPORTANCE Despite the clinical importance of urinary diseases in cats, the presence of resident urine microbes has not been demonstrated in cats, and the role of these microbes as a community in urinary health remains unknown. Here, we have shown that cats with and without urinary tract disease harbor unique microbial communities in their urine. We found no evidence to suggest that the bladder microbiome is implicated in the pathogenesis of feline idiopathic cystitis, a disease similar to bladder pain syndrome/interstitial cystitis in humans. However, cats with chronic kidney disease had dysbiosis of their bladder microbiome, which was predominated by Escherichia-Shigella and had a community structure similar to that of cats with Escherichia coli cystitis. These findings suggest that chronic kidney disease alters the bladder environment to favor Escherichia-Shigella colonization, potentially increasing the risk of overt clinical infection.

Evaluating extraction methods to study canine urine microbiota

The urinary microbiota is the collection of microbes present in urine that may play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes is present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of bacterial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and bacterial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia Kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species.

Assessment of bacterial and fungal populations in urine from clinically healthy dogs using next-generation sequencing

BACKGROUND

Urine from clinically healthy dogs is not sterile. Characterizing microbial diversity and abundance within this population of dogs is important to define normal reference ranges for healthy urine.

OBJECTIVES

To establish composition and relative representation of bacterial and fungal microbiomes in urine of clinically healthy dogs.

ANIMALS

Fifty clinically healthy dogs.

METHODS

Analytic study. Urine sampling via cystocentesis. Comprehensive evaluation of urine including standard urinalysis, culture and sensitivity, next-generation sequencing (NGS), and bioinformatics to define bacterial and fungal microbiome.

RESULTS

Culture did not yield positive results in any samples. Next-generation sequencing of urine established low presence of bacteria, fungi, or both in all samples. Diversity and abundance of bacterial and fungal communities varied between urine samples from different dogs. Struvite crystals were associated with bacterial community structure (P = .07) and there was a positive correlation between struvite crystals and pH.

CONCLUSIONS AND CLINICAL IMPORTANCE

The microbiome in urine of clinically healthy dogs has diverse bacterial and fungal species These findings highlight limitations of conventional culture testing and the need for culture-independent molecular diagnostics to detect microorganisms in urine.

Composition and Potential Function of Fecal Bacterial Microbiota from Six Bird Species

Gut microbial communities play a fundamental role in health and disease, but little is known about the gut microbiota of pet bird species. This is important to better understand the impact of microbes on birds’ health but may also be relevant in a context of zoonoses. Total genomic DNA samples from pooled fecal samples from 30 flocks (4–7 pet birds per flock) representing over 150 birds of six different species (two Passeriformes: Northern Mockingbird (Mimus polyglottos) and Zebra Finch (Taeniopygia guttata), and four Psittaciformes: Lovebird (Agapornis, different species), Cockatiel (Nymphicus hollandicus), Red-rumped Parrot (Psephotus haematonotus), and Rose-ringed Parakeet (Psittacula krameri) were used for 16S rRNA gene analysis. Several taxa were found to be different among the bird species (e.g., lowest median of Lactobacillus: 2.2% in Cockatiels; highest median of Lactobacillus: 79.4% in Lovebirds). Despite marked differences among individual pooled samples, each bird species harbored a unique fecal bacterial composition, based on the analysis of UniFrac distances. A predictive approach of metagenomic function and organism-level microbiome phenotypes revealed several differences among the bird species (e.g., a higher proportion of proteobacteria with the potential to form biofilms in samples from Northern Mockingbirds). The results provide a useful catalog of fecal microbes from pet birds and encourage more research on this unexplored topic.

Bacterial communities associated to the urethra of healthy gilts and pregnant sows undergoing different reproductive protocols

Nowadays, it is known that the urogenital microbiota plays a key role in the urinary health of mammalians. Despite the urinary infections affect the health and the welfare of breeding sows, the urethral microbiota of healthy sows remains unknown. Therefore, this work evaluates the urethral bacterial communities of healthy gilts and sows to determine the presence of Enterobacteriaceae populations, and the structure of this microbiota in gilts (G) and pregnant (P) sows. Samples were collected by scraping the urethral mucosa of G (n = 9) and P sows, which included natural mating (NM, n = 9) and artificial inseminated (AI, n = 7) sows. Samples were analyzed by culture-dependent techniques and 16S-rRNA gene high-throughput-sequencing. All females were positive for Enterobacteriaceae culture, without significant differences (Kruskal-Wallis) between G and P groups (median values: 2.78 and 3.09 log CFU/mL, respectively; P = 0.497). Also, the rate of Enterobacteriaceae/total mesophilic microorganisms was individually calculated, without significant differences between G and P sows (median values: 0.61 and 0.66, respectively; P = 0.497). When analyzing the bacterial communities, it was found similar richness in G, NM, and AI; however, diversity was lower in P sows than G (Mann Whitney/Kruskal-Wallis test, P < 0.01). The dominating phyla that constituted a "core microbiome" included Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, which were common for all the studied females. The relative abundance for phyla, families, and genera was estimated, and Firmicutes was significantly higher in NM than AI sows (P = 0.02, Mann-Whitney/Kruskal Wallis test for univariate statistical comparisons); Pseudomonadaceae and Enterobacteriaceae were higher in AI than in NM (Mann-Whitney/Kruskal-Wallis, P < 0.05). Lactobacillus and Pseudomonas were among the dominant genera; however, only Pseudomonas sp. was significantly higher in AI than NM (Mann-Whitney/Kruskal-Wallis, P = 0.006). The results represent the first evidence about the existence of a urethral microbiota that includes Enterobacteriaceae, as well as the patterns of this microbiota in G and P sows. The knowledge of this urethral microbiota might allow for future research to develop innovative protocols to restore and/or preserve the healthy ecology of the urinary microbiome to prevent diseases ensuring the welfare of breeding sows.

[Bacterial urinary tract infection and subclinical bacteriuria in the dog: a current review]

Bacterial urinary tract infection (UTI) is a common clinical presentation in dogs and a frequent reason for the prescription of antimicrobial drugs. UTI refers to adherence, multiplication and persistence of an infectious agent within the urogenital system. This causes an associated inflammatory response as well as the pertaining clinical signs. Depending on the site of infection, UTI's may be classified as bacterial cystitis, prostatitis or pyelonephritis. In contrast, subclinical bacteriuria (SB) is defined as the presence of a significant number of bacteria in the urine of an individual not showing clinical signs referrable to UTI. UTI's typically occur as a consequence of ascending pathogen migration from the host's own fecal or distal urogenital microbial flora. The most commonly isolated pathogen in cases of UTI and SB is Escherichia coli. The diagnosis is based on clinical signs and the results of urine examination and culture. The recently revised guidelines of the International Society for Companion Animal Infectious Diseases provide detailed recommendations for diagnosis and management of different forms of bacterial UTI's in dogs. Adherence to treatment guidelines will improve treatment success and is imperative in avoiding further deterioration of the antimicrobial resistance situation.

Subclinical bacteriuria and surgical site infections in dogs with cranial cruciate ligament disease

OBJECTIVE

To determine the prevalence of subclinical bacteriuria (SBU) in dogs with cranial cruciate ligament (CCL) disease, the clinical variables and clinicopathologic data associated with SBU, and the incidence of surgical site infections (SSI) in dogs with and without SBU.

STUDY DESIGN

Prospective, clinical cohort study.

ANIMALS

One hundred fifty-five dogs with CCL disease.

METHODS

Dogs had a urinalysis, sediment examination, and aerobic urine culture performed. Age, breed, sex, body weight, body condition score, clinical history, and physical examination findings were recorded. Dogs with SBU were not treated for bacteriuria or with postoperative antibiotics. Standard perioperative antimicrobials were provided for all dogs. Dogs that received nonsteroidal anti-inflammatory drugs were not excluded. Dogs that underwent an osteotomy were followed for at least 1 year to determine incidence of SSI. Outcomes and variables associated with SBU were assessed.

RESULTS

In 155 dogs with CCL disease, the prevalence of SBU was 6.5%, and SBU occurred exclusively in female dogs (11.4%). The incidence of SSI was 22.3% (25/112). Two of six dogs with SBU and 23/106 dogs without SBU developed SSI. Organisms isolated from SSI were different from those isolated from urine.

CONCLUSION

The prevalence of SBU in dogs with CCL disease was similar to that in other studies in which SBU was evaluated in various populations of dogs.

CLINICAL SIGNIFICANCE

Screening for and treatment of SBU may not be beneficial prior to tibial osteotomy for CCL disease. Additional studies are required to determine whether dogs with SBU have a greater risk of SSI.

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats

A growing number of studies suggest that the lower urinary tract of humans and dogs can harbor a urinary microbiota. Nevertheless, a certain concern has developed that the microbiota reported could be due to unaccounted contamination, especially in low-biomass samples. The aim of this study was to investigate the bacterial community which populates the urine of healthy cats using two approaches: a culture-dependent approach which consisted of the expanded quantitative urine culture (EQUC) techniques capable of identifying live bacteria not growing in standard urine cultures, and a culture-independent approach which consisted of 16S ribosomal RNA next generation sequencing (16S rRNA NGS) capable of identifying bacterial DNA and exploring microbial diversity with high resolution. To avoid confounding factors of possible bacterial contamination, the urine was sampled using ultrasound-guided cystocentesis, and several sample controls and negative controls were analyzed. The urine sampled from the 10 cats included in the study showed no bacterial growth in the EQUC procedure. Although several reads were successfully originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and the negative control, and no taxa were statistically accepted as non-contaminant. Taken together, the results obtained allowed stating that no viable bacteria were present in the urine of healthy cats without lower urinary tract disease and urinary tract infections, and that the bacterial DNA detected was of contaminant origin.

Akkermansia and Microbial Degradation of Mucus in Cats and Dogs: Implications to the Growing Worldwide Epidemic of Pet Obesity

Akkermansia muciniphila is a mucin-degrading bacterium that has shown the potential to provide anti-inflammatory and anti-obesity effects in mouse and man. We here focus on companion animals, specifically cats and dogs, and evaluate the microbial degradation of mucus and its health impact in the context of the worldwide epidemic of pet obesity. A literature survey revealed that the two presently known Akkermansia spp., A. muciniphila and A. glycaniphila, as well as other members of the phylum of Verrucomicrobia seem to be neither very prevalent nor abundant in the digestive tract of cats and dog. While this may be due to methodological aspects, it suggests that bacteria related to Akkermansia are not the major mucus degraders in these pets and hence other mucus-utilizing taxa may deserve attention. Hence, we will discuss the potential of these endogenous mucus utilizers and dietary interventions to boost these as well as the use of Akkermansia spp. related bacteria or their components as strategies to target feline and canine obesity.

The Occurrence of Multidrug Resistant Bacteria in the Urine of Healthy Dogs and Dogs with Cystitis

Simple Summary

Antimicrobial resistance is a global health issue. The “One Health” concept describes animals and environments playing an important role in the resistance to antimicrobials. In this study, we survey healthy companion animals (dogs) as a potential source of multidrug resistant (MDR) bacteria, and compare them with dogs with cystitis. Both groups have a similar isolated genus profile and frequency of multidrug resistance. In our study, both healthy and cystitis animals were found to be carriers of MDR bacteria.

Abstract

The objectives of this study were to evaluate the occurrence of microorganisms, the antimicrobial susceptibility profile, and the presence of multidrug resistant (MDR) bacteria in the urine of clinically healthy dogs and dogs with cystitis. The urine was collected through cystocentesis. Subsequently, culture and antimicrobial susceptibility tests were performed. The isolates were classified based on their resistance profile, to evaluate the presence of MDR bacteria. Statistical analyses were performed using the chi-squared or Fisher’s exact tests. Bacterial isolates were present in 24.39% of the dogs in the control group, and 60.27% of the dogs in the cystitis group. The cystitis group was associated with a higher risk of bacterial isolates than the control group (odds ratio = 7.5; 95% confidence interval = 2.81–22.40). The main isolates were Staphylococcus spp., Escherichia coli, Proteus spp., and Enterobacter spp. in both groups. A high percentage of isolates were resistant to ampicillin in both groups. The lowest resistance presented by the isolates in both groups was to meropenem. Only the resistance to quinolones was different between the groups. The proportions of MDR isolates were 70% (7/10) and 65.91% (29/44) in the control and cystitis groups, respectively. The results showed the presence of MDR bacteria in the urine of both the healthy dogs, and the dogs with cystitis. The drug resistance was high, reinforcing the importance of establishing an effective treatment approach against urinary tract infections in pets, to minimize the spread of bacterial resistance and its impact on public health.

A clinical approach to multidrug-resistant urinary tract infection and subclinical bacteriuria in dogs and cats

Multidrug-resistant bacteria are increasingly isolated from the urinary tract of pets, particularly those that suffer from concurrent conditions, have been hospitalised, or were treated with antimicrobials in the recent past. Many of the multidrug-resistant bacteria encountered are resistant to all commonly used oral antibiotics. This poses both a therapeutic dilemma in the individual pet and a threat to public health. This article begins with an overview of multidrug resistance in organisms that are commonly isolated from the urinary tract of pets. This is followed by a proposed clinical approach to managing multidrug-resistant urinary bacteria, which summarises current knowledge regarding appropriate sampling and analysis, reviews the current guidelines regarding appropriate antimicrobial use and discusses treatment options that might be considered. The article highlights several shortcomings of the current knowledge to be considered when planning future clinical research and developing policies.

Urinary Tract Infection

"Urinary tract infection (UTI) is a common diagnosis in companion animal practice and is responsible for a significant proportion of antimicrobial use in veterinary medicine. The veterinary community has begun to follow the standards of care in human medicine and shift its definition of an UTI based on culture results and toward the presence of lower urinary tract symptoms. An improved understanding of the pathophysiology of UTI, risk factors for clinical disease, and the implementation of more reliable in-house diagnostic testing can lead to improved outcomes for patients and reduce inappropriate treatment. Investigation of antibiotic-sparing therapies holds some promise as well."

Agreement between Parallel Canine Blood and Urine Cultures: Is Urine Culture the Poor Man's Blood Culture?

Bloodstream infections are a significant cause of morbidity and mortality in critically ill dogs, but due to cost and difficulties in sample acquisition, blood cultures are infrequently obtained. In ill dogs, urine cultures may be recommended as surrogates for blood cultures. In order to determine the outcome agreement between parallel urine and blood cultures, we retrospectively analyzed parallel blood and urine specimens submitted for culture from dogs at the NC State Veterinary Hospital between 2011 and 2016. Positive cultures were reported from 15% of the submitted blood specimens and 23% of the submitted urine specimens. A total of 295 urine and blood samples were submitted in parallel, with positive growth demonstrated in 14 concordant and five discordant pairs. A kappa statistic comparing blood and urine culture outcomes was 0.266 (fair) when all parallel growth was included, including concordant and discordant results, and 0.170 (poor) when restricted to parallel concordant growth. The sensitivity of urine to reflect concordant bloodstream bacterial organisms was 30%, with a specificity of 87%. The positive and negative predictive values were 30% and 88%, respectively. Of dogs with both specimens positive on bacterial culture, 7 of 7 (100%) with suspected urogenital infection sources were concordant. All dogs with discordant bloodstream and urinary infections were immunosuppressed. Urinary coagulase-positive Staphylococcus isolates were most likely to be concordant with bloodstream infections. In conclusion, we found that urine culture is neither a substitute nor a screen for blood culture. Blood cultures should be performed in any potentially septic animal, especially those that are considered immunosuppressed.

Pyelonephritis in Dogs: Retrospective Study of 47 Histologically Diagnosed Cases (2005-2015)

Background

The clinicopathologic aspects of pyelonephritis have not been reported in companion animals.

Hypothesis/Objectives

To evaluate the prevalence of pyelonephritis diagnosed in dogs in a academic referral population, describe the clinical signs and the diagnostic test results in dogs with pyelonephritis, and identify concurrent disorders in order to determine potential risk factors for pyelonephritis.

Animals

Forty‐seven dogs with a histopathologic diagnosis of pyelonephritis from the teaching hospitals of three Canadian veterinary colleges.

Methods

Retrospective case series. Review of medical records and renal histologic sections.

Results

Pyelonephritis was diagnosed in 0.4–1.3% of the cases at necropsy. Clinical signs included anorexia or inappetence (n = 27, 57%), lethargy (n = 24, 51%), vomiting (n = 17, 36%), and dehydration (n = 12, 25%). Thirty‐five dogs (75%) had concomitant disease(s). Escherichia coli was the most common pathogen isolated (37%). Pyelonephritis was classified as acute (n = 12, 26%), subacute (n = 9, 19%), and chronic (n = 26, 55%) disease; and mild (n = 7, 15%), moderate (n = 11, 24%), and severe (n = 28, 61%). Fever was significantly associated with histopathologically subacute pyelonephritis (P = 0.01).

Conclusions

In referral hospitals, pyelonephritis has a very low prevalence at necropsy. Nonspecific clinical presentation, concomitant diseases, and high variability in the diagnostic tests results make the antemortem diagnosis of pyelonephritis challenging. Neither the histopathologic stage nor the severity of the pyelonephritis was associated with fever, lumbar pain, or signs of a urinary tract infection (ie, lower urinary tract infection, upper urinary tract infection, or both) except for subacute pyelonephritis which was associated with fever.