Genetic structure, antimicrobial resistance and frequency of human associated Escherichia coli sequence types among faecal isolates from healthy dogs and cats living in Canberra, Australia.
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SUBMITTER: Bourne JA
PROVIDER: S-EPMC6398920 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The purpose of this study was to analyse the prevalence and genetic characteristics of ESBL and acquired-AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick dogs in Portugal. Three hundred and sixty-one faecal samples from sick and healthy dogs were seeded on MacConkey agar supplemented with cefotaxime (2 µg/mL) for cefotaxime-resistant (CTXR) E. coli recovery. Antimicrobial susceptibility testing for 15 antibiotics was performed and the ESBL-phenotype of the E. coli isolates was screened. Detection of antimicrobial resistance and virulence genes, and molecular typing of the isolates (phylogroups, multilocus-sequence-typing, and specific-ST131) were performed by PCR (and sequencing when required). CTXRE. coli isolates were obtained in 51/361 faecal samples analysed (14.1%), originating from 36/234 sick dogs and 15/127 healthy dogs. Forty-seven ESBL-producing E. coli isolates were recovered from 32 sick (13.7%) and 15 healthy animals (11.8%). Different variants of blaCTX-M genes were detected among 45/47 ESBL-producers: blaCTX-M-15 (n = 26), blaCTX-M-1 (n = 10), blaCTX-M-32 (n = 3), blaCTX-M-55 (n = 3), blaCTX-M-14 (n = 2), and blaCTX-M-variant (n = 1); one ESBL-positive isolate co-produced CTX-M-15 and CMY-2 enzymes. Moreover, two additional CTXR ESBL-negative E. coli isolates were CMY-2-producers (qAmpC). Ten different sequence types were identified (ST/phylogenetic-group/β-lactamase): ST131/B2/CTX-M-15, ST617/A/CTX-M-55, ST3078/B1/CTX-M-32, ST542/A/CTX-M-14, ST57/D/CTX-M-1, ST12/B2/CTX-M-15, ST6448/B1/CTX-M-15 + CMY-2, ST5766/A/CTX-M-32, ST115/D/CMY-2 and a new-ST/D/CMY-2. Five variants of CTX-M enzymes (CTX-M-15 and CTX-M-1 predominant) and eight different clonal complexes were detected from canine ESBL-producing E. coli isolates. Although at a lower rate, CMY-2 β-lactamase was also found. Dogs remain frequent carriers of ESBL and/or qAmpC-producing E. coli with a potential zoonotic role.
| S-EPMC8388948 | biostudies-literature
Project description:BackgroundReproducible and reliable studies of cat and dog faecal microbiomes are dependent on many methodology-based variables including how the faecal stools are sampled and stored prior to processing. The current study aimed to establish an appropriate method for sampling and storing faecal stools from cats and dogs which may also be applied to privately-owned pets. The approach investigated the effects of storing faeces for up to 12 h at room temperature and sampling from various locations within the stool in terms of microbial diversity, relative taxa abundances and DNA yield. Faeces were collected from 10 healthy cats and 10 healthy dogs and stored at room temperature (20 °C). Samples were taken from various locations within the stool (the first emitted part (i), the middle (ii) and the last emitted end (iii), at either surface or core) at 0, 0.5, 1, 2, 3, 6 and 12 h, stabilised and stored at -80 °C. DNA was extracted from all samples, using Illumina NovaSeq.ResultsFaecal bacterial composition of dogs and cats shown no statistically significant differences in alpha diversity. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria were the most prevalent phyla. Cat and dog samples were characterized by a dominance of Prevotella, and a lack of Fusobacterium in feline stools. Room temperature storage of cat and dog faecal samples generally had no significant effect on alpha diversity, relative taxa abundance or DNA yield for up to 12 h. Sampling from regions i, ii or iii of the stool at the surface or core did not significantly influence the outcome. However, surface cat faecal samples stored at room temperature for 12 h showed a significant increase in two measures of alpha diversity and there was a tendency for a similar effect in dogs. When comparing samples with beta diversity measures, it appeared that for dog and cat samples, individual effect has the strongest impact on the observed microbial diversity (R2 0.64 and 0.88), whereas sampling time, depth and horizontal locations significantly affected the microbial diversity but with less impact.ConclusionCat and dog faeces were stable at room temperature for up to 12 h, with no significant changes in alpha diversity, relative taxa abundance and DNA concentration. Beta diversity analysis demonstrated that despite an impact of the sampling storing time and the surface of the sampling, we preserved the identity of the microbial structure linked to the individual. Finally, the data suggest that faecal stools stored for > 6 h at room temperature should be sampled at the core, not the surface.
| S-EPMC10724939 | biostudies-literature
Project description:Investigations of antimicrobial use in companion animals are limited. With the growing recognition of the need for improved antimicrobial stewardship, there is urgent need for more detailed understanding of the patterns of antimicrobial use in this sector.To investigate antimicrobial use for medical and surgical conditions in dogs and cats by Australian veterinarians.A cross-sectional study was performed over 4 months in 2011. Respondents were asked about their choices of antimicrobials for empirical therapy of diseases in dogs and cats, duration of therapy, and selection based on culture and susceptibility testing, for common conditions framed as case scenarios: 11 medical, 2 surgical, and 8 dermatological.A total of 892 of the 1,029 members of the Australian veterinary profession that completed the survey satisfied the selection criteria. Empirical antimicrobial therapy was more common for acute conditions (76%) than chronic conditions (24%). Overall, the most common antimicrobial classes were potentiated aminopenicillins (36%), fluoroquinolones (15%), first- and second-generation cephalosporins (14%), and tetracyclines (11%). Third-generation cephalosporins were more frequently used in cats (16%) compared to dogs (2%). Agreement with Australasian Infectious Disease Advisory Panel (AIDAP) guidelines (generated subsequently) was variable ranging from 0 to 69% between conditions.Choice of antimicrobials by Australian veterinary practitioners was generally appropriate, with relatively low use of drugs of high importance, except for the empirical use of fluoroquinolones in dogs, particularly for otitis externa and 3rd-generation cephalosporins in cats. Future surveys will determine whether introduction of the 2013 AIDAP therapeutic guidelines has influenced prescribing habits.
| S-EPMC5508328 | biostudies-literature
Project description:BackgroundEnterocytozoon bieneusi is one of the commonest microsporidians contributing to human microsporidiosis, and is frequently found in animals in various countries. However, there is limited epidemiological information on this microorganism in Australia. Here, we undertook the first molecular epidemiological study of E. bieneusi in cats and dogs in Victoria.ResultsGenomic DNAs were extracted from 514 individual faecal deposits from cats (n = 172) and dogs (n = 342) and then tested using PCR-based sequencing of the internal transcribed spacer (ITS) of nuclear ribosomal DNA. Four distinct genotypes (designated D, PtEb IX, VIC_cat1 and VIC_dog1) of E. bieneusi were identified in 20 of the 514 faecal samples (3.9%). Genotype D is known to have a broad host range (humans and other animals) and has a wide geographical distribution around the world. The identification of this genotype here suggests that companion animals might represent reservoir hosts that are able to transmit E. bieneusi infection to humans in Australia. A phylogenetic analysis of ITS sequence data revealed that the novel genotype VIC_cat1 is related to the known genotype type IV within Group 1, and the new genotype VIC_dog1 is linked to a contentious "Group 3", which includes genotypes reported previously in the published literature to represent Group 2 or 3.ConclusionsA future, large-scale phylogenetic study of all known E. bieneusi genotypes, including VIC_dog1, should aid in clarifying their relationships and assignment to Groups, and in the identification of new genotypes, thus assisting epidemiological investigations.
| S-EPMC6686557 | biostudies-literature
Project description:BackgroundCampylobacter spp. are among the leading foodborne bacterial pathogens. Pet animals may be an important reservoir for human infection.ObjectivesTo determine the prevalence and antimicrobial resistance profiles and mechanisms of Campylobacter isolates recovered from shelter-housed healthy and diarrheic cats and dogs in Erzurum province in Turkey.MethodsA total of 250 rectal swabs (from 124 cats and 126 dogs) collected between 2020 and 2021 were included in this study. The samples were cultured using a Campylobacter-selective agar medium. A single suspect colony from each plate was purified and species identification was performed by PCR. Minimum inhibitory concentration (MIC) values were determined against eight antibiotics. Specific antimicrobial resistance genes (tetO and aphA-3) and mutations (in gyrA) were screened by PCR and/or sequencing.ResultsA total of 26 (10.4%) isolates (25 Campylobacter jejuni and 1 Campylobacter coli) were obtained from the dogs; no Campylobacter was isolated from the cats. Of the C. jejuni isolates, 19.2% were resistant to nalidixic acid, 7.7% to ciprofloxacin and 3.8% to tetracycline and gentamicin per the CLSI interpretative criteria. The C. coli isolate was susceptible to all of the tested antibiotics. Thr-86-Ile mutation was the most common change detected in the gyrA gene in the quinolone-resistant isolates.ConclusionWhile geographic and population differences exist, Campylobacter carriage and associated antibiotic resistance in dogs is common, emphasising the need for continuous surveillance in this species, particularly given its zoonotic potential.
| S-EPMC10766042 | biostudies-literature
Project description:The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.
| S-EPMC5453527 | biostudies-literature
Project description:BackgroundBacterial urinary tract infections have been associated with comorbidities and increased antimicrobial resistance over time.ObjectiveTo identify bacterial species, antimicrobial susceptibility patterns and risk factors associated with antimicrobial resistance.AnimalsThree hundred sixty-three positive urine cultures from 308 cats.MethodsBacterial species and antimicrobial susceptibility data from positive aerobic bacterial urine cultures from cats with growth of ≥103 colony forming units per milliliter (cfu/ml) were included. Medical records were reviewed, and bacteriuria was classified as sporadic bacterial cystitis, recurrent bacterial cystitis or subclinical bacteriuria (SBU). Multivariable logistic regression analysis was used to evaluate antimicrobial resistance risk factors.ResultsA total of 444 bacterial isolates from 363 bacteriuric episodes were identified. Escherichia coli (52%) and SBU (59%) were the most common organism and classification, respectively. When compared to other classifications of bacteriuria, Enterococcus spp. were more likely to be isolated from SBU episodes (P < .001), whereas E. coli was more likely to be isolated from sporadic bacterial cystitis episodes (P < .001). Recurrent bacterial cystitis was associated with an increased risk of antimicrobial resistance to amoxicillin/clavulanic acid (odds ratio [OR], 3.9; 95% confidence interval [CI], 1.3-11.3). The percent susceptibilities of all bacterial isolates to commonly prescribed antimicrobials were amoxicillin/clavulanic acid (72%), cefazolin (49%), enrofloxacin (61%), and trimethoprim/sulfamethoxazole (75%). Multidrug resistance was highest for Enterococcus faecium isolates (65%).Conclusions and clinical importanceNo antimicrobial achieved >90% susceptible designation to all bacteria isolated highlighting the importance of performing urine culture and susceptibility testing, particularly for cats with recurrent bacterial cystitis.
| S-EPMC10229343 | biostudies-literature
Project description:We determined the population genetic structures of feline and canine Staphylococcus aureus strains in Japan by multilocus sequence typing (MLST). Ecological analyses suggested that multiple feline-related S. aureus clones, including ST133, naturally occur as commensals and can cause endogenous infections in felines. In contrast, S. aureus populations do not likely include any clone that exhibits tropism in domestic dogs. Even if S. aureus infections occur in dogs, the pathologies are likely exogenous infections.
| S-EPMC3372125 | biostudies-literature
Project description:Purpose: The study establishes normative data of tear volume (TV) and tear turnover rate (TTR) in healthy dogs and cats, 2 species commonly used for translational research in ophthalmology. Methods: Thirty-six dogs and 24 cats were enrolled, encompassing a variety of breeds with diverse skull conformations (brachycephalic, mesocephalic, and dolichocephalic). Two microliters of 10% fluorescein were instilled onto the upper bulbar conjunctiva of both eyes, followed by tear collection with 2-?L capillary tubes at 0, 2, 4, 6, 10, 15, and 20?min. Fluorescein concentrations were measured with a computerized scanning ocular fluorophotometer. The TV and TTR were estimated based upon nonlinear mixed-effects analysis of fluorescein decay curves. Results: In dogs, median (interquartile range) TV, basal TTR (bTTR), and reflex TTR (rTTR) were 65.3??L (42.3-87.9), 12.2%/min (3.7-22.1), and 50.0%/min (25.9-172.3), respectively. In cats, median (interquartile range) TV, bTTR, and rTTR were 32.1??L (29.5-39.9), 10.9%/min (3.0-23.7), and 50.0%/min (28.4-89.4), respectively. Body weight (r?=?0.44) and age (r?=?0.30) were positively correlated (P???0.019) with TV in dogs. Age was negatively correlated (P???0.018) with TTR in dogs (r?=?-0.33) and cats (r?=?-0.24). However, TV and TTR were not associated with skull conformation in either species. Conclusions: Dogs have greater TV than cats but similar basal and rTTR. Tear parameters were impacted by body weight and age, but not by skull conformation. In both clinical and research settings, successive lacrimal tests should be spaced by ?10?min to provide sufficient time for the tear film to replenish, as bTTR is ?11%/min-12%/min in both species.
| S-EPMC6842130 | biostudies-literature
Project description:The purpose of this study was the identification of RNAs contained in the urinary exosome (UExo) from dogs and cats. The quality of total RNA in isolated urinary exosome (UExo)-derived total RNAs obtained from the column-based method (urine 1 mL) was checked by using a Bioanalyzer, and samples from normal renal function (NR) group and kidney disease (KD) group were pooled as one sample for each group. We collected NR dogs (n = 37), KD dogs (n = 47), NR cats (n=43), and KD cats (n = 45). For the next generation sequencing, libraries were prepared according to the manufacturer’s protocols and sequenced using 50-base reads acquired by using a HiSeq 2000 platform. The December 2011 (GRCm38/mm10) mouse (Mus musculus) genome data were used as reference. As a result, we could identify the miRNA from these samples.
2018-12-10 | GSE121156 | GEO