Sequenciamento de nova geração : 16S rRNA do microbioma urinário e resistência antimicrobiana de isolados bacterianos na urina de cães saudáveis e com infecções urinárias e isolados bacterianos de cães com neoplasias submetidos a tratamento quimioterápico

Abstract

The urine of healthy individuals has always been considered a sterile environment until new diagnostic techniques started to be used to detect bacteria in this environment; techniques such as sequencing through the 16S rRNA gene, which allowed characterizing the urinary microbiome and changing the clinical paradigm that urine is sterile. The present study aimed to determine the presence of bacterial isolates in the urine of healthy dogs (control group) and with urinary tract infection (cystitis group), identify the microorganisms through the standard examination of urinary culture and antibiogram in addition to evaluate the presence of multidrug resistant bacteria; besides determining the main agents of the urine microbiome of healthy and urinary-infected dogs by sequencing the 16S rRNA gene, also aimed to evaluate the profile of microorganisms present in the urine, the antimicrobial susceptibility pattern and the covariates breed, sex and tumor type in the development of urinary tract infection in dogs that have undergone chemotherapy. The dogs' urine of the three groups was collected by cystocentesis technique as well as culture and antibiogram of all samples were performed; Randomly selected samples from healthy dogs with urinary tract infection were also sequenced by the 16S rRNA method through the new generation Illumina® sequencer. In the control group 24.39% (10/41) and in the cystitis group 60.27% (44/73) of the animals that had bacterial isolates, the cystitis group was associated with a higher risk of these compared to the control group ( OR = 7.5; 95% CI 2.81 - 22.40). The main isolates were Staphylococcus spp, E. coli, Proteus sp and Enterobacter, in both groups, with different isolation percentages between these, but without statistical significance. A high percentage of isolates were resistant to ampicillin (68,18%), enrofloxacin (61,36%) and marbofloxacin (59,09%) in the cystitis group and ampicillin (50%), nitrofurantoin (50%) and chloramphenicol (40%) in the control group. The number of multiresistant isolates was 70% (7/10) and 65.91 (29/44) in the control and cystitis groups, respectively. However, animals from the cystitis group had the highest chance of presenting an multiresistant bacterium (OR = 4.3; 95% CI 1.57-13.61). As for sequencing, the most commonly found phyla in both of the control and cystitis microbiomes were: Actinobacteria, Firmicutes and Proteobacteria. In the control group, the most abundant genera were: Propionibacterium, Streptococcus, Enterococcus, Sphingomonas, Acinetobacter and Pasteurella; and in the cystitis

group were: Staphylococcus, Rhodococcus, Bacillus and Luteimonas. When dogs with neoplasms were analyzed, positive culture was obtained in 68.75% of patients in at least one of the collections performed, with Staphylococcus bacteria being the most isolated. Antibiotics such as imipenem and meropenem were not resistant to the antimicrobial susceptibility pattern, and ampicillin, enrofloxacin and nitrofurantoin were the most resistant.Dogs of breed were more likely to develop infection than dogs SRD. The results of the study showed that there is a microbiome in the urine of healthy dogs, and that the research in this area is essential to understand the role of this microbiome in the health and disease in the urinary tract of dogs.