Caution at choosing a particular colony-forming unit from faecal Escherichia coli: it may not represent the sample profile.

Data about phylogenetic classification of Escherichia coli colonizing calves, lambs and foals are routinely neglected and restricted to outdated methodologies, even in the context of antimicrobial susceptibility (AS) testing. Thus, the aim of this study was to determine the phylogenetic diversity and the AS profile of E. coli colony-forming units (CFUs) from faecal samples of healthy animals. Five CFUs of E. coli were randomly selected from each faecal culture of calves (n = 13), foals (n = 13) and lambs (n = 13), totalizing 195 CFUs phylo-typed by quadruplex PCR. The AS profile of five CFUs from 15 samples (five from each animal species; n = 75 isolates) against nine drugs was determined by agar diffusion test. We found E. coli belonging to all phylo-groups already described, except D group, with the predominance of B1 (65% CFUs; 126/195) in the three-animal species sampled. Most faecal samples of calves (77%; 10/13) and foals (69%; 9/13) harboured both pathogenic and nonpathogenic E. coli. All faecal samples showed CFUs with diverse AS profile, highlighting the ineffectiveness of tetracycline, sulphonamide and ampicillin. As a key point, our data reinforce the importance to select at least four E. coli CFUs for AS testing. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides relevant data about the high phylogenetic and antimicrobial susceptibility diversity observed in Escherichia coli colony-forming units (CFUs) from a bacteriological culture of faeces from healthy calves, foals and lambs. The selection pressure exerted by the herd treatment may directly impact the intestinal microflora of animals that have never been treated. Finally, we emphasize the importance of Clinical Laboratory Standards Institute guidelines and we recommended to analyse at least four E. coli CFUs to determine, in particular, the antimicrobial susceptibility profile of faecal isolates, independent of the animal's health status.

Prevalence of Rhodococcus equi from the nasal cavity of 1010 apparently healthy horses.

BACKGROUND: Rhodococcus equi is an important cause of foal pneumonia. While its isolation from different sources has been widely evaluated, there is a need to better understand the R. equi epidemiology from samples of the nasal cavity of healthy horses. OBJECTIVES: To determine the prevalence of R. equi from the nasal cavity of healthy horses, along with its virulence profile, antimicrobial susceptibility and environmental variables associated. STUDY DESIGN: Cross-sectional study. METHODS: Swabs from the nasal cavity of 1010 apparently healthy horses from 341 farms were submitted for bacteriological analyses. The identity and virulence profile of the R. equi isolates were assessed by multiplex PCR; antimicrobial susceptibility was determined by the disk-diffusion method. The occurrence of R. equi was calculated at the level of both animal and farm. The association of seven specific environmental factors with R. equi isolation was assessed using logistic regression and by a spatial scan statistical method to determine the presence of local clusters. RESULTS: Antimicrobial-sensitive R. equi was isolated from 10 (1%) of 1010 horses ranging between 3 and 29 years old. Ten farms (3%) had at least one positive horse. Only one R. equi isolate (10%) was classified as virulent. Red-Yellow Argisol (PVA/PV) soils were significantly associated with R. equi isolation (odds ratio (OR) 8.02; CI95% , 1.98-32.50, P = 0.01), and areas with well-drained soil were less likely to be test positive (OR 0.85; CI95% , 0.76-0.96, P = 0.03). MAIN LIMITATIONS: The use of culture-based method instead of PCR-based assay and the lack of soil sampling. CONCLUSIONS: Antimicrobial-sensitive R. equi may be considered a minor part of the normal bacterial flora in the nasal cavity of healthy and immunologically functional horses breeding on pasture. Further studies are warranted to determine if soils rich in iron and well-drained are, in fact, associated with the occurrence of R. equi.