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

Abstract

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. AbstractData 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classification of Escherichia coli colonizing calves, lambs and foals are routinely neglected and restricted to outdated methodologies, even in the context of antimicrobial susceptibility (AS) testing.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 phylogroups 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.

Bacterial genomic epidemiology with mixed samples

“…mGEMS demonstrates the power of plate sweep sequencing in genomic epidemiology and enables a change in the currently dominant framework that confers multiple benefits over both whole-genome shotgun metagenomics and isolate sequencing. Studies of the population structures of opportunistic pathogens have revealed extensive strain-level within-host variation [21,23,27,67,68] with adverse implications for transmission analyses relying solely on isolate sequencing [31,69] and colony pick based longitudinal studies reporting the absence or re-emergence of strains in a host [30,38,70] or antimicrobial profiles [28,71]. While whole-genome shotgun metagenomics solves these issues to some extent [35,72], the culture-free nature suffers from issues with both bacterial and host DNA contamination particularly affecting the sensitivity for detecting strains in low abundance [29,33,34,73,74].…”

Genomic Epidemiology with Mixed Samples

“…mGEMS demonstrates the power of plate sweep sequencing in genomic epidemiology and enables a change in the currently dominant framework that confers multiple benefits over both whole-genome shotgun metagenomics and isolate sequencing. Studies of the population structures of opportunistic pathogens have revealed extensive strain-level within-host variation [20,22,26,54,55] with adverse implications for transmission analyses relying solely on isolate sequencing [30,56] and colony pick based longitudinal studies reporting the absence or re-emergence of strains in a host [29,37,57] or antimicrobial profiles [27,58]. While whole-genome shotgun metagenomics solves these issues to some extent [34,59], the culture-free nature suffers from issues with both bacterial and host DNA contamination particularly affecting the sensitivity for detecting strains in low abundance [28,32,33,60,61].…”

Non‐lactose‐fermenting uropathogenic Escherichia coli from dogs: virulence profile characterization

“…Finally, from the plates of each strain five colonies were selected (Maciel et al . 2019) and subjected to antimicrobial susceptibility test through the disk‐diffusion tests according to the Clinical Laboratory Standards Institute (CLSI 2012 – M02‐A11) guidelines with the following class drugs (Laborclin, Brazil): β‐Lactams—ampicillin (10 µg), amoxicillin–clavulanate (20/10 µg), cephalothin (30 µg); imipenem (10 µg); Macrolide – azithromycin (15 µg), erythromycin (15 µg); Aminoglycosides – amikacin (30 µg), gentamicin (10 µg), streptomycin (300 µg), tobramycin (10 µg); phenicols—chloramphenicol (30 µg); tetracyclines—doxycycline (30 µg); quinolones—enrofloxacin (10 µg), ciprofloxacin (5 µg); nitrofuran—nitrofurantoin (300 µg) and sulphonamides—trimethoprim/sulphamethoxazole (25 µg). Escherichia coli ATCC 25922 and ATCC 35218 were used as quality control strains.…”