Comparative Characteristics and Pathogenic Potential of Escherichia coli Isolates Originating from Poultry Farms, Retail Meat, and Human Urinary Tract Infection

Abstract

The pathogenicity of many bacterial strains is determined by the acquisition of virulence genes and depends on many factors. The aim of this study was to analyse the phylogenetic background, virulence patterns, and drug susceptibility of 132 E. coli isolates tested in the context of the ExPEC (Extraintestinal Pathogenic E. coli) pathotype and the correlation of these features with bacterial isolation source: food (retail meat), poultry farms (AFEC-Avian Faecal E. coli), and patients with UTI (urinary tract infection) symptoms. The drug-susceptibility results of tested E. coli isolates obtained indicate that the resistance profile-ampicillin/tetracycline/trimethoprim+sulfamethoxazole/ciprofloxacin (AMP/TE/SXT/CIP)-was most frequently observed. The multidrug resistance (MDR) phenotype was found in 31.8% of isolates from poultry farms, 36.8% of strains isolated from food, and 20% of clinical samples. The greatest similarity of virulence profiles applied to isolates derived from poultry farms and food. Most of the AFEC from poultry farms and food-derived isolates belonged to commensals from phylogroups A and B1, while among the isolates from patients with UTI symptoms, the most common was the B2 phylogroup. The collective analysis showed similarity of the three studied groups of E. coli isolates in terms of the presented patterns of antimicrobial resistance, while the virulence profiles of the isolates studied showed great diversity. The phylogroup analysis showed no similarity between the poultry/food isolates and the UTI isolates, which had significant pathogenic potential.

Keywords: Escherichia coli; ExPEC; MLST; UTI; antimicrobial resistance; poultry farms; retail food; virulence genes.

Figure 1

The percentage (%) share of E. coli (n = 132) isolates belonging to specific phylogroups. Note: AFEC—Poultry farms (n = 44), UTI—(n = 50) and FOOD—(n = 38).

Figure 2

(A) Occurrence of MDR and Non-MDR resistance in individual phylogroups in AFEC strains. (B) Occurrence of MDR and Non-MDR resistance in individual phylogroups in UTI strains. (C) Occurrence of MDR and Non-MDR resistance in individual phylogroups in strains isolated from food.

Figure 2

(A) Occurrence of MDR and Non-MDR resistance in individual phylogroups in AFEC strains. (B) Occurrence of MDR and Non-MDR resistance in individual phylogroups in UTI strains. (C) Occurrence of MDR and Non-MDR resistance in individual phylogroups in strains isolated from food.

Figure 3

(A) (AFEC) The number of E. coli isolates containing tested virulence genes representing a specific phylogenetic group. (B) (UTI) The number of E. coli isolates containing tested virulence genes representing a specific phylogenetic group. (C) (FOOD) The number of E. coli isolates containing tested virulence genes representing a specific phylogenetic group.

Figure 3

(A) (AFEC) The number of E. coli isolates containing tested virulence genes representing a specific phylogenetic group. (B) (UTI) The number of E. coli isolates containing tested virulence genes representing a specific phylogenetic group. (C) (FOOD) The number of E. coli isolates containing tested virulence genes representing a specific phylogenetic group.

Figure 4

Phylogenetic tree (according to the neighbour-joining algorithm based on Hamming distance) was generated from the allelic profiles of seven housekeeping genes: adk, gyrB, fumC, icd, mdh, purA, and recA of 25 E. coli strains isolated from poultry farms, food, and patients with UTI symptoms. The sequence types (ST) highlighted in red (seven housekeeping genes) and sequence types highlighted in green (six housekeeping genes). I–V phylogenetic branches.