Characterization of Escherichia coli isolated from poultry in the Chobe region of Botswana by molecular methods

Introduction: Diarrheal illness incidence is high in rural dryland environments, including the Chobe region of Botswana, where peaks are often associated with high rainfall events. Antibiotic resistance (ABR) is also a growing problem in the region. Contributions of poultry to diarrheal illness and ABR in the region are not well understood. Purpose: Characterize the virulence potential and ABR of E.coli isolated from chicken purchased from local vendors in Botswana using molecular techniques, including whole genome sequencing. Methods: Poultry was purchased in Kasane, Botswana and enriched within 24h. E.coli was isolated using MacConkey and EMB agar. Isolates were shipped to Virginia Tech for molecular and antibiotic resistance characterization. Multiplex PCR was used to detect presence of genes phoA (all E.coli), and diarrheagenic E.coli (eae, and est1b). Phenotypic ABR was determined using CLSI disk diffusion methods. Whole genome sequencing was performed using an Illumina MiSeq system and genome annotated using BV-BRC. Results: E.coli was isolated from 62% (38/61) of poultry samples. Five isolates were classified as diarrheagenic based on eae, none were positive for est1LB. Multidrug resistance (3+) was seen in 26 isolates and resistance to 1 or more antibiotics in 41 E.coli isolates. Resistance amongst chicken isolates was as follows: tetracycline (29), doxycycline (21), sulfamethoxazole (20), streptomycin (15), ampicillin (15), chloramphenicol (9), ciprofloxacin (6), gentamicin (4), c ceftriaxone (4), amoxicillin-clavulanic acid (3) and azithromycin (1). Comprehensive analysis of the genomes from chicken intestinal isolates revealed large numbers of virulence genes (125-252) common amongst diarrheagenic E.coli. Antibiotic resistance genes (65-85) were also present including those encoding resistance to ampicillin, ceftriaxone, doxycycline, streptomycin, and tetracycline.
Significance: While prevalence of diarrheagenic E.coli was low, antibiotic resistant E.coli were frequently isolated. E.coli may be an important sentinel species to evaluate ABR emergence and effectiveness of control strategies by Botswana poultry producers.