Prevalence and molecular characteristics of avian pathogenic Escherichia coli in “No Antibiotics Ever” broiler farms

Authors: FANCHER, C - Mississippi State University; THAMES, H - Mississippi State University; COLVIN, M - Mississippi State University; SMITH, M - Virginia-Maryland Regional College Of Veterinary Medicine (VMRCVM); EASTERLING, A - University Of Missouri; NUTHALAPATI, N - Mississippi State University; ZHANG, LI - Mississippi State University; KIESS, A - North Carolina State University; DINH, T - Mississippi State University; SUDUMARAN, A - Mississippi State University

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/29/2021
Publication Date: 12/8/2021
Citation: Fancher, C.A., Thames, H.T., Colvin, M.G., Smith, M., Easterling, A., Nuthalapati, N., Zhang, L., Kiess, A., Dinh, T., Sudumaran, A. 2021. Prevalence and molecular characteristics of avian pathogenic Escherichia coli in “No Antibiotics Ever” broiler farms. Microbiology Spectrum. 9(3):e00834-21. https://doi.org/10.1128/Spectrum.00834-21.
DOI: https://doi.org/10.1128/Spectrum.00834-21

Interpretive Summary: Escherichia coli (E. coli) is a bacteria that can cause major infections for poultry. Set backs such as this can take an economical toll on the poultry industry, therefore antibiotics have commonly been used as a preventative measure. Recently, however, there has been a push for “no antibiotics ever” in the food we consume, which has led to more observed E. coli outbreaks. This study aimed to determine E. coli prevalence and to identify antimicrobial properties of E. coli in poultry farms that do not use antibiotics. Various swabs were taken from four farms during the hottest times of year, and E. coli was isolated by PCR and then sampled for five genes that are associated with virulence. All isolated E. coli were tested against 11 antimicrobials. It was shown that E. coli prevalence was not affected by environmental factors; although, virulence factors decreased from spring to summer. The E. coli strains were the most resistance to tetracycline, a class of antibiotics that affects bacterial ribosomes. In conclusion, there is a high prevalence of dangerous E. coli in farms that do not use antibiotics, especially in the spring season.

Technical Abstract: Avian pathogenic Escherichia coli (APEC) causes significant economic and welfare concerns to the broiler industry. For several decades, prophylactic supplementation of antimicrobial growth promoters was the primary method to control APEC; however, the recent shift to no antibiotics ever (NAE) production has increased colibacillosis incidence. The objectives of this study were to determine the influence of season, flock age, and sample type on the prevalence and virulence of E. coli and to identify the serogroups and antimicrobial susceptibility of virulent and nonvirulent E. coli in NAE broiler farms. Litter, feces, cloacal swabs, and tracheal swabs were collected from 4 NAE farms during spring and summer seasons, and E. coli was isolated and confirmed by PCR. Confirmed E. coli isolates were tested for 5 APEC-virulence-associated genes (VAGs) using quantitative PCR (qPCR). Further, E. coli isolates with all five VAGs (100 isolates) and E. coli isolates without any VAGs (87 isolates) were screened against 11 antimicrobials through Kirby-Bauer disk diffusion assay, and their serogroups were tested using PCR. Data were analyzed using the GLIMMIX procedure of SAS 9.4, and statistical significance was determined at a P value of =0.05. Overall, the prevalence of E. coli was not affected by season, flock age, or sample type. However, the prevalence of all tested VAGs decreased from spring to summer (P'='0.002). The frequency of resistance was highest for tetracycline, and serogroups O8 (31%) and O78 (11%) were most frequent in virulent E. coli. In conclusion, there is a high prevalence of virulent E. coli in NAE farms, especially in the spring season.