Antimicrobial resistance, genetic diversity and multilocus sequence typing of Escherichia coli from humans, retail chicken and ground beef in Egypt

Authors: RAMADAN, HAZEM - Mansoura University; Jackson, Charlene; Frye, Jonathan; Hiott, Lari; SAMIR, MOHAMED - Zagazig University; AWAD, AMAL - Mansoura University; Woodley, Tiffanie

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2020
Publication Date: 5/8/2020
Citation: Ramadan, H., Jackson, C.R., Frye, J.G., Hiott, L.M., Samir, M., Awad, A., Woodley, T.A. 2020. Antimicrobial resistance, genetic diversity and multilocus sequence typing of Escherichia coli from humans, retail chicken and ground beef in Egypt. Pathogens. https://doi.org/10.3390/pathogens9050357.
DOI: https://doi.org/10.3390/pathogens9050357

Interpretive Summary: Contamination of retail foods with foodborne pathogens, particularly those that are resistant to antimicrobials, poses a persistent threat to human health. Little is known about Escherichia coli clones circulating among retail food and humans in Egypt. This study aimed to determine diversity of E. coli from humans, retail chicken, and ground beef from Mansoura, Egypt using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Antimicrobial resistance phenotypes, genotypes and phylogrouping of the isolates were also determined. Higher antimicrobial resistance levels were found among chicken isolates compared to beef and human isolates. Regardless of isolate source, the predominant antimicrobial resistances were found against ampicillin, tetracycline, sulfisoxazole, and streptomycin. The prevalent genes detected corresponded with resistance phenotypes. The majority of E. coli from humans, beef, and chicken belonged to commensal phylogroups instead of pathogenic groups. Using PFGE, genetic clusters were a mixture of isolates from different sources. MLST assigned E. coli isolates into both distinct and shared sequence types for the isolates. The existence of common genetic determinants among isolates from retail foods and humans in Egypt as well as the circulation of shared sequence types indicates a possible epidemiological link with potential zoonotic hazards. This data is useful for scientists from various disciplines in order to determine environmental niches of bacterial clones for development of mitigation strategies for foodborne illness.

Technical Abstract: Contamination of retail foods with foodborne pathogens, particularly the antimicrobial resistant ones, poses a persistent threat to human health. Little is known about the overlapped Escherichia coli lineages circulating among retail foods and humans in Egypt. This study aimed to determine the clonal diversity of 120 E. coli isolates from diarrheic patients (n=32), retail chicken carcasses (n=61) and ground beef (n=27) from Mansoura, Egypt using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Simpson index of diversity was calculated to compare the results of both typing methods. Antimicrobial resistance phenotypes, genotypes and phylogrouping of the isolates were also determined. Higher antimicrobial resistances were found among chicken isolates compared to beef and human isolates; regardless of isolate source, the predominant antimicrobial resistances were found against ampicillin (87/120, 72.5%), tetracycline and sulfisoxazole (82/120, 68.3%, each), and streptomycin (81/120, 67.5%). None of the isolates displayed resistance to meropenem. The prevalent genes detected were tetA (64.17%), blaTEM (62.5%), sul1 (56.6%), floR (53.3%), sul2 (50%), strB (48.3%) and strA (47.5%) corresponding with resistance phenotypes. Alarmingly, blaCTX was detected in 63.9% (39/61) of chicken isolates. The majority of E. coli isolates from humans (90.6%), beef (81.5%) and chicken (68.9%) belonged to commensal phylogroups (A, B1, C). Using PFGE analysis, 16 out of 24 clusters (66.7%) contained isolates from different sources at a similarity level =75%. MLST results assigned E. coli isolates into 25, 19 and 13 STs from chicken, human and beef isolates, respectively. Six shared STs were identified including ST1011, ST156, ST48, ST224 (chicken and beef), ST10 (human and chicken) and ST226 (human and beef). Simpson index of diversity was higher for MLST (0.98) than PFGE (0.94). In conclusion, the existence of common genetic determinants among isolates from retail foods and humans in Egypt as well as the circulation of shared STs indicate a possible epidemiological link with potential zoonotic hazards.