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Open AccessArticle

Antimicrobial Resistance, Genetic Diversity and Multilocus Sequence Typing of Escherichia coli from Humans, Retail Chicken and Ground Beef in Egypt

1
Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA 30605, USA
2
Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
3
Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
4
Bacteriology, Mycology and Immunology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
*
Authors to whom correspondence should be addressed.
Pathogens 2020, 9(5), 357; https://doi.org/10.3390/pathogens9050357
Received: 3 April 2020 / Revised: 28 April 2020 / Accepted: 6 May 2020 / Published: 8 May 2020
(This article belongs to the Special Issue Molecular Microbiology of Foodborne Pathogens)
Contamination of retail foods with foodborne pathogens, particularly the antimicrobial resistant ones, poses a persistent threat to human health. There is a dearth of information about the overlapping Escherichia coli (E. 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’s 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 frequencies of antimicrobial resistance 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 (79/120, 65.8%). None of the isolates displayed resistance to meropenem. The prevalent genes detected were tetA (64.2%), blaTEM (62.5%), sul1 (56.7%), 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 (70.5%) 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 sequence types (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’s 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 indicates a possible epidemiological link with potential zoonotic hazards. View Full-Text
Keywords: Escherichia coli; antimicrobial resistance; humans; retail food; multilocus sequence typing; Egypt Escherichia coli; antimicrobial resistance; humans; retail food; multilocus sequence typing; Egypt
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Ramadan, H.; Jackson, C.R.; Frye, J.G.; Hiott, L.M.; Samir, M.; Awad, A.; Woodley, T.A. Antimicrobial Resistance, Genetic Diversity and Multilocus Sequence Typing of Escherichia coli from Humans, Retail Chicken and Ground Beef in Egypt. Pathogens 2020, 9, 357.

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