Comparison of multidrug-resistant extraintestinal pathogenic Escherichia coli from human, foods and animals to investigate the possible chains of transmission

Background Globally, antimicrobial drug resistant Escherichia coli is the most common etiological agent of invasive disease in humans. In Europe, increasing proportions of infections due to third generation cephalosporins (3GCs) and/or fluoroquinolone resistant extraintestinal pathogenic E. coli (ExPEC) strains are reported. It has been shown that multidrug resistant (MDR) E. coli can be transmitted from animals to humans and based on existing evidence, poultry is the food animal source most closely linked to human E. coli. However, lack of reliable data makes it difficult to assess the attributable risk of different food sources and their impact on human health. Objectives In the present study, our objective was to investigate the antimicrobial resistance profile, phylogenetic background and virulence factors of E. coli isolates from broiler chicken meat sold at retail in Palermo, Italy and to compare with the geographically and temporally matched collection of isolates from humans with infections due to this bacterium. Materials and Methods Isolation of MDR E. coli was performed during April 2013-December 2014 on a total of 250 food samples including 180 raw broiler chicken meat , 17 pork meat , 14 cow meat 19 cheese and 20 ready to eat foods samples and a total of 200 de-identified FQ-R and ESBL-producing E. coli isolates were collected from Ospedale Civico in Palermo , Italy. Susceptibility to a panel of nine antimicrobial agents was determined and the isolates resistant to at least three classes of antibacterial drugs were defined as MDR. PCR assays were carried out to detect extended spectrum β-lactamase (ESBL), plasmid-mediated AmpC β-lactamase and plasmid-mediated quinolone resistance (PMQR) genes, phylogenetic group and ExPEC-associated traits. A single nucleotide polymorphism (SNP) PCR was done to detect E. coli sequence type (ST)131. Enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) and Raman spectroscopy were performed to analyze the relatedness among ExPEC isolates. Results E. coli were isolated from all of the chicken samples. However, multi-drug resistant (MDR) E. coli were isolated from 152 (84.4%) of the 180 chicken samples. No MDR E. coli isolates were found in other types of food samples. B1 was the most prevalent (114 isolates, 48.1%) followed by groups D (80 isolates, 33.7%), A (30 isolates, 12.7%) and B2 (13 isolates, 5.5%); phylogenetic group B2 was the most prevalent phylogroup among clinical isolates (136 isolates, 68.5%) followed by groups D (33 isolates, 16.8%), A (20 isolates, 10.6%) and B2 (9 isolates, 4.6%), respectively. ESBLs and AmpC β-lactamases were detected by PCR in 233 (98.3%) and 29 (12.2%) of chicken meat isolates and 194 (97.5%) and 34 (17.2%) of clinical isolates, respectively. PMQR determinants were detected in 215 (90.7%) of chicken isolates and 183 (91.9%) of clinical isolates, respectively. Based on the molecular definition of ExPEC, 58 and 156 isolates from chicken meat and clinical samples were attributed with the status of ExPEC . SNP-PCR results confirmed that a total of 91.9% (125/136) and 69.2% (9/13) of the clinical and chicken meat isolates of E. coli of B2 phylogroup population were identified as ST131, respectively. Both ERIC-PCR and Raman Spectroscopy analysis showed a large heterogeneity among isolates. Conlusion The results of this study show an alarmingly high prevalence of MDR E. coli and especially ExPEC isolates from broiler chicken meat in our geographic area. The ongoing use of antimicrobial drugs in livestock should be urgently revised and stopped, particularly in the poultry sector.