Antibiotic susceptibility and genomic analysis of ciprofloxacin-resistant and ESBLs-producing Escherichia coli in vegetables and their irrigation water and growing soil

Abstract

The rise of antibiotic resistance in Escherichia coli has become a major global public health concern. While there is extensive research on antibiotic-resistant E. coli from human and animal sources, studies on vegetables and their environments are limited. This study investigated the prevalence and characteristics of ciprofloxacin-resistant (CIP^R) E. coli in 13 types of edible raw vegetables, along with their irrigation water and soil in Shaanxi, China. Of 349 samples collected (157 vegetables, 59 water, and 133 soil), a total of 48 positive samples were detected, with one CIP^RE. coli strain isolated from each sample being selected for further analyses. A striking observation was its high prevalence in irrigation water at 44.1 %, markedly exceeding that in vegetables (12.0 %) and soil (4.5 %). The susceptibility of Forty-eight CIP^RE. coli isolates was evaluated using the disc diffusion method for 18 different antibiotics, all these isolates were not only resistant to the tested fluoroquinolones antibiotics (levofloxacin, nalidixic acid), but also displayed a multi-drug resistance (MDR) pattern. Twenty-eight (58.3 %) of 48 CIP^RE. coli isolates exhibited extended spectrum β-lactamases (ESBLs) (CIP^R-ESBLs) producing phenotype. Subsequently, whole-genome sequencing was performed on these 28 isolates. We identified 12 serotypes and STs each, with O101: H9 (35.7 %, 10/28) and ST10 (21.4 %, 6/28) being the most common. Further classification placed these isolates into five phylogenetic groups: A (57.1 %, 16/28), B1 (32.1 %, 9/28), D (3.6 %, 1/28), B2 (3.6 %,1/28), and F (3.6 %,1/28). Notelly, Identical ST types, serotypes and phylogroups were found in certain CIP^R-ESBLs-producing E. coli from both vegetables and adjacent irrigation water. Genomic analysis of the 28 CIP^R-ESBLs-producing E. coli isolates unveiled 73 resistance genes, associated with 13 amino acid mutations in resistance-determining regions (QRDRs) and resistance to 12 types of antibiotics. Each isolate was confirmed to carry both ESBLs and fluoroquinolone resistance genes, with the Ser83Ala mutation in GyrA (96.4 %, 27/28) being the most prevalent. A detailed analysis of Mobile Genetic Elements (MGEs) revealed that IncFIB and IncFII plasmid subtypes were most prevalent in 60.7 % and 67.9 % of isolates, respectively, with 75 % containing over 10 insertion sequences (IS) each. Furthermore, we observed that certain ESBL and PMQR genes were located on plasmids or in proximity to insertion sequences. In conclusion, our research highlights the widespread presence of CIP^RE. coli in irrigation water and thoroughly examines the genetic characteristics of CIP^R-ESBLs-producing E. coli strains, underlining the need for ongoing monitoring and management to reduce multidrug-resistant bacteria in vegetables and their environment.

Keywords: Ciprofloxacin-resistant Escherichia coli; ESBLs; Irrigation water; Soil, whole-genome sequencing; Vegetables.