Whole-genome sequencing and molecular analysis of carbapenem-resistant Escherichia coli from clinical samples collected in the framework of the EURGen-Net CCRE survey, Italy 2019.

INTRODUCTION

Carbapenem-resistant (CR)-Enterobacterales are a serious threat to public health worldwide. However, there are limited surveillance data on the molecular epidemiology of CR-Escherichia coli. To address this need, the European Centre for Disease Prevention and Control (ECDC) investigated the molecular epidemiology of CR-E. coli in the carbapenem- and/or colistin-resistant Enterobacterales (CCRE) survey launched in 2019, involving 37 European countries, including Italy.

METHODS

In 2019, 46 acute-care hospitals in Italy were enrolled to collect the first 10 non-duplicated consecutive isolates of carbapenem non-susceptible Klebsiella pneumoniae specie complex or E. coli isolates and 10 carbapenem-susceptible comparator isolates of the same species. Each isolate was subjected to antibiotic susceptibility testing. WGS analysis was performed using Illumina technology to determine the ST and to detect resistance genes, virulence factors, and plasmid content.

RESULTS

A total of 61 E. coli isolates were collected from 17 hospitals: 17 CR-E. coli isolates (from urine, 41.2%, and blood, 23.5%) and 44 carbapenem-susceptible (CS)-isolates (from blood, 43.2%, and urine, 38.6%). All the CR-E. coli isolates were resistant to amoxicillin/clavulanic acid, cefepime, ceftazidime and piperacillin/tazobactam; three were resistant to ceftazidime/avibactam and all were susceptible to amikacin and tigecycline. MLST analysis showed the presence of unrelated lineages: CR-E. coli isolates belonged to 8 different STs, with ST131 predominant (58.8%). All the CR-E. coli isolates carried one carbapenemase: KPC-3 (10 isolates), KPC-2 (three), NDM-5 (two), VIM-1 and OXA-181 (one each). Among CS-E. coli isolates, the highest resistance rates were observed for amoxicillin/clavulanic acid (36.4%) followed by ciprofloxacin, and trimethoprim/sulfamethoxazole, and ST131, carrying CTX-M-15, was the predominant clone.

DISCUSSION: CR-E. coli clones from infection showed a heterogeneous genetic background, ST131 being the most frequent. KPC was the most common carbapenemase but the presence of E. coli isolates carrying NDM-5 is worrisome, as it results in resistance to several novel beta-lactam-beta-lactamase combinations. Our study underlines the importance of genomic surveillance to monitor and prevent the spread of high-risk clones causing difficult-to-treat infections.