Epidemiology of multidrug resistant E. coli isolates from a German university hospital illustrates dominance of E. coli ST131

Our study characterized 301 extended-spectrum beta-lactamases (ESBL) Escherichia coli isolates collected a tertiary hospital in Germany during a during an 18-month period starting from March 2021. All isolates were subjected to long-read whole genome sequencing (lrWGS) to identify resistance genes, type strains and investigate genetic relatedness. Results showed that the sequence type (ST)131 subclade B2 dominates the E. coli population. While carbapenemase genes were rare (n = 7), the most common resistance genes identified were the extended-spectrum beta-lactamase (ESBL) encoding genes bla_CTX-M-15 (26.6 %), bla_CTX-M-27 (18.9 %) and bla_OXA-1 in combination with bla_CTX-M-15 (14.6 %). About half of the isolates were categorized as nosocomial. Epidemiological evaluation and genetic analysis of bacterial isolates identified five probable cases of transmission during hospital admission. 43,7 % (55 isolates) of the E. coli ST131 isolates were detected in urine samples. 23 % of respective patients received antibiotic treatment prior to sample collection. Moreover, we used lrWGS data to investigate the antimicrobial resistance plasmids in the E. coli ST131 isolates. In total, 68 E. coli ST131 carried at least one ESBL gene on a plasmid. Of these, the bla_CTX-M-27 carrying IncF plasmid was detected in 49 isolates. Taken together our study represents a detailed characterization of the ESBL E. coli population in the hospital setting and highlights the role of ST131 E. coli for hospital epidemiology.