Genetic Evaluation of ESBL E. coli Urinary Isolates in Otago

Abstract

The incidence of infections with extended spectrum beta-lactamase (ESBL)-producing E. coli in New Zealand is increasing. ESBL E. coli most commonly cause urinary tract infections and are seen in both community and hospital patients. The reason for the increasing incidence of ESBL E. coli infections is unknown. In this study, 66 urinary ESBL E. coli isolates from Otago in 2015 were fully genetically characterised to understand the mechanisms of transmission. The ESBL gene, E. coli sequence types, plasmid types, and genetic context (e.g. insertion sequences) of ESBL genes were determined by a combination of whole genome and plasmid sequencing. A bioinformatic pipeline was constructed for the hybrid assembly of Illumina short reads and MinION long reads of ESBL-encoding plasmids. Significant diversity of E. coli strains, plasmids, and the genetic context of ESBL genes was seen. This suggests multiple introductions of ESBL resistance genes or resistant bacterial strains accounts for the increased incidence of ESBL E. coli in this low prevalence area. Future studies should investigate modes of transmission of ESBL E. coli and the genes they encode in Otago.