Genomic characterisation of three GES-producing Enterobacterales isolated in the Czech Republic

Abstract

Objectives: The aim of the study is to characterise the genomic features of three GES-producing Enterobacterales isolates from Czech hospitals.

Methods: In 2020, during a routine screening of the hospital's surfaces in Prague General Hospital, two strains (CZ862 and CZ863) that belonged to the Enterobacter cloacae complex were found to be bla_GES positive. Another bla_GES positive strain identified as Klebsiella oxytoca was recovered from a patient hospitalised in Pilsen. Antibiotic susceptibility profiling was done with broth microdilution assay. Conjugation/transformation experiments were performed on all three strains. Genomic DNA of the three isolates was subjected to whole genome sequencing using PacBio platform.

Results: Multilocus sequence types typing of CZ862 and CZ863 identified the strains as ST837 and a novel ST (ST1622). Both bla_GES harbouring plasmids showed high sequence similarity and complete query coverage (100% and 99.98%) with pEcl-35771cz. Both plasmids had two copies of bla_GES instead of one copy as found in pEcl-35771cz. The clinical isolate CZ598 belonged to ST180. The plasmid harboured bla_GES-7 gene, cat and aac(6')-lb and the novel variant bla_OXA-1011. No similar sequences were observed, suggesting a novel plasmid.

Conclusion: The detection of the two bla_GES-positive plasmids in the same hospital environment, the first report after 3 years, suggests a hidden source. This highlights the importance of the hidden sources and evolution of such plasmids on the route of spreading into clinical settings. Also, the detection of the new bla_OXA-1011, which is thought in this case to be associated with carbapenem resistance, imposes a health risk if disseminated, limiting therapeutic options.

Keywords: Enterobacter cloacae; Klebsiella michiganensis; bla(GES-1); bla(GES-5); bla(GES-7); bla(OXA-1011).