Repatriation of a patient with COVID-19 contributed to the importation of an emerging carbapenemase producer

Abstract

BACKGROUND

Patients hospitalized abroad can become colonized with multidrug-resistant bacteria and import them to their home countries. In this work, we characterized an OXA-484 carbapenemase-producing Escherichia coli strain from a Swiss patient infected by SARS-CoV-2 and repatriated from India.

METHODS

At admission to Switzerland (April, 2021), the patient undertook a molecular nasopharyngeal swab to search for SARS-CoV-2 and a rectal swab to detect multidrug-resistant bacteria. Both SARS-CoV-2 and E. coli isolates were whole-genome sequenced and analyzed for phylogenetic relatedness.

RESULTS

The patient was infected with the SARS-CoV-2 B.1.617.2 lineage (VOC Delta), a lineage that started to be reported across Switzerland at that time. He was also colonized with a sequence type (ST) 410 E. coli strain (L3452210II) producing the OXA-484, a single amino acid variant of OXA-181. The blaOXA-484 was carried by a 51.5 kb IncX3 plasmid identical to those described in blaOXA-181-harboring ST410 E. coli strains. Core-genome analysis showed that L3452210II was identical (∆SNV ≤23) to two ST410 OXA-484 producers recently reported in Qatar and Germany, but differed from other ST410 OXA-181 producers reported worldwide.

CONCLUSIONS

The patient was infected by an emerging SARS-CoV-2 variant, and also imported an E.coli producing OXA-484, an OXA-48-like carbapenemase not yet reported in Switzerland. The genetic background of L3452210II indicated that the blaOXA-484 shared the same plasmid of blaOXA-181, but its bacterial host differed from most of the pandemic OXA-181-producing ST410 strains previously reported. This case description underlines that the COVID-19 crisis can contribute to the worldwide spread of emerging carbapenemase producers.