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

Abstract

Objectives: Patients hospitalised abroad can become colonised with multidrug-resistant bacteria and import them to their home countries. In this study, we characterised 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 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 analysed for phylogenetic relatedness.

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

Conclusion: 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 bla_OXA-484 shared the same plasmid as bla_OXA-181, but its bacterial host differed from most of the pandemic OXA-181-producing ST410 strains reported previously. This case description underlines that the COVID-19 crisis can contribute to the worldwide spread of emerging carbapenemase producers.

Keywords: Carbapenemase; IncX3; OXA-48; OXA-484; Plasmid; SARS-CoV-2.

Fig. 1

BLASTn comparison of plasmid pL3452210II_3 (GenBank accession no. CP076530) against similar sequences. Plasmid sequences were selected based on high homology to pL3452210II_3 in a BLASTn search against the NCBI non-redundant nucleotide database (date of access 9 June 2021). Rings were constructed using BRIG (BLAST Ring Image Generator) v.0.95. Coloured rings represent similarities to the reference sequence. For each sequence we report GenBank accession, species of isolation, sequence name, plasmid size and carbapenemase gene. Coding sequences (CDS) are represented as arrows in the outermost circle. Mobile genetic elements are depicted in blue, antimicrobial resistance genes in red, and other CDS in grey.

Fig. 2

Core genome analysis for Escherichia coli L3452210II (in red) and 75 E. coli ST410 possessing bla_OXA-484 or bla_OXA-181 obtained from the NCBI genome collection and Enterobase (date of access 15 June 2021). Core genome analysis of the whole-genome sequencing (WGS) assemblies is presented in a single nucleotide variant (SNV) hierarchical clustering dendrogram tree. The ΔSNV values correspond to the number of non-identical SNVs between two strains within a clade. We indicate association of the isolate with previous stay abroad (Link), country of origin, source of isolation and year of isolation. IND, India; QAT, Qatar; HKG, Hong Kong; NED, the Netherlands; PAK, Pakistan; DEN, Denmark; AUS, Australia; CAN, Canada; USA, United States of America; GBR, United Kingdom; SUI, Switzerland; GER, Germany; NGR, Nigeria; THA, Thailand; MYA, Myanmar; CRO, Croatia; LBN, Lebanon; SWE, Sweden; EGY, Egypt; ICU, intensive care unit; env., environment; na, not available.