1d - Hybrid plasmid caused a rapid increase of OXA-48 K. pneumoniae in Lithuania

Background : In 2023 Lithuania noticed a rapid increase in OXA-48-like carbapenemase producing Enterobacterales. An initial genomic investigation revealed a multi-cluster multi-hospital OXA-48 K. pneumoniae outbreak affecting most regions of the country. Such a sudden emergence of multiple clusters of OXA-48 carriers prompted us to expect a plasmid outbreak. To identify the plasmid, long-read sequencing of cluster representatives was conducted.

Methods : All clinical carbapenem-resistant Enterobacterales are referred to the National Reference Laboratory in Lithuania. K. pneumoniae isolates confirmed to carry OXA-48-like-encoding genes by PCR were sequenced using Illumina MiSeq. Clusters were determined with core-genome multi-locus sequence typing. Isolates with < 5 allelic differences were considered to belong to the same cluster. Cluster representatives were further sequenced using long-read Nanopore technology for plasmid determination.

Results : A total of 162 K. pneumoniae isolates from at least 21 Lithuanian hospitals were confirmed to carry OXA-48 and three clusters were identified: ST45 (n=53), ST392 (n=47), and ST395 (n=43). Analysis of short read assemblies also revealed that 149 of these isolates also carried iucABCD, iutA genes coding for the virulence factor aerobactin. Follow-up long read sequencing demonstrated that the OXA-48 gene and aerobactin gene locus are located on a 303 kb IncH1B hybrid plasmid. 

Conclusions : The sudden onset of a multi-cluster, multi-hospital outbreak of OXA-48 producing K. pneumoniae is attributed to the spread of an IncH1B plasmid carrying this carbapenemase gene. In addition, same plasmid also carries the gene locus for virulence factor aerobactin which likely contributed to the success of the pathogen. In light of these findings, an epidemiological investigation was launched to identify factors enabling the spread of this plasmid.