Genotypic and phylogenetic characterisation of a clinical Ralstonia pickettii strain carrying two novel OXA allelic variants, blaOXA-898 and blaOXA-899, isolated from a bloodstream infection in China

Abstract

ObjectivesRalstonia pickettii has been increasingly recognised as an emerging opportunistic pathogen in hospital settings in recent years, especially in patients with prolonged hospital stay. Clinical manifestations associated with R. pickettii infection range from mild infections to severe invasive life-threatening infections. Here we report the genome sequence of a clinical R. pickettii strain (PSLESD1) carrying two novel blaOXA allelic variants in China. MethodsWhole-genome sequencing of strain PSLESD1 was performed using an Illumina NovaSeq 6000 platform. Antimicrobial resistance genes were identified using the BacWGSTdb server. The phylogenetic relationship betweenR. pickettii PSLESD1 and a total of 17 R. pickettii strains deposited in the NCBI GenBank database was analysed using NJ (neighbour joining)/UPGMA (unweighted pair-group method with arithmetic mean) phylogeny (MAFFT v.7) based on core genome single nucleotide polymorphism (SNP) data. ResultsThe draft genome sequence of R. pickettii strain PSLESD1 consists of 25 contigs comprising 5 267 333 bp. Three antimicrobial resistance genes were identified in the genome, including blaOXA-898, blaOXA-899 and sul2. Strain PSLESD1 was resistant to aminoglycosides and carbapenems including meropenem. Phylogenetic analysis showed that all strains retrieved from the NCBI GenBank database were epidemiologically unrelated. The closest relative of strain PSLESD1 was H2Cu2, which differed by 2908 SNPs. ConclusionIn summary, we report the first genome sequence of a clinicalR. pickettii strain harbouring two novel class D β-lactamase genes (blaOXA-898 and blaOXA-899) recovered from a bloodstream infection in China. These data may help to understand the genomic features and antimicrobial resistance mechanisms of this bacterial pathogen.