Epidemiological and genomic features of clinical isolates of the Elizabethkingia genus in Taizhou City, China

Abstract

Objective: Elizabethkingia species usually exhibit resistance to multiple antibiotics, and inappropriate antimicrobial therapy is a major cause of mortality in patients with Elizabethkingia infection. Our study aimed to comprehensively analyse and compare the genomic and clinical features of three Elizabethkingia species. Methods: Matrix-assisted laser desorption/ionization–time of flight mass spectrometry and whole-genome sequencing were used to identify 88 Elizabethkingia isolates from 88 patients in the past 6 y. Phylogenetic tree and Sankey diagram analysis were used to compare the strains with metallo-β-lactamase resistance genes and 49 Elizabethkingia miricola strains with evolutionary relationships. Results: The identified Elizabethkingia species included Elizabethkingia anophelis (65/88, 73.9%), Elizabethkingia meningoseptica (8/88, 9.1%), and E. miricola (15/88, 17.0%). Multivariate analysis showed that co-isolated with Pseudomonas aeruginosa (odds ratio: 40.83, 95% confidence interval: 3.05–546.29, P = 0.005) and antimicrobial exposure to carbapenems (odds ratio: 5.76, 95% confidence interval: 1.00–248.32, P = 0.050) were independent risk factors for in-hospital mortality. Whole-genome sequencing and phylogenetic tree analysis revealed all 88 strains with 22 BlaBlaB and 19 BlaGOB variants. In particular, the specific combinations of BlaB and GOB subtypes differed in three Elizabethkingia species. All Elizabethkingia species harboured drug-resistance genes adeF, vanT, and vanW and shared 32 virulence-associated genes. Global phylogenetic evolution of E. miricola showed a dispersal in Chinese clinical isolates and did not display outbreak possibility. Conclusions: Variations in resistance and virulence genes are associated with the natural resistance and pathogenicity of Elizabethkingia. Increased genomic monitoring is recommended for a deeper understanding of the pathogenic mechanisms of Elizabethkingia spp.

Keywords

• Elizabethkingia
• Whole-genome sequencing
• Genomic features
• Metallo-β-lactamase