Clinical manifestations, antimicrobial resistance and genomic feature analysis of the multi-drug resistance Elizabethkingia strains

Abstract

Abstract Background Elizabethkingia are now emerging as an opportunistic pathogenic bacterium in human. The aim of this study is to investigate the clinical epidemiology, antimicrobial resistance, virulence factors, genome features, and comparative genomics of this pathogen. Methods Seven Elizabethkingia isolates were identified by MALDI-TOF MS, and antimicrobial susceptibility testing also was performed. They were conducted whole-genome sequencing (WGS) and compared with a global strain data set, including 83 Elizabethkingia whole-genomes sequences collected from NCBI database. Average nucleotide identity (ANI), pan-genome analysis, and KEGG analyses were performed, and orthologous groups were evaluated. Results A total of 71 Elizabethkingia strains were mainly obtained from the department of ICU (36.6%, 26/71) and emergency (32.4%, 23/71). The number of strains isolated from the respiratory tract specimens was the highest. The mean age of the infected patients was 56.9 years and 64.8% were male. All patients had a history of broad-spectrum antimicrobial exposure. Hospitalization for invasive mechanical ventilation or catheter insertion were found to be the risk factors for infection. Isolates displaced high susceptibility rate to levofloxacin, trimethoprim-sulfamethoxazole, and all were sensitive to minocycline. Genomics analysis revealed that five β-lactamase genes (blaGOB, blaB, blaCME, blaOXA, blaTEM) responsible for β-lactams resistance, seventeen virulence genes involve in stress adaption, adherence and immune modulation. The bulk of the core genomes in the Elizabethkingia genomes were associated with metabolism, according to a function study of the COGs, whereas the unique gene families were largely involved in "information storage and processing." The five type species of the Elizabethkingia genus were identified by pan-genome analysis to have a total of 2,077 clusters of orthologous groups. Conclusion The comparative analysis of the clinical data and associated genomes of patients infected with Elizabethkingia can provide a better understanding of this organism.