Molecular characteristics and comparative genomics analysis of a clinical Enterococcus casseliflavus with a resistance plasmid

Abstract

Purpose: The aim of this work was to investigate the molecular characterization of a clinical Enterococcus casseliflavus strain with a resistance plasmid.

Materials and methods: En. casseliflavus EC369 was isolated from a patient in a hospital in southern China. The minimum inhibitory concentration was found by means of the agar dilution method to determine the antimicrobial susceptibilities of the strains. Whole-genome sequencing and comparative genomics analysis were performed to analyze the mechanism of antibiotic resistance and the horizontal gene transfer of the resistance gene-related mobile genetic elements.

Results: En. casseliflavus EC369 showed resistance to erythromycin, kanamycin, and streptomycin, but was susceptible to vancomycin, ampicillin, and streptothricin and other antimicrobials. There were six resistance genes (aph3', ant6, bla, sat4, and two ermBs) carried by a transposon identified on the plasmid pEC369 and a complete resistance gene cluster of vancomycin and a tet (M) gene encoded on the chromosome. This is the first complete plasmid sequence reported in clinically isolated En. casseliflavus. The plasmid with the greatest sequence identity with pEC369 was the plasmid of Enterococcus sp. FDAARGOS_375, followed by the plasmids of Enterococcus faecium strains F12085 and pRE25, whereas the sequence with the greatest identity to the resistance genes carrying a transposon of pEC369 was on the chromosome of Staphylococcus aureus strain GD1677.

Conclusion: The resistance profiles of En. casseliflavus EC369 might contribute to the resistance genes encoded on the plasmid. The fact that the most similar sequence to the transposon carrying resistance genes of pEC369 was encoded in the chromosome of a S. aureus strain provides insights into the mechanism of dissemination of multidrug resistance between bacteria of different species or genera through horizontal gene transfer.

Keywords: Enterococcus casseliflavus; antimicrobial resistance; comparative genomics analysis; molecular characteristics; transposon.

Figure 1

The circular map of the pEC369 genome and comparative genomic analysis of the plasmids. Notes: Figuring from outside to inside: 1, the plasmid of Enterococcus sp. FDAARGOS_375; 2, the plasmid of pRE25; 3, the plasmid of Enterococcus faecium strain F12085; 4, the genes encoded on pEC369 with the hypothetical ORFs in brackets; 5, GC content with the G+C content >50% toward the outside rather than inside; 6, GC skew (G–C/G+C) with a positive GC skew toward the outside and a negative GC skew toward the inside; and 7, the most inner circle, scale in bp. Abbreviation: ORFs, open reading frames.

Figure 2

Comparative genomics analysis of the transposon-related region of pEC369. Notes: The sequence with the highest identity to the resistance gene-related region of pEC369 was that of the chromosome sequence of Staphylococcus aureus strain GD1677, and the sequence with the highest identity to the flanking regions of the transposon was the sequence of pVEF1. Black triangles represent the IRs at both ends of the transposon. Nucleotide letters under the black triangles represent DRs. The identical sequence regions are connected with light blue bars. The predicted proteins without direct gene names are illustrated as: orfA, tetronasin resistance protein; orfB, zeta-toxin; orfC, antitoxin; orfD and orfE, peptide-binding proteins; orfF, resolvase; orfG, FAD-dependent thymidylate synthase; and orfH dihydrofolate reductase. Abbreviation: DRs, direct repeats; IRs, inverted repeats.