Complete genome sequence of an Enterococcus devriesei strain isolated from Zophobas morio larvae

Objectives

Enterococcus spp. are typically found in multiple settings and are sometimes responsible for difficult-to-treat infections. In this context, very little is known about Enterococcus devriesei (E. devriesei), a rare species first isolated from a river lamprey. Importantly, no complete genome of E. devriesei currently exists in public repositories.

Methods

An E. devriesei strain (Ed-CK-24) was isolated from homogenized Zophobas morio (Z. morio) larvae. Initial species identification (ID) was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing (AST) was performed by broth microdilution. Whole-genome sequencing (WGS) was done using both Illumina NovaSeq 6000 and Nanopore MinION to generate a complete genome assembly. WGS data were used to confirm species ID, antimicrobial resistance genes (ARGs) and plasmid replicon sequences screening. A database search for other E. devriesei genomes in National Center for Biotechnology Information (NCBI) was performed and used for 16S rRNA and core-genome phylogeny analyses.

Results

WGS and bioinformatic analyses were performed, resulting in a complete genome assembly and allowing accurate taxonomic classification of Ed-CK-24 strain as E. devriesei. Alignment of 16S rRNA sequences of representative Enterococcus spp. further supported the ID of Ed-CK-24. A core-genome phylogenetic analysis revealed no clonal relationships between Ed-CK-24 and other E. devriesei derived from multiple sources. The Ed-CK-24 strain was resistant to clindamycin and quinupristin/dalfopristin. ARG screening identified the lsa(A) gene, carried on a 633,497 bp circular megaplasmid.

Conclusions

WGS of Ed-CK-24 allowed high-resolution genomic comparison and epidemiologic analysis of E. devriesei. Its isolation from Z. morio larvae, commonly used in pet food, warns for further surveillance as the human pathogenic potential of this species remains unknown.