Draft Genome Sequence of Kerstersia gyiorum CG1, Isolated from a Leg Ulcer.

We report the first draft genome sequence of Kerstersia gyiorum from a leg ulcer of a patient with diabetes and osteomyelitis. The 3.94-Mb genome assembly included 3,428 annotated coding sequences with an N50 of 223,310 bp and a plasmid encoding a type IV secretion system gene and two antitoxin genes.

GENOME ANNOUNCEMENT

Kerstersia gyiorum is a Gram-negative bacterium of the order Burkholderiales that is occasionally isolated from clinical samples. The Kerstersia genus was described in 2003 based on a polyphasic taxonomic study of Alcaligenes faecalis–like organisms that formed a unique clade (1). Kerstersia members are biochemically very similar to the Alcaligenaceae and can only be speciated by sequence, fatty acid composition, and whole-cell protein lysates. Isolation of K. gyiorum has been reported from a total of five cases of chronic otitis media and eight lower extremity wound infections (1–4). Recently, the first cases of K. gyiorum bacteremia and bronchoalveolar lavage fluid isolations were reported (5, 6).

Because of the lack of a genomic sequence from any members of the genus Kerstersia, we sequenced the first draft genome of K. gyiorum strain CG1. This strain originated from a leg ulcer specimen from a 57-year-old man with a history of diabetes and osteomyelitis. The isolate was identified as a K. gyiorum in our laboratory, based on partial 16S rRNA sequencing, in addition to MALDI-TOF MS analysis.

DNA from K. gyiorum was extracted using the Promega Genomic DNA Wizard kit, and paired-end libraries were constructed using the Nextera XT kit. Sequences were adapted and quality (Q30) trimmed using Cutadapt, de novo assembled using SPAdes version 3.5, and annotated via Prokka version 1.1 (7–10). A total of 5,228,748 paired-end reads with an average length of 208 nucleotides were recovered after trimming. De novo assembly yielded 32 contigs covering a total of 3,943,213 bp with an N50 of 223,310 bp, an average coverage of 260×, and a total of 3,428 annotated coding sequences. The assembled 16S sequence aligned 100% to K. gyiorum S7. Coverage of the rRNA locus suggests that there are likely five copies of rRNA dispersed throughout the genome.

Strain CG1 possesses a 9,094-nucleotide plasmid with 9× greater coverage than the genome and homology to Xanthomonas and Achromobacter spp. plasmids. The plasmid encodes a virB6 type IV secretion system with a putative adenylate kinase–like protein opposed by a VbhA-like antitoxin coding sequence. The plasmid also encodes a second antitoxin sequence in a pemI-like gene. The remaining sequence of the plasmid is devoted to repA (70% amino acid to Paracoccus sp. TRP), ParA, and DNA-invertase hin, along with 5 hypothetical proteins. Antibiotic resistance genes encoded on the chromosome included an aminoglycoside adenylyltransferase (69% amino acid to Mannheimia haemolytica MhSwine 2000) and a chloramphenicol acetyltransferase (80% amino acid to Morganella morganii MM1).

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LBNE00000000.