Abstract
Kingella kingae is a betaproteobacterium from the order Neisseriales, and it is an agent of invasive infections in children. We sequenced the genome from the septic arthritis strain 11220434. It is composed of a 1,990,794-bp chromosome but no plasmid, and it contains 2,042 protein-coding genes and 52 RNA genes, including 3 rRNA genes.
GENOME ANNOUNCEMENT
Kingella kingae is a commensal Gram-negative inhabitant of the human oropharyngeal epithelium, especially in young children (12). The organism is fastidious, and its detection has been recently improved by seeding bone and synovial fluid exudates into blood culture vials and an increasing use of nucleic acid amplification techniques (12). Use of these novel methods has revealed that K. kingae is the most common etiology of skeletal system infections in children ages 6 to 36 months (3).
The organism penetrates the upper respiratory tract mucosa, invades the bloodstream, and disseminates to bones, joints, or the endocardium (12). Kingella kingae is usually susceptible to β-lactam antibiotics, fluoroquinolones, and cotrimoxazole and, with the exception of cases of endocarditis, infections run a benign clinical course and leave no permanent sequelae (12). Despite the increasing recognition of the organism as an important human pathogen, our knowledge of the physiology of the bacterium and its virulence factors remains limited and, to the best of our knowledge, the genomes of only two K. kingae isolates have been fully sequenced so far (4). We report the draft genome of K. kingae strain 11220434, which was isolated from the knee joint of a 19-month-old boy with acute arthritis, and compare it to those of strains PYKK081 and ATCC 23330 (4).
Genomic DNA isolated from K. kingae strain 11220434 grown on chocolate agar (bioMérieux) was pyrosequenced using the 454 GS FLX titanium platform (Roche, Branford, CT) and both the shotgun and paired-end strategies (7). The information was assembled using the Newbler software (Roche). A total of 534,235 reads (99,350,913 bp) were obtained (ca. 59-fold coverage). The draft genome of K. kingae 11220434 consists of 159 unique contigs, arranged into one final scaffold, and contains 1,990,794 bp with a G+C content of 46.7%. Potential coding sequences (CDSs) were predicted using Prodigal (http://prodigal.ornl.gov/) using the default parameters, but the predicted open reading frames were excluded if they spanned a sequencing gap region. Assignment of protein functions was performed by searching against the GenBank, Clusters of Orthologous Groups, and Pfam databases by using BLASTP (1, 9, 10, 11). Of the 2,042 CDSs that were identified, representing a coding capacity of 1,722,045 bp (88.1% of the complete genome), 1,518 were assigned a putative function (74.3%). Using BLASTN, tRNAscan-SE (6), and RNAmmer, the genome was shown to contain 52 RNA genes, including a single rRNA operon, 48 tRNAs, and 1 tmRNA.
Comparison with the genomes from K. kingae strains PYKK081 (GenBank accession number AJGB00000000), another arthritis strain, and the nasal strain ATCC 23330 (AFHS01000000) by using RAST (2) showed that the synteny was almost perfectly conserved. Comparison with strain PYKK081 showed that strain 11220434 exhibited 111 unique genes, including genes encoding proteins classified within the following functional categories: toxin-antitoxins (7), conjugation (3), virulence (7), phages (6), transposases (1), and hypothetical proteins (74).
Nucleotide sequence accession number.
The K. kingae 11220434 genome sequence was deposited in GenBank under accession number ALIJ00000000.
ACKNOWLEDGMENT
This research did not benefit from any external funding.
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