Genome Sequence of Klebsiella oxytoca 11492-1, a Nosocomial Isolate Possessing a FOX-5 AmpC β-Lactamase

Abstract

Klebsiella oxytoca strain 11492-1 was isolated from a perianal swab culture from a patient at the University of Maryland Medical Center in 2005. The K. oxytoca 11492-1 draft genome contains multiple antibiotic resistance genes, including a FOX-5 AmpC β-lactamase encoded on a large IncA/C plasmid.

GENOME ANNOUNCEMENT

The genus Klebsiella is comprised of diverse organisms that range from nitrogen-fixing plant endosymbionts (6, 11) to nosocomial pathogens capable of causing pneumonia, septicemia, meningitis, and urinary tract infections in humans (12, 14). In addition, K. pneumoniae has been linked to the occurrence of pyogenic liver abscesses, which were originally described in Taiwan but have been reported globally in recent years (5, 9, 13). K. pneumoniae is a significant nosocomial pathogen often encoding multiple antibiotic resistance markers. K. oxytoca is less frequently associated with human disease (7, 12); however, K. oxytoca has recently been linked to antibiotic-associated hemorrhagic colitis (8).

K. oxytoca 11492-1 was isolated from a perianal swab culture from a patient in the intensive care unit (ICU) at the University of Maryland Medical Center (UMMC) in April 2005. There were no K. oxytoca isolates cultured from this patient on either surveillance cultures or clinical cultures upon admission of the patient to the UMMC ICU, suggesting that the patient most likely acquired the isolate while residing in the ICU. K. oxytoca was also isolated from a blood culture during the same admission, suggesting that this patient had a systemic K. oxytoca infection.

K. oxytoca was identified by API 20E and Vitek 2 biochemical assays (bioMérieux). In addition, K. oxytoca 11492-1 was indole positive, as are other K. oxytoca isolates, and encodes a bla_OXY-2 β-lactamase (10). BLAST analysis of a partial 16S rRNA gene sequence (991 nucleotides) from the draft genome of K. oxytoca 11492-1 exhibited 99% nucleotide identity over the entire sequence length to the 16S rRNA gene of K. oxytoca ATCC 13182T (KOU78183). Genomic DNA was isolated from an overnight culture using the Sigma GenElute kit (Sigma-Aldrich). The genome sequence of K. oxytoca 11492-1 was generated using paired-end libraries with 300-bp inserts on the Illumina HiSeq2000. The draft genome is 6.18 Mb with approximately 95× sequence coverage and was assembled using the Velvet assembly program (15). The final assembly includes 213 contigs after filtering for contigs of >200 bp.

Antibiotic susceptibility was determined by disk diffusion assays (4), which demonstrated that K. oxytoca 11492-1 is resistant to broad-spectrum cephalosporins and sulfamethoxazole-trimethoprim. K. oxytoca 11492-1 also contains a large IncA/C plasmid encoding a FOX-5 AmpC β-lactamase.

Bioinformatic detection of previously identified K. pneumoniae virulence-associated genes demonstrated that K. oxytoca 11492-1 does not carry genes associated with the mucoid phenotype (1). Interestingly, the K. oxytoca 11492-1 genome does contain genes for allantoin metabolism, which is an anaerobic process associated primarily with K. pneumoniae isolates from liver abscesses (3). Additionally, the K. oxytoca 11492-1 genome has citrate fermentation genes, which were previously identified in some clinical K. pneumoniae isolates such as the MGH 78578 sputum isolate (2) and the nitrogen-fixing plant endosymbiont K. pneumoniae 342 (6).

K. oxytoca 11492-1 possesses a unique combination of virulence, antibiotic resistance, and metabolic genes that highlight the need for additional studies into the genomic diversity of K. oxytoca. To our knowledge, this is the first-described K. oxytoca genome in the public domain.

Nucleotide sequence accession number.

The 11492-1 draft genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession number AIEM01000000.