Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source

Abstract

We report here the draft genome sequence of a multidrug-resistant clinical isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, KP_Z4175. This strain, isolated as part of a hospital infection-control screening program, is resistant to multiple β-lactam antibiotics, aminoglycosides, and trimethoprim-sulfamethoxazole.

GENOME ANNOUNCEMENT

Klebsiella quasipneumoniae, formerly Klebsiella pneumoniae phylogroup KpII, was recently taxonomically reclassified as a new sister species of K. pneumoniae with two subspecies, K. quasipneumoniae subsp. quasipneumoniae and K. quasipneumoniae subsp. similipneumoniae (1). K. quasipneumoniae, like K. pneumoniae, can cause human infections but is considered less pathogenic and more often associated with carriage than clinical disease (1, 2). However, severe human infections with K. quasipneumoniae have been reported (3, 4). Here, we report the draft genome sequence of a multidrug-resistant K. quasipneumoniae subsp. similipneumoniae strain, isolated from the gastrointestinal tract of a hospitalized patient.

K. quasipneumoniae subsp. similipneumoniae strain KP_Z4175 was isolated from a screening rectal culture obtained for infection control purposes from a 53-year-old patient. The patient had a remote history of simultaneous pancreas-kidney transplant, was currently receiving immunosuppressive treatment, and had recently undergone colectomy for an obstructing cecal lymphoma. He was admitted to a tertiary care hospital with increased ostomy output that resolved with medical management. There were no signs of active infection throughout the hospitalization. The isolate was identified as having extended-spectrum β-lactamase activity by CLSI double-disk diffusion Kirby-Bauer testing (5).

KP_Z4175 DNA was sequenced on the MiSeq platform (Illumina Inc., San Diego, CA, USA) generating 2 × 301-bp paired-end reads. A total of 15,256,306 reads were produced comprising 1,540,886,906 bases after adapter sequence trimming. De novo assembly was performed using SPAdes version 3.6.2 (6, 7) to generate 97 contigs at least 200 bp in length for a total sequence of 5,598,139 bp. The assembly N₅₀ was 332,350 bp, and the average GC content was 57.6%. Annotation was performed by the NCBI Prokaryotic Genome Annotation Pipeline and contained 5,398 coding sequences. Speciation was confirmed by fusA, gapA, gyrA, leuS, and rpoB analysis (1) and predicted DNA-DNA hybridization of 93.7% against K. quasipneumoniae subsp. similipneumoniae strain 07A044 (accession no. CBZR00000000) using the GGDC 2.1 software (8).

To examine the antibiotic resistance profile of K. quasipneumoniae subsp. similipneumoniae strain KP_Z4175, antibiotic resistance genes were identified using ResFinder version 2.1 (9). In addition to bla_OKP-B-1, a β-lactamase characteristic of K. quasipneumoniae (10), β-lactamase bla_OXA-10 and the extended-spectrum β-lactamase bla_SHV-12 were identified. Also identified were three aminoglycoside resistance genes (aadA1, aacA4, and aac(6′)-IIc), two fluoroquinolone resistance genes (aac(6′)Ib-cr and QnrB4), one macrolide-lincosamide-streptogramin B resistance gene (ere(A)), two phenicol resistance genes (cmlA1 and floR), one rifampin resistance gene (ARR-2), two sulfonamide resistance genes (sul1 and sul2), one tetracycline resistance gene (tet(D)), and one trimethoprim resistance gene (dfrA14). All identified resistance genes had nucleotide identities of 98.35 to 100% over 85 to 100% of the reference gene lengths. Broth microdilution testing using CLSI breakpoints for Enterobacteriaceae indicated that KP_Z4175 is resistant to gentamicin (MIC >64), tobramycin (=32), cefazolin (>64), ceftriaxone (>64), aztreonam (>64), and trimethoprim-sulfamethoxazole (>64). The isolate had intermediate resistance to ampicillin-sulbactam (=16) and pipericillin/tazobactam (=32), and was sensitive to ertapenem (≤0.03), imipenem (=1), meropenem (≤0.03), amikacin (=0.5), cefepime (=8), and ciprofloxacin (=1).

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number LVCD00000000. The version described in this paper is version LVCD01000000.