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.
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
blaOKP-B-1, a β-lactamase characteristic of
K. quasipneumoniae (
10), β-lactamase
blaOXA-10 and the extended-spectrum β-lactamase
blaSHV-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).