Klebsiella grimontii, a New Species Acquired Carbapenem Resistance

Abstract

Klebsiella grimontii is a newly identified species closely related to Klebsiella oxytoca, but carbapenem resistance was not identified in the species before. We found a carbapenem-resistant K. oxytoca-like clinical strain, WCHKG020121. The strain was subjected to whole genome sequencing using Illumina HiSeq X10. The precise species identification was established based on average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) between strain WCHKG020121 and type strains of Klebsiella species. Antimicrobial resistance genes were identified from the genome sequence. The sequence of the bla _KPC-2-carrying plasmid was completed using PCR and Sanger sequencing. Conjugation experiments were performed to obtain the plasmid carrying bla _KPC-2. All K. grimontii genomes were retrieved from GenBank and were analyzed for antimicrobial resistance genes. Strain WCHKG020121 was resistant to imipenem and meropenem (MIC for both, 32 μg/ml) but was susceptible to colistin (1 μg/ml). Strain WCHKG020121 was initially identified as K. oxytoca using Vitek II but it actually belongs to K. grimontii as it had a 98.81% ANI and 83.4% isDDH value with K. grimontii type strain. Strain WCHKG020121 had bla _KPC-2; by contrast, none of other K. grimontii genomes carry any known carbapenemase genes. bla _KPC-2 was carried by a 95,734-bp plasmid, designated pKPC2_020121, which contained two different FII(Y) replicons. pKPC2_020121 was closest (93% coverage, 99% identity) to bla _KPC-2-carrying plasmids from Enterobacter hormaechei recovered in 2014 at the same hospital. pKPC2_020121 was not self-transmissible, which could be explained by the absence of a conjugation essential gene, traY. In conclusion, we reported the first K. grimontii strain that produced the KPC carbapenemase. Carbapenem resistant K. grimontii may represent a new threat.

Keywords: KPC-2; Klebsiella; Klebsiella grimontii; Klebsiella oxytoca; carbapenemase.

FIGURE 1

pKPC2_020121 vs. pKPC2-EC14653. pKPC2_020121 (in pink) is aligned with pKPC2-EC14653 (GenBank accession no. KP868646; in light blue), a plasmid from E. hormaechei recovered in 2014 at our hospital, using BRIG (Alikhan et al., 2011). pKPC2_020121 has two FII(Y) replicon, while pKPC2-EC14653 has one. GC content and GC skew are indicated. The genetic context of bla_KPC-2 is shown in Figure 2. The annotation of the genetic components were added manually using the Microsoft PowerPoint program.

FIGURE 2

The genetic context of bla_KPC-2 on pKPC2_020121 and pKPC2-EC14653. The genetic context of bla_KPC-2 on pKPC2_020121 is compared with that on pKPC2-EC14653 with the identical region highlighted in gray. Poles in black are the inverted repeats (IR) of Tn3, while poles in cyan are the IR of Tn1722. orfs without known function are indicated by numbers 1–5. This figure was drawn manually using the Microsoft PowerPoint program.