Emergence of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Coharboring a blaNDM-1-Carrying Virulent Plasmid and a blaKPC-2-Carrying Plasmid in an Egyptian Hospital

Abstract

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and analysis of the plasmids associated with carbapenem-resistant hypervirulent K. pneumoniae (CR-HvKP) in Egypt have not been presented. Therefore, we attempted to decipher the plasmid sequences that are responsible for transferring the determinants of carbapenem resistance, particularly bla_NDM-1 and bla_KPC-2 Out of 34 K. pneumoniae isolates collected from two tertiary hospitals in Egypt, 31 were CRKP. Whole-genome sequencing revealed that our isolates were related to 13 different sequence types (STs). The most prevalent ST was ST101, followed by ST383 and ST11. Among the CRKP isolates, one isolate named EBSI036 has been reassessed by Nanopore sequencing. Genetic environment analysis showed that EBSI036 carried 20 antibiotic resistance genes and was identified as a CR-HvKP strain: it harbored four plasmids, namely, pEBSI036-1-NDM-VIR, pEBSI036-2-KPC, pEBSI036-3, and pEBSI036-4. The two carbapenemase genes bla_NDM-1 and bla_KPC-2 were located on plasmids pEBSI036-1-NDM-VIR and pEBSI036-2-KPC, respectively. The IncFIB:IncHI1B hybrid plasmid pEBSI036-1-NDM-VIR also carried some virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA). Thus, we set out in this study to analyze in depth the genetic basis of the pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. We report a high-risk clone ST11 KL47 serotype of a CR-HvKP strain isolated from the blood of a 60-year-old hospitalized female patient from the intensive care unit (ICU) in a tertiary care hospital in Egypt, which showed the cohabitation of a novel hybrid plasmid coharboring the bla_NDM-1 and virulence genes and a bla_KPC-2-carrying plasmid.IMPORTANCE CRKP has been registered in the critical priority tier by the World Health Organization and has become a significant menace to public health. The emergence of CR-HvKP is of great concern in terms of both disease and treatment. In-depth analysis of the carbapenemase-encoding and virulence plasmids may provide insight into ongoing recombination and evolution of virulence and multidrug resistance in K. pneumoniae Thus, this study serves to alert contagious disease clinicians to the presence of hypervirulence in CRKP isolates in Egyptian hospitals.

Keywords: Egypt; KPC-2; Klebsiella pneumoniae; NDM-1; hybrid plasmid; virulent plasmid.

FIG 1

Structure analysis of pEBSI036-1-NDM-VIR. Major structural features of plasmid pEBSI036-1-NDM-VIR were compared with those of plasmids pKpvST101_5 (GenBank accession no. CP031372.2) and pJX6-1 (GenBank accession no. CP064230.1). The comparative schematic diagrams of resistance regions and virulence regions in plasmids pEBSI036-1-NDM-VIR, pKpvST383L (GenBank accession no. CP034201.2), pKpvST147B_virulence (GenBank accession no. CP040726.1), and p51015_NDM_1 (GenBank accession no. CP050380.1) are shown. Gray shading indicates shared regions with a high degree of homology. Red and purple represent the antibiotic resistance and virulence genes, respectively, and yellow represents the insertion sequences and transposons.

FIG 2

Sequence alignment analysis among plasmids pEBSI036-2-KPC, pKPC2_040035 (GenBank accession no. CP028796.1), and p3_L382 (GenBank accession no. CP033962.1). Red and green represent the antibiotic resistance and heavy metal resistance genes, respectively, and yellow represents the insertion sequences and transposons.