Emergence of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Coharboring a bla _NDM-1 -Carrying Virulent Plasmid and a bla _KPC-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 blaNDM-1 and blaKPC-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 blaNDM-1 and blaKPC-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 blaNDM-1 and virulence genes and a blaKPC-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.

Anatomy of an extensively drug-resistant Klebsiella pneumoniae outbreak in Tuscany, Italy

“…Furthermore, we also confirm the early concern about cross-border spread ( 17 ), as highly genetically related isolates and/or near-identical plasmids ( SI Appendix , Fig. S3 ) are detected in emerging, convergent K. pneumoniae from hospitals around the globe ( 6 , 14 , 16 , 22 , 33 ).…”

“…While WGS allows for the detection of convergence events in K. pneumoniae , the definitive impact on pathogenicity often remains unclear ( 3 , 32 ). Compared with this ST-147 clone from Italy, the acquisition of the same combination of virulence genes was reported in distinct lineages of K. pneumoniae ST-11 from China and Egypt ( 15 , 16 ) and ST-307 from Germany ( 6 ). Comparable virulence was observed in a Galleria insect model at 10 6 CFU of ST-11 strains with and without the virulence plasmid ( 15 ).…”

“…Importantly, near-identical hybrid plasmids carrying determinants for virulence, carbapenem ( bla NDM ), and broad-spectrum aminoglycoside resistances are now emerging in isolates from various countries in both ST-147 and distinct convergent K. pneumoniae lineages ( SI Appendix , Fig. S3 ) ( 6 , 14 , 16 , 22 ).…”

“…Genotypic convergence most frequently occurs when MDR-cKp lineages acquire mobile genetic elements that carry the aforementioned virulence biomarker genes ( 11 ). Alarmingly, large hybrid plasmids that harbor both antimicrobial resistance and virulence genes have recently been reported in MDR isolates from multiple countries ( 6 , 12 – 16 ). This includes sporadic instances of convergent bla NDM -carrying ST-147 isolates detected in the United Kingdom in 2018 and 2019 ( 13 , 14 ).…”

Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region

“…K. pneumoniae represents an important reservoir for class A (KPC, SHV, GES, IMI, and NMCA), class B (i.e., VIM, IMP, and NDM), class D carbapenemases (OXA-48), and extended-spectrum β-lactamases (ESBLs) such as CTX-M variants [ 5 , 9 ]. Carbapenem-resistant K. pneumoniae is largely disseminated around the world [ 10 , 11 , 12 , 13 , 14 ]. One reason for the rapid dissemination of K. pneumoniae is the presence of antibiotic resistance genes in mobile genetic elements and the Inc-groups, which belong to plasmids IncF, IncFII(K1), IncR, IncX, IncX3, IncI2, and ColE1 [ 15 , 16 , 17 , 18 , 19 ].…”