Within-Host Resistance and Virulence Evolution of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST11 Under Antibiotic Pressure

Abstract

Background

Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) has recently aroused an extremely severe health challenge and public concern. However, the underlying mechanisms of fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we report a hv-CRKP-associated fatal infection and reveal a reduction in virulence due to the acquisition of aminoglycoside resistance.

Methods

The bacterial identification, antimicrobial susceptibility, hypermucoviscosity, virulence factors, MLST and serotypes were profiled.The clonal homology and plasmid acquisition among hv-CRKP strains were detected by XbaI and S1-PFGE. The virulence potential of the strains was evaluated using Galleria mellonella larvae infection model, serum resistance assay, capsular polysaccharide quantification, and biofilm formation assay. Genomic variations were identified using whole-genome sequencing (WGS).

Results

Four K. pneumoniae carbapenemase (KPC)-producing CRKP strains were consecutively isolated from an 86-year-old patient with severe pneumonia. Whole-genome sequencing (WGS) showed that all four hv-CRKP strains belonged to the ST11-KL64 clone. PFGE analysis revealed that the four ST11-KL64 hv-CRKP strains could be grouped into the same PFGE type. Under the pressure of antibiotics, the antimicrobial resistance of the strains increased and the virulence potential decreased. Further sequencing, using the Nanopore platform, was performed on three representative isolates (WYKP586, WYKP589, and WYKP594). Genomic analysis showed that the plasmids of these three strains underwent a large number of breaks and recombination events under antibiotic pressure. We found that as aminoglycoside resistance emerged via acquisition of the rmtB gene, the hypermucoviscosity and virulence of the strains decreased because of internal mutations in the rmpA and rmpA2 genes.

Conclusion

This study shows that ST11-KL64 hv-CRKP can further evolve to acquire aminoglycoside resistance accompanied by decreased virulence to adapt to antibiotic pressure in the host.

Keywords:

• hypervirulent carbapenem-resistant Klebsiella pneumoniae
• within-host evolution
• plasmids
• whole-genome sequencing

Data Sharing Statement

The genome data of the four hv-CRKP strains were submitted to the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA962850.

Ethics Approval and Informed Consent

This study was approved by the Medical Ethics Council of Shanghai Fifth People’s Hospital (Approval No. 11, 2022), and written informed consent has been provided by the patient’s son to have the case details published.

Acknowledgments

We thank the authority of NTUH-K2044 by Jin-Town Wang from National Taiwan University Hospital.

We extend our thanks to Personal Biotechnology Co., Ltd. Shanghai, China, for the support of whole-genome sequencing and the prediction of coding DNA sequences in the genome.

Disclosure

The authors report no conflicts of interest in this work.

Additional information

Funding

This study was supported by the Outstanding Young Medical Technical Talents and Pharmaceutical Talents Training Program supported by Health Commission of Minhang District, Shanghai (No. MWYJYX07), Natural Science Research Funds of Minhang District, Shanghai(No. 2023MHZ042), Medical Specialty Construction Project of Minhang District, Shanghai (No. 2020MWTZB04), Key Medical Specialty funded by Shanghai Fifth People’s Hospital, Fudan University (No. 2020WYZDZK08).