Concurrent classical and hypervirulent Klebsiella pneumoniae infection in distinct host niches revealed by a rapid nanopore whole-genome and plasmid sequencing method

TL;DR

A patient was infected with two distinct Klebsiella pneumoniae strains in different body parts, revealed through rapid nanopore sequencing.

Contribution

A rapid nanopore sequencing method was used to identify dual-strain K. pneumoniae infections in distinct host niches.

Findings

The lung isolate was a hypervirulent strain with specific virulence plasmids.

The eye isolate was a classical strain lacking hypervirulence markers but causing severe infection.

The two isolates were not clonally related, suggesting niche-specific adaptation.

Abstract

This study reports a rare case of dual-strain Klebsiella pneumoniae infection involving genetically distinct isolates from the lung and eye of a previously immunocompetent patient.

A rapid nanopore sequencing workflow on the Gseq-500 platform was used for whole-genome and plasmid sequencing. Comparative genomic and phylogenetic analyses assessed isolate relatedness and identified virulence and resistance determinants.

The lung isolate (KP-L) belonged to the hypervirulent ST23/KL1 lineage and carried a large non-conjugative plasmid encoding rmpA, rmpA2, iuc, iro, and peg-344, together with chromosomal yersiniabactin. In contrast, the eye isolate (KP-E) was a classical ST133/KL116 strain lacking known hypervirulence markers but harboring plasmids encoding heavy-metal resistance genes. Despite the absence of hypervirulence factors, KP-E caused severe endophthalmitis requiring enucleation, underscoring the pathogenic potential of classical strains in immune-privileged sites. Comparative genomic and phylogenetic analyses confirmed that the two isolates were not clonally related.

We propose a plausible infection trajectory involving initial hypervirulent K. pneumoniae (hvKp) dissemination followed by niche-specific replacement by Classical K. pneumoniae (cKp) under antibiotic pressure. This case underscores that severe infections can arise from genetically “low-virulence” strains in certain host environments. Comprehensive genomic surveillance and aggressive clinical management strategies remain crucial for improving patient prognosis and understanding pathogen adaptation mechanisms within host niches.

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