Concurrent Classical and Hypervirulent Klebsiella pneumoniae Infection in Distinct Host Niches Revealed by a Rapid Nanopore Whole-Genome and Plasmid Sequencing Method

Lu Wang¹QI-qi Wang²Zizhen Tang³Yuyun Wang¹Yuanqing Qu¹Danli Wen¹Qiulei Zhong²Huan Hu⁴Yuan Liu^1*Miao He^2*

• ¹Chinese People's Liberation Army Western Theater General Hospital, Chengdu, China
• ²Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
• ³Sichuan University College of Life Sciences, Chengdu, China
• ⁴Geneus Technologies Co., Ltd., Chengdu, China

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 method using Gseq-500 platform was used to reveal the pathogenesis of this case. The whole-genome and plasmid sequencing results showed that the lung isolate (KP-L) belonged to the hypervirulent ST23/KL1 lineage, carrying a large non-conjugative plasmid encoding rmpA, rmpA2 iuc, iro, and peg-344, along 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, highlighting the pathogenic potential of classical strains in immune-privileged sites. Comparative genomic and phylogenetic analysis 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.