Comprehensive metataxonomic analysis of Klebsiella pneumoniae pulmonary 16S rRNA full- sequences

Most clinically used antimicrobials fail to eradicate multidrug-resistant Klebsiella pneumoniae, and the limited availability of genomic data on clinical strains hinders the development of new interventions. This study reports and characterizes long-read 16S rRNA sequences from clinical multidrug-resistant K. pneumoniae sequences associated with mechanical-ventilated pneumonia infections in intensive care unit (ICU) hospitals in Saudi Arabia. Phylogenetic analysis of the 63 sequences was conducted, followed by exploratory screening by comparing the 16S rRNA sequences against the Comprehensive Antibiotic Resistance Database (CARD). This screening aimed solely to identify any incidental sequence similarities within the 16S region and its immediate flanking sequences that might have been captured by long-read sequencing. Given the inherent limitations of applying whole-genome analysis tools to 16S data, these results are presented as computational observations of sequence similarity only and do not confirm the presence of functional resistance genes. Phylogenetic trees showed that the 63 sequences formed well-supported clusters distinct from many global K. pneumoniae reference genomes in NCBI yet closely related to locally reported Saudi K. pneumoniae genomes, suggesting regionally adapted lineages. These findings highlight the convergence of hypervirulence and multidrug resistance in ICU-associated pneumonia and point to the need for ongoing genomic surveillance and development of targeted diagnostics and therapeutics for high-risk lineages.