A Pilot Study of Klebsiella pneumoniae in Community-Acquired Pneumonia: Comparative Insights from Culture and Targeted Next-Generation Sequencing

Beloussov V. Strochkov V. Sandybayev N. Lavrinenko A. Solomadin M.
January 2026 Multidisciplinary Digital Publishing Institute (MDPI)

Diagnostics
2026 #16 Issue 1

Background/Objectives: Klebsiella pneumoniae is a major Gram-negative pathogen associated with community-acquired pneumonia (CAP) and a critical contributor to antimicrobial resistance (AMR). Culture-based diagnostics remain the clinical standard but may underestimate microbial diversity and resistance gene profiles. This pilot study compared pathogen detection and antimicrobial resistance gene (ARG) repertoires in matched K. pneumoniae pure cultures and primary sputum samples using targeted next-generation sequencing (tNGS). Methods: We analyzed 153 sputum samples from patients with CAP. Among 48 culture-positive cases, 22 (14% overall; 54% culture-positive) yielded K. pneumoniae. MALDI-TOF MS, phenotypic drug susceptibility testing, and tNGS were conducted on both culture isolates and matched sputum specimens. Microbial composition, ARG diversity, and method concordance were evaluated, with focused analysis of discordant and fatal cases. Results: K. pneumoniae was detected in 14.4% of all CAP cases and accounted for 54.2% of culture-positive samples. Identification rates differed across methods: 35% by MALDI-TOF MS, 45% by culture tNGS, and 29% by sputum tNGS. Sputum tNGS revealed substantially higher microbial diversity than cultures (3.04 vs. 1.42 species per sample) and detected more than sixfold unique ARGs (38 vs. 7), including clinically relevant determinants that were absent from culture isolates. Concordance was high between MALDI-TOF MS and culture tNGS (κ = 0.712), but low between sputum and culture tNGS (κ = 0.279). Among twelve K. pneumoniae isolates included in AMR analysis, all showed resistance to β-lactams, and two-thirds exhibited MDR/XDR phenotypes. Genotypic screening identified seven ARGs, but major ESBL and carbapenemase genes were not detected, suggesting the presence of alternative resistance mechanisms. Overall, sputum tNGS provided additional etiological and resistome information not captured by cultivation and complemented classical diagnostics in CAP involving K. pneumoniae. Conclusions: Culture-based diagnostics and tNGS provide complementary insights into the detection and resistance profiling of K. pneumoniae in CAP, with sputum tNGS revealing broader microbial and resistome information than pure cultures, while classical methods remain essential for species confirmation and phenotypic AST. An integrated diagnostic approach combining both methodologies may improve pathogen detection, guide antimicrobial therapy, and enhance AMR surveillance in K. pneumoniae-associated CAP.

AMR , ARGs , community-acquired pneumonia , DDM , Klebsiella pneumoniae , MALDI-TOF MS , resistome , tNGS

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Molecular Genetic Laboratory TreeGene, Almaty, 050008, Kazakhstan
Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University, Almaty, 050010, Kazakhstan
Scientific Research Laboratory, Karaganda Medical University, Karaganda, 100000, Kazakhstan

Molecular Genetic Laboratory TreeGene
Kazakhstan-Japan Innovation Centre
Scientific Research Laboratory

10 лет помогаем публиковать статьи Международный издатель

Книга Публикация научной статьи Волощук 2026 Book Publication of a scientific article 2026