Concordance of next-generation sequencing and conventional microbiology for pathogen detection and antimicrobial resistance prediction in pneumonia

Nurlan T. Sandybayev, Radmir Sarsenov, Vitaliy M. Strochkov, Alyona V. Lavrinenko, Vyacheslav Beloussov, Maxim Solomadin, Shynggys Orkara, Sergey Yegorov

Data confidence 85 high

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Abstract

Abstract Delays in pathogen and antimicrobial resistance (AMR) profiling adversely affect patient outcomes. Next-generation sequencing (NGS) may complement conventional microbiology (CM), yet real-world value of NGS in pneumonia diagnosis remains unclear. We quantified concordance between a commercial NGS panel and CM for pathogen detection and genotypic AMR prediction in 48 pneumonia inpatients with culture-confirmed infections. Archived sputum was analysed using the Ion AmpliSeq Pan-Bacterial targeted panel with 16S rRNA profiling. CM comprised culture, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) identification and disc-diffusion antibiotic susceptibility testing. NGS recovered 27/50 pathogens detected by CM (54.0%, 95% CI 40.4–67.0), with more organisms per sample than CM (mean 2.42 versus 1.04), including uncultured taxa, indicating broader detection. AMR sensitivity of NGS was low (41.2%, 105/255; 95% CI 35.3–47.3; ranging from 1.1% for fluoroquinolones to 100% for cephamycins/lincosamides/tetracyclines) and remained low (37.6–69.8%) across alternative read and abundance cut-offs. Overall, the commercial NGS panel expanded pathogen detection beyond culture but showed only moderate concordance with CM and limited sensitivity for AMR phenotypes; it is therefore best regarded as an adjunct to CM and phenotypic susceptibility testing in pneumonia, not a replacement.