Concordance of next-generation sequencing and conventional microbiology for pathogen detection and antimicrobial resistance prediction in pneumonia
4 affiliations
- 1Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University (KazNARU) 1 , Almaty, Kazakhstan
- 2Department of Biological and Biomedical Sciences, School of Medicine, Nazarbayev University 3 , Astana, Kazakhstan
- 3Research Laboratory, Karaganda Medical University 4 , Karaganda, Kazakhstan
- 4International Center for Vaccinology, Kazakh National Agrarian Research University (KazNARU) 2 , Almaty, Kazakhstan
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.
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BibTeX
@article{sandybayev2026concordance,
title = {{Concordance of next-generation sequencing and conventional microbiology for pathogen detection and antimicrobial resistance prediction in pneumonia}},
author = {Nurlan Sandybayev and Radmir Sarsenov and Vitaliy Strochkov and Alyona Lavrinenko and Vyacheslav Beloussov and Maxim Solomadin and Shynggys Orkara and Sergey Yegorov},
journal = {Royal Society Open Science},
year = {2026},
month = sep,
doi = {10.1098/rsos.260772},
url = {https://royalsocietypublishing.org/rsos/article/13/9/260772/483434/Concordance-of-next-generation-sequencing-and},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Concordance of next-generation sequencing and conventional microbiology for pathogen detection and antimicrobial resistance prediction in pneumonia
AU - Nurlan Sandybayev
AU - Radmir Sarsenov
AU - Vitaliy Strochkov
AU - Alyona Lavrinenko
AU - Vyacheslav Beloussov
AU - Maxim Solomadin
AU - Shynggys Orkara
AU - Sergey Yegorov
PY - 2026
DA - 2026/09/30
JO - Royal Society Open Science
DO - 10.1098/rsos.260772
UR - https://royalsocietypublishing.org/rsos/article/13/9/260772/483434/Concordance-of-next-generation-sequencing-and
AB - 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.
SN - 2054-5703
ER -