{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University (KazNARU) 1 , Almaty, Kazakhstan",
    "Department of Biological and Biomedical Sciences, School of Medicine, Nazarbayev University 3 , Astana, Kazakhstan",
    "Research Laboratory, Karaganda Medical University 4 , Karaganda, Kazakhstan",
    "International Center for Vaccinology, Kazakh National Agrarian Research University (KazNARU) 2 , Almaty, Kazakhstan"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Nurlan Sandybayev",
      "orcid": "0000-0003-1814-2798"
    },
    {
      "affs": [
        1
      ],
      "name": "Radmir Sarsenov"
    },
    {
      "affs": [
        0
      ],
      "name": "Vitaliy Strochkov",
      "orcid": "0000-0003-3399-2942"
    },
    {
      "affs": [
        2
      ],
      "name": "Alyona Lavrinenko"
    },
    {
      "affs": [
        0
      ],
      "name": "Vyacheslav Beloussov"
    },
    {
      "affs": [
        3
      ],
      "name": "Maxim Solomadin"
    },
    {
      "affs": [
        0
      ],
      "name": "Shynggys Orkara"
    },
    {
      "affs": [
        1
      ],
      "name": "Sergey Yegorov",
      "orcid": "0000-0002-7136-7921"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5635n42abye28.bib",
  "cited_by": 0,
  "doi": "10.1098/rsos.260772",
  "fulltext_url": null,
  "id": "5635n42abye28",
  "issns": [
    "2054-5703"
  ],
  "landing_url": "https://royalsocietypublishing.org/rsos/article/13/9/260772/483434/Concordance-of-next-generation-sequencing-and",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1308|Bacterial Identification and Susceptibility Testing"
    ]
  ],
  "openalex": "W7153485146",
  "pdf_url": "https://royalsocietypublishing.org/rsos/article-pdf/doi/10.1098/rsos.260772/6167998/rsos.260772.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-30",
  "publisher": "The Royal Society",
  "ris": "https://research.draconitic.com/paper/5635n42abye28.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:45Z",
      "native_id": "10.1098/rsos.260772",
      "source": "crossref",
      "url": "https://royalsocietypublishing.org/rsos/article/13/9/260772/483434/Concordance-of-next-generation-sequencing-and"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:1308|Bacterial Identification and Susceptibility Testing",
      "subfield": "general"
    }
  ],
  "title": "Concordance of next-generation sequencing and conventional microbiology for pathogen detection and antimicrobial resistance prediction in pneumonia",
  "title_text": "Concordance of next-generation sequencing and conventional microbiology for pathogen detection and antimicrobial resistance prediction in pneumonia",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:45Z",
  "url": "https://research.draconitic.com/paper/5635n42abye28",
  "venue": "Royal Society Open Science",
  "versions": []
}