{
  "abstract": "Diarrhea is a leading cause of pediatric morbidity and mortality worldwide, frequently caused by various bacterial, viral, and protozoan pathogens. Identification of these pathogens is important in clinical settings for proper management of the infection. Conventional stool culture technique is time-consuming for the detection of diarrheagenic pathogens. In addition, these traditional procedures lack sensitivity, require a specific laboratory structure, and well-trained staff. Conversely, multiplex molecular detection methods offer rapid results with less hands-on time and more sensitivity. This study compared the diagnostic performance of conventional microbiological methods and GastroFinder 2SMART multiplexed real-time PCR (real-time PCR) assay for detecting enteric pathogens in pediatric stool samples. Overall pathogen detection was significantly higher using this real-time PCR (81%) compared to the conventional assays (43.1%), reflecting differences in both sensitivity and pathogen panel breadth. Rotavirus, adenovirus, Shigella, and Giardia lamblia were frequently identified by conventional methods, whereas real-time PCR commonly detected adenovirus, Campylobacter, EPEC, ETEC, and norovirus. Certain pathogens such as Yersinia enterocolitica, Clostridioides difficile, STEC, and Dientamoeba fragilis were not tested in the conventional panel and therefore excluded for comparison. Sensitivity estimates varied, with lower sensitivity observed for EPEC, Cryptosporidium, G. lamblia, and rotavirus, partly due to the small sample numbers and wide confidence intervals. Specificity exceeded 90% for most pathogens, and diagnostic accuracy was > 90% for Shigella/EIEC, Salmonella, Cryptosporidium, Giardia lamblia, and astrovirus. Bayesian latent class analysis demonstrated the highest sensitivity for Shigella/EIEC (93.2%), followed by norovirus and adenovirus, while overall test performance, measured by the Youden Index, was greatest for Shigella/EIEC. These findings highlight the diagnostic use of real-time PCR and support its integration into routine diarrheal diagnostics to improve pathogen detection and clinical management. Author summary: Diarrhea remains a leading cause of childhood death in low-resource settings. Less sensitive conventional diagnostics methods often fail to identify the diarrheal pathogens. We compared a multiplex real-time PCR (GastroFinder 2SMART) assay with standard laboratory methods using stool specimens collected from 153 children with diarrhea. Using conventional diagnostic accuracy metrics and Bayesian latent class analysis—which estimates true test performance without assuming a perfect gold standard—we found that real-time PCR detected pathogens in 81% of samples versus 43.1% by conventional methods (p < 0.001). Detection improved substantially for bacteria (61% vs. 12%) and viruses (67% vs. 27%). Mixed infections were more common by the real-time PCR (75.8% vs. 12.1%). Performance varied by pathogen type: Shigella/EIEC showed excellent discriminatory ability (Youden Index 0.88; sensitivity 93.2%, specificity 95.4%), and negative predictive values exceeded 95% for most pathogens, indicating the use of GastroFinder 2SMART as a screening tool. However, rotavirus sensitivity was unexpectedly low (15%), a critical limitation for pediatric populations. These findings support the integration of molecular methods into routine diarrheal testing to improve pathogen detection and also highlight the need for additional rotavirus testing and careful pathogen-specific interpretation of results.",
  "abstract_shown": true,
  "affiliations": [
    "ICMR-National Institute for Research in Bacterial Infections, Kolkata, India"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Goutam Chowdhury"
    },
    {
      "name": "Melissa Glenda Lewis"
    },
    {
      "name": "Alok Deb"
    },
    {
      "name": "Mamta Chawla-Sarkar"
    },
    {
      "name": "Sandipan Ganguly"
    },
    {
      "name": "Paulami Dutta"
    },
    {
      "name": "Santasabuj Das"
    },
    {
      "name": "Asish K. Mukhopadhyay"
    },
    {
      "name": "Thandavarayan Ramamurthy"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/eadfhsy8jd9zz.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pntd.0014823",
  "fulltext_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014823",
  "id": "eadfhsy8jd9zz",
  "issns": [
    "1935-2735"
  ],
  "landing_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014823",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2725|Viral gastroenteritis research and epidemiology"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Shigella"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Viral pathogens"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Shigella"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Viral pathogens"
    ],
    [
      "plos",
      "/Medicine and health sciences/Clinical medicine/Signs and symptoms/Diarrhea"
    ],
    [
      "plos",
      "/Medicine and health sciences/Gastroenterology and hepatology/Diarrhea"
    ],
    [
      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Pediatric infections"
    ],
    [
      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Viral diseases/Rotavirus infection"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Shigella"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Viral pathogens"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pediatrics"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pediatrics/Pediatric infections"
    ]
  ],
  "openalex": "W7225107193",
  "pdf_url": "https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0014823&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-02",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/eadfhsy8jd9zz.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T12:20:16Z",
      "native_id": "10.1371/journal.pntd.0014823",
      "source": "plos",
      "url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014823"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:microbiology",
      "subfield": "microbiology"
    },
    {
      "field": "medicine",
      "origin": "plos:infectious diseases",
      "subfield": "infectious-disease"
    },
    {
      "field": "medicine",
      "origin": "plos:pediatrics",
      "subfield": "reproductive-child"
    }
  ],
  "title": "Enhancing pathogen detection in pediatric diarrheal stools: The case of molecular multiplexing with a real-time PCR assay",
  "title_text": "Enhancing pathogen detection in pediatric diarrheal stools: The case of molecular multiplexing with a real-time PCR assay",
  "type": "peer-reviewed",
  "updated_at": "2026-11-04T12:20:44Z",
  "url": "https://research.draconitic.com/paper/eadfhsy8jd9zz",
  "venue": "PLOS Neglected Tropical Diseases",
  "versions": []
}