Stepwise model to differentiate pathogenic from non-pathogenic organisms in lower-respiratory isolates: Effectiveness and feasibility prospective cohort study

doi:10.5662/wjm.115598

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World Journal of Methodology

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2222-0682

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

Prospective Study

Copyright: ©Author(s) 2026. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution-NonCommercial (CC BY-NC 4.0) license. No commercial re-use. See permissions. Published by Baishideng Publishing Group Inc.

World J Methodol. Sep 20, 2026; 16(3): 115598
Published online Sep 20, 2026. doi: 10.5662/wjm.115598

Stepwise model to differentiate pathogenic from non-pathogenic organisms in lower-respiratory isolates: Effectiveness and feasibility prospective cohort study

Shivnarayan Sahu, Balram Ji Omar, Mukesh Bairwa, Prakhar Sharma, Partha Sahu, Prasan Kumar Panda

Shivnarayan Sahu, Partha Sahu, Department of Medicine, All India Institute of Medical Sciences, Rishikesh 249203, India

Balram Ji Omar, Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, India

Mukesh Bairwa, Division of Internal Medicine, All India Institute of Medical Sciences, Rishikesh 249203, India

Prakhar Sharma, Division of Pulmonary, Sleep and Critical Care Medicine, All India Institute of Medical Sciences Rishikesh, Rishikesh 249203, India

Prasan Kumar Panda, Internal Medicine (ID Division), All India Institute of Medical Sciences, Rishikesh 249203, India

Author contributions: Sahu S and Sahu P designed, collected data, analysed, wrote, reviewed, and approved the manuscript; Panda PK, Omar BJ, Bairwa M, and Sharma P gave the concept, designed, analysed, critically reviewed, and approved the manuscript.

Institutional review board statement: The study was reviewed and approved by Institutional Ethics Committee of All India Institute of Medical Sciences, Rishikesh, India.

Clinical trial registration statement: Considering observational study, it was not registered.

Informed consent statement: All study participants, or their legal guardian, provided informed written consent prior to study enrollment.

Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.

CONSORT 2010 statement: The authors have read the CONSORT 2010 Statement, and the manuscript was prepared and revised according to the CONSORT 2010 Statement.

Data sharing statement: All data was shared in the published article; the corresponding authors can be reached for any other clarification.

Corresponding author: Prasan Kumar Panda, MD, MBBS, Professor, Internal Medicine (ID Division), All India Institute of Medical Sciences, Room No. 409, College Block, Rishikesh 249203, India. motherprasanna@rediffmail.com

Received: October 21, 2025
Revised: December 11, 2025
Accepted: March 4, 2026
Published online: September 20, 2026
Processing time: 263 Days and 0.2 Hours

Abstract

BACKGROUND

Lower respiratory tract infections remain a major cause of morbidity and mortality among hospitalized patients. However, isolating organisms from respiratory samples often leads to diagnostic uncertainty due to the coexistence of colonizers, commensals, and contaminants. To address this challenge, this study employed a structured, stepwise exploratory model to differentiate true pathogens from non-pathogens in aerobic respiratory cultures and multiplex polymerase chain reaction (Biofire FilmArray) results.

AIM

To determine pathogen vs non-pathogen in lower respiratory tract isolates.

METHODS

This prospective, longitudinal time-bound study was conducted over three months (August 2024 to October 2024) at a tertiary care center in Northern India. Adult patients (≥ 18 years) with positive lower respiratory tract samples were enrolled. Each isolate was independently classified by the treating clinician, microbiologist, and study investigator using a six-step clinical-microbiological algorithm that incorporated clinical signs, Sequential Organ Failure Assessment score trends, alternative infection sources, host factors, and outcome data. The final classification was determined by the investigator. Outcomes, including treatment response and mortality at 28 days, were compared across pathogen and non-pathogen groups.

RESULTS

Of the 145 included patients, 131 (90.3%) were classified as pathogens and 14 (9.7%) as non-pathogens. Cohen’s Kappa between investigator and microbiologist classifications was 0.28, indicating fair agreement. Among pathogen cases, 68 (51.9%) responded to treatment. In contrast, 12 of 14 non-pathogen cases (85.7%) were not treated, with favorable outcomes in most, and only one unrelated death (7.1%).

CONCLUSION

The structured clinico-microbiological model strongly correlates with treatment outcomes, making it useful for differentiating infection from colonization. Crucially, microbiological detection alone doesn’t determine pathogenicity. Integrating clinical, laboratory, and outcome data is essential for rational antibiotic use and effective antimicrobial stewardship.

Keywords: Aerobic respiratory culture; Biofire FilmArray; Pathogen classification; Lower respiratory tract infections; Antimicrobial stewardship; Sequential Organ Failure Assessment score

Core Tip: This prospective cohort study developed a structured clinico-microbiological model to distinguish true pathogens from colonizers in lower respiratory tract infections. Among 145 cases, 90% were identified as pathogens, with treatment outcomes aligning closely with the model’s classifications. The findings highlight that microbiological detection alone is insufficient for diagnosing infection - integrating clinical context and outcome data is crucial for rational antibiotic use and effective antimicrobial stewardship.