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©The Author(s) 2025. Published by Baishideng Publishing Group Inc. All rights reserved.
Stepwise model to differentiate pathogenic from non-pathogenic organisms in urinary isolates: Effectiveness, safety, and feasibility prospective study
Bimalesh Yadav, Jaideep Pilania, Ravi Kant, Balram Ji Omar, Sandeep Saini, Vikas Kumar Panwar, Yogesh Bahurupi, Prasan Kumar Panda
Bimalesh Yadav, Jaideep Pilania, Ravi Kant, Prasan Kumar Panda, Department of Medicine, All India Institute of Medical Sciences, Rishikesh 249203, Uttarākhand, India
Balram Ji Omar, Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, Uttarākhand, India
Sandeep Saini, Department of Nephrology, All India Institute of Medical Sciences, Rishikesh 249203, Uttarākhand, India
Vikas Kumar Panwar, Department of Urology, All India Institute of Medical Sciences, Rishikesh 249203, Uttarakhand, India
Yogesh Bahurupi, Department of Community Medicine, All India Institute of Medical Sciences, Nagpur 441108, Mahārāshtra, India
Author contributions: Yadav B and Pilania J contributed to the data collection and data analysis and was involved in manuscript writing; Omar BJ, Saini S, Panwar VK, Bahurupi Y and Panda PK provided the concept, interpreted the analysis, critically reviewed the draft; and all authors approved it for publication.
Institutional review board statement: The study was reviewed and approved by Institutional Ethics Committee, AIIMS Rishikesh, ensuring patient confidentiality, data protection, and adherence to ethical standards in research involving human participants.
Informed consent statement: All study participants, or their legal guardian, provided informed written consent prior to study enrollment.
Conflict-of-interest statement: We declare that we have no conflicts of interest.
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: It will be made available to others upon request to the corresponding author.
Open Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:
https://creativecommons.org/Licenses/by-nc/4.0/ Corresponding author: Prasan Kumar Panda, Professor, Department of Internal Medicine, All India Institute of Medical Sciences, Room No. 409, College Block, Rishikesh 249203, Uttarākhand, India.
motherprasanna@rediffmail.com
Received: April 30, 2025
Revised: June 9, 2025
Accepted: October 15, 2025
Published online: December 20, 2025
Processing time: 233 Days and 18.6 Hours
BACKGROUND
Clinical decision-making in urinary tract infections depends heavily on accurately distinguishing between pathogenic and non-pathogenic organisms. The interpretation of urine culture results is influenced by proper sample collection, the patient's clinical context, and organism-specific characteristics. However, there is currently no definitive method to determine whether a urinary isolate is truly pathogenic. This distinction is critical, as treatment decisions hinge on it. This pioneering study systematically applies a stepwise model to differentiate pathogenic from non-pathogenic urinary isolates—an approach not previously described.
AIM
To determine whether a urinary isolate is pathogenic (commensal, colonizer, or direct pathogen) or non-pathogenic (commensal, colonizer, or contaminant) using a structured, stepwise approach.
METHODS
This prospective, longitudinal, exploratory study was conducted over 24 months, starting in January 2022, at All India Institute of Medical Sciences Rishikesh, following approval from the Institutional Ethics Committee. A stepwise model developed by the investigators was applied to assess the nature of the isolates. Data recorded using REDCap, and analysis was performed using SPSS Version 25.
RESULTS
A total of 275 consecutive patients aged over 18 years with positive urine cultures—initially treated with antibiotics based on microbiological and clinical assessment—were included. The stepwise model classified 90.54% of cases as pathogenic (commensals: 61.81%, colonizers: 14.18%, and direct pathogens: 14.54%) and 9.45% as non-pathogenic. The model showed that there could be a significant reduction in average hospital stay by over 13 days, along with saving approximately Rs. 981 per patient in antibiotic costs in non-pathogenic cohort.
CONCLUSION
This novel model identified that approximately one in ten urinary isolates, initially considered pathogenic and treated with antibiotics, were in fact non-pathogenic. The model is safe, feasible, and potentially valuable in resource-limited settings, warranting broader validation and implementation.
Core Tip: Differentiating true pathogens from colonizers or contaminants in urinary cultures remains a major challenge in clinical practice. This study presents a novel, stepwise model to assess the true pathogenicity of urinary isolates in hospitalized adults. The model identified nearly 10% of culture-positive cases—previously treated as infections—as non-pathogenic. This approach is safe, feasible, and potentially reduces unnecessary antibiotic use, especially in resource-limited settings.
