Identification of Uropathogens: A Journey from Conventional to Molecular Level

Abstract

Background: During the course of bacterial infection, the rapid and accurate identification of the causative agent is essential to determine the effective treatment option. Now, the question arises, is it necessary to identify the microbial pathogens up to the species level? Objective: The present prospective study involving uropathogens has been designed to highlight the journey from well-adapted, inexpensive but time-consuming and labor-intensive gold-standard conventional (biochemical) diagnostic methods to the rapid and specific upcoming rival in the form of molecular methods (16s rRNA sequencing). Materials and Methods: The study was carried out for a period of 12 months. Clean catch, midstream urine samples from 1101 admitted patients clinically suspected of urinary tract infection (UTI) were subjected to microscopy and culture on blood agar, MacConkey agar, and UTI chromogenic media (HiMedia, Mumbai). The uropathogens isolated from the culture-positive samples were identified up to the species level by the conventional method (Biochemical testing). The isolates were further confirmed by automated method (Vitek 2-Compact System, BioMérieux Inc., France). If required, then, further confirmation was done by molecular method (16S rRNA sequencing) (Yaazh Xenomics, Mumbai and Chennai). Results: A total of 463 (42%) urine samples were found to be culture positive out of 1101 patient samples processed. Four hundred and eighty-nine uropathogens were isolated from 463 culture-positive samples (26 samples had mixed flora i.e., two pathogens per sample). Conclusions: Although genotypic characterization of bacterial pathogen is advantageous when compared to phenotypic method, it is recommendable to use the combination of a traditional culture-based assays and rapid molecular diagnostic tool.