Abstract

Successful treatment against infectious agents depends on rapid and accurate detection of the causative organisms. Lack of proper identification may facilitate improper antibiotic recommendations. Apart from a few advanced diagnostic facilities in developing countries, most facilities identify pathogens through culture-based methods and suggest antibiotics based solely on the results of disk-diffusion tests. In this pilot study, we tried to validate the identity of the clinical isolates precharacterized by diagnostic facilities. One hundred precharacterized clinical isolates were collected and analyzed phenotypically, biochemically, and genotypically. We employed random amplified polymorphic DNA-polymerase chain reaction (PCR), rcsA, and phoA genes-based PCR and loop-mediated isothermal amplification (LAMP) methods to validate the identification of Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli), respectively. Further validation through phylogenetic analysis based on 16S ribosomal deoxyribonucleic acid (rDNA) sequencing was also performed. Phenotypical, biochemical, and phylogenetic analyses found that 30% and 46% misidentification among the diagnostic center identified E. coli and Klebsiella spp., respectively. Moreover, 16S rDNA sequencing confirmed that the representatives of the misidentified organisms belonged to Enterobacter, Acinetobacter, and Pseudomonas genus. Furthermore, LAMP successfully detected the clinical E. coli within 60 minutes. In this study, we recommend proper monitoring and validation of different tests performed in clinical facilities to avoid misidentification, thus facilitating the avoidance of possible routes responsible for developing antimicrobial resistance.

Key words: Misidentification; 16S rDNA Sequencing; Loop-Mediated Isothermal Amplification; Antibiotic Resistance