OP4 - Abstract Use of the rapid, multiplex PCR panel for the identification of respiratory pathogens and the resistance genes among patients admitted to a Tertiary care hospital in Southern Province, Sri Lanka

Abstract

Introduction

Lower respiratory tract infections (LRTIs) cause significant morbidity and mortality in patients worldwide, and their etiology is often unknown. The conventional culture-based methods are time-consuming and have low positivity rates.

Objectives

This study aimed to evaluate the etiology and the genotypic resistance using the BIOFIRE^® FILMARRAY^® Pneumonia plus Panel, a multiplex polymerase chain reaction assay, in community-acquired LRTI among hospitalized patients. 

 Design, setting, and methods

We enrolled children and adults hospitalized with clinically confirmed LRTIs at a Tertiary care hospital in Southern Sri Lanka from 2019 to 2021. Demographic and clinical data were collected, and a sputum sample from each patient was tested by culture and the Pneumonia plus Panel. 

 Results

Of 267 patients, 253 (94.8%) were ³18 years of age and 120 (44.9%) were female. Of all (n=267) sputum samples, the majority were positive for Gram-negatives (n=211, 79.0%), and 142 (53.2%) were detected with ³1 antibacterial resistance genes. The predominant organism was K. pneumoniae (KP) (41.9% of total patients), followed by S. aureus (34.5%), A. calcoaceticus-baumannii complex (ACBC)(32.6%), P. aeruginosa (26.6%) and Mycoplasma pneumoniae (1.1%). A total of 96 patients (40.0%) had at least one carbapenem resistance gene target, 56 (21.0%) had an extended-spectrum beta-lactamase related gene, and 42 (15.7%) had a methicillin resistance gene target. The most commonly co-detected antibacterial resistance genes were NDM and VIM (10.1%) and NDM with CTX-M (9.7%). The most commonly co-detected resistant bacteria and resistance genes were ACBC with OXA-48-like (n=48, 18.0%) and the KP group with CTX-M or NDM (n=48, 18.0%). ­­ PCR Panel results of 15 patients (5.6%) matched with sputum culture results.

 Conclusions

Our findings showed a predominance of Gram-negative bacteria as well as carbapenem resistance-encoding gene targets in the sputum samples of patients with LRTI. While discordant results among positive panel findings and negative culture results will be challenging to clinicians regarding management, these results point towards drug-resistant, Gram-negative aetiologies, which should be considered in treatment.