A-063 Performance evaluation of a molecular RT-PCR pneumonia panel in addition to traditional microbiological culturing methods

Abstract

Pneumonia infections pose a significant global health challenge, accounting for more than 1.2 million emergency department visits and 41,000 deaths in the U.S. annually. Given the low vaccination rates, significant increase in childhood cases over the last couple years, and that untreated infections can result in severe and long-term consequences, early and proper diagnosis is very important for preventing disease spreading and improving public health outcomes. We recently verified a pneumonia panel nucleic acid screening assay to supplement our current traditional microbiological culture methods in order to identify common infection organisms with increased efficiency and their possible antimicrobial resistance gene presence. The Biomerieux Pneumonia Panel is an automated, nested multiplexed real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay used for the simultaneous detection and differentiation against many of the common infection causes of pneumonia. The panel targets 15 common bacterial strains, 3 atypical bacterial strains, 8 viruses, as well as 7 prominent antimicrobial resistance genes. The assay was evaluated for precision, reproducibility, and accuracy using microbiological specimens with culturing identification results, external validation material spiking, a carbapenemase bacterial library, and specimens from partner laboratories with previously-run known panel results. The percentage agreements were statistically calculated and any non-concordant samples were re-tested on the panel and/or re-cultured for microbiological identification. Overall sensitivity of the Pneumonia Panel was 98.3% (98.5% for typical bacteria, 100% for atypical bacteria, and 97.1% for viruses), specificity was 100%, and accuracy was 99.7% across 66 total targeted assay runs using collected patient specimens, pooled external material spiking, and a CDC bacterial library collection. Sensitivity, specificity, and accuracy for the antimicrobial resistance genes was 100%, however resistance gene screening in the panel is dependent on preceding typical bacteria positivity in order to be tested. It is of note that during the verification the pneumonia panel assay actually found a mis-identified bacterial species and a previously undetected bacterial infection within a couple of the cultured patient specimens, both of which were confirmed by re-culturing methods and MALDI-ToF identification. The Biomerieux Pneumonia Panel provided an automated, high precision, accurate, and sensitive assay for the detection and identification of common pneumonia targets. While it has the ability to assist co-culture microbiological methods, the assay also has the benefit of a faster turnaround time (hours instead of days), viral identification, and antimicrobial resistance gene detection. This allows the panel to be used as a critical tool toward allowing quicker diagnosis with earlier and more specific treatment to help prevent disease spread and serious long-term consequences of pneumonia infection.