Laboratory diagnosis of pneumonia in the molecular age

Abstract

Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.

Comparison of ePlex Respiratory Pathogen Panel with Laboratory-Developed Real-Time PCR Assays for Detection of Respiratory Pathogens

“…The etiological agent in such infections differs greatly according to season and age of patient, with highest prevalences being those of respiratory syncytial virus (RSV) in children and influenza virus in adults. Rapid microbiological diagnosis of a respiratory infection is important to ensure appropriate antimicrobial therapy and for the effective implementation of isolation precautions (1). …”

The past decade in bench research into pulmonary infectious diseases: What do clinicians need to know?

“…Existing diagnostics are limited—blood culture are rarely positive and strongly affected by prior antibiotic treatment . Sputum cultures are unreliable, and urinary antigen tests are sensitive but only available widely for Streptococcus pneumoniae and Legionella pneumophila . PCR assays for respiratory viruses have greatly enhanced detection of these organisms along with some atypical pathogens such as Mycoplasma pneumoniae .…”

“…pneumoniae was found in 5% as the most common bacteria . Therefore, superior technology is needed to identify pathogenic microorganisms during acute infections, including CAP, but also hospital‐ and ventilator‐associated pneumonia, exacerbations of chronic respiratory diseases and any other circumstance where antibiotics are prescribed without documented evidence of bacterial infection …”

Fluorescence Imaging of Streptococcus pneumoniae with the Helix pomatia agglutinin (HPA) As a Potential, Rapid Diagnostic Tool

“…Unfortunately, this is time consuming (24–72 h) and includes the inoculation of appropriate media, subculturing, and phenotype-based characterization via biochemical testing, along with antibiotic susceptibility testing. Currently, bacteriological diagnosis is making progress in molecular biology techniques such as PCR, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and whole genome sequencing (Clark, 2015; Pai et al, 2015; McGill et al, 2016; Torres et al, 2016). These techniques have been developed to decrease the time for the initiation of an optimal antimicrobial therapy for improving clinical outcomes.…”