Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections

Abstract

While most diagnostic processes cease with the detection of the first relevant infectious agent, newer multiplexed molecular methods which provide simultaneous analysis of multiple agents may give a more accurate representation of the true pathogen spectrum in these samples. To examine this in the context of respiratory infections, acute-phase respiratory specimens submitted to our clinical diagnostic microbiology/virology laboratory for our routine VIRAP diagnosis protocol during the spring 2006 peak respiratory infection season were processed in parallel by analysis with Genaco (QiaPlex) ResPlex I and ResPlex II molecular diagnostic panels. A total of 1,742 specimens were examined for 21 relevant targets each. The resulting data reveal that multiple infections are frequent and provide evidence for complex interactions between different infectious agents. Statistically relevant association patterns (both positive and negative) were observed between particular pathogens. While some interactions we observed are substantiated by prior reports in the literature, several specific patterns do not appear to have been reported previously. In addition, we report preliminary clinical evidence which supports a hypothesis that these coinfections are medically relevant and that effective treatment for severe respiratory tract infections will increasingly require diagnosis of all involved pathogens, as opposed to single-pathogen reporting.

FIG. 1.

Pathogen prevalence per sample. The histogram shows the number of pathogens detected per sample by ResPlex I/II assay of 1,742 total specimens.

FIG. 2.

Pathogen prevalence by ResPlex I/II assay and VIRAP DFA (as obtained with the SimulFluor assay according to the manufacturer's protocols). Light bars, ResPlex I/II prevalence values for all samples; dark bars, VIRAP DFA prevalence values for the same sample set. Note that VIRAP examines only adenovirus, RSV, influenza A virus, influenza B virus, and PIV-1 to PIV-3 and that it groups RSV-A and RSV-B together; the indicated VIRAP RSV-A prevalence should thus be compared against the ResPlex RSV-A and RSV-B prevalence values combined. Abbreviations: M. pneumo, Mycoplasma pneumoniae; C. pneumo, Chlamydia pneumoniae; L. pneumo, Legionella pneumophila; S. pneumo, Streptococcus pneumoniae; N. meningo, Neisseria meningitidis; H. flu 1, Haemophilus influenzae (all types); H. flu 2, Haemophilus influenzae (strains a, b, c, and d); H. flu 3, Haemophilus influenzae (strains e and f); AdV, adenovirus; RSV, respiratory syncytial virus; Flu, influenza virus; PIV, parainfluenza virus; hMPV, human metapneumovirus; CVEV, coxsackie virus/echovirus family; Rhino, rhinovirus.