Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens

Prevalence and clinical course of upper airway respiratory virus infection in critically ill patients with hematologic malignancies

Background

The clinical significance of upper airway respiratory virus (RV) detection in patients with hematologic malignancies remains unclear. We aimed to investigate the association between upper airway RV detection and prognosis in critically ill patients with hematologic malignancies.

Methods

This retrospective observational study included 331 critically ill patients with hematologic malignancies who presented respiratory symptoms and their nasopharyngeal swab was tested using a multiplex PCR assay between January 2017 and December 2018. A logistic regression model was used to adjust for potential confounding factors in the association between assay positivity and in-hospital mortality.

Results

Among the 331 analyzed patients, RVs were detected in 29.0%. The overall mortality rates in the intensive care unit and hospital were 56.8% and 65.9%, respectively. Positive upper airway RV detection was associated with relapsed hematologic malignancies, higher level of C-reactive protein, and prior use of high dose steroids and anti-cancer chemotherapeutic drugs. Furthermore, it was independently associated with in-hospital mortality (adjusted odds ratio, 2.36; 95% confidence interval, 1.23 to 4.54). Among different RVs, parainfluenza virus was more prevalent among patients who died in the hospital than among those who survived (11.5% vs. 3.5%, P = 0.027).

Conclusions

RV detection in the upper respiratory tract was relatively common in our cohort and was significantly associated with a poor prognosis. Thus, it can be used as a predictor of prognosis. Moreover, RV presence in the upper respiratory tract should be examined in patients who have previously been prescribed with high dose corticosteroids and anti-cancer drugs.

Polymerase-chain reaction/electrospray ionization-mass spectrometry for the detection of bacteria and fungi in bronchoalveolar lavage fluids: a prospective observational study

PLEX-ID uses polymerase chain reaction-electrospray ionization/mass spectrometry for rapid identification of infectious agents in clinical samples. We evaluated its concordance with our centre's standard methods (SM) for bacterial and fungal detection in bronchoalveolar lavage (BAL) fluid in a prospective observational cohort study. The primary outcome was concordance (%) between SM and PLEX-ID. Secondary outcomes included concordance when excluding commensal oral flora, detection of resistance genes, and PLEX-ID's potential impact on clinical management, as determined by two independent reviewers. Included were 101 specimens from 94 patients. BALs were performed primarily for suspected pneumonia (76/101, 75%) and lung transplant work-ups (12/101, 12%). Most specimens yielded at least one organism by either method (92/101, 91%). Among all microorganisms detected (n = 218), 83% and 17% were bacterial and fungal, respectively. Overall concordance between SM and PLEX-ID was 45% (45/101). Concordance increased to 66% (67/101) when discordance for commensal flora was excluded. PLEX-ID failed to detect 21% of all 183 SM-identified organisms, while SM did not identify 28% of the 191 PLEX-ID-identified organisms (p <0.001). There was low concordance for mecA detection. Two infectious-disease specialists' analyses concluded that in most of the 31 discordant, non-commensal cases, PLEX-ID results would have had little or no impact on patient management; in eight cases, however, PLEX-ID would have led to ‘wrong decision-making’. The tested version of PLEX-ID concurred weakly with standard methods in the detection of bacteria and fungi in BAL specimens, and is not likely to be useful as a standalone tool for microbiological diagnosis in suspected respiratory infections.

Application of mass spectrometry to molecular diagnostics of viral infections

Mass spectrometry (MS) has found numerous applications in life sciences. It has high accuracy, sensitivity and wide dynamic range in addition to medium- to high-throughput capabilities. These features make MS a superior platform for analysis of various biomolecules including proteins, lipids, nucleic acids and carbohydrates. Until recently, MS was applied for protein detection and characterization. During the last decade, however, MS has successfully been used for molecular diagnostics of microbial and viral infections with the most notable applications being identification of pathogens, genomic sequencing, mutation detection, DNA methylation analysis, tracking of transmissions, and characterization of genetic heterogeneity. These new developments vastly expand the MS application from experimental research to public health and clinical fields. Matching of molecular techniques with specific requirements of the major MS platforms has produced powerful technologies for molecular diagnostics, which will further benefit from coupling with computational tools for extracting clinical information from MS-derived data.

Evolving gene targets and technology in influenza detection

Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.

Evaluation of a polymerase chain reaction-electrospray ionization time-of-flight mass spectrometry for the detection and subtyping of influenza viruses in respiratory specimens

Background

PCR coupled to electrospray ionization mass spectrometry technology (PCR/ESI-TOF-MS) (PLEX-ID system, Abbott Ibis Biosciences) was developed to characterize microbial pathogens.

Objectives

To evaluate the performance of the PLEX-ID flu detection™ kit for detecting Influenza viruses by comparison with the multiplex RespiFinder^® Kit (PathoFinder).

Study design

Acute-phase respiratory samples (n = 293) were analysed for this purpose. A subpopulation of influenza type A positive samples, identified with the RespiFinder^® kit (n = 64), were subtyped with the RealTime ready Inf A/H1N1 Detection Set^® (Roche Molecular Diagnostics) and results were compared to the PLEX-ID Flu Detection™ kit.

Results

274 samples gave concordant results (93.5%, p < 0.0001): 65 influenza A-positive, 18 influenza B-positive and 191 negative samples. Of these, 7 samples were PLEX-ID positive/RespiFinder^® negative (5 influenza A and 2 influenza B) and 12 were PLEX-ID positive/RespiFinder^® negative (10 influenza A and 2 influenza B). PLEX-ID showed one sample as an influenza A and B co-infection while the RespiFinder^® assay showed it to be influenza A-positive. The sensitivity, specificity, positive and negative predictive values of the PLEX-ID™ system were 87.4%, 96.5%, 92.2% and 94.1% respectively. Thirteen of 19 discordant samples available for retesting were investigated further with the Anyplex™II RV16 Detection kit (Seegene): seven were RespiFinder^® concordant, while six were PLEX-ID™ concordant. Subtyping of 61/64 influenza A samples was concordant (95.3%): 55 were H1N1pdm09 and six were non-H1N1pdm09. Three samples gave negative PLEX-ID™ results (one H1N1pdm09 and two non-H1N1pdm09).

Conclusions

PCR/ESI-TOF-MS technology showed good diagnostic performances to detect and subtype influenza viruses.

Point: is the era of viral culture over in the clinical microbiology laboratory?

Conventional tube culture systems have long been the mainstay in clinical virology for the growth and identification of viruses from clinical specimens. Innovations such as centrifugation-enhanced shell vial and multiwell plate cultures and the use of genetically engineered and mixed cell lines, coupled with faster detection of viral replication, have allowed for reasonable turnaround times for even some of the most slowly growing clinically important human viruses. However, molecular methods, in particular, the PCR, have usurped the role of viral culture in many laboratories, limiting the use of this traditional method of virus detection or replacing it altogether. Advances and improvements in molecular technology over time have also resulted in newer generations of more rapid and accurate molecular assays for the detection, quantification, and genetic characterization of viruses. For this point-counterpoint, we have asked two individuals, Richard L. Hodinka of the Children's Hospital of Philadelphia, a clinical virologist whose laboratory has completely eliminated viral culture in favor of molecular methods, and Laurent Kaiser, head of the Virology Laboratory at the University of Geneva Hospital, who continues to be a strong advocate of viral culture, to discuss the relevance of viral culture in the molecular age.