Multiplex PCR implementation as point-of-care testing in a French emergency department

Laboratory assessment of a multi-target assay for the rapid detection of viruses causing vesicular diseases

BACKGROUND

The recent mpox outbreak has highlighted the need to rapidly diagnose the causative agents of viral vesicular disease to inform treatment and control measures. Common causes of vesicular disease include Monkeypox virus (MPXV), clades I and II, Herpes simplex viruses Type 1 and Type 2 (HSV-1, HSV-2), human herpes virus 6 (HHV-6), Varicella-zoster virus (VZV) and Enteroviruses (EVs). Here, we assessed a syndromic viral vesicular panel for rapid and simultaneous detection of these 7 targets in a single cartridge.

OBJECTIVE

The aim of this study was to evaluate the QIAStat-Dx ® viral vesicular (VV) panel and compare with laboratory developed tests (LDTs). Limit of detection, inter-run variability, cross-reactivity and specificity were assessed. Positive and negative percent agreement, and correlation between assays was determined using 124 clinical samples from multiple anatomical sites.

RESULTS

The overall concordance between the QIAstat and LDTs was 96%. Positive percent agreement was 82% for HHV-6, 89% for HSV-1 and 100% for MPXV, HSV-2, EV and VZV. Negative percent agreement was 100% for all targets assessed. There was no cross-reactivity with Vaccinia, Orf, Molluscum contagiosum viruses, and a pooled respiratory panel.

CONCLUSION

The QIAstat VV multi-target syndromic panel combine ease of use, rapid turnaround, good sensitivity and specificity for enhanced diagnosis, clinical care and public health responses.

Rhinoviruses: molecular diversity and clinical characteristics

BACKGROUND

Rhinoviruses are commonly considered simple "common cold" agents. The link between their molecular epidemiology and patient clinical presentation and outcomes remains unclear in adult populations.

MATERIALS/METHODS

All nasopharyngeal or bronchoalveolar lavages were screened using multiplex PCR in three Parisian hospitals from January to September 2018. For all detected rhinoviruses, the VP2/VP4 region was subtyped by sequencing.

RESULTS

The study included 178 human rhinovirus (HRV) positive unique patients. They were primarily male (56%), with a median age of 62.2 [IQR: 46.8-71.4], frequently presenting chronic respiratory diseases (56%) and/or immunosuppression (46%). Of these, 63% were admitted for respiratory distress, including pneumonia for 25%; 95 (53%), 27 (15%), and 56 (32%) were positive for HRV-A, -B, and -C, respectively. HRV-B appeared more associated with immunosuppressive treatments (58% vs. 30% and 36% of patients for HRV-A and -C, respectively, p = 0.038), higher coinfection rates (54% vs. 34% and 23%, p = 0.03), and higher ICU admission rates (35% vs. 17% and 13%, p = 0.048). Conversely, HRV-A was more frequently associated with pneumonia (54% vs. 31% and 11% for HRV-B and -C, respectively, p = 0.01).

CONCLUSIONS

This study highlights the high proportion of chronic respiratory diseases or immunosuppression among hospitalized patients infected with a rhinovirus.

Place des virus respiratoires dans les pneumonies aiguës communautaires de l'adulte : quels changements depuis la Covid-19 ?

L’émergence du SARS-CoV-2 a renforcé l'intérêt pour la place des virus respiratoires, dans les pneumonies aiguës communautaires, en mettant en exergue de nombreux points encore mal connus tels que la part des infections asymptomatiques, les interactions entre virus respiratoires et pathogènes non viraux, leurs périodes d'incubation, leur pathogénicité ou encore la durée d'excrétion variable.

La présentation clinique et radiologique des pneumonies aiguës communautaires ne permet pas toujours de distinguer l'origine virale de l'origine bactérienne.

L'absence de réelle conséquence thérapeutique semble un frein à l'utilisation des PCR multiplex dans la pratique quotidienne. Toutefois, l'amélioration en termes de délai de rendu des résultats et du nombre de pathogènes inclus dans les panels, ainsi que l'accumulation récente de données épidémiologiques et cliniques, devraient aider à rationaliser l'utilisation de ces tests, faciliter l'interprétation de leurs résultats et guider l'utilisation des molécules antivirales en développement.

Added value of rapid respiratory syndromic testing at point of care versus central laboratory testing: a controlled clinical trial

Background

Virus-associated respiratory infections are in the spotlight with the emergence of SARS-CoV-2 and the expanding use of multiplex PCR (mPCR). The impact of molecular testing as a point-of-care test (POCT) in the emergency department (ED) is still unclear.

Objectives

To compare the impact of a syndromic test performed in the ED as a POCT and in the central laboratory on length of stay (LOS), antibiotic use and single-room assignment.

Methods

From 19 November 2019 to 9 March 2020, adults with acute respiratory illness seeking care in the ED of a large hospital were enrolled, with mPCR performed with a weekly alternation in the ED as a POCT (week A) or in the central laboratory (week B).

Results

474 patients were analysed: 275 during A weeks and 199 during B weeks. Patient characteristics were similar. The hospital LOS (median 7 days during week A versus 7 days during week B, P = 0.29), the proportion of patients with ED-LOS <1 day (63% versus 60%, P = 0.57) and ED antibiotic prescription (59% versus 58%, P = 0.92) were not significantly different. Patients in the POCT arm were more frequently assigned a single room when having a positive PCR for influenza, respiratory syncytial virus and metapneumovirus [52/70 (74%) versus 19/38 (50%) in the central testing arm, P = 0.012].

Conclusions

Syndromic testing performed in the ED compared with the central laboratory failed to reduce the LOS or antibiotic consumption in patients with acute respiratory illness, but was associated with an increased single-room assignment among patients in whom a significant respiratory pathogen was detected.

Performance evaluation of the QIAstat-Dx® Respiratory SARS-CoV-2 Panel

Objective

The aim of this study was to evaluate the QIAstat-Dx® Respiratory SARS-CoV-2 Panel (QIAstat-SARS-CoV-2), which is a closed, fully automated, multiplex polymerase chain reaction (PCR) assay that detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and 21 other pathogens that cause respiratory disease.

Methods

Nasopharyngeal swabs from patients with or suspected of having coronavirus disease 2019 were collected and tested at Bichat–Claude Bernard Hospital, Paris, France. Using the World Health Organisation-approved real-time-PCR assay developed by the Charité Institute of Virology as the reference, positive percent agreement (PPA) and negative percent agreement (NPA) were calculated.

Results

In total, 189 negative and 88 positive samples were analyzed. QIAstat-SARS-CoV-2 had an NPA of 90.48% (95% confidence interval (CI), 85.37%, 94.26%) and a PPA of 94.32% (95% CI, 87.24%, 98.13%). Co-infections were detected by QIAstat-SARS-CoV-2 in 4/277 specimens. The methods exhibited comparable failure rates (23/307 [7.5%] vs. 6/298 [2.0%] for QIAstat-SARS-CoV-2 and reference methods, respectively). The turnaround time was shorter for QIAstat-SARS-CoV-2 compared with the reference method (difference in mean –14:30 h [standard error, 0:03:23; 95% CI, –14:37, –14:24]; P < 0.001).

Conclusions

QIAstat-SARS-CoV-2 shows good agreement with the reference assay, providing faster and accurate results for detecting SARS-CoV-2.

Management of Crohn's disease in an immunosuppressed COVID-19-positive patient: safety-driven prioritisation of nutritional therapy as a bridge to restarting immunosuppression

Active inflammatory bowel disease (IBD), combined immunosuppression and corticosteroid therapy have all been identified as risk factors for a poor outcome in COVID-19 infection. The management of patients with both COVID-19 infection and active IBD is therefore complex. We present the case of a 31-year-old patient with Crohn's disease, on dual immunosuppression with infliximab and mercaptopurine presenting with inflammatory small bowel obstruction and COVID-19 infection. The case highlights the use of nutritional therapy, which remains underused in the management of adults with IBD, to manage his flare acutely. Following negative SARS-CoV-2 PCR testing and SARS-CoV-2 IgG testing confirming an antibody response, ustekinumab (anti-interleukin 12/23) was prescribed for long-term maintenance.

Analysis of Emergency Department Visits and Hospital Activity during Influenza Season, COVID-19 Epidemic, and Lockdown Periods in View of Managing a Future Disaster Risk: A Multicenter Observational Study

ED-visits and through-ED admissions to medical/surgical wards (MSW) and intensive care unit (ICU) during influenza, COVID-19 and lockdown periods were evaluated in a four-hospital prospective observational study from November 2018 to March 2020. ED visit characteristics and main diagnostic categories were assessed. Analysis of 368,262 ED-visits highlighted a significantly increasing trend in ED-visits during influenza followed by a significantly decreasing trend after lockdown. For MSW-admissions, a pattern of growth during influenza was followed by a fall that began during COVID-19 pandemic and intensified during the lockdown. For ICU-admissions, a significant rise during the COVID-19 pandemic was followed by diminution during the lockdown period. During lockdown, significantly diminishing trends were shown for all diagnostic categories (between -40.8% and -73.6%), except influenza-like illness/COVID cases (+31.6%), Pulmonary embolism/deep vein thrombosis (+33.5%) and frequent users (+188.0%). The present study confirms an increase in demand during the influenza epidemic and during the initial phase of the COVID-19 epidemic, but a drop in activity during the lockdown, mainly related to non-COVID conditions. Syndromic surveillance of ILI cases in ED is a tool for monitoring influenza and COVID-19, and it can predict ED activity and the need for MSW and ICU beds.

Factors associated with single-room assignment among patients admitted through the emergency department during influenza epidemics

INTRODUCTION

Every winter, emergency departments (EDs) face overcrowding with patients presenting influenza-like symptoms, and organisational issues such as single room assignment and droplet precautions to avoid hospital-acquired influenza. Our main objective was to assess the impact of PCR results and patient's severity on single room assignment.

METHODS

All patients admitted to Bichat-Claude Bernard Hospital through the ED and tested for influenza by PCR (GenXpert, Cepheid) or (FilmArray, BioMérieux) on a nasopharyngeal swab were retrospectively included during three influenza seasons (2015-2018.

RESULTS

Of 1,330 included patients, 278 (20.9%) had a positive PCR for influenza. The median time to obtain a PCR result was 19 hours, and 238 (18.3%) patients were assigned a single room. Among patients with positive and negative influenza PCR, 22.3% and 16.7% were assigned a single room (p = 0.03). The multivariable analysis was performed on the two first epidemic periods, excluding the third epidemic because of the concomitant use of influenza immune-chromatic test. Only level 1 of the Emergency severity index (ESI) (aOR, 1.9; 95% CI, 1.3-2.8; p < 0.01) was associated with single-room assignment. PCR result was not statistically associated with the decision of single room assignment (aOR, 1.4; 95%CI, 1.0-1.4; p = 0.07).

CONCLUSION

A PCR positive for influenza was not significantly associated with single-room assignment. Less than one quarter of influenza patients were adequately assigned a single room, likely due to the long turnaround time of PCR result and other conflicting indications for single room-assignment. Accelerating biological diagnosis could improve single-room assignment.

Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the First Rapid Multiplex PCR Commercial Assay for SARS-CoV-2 Detection

In the race to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), efficient detection and triage of infected patients must rely on rapid and reliable testing. In this work, we performed the first evaluation of the QIAstat-Dx respiratory SARS-CoV-2 panel (QIAstat-SARS) for SARS-CoV-2 detection. This assay is the first rapid multiplex PCR (mPCR) assay, including SARS-CoV-2 detection, and is fully compatible with a non-PCR-trained laboratory or point-of-care (PoC) testing. This evaluation was performed using 69 primary clinical samples (66 nasopharyngeal swabs [NPS], 1 bronchoalveolar lavage fluid sample [BAL], 1 tracheal aspirate sample, and 1 bronchial aspirate sample) comparing SARS-CoV-2 detection with the currently WHO-recommended reverse transcription-PCR (RT-PCR) (WHO-RT-PCR) workflow. Additionally, a comparative limit of detection (LoD) assessment was performed for QIAstat-SARS and WHO-RT-PCR using a quantified clinical sample. Compatibility of sample pretreatment for viral neutralization or viscous samples with the QIAstat-SARS system were also tested. The QIAstat-Dx respiratory SARS-CoV-2 panel demonstrated a sensitivity comparable to that of the WHO-recommended assay with a limit of detection at 1,000 copies/ml. The overall percent agreement between QIAstat-Dx SARS and WHO-RT-PCR on 69 clinical samples was 97% with a sensitivity of 100% (40/40) and specificity at 93% (27/29). No cross-reaction was encountered for any other respiratory viruses or bacteria included in the panel. The QIAstat-SARS rapid multiplex PCR panel provides a highly sensitive, robust, and accurate assay for rapid detection of SARS-CoV-2. This assay allows rapid decisions even in non-PCR-trained laboratory or point-of-care testing, allowing innovative organization.