Performance of MassARRAY system for the detection of SARS-CoV-2 compared to real-time PCR.

Background: Early identification of COVID-19 (coronavirus disease of 2019) by diagnostic tests played an important role in the isolation of infectious patients and management of this pandemic. Various methodologies and diagnostic platforms are available. The current "gold standard" for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) diagnosis is real-time reverse transcriptase-polymerase chain reaction (RT-PCR). To overcome the limitations posed by the short supply experienced early during the pandemic and to increase our capacity, we assessed the performance of the MassARRAY System (Agena Bioscience). Methods: MassARRAY System (Agena Bioscience) combines RT-PCR (reverse transcription-polymerase chain reaction) with high-throughput mass spectrometry processing. We compared the MassARRAY performance to a research-use-only E-gene/EAV (Equine Arteritis Virus) assay and RNA Virus Master PCR. Discordant results were tested with a laboratory-developed assay using the Corman et al. E-gene primers and probes. Results: 186 patient specimens were analyzed using the MassARRAY SARS-CoV-2 Panel. The performance characteristics were as follows: the positive agreement was 85.71%, 95% CI (78.12 - 91.45), and the negative agreement was 96.67%, 95% CI (88.47 - 99.59). 19/186 (10.2%) results were found to be discordant and assessed by a different assay with the exception of 1, where the sample was not available for repeat testing. 14 out of 18 agreed with the MassARRAY after testing with the secondary assay. The overall performance after discordance testing was as follows: the positive agreement was 97.3%, 95% CI (90.58 - 99.67), and the negative agreement was 97.14%, 95% CI (91.88 - 99.41). Conclusion: Our study demonstrates that the MassARRAY System is an accurate and sensitive method for SARS-CoV-2 detection. Following the discordant agreement with an alternate RT-PCR test, the performance was found to have sensitivity, specificity, and accuracy exceeding 97%, making it a viable diagnostic tool. It can be used as an alternative method during periods when real-time RT-PCR reagent supply chains are disrupted.

Yokenella regensburgei infection in an immunocompetent individual after trauma following a fall from a personal conveyance.

Background: Yokenella regensburgei infections have been documented in several immunocompromised individuals with numerous associated risk factors including soft tissue infections, organ transplants, and metabolic disorders. Our report presents a rare case of Y. regensburgei infection in an immunocompetent individual. Methods: In September 2020, a 38-year-old man who was otherwise healthy fell from a personal conveyance causing a puncture of his elbow. Two months later, he was admitted to the hospital with a chronic draining wound on his left arm with no fever (36.7°C) and stable vital signs. The patient underwent white blood cell (WBC) imaging, and single-photon emission computed tomography (SPECT/CT) to rule out osteomyelitis. Incision and drainage were performed, and the collected fluid was sent to a microbiology lab for culture diagnosis. Subsequently, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis and antimicrobial susceptibility testing were performed. Results: A WBC image and SPECT/CT test showed an increase in WBC uptake and activity in the subcutaneous tissue of the left arm. The culture diagnosis identified the isolate as Y. regensburgei and the patient received 2 weeks of sulfamethoxazole 800 mg and trimethoprim 160 mg orally twice daily based on the results of the antimicrobial susceptibility testing. He demonstrated clinical improvements shown through wound healing and reduced pain. Conclusion: This report supports the potential of Y. regensburgei to act as an opportunistic pathogen even in hosts with no prior underlying diseases or conditions.

Historique: Les infections à Yokenella regensburgei, qui ont été diagnostiquées chez plusieurs personnes immunodéprimées, sont associées à des facteurs de risque, y compris des infections des tissus mous, des transplantations d'organes et des troubles métaboliques. Le présent rapport expose un rare cas d'infection à Y. regensburgei chez une personne immunocompétente. Méthodologie: En septembre 2020, un homme de 38 ans en bonne santé a subi une blessure ponctiforme sur le coude gauche à cause d'une chute en vélo de montagne. Deux mois plus tard, il a été hospitalisé en raison d'une plaie purulente chronique sur le bras gauche. Il ne faisait pas de fièvre (36,7°C), et ses signes vitaux étaient stables. Il a été soumis à une scintigraphie aux globules blancs et une tomographie par émission monophotonique pour écarter la possibilité d'ostéomyélite. Après une incision et un drainage, le liquide recueilli a été envoyé à un laboratoire de microbiologie pour poser un diagnostic par culture. Une analyse de la spectrométrie de masse à temps de vol selon la technique de désorption-ionisation laser assistée par matrice (MALDI-TOF) et un test de susceptibilité antimicrobienne ont ensuite été exécutés. Résultats: La scintigraphie aux globules blancs et la tomographie par émission monophotonique ont révélé une augmentation de la numération et de l'activité des globules blancs dans les tissus sous-cutanés du bras gauche. La culture a identifié que l'isolat était l'Y. regensburgei, et le patient a reçu un traitement de 800 mg de sulfaméthoxazole et de 160 mg de triméthoprime par voie orale deux fois par jour pendant deux semaines, en fonction du test de susceptibilité antimicrobienne. Son état clinique s'est amélioré, car sa plaie a guéri et sa douleur a diminué. Conclusion: Le présent rapport appuie la possibilité que l'infection à Y. regensburgei agisse comme agent pathogène opportuniste, même chez des hôtes sans maladie ou affection sous-jacente.

Tracheal Aspirate and Bronchoalveolar Lavage as Potential Specimen Types for COVID-19 Testing Using the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV.

Xpert Xpress SARS-CoV-2/Flu/RSV is a rapid diagnostic test currently approved for the detection of SARS-CoV-2 using upper respiratory tract specimens. This study attempts to assess the performance of this assay using upper and lower respiratory tract specimens by comparing its results to the lab-developed PCR test. We assessed the performance of GeneXpert for the detection of SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus for upper respiratory tract specimens. In addition, the SARS-CoV-2 detection was evaluated for lower respiratory tract specimens (bronchoalveolar lavage and tracheal aspirate). Precision and reproducibility of the test were also assessed using samples with varying cycle threshold values. Xpert Xpress SARS-CoV-2/Flu/RSV shows 100% positive and negative agreements for all four targets when tested using upper respiratory tract specimens. For lower respiratory tract specimens, tracheal aspirate and bronchoalveolar lavage samples respectively show 96% and 100% positive percent agreement for SARS-Cov-2 target only. No positive flu/RSV samples were included for lower respiratory tract specimens. Both samples show 100% negative percent agreement. The precision and reproducibility assay also showed 100% correspondence. Xpert Xpress SARS-CoV-2/Flu/RSV can be potentially used for SARS-Cov-2 detection in lower respiratory tract specimens. Performance passed our study acceptance criteria and shows promising implications as a point of care detection assay. IMPORTANCE Cepheid's Xpert Xpress SARS-CoV-2/Flu/RSV provides a means of rapid diagnosis that can help in hospital bed management and patient flow. It is also important for each microbiology lab to increase its capacity and most importantly have a different platform to overcome the anticipated reagent shortage at times of peak community transmission. There is limited evidence on using it for lower respiratory tract specimens. Here we present our validation for upper respiratory tract specimens as well as a potential use for lower respiratory specimens (BAL and TA), and we discuss some of the applications we have been using in our organization.

Comamonas kerstersii Bacteremia of Unknown Origin.

Comamonas kerstersii (C. kerstersii) is a Gram-negative bacillus abundant in the environment and rarely implicated in human disease. Previously considered nonpathogenic, its scarcity in literature may be partly due to the unreliability of past phenotypic tests used for its identification. In recent years, the development of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has enabled fast and accurate laboratory identification of C. kerstersii. Since the first report of human infection in 2013, several others have emerged, with most cases involving peritoneal infection. Here, we present a rare case of C. kerstersii bacteremia in an 82-year-old male patient. With no clear predisposing conditions, the source of his infection is unclear. We accompany this report with a review of C. kerstersii bacteremia cases found in the literature.

Validation of the Cepheid Xpert® Xpress SARS-CoV-2 using upper and lower respiratory tract specimens.

This study validated the performance of the reverse transcriptase-polymerase chain reaction (rRT-PCR) based Cepheid Xpert® Xpress SARS-CoV-2 assay against the TIB MOLBIOL E-gene/EAV, a standard laboratory rRT-PCR SARS-CoV-2 assay. Upper and lower respiratory tract samples (nasopharyngeal and nasal swabs, bronchoalveolar lavage, and tracheal aspirate) were obtained from patients suspected to have contracted COVID-19. Results from the Xpert® Xpress and standard rRT-PCR assays were compared for positive and negative agreement and analyzed for precision, reproducibility, 95% confidence intervals, and coefficients of variation. The Xpert® Xpress assay demonstrated 100% agreement with the standard lab rRT-PCR for both upper and lower respiratory tract samples. Both the Xpert® Xpress and lab rRT-CPR identified weakly positive (Ct values 35-39) sample replicates with 100% reproducibility and showed 100% precision in identifying triplicates of upper respiratory tract samples. The single-cartridge Xpert® Xpress system has a short turnaround time and can be employed to improve patient management and hospital bed allocation. Further verification of the system is required before implementation and consideration must be paid to its higher cost and impracticality for high-throughput use.