An evaluation of the Luminex NxTAG Respiratory Pathogen Panel was performed on 404 clinical respiratory specimens. Clinical sensitivities and specificities of the assay compared to those of the ...reference methods were 80.0% to 100.0% and 98.9% to 100.0%, respectively. Correct genotyping information was provided for 95.5% of influenza virus A specimens. The closed-tube format of the assay simplified the workflow and minimized carryover contamination.
Clostridium difficile is the most common cause of health care-associated diarrhea. Accurate and rapid diagnosis is essential to improve patient outcome and prevent disease spread. We compared our ...two-step diagnostic algorithm, an enzyme immunoassay for glutamate dehydrogenase (GDH) followed by the cytotoxin neutralization test (CYT) with a turnaround time of 24 to 48 h, versus the Cepheid Xpert C. difficile Epi assay, a PCR-based assay with a turnaround time of <1 h. In the first phase of the study, only GDH-positive stool samples were tested by both CYT and Xpert PCR. Discordant results were resolved by toxigenic culture. In the second phase, all stool samples were tested by GDH and Xpert PCR. Only GDH-positive stools were further tested by CYT. Genotypic characterization of 45 Xpert PCR-positive stools was performed by sequencing of the tcdC gene and PCR ribotyping. In phase 1, the agreement between the GDH-CYT and the GDH-Xpert PCR was 72%. The sensitivities and specificities of GDH-CYT and GDH-Xpert PCR were 57% and 97% and 100% and 97%, respectively. In phase 2, the agreement between GDH-CYT and Xpert PCR alone was 95%. As in phase 1, sensitivity of the Xpert PCR was higher than that of the GDH-CYT. The correlation between PCR-ribotyping, sequencing, and Xpert PCR for detection of NAP1 strains was excellent (>90%). The excellent sensitivity and specificity and the rapid turnaround time of the Xpert PCR assay as well as its strain-typing capability make it an attractive option for diagnosis of C. difficile infection.
SARS-CoV-2 was identified and diagnostic methods developed at an impressive speed due in great part to the wider use of molecular methods in 2019 compared with 2002 during the SARS pandemic. The ...development of rapid and novel molecular diagnostic assays, leveraging of the high adaptability of molecular tests, and the integration of SARS-CoV-2 genotyping into public health, clinical, and research laboratories have been some of the successes in SARS-CoV-2 molecular testing. The main challenges are related to regulatory hurdles, supply chain constraints, and laboratory preparation.
The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates that the global scientific community monitor, assess, and respond to the evolving coronavirus ...disease (COVID-19) pandemic. But the current reactive approach to emerging variants is ill-suited to address the quickly evolving and ever-changing pandemic. To tackle this challenge, investments in pathogen surveillance, systematic variant characterization, and data infrastructure and sharing across public and private sectors will be critical for planning proactive responses to emerging variants. Additionally, an emphasis on incorporating real-time variant identification in point-of-care diagnostics can help inform patient treatment. Active approaches to understand and identify “immunity gaps” can inform design of future vaccines, therapeutics, and diagnostics that will be more resistant to novel variants. Approaches where the scientific community actively plans for and anticipates changes to infectious diseases will result in a more resilient system, capable of adapting to evolving pathogens quickly and effectively.
•Respiratory tract infections are a common cause of visits to emergency departments and outpatient settings.•More recently, rapid molecular tests for the detection of influenza viruses A and B have ...become commercially available as point-of-care platforms.•Challenges and opportunities for implementation of CLIA-waived Flu tests (e.g. testing locations, economic and clinical impact) are discussed.
Respiratory tract infections are a common cause of visits to emergency departments and outpatient settings. Infections with influenza viruses A and B in particular, are responsible for significant morbidity and mortality in both pediatric and adult populations worldwide. A significant number of influenza diagnoses occur in the emergency departments with many being performed using rapid influenza diagnostic tests (RIDT) which have sensitivities as low as 30% depending on the specific RIDT and patient population. More recently, rapid molecular tests for the detection of influenza viruses A and B have become commercially available as point-of-care platforms. In the United States, several of these new tests are approved by the Food and Drug Administration as CLIA-waived tests. In this report, we review the data on the analytical and clinical performance of RIDTs and CLIA-waived molecular tests, present and discuss potential key challenges and opportunities for implementation of CLIA-waived molecular tests at or near point of care in the emergency departments and outpatient settings.
Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a ...particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
Clostridium difficile 027/NAP1/BI is the most common C. difficile strain in the United States. The Xpert C. difficile/Epi assay allows rapid, presumptive identification of C. difficile NAP1. We ...compared Xpert C. difficile/Epi to multilocus sequence typing for identification of C. difficile NAP1 and found "very good" agreement at 97.9% (κ = 0.86; 95% confidence interval, 0.80 to 0.91).
Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing ...appropriate therapy, it can be slow and laborious and often relies on subjective morphological criteria. The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has the potential to speed up and improve the accuracy of identification. In this multicenter study, we evaluated the accuracy of the Vitek MS v3.0 system in identifying 1,601 clinical mold isolates compared to identification by DNA sequence analysis and supported by morphological and phenotypic testing. Among the 1,519 isolates representing organisms in the v3.0 database, 91% (
= 1,387) were correctly identified to the species level. An additional 27 isolates (2%) were correctly identified to the genus level. Fifteen isolates were incorrectly identified, due to either a single incorrect identification (
= 13) or multiple identifications from different genera (
= 2). In those cases, when a single identification was provided that was not correct, the misidentification was within the same genus. The Vitek MS v3.0 was unable to identify 91 (6%) isolates, despite repeat testing. These isolates were distributed among all the genera. When considering all isolates tested, even those that were not represented in the database, the Vitek MS v3.0 provided a single correct identification 98% of the time. These findings demonstrate that the Vitek MS v3.0 system is highly accurate for the identification of common molds encountered in the clinical mycology laboratory.
Clostridioides difficile infection (CDI) is prevalent in pediatric oncology patients, but the transmission risk to peers is unknown. In 224 children with CDI, multilocus sequence typing (MLST) ...identified only 7 alleged transmission events (18%) originating from children <3 years old. None of these events were corroborated by WGS.
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