Access to rapid and accurate detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA is essential for controlling the current global pandemic of Coronavirus Disease 2019 (COVID-19). In this study, the use of oral rinses and posterior oropharyngeal saliva as an alternative to swab collection methods from symptomatic and asymptomatic healthcare workers for the detection of SARS-CoV-2 RNA by RT-PCR was evaluated. For saliva samples, the overall agreement with oropharyngeal swabs (OPS) was 93% (Ƙ=0.84) with a sensitivity of 96.7% (95%CI:83.3-99.8%). The agreement between saliva and nasopharyngeal swabs was 97.7% (Ƙ=0.93) with a sensitivity of 94.1% (95% CI:73.0-99.7%). Oral rinses were compared with NPS only, with an overall agreement of 85.7% (Ƙ=0.65), and a sensitivity of 63% (95% CI:46.6-77.8%). The agreement between a laboratory-developed test based on the CDC RT-PCR and two commercial assays, the Xpert Xpress SARS-CoV-2 and the Cobas SARS-CoV-2 was also evaluated. The overall agreement was higher than 90%. Finally, SARS-CoV-2 RNA in saliva samples was shown to be stable, with no changes in viral loads over 24 hours at both room temperature and 4ºC. While the dilution of SARS-CoV-2 in oral rinses precluded its acceptability as a sample type, posterior oropharyngeal saliva was an acceptable alternative sample type for SARS-CoV-2 RNA detection.

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We evaluated the performance characteristics of the FilmArray respiratory panel and the eSensor respiratory viral panel on clinical and spiked lower respiratory tract specimens (LRTS). The overall agreement between the two methods was 89.5% (51/57). The lower limit of detection of both assays for all targets in LRTS was comparable to that for nasopharyngeal swab specimens. Lower respiratory tract infections, especially pneumonia, can be particularly severe and a cause of high morbidity and mortality in cancer and hematopoietic stem cell transplant (HSCT) patients (1). In HSCT recipients, progression of respiratory viral infections from the upper to the lower respiratory tract occurs most frequently with respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza viruses (PIV), and influenza viruses (2, 3). Two of the several multiplexed molecular assays cleared by the Food and Drug Administration (FDA) for the detection of respiratory pathogens include the FilmArray respiratory panel (FA RP) test (BioFire Diagnostics, Salt Lake City, UT) and the eSensor respiratory virus panel (eS RVP) test (GenMark Diagnostics, Carlsbad, CA). However, both assays are cleared only for testing on nasopharyngeal swab (NPS) specimens. A few studies evaluating both the FA RP and the eS RVP have included a small number of other specimen types, including bronchoalveolar lavage (BAL) fluids, bronchial washes (BW), sputum (SPT), throat swabs, and tracheal aspirates (4-8). In this study, we compare the performances of both the FA RP and the eS RVP exclusively with lower respiratory tract specimens (BAL fluids, BW, and SPT) from cancer patients with symptoms of pneumonia. In addition to accuracy, the lower limit of detection (LOD) of the assays for each target in BAL fluids was compared to the LOD for NPS specimens.This was a retrospective study performed with specimens collected from July 2010 to March 2013 and stored at Ϫ80°C following testing by direct fluorescent antibody assay and viral culture as previously described (4). A total of 52 samples (31 BAL fluid, 17 BW, and 4 SPT) from 45 patients were included: 32 consecutive positive samples and 20 randomly selected negative specimens. Patients' ages ranged from 25 to 89 years old, with 25 liquid-tumor patients (12 with leukemia and 13 with lymphoma) and 20 solidtumor patients (12 with lung cancer and 8 with other types of cancer). The most common symptoms included radiological evidence of lung abnormality (infiltrates or nodules) and/or fever and cough. The study was granted a waiver of the HIPPA authorization and informed consent by the Memorial Sloan-Kettering Cancer Center (MSKCC) institutional review board.To increase the number of positive specimens tested, BAL fluids (n ϭ 14) negative for all 20 targets detected by the FA RP were combined, split into 4 pools, and spiked with organisms from the Zeptometrix respiratory panel (Zeptometrix, Buffalo, NY). This panel includes all the targets listed in Table 1. The concentration of each viral stock solution varied fr...

Utilization of UV disinfection to supplement routine terminal cleaning of rooms was not effective in reducing hospital-acquired VRE and C. difficile among SCT recipients.

This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of and species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the ,, and complexes and within the and groups could be differentiated. Among the 312 isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the and complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of and species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and in clinical practice.