RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens.

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.

Asymptomatic rectal colonization with carbapenem-resistant Enterobacteriaceae and Clostridium difficile among residents of a long-term care facility in New York City.

BACKGROUND: Residents of long-term care facilities (LTCFs) are at increased risk for colonization and development of infections with multidrug-resistant organisms. This study was undertaken to determine prevalence of asymptomatic rectal colonization with Clostridium difficile (and proportion of 027/NAP1/BI ribotype) or carbapenem-resistant Enterobacteriaceae (CRE) in an LTCF population. METHODS: Active surveillance was performed for C difficile and CRE rectal colonization of 301 residents in a 320-bed (80-bed ventilator unit), hospital-affiliated LTCF with retrospective chart review for patient demographics and potential risk factors. RESULTS: Over 40% of patients had airway ventilation and received enteral feeding. One-third of these patients had prior C difficile-associated infection (CDI). Asymptomatic rectal colonization with C difficile occurred in 58 patients (19.3%, one-half with NAP1+), CRE occurred in 57 patients (18.9%), and both occurred in 17 patients (5.7%). Recent CDI was significantly associated with increased risk of C difficile ± CRE colonization. Multivariate logistic regression analysis revealed presence of tracheostomy collar to be significant for C difficile colonization, mechanical ventilation to be significant for CRE colonization, and prior CDI to be significant for both C difficile and CRE colonization. CONCLUSIONS: The strong association of C difficile or CRE colonization with disruption of normal flora by mechanical ventilation, enteral feeds, and prior CDI carries important implications for infection control intervention in this population.

Evaluation of Remel Spectra CRE Agar for Detection of Carbapenem-Resistant Bacteria from Rectal Swabs Obtained from Residents of a Long-Term-Care Facility.

We compared the Remel Spectra CRE agar plate to CDC standard methodology for the isolation of carbapenem-resistant Enterobacteriaceae (CRE) from 300 rectal swab specimens obtained from patients residing in a long-term-care facility (LTCF). Multiplex PCR experiments were performed on isolates to identify specific Klebsiella pneumoniae carbapenemases (KPC) and additional ß-lactamases. Of the 300 patients, 72 (24%) harbored CRE and were PCR positive for KPC enzymes. The Remel Spectra CRE plates detected KPC-type CRE in isolates from 70 of 72 patients (97.2%), while the CDC method detected CRE in 56 of 72 (77.8%). CRE identification results were available in 18 h compared to 36 h for the CDC method. Remel Spectra CRE agar plates can provide useful means for a fast and reliable method for detecting KPC-type CRE and for accelerated institution of appropriate infection control precautions.