During the Coronavirus disease 2019 (COVID-19) pandemic, logistic problems associated with specimen collection limited the SARS-CoV-2 testing especially in the community. In this study, we assessed the use of posterior oropharyngeal saliva as specimens for the detection of SARS-CoV-2 in an automated point-of-care molecular assay. Archived nasopharyngeal swab (NPS) and posterior oropharyngeal saliva specimens of 58 COVID-19 patients were tested with the Xpert^® Xpress SARS-CoV-2 assay. SARS-CoV-2 was detected in either NPS or saliva specimens of all patients. Among them, 84.5% (49/58) tested positive in both NPS and saliva, 10.3% (6/58) tested positive in NPS only, and 5.2% (3/58) tested positive in saliva only. No significant difference in detection rate was observed between NPS and saliva (McNemar’s test p=0.5078). The detection rate was slightly higher for N2 (NPS 94.8% and Saliva 93.1%) than that of the E gene target (Saliva:89.7% vs 82.8%) on both specimen types. Significant earlier median Ct value was observed for NPS comparing to that of saliva on both E (26.8 vs 29.7, p=0.0002) and N2 gene target (29.3 vs 32.3, p=0.0002). The median Ct value of E gene target was significantly earlier than that of the N2 gene target for both NPS (26.8 vs 29.3, p<0.0001) and saliva (29.7 vs 32.3, p<0.0001). In conclusion, posterior oropharyngeal saliva and NPS were found to have similar detection rates in the point-of-care test for SARS-CoV-2 detection. Due to the easy collection of posterior oropharyngeal saliva, the use of saliva as an alternative specimen type for SARS-CoV-2 detection is recommended.

A broad range of viral and bacterial pathogens can cause acute respiratory tract infection. For rapid detection of a broad respiratory pathogen spectrum, multiplex real-time PCR is ideal. This study evaluated the performance of the new Luminex NxTAG Respiratory Pathogen Panel (NxTAG-RPP) in comparison with the BioFire FilmArray Respiratory Panel (FA-RP) or singleplex real-time PCR as reference. A total of 284 clinical respiratory specimens and 3 influenza A/H7N9 viral culture samples were tested. All clinical specimens were processed and analyzed in parallel using NxTAG-RPP and the reference standard method. The H7N9 viral culture samples were tested using NxTAG-RPP only. Overall, the NxTAG-RPP demonstrated ≥93% sensitivity and specificity for all respiratory targets except human coronavirus OC43 (HCoV-OC43) and HCoV-HKU1. The H7N9 virus was detected by the influenza A virus matrix gene target, while other influenza A virus subtyping gene targets in the panel remained negative. Complete concordance between NxTAG-RPP and FA-RP was observed in 98.8% (318/322) of positive results (kappa = 0.92). Substantial agreement was found for most respiratory targets, but significant differences were observed in human metapneumovirus ( P = 0.001) and parainfluenza virus type 3 ( P = 0.031). NxTAG-RPP has a higher sample throughput than FA-RP (96 samples versus 1 sample per run) while the turnaround times for NxTAG-RPP and FA-RP were 5 h (up to 96 samples) and 1 h (for one sample), respectively. Overall, NxTAG-RPP demonstrated good diagnostic performance for most respiratory pathogens. The high sample throughput with reasonable turnaround time of this new assay makes it a suitable multiplex platform for routine screening of respiratory specimens in hospital-based laboratories.

Background: The relative contribution of long term care facilities (LTCFs) and hospitals in the transmission of methicillin-resistant Staphylococcus aureus (MRSA) is unknown. Methods: Concurrent MRSA screening and spa type analysis was performed in LTCFs and their network hospitals to estimate the rate of MRSA acquisition among residents during their stay in LTCFs and hospitals, by colonization pressure and MRSA transmission calculations. Results: In 40 LTCFs, 436 (21.6%) of 2020 residents were identified as ‘MRSA-positive’. The incidence of MRSA transmission per 1000-colonization-days among the residents during their stay in LTCFs and hospitals were 309 and 113 respectively, while the colonization pressure in LTCFs and hospitals were 210 and 185 per 1000-patient-days respectively. MRSA spa type t1081 was the most commonly isolated linage in both LTCF residents (76/121, 62.8%) and hospitalized patients (51/87, 58.6%), while type t4677 was significantly associated with LTCF residents (24/121, 19.8%) compared with hospitalized patients (3/87, 3.4%) (p < 0.001). This suggested continuous transmission of MRSA t4677 among LTCF residents. Also, an inverse linear relationship between MRSA prevalence in LTCFs and the average living area per LTCF resident was observed (Pearson correlation −0.443, p = 0.004), with the odds of patients acquiring MRSA reduced by a factor of 0.90 for each 10 square feet increase in living area. Conclusions: Our data suggest that MRSA transmission was more serious in LTCFs than in hospitals. Infection control should be focused on LTCFs in order to reduce the burden of MRSA carriers in healthcare settings.

Prolonged asymptomatic carriage of vancomycin-resistant enterococci (VRE) in the gastrointestinal tract and the lack of effective decolonization regimen perpetuate the endemicity of VRE in the healthcare settings. We report a regimen for decolonization of gastrointestinal carriage of VRE by a combination of environmental disinfection, patient isolation, bowel preparation to wash-out the fecal bacterial population using polyethylene glycol, a five-day course of oral absorbable linezolid and non-absorbable daptomycin to suppress any remaining VRE, and subsequent oral Lactobacillus rhamnosus GG to maintain the colonization resistance in four patients, including two patients with end-stage liver cirrhosis, one patient with complication post liver transplant, and one patient with complicated infective endocarditis. All patients had clearance of VRE immediately after decolonization, and 3 of them remained VRE-free for 23 to 137 days of hospitalization, despite subsequent use of intravenous broad-spectrum antibiotics without anti-VRE activity. This strategy should be further studied in settings of low VRE endemicity with limited isolation facilities.