A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay.

OBJECTIVES: The optimal diagnostic specimen to detect SARS-CoV-2 by PCR in the upper respiratory tract is unclear. Mouthwash fluid has been reported as an alternative to nasopharyngeal and oropharyngeal swabs. We compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding test performance. METHODS: In a large refugee facility, we retested individuals with a previous positive test for SARS-CoV-2 and their quarantined close contacts. All individuals were asymptomatic at the time of testing. First, a mouthwash (gargling for at least 5 s) with sterile water was performed. Then, with a single flocked swab the back of the throat and subsequently the nasopharynx were sampled. Samples were inactivated and analysed on a Roche cobas 6800® system with the Roche SARS-CoV-2 test. RESULTS: Of 76 individuals, 39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 of 76 (17%) infections, but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs. CONCLUSION: Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection.

Determining the optimal frequency of SARS-CoV-2 regular asymptomatic testing: A randomized feasibility trial in a home care setting.

BACKGROUND: The SARS-CoV-2 pandemic presented a challenge for caregiving relatives in the home care setting. Caregivers can transmit SARS-CoV-2 to their relatives who are often at high risk for a severe course of COVID-19. Regular testing of asymptomatic caregivers for SARS-CoV-2 may reduce the risk of transmission. The optimal method and frequency of regular asymptomatic testing is unknown. We conducted a prospective, randomised trial to assess the feasibility, recruitment and acceptance of different testing frequencies. This serves to inform a future definitive randomised controlled trial. METHODS: We carried out a parallel three-armed feasibility trial, enrolling adult participants who provided home-based care for a relative at least twice a week. Participants were randomly assigned using sealed envelopes to either conduct saliva-based antigen self-testing at a frequency of once a week (group I), twice a week (group II), or every two days (group III). The participants completed questionnaires on a weekly basis. Main outcome measures were feasibility of recruitment, adherence to self-tests and distress caused by self-testing. We further collected data on the use of mouth-nose mask. RESULTS: From 25 March to 7 May 2021 we assessed 27 participants and randomised 26 in the study: 8 participants in group I, 8 in group II and 10 in group III. All participants completed the study. In group I 48/48 (100.0%; 95% CI 92.6% to 100.0%), in group II 93/96 (96.9%; 95% CI 91.2% to 98.9%) and in group III 209/210 (99.5%; 95% CI 97.4% to 99.9%) self-tests were carried out at home. Participants did not perceive regular self-testing as burdensome in any of the study arms. We did not observe any infection with SARS-CoV-2. During the study, mask adherence decreased from 35% to 19% in all groups. CONCLUSION: Conducting such a study was feasible. The participants tolerated regular self-testing well, which was reflected in a high level of test adherence. However, regular self-testing may have led to decreased protective behaviour. To demonstrate that regular asymptomatic testing reduces infection transmission, a future definitive trial should be performed at a time of a high prevalence of SARS-CoV-2 and be implemented as a multicentre study. TRIAL REGISTRATION: The trial is registered with the German Clinical Trials Register, DRKS00026234.

Whole genomes from bacteria collected at diagnostic units around the world 2020.

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

Human Erysipelothrix rhusiopathiae infection via bath water - case report and genome announcement.

Erysipelothrix rhusiopathiae is a facultative anaerobic, environmentally stable, Gram-positive rod that causes swine and avian erysipelas as a zoonotic pathogen. In humans, the main manifestations described are circumscribed erysipeloid, generalized erysipeloid, and endocarditis. Here, we report a 46-year-old female patient who presented to the physician because of redness and marked functio laesa of the hand, in terms of a pain-related restricted range of motion, and was treated surgically. E. rhusopathiae was detected in tissue biopsy. The source of infection was considered to be a pond in which both swine and, later, her dog bathed. The genome of the isolate was completely sequenced and especially the presumptive virulence associated factors as well as the presumptive antimicrobial resistance genes, in particular a predicted homologue to the multiple sugar metabolism regulator (MsmR), several predicted two-component signal transduction systems, three predicted hemolysins, two predicted neuraminidases, three predicted hyaluronate lyases, the surface protective antigen SpaA, a subset of predicted enzymes that potentially confer resistance to reactive oxygen species (ROS), several predicted phospholipases that could play a role in the escape from phagolysosomes into host cell cytoplasm as well as a predicted vancomycin resistance locus (vex23-vncRS) and three predicted MATE efflux transporters were investigated in more detail.