Rapid, adaptable and sensitive Cas13-based COVID-19 diagnostics using ADESSO.

During the ongoing COVID-19 pandemic, PCR testing and antigen tests have proven critical for helping to stem the spread of its causative agent, SARS-CoV-2. However, these methods suffer from either general applicability and/or sensitivity. Moreover, the emergence of variant strains creates the need for flexibility to correctly and efficiently diagnose the presence of substrains. To address these needs we developed the diagnostic test ADESSO (Accurate Detection of Evolving SARS-CoV-2 through SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) Optimization) which employs Cas13 to diagnose patients in 1 h without sophisticated equipment. Using an extensive panel of clinical samples, we demonstrate that ADESSO correctly identifies infected individuals at a sensitivity and specificity comparable to RT-qPCR on extracted RNA and higher than antigen tests for unextracted samples. Altogether, ADESSO is a fast, sensitive and cheap method that can be applied in a point of care setting to diagnose COVID-19 and can be quickly adjusted to detect new variants.

A case series of severe breakthrough infections observed in nine patients with COVID-19 in a southwestern German university hospital.

PURPOSE: Vaccination is the key element for protection against COVID-19. Increased vaccination breakthroughs raise the question of whether additional prevention is necessary in case of individual risk factors for a severe course with hospitalization or death despite vaccination. METHODS: Since July 13, 2021, there is an extended reporting requirement by German law. We analyzed our hospitalized patients with vaccine breakthrough infection during the first 8 weeks. RESULTS: Nine of 67 patients (13.4%) hospitalized for COVID-19 (median age 75 years) were fully vaccinated. Five of these patients received intensive care; two patients died. All had received two doses of BNT162b2 vaccines (Pfizer-BioNTech). There was a median of 99 days between complete immunization and symptom onset. All patients suffered from ≥ three comorbidities. Six patients (66.7%) showed a negative Anti-SARS-CoV-2-N titer at the time of vaccine breakthrough, five of these also had Anti-SARS-CoV-2-S titers < 100 U/ml. All determinable cases were Delta variant B.1.617.2. CONCLUSION: Advanced age, underlying cardiorespiratory disease, and the Delta variant of SARS-CoV-2 were associated with hospitalization of our patients, suffering from vaccine breakthrough infection. Avoidance of face masks, lack of immunization of close contacts, and travel to high-risk areas have been observed as modifiable behavioural circumstances. Consistent personal protective measures, vaccination of close caregivers, and increased awareness might be effective measures in addition to COVID-19 booster vaccination for patients at a high risk to suffer a severe course of infection.

Emergence of Macrolide-Resistant Mycoplasma pneumoniae during an Outbreak in a Primary School: Clinical Characterization of Hospitalized Children.

Mycoplasma pneumoniae (M. pneumoniae) is a common causative pathogen of community-acquired pneumonia. Here, we report the development of macrolide resistance during a school outbreak of severe M. pneumoniae infections in southwest Germany. We conducted a case series to assess the clinical and laboratory characteristics of hospitalized children with M. pneumonia infection and the prevalence of macrolide-resistant M. pneumoniae (MRMP) in this patient group. We retrospectively analyzed 23 children with serologically (19 patients) and/or PCR (eight patients) confirmed M. pneumoniae infection between October 2019 and December 2019. Most of the 15 hospitalized patients had lower respiratory tract infection (n = 10) and required oxygen therapy (83%). The median length of hospitalization was 7 days (range 3-10 days). In 8/15 patients (53.3%) azithromycin and in 4/15 (26.6%) clarithromycin treatment was applied. However, among the five patients for which extended molecular characterization was performed, sequencing of 23S rRNA revealed no mutation only in the first case, but development of macrolide resistance A2058G in four subsequent cases. Hence, we identified a cluster of hospitalized patients with emerging MRMP. Further studies are warranted to confirm a potential link between macrolide resistance and disease severity.

Emergence of carbapenem-resistant ST131 Escherichia coli carrying blaOXA-244 in Germany, 2019 to 2020.

The dissemination of carbapenem-producing Gram-negative bacteria is a major public health concern. We report the first detection of OXA-244-producing ST131 O16:H5 Escherichia coli in three patients from two tertiary hospitals in the south-west of Germany. OXA-244 is emerging in Europe. Because of detection challenges, OXA-244-producing E. coli may be under-reported. The emergence of carbapenem resistance in a globally circulating high-risk clone, such as ST131 E. coli is of clinical relevance and should be monitored closely.

Reconstitution of mRNA editing in yeast using a Gal4-apoB-Gal80 fusion transcript as the selectable marker.

We describe a fusion transcript of Gal4 linked to its specific inhibitor protein Gal80 by 276 nucleotides of apolipoprotein (apo) B sequence as a selectable marker for mRNA editing. Editing of apoB mRNA is catalyzed by an editing enzyme complex that introduces a stop codon by deamination of C to U. The catalytic subunit APOBEC-1 is a cytidine deaminase and requires a second essential component recently cloned and termed APOBEC-1 complementing factor (ACF) or APOBEC-1-stimulating protein (ASP). The aim of this study was to demonstrate that APOBEC-1 plus ACF/ASP comprise all that is required for editing of apoB mRNA in vivo. Expression of APOBEC-1 and Gal4 fused to its inhibitor Gal80 by an intervening unedited apoB sequence (Gal4-apoB(C)-Gal80) did not result in the Gal4-dependent expression of HIS3 and beta-galactosidase in the yeast strain CG1945. Co-expression of APOBEC-1 and ACF/ASP induced editing of the apoB site in up to 13% of the Gal4-apoB(C)-Gal80 transcripts and enabled selection of yeast cells for robust expression of HIS3 and beta-galactosidase. Additional expression of the alternative splicing regulatory protein KSRP increased the editing of the apoB site by APOBEC-1 and ACF/ASP to 21%. Thus, APOBEC-1 and ACF/ASP represent the core apoB mRNA editing enzyme in vivo. This study demonstrates for the first time the successful use of a selectable marker for mRNA editing. The Gal4-Gal80 system is analogous to the two-hybrid assay and may have broader applications for the study of other mRNA processing reactions.