In late November 2021, an outbreak of Omicron SARS-CoV-2 following a Christmas party with 117 attendees was detected in Oslo, Norway. We observed an attack rate of 74% and most cases developed symptoms. As at 13 December, none have been hospitalised. Most participants were 30–50 years old. Ninety-six percent of them were fully vaccinated. These findings corroborate reports that the Omicron variant may be more transmissible, and that vaccination may be less effective in preventing infection compared with Delta.

Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and bla CTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes. Bloodstream infections (BSIs) and sepsis are major causes of morbidity and mortality worldwide. Epidemiological data are scarce, but a recent estimate indicated that 31.5 million cases of sepsis and 5.3 million sepsis attributable deaths occur annually 1. This estimate is only based on data collected from high-income countries, and it therefore likely underestimates the true burden of disease worldwide, especially in low-and-middle-income countries 2. Most studies on sepsis and BSIs report an increasing incidence over the last two decades 3 , particularly among the immunocompromised, multimorbid, and elderly patients, or due to failure of empiric antibiotic regimens as result of antimicrobial resistance (AMR) 4. With multi drug resistant pathogens spreading at an alarming rate, widely adopted empirical antibiotic treatment regimens for sepsis based on penicillin (or aminopenicillin) in combination with gentamicin 5 are being challenged. In particular, the escalating burden of infections due to extended-spectrum β-lactamase (ESBL) producing Gram negative bacteria represents a major health concern. These bacteria, mainly Escherichia coli and Klebsiella pneumoniae, are not only resistant to all penicillins and third generation cephalosporins, but also frequently express co-resistance to gentamicin. Consequently, treatment failure may occur, and clinicians increasingly prescribe last-resort antibiotics such as carbapenems as initial antibiotic treatment of sepsis. This in turn contributes to development and spread of AMR and to a further increase in the burden of infections caused by resistant bacteria. Current state-of-...

5Enterotoxigenic Escherichia coli (ETEC) is responsible for 280 million to 400 million episodes of diarrhea and about 380,000 deaths annually. Epidemiological data suggest that ETEC strains which secrete heat-stable toxin (ST), alone or in combination with heat-labile toxin (LT), induce the most severe disease among children in developing countries. This makes ST an attractive target for inclusion in an ETEC vaccine. ST is released upon colonization of the small intestine and activates the guanylate cyclase C receptor, causing profuse diarrhea. To generate a successful toxoid, ST must be made immunogenic and nontoxic. Due to its small size, ST is nonimmunogenic in its natural form but becomes immunogenic when coupled to an appropriate large-molecular-weight carrier. This has been successfully achieved with several carriers, using either chemical conjugation or recombinant fusion techniques. Coupling of ST to a carrier may reduce toxicity, but further reduction by mutagenesis is desired to obtain a safe vaccine. More than 30 ST mutants with effects on toxicity have been reported. Some of these mutants, however, have lost the ability to elicit neutralizing immune responses to the native toxin. Due to the small size of ST, separating toxicity from antigenicity is a particular challenge that must be met. Another obstacle to vaccine development is possible cross-reactivity between anti-ST antibodies and the endogenous ligands guanylin and uroguanylin, caused by structural similarity to ST. Here we review the molecular and biological properties of ST and discuss strategies for developing an ETEC vaccine that incorporates immunogenic and nontoxic derivatives of the ST toxin.

g Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrheal disease and death in children <5 years old. ETEC strains that express the heat-stable toxin (ST), with or without the heat-labile toxin, are among the four most important diarrhea-causing pathogens. This makes ST an attractive target for an ETEC vaccine. An ST vaccine should be nontoxic and elicit an immune response that neutralizes native ST without cross-reacting with the human endogenous guanylate cyclase C receptor ligands. To identify variants of ST with no or low toxicity, we screened a library of all 361 possible single-amino-acid mutant forms of ST by using the T84 cell assay. Moreover, we identified mutant variants with intact epitopes by screening for the ability to bind neutralizing anti-ST antibodies. ST mutant forms with no or low toxicity and intact epitopes are termed toxoid candidates, and the top 30 candidates all had mutations of residues A14, N12, and L9. The identification of nontoxic variants of L9 strongly suggests that it is a novel receptor-interacting residue, in addition to the previously identified N12, P13, and A14 residues. The screens also allowed us to map the epitopes of three neutralizing monoclonal antibodies, one of which cross-reacts with the human ligand uroguanylin. The common dominant epitope residue for all non-cross-reacting antibodies was Y19. Our results suggest that it should be possible to rationally design ST toxoids that elicit neutralizing immune responses against ST with minimal risk of immunological cross-reactivity. D iarrhea caused by enterotoxigenic Escherichia coli (ETEC)contributes to the almost 600,000 annual child deaths due to diarrheal disease in low-and middle-income countries (1). In addition, the 280 to 400 million annual episodes of ETEC diarrhea in children Ͻ5 years old (2, 3) contribute to malnutrition and a failure to thrive (4). Thus, the World Health Organization strongly encourages the development of an ETEC vaccine (2). ETEC is also the most common cause of traveler's diarrhea (5).ETEC causes diarrhea by colonizing the small intestine with subsequent expression of heat-labile (LT) and/or heat-stable toxins (ST; variants STh and STp) that elicit a net efflux of salt and water into the intestinal lumen (6). Both LT and ST are potential vaccine targets, in addition to the many surface-exposed antigens, including the colonization factors. ETEC vaccine development has primarily targeted colonization factors and LT (7,8), and the most promising vaccine candidate to date is a killed whole-cell vaccine comprising five different ETEC strains that express the most prevalent colonization factors, coadministered with the cholera toxin B subunit, which is a homologue of the LT B subunit (9). This vaccine was found to be efficacious against serious diarrhea among American travelers to Guatemala (10) but not protective when evaluated in Egyptian children (11).A recently conducted large global multicenter study designed to analyze the etiology of enteric pathogens in children ranked ...

Some variants of SARS-CoV-2 are associated with increased transmissibility, increased disease severity or decreased vaccine effectiveness (VE). In this population-based cohort study (n = 4,204,859), the Delta variant was identified in 5,430 (0.13%) individuals, of whom 84 were admitted to hospital. VE against laboratory confirmed infection with the Delta variant was 22.4% among partly vaccinated (95% confidence interval (CI): 17.0−27.4) and 64.6% (95% CI: 60.6−68.2) among fully vaccinated individuals, compared with 54.5% (95% CI: 50.4−58.3) and 84.4% (95%CI: 81.8−86.5) against the Alpha variant.

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Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.