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.

The ongoing global spread and increased prevalence of CTX-M-type extended-spectrum β-lactamases in Enterobacteriaceae is of great concern. The successful distribution of CTX-M enzymes mainly involves Escherichia coli causing systemic as well as urinary tract infections in patients worldwide. CTX-M expression is often associated with coresistance that critically reduces treatments options. The mobilization of bla(CTX-M) genes from their original chromosomal position in various Kluyvera species has been facilitated by mobile genetic elements such as ISEcp1 or ISCR1. Molecular epidemiological studies have revealed a thriving linkage of bla(CTX-M) genes to conjugative plasmids and successful bacterial clones. Multireplicon FII plasmids are shown to carry the most widely distributed bla(CTX-M-15) across continents, paving the way for bla(CTX-M-15) into different genetic lineages of E. coli. Dissemination of virulent clones ST131-O25:H4-B2 and ST405-O102:H6-D is now being described worldwide. Importantly, CTX-M-producing strains are uncovering their ability of long-term gastrointestinal colonization often associated with travel to high-prevalent areas. Thus, we are witnessing a global epidemic of bla(CTX-M)-encoding E. coli strains and plasmids, which require serious attention and efficient infection control measures.

The emergence of KPC-producing isolates of K. pneumoniae in Norway and Sweden is associated with multiple import events and probable local transmission of a successful multiresistant ST258 clone, closely related to the CTX-M-15-producing ST11 clone previously described in Hungary.

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-...

BackgroundTo study the molecular characteristics of a long-term, low frequency outbreak of bla KPC-2 in a low prevalence setting involving the hospital environment.Methodology/Principal FindingsKPC-producing bacteria were screened by selective chromogenic agar and Real-Time PCR. The presence of antibiotic resistance genes was ascribed by PCRs and subsequent sequencing, and the KPC-producing isolates were phylogenetically typed using PFGE and multi-locus sequence typing. Bla KPC-2-plasmids were identified and analysed by S1-nuclease-PFGE hybridization and PCR based replicon typing. A ∼97 kb IncFII plasmid was seen to carry bla KPC-2 in all of the clinical isolates, in one of the isolates recovered from screened patients (1/136), and in the Klebsiella pneumoniae and Enterobacter asburiae isolates recovered from the environment (sinks) in one intensive care unit. The K. pneumoniae strain ST258 was identified in 6 out of 7 patients. An intergenus spread to E. asburiae and an interspecies spread to two different K. pneumoniae clones (ST27 and ST461) of the bla KPC-2 plasmid was discovered. K. pneumoniae ST258 and genetically related E. asburiae strains were found in isolates of both human and environmental origins.Conclusions/SignificanceWe document a clonal transmission of the K. pneumoniae ST258 strain, and an intergenus plasmid diffusion of the IncFII plasmid carrying bla KPC-2 in this outbreak. A major reservoir in the patient population could not be unveiled. However, the identification of a persisting environmental reservoir of strains with molecular determinants linked to human isolates, suggests a possible role of the environment in the maintenance of this long-term outbreak.