The population structure of vancomycin-resistant and -susceptible in a low-prevalence antimicrobial resistance setting is highly influenced by circulating global hospital-associated clones.

Between 2010 and 2015 the incidence of vancomycin-resistant (VRE) in Norway increased dramatically. Hence, we selected (1) a random subset of vancomycin-resistant enterococci (VRE) from the Norwegian Surveillance System for Communicable Diseases (2010-15; =239) and (2) Norwegian vancomycin-susceptible (VSE) bacteraemia isolates from the national surveillance system for antimicrobial resistance in microbes (2008 and 2014; =261) for further analysis. Whole-genome sequences were collected for population structure, gene cluster, mobile genetic element and virulome analysis, as well as antimicrobial susceptibility testing.

Investigating the human jejunal microbiota.

Descriptions of the small intestinal microbiota are deficient and conflicting. We aimed to get a reliable description of the jejunal bacterial microbiota by investigating samples from two separate jejunal segments collected from the luminal mucosa during surgery. Sixty patients with morbid obesity selected for elective gastric bypass surgery were included in this survey.

Managing Contamination and Diverse Bacterial Loads in 16S rRNA Deep Sequencing of Clinical Samples: Implications of the Law of Small Numbers.

In this article, we investigate patterns of microbial DNA contamination in targeted 16S rRNA amplicon sequencing (16S deep sequencing) and demonstrate how this can be used to filter background bacterial DNA in diagnostic microbiology. We also investigate the importance of sequencing depth. We first determined the patterns of contamination by performing repeat 16S deep sequencing of negative and positive extraction controls.

Characterization of abscesses from liver, pancreas and kidney using deep sequencing of the 16S rRNA gene.

To characterize the microbial communities in abscess material from liver, pancreas, and kidneys, we performed deep sequencing of the 16S rRNA gene, in addition to cultivation and Sanger based 16S rRNA gene sequencing directly from the samples. Fifty-nine abscess samples were investigated, 38 from liver, 11 from pancreas, 10 from kidney. Using deep sequencing we made 227 bacterial identifications in 52 specimens, as compared to 69 identifications from the 44 specimens positive by culture.

sp. nov., isolated from brain abscess and blood.

We herein describe the first novel species within the genus since it was established in 1972 by the reclassification of ' to . From a polymicrobial brain abscess, we encountered an isolate, PXX, that could not validly be named . The isolate grew on blood agar with small, translucent, pitting colonies after 3 days of anaerobic incubation.

The 'Finnish new variant of ' escaping detection in the Aptima Combo 2 assay is widespread across Norway, June to August 2019.

The 'Finnish new variant of ' (FI-nvCT), escaping detection in the Aptima Combo 2 assay (AC2), is widespread across Norway. From June to August 2019, 84% (81/97) of available AC2/Aptima CT discordant samples from five laboratories were confirmed as FI-nvCT. Two additional CT variants (CT 23S rRNA C1514T and G1523A) also escaped AC2 detection.

Bacteria and fungi in acute cholecystitis. A prospective study comparing next generation sequencing to culture.

Objectives: Guidelines for antibiotic treatment of acute cholecystitis are based on studies using culture techniques for microbial identification. Microbial culture has well described limitations and more comprehensive data on the microbial spectrum may support adjustments of these recommendations. We used next generation sequencing to conduct a thorough microbiological characterization of bile-samples from patients with moderate and severe acute cholecystitis.