Antiviral combination treatment of SARS-CoV-2 after repeated treatment failures of remdesivir monotherapy: A case report.

Immunocompromised patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can have a longer duration of viral shedding and persistence of symptoms. The optimal treatment strategy for these patients remains to be established. This case describes a male in his late sixties with follicular lymphoma and persistent symptoms of infection with SARS-CoV-2 variant BA.

MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis.

Background: The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for single-isolate genomes. As result quality depends on sequence quality, performance of tools for single-isolate genomes on MAGs should be tested beforehand. Bioinformatics can be leveraged to quickly create varied synthetic test sets with known composition for this purpose.

Contaminated dicloxacillin capsules as the source of an NDM-5/OXA-48-producing ST79 outbreak, Denmark and Iceland, 2022 and 2023.

From October 2022 through January 2023, nine patients with NDM-5/OXA-48-carbapenemase-producing ST79 were detected in Denmark and subsequently one patient in Iceland. There were no nosocomial links between patients, but they had all been treated with dicloxacillin capsules. An NDM-5/OXA-48-carbapenemase-producing ST79, identical to patient isolates, was cultured from the surface of dicloxacillin capsules in Denmark, strongly implicating them as the source of the outbreak.

Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022.

Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark.

Rectally shed SARS-CoV-2 in COVID-19 inpatients is consistently lower than respiratory shedding and lacks infectivity.

Objectives: Assessment of whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been propagated during intestinal passage and infectivity is conserved when shed rectally by hospitalized individuals.

Methods: An exploratory cohort study including 28 inpatients with coronavirus disease 2019 with estimation of RNA levels by RT-PCR and of viral infectivity by culturing of viral material sampled concomitantly and identically from pharynx and rectum.

Results: SARS-CoV-2 RNA was detected more frequently (91%, 30/33 versus 42%, 14/33, p <0.

Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex.

Microbes produce a plethora of secondary (or specialized) metabolites that, although not essential for primary metabolism, benefit them to survive in the environment, communicate, and influence cell differentiation. Biosynthetic gene clusters (BGCs), responsible for the production of these secondary metabolites, are readily identifiable on bacterial genome sequences. Understanding the phylogeny and distribution of BGCs helps us to predict the natural product synthesis ability of new isolates.

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.

AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential.

Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular.