Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors.

Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing.

The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo.

With the increasing prevalence of antimicrobial-resistant bacterial infections, there is interest in using bacteriophages (phages) to treat such infections. However, the factors that govern bacteriophage pharmacokinetics in vivo remain poorly understood. Here, we have examined the contribution of neutrophils, the most abundant phagocytes in the body, to the pharmacokinetics of i.

Diversity, functional classification and genotyping of SHV β-lactamases in .

Interpreting the phenotypes of alleles in genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal alleles or additional plasmid-borne alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood.

Point-of-care Testing in Complicated Urinary Tract Infection: Evaluation of the Vivalytic One Urinary Tract Infection Analyser for Detecting Uropathogenic Bacteria and Antimicrobial Resistance in Urine Samples of Urological Patients in a Point-of-care Setting.

Background And Objective: Urinary tract infections (UTIs) are some of the most encountered infections in clinical practice, exhibiting increasing antimicrobial resistance. Bacterial species identification and antimicrobial resistance testing at point of care (POCT) could improve adequate initial antibiotic therapy and antimicrobial stewardship. In this work, the Vivalytic UTI test, which represents a qualitative PCR-based microarray test, able to detect specific uropathogenic bacteria and associated antimicrobial resistance genes was evaluated at POCT.

Post-COVID-19-pandemic changes and clinical characteristics of invasive group a streptococcal infections from 2015 to 2023.

Purpose: Since winter 2022, invasive GAS (iGAS) infections have re-emerged in Europe, causing severe diseases in children and adults. We aimed to examine whether this reported post-pandemic increase was associated with an increased disease severity and/or a shift in clinical disease phenotypes.

Methods: We performed detailed clinical phenotyping of patients hospitalized with iGAS infections at a 1410-bed tertiary German Medical Center from 01/2015 to 09/2023.

GPT-4-based AI agents-the new expert system for detection of antimicrobial resistance mechanisms?

Unlabelled: The European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommends two steps for detecting beta-lactamases in Gram-negative bacteria. Screening for potential extended-spectrum beta-lactamase (ESBL), plasmid-mediated AmpC beta-lactamase, or carbapenemase production is confirmed. We aimed to validate generative pre-trained transformer (GPT)-4 and GPT-agent for pre-classification of disk diffusion to indicate potential beta-lactamases.

Evaluation of the Eazyplex ID LAMP Assay for the Rapid Diagnosis of Positive Blood Cultures.

Rapid molecular assays can be used to identify pathogens directly from positive blood cultures (BCs) in a timely manner compared to standard methods using subcultures. In this study, the eazyplex ID assay, which is based on loop-mediated amplification (LAMP) and is currently for research use only, was evaluated for the identification of the most common fungal species. A total of 190 BCs were analysed.

Endothelial ENaC-α Restrains Oxidative Stress in Lung Capillaries in Murine Pneumococcal Pneumonia-associated Acute Lung Injury.

Infection of lung endothelial cells with pneumococci activates the superoxide-generating enzyme NADPH oxidase 2 (NOX2), involving the pneumococcal virulence factor pneumolysin (PLY). Excessive NOX2 activity disturbs capillary barriers, but its global inhibition can impair bactericidal phagocyte activity during pneumococcal pneumonia. Depletion of the α subunit of the epithelial sodium channel (ENaC) in pulmonary endothelial cells increases expression and PMA-induced activity of NOX2.

Microbial imbalance in Darier disease: Dominance of various staphylococcal species and absence of Cutibacteria.

Darier disease (DD) is a rare autosomal dominant genodermatosis characterized by erythematous papules and plaques mainly involving sebaceous areas, such as the face, chest and back. Skin microbiome plays an essential role in maintaining skin homeostasis. A disturbed skin microbiome may contribute to the exacerbation of DD.

Innate players in Th2 and non-Th2 asthma: emerging roles for the epithelial cell, mast cell, and monocyte/macrophage network.

Asthma is one of the most common chronic respiratory diseases and is characterized by airway inflammation, increased mucus production, and structural changes in the airways. Recently, there is increasing evidence that the disease is much more heterogeneous than expected, with several distinct asthma endotypes. Based on the specificity of T cells as the best-known driving force in airway inflammation, bronchial asthma is categorized into T helper cell 2 (Th2) and non-Th2 asthma.

-derived metabolites protect mice against colonic inflammation.

Gut microbiota-derived metabolites play a pivotal role in the maintenance of intestinal immune homeostasis. Here, we demonstrate that the human commensal possesses a specific metabolic fingerprint, consisting predominantly of the tryptophan catabolite indole-3-propionic acid (IPA), the branched-chain acids (BCFAs) isobutyrate and isovalerate and the short-chain fatty acids (SCFAs) acetate and propionate. Mono-colonization of germ-free mice with (CS mice) affected colonic mucosal immune cell phenotypes, including up-regulation of gene expression, and increased abundance of transcriptionally active colonic tuft cells and Foxp3 regulatory T cells (Tregs).

Non-pharmaceutical infection prevention measures in nosocomial SARS-CoV-2 outbreaks: a retrospective multi-centre cohort study.

Background: Hospital severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks are relevant for patients and healthcare systems within and beyond the pandemic.

Aim: To explore the characteristics of SARS-CoV-2 outbreaks and their infection prevention and control (IPC) measures during the different pandemic waves.

Methods: A comprehensive structured template for SARS-CoV-2 outbreaks was developed and filled out by six university hospitals.

How long do bacteria, fungi, protozoa, and viruses retain their replication capacity on inanimate surfaces? A systematic review examining environmental resilience versus healthcare-associated infection risk by "fomite-borne risk assessment".

SUMMARYIn healthcare settings, contaminated surfaces play an important role in the transmission of nosocomial pathogens potentially resulting in healthcare-associated infections (HAI). Pathogens can be transmitted directly from frequent hand-touch surfaces close to patients or indirectly by staff and visitors. HAI risk depends on exposure, extent of contamination, infectious dose (ID), virulence, hygiene practices, and patient vulnerability.