Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics.

Infection in the central nervous system is a severe condition associated with high morbidity and mortality. Despite ample testing, the majority of encephalitis and meningitis cases remain undiagnosed. Metagenomic sequencing of cerebrospinal fluid has emerged as an unbiased approach to identify rare microbes and novel pathogens.

Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2).

Objective: Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data.

Design: Retrospective cohort study.

Recurrent and persistent infection with SARS-CoV-2 - epidemiological data and case reports from Western Sweden, 2020.

Background: Reinfections with SARS-CoV-2 have been reported and most cases were classified as mild. Reports of persistent infection with SARS-CoV-2 are rare.

Aim: To investigate the frequency of recurrent and persistent infection with SARS-CoV-2.

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies.

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198 and CCUG 4207, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198 and CCUG 4207 are derived from deposit of the same strain at two different culture collections.

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping.

Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses.

gen. nov., sp. nov., a New Member of the Family Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant.

The family is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family , isolated from a wound infection of an adult patient, in Sweden.

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics.

A range of methodologies may be used for analyzing bacteria, depending on the purpose and the level of resolution needed. The capability for recognition of species distinctions within the complex spectrum of bacterial diversity is necessary for progress in microbiological research. In clinical settings, accurate, rapid and cost-effective methods are essential for early and efficient treatment of infections.

Draft Genome Sequences of Six Strains of from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.

is a pathogenic bacterium found most commonly in the respiratory tract of humans and is a common cause of pneumonia and bacterial meningitis. Here, we report the draft genome sequences of six strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272.

Draft Genome Sequence of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample.

The draft genome sequence has been determined for an extended-spectrum-β-lactamase (ESBL)-producing (bla) Escherichia coli strain (CCUG 62462), composed of 119 contigs and a total size of 5.27 Mb. This E.

Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.

Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human respiratory tract. It is associated with otitis media and respiratory tract infections. Here, we report the draft genome sequence of M.

Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.

Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41 contigs of a total size of 2.

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization.

The intestinal mucus layer provides a barrier limiting bacterial contact with the underlying epithelium. Mucus structure is shaped by intestinal location and the microbiota. To understand how commensals modulate gut mucus, we examined mucus properties under germ-free (GF) conditions and during microbial colonization.

The composition of the gut microbiota shapes the colon mucus barrier.

Two C57BL/6 mice colonies maintained in two rooms of the same specific pathogen-free (SPF) facility were found to have different gut microbiota and a mucus phenotype that was specific for each colony. The thickness and growth of the colon mucus were similar in the two colonies. However, one colony had mucus that was impenetrable to bacteria or beads the size of bacteria-which is comparable to what we observed in free-living wild mice-whereas the other colony had an inner mucus layer penetrable to bacteria and beads.

DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.

The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips.

Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section.

Objective: The early intestinal microbiota exerts important stimuli for immune development, and a reduced microbial exposure as well as caesarean section (CS) has been associated with the development of allergic disease. Here we address how microbiota development in infants is affected by mode of delivery, and relate differences in colonisation patterns to the maturation of a balanced Th1/Th2 immune response.

Design: The postnatal intestinal colonisation pattern was investigated in 24 infants, born vaginally (15) or by CS (nine).

Low diversity of the gut microbiota in infants with atopic eczema.

Background: It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts.

Objective: We sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development.

Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.

Antibiotic administration is the standard treatment for the bacterium Helicobacter pylori, the main causative agent of peptic ulcer disease and gastric cancer. However, the long-term consequences of this treatment on the human indigenous microbiota are relatively unexplored. Here we studied short- and long-term effects of clarithromycin and metronidazole treatment, a commonly used therapy regimen against H.

Comparative analysis of human gut microbiota by barcoded pyrosequencing.

Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed.

Macrolide resistance in the normal microbiota after Helicobacter pylori treatment.

Large-scale chemoprevention of peptic ulcer disease and gastric cancer through eradication of Helicobacter pylori would expose large population groups to antibiotics, which raises concerns about possible dissemination of antibiotic resistance. The objective of this cohort study was to determine whether a triple therapy, containing omeprazole, clarithromycin, and metronidazole, of H. pylori infection increases the prevalence of macrolide resistance in the normal microbiota.