The complete genome sequence of unculturable obtained through clinical metagenomic next-generation sequencing.

Introduction: Diagnosing poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.

Methods: This study analyzes the complete genome sequence of , obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.

Results: Genome analysis revealed limited therapeutic options for the infection, primarily susceptibility to tetracyclines.

Case Report: Necrotizing fasciitis caused by positive for a new sequence variant of exfoliative toxin E.

Necrotizing fasciitis (NF) caused by is a rare, aggressive and rapidly progressing superficial fascia infection with a high mortality rate. The aim of this study was to identify virulence-related genes from a complete genome sequence of a methicillin-susceptible (MSSA) isolate recovered from a monomicrobial case of NF. The MSSA isolate UMCG579 was cultured from a pus collection from the subcutis of a patient with NF.

Insight Into the Anti-staphylococcal Activity of JBC 1847 at Sub-Inhibitory Concentration.

Multidrug-resistant pathogens constitute a serious global issue and, therefore, novel antimicrobials with new modes of action are urgently needed. Here, we investigated the effect of a phenothiazine derivative (JBC 1847) with high antimicrobial activity on , using a wide range of assays, flow cytometry, and RNA transcriptomics. The flow cytometry results showed that JBC 1847 rapidly caused depolarization of the cell membrane, while the macromolecule synthesis inhibition assay showed that the synthesis rates of DNA, RNA, cell wall, and proteins, respectively, were strongly decreased.

Misidentification of meticillin-resistant by the Cepheid Xpert MRSA NxG assay, the Netherlands, February to March 2021.

We describe two false-negative results in the detection of meticillin-resistant (MRSA) of sequence type 398 and type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations between the two isolate genomes indicate that this MRSA strain might have been spreading for some time and could have disseminated to other regions of the Netherlands and other European countries.

Staphylococcal cassette chromosome mec containing a novel mec gene complex, B4.

Objectives: To describe a new subclass of mec class B complex identified in Staphylococcus epidermidis.

Methods: Four S. epidermidis isolates obtained from bloodstream infections in patients at University Medical Center Groningen (UMCG) were analysed by phenotypic antibiotic susceptibility testing and WGS.

Development of a reference data set for assigning and species based on next generation sequencing of the 16S-23S rRNA region.

Background: Many members of and genera are clinically relevant opportunistic pathogens warranting accurate and rapid identification for targeted therapy. Currently, the developed method based on next generation sequencing (NGS) of the 16S-23S rRNA region proved to be a rapid, reliable and precise approach for species identification directly from polymicrobial and challenging clinical samples. The introduction of this new method to routine diagnostics is hindered by a lack of the reference sequences for the 16S-23S rRNA region for many bacterial species.

Development and Validation of a Reference Data Set for Assigning Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region.

Many members of the genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, and genes and NGS of the 16S-23S rRNA region.

Daptomycin Resistant Clinical Strain With Novel Non-synonymous Mutations in the and Genes: A New Insight Into Daptomycin Resistance.

Daptomycin (DAP) resistance in is uncommon but there are increasing reports of the emergence of resistance during DAP therapy. Most clinical DAP-resistant isolates investigated carried mutations in the gene. The aim of this study was to identify mutations between a clinical pair of methicillin-susceptible (MSSA) isolates (DAP-susceptible and DAP-resistant).

Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Strains.

is an opportunistic pathogen of humans and warm-blooded animals and presents a growing threat in terms of multi-drug resistance. Despite numerous studies, the basis of staphylococcal virulence and switching between commensal and pathogenic phenotypes is not fully understood. Using genomics, we show here that strains exhibiting virulent (VIR) and non-virulent (NVIR) phenotypes in a chicken embryo infection model genetically fall into two separate groups, with the VIR group being much more cohesive than the NVIR group.

PVL overexpression due to genomic rearrangements and mutations in the S. aureus reference strain ATCC25923.

Objective: ATCC25923 is a Staphylococcus aureus strain that is positive for the Panton Valentin leukocidin. It has been used for decades as reference strain. We observed that two separately maintained clones of ATCC25923 ("G477 and G478") differed grossly in the expression of this toxin.

Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species.

The aim of this study was to develop an easy-to-use culture-free diagnostic method based on next generation sequencing (NGS) of PCR amplification products encompassing whole 16S-23S rRNA region to improve the resolution of bacterial species identification. To determine the resolution of the new method 67 isolates were subjected to four identification methods: Sanger sequencing of the 16S rRNA gene; NGS of the 16S-23S rRNA region using MiSeq (Illumina) sequencer; Microflex MS (Bruker) and VITEK MS (bioMérieux). To evaluate the performance of this new method when applied directly on clinical samples, we conducted a proof of principle study with 60 urine samples from patients suspected of urinary tract infections (UTIs), 23 BacT/ALERT (bioMérieux) positive blood culture bottles and 21 clinical orthopedic samples.

Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.

We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP.

Clonal Structure and Characterization of Staphylococcus aureus Strains from Invasive Infections in Paediatric Patients from South Poland: Association between Age, spa Types, Clonal Complexes, and Genetic Markers.

The aim of current study was to examine clonal structure and genetic profile of invasive Staphylococcus aureus isolates recovered from infants and children treated at the Jagiellonian University Children's Hospital of Krakow, Poland. The 107 invasive S. aureus isolates, collected between February 2012 and August 2014, were analysed retrospectively.

Whole-genome analysis of an oxacillin-susceptible CC80 mecA-positive Staphylococcus aureus clinical isolate: insights into the mechanisms of cryptic methicillin resistance.

Objectives: The mec and bla systems, among other genetic factors, are critical in regulating the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the mechanism conferring oxacillin susceptibility.

Genome-wide analysis reveals two novel mosaic regions containing an ACME with an identical DNA sequence in the MRSA ST398-t011 and MSSA ST8-t008 isolates.

Objectives: The presence of the arginine catabolic mobile element (ACME) in Staphylococcus aureus has been reported to enhance the colonization of the human host. The aim of this study was to determine the genetic organization of composite islands harbouring ACME.

Methods: Two ACME-positive S.

Carriage of Staphylococcus aureus in Thika Level 5 Hospital, Kenya: a cross-sectional study.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen but little is known about its circulation in hospitals in developing countries. We aimed to describe carriage of S.aureus amongst inpatients in a mid-sized Kenyan government hospital.

Novel organization of the arginine catabolic mobile element and staphylococcal cassette chromosome mec composite island and its horizontal transfer between distinct Staphylococcus aureus genotypes.

In this study, 425 methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in the Dutch-German Euregio were investigated for the presence of the arginine catabolic mobile element (ACME). Sequence analysis by whole-genome sequencing revealed an entirely new organization of the ACME-staphylococcal cassette chromosome mec composite island (SCCmec-CI), with truncated ACME type II located downstream of SCCmec. An identical nucleotide sequence of ACME-SCCmec-CI was found in two distinct MRSA lineages (t064-ST8 and t002-ST5), which has not been reported previously in S.

Detection of new methicillin-resistant Staphylococcus aureus strains that carry a novel genetic homologue and important virulence determinants.

In this study, 18 methicillin-resistant Staphylococcus aureus (MRSA) isolates harboring staphylococcal cassette chromosome mec (SCCmec) type XI, recovered in the Dutch-German Euregio, were characterized by DNA microarrays. In contrast to previous data, we found two MRSA strains of different clonal lineages possessing SCCmec XI that carried important virulence determinants. The worrisome emergence of such toxigenic MRSA strains raises concerns that MRSA strains with enhanced virulence potential and impaired detectability by standard molecular assays may spread in Europe.