Toxigenic Corynebacterium diphtheriae Infections in Low-Risk Patients, Switzerland, 2023.

We report a cluster of infections with genetically related toxigenic Corynebacterium diphtheriae linked to an outbreak among asylum seekers in Switzerland that subsequently affected patients without known exposure. This discovery highlights the importance of rapid, interdisciplinary outbreak investigations and regular vaccination status assessment, especially in elderly populations with waning immunity.

Diphtheria in a Swiss Asylum Seeker Reception Centre: Outbreak Investigation and Evaluation of Testing and Vaccination Strategies.

To describe a suspected diphtheria outbreak in a Swiss asylum seeker reception centre, and to analyse its management response regarding testing and vaccination. We retrospectively analysed clinical, microbiology, and case management data of all asylum seekers tested for between 28th August and 31st December 2022 while residing at the centre. Results are reported descriptively.

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.

Background: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).

Results: We identified a total of 35 bacterial strains that represent potentially novel species.

Cefepime versus carbapenems for treatment of AmpC beta-lactamase-producing Enterobacterales bloodstream infections.

Purpose: Cefepime is recommended for treating infections caused by AmpC beta-lactamase-producing Enterobacterales (AmpC-PE), though supporting evidence is limited. Therefore, this study compared outcomes associated with cefepime versus carbapenem therapy for bloodstream infections (BSIs) caused by AmpC-PE after phenotypic exclusion of ESBL-co-producing isolates.

Methods: This retrospective cohort study compared definite cefepime versus carbapenem treatment for AmpC-PE BSI in hospitalized patients of the University Hospital Basel, Switzerland, between 01/2015 and 07/2020.

Evaluation of the clinical relevance of the Biofire FilmArray pneumonia panel among hospitalized patients.

Purpose: Panel PCR tests provide rapid pathogen identification. However, their diagnostic performance is unclear. We assessed the performance of the Biofire FilmArray pneumonia (PN)-panel against standard culture in broncho-alveolar lavage (BAL) samples.

Epidemiology of patients harboring carbapenemase-producing bacteria and comparison with patients with detection of extended-spectrum beta-lactamase-producing Enterobacterales-A retrospective cohort study.

Objective: We evaluated the epidemiology of carbapenemase-producing bacteria (CPB) in Switzerland by comparing risk factors between patients colonized with CPB and patients colonized with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE).

Methods: This retrospective cohort study was conducted at the University Hospital Basel in Switzerland. Hospitalized patients with CPB in any sample between January 2008 and July 2019 were included.

Patients exposed to vancomycin-resistant enterococci during in-hospital outbreaks in a low endemic setting: a proposal for risk-based screening.

Background: The optimal extent of screening of contact patients (CoPat) after exposure to patients infected or colonized with vancomycin-resistant enterococci (VRE) remains controversial.

Methods: We retrospectively developed a new risk stratification for screening patients exposed to VRE, based on data from three outbreaks-two with Enterococcus faecium vanB and one with Enterococcus faecium vanA involving 1096 CoPat-in a low endemic setting. We classified them into four risk groups: three on environmental exposure, one by healthcare exposure: high (sharing the same room/bathroom with a VRE-colonized patient), medium (hospitalization in the same room after a VRE-colonized patient's discharge until terminal disinfection including ultraviolet C (UVc)-disinfection), low (hospitalized in the same room within three weeks before the VRE-colonized patient), and "staff" (screening of patients having the same medical care team).

Distribution of Species and Prevalence of Azole Resistance in Respiratory Samples From Swiss Tertiary Care Hospitals.

Among 400 species from respiratory samples in Switzerland, was the most frequent species. Non- spp were more prevalent among solid organ transplant recipients and after azole exposure. Azole resistance was detected in 4 isolates, 3 of them with the "environmental" mutation TR/L98H in the gene.

Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov.

We present polyphasic taxonomic data to demonstrate that strain 125703-2019, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as Pseudoclavibacter albus comb. nov.

Trends of the Epidemiology of Candidemia in Switzerland: A 15-Year FUNGINOS Survey.

Background: The increasing incidence of candidemia and emergence of drug-resistant species are major concerns worldwide. Long-term surveillance studies are needed.

Methods: The Fungal Infection Network of Switzerland (FUNGINOS) conducted a 15-year (2004-2018), nationwide, epidemiological study of candidemia.

Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections.

We present genomic, phylogenomic, and phenotypic taxonomic data to demonstrate that three human ear isolates represent a novel species within the genus Gulosibacter. These isolates could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that they belonged to the genus Gulosibacter. Overall genomic relatedness indices between the draft genome sequences of the three isolates and of the type strains of established Gulosibacter species confirmed that the three isolates represented a single novel Gulosibacter species.

Ongoing evolution of lymphogranuloma venereum: exploring the genomic diversity of circulating strains.

Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) , is caused by strains from the LGV biovar, most commonly represented by -genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (=321) from eight countries collected between 2011 and 2017 (Spain =97, Netherlands =67, Switzerland =64, Australia =53, Sweden =37, Hungary =31, Czechia =30, Slovenia =10) were genotyped for and variants.

Cutibacterium modestum and "Propionibacterium humerusii" represent the same species that is commonly misidentified as Cutibacterium acnes.

Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp.

Unexpectedly High False-Positive Rates for Using a Meningoencephalitis Syndromic PCR Panel in Two Tertiary Centers.

False-positive results in the diagnostic of meningitis and encephalitis pose important challenges. This study aimed to determine false-positive rates for in cerebrospinal fluids evaluated by the BioFire FilmArray Meningitis/Encephalitis Panel. We conducted a retrospective study of all -positive FilmArray.

First case of IMP-15-producing in Switzerland: Challenging laboratory diagnosis using whole genome sequencing (WGS).

We report on the first case of multiresistant harbouring the metallo-β-lactamase IMP-15 isolated in Switzerland from a patient repatriated from Cambodia. The laboratory diagnosis of IMP-15 was hampered by two negative tests for carbapenemase detection. The carbapenemase gene was subsequently detected by whole genome sequencing and the isolate further characterised by various phenotypic and genotypic analyses.

Multicenter Prevalence Study Comparing Molecular and Toxin Assays for Clostridioides difficile Surveillance, Switzerland.

Public health authorities in the United States and Europe recommend surveillance for Clostridioides difficile infections among hospitalized patients, but differing diagnostic algorithms can hamper comparisons between institutions and countries. We compared surveillance based on detection of C. difficile by PCR or enzyme immunoassay (EIA) in a nationwide C.

Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay.

The clinical and epidemiologic management of the SARS-CoV-2 pandemic is critically dependent on molecular assays with short turn-around time. We validated the novel Xpert Xpress SARS-CoV-2 assay using a commercial nucleic acid testing (Roche Cobas 6800). We found an excellent concordance over a range of SARS-CoV-2 loads and across established human coronaviruses.

Results of the phase I open label clinical trial SAKK 06/14 assessing safety of intravesical instillation of VPM1002BC, a recombinant mycobacterium Bacillus Calmette Guérin (BCG), in patients with non-muscle invasive bladder cancer and previous failure of conventional BCG therapy.

: VPM1002BC is a modified mycobacterium Bacillus Calmette Guérin (BCG) for the treatment of non-muscle invasive bladder cancer (NMIBC). The genetic modifications are expected to result in better immunogenicity and less side effects. We report on patient safety and immunology of the first intravesical application of VPM1002BC in human.

Tick-Borne Relapsing Fever Caused by Borrelia persica in Traveler to Central Asia, 2019.

We report a case of tick-borne relapsing fever caused by Borrelia persica in a traveler returning to Switzerland from central Asia. After the disease was diagnosed by blood smear microscopy, the causative Borrelia species was confirmed by shotgun metagenomics sequencing. PCR and sequencing techniques provide highly sensitive diagnostic tools superior to microscopy.

First report of sexually transmitted multi-drug resistant Shigella sonnei infections in Switzerland, investigated by whole genome sequencing.

Shigella sonnei causes foodborne infections, but has recently also been described as a sexually transmitted infection (STI), with increased levels of antimicrobial resistance. We describe three cases of sexually acquired Shigella sonnei infection - the first report of this emerging infection in Switzerland. We used in-house whole genome sequencing (WGS) to investigate possible transmission routes and epidemiological correlations between the three cases.

Diagnosis of invasive mold diseases in patients with hematological malignancies using Aspergillus, Mucorales, and panfungal PCR in BAL.

Background: Accurate diagnosis of invasive mold diseases (IMD) remains challenging. Here, the performance of panfungal PCR, Aspergillus and MucoralesPCR in bronchoalveolar lavage (BAL) was evaluated.

Methods: We conducted a single-center study including 167 hematologic patients at risk for IMD with BAL performed 2011-2014.

Fungemia and necrotic lymph node infection with Sporopachydermia cereana in a patient with acute myeloid leukemia.

Sporopachydermia cereana is a rare yeast found in necrotic cactus tissue, predominantly in the Americas. Infection in humans with clinical data has only been reported in four patients so far, all of whom died, either directly from the pathogen or from other complications of immunosuppression. Treatment of the yeast is complicated by difficulties in identification of the pathogen with conventional diagnostic techniques and by intrinsic resistance to echinocandins.