NGS-Based Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test.

Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing.

Unexpected Mycoplasma hominis infection in two renal transplant recipients traced back to the same donor by whole-genome sequencing.

Mycoplasma hominis is a common colonizer of the lower genitourinary tract. Although its clinical relevance for causing urogenital infections in immunocompetent individuals is controversial, this bacterium has been involved in severe invasive infections in allograft recipients. In this report, we describe two cases of M.

Burden, epidemiology, and outcomes of microbiologically confirmed respiratory viral infections in solid organ transplant recipients: a nationwide, multi-season prospective cohort study.

Solid organ transplant (SOT) recipients are exposed to respiratory viral infection (RVI) during seasonal epidemics; however, the associated burden of disease has not been fully characterized. We describe the epidemiology and outcomes of RVI in a cohort enrolling 3294 consecutive patients undergoing SOT from May 2008 to December 2015 in Switzerland. Patient and allograft outcomes, and RVI diagnosed during routine clinical practice were prospectively collected.

COVID-19 Triage and Test Center: Safety, Feasibility, and Outcomes of Low-Threshold Testing.

This prospective observational study evaluated the safety and feasibility of a low threshold testing process in a Triage and Test Center (TTC) during the early course of the coronavirus disease 19 (COVID-19) pandemic. In addition, we aimed to identify clinical predictors for a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) swab result. Patients underwent informal triage, standardized history taking, and physician evaluation, only where indicated.

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.

from Canine and Bovine Cases of Campylobacteriosis Express High Antimicrobial Resistance Rates against (Fluoro)quinolones and Tetracyclines.

() spp. from poultry is the main source of foodborne human campylobacteriosis, but diseased pets and cattle shedding spp. may contribute sporadically as a source of human infection.

Identification of a Cluster of Extended-spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Sequence Type 101 Isolated From Food and Humans.

We report a cluster of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae sequence type 101, derived from 1 poultry and 2 clinical samples collected within the setting of a prospective study designed to determine the diversity and migration of ESBL-producing Enterobacterales between humans, foodstuffs, and wastewater.

Comorbidities, clinical signs and symptoms, laboratory findings, imaging features, treatment strategies, and outcomes in adult and pediatric patients with COVID-19: A systematic review and meta-analysis.

Introduction: Since December 2019, a novel coronavirus (SARS-CoV-2) has triggered a world-wide pandemic with an enormous medical and societal-economic toll. Thus, our aim was to gather all available information regarding comorbidities, clinical signs and symptoms, outcomes, laboratory findings, imaging features, and treatments in patients with coronavirus disease 2019 (COVID-19).

Methods: EMBASE, PubMed/Medline, Scopus, and Web of Science were searched for studies published in any language between December 1st, 2019 and March 28th, 2020.

Successful management of a Clostridioides difficile ribotype 027 outbreak with a lean intervention bundle.

Background: In a 2015 point-prevalence study, Clostridioides difficile 027, a hypervirulent ribotype, was absent from healthcare institutions in Switzerland. In late 2016, we detected an outbreak of C. difficile infection (CDI) with ribotype 027 occurring across several hospitals in the same hospital network.

Relevance of Dermabacter hominis isolated from clinical samples, 2012-2016: a retrospective case series.

We investigated the clinical relevance of Dermabacter hominis isolated from samples of 108 patients. Polymicrobial growth was evident in 88% of specimens. Isolation of D.

Emerging echinocandin-resistant Candida albicans and glabrata in Switzerland.

Echinocandins represent the first-line therapy of candidemia. Echinocandin resistance among Candida spp. is mainly due to acquired FKS mutations.

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra.

Motivation: Microbial species identification based on matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a standard tool in clinical microbiology. The resulting MALDI-TOF mass spectra also harbour the potential to deliver prediction results for other phenotypes, such as antibiotic resistance. However, the development of machine learning algorithms specifically tailored to MALDI-TOF MS-based phenotype prediction is still in its infancy.

Independent, external validation of clinical prediction rules for the identification of extended-spectrum β-lactamase-producing Enterobacterales, University Hospital Basel, Switzerland, January 2010 to December 2016.

BackgroundAlgorithms for predicting infection with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) on hospital admission or in patients with bacteraemia have been proposed, aiming to optimise empiric treatment decisions.AimWe sought to confirm external validity and transferability of two published prediction models as well as their integral components.MethodsWe performed a retrospective case-control study at University Hospital Basel, Switzerland.

Cefiderocol for Extensively Drug-Resistant Gram-Negative Bacterial Infections: Real-world Experience From a Case Series and Review of the Literature.

Cefiderocol is a new siderophore cephalosporin with activity against carbapenem-resistant gram-negative bacteria. Data on its clinical efficacy are limited to complicated urinary tract infections. We present a series of 3 patients successfully treated with cefiderocol for complicated health care-associated infections and review published case reports.

complex outbreak originating from contaminated wash gloves.

complex isolates were detected from four patients who were admitted to the heart centre of southern Switzerland, between April and June 2019. An outbreak investigation was conducted. The three available patient samples were whole genome sequenced, showing that they all are species, and that two are identical.

Emendation of the Genus Yassin et al. 2011 and Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis.

is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from IMMIB L-1656 (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus .

Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation.

Whole genome sequencing (WGS) has become the new gold standard for bacterial outbreak investigation, due to the high resolution available for typing. While sequencing is currently predominantly performed on Illumina devices, the preceding library preparation can be performed using various protocols. Enzymatic fragmentation library preparation protocols are fast, have minimal hands-on time, and work with small quantities of DNA.

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings.

() is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by and .