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Comparing Vaginal and Endometrial Microbiota Using Culturomics: Proof of Concept Vrije Universiteit Brussel

Robin Vanstokstraeten, Ellen Callewaert, Susanne Blotwijk, Eleni Rombauts, Florence Crombé, Kristof Emmerechts, Oriane Soetens, Kristof Vandoorslaer, Deborah De Geyter, Camille Allonsius, et al.
It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal–cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is ...

Genotypic resistance determined by whole genome sequencing versus phenotypic resistance in 234 Escherichia coli isolates Vrije Universiteit Brussel

Robin Vanstokstraeten, Denis Pierard, Florence Crombé, Deborah De Geyter, Ingrid Wybo, Astrid Muyldermans, Lucie Seyler, Ben Caljon, Toon Janssen, Thomas Demuyser, et al.

Whole genome sequencing (WGS) enables detailed characterization of bacteria at single nucleotide resolution. It provides data about acquired resistance genes and mutations leading to resistance. Although WGS is becoming an essential tool to predict resistance patterns accurately, comparing genotype to phenotype with WGS is still in its infancy. Additional data and validation are needed. In this retrospective study, we analysed 234 E. coli ...

Molecular characterization of extraintestinal and diarrheagenic Escherichia coli blood isolates Vrije Universiteit Brussel

Robin Vanstokstraeten, Florence Crombé, Denis Pierard, Angela Castillo Moral, Ingrid Wybo, Deborah De Geyter, Toon Janssen, Ben Caljon, Thomas Demuyser

Pathogenic E. coli strains can be classified into two major groups, based on the presence of specific virulence factors: extraintestinal pathogenic E. coli (ExPEC) and diarrheagenic E. coli (DEC). Several case reports describe that DEC can cause bloodstream infections in some rare cases. This mainly concerns a few specific sequence types that express virulence factors from both ExPEC and DEC. In this study, we retrospectively analysed 234 E. ...

Healthcare-Associated COVID-19 across Five Pandemic Waves Vrije Universiteit Brussel

Thomas Demuyser, Lucie Seyler, Oriane Soetens, Ben Caljon, Joost Boeckmans, Robin Vanstokstraeten, Helena Martini, Florence Crombé, Denis Pierard, Sabine Allard, et al.

BACKGROUND: Healthcare-associated SARS-CoV-2 infections need to be explored further. Our study is an analysis of hospital-acquired infections (HAIs) and ambulatory healthcare workers (aHCWs) with SARS-CoV-2 across the pandemic in a Belgian university hospital.

METHODS: We compared HAIs with community-associated infections (CAIs) to identify the factors associated with having an HAI. We then performed a genomic cluster analysis of HAIs ...

Culturomics to investigate the Endometrial Microbiome: Proof-of-Concept Vrije Universiteit Brussel

Robin Vanstokstraeten, Shari Mackens, Ellen Callewaert, Susanne Blotwijk, Kristof Emmerechts, Florence Crombé, Oriane Soetens, Ingrid Wybo, Kristof Vandoorslaer, Laurence Evelyne Mostert, et al.
Abstract: The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endome-trial microbiome is of particular interest given the potential impact on the embryo implanta-tion. To date, all endometrial microbiome studies have applied a metagenomics approach. A se-quencing-based technique, however, has its limitations, more specifically ...

Beyond Guidelines and Reports on Bacterial Co-/Superinfections in the Context of COVID-19 Vrije Universiteit Brussel

Johan Van Laethem, Denis Pierard, Sabine Allard

BACKGROUND: In the period following the declaration of the COVID-19 pandemic, more evidence became available on the epidemiology of bacterial co-/superinfections (bCSs) in hospitalized COVID-19 patients. Various European therapeutic guidelines were published, including guidance on rational antibiotic use.

METHODS: In this letter to the editor, we provide an overview of the largest meta-analyses or prospective studies reporting on bCS ...

Identification of Five Serotypes of Enteropathogenic Escherichia coli from Diarrheic Calves and Healthy Cattle in Belgium and Comparative Genomics with Shigatoxigenic E. coli Vrije Universiteit Brussel Universiteit Gent

Audrey Habets, Fabrice Touzain, Pierrick Lucas, Nguyen Thi Thu Huong, Atsushi Iguchi, Florence Crombé, Nicolas Korsak, Denis Pierard, Marc Saulmont, Eric Cox, et al.

Enteropathogenic Escherichia coli (EPEC) produce attaching/effacing (AE) lesions and cause non-bloody diarrhea in mammals. A minority of bovine EPEC belong to one of the ten classical serotypes of human and bovine AE-STEC. The purpose of this study was to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) among bovine EPEC and to characterize their virulence repertoires by whole genome sequencing. Around 40% of the ...

Healthcare-Associated SARS-CoV-2 Reinfection after 3 Months with a Phylogenetically Distinct Omicron Variant Vrije Universiteit Brussel

Anke Stoefs, Dimitri Stylemans, Oriane Soetens, Florence Crombé, Ellen Vancutsem, Hideo Imamura, Ingrid Wybo, Deborah De Geyter, Denis Pierard, Astrid Muyldermans, et al.

This case report describes a 60-year-old female patient suffering from systemic sclerosis, for which she received immunomodulatory drugs. Her first SARS-CoV-2-positive nasopharyngeal sample was obtained in the emergency department, on 31 January 2022. Whole genome sequencing confirmed infection with Omicron BA.1.1. Her hospital stay was long and punctuated by many complications, including admission to the intensive care unit. At the beginning ...

Validation of the Colibrí Instrument for Automated Preparation of MALDI-TOF MS Targets for Yeast Identification Vrije Universiteit Brussel

Robbe Heestermans, Pauline Herroelen, Kristof Emmerechts, Kristof Vandoorslaer, Deborah De Geyter, Thomas Demuyser, Ingrid Wybo, Denis Pierard, Astrid Muyldermans
Recently, Copan (Italy) introduced the Colibrí instrument for automated colony picking and preparation of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) target plates. Our study aimed to validate this system for yeasts as such testing has not been performed yet and is a missing link needed to implement the system for routine use. Fifty-five Candida strains were selected to evaluate the accuracy of Colibrí. For each ...

Validation of Rapid Antimicrobial Susceptibility Testing directly from blood cultures using WASPLab®, including Colibrí™ and Radian® in-Line Carousel Vrije Universiteit Brussel

Pauline Herroelen, Robbe Heestermans, Kristof Emmerechts, Kristof Vandoorslaer, Ingrid Wybo, Denis Pierard, Astrid Muyldermans
With the increase in antimicrobial resistance, fast reporting of antimicrobial susceptibility testing (AST) results is becoming increasingly important. EUCAST developed a method for rapid AST (RAST) directly from the broth of positive blood cultures (BC). Inhibition zones are read after 4, 6, and 8 h, with specific breakpoints per time point. We evaluated the RAST method based on EUCAST disk diffusion methodology with inoculation of BC broth ...