Fernanda L. Paganelli
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View article: Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity
Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity Open
The influence of SARS-CoV-2 on the nasopharyngeal microbiome, or vice-versa, is unclear. Nasopharyngeal swabs from Dutch healthcare workers (N = 257) and hospital outpatients with respiratory symptoms (N = 143), leftover after SARS-CoV-2 t…
View article: Probiotic Bifidobacterium bifidum strains desialylate MUC13 and increase intestinal epithelial barrier function
Probiotic Bifidobacterium bifidum strains desialylate MUC13 and increase intestinal epithelial barrier function Open
View article: Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation
Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation Open
View article: Dissemination of IncQ1 Plasmids Harboring NTEKPC-IId in a Brazilian Hospital
Dissemination of IncQ1 Plasmids Harboring NTEKPC-IId in a Brazilian Hospital Open
KPC is a clinically significant serine carbapenemase in most countries, and its rapid spread threatens global public health. blaKPC transmission is commonly mediated by Tn4401 transposons. The blaKPC gene has also been found in non-Tn4401 …
View article: Gut microbiome and immune checkpoint inhibitor toxicity
Gut microbiome and immune checkpoint inhibitor toxicity Open
Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.
View article: Colonization of vancomycin-resistant <i>Enterococcus faecium</i> in human-derived colonic epithelium: unraveling the transcriptional dynamics of host–enterococcal interactions
Colonization of vancomycin-resistant <i>Enterococcus faecium</i> in human-derived colonic epithelium: unraveling the transcriptional dynamics of host–enterococcal interactions Open
Enterococcus faecium is an opportunistic pathogen able to colonize the intestines of hospitalized patients. This initial colonization is an important step in the downstream pathogenesis, which includes outgrowth of the intestinal microbiot…
View article: YajC, a predicted membrane protein, promotes <i>Enterococcus faecium</i> biofilm formation <i>in vitro</i> and in a rat endocarditis model
YajC, a predicted membrane protein, promotes <i>Enterococcus faecium</i> biofilm formation <i>in vitro</i> and in a rat endocarditis model Open
Biofilm formation is a critical step in the pathogenesis of difficult-to-treat Gram-positive bacterial infections. We identified that YajC, a conserved membrane protein in bacteria, plays a role in biofilm formation of the clinically relev…
View article: Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts
Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts Open
This study investigated the gut microbiome dynamics of index patients colonized with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) ( n = 5) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-K…
View article: Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition
Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition Open
The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated w…
View article: Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone
Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone Open
The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin Amer…
View article: BCG Vaccination of Health Care Workers Does Not Reduce SARS-CoV-2 Infections nor Infection Severity or Duration: a Randomized Placebo-Controlled Trial
BCG Vaccination of Health Care Workers Does Not Reduce SARS-CoV-2 Infections nor Infection Severity or Duration: a Randomized Placebo-Controlled Trial Open
While several BCG trials in adults were conducted during the 2019 coronavirus disease epidemic, our data set is the most comprehensive to date, because we included serologically confirmed infections in addition to self-reported positive SA…
View article: The endometrial microbiota of women with or without a live birth within 12 months after a first failed IVF/ICSI cycle
The endometrial microbiota of women with or without a live birth within 12 months after a first failed IVF/ICSI cycle Open
View article: BCG vaccination of healthcare workers does not reduce SARS-CoV-2 infections nor infection severity or duration: a randomised placebo-controlled trial
BCG vaccination of healthcare workers does not reduce SARS-CoV-2 infections nor infection severity or duration: a randomised placebo-controlled trial Open
Background Bacillus Calmette-Guerin (BCG) vaccination has been hypothesised to reduce SARS-CoV-2 infection, severity, and/or duration via trained immunity induction. Methods Healthcare workers (HCWs) in 9 Dutch hospitals were randomised to…
View article: Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits
Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits Open
Diet is an important modulator of the human gut microbiome, which is susceptible to increased consumption of plant fibers in vegan or vegetarian lifestyles. To investigate this, we compared the gut microbiome of Dutch adults following omni…
View article: Air pollution from livestock farms and the oropharyngeal microbiome of COPD patients and controls
Air pollution from livestock farms and the oropharyngeal microbiome of COPD patients and controls Open
View article: The oropharyngeal microbiome of COPD patients and controls in a livestock dense area
The oropharyngeal microbiome of COPD patients and controls in a livestock dense area Open
This ready to load phyloseq R S4 object contains the ASV table, taxonomy table and sample metadata. This dataset was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 s…
View article: The oropharyngeal microbiome of COPD patients and controls in a livestock dense area
The oropharyngeal microbiome of COPD patients and controls in a livestock dense area Open
This ready to load phyloseq R S4 object contains the ASV table, taxonomy table and sample metadata. This dataset was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 s…
View article: Impact of long-term dietary habits on the human gut resistome in the Dutch population
Impact of long-term dietary habits on the human gut resistome in the Dutch population Open
View article: CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens
CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens Open
The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreig…
View article: CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens
CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens Open
The acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic ma…
View article: Table S6 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S6 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Posterior distributions for individual species-specific Bayesian Poisson generalised linear models of ABR gene count with fixed effects of CRISPR-Cas type (Prediction) and spacer count, and controlling for genetic distance.
View article: Table S2 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S2 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
AIC selection tables for binomial generalised linear model of CRISPR-Cas presence/absence with fixed effects of number of ABR genes, ICEs, IntI1 copies and plasmid replicons, as well as species as fixed effects. The fixed effect pre…
View article: Table S10 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S10 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Posterior distributions for Bayesian Poisson generalised linear model of ABR gene count with fixed effects of CRISPR-Cas type (Prediction) and proportion of spacers targeting MGEs that target ABR.
View article: Table S8 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S8 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Posterior distributions for individual species-specific Bayesian Poisson generalised linear models of ABR gene count with the fixed effects of CRISPR-Cas type (Prediction), ICE count and their interaction terms, controlling for genetic dis…
View article: Table S3 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S3 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Model estimates for linear model of genome lengths with fixed effects of CRISPR-Cas presence/absence (binomial), species (categorical) and an interaction term between the two. *Predictions were not made for this species, as it lacks CRISPR…
View article: Table S1 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S1 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
AIC selection tables for linear model of genome lengths with fixed effects of CRISPR-Cas presence/absence (binomial), species (categorical) and an interaction term between the two. The fixed effect presence/absence from the model is indica…
View article: Table S5 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S5 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Posterior distributions for individual species-specific Bayesian Poisson generalised linear models of ABR gene count with the fixed effect of CRISPR-Cas type (Prediction), and controlling for genetic distance. Intercept is always “None” i.…
View article: Table S7 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S7 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Posterior distributions for individual species-specific Bayesian Poisson generalised linear models of ABR gene count with the fixed effects of CRISPR-Cas type (Prediction), acr count and their interaction terms, controlling for genetic dis…
View article: Table S4 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S4 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Model estimates for binomial generalised linear model of CRISPR-Cas presence/absence with fixed effects of number of ABR genes, ICEs, IntI1 copies and plasmid replicons as well as species, and interaction terms between species and e…
View article: Table S9 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens
Table S9 from <i>CRISPR-Cas</i> is associated with fewer antibiotic resistance genes in bacterial pathogens Open
Posterior distributions for Bayesian Poisson generalised linear model of ABR gene count with fixed effects of CRISPR-Cas type (Prediction) and proportion of spacers targeting MGEs that do not target ABR.