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Université de Fribourg

NGS-based S. aureus typing and outbreak analysis in clinical microbiology laboratories : Lessons learned from a Swiss-wide proficiency test

Dylus, David ; Pillonel, Trestan ; Opota, Onya ; Wüthrich, Daniel ; Seth-Smith, Helena M. B. ; Egli, Adrian ; Leo, Stefano ; Lazarevic, Vladimir ; Schrenzel, Jacques ; Laurent, Sacha ; Bertelli, Claire ; Blanc, Dominique S. ; Neuenschwander, Stefan ; Ramette, Alban ; Falquet, Laurent ; Imkamp, Frank ; Keller, Peter M. ; Kahles, Andre ; Oberhaensli, Simone ; Barbié, Valérie ; Dessimoz, Christophe ; Greub, Gilbert ; Lebrand, Aitana

In: Frontiers in Microbiology, 2020, vol. 11, p. 591093

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...

Université de Fribourg

Identification of avoidance genes through neural pathway-specific forward optogenetics

Marques, Filipe ; Saro, Gabriella ; Lia, Andrei-Stefan ; Poole, Richard J. ; Falquet, Laurent ; Glauser, Dominique A.

In: PLOS Genetics, 2019, vol. 15, no. 12, p. e1008509

Understanding how the nervous system bridges sensation and behavior requires the elucidation of complex neural and molecular networks. Forward genetic approaches, such as screens conducted in C. elegans, have successfully identified genes required to process natural sensory stimuli. However, functional redundancy within the underlying neural circuits, which are often organized with multiple...

Université de Fribourg

Cell cycle constraints and environmental control of local DNA hypomethylation in α-proteobacteria

Ardissone, Silvia ; Redder, Peter ; Russo, Giancarlo ; Frandi, Antonio ; Fumeaux, Coralie ; Patrignani, Andrea ; Schlapbach, Ralph ; Falquet, Laurent ; Viollier, Patrick H.

In: PLOS Genetics, 2016, vol. 12, no. 12, p. e1006499

Heritable DNA methylation imprints are ubiquitous and underlie genetic variability from bacteria to humans. In microbial genomes, DNA methylation has been implicated in gene transcription, DNA replication and repair, nucleoid segregation, transposition and virulence of pathogenic strains. Despite the importance of local (hypo)methylation at specific loci, how and when these patterns are...

Université de Fribourg

Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation

Thoms, Matthias ; Mitterer, Valentin ; Kater, Lukas ; Falquet, Laurent ; Beckmann, Roland ; Kressler, Dieter ; Hurt, Ed

In: Nature Communications, 2018, vol. 9, no. 1, p. 4094

During eukaryotic 60S biogenesis, the 5S RNP requires a large rotational movement to achieve its mature position. Cryo-EM of the Rix1-Rea1 pre-60S particle has revealed the post-rotation stage, in which a gently undulating α-helix corresponding to Cgr1 becomes wedged between Rsa4 and the relocated 5S RNP, but the purpose of this insertion was unknown. Here, we show that cgr1 deletion in...

Université de Fribourg

Whole-genome sequence of a colombian Acinetobacter baumannii strain, a coproducer of OXA-72 and OXA-255-like carbapenemases

Saavedra, Sandra Yamile ; Prada-Cardozo, Diego ; Rincón, Verónica ; Pérez-Cardona, Hermes ; Hidalgo, Andrea Melissa ; González, María Nilse ; Reguero, María T. ; Silva, Emilia M. Valenzuela de ; Mantilla, José R. ; Falquet, Laurent ; Barreto-Hernández, Emiliano ; Duarte, Carolina

In: Genome Announcements, 2017, vol. 5, no. 7, p. e01558-16

Colombian Acinetobacter baumannii strain ST920 was isolated from the sputum of a 68-year-old male patient. This isolate possessed blaOXA-72 and blaOXA-255-like genes. The assembled genome contained 4,104,098 pb and 38.79% G+C content. This is the first case reported of the coproduction (blaOXA-72 and blaOXA-255-like) of carbapenem-hydrolyzing class D β-lactamases (CHDLs) in Acinetobacter...

Université de Fribourg

Draft genome sequence of the virulent Clostridium chauvoei reference strain JF4335

Falquet, Laurent ; Calderon-Copete, Sandra P. ; Frey, Joachim

In: Genome Announcements, 2013, vol. 1, no. 4, p. -

Clostridium chauvoei is the etiological agent of blackleg, a disease of cattle and sheep with high mortality rates, causing severe economic losses in livestock production. Here, we report the draft genome sequence of the virulent C. chauvoei strain JF4335 (2.8 Mbp and 28% G+C content) and the annotation of the genome.

Université de Fribourg

Draft genome sequences of multidrug-resistant acinetobacter sp. strains from colombian hospitals

Barreto-Hernández, Emiliano ; Falquet, Laurent ; Reguero, María T. ; Mantilla, José R. ; Valenzuela, Emilia M. ; González, Elsa ; Cepeda, Alexandra ; Escalante, Andrea

In: Genome Announcements, 2013, vol. 1, no. 6, p. -

The draft genome sequences of the strains Acinetobacter baumannii 107m, Acinetobacter nosocomialis 28F, and Acinetobacter pittii 42F, isolated from Colombian hospitals, are reported here. These isolates are causative of nosocomial infections and are classified as multidrug resistant, as they showed resistance to four different antibiotic groups.

Université de Fribourg

Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases

Piza-Buitrago, Adriana ; Rincón, Verónica ; Donato, John ; Saavedra, Sandra Yamile ; Duarte, Carolina ; Morero, Jaime ; Falquet, Laurent ; Reguero, María Teresa ; Barreto-Hernández, Emiliano

In: BMC Microbiology, 2020, vol. 20, no. 1, p. 345

Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of...

Université de Fribourg

Genome assembly of the ragweed leaf beetle, a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties

Bouchemousse, Sarah ; Falquet, Laurent ; Müller-Schärer, Heinz

In: Genome Biology and Evolution, 2020, vol. 12, no. 7, p. 1167–1173

Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of nontargeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled...

Université de Fribourg

Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes — a prospective cohort study among children born at term

Volery, Maryse ; Scherz, Valentin ; Jakob, William ; Bandeira, Diane ; Deggim-Messmer, Vanessa ; Lauber-Biason, Anna ; Wildhaber, Johannes ; Falquet, Laurent ; Curtis, Nigel ; Zimmermann, Petra

In: BMJ Open, 2020, vol. 10, no. 6, p. e036275

Introduction: There is compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. Antibiotics cause profound changes in the microbiome. However, the effect of intrapartum and early-life antibiotics on the maternal intestinal and breast milk microbiome, and the infant oral and intestinal microbiome, and whether...