Gilbert Greub, MD-PhD, FAMH
Claire Bertelli, PhD, head bioinformatics
Sébastien Aeby, Head laboratory technician
Virginie Martin, Laboratory technician
Nicolas Jacquier, PhD
Trestan Pillonel, PhD
The laboratory of genomics and metagenomics has started its activity in January 2012, thanks to an Institutional support. The current team, led by Prof Greub, mainly includes 3 bioinformaticians and one lab technician. However, several other investigators of the diagnostic and research laboratories are actively participating to the development of this young diagnostic laboratory. The laboratory is currently using an Illumina MiSeq system to perform most next generation sequencing tasks, taking advantage of both local CHUV computing facilities as well as those from the Swiss Institute of Bioinformatics.
The main objective of this laboratory is to provide an efficient and rapid tool to sequence microbial genomes, mainly bacterial, and to provide key informations on strains relatedness (typing), virulence factors (virulome) and/or resistance to antibiotics (resistome) within a few days. In addition to these fundamental aspects, genomic analysis is used to identify genes as targets for molecular diagnosis (see R&D), as well as to provide metagenomic data for research and/or diagnostic purposes.
As a complement, we have a functional genomics facility to study the biological impact of single nucleotide polymorphisms (SNPs) identifed by sequencing.
Prices of these investigations are highly dependent on the number of analyses and type of sample/microbial species. Information on prices may be obtained upon request to the lab technicians.
Rochat E, Vuilleumier S, Aeby S, Greub G, Joost S
Appl Environ Microbiol. 2020 Dec 17;87(1)
Dylus D, Pillonel T, Opota O, Wüthrich D, Seth-Smith HMB, Egli A, Leo S, Lazarevic V, Schrenzel J, Laurent S, Bertelli C, Blanc DS, Neuenschwander S, Ramette A, Falquet L, Imkamp F, Keller PM, Kahles A, Oberhaensli S, Barbié V, Dessimoz C, Greub G, Lebran
Front Microbiol. 2020;11:591093
Ardissone S, Scherler A, Pillonel T, Martin V, Kebbi-Beghdadi C, Greub G
Microorganisms. 2020 Nov 24;8(12)
Duss FR, Jaton K, Vollenweider P, Troillet N, Greub G
Clin Microbiol Infect. 2020 Sep 4
Laurent S, Zakham F, Bertelli C, Merz L, Nicod L, Mazza-Stalder J, Greub G, Jaton K, Opota O
Int J Antimicrob Agents. 2020 Aug;56(2):106068
Marizzoni M, Gurry T, Provasi S, Greub G, Lopizzo N, Ribaldi F, Festari C, Mazzelli M, Mombelli E, Salvatore M, Mirabelli P, Franzese M, Soricelli A, Frisoni GB, Cattaneo A
Front Microbiol. 2020;11:1262
van Dooremalen WTM, Verweij SP, den Hartog JE, Kebbi-Beghdadi C, Ouburg S, Greub G, Morré SA, Ammerdorffer A
Microorganisms. 2020 Jun 17;8(6)
Kebbi-Beghdadi C, Pilloux L, Martin V, Greub G
Microorganisms. 2020 Mar 3;8(3)
Magalhães B, Valot B, Abdelbary MMH, Prod'hom G, Greub G, Senn L, Blanc DS
Front Public Health. 2020;8:3
Scherler A, Jacquier N, Kebbi-Beghdadi C, Greub G
Microorganisms. 2020 Jan 9;8(1)
Pillonel T, Tagini F, Bertelli C, Greub G
Nucleic Acids Res. 2020 Jan 8;48(D1):D526-D534
Thiévent K, Szentiványi T, Aeby S, Glaizot O, Christe P, Greub G
Parasite. 2020;27:54
Bayramova F, Jacquier N, Greub G
Microorganisms. 2019 Nov 26;7(12)
Jacquier N, Yadav AK, Pillonel T, Viollier PH, Cava F, Greub G
mBio. 2019 Jul 16;10(4)
Zakham F, Laurent S, Esteves Carreira AL, Corbaz A, Bertelli C, Masserey E, Nicod L, Greub G, Jaton K, Mazza-Stalder J, Opota O
New Microbes New Infect. 2019 Sep;31:100582
Tagini F, Aeby S, Bertelli C, Droz S, Casanova C, Prod'hom G, Jaton K, Greub G
Int J Syst Evol Microbiol. 2019 Jun;69(6):1696-1704
Abdelbary MHH, Senn L, Greub G, Chaillou G, Moulin E, Blanc DS
Eur J Clin Microbiol Infect Dis. 2019 Jun;38(6):1163-1170
Pillonel T, Bertelli C, Aeby S, de Barsy M, Jacquier N, Kebbi-Beghdadi C, Mueller L, Vouga M, Greub G
Genome Biol Evol. 2019 Apr 1;11(4):1334-1344
de Barsy M, Herrgott L, Martin V, Pillonel T, Viollier PH, Greub G
Sci Rep. 2019 Mar 20;9(1):4885