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    Laboratoires de Diagnostic de l’Institut de Microbiologie (Diagnostic Laboratories of the Institute of Microbiology)

    2. Where is it located (include both address and geographical location)?

    Laboratoires de Diagnostic de l’Institut de Microbiologie, Département de Pathologie et Médecine de Laboratoire, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 48, CH-1011 Lausanne, Switzerland

    N 46° 31' 30.57", E 6° 38' 29.15"

    3. Floor area of laboratory areas by containment level
    BL 3 , 93.00 SqM
    BL 2 , 596.00 SqM
    Total laboratory floor area (SqM): 
    689

    4. The organizational structure of each facility

    Personnel
    (i) Total number of personnel: 
    19

    (ii) Division of personnel

    Military: 
    0
    Civilian: 
    19

    (iii) Division of personnel by category

    Scientists: 
    5
    Engineers: 
    0
    Technicians: 
    14
    Administrative and support staff: 
    0
    (iv) List the scientific disciplines represented in the scientific/engineering staff

    Bacteriology, mycology, parasitology, virology, biosafety, bioinformatics

    (v) Are contractor staff working in the facility? If so, provide an approximate number.
    0
    Funding
    (vi) What is (are) the source(s) of funding for the work conducted in the facility, including indication if activity is wholly or partly financed by the Ministry of Defence?

    Cantons of Fribourg, Genève, Neuchâtel, Valais, Vaud.

    Research
    Development
    Test & Evaluation
    Analysis / Diagnosis
    Education & Training
    Other activities

    0 %
    5 %
    10 %
    50 %
    15 %
    20 %

    (vii) What are the funding levels for the following programme areas:

    Research: 
    0 %
    Development: 
    5 %
    Test and evaluation: 
    10 %
    (viii) Briefly describe the publication policy of the facility

    Publication in peer-reviewed open literature.

    (ix) Provide a list of publicly-available papers and reports resulting from the work published during the previous 12 months. (To include authors, titles and full references)

    Impact of different SARS-CoV-2 assays on laboratory turnaround time.
    Marquis B, Opota O, Jaton K, Greub G
    Med Microbiol. 2021 May;70(5)

    Aequorin as a Useful Calcium-Sensing Reporter in Candida albicans.
    Sanglard D
    J Fungi (Basel). 2021 Apr 20;7(4)

    Fecal microbiota transplantation: from the evidence to the realty of the field.
    Ballif A, Gerber S, Carrez L, Audry M, Sadeghipour F, Mitouassiwou A, Croxatto A, Opota O, Prod'hom G, Henchoz S, Schoepfer A, Cavassini M, Galpérine T
    Rev Med Suisse. 2021 Apr 14;17(734):726-731

    Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study.
    Caruana G, Croxatto A, Kampouri E, Kritikos A, Opota O, Foerster M, Brouillet R, Senn L, Lienhard R, Egli A, Pantaleo G, Carron PN, Greub G
    Microorganisms. 2021 Apr 10;9(4)

    Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
    Kubik S, Marques AC, Xing X, Silvery J, Bertelli C, De Maio F, Pournaras S, Burr T, Duffourd Y, Siemens H, Alloui C, Song L, Wenger Y, Saitta A, Macheret M, Smith EW, Menu P, Brayer M, Steinmetz LM, Si-Mohammed A, Chuisseu J, Stevens R, Constantoulakis P,
    Clin Microbiol Infect. 2021 Apr 1

    Navigating the uncertainties of COVID-19 associated aspergillosis (CAPA): A comparison with influenza associated aspergillosis (IAPA).
    Lamoth F, Lewis RE, Walsh TJ, Kontoyiannis DP
    J Infect Dis. 2021 Mar 26

    Invasive aspergillosis in solid organ transplant patients: diagnosis, prophylaxis, treatment, and assessment of response.
    Neofytos D, Garcia-Vidal C, Lamoth F, Lichtenstern C, Perrella A, Vehreschild JJ
    BMC Infect Dis. 2021 Mar 24;21(1):296

    Assessment of the Role of 1,3-β-d-Glucan Testing for the Diagnosis of Invasive Fungal Infections in Adults.
    Lamoth F, Akan H, Andes D, Cruciani M, Marchetti O, Ostrosky-Zeichner L, Racil Z, Clancy CJ
    Clin Infect Dis. 2021 Mar 12;72(Supplement_2):S102-S108

    Guidance on Imaging for Invasive Pulmonary Aspergillosis and Mucormycosis: From the Imaging Working Group for the Revision and Update of the Consensus Definitions of Fungal Disease from the EORTC/MSGERC.
    Alexander BD, Lamoth F, Heussel CP, Prokop CS, Desai SR, Morrissey CO, Baddley JW
    Clin Infect Dis. 2021 Mar 12;72(Supplement_2):S79-S88

    Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae.
    Colpaert M, Kadouche D, Ducatez M, Pillonel T, Kebbi-Beghdadi C, Cenci U, Huang B, Chabi M, Maes E, Coddeville B, Couderc L, Touzet H, Bray F, Tirtiaux C, Ball S, Greub G, Colleoni C
    Commun Biol. 2021 Mar 5;4(1):296

    Novel ERG11 and TAC1b mutations associated with azole resistance in Candida auris.
    Li J, Coste AT, Liechti M, Bachmann D, Sanglard D, Lamoth F
    Antimicrob Agents Chemother. 2021 Feb 22

    Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer.
    Tagini F, Pillonel T, Bertelli C, Jaton K, Greub G
    Microorganisms. 2021 Feb 10;9(2)

    Letter on "(1,3)-β-D-Glucan-based empirical antifungal interruption in suspected invasive candidiasis: a randomized trial".
    Kritikos A, Lamoth F
    Crit Care. 2021 Feb 9;25(1):55

    Insights in the molecular mechanisms of an azole stress adapted laboratory-generated Aspergillus fumigatus strain.
    Aruanno M, Gozel S, Mouyna I, Parker JE, Bachmann D, Flamant P, Coste AT, Sanglard D, Lamoth F
    Med Mycol. 2021 Feb 7

    Invasive Pulmonary Aspergillosis Goes Viral Again?
    Wauters J, Lamoth F, Rijnders BJA, Calandra T
    Am J Respir Crit Care Med. 2021 Feb 1;203(3):275-277

    Camphor and Eucalyptol-Anticandidal Spectrum, Antivirulence Effect, Efflux Pumps Interference and Cytotoxicity.
    Ivanov M, Kannan A, Stojković DS, Glamočlija J, Calhelha RC, Ferreira ICFR, Sanglard D, Soković M
    Int J Mol Sci. 2021 Jan 6;22(2)

    Future challenges and chances in the diagnosis and management of invasive mould infections in cancer patients.
    Vehreschild JJ, Koehler P, Lamoth F, Prattes J, Rieger C, Rijnders BJA, Teschner D
    Med Mycol. 2021 Jan 4;59(1):93-101

    Notes
    N/A
    Attachments
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    5. Briefly describe the biological defence work carried out at the facility, including type(s) of micro-organisms(9) and/or toxins studied, as well as outdoor studies of biological aerosols.

    The Diagnostic Laboratories of the Institute of Microbiology, which are part of the University Hospital of Lausanne, are the Regional Competence Center for the primary analysis of samples suspicious of a bioterror-related background. Due to its other diagnostic activities, it is able to cover the whole spectrum of microbiology, namely virology, bacteriology, mycology and parasitology. Bacteriology also includes mycobacteriology, for which the Institute of Microbiology acts as a regional center.

    Moreover, in 2017, we obtained the necessary funds for the up-grade and the expansion of our BSL3 level laboratory in the Institute of Microbiology. The construction started in September 2018 and finished in March 2020. During this period all these activities were carried out in the research BSL3 laboratory of our Institute according to the good laboratories practices recommended.

    The new BSL3 laboratory stand as the reference BSL3 laboratory of the hospital (CHUV) for the diagnosis and manipulation of BSL3 samples, strains, microorganisms that may be encountered in daily work as well as the samples of the environment for the regional laboratory network.

    For further information please visit:
    https://www.chuv.ch/en/microbiologi e/imu-home/diagnostics/

    (9) Including viruses and prions.

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