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 , 77.00 SqM
Total laboratory floor area (SqM)

4. The organizational structure of each facility

(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)

Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results. 
Caruana G, Croxatto A, Coste AT, Opota O, Lamoth F, Jaton K, Greub G.
Clin Microbiol Infect. 2020 Sep;26(9):1178-1182. doi: 10.1016/j.cmi.2020.06.019. Epub 2020 Jun 25.
PMID: 32593741 Free PMC article. Review. 

Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium. 
Donnelly JP, Chen SC, Kauffman CA, Steinbach WJ, Baddley JW, Verweij PE, Clancy CJ, Wingard JR, Lockhart SR, Groll AH, Sorrell TC, Bassetti M, Akan H, Alexander BD, Andes D, Azoulay E, Bialek R, Bradsher RW, Bretagne S, Calandra T, Caliendo AM, Castagnola E, Cruciani M, Cuenca-Estrella M, Decker CF, Desai SR, Fisher B, Harrison T, Heussel CP, Jensen HE, Kibbler CC, Kontoyiannis DP, Kullberg BJ, Lagrou K, Lamoth F, Lehrnbecher T, Loeffler J, Lortholary O, Maertens J, Marchetti O, Marr KA, Masur H, Meis JF, Morrisey CO, Nucci M, Ostrosky-Zeichner L, Pagano L, Patterson TF, Perfect JR, Racil Z, Roilides E, Ruhnke M, Prokop CS, Shoham S, Slavin MA, Stevens DA, Thompson GR, Vazquez JA, Viscoli C, Walsh TJ, Warris A, Wheat LJ, White PL, Zaoutis TE, Pappas PG.
Clin Infect Dis. 2020 Sep 12;71(6):1367-1376. doi: 10.1093/cid/ciz1008.
PMID: 31802125 Free PMC article. 

Second-Trimester Miscarriage in a Pregnant Woman With SARS-CoV-2 Infection. 
Baud D, Greub G, Favre G, Gengler C, Jaton K, Dubruc E, Pomar L.
JAMA. 2020 Jun 2;323(21):2198-2200. doi: 10.1001/jama.2020.7233.
PMID: 32352491 Free PMC article. 

[Novelties in HIV prevention and treatment in 2019]. 
Kampouri E, Papadimitriou-Olivgeris M, Calmy A, Ciuffi A, Cavassini M.
Rev Med Suisse. 2020 Jan 15;16(676-7):92-98.
PMID: 31961093 French. 

Letter to the editor: SARS-CoV-2 detection by real-time RT-PCR. 
Pillonel T, Scherz V, Jaton K, Greub G, Bertelli C.
Euro Surveill. 2020 May;25(21):2000880. doi: 10.2807/1560-7917.ES.2020.25.21.2000880.
PMID: 32489175 Free PMC article. No abstract available. 

Collapsing glomerulopathy in a COVID-19 patient. 
Kissling S, Rotman S, Gerber C, Halfon M, Lamoth F, Comte D, Lhopitallier L, Sadallah S, Fakhouri F.
Kidney Int. 2020 Jul;98(1):228-231. doi: 10.1016/j.kint.2020.04.006. Epub 2020 Apr 15.
PMID: 32471639 Free PMC article. No abstract available. 

Risk factors for candidemia: a prospective matched case-control study. 
Poissy J, Damonti L, Bignon A, Khanna N, Von Kietzell M, Boggian K, Neofytos D, Vuotto F, Coiteux V, Artru F, Zimmerli S, Pagani JL, Calandra T, Sendid B, Poulain D, van Delden C, Lamoth F, Marchetti O, Bochud PY; FUNGINOS; Allfun French Study Groups.
Crit Care. 2020 Mar 18;24(1):109. doi: 10.1186/s13054-020-2766-1.
PMID: 32188500 Free PMC article. 

Digital microbiology. 
Egli A, Schrenzel J, Greub G.
Clin Microbiol Infect. 2020 Oct;26(10):1324-1331. doi: 10.1016/j.cmi.2020.06.023. Epub 2020 Jun 27.
PMID: 32603804 Free PMC article. Review. 

Invasive aspergillosis due to Aspergillus section Usti: a multicenter retrospective study. 
Glampedakis E, Cassaing S, Fekkar A, Dannaoui E, Bougnoux ME, Bretagne S, Neofytos D, Schreiber PW, Hennequin C, Morio F, Shadrivova O, Bongomin F, Fernández-Ruiz M, Bellanger AP, Arikan-Akdagli S, Erard V, Aigner M, Paolucci M, Khanna N, Charpentier E, Bonnal C, Brun S, Gabriel F, Riat A, Zbinden R, Le Pape P, Klimko N, Lewis RE, Richardson M, İnkaya AC, Coste AT, Bochud PY, Lamoth F.
Clin Infect Dis. 2020 Mar 10:ciaa230. doi: 10.1093/cid/ciaa230. Online ahead of print.
PMID: 32155262 

COVID-19 et médecine ambulatoire - Migrations forcées : enjeux d’équité en santé. 
Morisod K, Bodenmann P.
Rev Med Suisse. 2020 Aug 5;16(701):1446-1447.
PMID: 32833365 French. No abstract available. 

Incidence of invasive pulmonary aspergillosis among critically ill COVID-19 patients. 
Lamoth F, Glampedakis E, Boillat-Blanco N, Oddo M, Pagani JL.
Clin Microbiol Infect. 2020 Dec;26(12):1706-1708. doi: 10.1016/j.cmi.2020.07.010. Epub 2020 Jul 10.
PMID: 32659385 Free PMC article. No abstract available. 
Pneumocystis jirovecii. 

Nevez G, Hauser PM, Le Gal S.
Trends Microbiol. 2020 Dec;28(12):1034-1035. doi: 10.1016/j.tim.2020.03.006. Epub 2020 Apr 21.
PMID: 33171104 No abstract available. 

Signaling Pathways Governing the Caspofungin Paradoxical Effect in Aspergillus fumigatus. 
Papon N, Morio F, Sanglard D.
mBio. 2020 Aug 18;11(4):e01816-20. doi: 10.1128/mBio.01816-20.
PMID: 32817108 Free PMC article. 

Ability of quantitative PCR to discriminate Pneumocystis jirovecii pneumonia from colonization. 
Perret T, Kritikos A, Hauser PM, Guiver M, Coste AT, Jaton K, Lamoth F.
J Med Microbiol. 2020 May;69(5):705-711. doi: 10.1099/jmm.0.001190. Epub 2020 Apr 28.
PMID: 32369002 Free PMC article. 

Emerging echinocandin-resistant Candida albicans and glabrata in Switzerland. 
Coste AT, Kritikos A, Li J, Khanna N, Goldenberger D, Garzoni C, Zehnder C, Boggian K, Neofytos D, Riat A, Bachmann D, Sanglard D, Lamoth F; Fungal Infection Network of Switzerland (FUNGINOS).
Infection. 2020 Oct;48(5):761-766. doi: 10.1007/s15010-020-01475-8. Epub 2020 Jul 13.
PMID: 32661647 Free PMC article. 

A novel circulating tamiami mammarenavirus shows potential for zoonotic spillover. 
Moreno H, Rastrojo A, Pryce R, Fedeli C, Zimmer G, Bowden TA, Gerold G, Kunz S.
PLoS Negl Trop Dis. 2020 Dec 28;14(12):e0009004. doi: 10.1371/journal.pntd.0009004. eCollection 2020 Dec.
PMID: 33370288 Free PMC article. 

Waddlia chondrophila and Male Infertility. 
Baud D, Vulliemoz N, Zapata MVM, Greub G, Vouga M, Stojanov M.
Microorganisms. 2020 Jan 17;8(1):136. doi: 10.3390/microorganisms8010136.
PMID: 31963568 Free PMC article. 

[SARS-CoV-2, a point in the storm]. 
Tadini E, Papamidimitriou-Olivgeris M, Opota O, Moulin E, Lamoth F, Manuel O, Lhopitallier L, Jaton K, Croxatto A, Grandbastien B, Senn L, Guery B.
Rev Med Suisse. 2020 May 6;16(692):917-923.
PMID: 32374537 French. 

Comparison of SARS-CoV-2 serological tests with different antigen targets. 
Coste AT, Jaton K, Papadimitriou-Olivgeris M, Greub G, Croxatto A.
J Clin Virol. 2021 Jan;134:104690. doi: 10.1016/j.jcv.2020.104690. Epub 2020 Nov 17.
PMID: 33253926 Free PMC article. 

Letter to the Editor. The COVID-19 pandemic in Singapore. 
Schiariti M, Restelli F, Broggi M, Acerbi F, Vetrano IG, Ciuffi A, Raccuia G, Ferroli P.
J Neurosurg. 2020 Jul 24:1-2. doi: 10.3171/2020.4.JNS201436. Online ahead of print.
PMID: 32707546 No abstract available. 

Les étudiant·e·s en médecine mènent une recherche dans la communauté. 
Daeppen JB, Gaume J, Bodenmann P, Buclin T, Fauvel A, Paroz S, Widmer D, Baumann M.
Rev Med Suisse. 2020 Oct 21;16(711):2007.
PMID: 33085258 French. No abstract available. 

Venous thromboembolism in critically Ill patients with COVID-19: Results of a screening study for deep vein thrombosis. 
Longchamp A, Longchamp J, Manzocchi-Besson S, Whiting L, Haller C, Jeanneret S, Godio M, Garcia Martinez JJ, Bonjour T, Caillat M, Maitre G, Thaler JM, Pantet R, Donner V, Dumoulin A, Emonet S, Greub G, Friolet R, Robert-Ebadi H, Righini M, Sanchez B, Delaloye J.
Res Pract Thromb Haemost. 2020 Jun 30;4(5):842-847. doi: 10.1002/rth2.12376. eCollection 2020 Jul.
PMID: 32685893 Free PMC article. 

[Left behind populations, COVID-19 and risks of health inequities : a guide of the local social-health network (Vaud, Switzerland)]. 
Bodenmann P, Pahud-Vermeulen B, Bouche L, Sanchis Zozaya J, Bauermeister M, Berzig A.
Rev Med Suisse. 2020 Apr 29;16(N° 691-2):859-862.
PMID: 32348054 French. 

Clinical Relevance and Characteristics of Aspergillus calidoustus and Other Aspergillus Species of Section Usti. 
Glampedakis E, Erard V, Lamoth F.
J Fungi (Basel). 2020 Jun 12;6(2):84. doi: 10.3390/jof6020084.
PMID: 32545485 Free PMC article. Review. 

Incidentally discovered COVID-19 pneumonia: the role of diagnostic imaging. 
Pozzessere C, Rotzinger DC, Ghaye B, Lamoth F, Beigelman-Aubry C.
Eur Radiol. 2020 Sep;30(9):5211-5213. doi: 10.1007/s00330-020-06914-6. Epub 2020 May 4.
PMID: 32367421 Free PMC article. No abstract available. 

[Risk communication in healthcare: literature review and recommendations for clinical practice]. 
Durand MA, Selby K, Bodenmann P, Zaman K, Ducros C, Cornuz J.
Rev Med Suisse. 2020 Nov 4;16(713):2092-2098.
PMID: 33146957 Review. French. 

Invasive Pulmonary Aspergillosis Goes Viral Again? 
Wauters J, Lamoth F, Rijnders BJ, Calandra T.
Am J Respir Crit Care Med. 2020 Dec 22. doi: 10.1164/rccm.202012-4413ED. Online ahead of print.
PMID: 33352060 No abstract available. 

Identification and Characterization of Mediators of Fluconazole Tolerance in Candida albicans. 
Delarze E, Brandt L, Trachsel E, Patxot M, Pralong C, Maranzano F, Chauvel M, Legrand M, Znaidi S, Bougnoux ME, d'Enfert C, Sanglard D.
Front Microbiol. 2020 Nov 11;11:591140. doi: 10.3389/fmicb.2020.591140. eCollection 2020.
PMID: 33262748 Free PMC article. 

Evaluation of the BD Phoenix™ CPO Detect Test for the detection of carbapenemase producers. 
Croxatto A, Coste AT, Pillonel T, Bertelli C, Greub G, Prod'hom G.
Clin Microbiol Infect. 2020 May;26(5):644.e9-644.e15. doi: 10.1016/j.cmi.2019.10.002. Epub 2019 Oct 18.
PMID: 31634549 

Performance of the T2Candida Panel for the Diagnosis of Intra-abdominal Candidiasis. 
Lamoth F, Clancy CJ, Tissot F, Squires K, Eggimann P, Flückiger U, Siegemund M, Orasch C, Zimmerli S, Calandra T, Marchetti O, Nguyen MH, Bochud PY.
Open Forum Infect Dis. 2020 Feb 27;7(3):ofaa075. doi: 10.1093/ofid/ofaa075. eCollection 2020 Mar.
PMID: 32195291 Free PMC article. 

Impact of the Beta-Glucan Test on Management of Intensive Care Unit Patients at Risk for Invasive Candidiasis. 
Kritikos A, Poissy J, Croxatto A, Bochud PY, Pagani JL, Lamoth F.
J Clin Microbiol. 2020 May 26;58(6):e01996-19. doi: 10.1128/JCM.01996-19. Print 2020 May 26.
PMID: 32238435 Free PMC article. 

Role and Interpretation of Antifungal Susceptibility Testing for the Management of Invasive Fungal Infections. 
Lamoth F, Lewis RE, Kontoyiannis DP.
J Fungi (Basel). 2020 Dec 30;7(1):17. doi: 10.3390/jof7010017.
PMID: 33396870 Free PMC article. Review. 

Long lasting hypercoagulability after subclinical COVID-19. 
Ferroli P, Villa C, Ciuffi A, Gubertini G, Broggi M.
J Thromb Thrombolysis. 2020 Nov;50(4):822-824. doi: 10.1007/s11239-020-02215-3.
PMID: 32757154 Free PMC article. No abstract available. 

Whipple disease: a 15-year retrospective study on 36 patients with positive polymerase chain reaction for Tropheryma whipplei. 
Duss FR, Jaton K, Vollenweider P, Troillet N, Greub G.
Clin Microbiol Infect. 2020 Sep 4:S1198-743X(20)30519-X. doi: 10.1016/j.cmi.2020.08.036. Online ahead of print.
PMID: 32896657 

Universal admission screening strategy for COVID-19 highlighted the clinical importance of reporting SARS-CoV-2 viral loads. 
Moraz M, Jacot D, Papadimitriou-Olivgeris M, Senn L, Greub G, Jaton K, Opota O.
New Microbes New Infect. 2020 Nov;38:100820. doi: 10.1016/j.nmni.2020.100820. Epub 2020 Nov 19.
PMID: 33235799 Free PMC article. 

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. 
Wan C, Bachmann N, Mitov V, Blanquart F, Céspedes SP, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Walti L, Calmy A, Vernazza P, Bernasconi E, Cavassini M, Metzner KJ, Günthard HF, Kouyos RD; Swiss HIV Cohort Study.
Nat Commun. 2020 Nov 2;11(1):5542. doi: 10.1038/s41467-020-19198-7.
PMID: 33139735 Free PMC article. 

Serum antibody response in critically ill patients with COVID-19. 
Longchamp A, Longchamp J, Croxatto A, Greub G, Sanchez B, Delaloye J; Study Group.
Intensive Care Med. 2020 Oct;46(10):1921-1923. doi: 10.1007/s00134-020-06171-7. Epub 2020 Jul 8.
PMID: 32642784 Free PMC article. No abstract available. 

Nested Species Distribution Models of Chlamydiales in Ixodes ricinus (Tick) Hosts in Switzerland. 
Rochat E, Vuilleumier S, Aeby S, Greub G, Joost S.
Appl Environ Microbiol. 2020 Dec 17;87(1):e01237-20. doi: 10.1128/AEM.01237-20. Print 2020 Dec 17.
PMID: 33067199 Free PMC article. 

SPHN/PHRT: Forming a Swiss-Wide Infrastructure for Data-Driven Sepsis Research. 
Egli A, Battegay M, Büchler AC, Bühlmann P, Calandra T, Eckert P, Furrer H, Greub G, Jakob SM, Kaiser L, Leib SL, Marsch S, Meinshausen N, Pagani JL, Pugin J, Rätsch G, Schrenzel J, Schüpbach R, Siegemund M, Zamboni N, Zbinden R, Zinkernagel A, Borgwardt K.
Stud Health Technol Inform. 2020 Jun 16;270:1163-1167. doi: 10.3233/SHTI200346.
PMID: 32570564 

Single yeast cell nanomotions correlate with cellular activity. 
Willaert RG, Vanden Boer P, Malovichko A, Alioscha-Perez M, Radotić K, Bartolić D, Kalauzi A, Villalba MI, Sanglard D, Dietler G, Sahli H, Kasas S.
Sci Adv. 2020 Jun 24;6(26):eaba3139. doi: 10.1126/sciadv.aba3139. eCollection 2020 Jun.
PMID: 32637604 Free PMC article. 

SARS-CoV-2 ACE-receptor detection in the placenta throughout pregnancy. 
Gengler C, Dubruc E, Favre G, Greub G, de Leval L, Baud D.
Clin Microbiol Infect. 2020 Oct 3:S1198-743X(20)30603-0. doi: 10.1016/j.cmi.2020.09.049. Online ahead of print.
PMID: 33022363 Free PMC article. No abstract available. 

[Racism and the practice of medicine : elements for a required learning]. 
Bodenmann P, Hrasnica F, Prod'hom D, Perrin ÈM, Ishii A, Porret R, Fricker C, Morisod K, Sanchis Zozaya J, Malebranche ME, Green A, Bart PA.
Rev Med Suisse. 2020 Jul 15;16(700):1373-1379.
PMID: 32672017 French. 

Machine Learning Approach for Candida albicans Fluconazole Resistance Detection Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. 
Delavy M, Cerutti L, Croxatto A, Prod'hom G, Sanglard D, Greub G, Coste AT.
Front Microbiol. 2020 Jan 14;10:3000. doi: 10.3389/fmicb.2019.03000. eCollection 2019.
PMID: 32010083 Free PMC article. 

New Data on the In Vitro Activity of Fenticonazole against Fluconazole-Resistant Candida Species. 
Cacaci M, Menchinelli G, Torelli R, Sanglard D, Sanguinetti M, Posteraro B.
Antimicrob Agents Chemother. 2020 Nov 17;64(12):e01459-20. doi: 10.1128/AAC.01459-20. Print 2020 Nov 17.
PMID: 32988826 Free PMC article. No abstract available. 

Genome sequencing of Mycobacterium tuberculosis clinical isolates revealed isoniazid resistance mechanisms undetected by conventional molecular methods. 
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. doi: 10.1016/j.ijantimicag.2020.106068. Epub 2020 Jun 27.
PMID: 32603684 

Determination of carbapenem antibiotics using a purpose-made capillary electrophoresis instrument with contactless conductivity detection. 
Pham TNM, Le TB, Le DD, Ha TH, Nguyen NS, Pham TD, Hauser PC, Nguyen TAH, Mai TD.
J Pharm Biomed Anal. 2020 Jan 30;178:112906. doi: 10.1016/j.jpba.2019.112906. Epub 2019 Oct 3.
PMID: 31634756 

Epidemiology of sexually transmitted infections among female sex workers in Switzerland: a local, exploratory, cross-sectional study. 
Vu F, Cavassini M, D'Acremont V, Greub G, Jaton K, Masserey E, Pongelli S, Bouche L, Ngarambe C, Bize R, Bodenmann P.
Swiss Med Wkly. 2020 Dec 30;150:w20357. doi: 10.4414/smw.2020.20357. eCollection 2020 Dec 14.
PMID: 33378545 

Symposium report: One Health meets sequencing. 
Egli A, Koch D, Danuser J, Hendriksen RS, Driesen S, Schmid DC, Neher R, Mäusezahl M, Seth-Smith HMB, Bloemberg G, Tschudin-Sutter S, Endimiani A, Perreten V, Greub G, Schrenzel J, Stephan R.
Microbes Infect. 2020 Jan-Feb;22(1):1-7. doi: 10.1016/j.micinf.2019.07.004. Epub 2019 Aug 8.
PMID: 31401354 No abstract available. 

Performance evaluation of the Becton Dickinson Kiestra™ IdentifA/SusceptA. 
Jacot D, Sarton-Lohéac G, Coste AT, Bertelli C, Greub G, Prod'hom G, Croxatto A.
Clin Microbiol Infect. 2020 Oct 5:S1198-743X(20)30604-2. doi: 10.1016/j.cmi.2020.09.050. Online ahead of print.
PMID: 33031951 

Screening of Chlamydia trachomatis and Waddlia chondrophila Antibodies in Women with Tubal Factor Infertility. 
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):918. doi: 10.3390/microorganisms8060918.
PMID: 32560559 Free PMC article. 

The Role of Receptor Tyrosine Kinases in Lassa Virus Cell Entry. 
Fedeli C, Moreno H, Kunz S.
Viruses. 2020 Aug 6;12(8):857. doi: 10.3390/v12080857.
PMID: 32781509 Free PMC article. 

Validation and clinical application of a multiplex high performance liquid chromatography - tandem mass spectrometry assay for the monitoring of plasma concentrations of 12 antibiotics in patients with severe bacterial infections. 
Decosterd LA, Mercier T, Ternon B, Cruchon S, Guignard N, Lahrichi S, Pesse B, Rochat B, Burger R, Lamoth F, Pagani JL, Eggimann P, Csajka C, Choong E, Buclin T, Widmer N, André P, Marchetti O.
J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Nov 10;1157:122160. doi: 10.1016/j.jchromb.2020.122160. Epub 2020 May 17.
PMID: 32891946 

Longitudinal panel data study of self-rated health among migrants in French-speaking Switzerland, 2003-2017. 
Mota P, Saez M, Selby K, Bodenmann P.
BMJ Open. 2020 Aug 13;10(8):e035812. doi: 10.1136/bmjopen-2019-035812.
PMID: 32792430 Free PMC article. 

Single-Cell Analysis Reveals Heterogeneity of Virus Infection, Pathogenicity, and Host Responses: HIV as a Pioneering Example. 
Brandt L, Cristinelli S, Ciuffi A.
Annu Rev Virol. 2020 Sep 29;7(1):333-350. doi: 10.1146/annurev-virology-021820-102458.
PMID: 32991268 

Glucuronoxylomannan in the Cryptococcus species capsule as a target for Chimeric Antigen Receptor T-cell therapy. 
da Silva TA, Hauser PJ, Bandey I, Laskowski T, Wang Q, Najjar AM, Kumaresan PR.
Cytotherapy. 2020 Dec 7:S1465-3249(20)30933-6. doi: 10.1016/j.jcyt.2020.11.002. Online ahead of print.
PMID: 33303326 

Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses. 
Jacot D, Greub G, Jaton K, Opota O.
Microbes Infect. 2020 Nov-Dec;22(10):617-621. doi: 10.1016/j.micinf.2020.08.004. Epub 2020 Sep 7.
PMID: 32911086 Free PMC article. 

Clinical bioinformatics for microbial genomics and metagenomics: an ESCMID Postgraduate Technical Workshop. 
Greub G, Palagi PM, Dylus D, Egli A, Pillonel T, Rossen JWA, Seth-Smith HMB, Lebrand A; ESGMD Study Group.
Microbes Infect. 2020 Nov-Dec;22(10):626-634. doi: 10.1016/j.micinf.2020.07.008. Epub 2020 Aug 22.
PMID: 32841729 No abstract available. 

Presence and diversity of Chlamydiae bacteria in Spinturnix myoti, an ectoparasite of bats. 
Thiévent K, Szentiványi T, Aeby S, Glaizot O, Christe P, Greub G.
Parasite. 2020;27:54. doi: 10.1051/parasite/2020052. Epub 2020 Nov 2.
PMID: 33135998 Free PMC article. 

Impact of Genetic and Nongenetic Factors on Body Mass Index and Waist-Hip Ratio Change in HIV-Infected Individuals Initiating Antiretroviral Therapy. 
Barceló C, Guidi M, Thorball CW, Hammer C, Chaouch A, Scherrer AU, Hasse B, Cavassini M, Furrer H, Calmy A, Haubitz S, Bernasconi E, Buclin T, Fellay J, Tarr PE, Csajka C; Swiss HIV Cohort Study.
Open Forum Infect Dis. 2020 Jan 22;7(1):ofz464. doi: 10.1093/ofid/ofz464. eCollection 2020 Jan.
PMID: 31988971 Free PMC article. 

Emergence of Drug Resistance in the Swiss HIV Cohort Study Under Potent Antiretroviral Therapy Is Observed in Socially Disadvantaged Patients. 
Abela IA, Scherrer AU, Böni J, Yerly S, Klimkait T, Perreau M, Hirsch HH, Furrer H, Calmy A, Schmid P, Cavassini M, Bernasconi E, Günthard HF; Swiss HIV Cohort Study.
Clin Infect Dis. 2020 Jan 2;70(2):297-303. doi: 10.1093/cid/ciz178.
PMID: 30843028 

ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. 
Pillonel T, Tagini F, Bertelli C, Greub G.
Nucleic Acids Res. 2020 Jan 8;48(D1):D526-D534. doi: 10.1093/nar/gkz924.
PMID: 31665454 Free PMC article. 

Large-scale genome mining allows identification of neutral polymorphisms and novel resistance mutations in genes involved in Candida albicans resistance to azoles and echinocandins. 
Sitterlé E, Coste AT, Obadia T, Maufrais C, Chauvel M, Sertour N, Sanglard D, Puel A, D'Enfert C, Bougnoux ME.
J Antimicrob Chemother. 2020 Apr 1;75(4):835-848. doi: 10.1093/jac/dkz537.
PMID: 31923309 

Expression pattern of the Pneumocystis jirovecii major surface glycoprotein superfamily in patients with pneumonia. 
Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M, Hauser PM.
J Infect Dis. 2020 Jun 19:jiaa342. doi: 10.1093/infdis/jiaa342. Online ahead of print.
PMID: 32561915 

Vertical transmission and materno-fetal outcomes in 13 patients with coronavirus disease 2019. 
Masmejan S, Pomar L, Favre G, Panchaud A, Giannoni E, Greub G, Baud D.
Clin Microbiol Infect. 2020 Nov;26(11):1585-1587. doi: 10.1016/j.cmi.2020.06.035. Epub 2020 Jul 8.
PMID: 32652239 Free PMC article. No abstract available. 

Eukaryotic Cell Permeabilisation to Identify New Putative Chlamydial Type III Secretion System Effectors Secreted within Host Cell Cytoplasm. 
Kebbi-Beghdadi C, Pilloux L, Martin V, Greub G.
Microorganisms. 2020 Mar 3;8(3):361. doi: 10.3390/microorganisms8030361.
PMID: 32138376 Free PMC article. 

COVID-19 Pandemics: A Surprising Link to Bread Flour With Collateral Damage to a Prosthetic Heart Valve. 
Tozzi P, Kampouri EE, Tzimas G, Prior JO, Monney P, Kamani C, Lamoth F.
Circ Cardiovasc Imaging. 2020 Oct;13(10):e011395. doi: 10.1161/CIRCIMAGING.120.011395. Epub 2020 Oct 2.
PMID: 33003958 No abstract available. 

Transcriptional Landscape of Waddlia chondrophila Aberrant Bodies Induced by Iron Starvation. 
Ardissone S, Scherler A, Pillonel T, Martin V, Kebbi-Beghdadi C, Greub G.
Microorganisms. 2020 Nov 24;8(12):1848. doi: 10.3390/microorganisms8121848.
PMID: 33255276 Free PMC article. 

Piperacillin/tazobactam selects an ampC derepressed E. cloacae complex mutant in a diabetic osteoarticular infection. 
Moraz M, Bertelli C, Prod'hom G, Croxatto A, Greub G, Abou-Khalil S, Borens O, Meylan S.
Clin Microbiol Infect. 2020 Sep 4:S1198-743X(20)30518-8. doi: 10.1016/j.cmi.2020.08.035. Online ahead of print.
PMID: 32891764 No abstract available. 

Flavones, Flavonols, and Glycosylated Derivatives-Impact on Candida albicans Growth and Virulence, Expression of CDR1 and ERG11, Cytotoxicity. 
Ivanov M, Kannan A, Stojković DS, Glamočlija J, Calhelha RC, Ferreira ICFR, Sanglard D, Soković M.
Pharmaceuticals (Basel). 2020 Dec 30;14(1):27. doi: 10.3390/ph14010027.
PMID: 33396973 Free PMC article. 

Prevalence and Clinical Outcomes of Poor Immune Response Despite Virologically Suppressive Antiretroviral Therapy Among Children and Adolescents With Human Immunodeficiency Virus in Europe and Thailand: Cohort Study. 
European Pregnancy and Paediatric HIV Cohort Collaboration (EPPICC) Study Group in EuroCoord.
Clin Infect Dis. 2020 Jan 16;70(3):404-415. doi: 10.1093/cid/ciz253.
PMID: 30919882 

Diverse Stress-Inducing Treatments cause Distinct Aberrant Body Morphologies in the Chlamydia-Related Bacterium, Waddlia chondrophila. 
Scherler A, Jacquier N, Kebbi-Beghdadi C, Greub G.
Microorganisms. 2020 Jan 9;8(1):89. doi: 10.3390/microorganisms8010089.
PMID: 31936490 Free PMC article. 

Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units. 
Magalhães B, Valot B, Abdelbary MMH, Prod'hom G, Greub G, Senn L, Blanc DS.
Front Public Health. 2020 Jan 28;8:3. doi: 10.3389/fpubh.2020.00003. eCollection 2020.
PMID: 32047733 Free PMC article. 

Multisystem inflammatory syndrome with refractory cardiogenic shock due to acute myocarditis and mononeuritis multiplex after SARS-CoV-2 infection in an adult. 
Othenin-Girard A, Regamey J, Lamoth F, Horisberger A, Glampedakis E, Epiney JB, Kuntzer T, de Leval L, Carballares M, Hurni CA, Rusca M, Pantet O, Di Bernardo S, Oddo M, Comte D, Piquilloud L.
Swiss Med Wkly. 2020 Nov 11;150:w20387. doi: 10.4414/smw.2020.20387. eCollection 2020 Nov 2.
PMID: 33181855 

NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. 
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, Lebrand A.
Front Microbiol. 2020 Nov 24;11:591093. doi: 10.3389/fmicb.2020.591093. eCollection 2020.
PMID: 33424794 Free PMC article. 

Comparison of SARS-CoV-2 RT-PCR on a high-throughput molecular diagnostic platform and the cobas SARS-CoV-2 test for the diagnostic of COVID-19 on various clinical samples. 
Opota O, Brouillet R, Greub G, Jaton K.
Pathog Dis. 2020 Nov 11;78(8):ftaa061. doi: 10.1093/femspd/ftaa061.
PMID: 33030200 Free PMC article. 

Prevalence and phylogeny of Chlamydiae and hemotropic mycoplasma species in captive and free-living bats. 
Fritschi J, Marti H, Seth-Smith HMB, Aeby S, Greub G, Meli ML, Hofmann-Lehmann R, Mühldorfer K, Stokar-Regenscheit N, Wiederkehr D, Pilo P, Van Den Broek PR, Borel N.
BMC Microbiol. 2020 Jun 26;20(1):182. doi: 10.1186/s12866-020-01872-x.
PMID: 32590949 Free PMC article. 

International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae, minutes of the closed meeting, 10 September 2020, via Zoom. 
Borel N, Greub G.
Int J Syst Evol Microbiol. 2020 Dec 17. doi: 10.1099/ijsem.0.004620. Online ahead of print.
PMID: 33332256 No abstract available. 

Exonuclease resistant 18S and 25S ribosomal RNA components in yeast are possibly newly transcribed by RNA polymerase II. 
Fleischmann J, Rocha MA, Hauser PV, Gowda BS, Pilapil MGD.
BMC Mol Cell Biol. 2020 Aug 1;21(1):59. doi: 10.1186/s12860-020-00303-z.
PMID: 32738873 Free PMC article. 

Evaluation of the performance of rapid tests for screening carriers of acquired ESBL producers and their impact on the turnaround time. 
Blanc DS, Poncet F, Grandbastien B, Greub G, Senn L, Nordmann P.
J Hosp Infect. 2020 Oct 24:S0195-6701(20)30494-1. doi: 10.1016/j.jhin.2020.10.013. Online ahead of print.
PMID: 33122041 

[Myases from here and elsewhere : pseudo-furonculosis and Ignatzschineria larvae bacteremia]. 
Berthod D, Duss FR, Palazzuolo M, Eyer M, Onya O, Aellen S, Bettschart V, Schmid T, Greub G, Troillet N.
Rev Med Suisse. 2020 Oct 14;16(710):1932-1936.
PMID: 33058580 French. 

Comparison of Bioinformatics Pipelines and Operating Systems for the Analyses of 16S rRNA Gene Amplicon Sequences in Human Fecal Samples. 
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 Jun 17;11:1262. doi: 10.3389/fmicb.2020.01262. eCollection 2020.
PMID: 32636817 Free PMC article. 

Changes in SARS-CoV-2 Spike versus Nucleoprotein Antibody Responses Impact the Estimates of Infections in Population-Based Seroprevalence Studies. 
Fenwick C, Croxatto A, Coste AT, Pojer F, André C, Pellaton C, Farina A, Campos J, Hacker D, Lau K, Bosch BJ, Gonseth Nussle S, Bochud M, D'Acremont V, Trono D, Greub G, Pantaleo G.
J Virol. 2021 Jan 13;95(3):e01828-20. doi: 10.1128/JVI.01828-20. Print 2021 Jan 13.
PMID: 33144321 

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. doi: 10.1093/mmy/myaa079.
PMID: 32898264 Free PMC article. 

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):483. doi: 10.3390/ijms22020483.
PMID: 33418931 Free PMC article. 

The Effect of Nutritional Support on the Disease Progression and Survival in Pediatric Patients with Solid Tumors. 
Gallo N, Czuppon K, Tomsits E, Garami M, Hauser P, Jakab Z, Nagy K, Kovacs GT.
Nutr Cancer. 2021 Jan 12:1-9. doi: 10.1080/01635581.2020.1869275. Online ahead of print.
PMID: 33432830 

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.

Moreover, in 2017, the laboratory obtained the necessary funds for the up-grade and the expansion of its 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 the 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 RLN group.

For further information please visit: e/imu-home/diagnostics/

(9) Including viruses and prions.