applied microbiology research lab

Publications

GPT-4-based AI agents—the new expert system for detection of antimicrobial resistance mechanisms?

Giske CG, Bressan M, Fiechter F, Hinic V, Mancini S, Nolte O, Egli A.

Journal of Clinical Microbiology. 2024 Oct 17:e00689-24. https://doi.org/10.1128/jcm.00689-24

Usage of Bacterial Whole Genome Sequencing: Outbreaks and Beyond in Pediatric Patients

Seth-Smith H, Roloff T, Benvenga V, Egli A.

The Pediatric Infectious Disease Journal. 2024:10-97. doi.org/10.1097/INF.0000000000004588.

Potent in-vitro activity of sulbactam-durlobactam against NDM-producing Escherichia coli including cefiderocol and aztreonam-avibactam-resistant isolates

Terrier CL, Nordmann P, Delaval A, Lienhard R, Vonallmen L, Schilt C, Scherler A, Lucke K, Jutzi M, Reichmuth M, Slutter V, Gras PA, Suter B, Schibli U, Fricker C, Pranghofer S, Graff K, Graf S, Greub G, Blanc D, Vitale A, Lemaire B, Fatoux M, Tritten M, Simonet T, Rumebe L, Liassine N, Jost G, Rosselin M, Wohlwend N, Schultze D, Burren K, Westers A, Imperiali M, Pozzi L, Balzari D, Vaninetti G, Cirillo C, Gaia V, Pianezzi E, Mueller GL, Jayol A, Guyon C, Hyden D, Maitrejean M, Deggi-Messmer V, Bandeira D, Fournier C, Assman H, Nusbaumer C, Bertaiola Monnerat L, Schrenzel J, Renzi G, Cherkaoui A, Andrey D, Nguyen A, Emonet S, Eyer M, Maret R, Belo AV, Mabillard D, Moraz M, Herzog K, Gisler V, Hitz E, Oberle M, Fankhauser H, Dubey N, Capaul R, Guler C, Schoenenberger M, Karrer U, Imeri F, Hinrikson H, Piran F, Ergani A, Andreutti C, Dessauges M, Schmid T, Mitrovic I, Gruner E, Bruderer V, Dimitrijevic D, Guillod Y, Maffioli C, Maurer J, Michel Blanco M, Vogel M, Wampfler R, Staehli P, Schnell B, Zehnder C, Di Lorenzo V, Payen C, Boschung D, Comte L, Schacher M, Brandenberger M, Zowa C, Marti CO, Trachsel S, Descombes MC, Steffen I, Kurmann C, von Arb B, Wehrli M, Elmer B, Imhof A, Preiswerk B, Mathis B, Martinotti L, Basilico L, Togni G, Minkova P, Kuegler M, Povolo V, Droz S, Elzi M, Casanova C, Goldenberger D, Keller P, Lang C, Blaich A, Schmid S, Ivan B, Egli A, Mancini S, Dubuis O, Narr K, Schoch S, Ellenberger S, Castelberg C, Seiffert S, Poirel L.

Clinical Microbiology and Infection. 2024 Oct 22. 10.1016/j.cmi.2024.10.012

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

Tsang KK, Lam MM, Wick RR, Wyres KL, Bachman M, Baker S, Barry K, Brisse S, Campino S, Chiaverini A, Cirillo DM, Clark T, Corander J, Corbella M, Cornacchia A, Cuénod A, D'Alterio N, Di Marco F, Donado-Godoy P, Egli A, Farzana R, Feil EJ, Fostervold A, Gorrie CL, Hassan B, Klokkhammer Hetland MA, Hoa LNM, Hoi LT, Howden B, Ikhimiukor OO, Jenney AWJ, Kaspersen H, Khokhar F, Leangapichart T, Ligowska-Marzęta M, Høyland Löhr I, Long SW, Mathers AJ, McArthur AG, Nagaraj G, Oaikhena AO, Okeke IN, Perdigão J, Parikh H, Pham MH, Pomilio F, Raffelsberger N, Rakotondrasoa A, Kumar KLR, Roberts LW, Rodrigues C, Samuelsen Ø, Sands K, Sassera D, Seth-Smith HMB, Shamanna V, Sherry N, Sia S, Spadar A, Stoesser N, Sunde M, Sundsfjord A, Thach PN, Thomson NR, Thorpe HA, Torok ME, Trang VD, Trung NV, Vornhagen J, Walsh T, Warne B, Wilson H, Wright GD, Holt KE and KlebNET-GSP AMR Genotype-Phenotype Group.

Microbial genomics. 2024 Oct 21;10(10):001294. https://doi.org/10.1099/mgen.0.001294

Outbreak with OXA-23-producing Acinetobacter baumannii in a COVID-19 ICU cohort: unraveling routes of transmission

Zingg S, Kuster S, von Rotz M, Portmann A, Egli A, Seth-Smith HM, Schlaepfer P, Goldenberger D, Bassetti S, Marsch S, Pargger H, Kuehl R & Tschudin-Sutter S.

Antimicrobial Resistance & Infection Control. 2024 Oct 19;13(1):127. https://doi.org/10.1186/s13756-024-01485-3

Quantifying aminoglycoside resistance in extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales clinical isolates: a retrospective cohort study

Vock I, Aguilar-Bultet L, Khanna N, Egli A, Wehrle-Wieland E, Tamma PD, Sutter ST.

Swiss Medical Weekly 2024 Oct 9;154(10):3904-. https://doi.org/10.57187/s.3904

Target Attainment and Population Pharmacokinetics of Cefazolin in Patients with Invasive Staphylococcus aureus Infections: A Prospective Cohort Study

Bausch S, Dräger S, Charitos-Fragkakis P, Egli A, Moser S, Hinic V, Kuehl R, Bassetti S, Siegemund M, Rentsch KM, Hermann L, Schöning V, Hammann F, Sendi P and Osthoff M.

2024 Sep 29;13(10):928. https://doi.org/10.3390/antibiotics13100928

Colonization with resistant bacteria in hospital employees: an epidemiological surveillance and typing study

Badinski T, Seiffert SN, Grässli F, Babouee Flury B, Besold U, Betschon E, Biggel M, Brucher A, Cusini A, Dörr T, Egli A, Goppel S, Güsewell S, Keller J, von Kietzell M, Möller JC, Nolte O, Ortner M, Roloff T, Ruetti M, Schlegel M, Seth-Smith HMB, Stephan R, Stocker R, Vuichard-Gysin D, Willi B, Kuster SP, Kahlert CR, Kohler P, on behalf of the SURPRISE Study Group.

Antimicrobial Agents and Chemotherapy. 2024 Sep 26:e00985-24. https://doi.org/10.1128/aac.00985-24

A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities

Dommann J, Kerbl-Knapp J, Albertos Torres D, Egli A, Keiser J, Schneeberger PH.

mSystems. 2024 Sep 10:e00859-24. https://doi.org/10.1128/msystems.00859-24

Conference report: The first Bacterial Genome Sequencing Pan-European Network Conference

Germuskova Z, Sosa E, Lagos AC, Aamot HV, Beale MA, Bertelli C, Björkmann J, Couto N, Feige L, Greub G, Hallbäck ET, Hodcroft EB, Harmsen D, Jacob L, Jolley KA, Kahles A, Mather AE, Neher RA, Neves A, Nieman S, Nolte O, Peacock SJ, Razavi M, Roloff T, Schrenzel J, Sikora P, Sundqvist M, Mölling P, Egli A.

Microbes and infection. 2024 Aug 30:105410. https://doi.org/10.1016/j.micinf.2024.105410

Clinical Presentation of Enterovirus D68 in a Swiss Pediatric University Center

Ott C, Dutilh G, Reist J, Bingisser R, Egli A, Heininger U.

The Pediatric Infectious Disease Journal.:10-97. 10.1097/INF.0000000000004503

Towards unified reporting of genome sequencing results in clinical microbiology

Mutschler E, Roloff T, Neves A, Aamot HV, Rodriguez-Sanchez B, Ramirez M, Rossen J, Couto N, Novais Â, Howden BP, Brisse S, Reuter S, Nolte O, Egli A, Seth-Smith HMB, and the ESCMID Study Group for Epidemiological Markers (ESGEM), and ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD)

PeerJ. 2024 Aug 8;12:e17673. 10.7717/peerj.17673

Prospective One-Health investigation into low-abundant extended-spectrum β-lactamase producing Enterobacterales enables detection of potential dissemination events and persistence

García-Martín AB, Aguilar-Bultet L, Gómez-Sanz E, Hug MA, Furger R, Eichenberger L, Schindler R, Steffen I, Egli A, Stadler T, Bagutti C, Tschudin-Sutter S.

Science of The Total Environment. 2024 Nov 10;950:175078. https://doi.org/10.1016/j.scitotenv.2024.175078

Anti-SARS-CoV-2 total immunoglobulin and neutralising antibody responses in healthy blood donors throughout the COVID-19 pandemic: a longitudinal observational study

Gütlin Y, Torres DA, Gensch A, Schlotterbeck AK, Stöger L, Heller S, Infanti L, Barut GT, Thiel V, Leuzinger K, Hirsch HH, Buser A, Egli A.

Swiss Medical Weekly. 2024 Jul 1;154(7):3408-. https://doi.org/10.57187/s.3408

Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution

Fernandez JE, Egli A, Overesch G & Perreten V.

Nature Communications. 2024 Jul 1;15(1):5526. https://doi.org/10.1038/s41467-024-49644-9

Schätze für die Gesundheit bewahren

Gautschi L, Steiger D, Egli A.

BIOspektrum. 2024 Jun;30(4):469-. https://doi.org/10.1007/s12268-024-2214-x

Molecular epidemiology of invasive Group A Streptococcal infections before and after the COVID-19 pandemic in Switzerland

Andrianaki AM, Andreoni F, Franz J, Bergada-Pijuan J, Scheier TC, Duwe T, Pfister M, Vostokova E, Seth-Smith H, Roloff T, Kolesnik-Goldmann N, Burkhard SH, Cusini A, Karrer U, Rüegg C, Schibli A, Schrenzel J, Musumeci S, Kouyos RD, Egli A, Brugger SD, Zinkernagel AS.

CMI Communications. 2024 May 23:100004. https://doi.org/10.1016/j.cmicom.2024.100004

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans

Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R.

Cell Host & Microbe. 2024 May 7. https://doi.org/10.1016/j.chom.2024.04.016

Utilization of a Meningitis/Encephalitis PCR panel at the University Hospital Basel – a retrospective study to develop a diagnostic decision rule

Erba A, Franzeck FC, Hinic V, Egli A, Osthoff M.

Frontiers in Medicine. 2024 Apr 17;11:1351903. https://doi.org/10.3389/fmed.2024.1351903

Rapid detection of plasmid-mediated AmpC-producers by eazyplex® SuperBug AmpC assay compared to whole-genome sequencing

Hinić V, Seth-Smith HM, Stammler S, Egli A.

Journal of Microbiological Methods. 2024 Apr 19:106938. https://doi.org/10.1016/j.mimet.2024.106938

How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort

Wegner F, Cabrera-Gil B, Tanguy A, Beckmann C, Beerenwinkel N, Bertelli C, Carrara M, Cerutti L, Chen C, Cordey S, Dumoulin A, du Plessis L, Friedli M, Gerth Y, Greub G, Härri A, Hirsch H, Howald C, Huber M, Imhof A, Kaiser L, Kufner V, Leib SL, Leuzinger K, Lleshi E, Martinetti G, Mäusezahl M, Moraz M, Neher R, Nolte O, Ramette A, Redondo M, Risch L, Rohner L, Roloff T , Schläepfer P, Schneider K, Singer F, Spina V, Stadler T, Studer E, Topolsky I, Trkola A, Walther D, Wohlwend N, Zehnder C, Neves A, Egli A, the SPSP consortium.

Microbiology spectrum. 2024 Mar 18:e03628-23. https://doi.org/10.1128/spectrum.03628-23

Tularemia on the rise in Switzerland? A one health approach is needed!

Buettcher M, Egli A, Albini S, Altpeter E, Labutin A, Guidi V, Tonolla M, Lienhard R, Opota O, Schmid P, Wuethrich T,

Schmidt CM on behalf of the TULAR-CH working group.

Infection. 2024 Mar 14:1-5. https://doi.org/10.1007/s15010-024-02218-9

Pneumonia outbreaks due to re-emergence of Mycoplasma pneumoniae

Meyer Sauteur PM, Beeton ML on behalf of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycoplasma and Chlamydia Infections (ESGMAC), and the ESGMAC Mycoplasma pneumoniae Surveillance (MAPS) study group

The Lancet Microbe. 2024 Feb 8. https://doi.org/10.1016/S2666-5247(23)00406-8

S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5

Hilti D, Wehrli F, Berchtold S, Bigler S, Bodmer T, Seth-Smith HM, Roloff T, Kohler P, Kahlert CR, Kaiser L, Egli A, Risch L, Risch M & Wohlwend N.

Microorganisms. 2024 Feb 3;12(2):321. https://doi.org/10.3390/microorganisms12020321

Molecular analysis of metallo-beta-lactamase-producing Pseudomonas aeruginosa in Switzerland 2022–2023

Findlay J, Raro OH, Poirel L, Nordmann P & NARA Network.

European Journal of Clinical Microbiology & Infectious Diseases. 2024 Jan 18:1-7. https://doi.org/10.1007/s10096-024-04752-8

Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

Benvenga V, Cuénod A, Purushothaman S, Dasen G, Weisser M, Bassetti S, Roloff T, Siegemund M, Heininger U, Bielicki J, Wehrli M, Friderich P, Frei R, Widmer A, Herzog K, Fankhauser H, Nolte O, Bodmer T, Risch M, Dubuis O, Pranghofer S, Calligaris-Maibach R, Graf S, Perreten V, Seth-Smith HMB & Egli A.

Genome Medicine. 2024 Feb 5;16(1):23. https://doi.org/10.1186/s13073-024-01292-w

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

Muigg V, Seth-Smith H, Adam KM, Weisser M, Hinić V, Blaich A, Roloff T, Heininger U, Schmid H, Kohler M, Graf L, Winterflood DM, Schlaepfer P & Goldenberger D.

BMC microbiology. 2024 Dec;24(1):1-1. https://doi.org/10.1186/s12866-023-03163-7

Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions

Sollier J, Basler M, Broz P, Dittrich PS, Drescher K, Egli A, Harms A, Hierlemann A, Hiller S, King CG, McKinney JD, Moran-Gilad J, Neher RA, Page MGP, Panke S, Persat A, Picotti P, Rentsch KM, Rivera-Fuentes P, Sauer U, Stolz D, Tschudin-Sutter S, van Delden C, van Nimwegen E, Veening JW, Zampieri M, Zinkernagel AS, Khanna N, Bumann D, Jenal U & Dehio C.

Nature Microbiology. 2024 Jan 4:1-3. https://doi.org/10.1038/s41564-023-01566-w

Regional spread of an atypical ESBL-producing Escherichia coli ST131H89 clone among different human and environmental reservoirs in Western Switzerland

Martischang R, Seth-Smith H, Verschuuren TD, Héquet D, Gaïa N, François P, Fluit AC, Kluytmans JA, Seiffert SN, Tacconelli E, Cherkaoui A, Harbarth S, Egli A, Kohler P.

Antimicrobial Agents and Chemotherapy. 2024 Jan 3:e00925-23. https://doi.org/10.1128/aac.00925-23

Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication

Maffei E, Woischnig AK, Burkolter MR, Heyer Y, Humolli D, Thürkauf N, Bock T, Schmidt A, Manfredi P, Egli A, Khanna N, Jenal U & Harms A.

Nature Communications. 2024 Jan 2;15(1):175. https://doi.org/10.1038/s41467-023-44157-3

SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing

Seth-Smith H, Vesenbeckh S, Egli A, Ott S.

BMJ Case Reports CP 2023;16:e255255. https://doi.org/10.1136/bcr-2023-255255

Surgical site infections after kidney transplantation are independently associated with graft loss

Schreiber PW, Hoessly LD, Boggian K, Neofytos D, van Delden C, Egli A, Dickenmann M, Hirzel C, Manuel O, Koller M, Rossi S, Banz V, Schmied B, Guerke L, Matter M, de Rougemont O, Bonani M, Golshayan D, Schnyder A, Sidler D, Haidar F, Kuster SP, Stampf S, Mueller NJ, members of the Swiss Transplant Cohort Study (STCS).

American Journal of Transplantation. 2023 Nov 30. https://doi.org/10.1016/j.ajt.2023.11.013

SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay

Hilti D, Wehrli F, Roditscheff A, Risch M, Risch L, Egli A, Bodmer T, Wohlwend N.

Pathogens. 2023 Nov 24;12(12):1383. https://doi.org/10.3390/pathogens12121383

Mycoplasma pneumoniae: delayed re-emergence after COVID-19 pandemic restrictions

Meyer Sauteur PM, Beeton ML; on behalf of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycoplasma and Chlamydia Infections (ESGMAC), and the ESGMAC Mycoplasma pneumoniae Surveillance (MAPS) study group

The Lancet Microbe. 2023 Nov 23.https://doi.org/10.1016/S2666-5247(23)00344-0

Investigation of an international water polo tournament in Czechia as a potential source for early introduction of the SARS-CoV-2 Omicron variant into Belgium, Switzerland and Germany, November 2021

Rudin C, Bollen N, Hong SL, Wegner F, Politi L, Mellou K, Geenen C, Gorissen S, Verhasselt B, Durkin K, Henin C, Logist AS , Dellicour S, Resa T, Stadler T, Maes P, Cuypers L , André E, Egli A, Baele G.

Eurosurveillance. 2023 Nov 9;28(45):2300018. https://doi.org/10.2807/1560-7917.ES.2023.28.45.2300018

Identification of microorganisms by a rapid PCR panel from positive blood cultures leads to faster optimal antimicrobial therapy – a before-after study

Agnetti J, Büchler AC, Osthoff M, Helfenstein F, Weisser M, Siegemund M, Bassetti S, Bingisser R, Schaefer DJ, Clauss M, Hinic V, Tschudin-Sutter S, Bättig V, Khanna N & Egli A.

BMC Infectious Diseases. 2023 Oct 26;23(1):730. https://doi.org/10.1186/s12879-023-08732-9

Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis

Cuénod A, Agnetti J, Seth-Smith HMB, Roloff T, Wälchli D, Shcherbakov D, Akbergenov R, Tschudin-Sutter S, Bassetti S, Siegemund M, Nickel CH, Moran-Gilad J, Keys TG, Pflüger V, Thomson NR, Egli A.

Genome Med 15, 89 (2023). https://doi.org/10.1186/s13073-023-01243-x

High-Fluence Accelerated PACK-CXL for Bacterial Keratitis Using Riboflavin/UV-A or Rose Bengal/Green in the Ex Vivo Porcine Cornea

Lu NJ, Koliwer-Brandl H, Hillen M, Egli A, Hafezi F.

Translational Vision Science & Technology. 2023 Sep 1;12(9):14-. https://doi.org/10.1167/tvst.12.9.14

Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation

Scheier TC, Franz J, Boumasmoud M, Andreoni F, Chakrakodi B, Duvnjak B, Egli A, Zingg W, Ramette A, Wolfensberger A, Kouyos RD, Brugger SD.

Microbiology spectrum. 2023 Sep 22:e00984-23. https://doi.org/10.1128/spectrum.00984-23

IVDR: Analysis of the Social, Economic, and Practical Consequences of the Application of an Ordinance of the In Vitro Diagnostic Ordinance in Switzerland

Coste AT, Egli A, Schrenzel J, Nickel B, Zbinden A, Lienhard R, Dumoulin A, Risch M, Greub G on behalf of Coordinated Clinical Commission of Microbiology (CCCM).

Diagnostics. 2023; 13(18):2910. https://doi.org/10.3390/diagnostics13182910

Immunogenicity of High-Dose vs. MF59-adjuvanted vs. Standard Influenza Vaccine in Solid Organ Transplant Recipients: The STOP-FLU trial

Mombelli M, Neofytos D, Huynh-Do U, Sánchez-Céspedes J, Stampf S, Golshayan D, Dahdal S, Stirnimann G, Schnyder A, Garzoni C, Venzin RM, Magenta L, Schönenberger M, Walti L, Hirzel C, Munting A, Dickenmann M, Koller M, Aubert JD, Steiger J, Pascual M, Mueller TF, Schuurmans M, Berger C, Binet I, Villard J, Mueller NJ, Egli A, Cordero E, van Delden C, Manuel O; Swiss Transplant Cohort Study.

Clin Infect Dis. 2023 Aug 16:ciad477. https://doi.org/10.1093/cid/ciad477

Evaluation of the clinical relevance of the Biofire© FilmArray pneumonia panel among hospitalized patients

Søgaard KK, Hinic V, Goldenberger D, Gensch A, Schweitzer M, Bättig V, Siegemund M, Bassetti S, Bingisser R, Tamm M, Battegay M, Weisser M, Stolz D, Khanna N & Egli A.

Infection. 2023 Aug 12:1-9. https://doi.org/10.1007/s15010-023-02080-1

Evaluation of the RESIST ACINETO multiplex immunochromatographic assay for detection of OXA-23-like, OXA-40/58-like and NDM carbapenemase production in Acinetobacter baumannii

Mancini S, Seth-Smith HM, Kolesnik-Goldmann N, Hinic V, Roloff T, Imkamp F, Egli A.

Journal of Antimicrobial Chemotherapy. 2023 Aug 11:dkad253. https://doi.org/10.1093/jac/dkad253

Factors associated with non-carbapenemase mediated carbapenem resistance of Gram-negative bacteria: a retrospective case-control study

Müller M, Wiencierz A, Gehringer C, Muigg V, Bassetti S, Siegemund M, Hinic V, Tschudin-Sutter S, Egli A.

Int Microbiol (2023). https://doi.org/10.1007/s10123-023-00405-6

Comparison of Disk Diffusion, E-Test, and Broth Microdilution Methods for Testing In Vitro Activity of Cefiderocol in Acinetobacter baumannii

Kolesnik-Goldmann N, Seth-Smith HMB, Haldimann K, Imkamp F, Roloff T, Zbinden R, Hobbie SN, Egli A, Mancini S.

Antibiotics. 2023; 12(7):1212. https://doi.org/10.3390/antibiotics12071212

ChatGPT, GPT-4, and other large language models – the next revolution for clinical microbiology?

Egli A.

Clinical Infectious Diseases. 2023 Jul 3;ciad407. https://doi.org/10.1093/cid/ciad407

The Swiss Pathogen Surveillance Platform – towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata

Neves A, Walther D, Martin-Campos T, Barbie V, Bertelli C, Blanc D, Bouchet G, Erard F, Greub G, Hirsch HH, Huber M, Kaiser L, Leib SL, Leuzinger K, Lazarevic V, Mäusezahl M, Molina J, Neher RA, Perreten V, Ramette A, Roloff T, Schrenzel J, Seth-Smith HMB, Stephan R, Terumalai D, Wegner F, Egli A.

Microb Genom. 2023 May;9(5). doi: 10.1099/mgen.0.001001.

A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center

von Rotz M, Kuehl R, Durovic A, Zingg S, Apitz A, Wegner F, Seth-Smith HM, Roloff T, Leuzinger K, Hirsch HH, Kuster S.

Antimicrobial Resistance & Infection Control. 2023 Apr 21;12(1):38. https://doi.org/10.1186/s13756-023-01242-y

Automatic Discrimination of Species within the Enterobacter cloacae Complex Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Supervised Algorithms

Candela A, Guerrero-López A, Mateos M, Gómez-Asenjo A, Arroyo MJ, Hernandez-García M, Del Campo R, Cercenado E, Cuénod A, Méndez G, Mancera L, Caballero JD, Martínez-García L, Gijón D, Morosini MI, Ruiz-Garbajosa P, Egli A, Cantón R, Muñoz P, Rodríguez-Temporal D, Rodríguez-Sánchez B.

J Clin Microbiol. 2023 Apr 20;61(4):e0104922. doi: 10.1128/jcm.01049-22.

Factors impacting the pre-analytical quality of blood cultures—Analysis at a tertiary medical center

Romann L, Werlen L, Rommers N, Hermann A, Gisler I, Bassetti S, Bingisser R, Siegemund M, Roloff T, Weisser M, Muigg V, Hinic V, Osthoff M, Franzeck FC, Egli A.

Plos one. 2023 Mar 16;18(3):e0282918. https://doi.org/10.1371/journal.pone.0282918

Legionnaires’ disease in Switzerland: rationale and study protocol of a prospective national case–control and molecular source attribution study (SwissLEGIO)

Fischer FB, Bigler M, Mäusezahl D, Hattendorf J, Egli A, Julian TR, Rölli F, Gaia V, Wymann M, Fridez F, Bertschi S; SwissLEGIO Hospital Network.

Infection. 2023 Mar 11. https://doi.org/10.1007/s15010-023-02014-x

A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia

Asare PT, Lee CH, Hürlimann V, Teo Y, Cuénod A, Akduman N, Gekeler C, Afrizal A, Corthesy M, Kohout C, Thomas V, de Wouters T, Greub G, Clavel T, Pamer EG, Egli A, Maier L and Vonaesch P.

Front Microbiol. 2023 Feb 21;14:1104707. https://doi.org/10.3389/fmicb.2023.1104707

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

Ghielmetti G, Seth-Smith HMB, Roloff T, Cernela N, Biggel M, Stephan R, Egli A.

Microb Genom. 2023 Feb;9(2). https://doi.org/10.1099/mgen.0.000941

Detection of mostly viral pathogens and high proportion of antibiotic treatment initiation in hospitalised children with community-acquired pneumonia in Switzerland – baseline findings from the first two years of the KIDS-STEP trial

Kohns Vasconcelos M, Meyer Sauteur PM, Keitel K, Santoro R, Egli A, Coslovsky M, Seiler M, Lurà M, Köhler H, Loevy N, Kahlert CR, Heininger U, van den Anker J, Bielicki JA.

Swiss Med Wkly. 2023 Feb 20;153:40040. https://doi.org/10.57187/smw.2023.40040

Dynamics of antibody titers to SARS-CoV-2 and clinical outcomes after sotrovimab pre-exposure prophylaxis early after allogeneic hematopoietic stem cell transplantation

Capoferri G, Walti CS, Urwyler P, Ragozzino S, Passweg JR, Halter J, Battegay M, Baettig V, Weisser M, Arnold B, Morin B, Guetlin Y, Albertos Torres D, Gueliz TB, Volker T, Egli A, Drexler B and Khanna N.

Bone marrow transplantation. 2023 May;58(5):597-9. https://doi.org/10.1038/s41409-023-01936-2

The Antibacterial Efficacy of High-Fluence PACK Cross-Linking Can Be Accelerated

Lu NJ, Koliwer-Brandl H, Gilardoni F, Hafezi N, Knyazer B, Achiron A, Zbinden R, Egli A, Hafezi F.

Transl Vis Sci Technol. 2023 Feb 1;12(2):12. https://doi.org/10.1167/tvst.12.2.12

PorinPredict: In Silico Identification of OprD Loss from WGS Data for Improved Genotype-Phenotype Predictions of P. aeruginosa Carbapenem Resistance

Biggel M, Johler S, Roloff T, Tschudin-Sutter S, Bassetti S, Siegemund M, Egli A, Stephan R, Seth-Smith HMB.

Microbiol Spectr. 2023 Jan 30:e0358822. https://doi.org/10.1128/spectrum.03588-22

Aerococcus urinae - significance of detection in the paediatric urinary tract: a case series

Rast D, Evers KS, Egli A, Rudin C, Goischke A and Ritz N.

Eur J Pediatr. 2022 Dec 6. https://doi.org/10.1007/s00431-022-04730-2

Outbreak investigation including molecular characterization of community associated methicillin-resistant Staphylococcus aureus in a primary and secondary school in Eastern Switzerland

Waldeck F, Seiffert SN, Manser S, Zemp D, Walt A, Berger C, Albrich WC, Schlegel M, Roloff T, Egli A, Nolte O and Kahlert CR.

Sci Rep. 2022 Nov 18;12(1):19826. https://doi.org/10.1038/s41598-022-24363-7

Impact of SARS-CoV-2 Omicron on Rapid Antigen Testing Developed for Early-Pandemic SARS-CoV-2 Variants

Leuzinger K, Roloff T, Egli A, Hirsch HH.

Microbiology Spectrum. 2022 Aug 31;10(4):e02006-22. https://doi.org/10.1128/spectrum.02006-22

A Case Study of Zoonotic Chlamydia abortus Infection: Diagnostic Challenges From Clinical and Microbiological Perspectives

Burgener AV, Seth-Smith HMB, Kern-Baumann S, Durovic A, Blaich A, Menter T, Bruder E, Roloff T, Martinez A, Borel N, Albini S, Hösli I, Egli A, Weisser M, Hinić V

Open Forum Infectious Diseases, Volume 9, Issue 10, October 2022, ofac524. https://doi.org/10.1093/ofid/ofac524

ESBL Displace: A Protocol for an Observational Study to Identify Displacing Escherichia coli Strain Candidates from ESBL-Colonized Travel Returners Using Phenotypic, Genomic Sequencing and Metagenome Analysis

Schweitzer M, Mari A, Roloff T, Künzli E, Heller S, Albertos Torres D, Meola M, Nogarth D, Laganenka L, Prampolini L, Seth-Smith HMB, Grüninger O, Gensch A, Reist J, Bonhoeffer S, Hardt WD and Egli A.

Microbiology Research. 2023; 14(1):177-189. https://doi.org/10.3390/microbiolres14010015

Multifactorial resistance mechanisms associated with resistance to ceftazidime-avibactam in clinical Pseudomonas aeruginosa isolates from Switzerland

Babouee Flury B, Bösch A, Gisler V, Egli A, Seiffert SN, Nolte O, Findlay J.

Frontiers in Cellular and Infection Microbiology. 2023 Apr 25;13:448. https://doi.org/10.3389/fcimb.2023.1098944

Spatiotemporal dissemination of ESBL-producing Enterobacterales in municipal sewer systems: a prospective, longitudinal study in the city of Basel, Switzerland

Gómez-Sanz E, Bagutti C, Roth JA, Alt Hug M, García-Martín AB, Maurer Pekerman L, Schindler R, Furger R, Eichenberger L, Steffen I, Egli A, Hübner P, Stadler T, Aguilar-Bultet L, Tschudin-Sutter S.

Frontiers in Microbiology. 2023 Jan 1;14. https://doi.org/10.3389/fmicb.2023.1174336

Air temperature and incidence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae

Bock L, Aguilar-Bultet L, Egli A, Battegay M, Kronenberg A, Vogt R, Kaufmann C, Tschudin-Sutter S.

Environmental research. 2022 Dec 1;215:114146. https://doi.org/10.1016/j.envres.2022.114146

Gut microbiota composition as a candidate risk factor for dimethyl fumarate-induced lymphopenia in multiple sclerosis

Diebold M, Meola M, Purushothaman S, Siewert LK, Pössnecker E, Roloff T, Lindberg RL, Kuhle J, Kappos L, Derfuss T, Egli A and Pröbstel AK.

Gut Microbes, November 18,2022, 2022;14(1):2147055. https://doi.org/10.1080/19490976.2022.2147055

Rapid Bacteria Detection from Patients’ Blood Bypassing Classical Bacterial Culturing

Huber F, Lang HP, Heller S, Bielicki JA, Gerber C, Meyer E and Egli A.

Biosensors, November 9,2022, 2022;12(11):994. https://doi.org/10.3390/bios12110994.

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.

Purushothaman S, Meola M and Egli A.

International journal of molecular sciences, August 30, 2022, 23(17), 9834. https://doi.org/10.3390/ijms23179834.

Diagnostic challenges within the Bacillus cereus-group: finding the beast without teeth

Muigg V, Cuénod A, Purushothaman S, Siegemund M, Wittwer M, Pflüger V, Schmidt KM, Weisser M, Ritz N, Widmer A, Goldenberger D, Hinic V, Roloff T, Søgaard KK, Egli A and Seth-Smith HMB

New Microbes New Infect. October 26, 2022, 26;49-50:101040. https://doi.org/10.1016/j.nmni.2022.101040

Do We Need Blood Culture Stewardship Programs? A Quality Control Study and Survey to Assess the Appropriateness of Blood Culture Collection and the Knowledge and Attitudes among Physicians in Swiss Hospitals

Dräger S, Giehl C, Søgaard KK, Egli A, de Roche M, Huber LC and Osthoff M.

European Journal of Internal Medicine, June 14, 2022, S0953-6205(22)00191-1. https://doi.org/10.1016/j.ejim.2022.04.028.

Performance of Four Bacterial Cell Counting Apps for Smartphones

Moucka M, Muigg V, Schlotterbeck A-K, Stöger L, Gensch A, Heller A and Egli A.

Journal of Microbiological Methods 199 (June 9, 2022): 106508. https://doi.org/10.1016/j.mimet.2022.106508.

Evolution, Geographic Spreading, and Demographic Distribution of Enterovirus D68

Hodcroft EB, Dyrdak R, Andrés C, Egli A, Reist J, García Martínez de Artola D, Alcoba-Flórez J, Niesters HGM, Antón A, Poelman R, Reynders M, Wollants E, Neher RA and Albert J

PLoS Pathogens 18, no. 5 (May 2022): e1010515. https://doi.org/10.1371/journal.ppat.1010515.

SARS-CoV-2 Vaccine Alpha and Delta Variant Breakthrough Infections Are Rare and Mild but Can Happen Relatively Early after Vaccination

Peter JK, Wegner F, Gsponer S, Helfenstein F, Roloff T, Tarnutzer R, Grosheintz K, Back M, Schaubhut C, Wagner S, Seth-Smith HMB, Scotton P, Redondo M, Beckmann C, Stadler T, Salzmann A, Kurth H, Leuzinger K, Bassetti S, Bingisser R, Siegemund M, Weisser M, Battegay M, Tschudin-Sutter S, Lebrand A, Hirsch HH, Fuchs S and Egli A

Microorganisms 10, no. 5 (April 21, 2022): 857. https://doi.org/10.3390/microorganisms10050857.

Quality of MALDI-TOF Mass Spectra in Routine Diagnostics: Results from an International External Quality Assessment Including 36 Laboratories from 12 Countries Using 47 Challenging Bacterial Strains

Cuénod A, Aerni M, Bagutti C, Bayraktar B, Boz ES, Beisert Carneiro C, Casanova C, Coste AT, Damborg P, van Dam DW, Demirci M, Drevinek P, Dubuis O, Fernandez J, Greub G, Hrabak J, Hürkal Yigitler G, Hurych J, Jensen TG, Jost G, Kampinga GA, Kittl S, Lammens C, Lang C, Lienhard R, Logan J, Maffioli C, Marekovic I, Marschal M, Moran-Gilad J, Nolte O, Oberle M, Pedersen M, Pflüger V, Pranghofer S, Reichl J, Rentenaar RJ, Riat A, Rodríguez-Sánchez B, Schilt C, Schlotterbeck A-K, Schrenzel J, Troib S, Willems E, Wootton M, Ziegler D and Egli A.

Clinical Microbiology and Infection May 24, 2022, S1198-743X(22)00273-7. https://doi.org/10.1016/j.cmi.2022.05.017.

Mycoplasma Pneumoniae Detections before and during the COVID-19 Pandemic: Results of a Global Survey, 2017 to 2021

Meyer Sauteur PM, Beeton ML, Uldum SA, Bossuyt N, Vermeulen M, Loens K, Pereyre S, Bébéar C, Keše, D, Day J, Afshar B, Chalker VJ, Greub G, Nir-Paz R, Dumke R and ESGMAC–MyCOVID Study Team

Euro Surveillance: European Communicable Disease Bulletin 27, no. 19 (May 2022). https://doi.org/10.2807/1560-7917.ES.2022.27.19.2100746.

Potent Neutralization by Monoclonal Human IgM against SARS-CoV-2 Is Impaired by Class Switch

Callegari I, Schneider M, Berloffa G, Mühlethaler T, Holdermann S, Galli E, Roloff T, Boss R, Infanti L, Khanna N, Egli A, Buser A, Zimmer G, Derfuss T and Sanderson NSR

EMBO Reports, May 12, 2022, e53956. https://doi.org/10.15252/embr.202153956.

Alpha Variant Coronavirus Outbreak in a Nursing Home despite High Vaccination Coverage: Molecular, Epidemiological and Immunological Studies

Zürcher K, Abela IA, Stange M, Dupont C, Mugglin C, Egli A, Trkola A, Egger M and Fenner L.

Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, May 6, 2022, ciab1005. https://doi.org/10.1093/cid/ciab1005.

Patients Exposed to Vancomycin-Resistant Enterococci during in-Hospital Outbreaks in a Low Endemic Setting: A Proposal for Risk-Based Screening

Büchler AC, Ragozzino S, Wicki M, Spaniol V, Jäger S, Seth-Smith HMB, Goldenberger D, Hinic V, Egli A, Frei R and Widmer AF.

Antimicrobial Resistance and Infection Control 11, no. 1 (April 13, 2022): 60. https://doi.org/10.1186/s13756-022-01089-9.

Determinants of SARS-CoV-2 Transmission to Guide Vaccination Strategy in an Urban Area

Brüningk SC, Klatt J, Stange M, Mari A, Brunner M, Roloff T-C, Seth-Smith HMB, Schweitzer M, Leuzinger K, Søgaard KK, Albertos Torres D, Gensch A, Schlotterbeck A-K, Nickel CH, Ritz N, Heininger U, Bielicki J, Rentsch, K, Fuchs S, Bingisser R, Siegemund M, Pargger H, Ciardo D, Dubuis O, Buser A, Tschudin-Sutter S, Battegay M, Schneider-Sliwa R, Borgwardt KM, Hirsch HH and Egli A.

Virus Evolution 8, no. 1 (2022): veac002. https://doi.org/10.1093/ve/veac002.

Agrobacterium Species Bacteraemia, Switzerland, 2008 to 2019: A Molecular Epidemiological Study

Balmer L, Seth-Smith HMB, Egli A, Casanova C, Kronenberg A, Schrenzel J, Marschall J, and Sommerstein R.

Antimicrobial Resistance and Infection Control 11, no. 1 (March 9, 2022): 47. https://doi.org/10.1186/s13756-022-01086-y.

Optimizing Antibiotic Therapies to Reduce the Risk of Bacterial Resistance

Bassetti S, Tschudin-Sutter S, Egli A, and Osthoff M.

European Journal of Internal Medicine 99 (May 2022): 7–12. https://doi.org/10.1016/j.ejim.2022.01.029.

Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov.

Vandamme P, Peeters C, Seth-Smith HMB, Schmid H, Cnockaert M, Egli A, and Goldenberger D

Antonie Van Leeuwenhoek, February 2, 2022.

Model-based inference of neutralizing antibody avidities against influenza virus

Linnik J, Syedbasha M, Hollenstein Y, Halter J, Egli A, and Stelling J

PLOS Pathogens 18, no. 1 (January 31, 2022): e1010243. https://doi.org/10.1371/journal.ppat.1010243.

High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota

Dreier M, Meola M, Berthoud H, Shani N, Wechsler D, Junier P

BMC Microbiol 22, 48 (2022). https://doi.org/10.1186/s12866-022-02451-y

SARS-CoV-2 in schools: genome analysis shows that concurrent cases in the second and third wave were often unconnected

Stange M, Wuerfel E, Peter JK, Seth-Smith H, Roloff T, Gsponer S, Mari A, Gil BC, Lebrand A, Wegner F, Heininger U, Bielicki J, Tschudin Sutter S, Stadler T, Leuzinger K, Hirsch HH, Ledergerber M, Fuchs S, Egli A

medRxiv posted January 28, 2022. doi: https://doi.org/10.1101/2022.01.26.22269824

Direct Antimicrobial Resistance Prediction from Clinical MALDI-TOF Mass Spectra Using Machine Learning

Weis C, Cuénod A, Rieck B, Dubuis D, Graf S, Lang C, Oberle M, Brackmann M, Søgaard KK, Osthoff M, Borgwardt K and Egli A

Nature Medicine, January 10, 2022, 1–11. https://doi.org/10.1038/s41591-021-01619-9

Prediction of Acute COPD Exacerbation in the Swiss Multicenter COPD Cohort Study (TOPDOCS) by Clinical Parameters, Medication Use, and Immunological Biomarkers

Huebner ST, Henny S, Giezendanner S, Brack T, Brutsche M, Chhajed P, Clarenbach C, Dieterle T, Egli A, Frey M, Heijnen I, Irani A, Sievi NA, Thurnheer R, Trendelenburg M, Kohler M, Leuppi-Taegtmeyer AB, Leuppi JD

Respiration, December 23, 2021, 1–14. https://doi.org/10.1159/000520196

Mycobacterium chelonae Infection Identified by Metagenomic Next-Generation Sequencing as the Probable Cause of Acute Contained Rupture of a Biological Composite Graft - A Case Report.

Büchler AC, Lazarevic V, Gaïa N, Girard M, Eckstein F, Egli A, Tschudin Sutter S, and Schrenzel J

International Journal of Molecular Sciences 23, no. 1 (January 2022): 381. https://doi.org/10.3390/ijms23010381

Scarce Data on Skin Microbiome in Graft-versus-Host Disease after Allogenic Haematopoietic Cell Transplantation - a Systematic Review.

Schumacher, M, Egli A, Mari A, Navarini AA, Halter JP, and Müller SM

Journal of the European Academy of Dermatology and Venereology n/a, no. n/a. Accessed January 11, 2022. https://doi.org/10.1111/jdv.17869

PCR Performance in the SARS-CoV-2 Omicron Variant of Concern?

Metzger CMJA, Lienhard R, Seth-Smith HMB, Roloff T, Wegner F, Sieber J, Bel M, Greub G, and Egli A

Swiss Medical Weekly, no. 49 (December 10, 2021). https://doi.org/10.4414/smw.2021.w30120.

Multicenter Technical Validation of 30 Rapid Antigen Tests for the Detection of SARS-CoV-2 (VALIDATE).

Greub G, Caruana G, Schweitzer M, Imperiali M, Muigg V, Risch M, Croxatto A, Opota O, Heller S, Albertos Torres D, Tritten M-L, Leuzinger K, Hirsch HH, Lienhard R and Egli A

Microorganisms 9, no. 12 (December 2021): 2589. https://doi.org/10.3390/microorganisms9122589.

Risk Factors for Colonization with Multiple Species of Extended-Spectrum Beta-Lactamase Producing Enterobacterales: A Case-Case–Control Study.

Vock I, Aguilar-Bultet L, Egli A, Tamma PD, and Tschudin-Sutter S

Antimicrob Resist Infect Control 10, 153 (2021). https://doi.org/10.1186/s13756-021-01018-2

Comparing Immunoassays for SARS-CoV-2 Antibody Detection in Patients with and without Laboratory-Confirmed SARS-CoV-2 Infection

Leuzinger K, Osthoff M, Dräger S, Pargger H, Siegemund M, Bassetti S, Bingisser R, Nickel CH, Tschudin-Sutter S, Khanna N, Rentsch K, Battegay M, Egli A, Hirsch HH

Journal of Clinical Microbiology, September 15, 2021. https://doi.org/10.1128/JCM.01381-21

External Quality Assessment of SARS-CoV-2-Sequencing: An ESGMD-SSM Pilot Trial across 15 European Laboratories.

Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bitte P, Neuenschwander P, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Klokkhammer Hetland MA, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Vangstein Aamot H, Hirsch HH, Greub G, Egli A

Journal of Clinical Microbiology, November 10, 2021. https://doi.org/10.1128/JCM.01698-21.

Epidemiology and Outcomes of Medically Attended and Microbiologically Confirmed Bacterial Foodborne Infections in Solid Organ Transplant Recipients.

van den Bogaart L, Lang BM, Neofytos D, Egli A, Walti LN, Boggian K, Garzoni C, Berger C, Pascual M, van Delden C, Mueller NJ, Manuel O, Mombelli M, Swiss Transplant Cohort Study

American Journal of Transplantation 22, no. 1 (2022): 199–209. https://doi.org/10.1111/ajt.16831.

Functional Activity of the Complement System in Hospitalized COVID-19 Patients: A Prospective Cohort Study.

Panteleimon C, Heijnen IAFM, Egli A, Bassetti S, Trendelenburg M, and Osthoff M

Frontiers in Immunology 12 (2021): 765330. https://doi.org/10.3389/fimmu.2021.765330.

Interseasonal RSV Infections in Switzerland - Rapid Establishment of a Clinician-Led National Reporting System (RSV EpiCH)

Hammerstein AL. von, Aebi C, Barbey F, Berger C, Buettcher M, Casaulta C, Egli A, Gebauer M, Guerra B, Kahlert C, Kellner E, Kottanattu L, Opota O, Mann C, Meyer Sauteur P, Plebani M, Ritz N, Testi C, von Niederhäusern V, Wagner N, Zimmermann P, Zucol F, Agyeman PKA, Trück J

Swiss Medical Weekly 151 (August 30, 2021): w30057. https://doi.org/10.4414/SMW.2021.w30057.

Colistin Resistance in Gram-Negative Bacteria Analysed by Five Phenotypic Assays and Inference of the Underlying Genomic Mechanisms

Albertos Torres D, Seth-Smith HMB, Joosse N, Lang C, Dubuis D, Nüesch-Inderbinen M, Hinic V, and Egli A.

BMC Microbiology 21, no. 1 (November 20, 2021): 321. https://doi.org/10.1186/s12866-021-02388-8.

Real-Time Respiration Changes as a Viability Indicator for Rapid Antibiotic Susceptibility Testing in a Microfluidic Chamber Array.

Jusková P, Schmitt S, Kling A, Rackus S, HeldM, Egli A, and Dittrich PS

ACS Sensors 6, no. 6 (June 25, 2021): 2202–10. https://doi.org/10.1021/acssensors.1c00020.

Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections.

Vandamme P, Peeters C, Seth-Smith HMB, Graf L, Cnockaert M, Egli A, Goldenberger D, 2021. Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections.

Antonie van Leeuwenhoek. https://doi.org/10.1007/s10482-021-01644-1

Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study.

Cuénod A, Wüthrich D, Seth-Smith HMB, Ott C, Gehringer C, Foucault F, Mouchet R, Kassim A, Revathi G, Vogt DR, von Felten S, Bassetti S, Tschudin-Sutter S, Hettich T, Schlotterbeck G, Homberger C, Casanova C, Moran-Gilad J, Sagi O, Rodríguez-Sánchez B, Müller F, Aerni M, Gaia V, van Dessel H, Kampinga GA, Müller C, Daubenberger C, Pflüger V, Egli A, 2021. Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study.

Genome Medicine 13, 150. https://doi.org/10.1186/s13073-021-00960-5

Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains.

Seth-Smith HMB, Bénard A, Bruisten SM, Versteeg B, Herrmann B, Kok J, Carter I, Peuchant O, Bébéar C, Lewis DA, Puerta T, Keše D, Balla E, Zákoucká H, Rob F, Morré SA, de Barbeyrac B, Galán JC, de Vries HJC, Thomson NR, Goldenberger D, Egli A, 2021. Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains.

Microbial Genomics 7. https://doi.org/10.1099/mgen.0.000599

Molecular Epidemiology and Risk Factors for Extended-Spectrum β-Lactamase–Producing Enterobacterales in Long-Term Care Residents.

Kohler P, Seiffert SN, Kessler S, Rettenmund G, Lemmenmeier E, Qalla Widmer L, Nolte O, Seth-Smith HMB, Albrich WC, Babouee Flury B, Gardiol C, Harbarth S, Münzer T, Schlegel M, Petignat C, Egli A, Héquet D, 2021. Molecular Epidemiology and Risk Factors for Extended-Spectrum β-Lactamase–Producing Enterobacterales in Long-Term Care Residents.

Journal of the American Medical Directors Association. https://doi.org/10.1016/j.jamda.2021.06.030

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, 2021. Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study.

Microorganisms 9, 798. https://doi.org/10.3390/microorganisms9040798

Distribution of pathogens and antimicrobial resistance in bacteraemia according to hospitalization duration: a nationwide surveillance study in Switzerland.

Buetti N, Marschall J, Timsit JF, Atkinson A, Kronenberg A, Sommerstein R, Burnens A, Cherkaoui A, Corradi C, Dubuis O, Egli A, Gaia V, Koch D, Kronenberg A, Leib SL, Marschall J, Nordmann P, Perreten V, Piffaretti JC, Prod’hom G, Schrenzel J, Widmer AF, Zanetti G, Zbinden R, 2021. Distribution of pathogens and antimicrobial resistance in bacteraemia according to hospitalization duration: a nationwide surveillance study in Switzerland.

Clinical Microbiology and Infection. https://doi.org/10.1016/j.cmi.2021.04.025

Does high adherence to contact precautions lead to low in-hospital transmission of multi-drug-resistant micro-organisms in the endemic setting?

Büchler AC, Dangel M, Frei R, Jäger S, Roth JA, Seth-Smith HMB, Egli A, Widmer AF, 2021. Does high adherence to contact precautions lead to low in-hospital transmission of multi-drug-resistant micro-organisms in the endemic setting?

Journal of Hospital Infection 116, 53–59. https://doi.org/10.1016/j.jhin.2021.07.002

Association of Host Factors with Antibody Response to Seasonal Influenza Vaccination in Allogeneic Hematopoietic Stem Cell Transplant (HSCT) Patients.

Linnik J, Syedbasha M, Kaltenbach H-M, Vogt D, Hollenstein Y, Kaufmann L, Cantoni N, Ruosch-Girsberger S, Müller AMS, Schanz U, Müller Pabst T, Stüssi G, Weisser M, Halter J, Stelling J, Egli A

The Journal of Infectious Diseases, August 20, 2021, jiab391. https://doi.org/10.1093/infdis/jiab391

Outer Membrane Permeability: Antimicrobials and Diverse Nutrients Bypass Porins in Pseudomonas Aeruginosa

Ude J, Tripathi V, Buyck JM, Söderholm S, Cunrath O, Fanous J, Claudi B, Egli A, Schleberger C, Hiller S and Bumann D.

Proceedings of the National Academy of Sciences 118, no. 31 (August 3, 2021). https://doi.org/10.1073/pnas.2107644118.

Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides Difficile

Seth-Smith HMB, Biggel M, Roloff T, Hinic V, Bodmer T, Risch M, Casanova C, Widmer A, Sommerstein R, Marschall J, Tschudin-Sutter S, Egli A

Frontiers in Cellular and Infection Microbiology 11 (2021). https://doi.org/10.3389/fcimb.2021.681518.

A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants

Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt W-D, Slack E

Nature Microbiology, May 27, 2021, 1–12. https://doi.org/10.1038/s41564-021-00911-1

Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance

Mari A, Roloff T, Stange M, Søgaard KK, Asllanaj E, Tauriello G, Alexander LT, Schweitzer M, Leuzinger K, Gensch A, Martinez AE, Bielicki J, Pargger H, Siegemund M, Nickel CH, Bingisser R, Osthoff M, Bassetti S, Sendi P, Battegay M, Marzolini C, Seth-Smith HMB, Schwede T, Hirsch HH, Egli A

Microorganisms 9, no. 5 (May 2021): 1094. https://doi.org/10.3390/microorganisms9051094

SARS-CoV-2 Outbreak in a Tri-National Urban Area Is Dominated by a B.1 Lineage Variant Linked to a Mass Gathering Event

Stange M, Mari A, Roloff T, Seth-Smith HMB, Schweitzer M, Brunner M, Leuzinger K, Søgaard KK, Gensch A, Tschudin-Sutter S, Fuchs S, Bielicki J, Pargger H, Siegemund M, Nickel CH, Bingisser R, Osthoff M, Bassetti S, Schneider-Sliwa R, Battegay M, Hirsch HH, Egli A

PLOS Pathogens 17, no. 3 (March 19, 2021): e1009374. https://doi.org/10.1371/journal.ppat.1009374

Cutibacterium Modestum and ‘Propionibacterium Humerusii’ Represent the Same Species That Is Commonly Misidentified as Cutibacterium Acnes

Goldenberger D, Søgaard KK, Cuénod A, Seth-Smith HMB, de Menezes D, Vandamme P, and Egli A

Antonie Van Leeuwenhoek, May 7, 2021. https://doi.org/10.1007/s10482-021-01589-5

Systematic Screening on Admission for SARS-CoV-2 to Detect Asymptomatic Infections

Stadler RN, Maurer L, Aguilar-Bultet L, Franzeck F, Ruchti C, Kühl R, Widmer AF, Schindler R, Bingisser R, Rentsch KM, Pargger H, Sutter R, Steiner L, Meier C, Kübler W, Hirsch HH, Egli A, Battegay M, Bassetti S, Tschudin-Sutter S

Antimicrobial Resistance & Infection Control 10, no. 1 (February 27, 2021): 44. https://doi.org/10.1186/s13756-021-00912-z

Bilateral Acute Renal Cortical Necrosis after a Dog Bite: Case Report

Amacher SA, Søgaard KK, Nkoulou C, Sutter R, Weisser M, Zingg SS, Egli A, Hollinger A, and Siegemund M

BMC Infectious Diseases 21, no. 1 (February 27, 2021): 231. https://doi.org/10.1186/s12879-021-05901-6

Accuracy of Urine Flow Cytometry and Urine Test Strip in Predicting Relevant Bacteriuria in Different Patient Populations

Gehringer C, Regeniter A, Rentsch K, Tschudin-Sutter S, Bassetti S, and Egli A

BMC Infectious Diseases 21, no. 1 (February 25, 2021): 209. https://doi.org/10.1186/s12879-021-05893-3

Community-Acquired and Hospital-Acquired Respiratory Tract Infection and Bloodstream Infection in Patients Hospitalized with COVID-19 Pneumonia

Søgaard KK, Baettig V, Osthoff M, Marsch S, Leuzinger K, Schweitzer M, Meier J, Bassetti S, Bingisser R, Nickel CH, Khanna N, Tschudin-Sutter S, Weisser M, Battegay M, Hirsch HH, Pargger H, Siegemund M, Egli A

Journal of Intensive Care 9, no. 1 (January 18, 2021): 10. https://doi.org/10.1186/s40560-021-00526-y.

SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

Goncalves Cabecinhas AR, Roloff T, Stange M, Bertelli C, Huber M, Ramette A, Chen C, Nadeau S, Gerth Y, Yerly S, Opota O, Pillonel T, Schuster T, Metzger CMJA, Sieber J, Bel M, Wohlwend N, Baumann C, Koch MC, Bittel P, Leuzinger K, Brunner M, Suter-Riniker F, Berlinger L, Søgaard KK, Beckmann C, Noppen C, Redondo M, Steffen I, Seth-Smith HMB, Mari A, Lienhard R, Risch M, Nolte O, Eckerle I, Martinetti Lucchini G, Hodcroft EB, Neher RA, Stadler T, Hirsch HH, Leib SL, Risch L, Kaiser L, Trkola A, Greub G, Egli A

Microorganisms 9, no. 4 (April 2021): 677. https://doi.org/10.3390/microorganisms9040677.

Unexpectedly High False-Positive Rates for Haemophilus Influenzae Using a Meningoencephalitis Syndromic PCR Panel in Two Tertiary Centers.

Zanella M-C, Cherkaoui A, Hinic V, Renzi G, Goldenberger D, Egli A, and Schrenzel J

Frontiers in Cellular and Infection Microbiology 11 (2021). https://doi.org/10.3389/fcimb.2021.639658

Plasmid- and Strain-Specific Factors Drive Variation in ESBL-Plasmid Spread in Vitro and in Vivo

Benz F, Huisman JS, Bakkeren E, Herter JA, Stadler T, Ackermann M, Diard M, Egli A, Hall AR, Hardt W-D, Bonhoeffer S

The ISME Journal 15, no. 3 (March 2021): 862–78. https://doi.org/10.1038/s41396-020-00819-4

Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas Aeruginosa Infections

Santi I, Manfredi P, Maffei E, Egli A, and Jenal U

MBio 12, no. 1 (February 23, 2021). https://doi.org/10.1128/mBio.03482-20.

Nosocomial Transmission of a BlaVIM-2 Carbapenemase Integron between Isolates of Two Different Pseudomonas Species.

Büchler AC, Wüthrich D, Wicki Jauslin M, Egli A, and Widmer AF

Infection Control & Hospital Epidemiology, undefined/ed, 1–3. https://doi.org/10.1017/ice.2021.39.

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Cuénod A, Foucault F, Pflüger V, and Egli A

Frontiers in Cellular and Infection Microbiology 11 (2021). https://doi.org/10.3389/fcimb.2021.646648.

Unexpected Mycoplasma Hominis Infection in Two Renal Transplant Recipients Traced Back to the Same Donor by Whole-Genome Sequencing

Hinić V, Seth-Smith HMB, Damm S, Amico P, Khanna N, Egli A, and Bättig V

European Journal of Clinical Microbiology & Infectious Diseases, December 23, 2020. https://doi.org/10.1007/s10096-020-04116-y.

Rapid and Ultrasensitive Detection of Mutations and Genes Relevant to Antimicrobial Resistance in Bacteria

Huber F, Lang HP, Lang D, Wüthrich D, Hinić V, Gerber C, Egli A and Meyer E

Global Challenges 5, no. 2 (2021): 2000066. https://doi.org/10.1002/gch2.202000066.

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

Frontiers in Microbiology 11 (2020). https://doi.org/10.3389/fmicb.2020.591093

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

Müller NF, Wüthrich D, Goldman N, Sailer N, Saalfrank C, Brunner M, Augustin N, Seth-Smith HMB, Hollenstein Y, Syedbasha M, Lang D, Neher RA, Dubuis O, Naegele M, Buser A, Nickel CH, Ritz N, Zeller A, Lang BM, Hadfield J, Bedford T, Battegay M, Schneider-Sliwa R, Egli A, Stadler T

PLOS Pathogens 16, e1008984. https://doi.org/10.1371/journal.ppat.1008984

Burden, Epidemiology, and Outcomes of Microbiologically Confirmed Respiratory Viral Infections in Solid Organ Transplant Recipients: A Nationwide, Multi-Season Prospective Cohort Study

Mombelli M, Lang BM, Neofytos D, Aubert J-D, Benden C, Berger C, Boggian K, Egli A, Soccal PM, Kaiser L, Hirzel C, Pascual M, Koller M, Mueller NJ, van Delden C, Hirsch HH, Manuel O

American Journal of Transplantation, October 2020, https://doi.org/10.1111/ajt.16383.

COVID-19 Triage and Test Center: Safety, Feasibility, and Outcomes of Low-Threshold Testing

Mansella G, Rueegg M, Widmer AF, Tschudin-Sutter S, Battegay M, Hoff J, Søgaard, KK, Egli A, Stieltjes B, Leuzinger K, Hirsch HH, Meienberg A, Burkard T, Mayr M, Bingisser R, Nickel CH

Journal of Clinical Medicine 9, no. 10 (October 2020): 3217. https://doi.org/10.3390/jcm9103217

Interferon-λ Enhances the Differentiation of Naive B Cells into Plasmablasts via the MTORC1 Pathway

Syedbasha M, Bonfiglio F, Linnik J, Stuehler C, Wüthrich D, and Egli A

Cell Reports 33, no. 1 (October 6, 2020): 108211. https://doi.org/10.1016/j.celrep.2020.108211.

Multicenter Prevalence Study Comparing Molecular and Toxin Assays for Clostridioides Difficile Surveillance, Switzerland.

Widmer AF, Frei R, Kuijper EJ, Wilcox MH, Schindler R, Spaniol V, Goldenberger D, Egli A, and Tschudin-Sutter S

Emerging Infectious Diseases 26, no. 10 (October 2020): 2370–77. https://doi.org/10.3201/eid2610.190804.

Diagnostic Performance of Multiplex Bacterial PCR in BAL for Bacterial Pneumonia Varies across Molecular Assays

Darie A, Schumann D, Egli A, Khanna N, Tamm M, and Stolz D

European Respiratory Journal 56, no. suppl 64 (September 7, 2020). https://doi.org/10.1183/13993003.congress-2020.2350

A Novel Lineage of Ceftriaxone-Resistant Salmonella Typhi From India That Is Closely Related to XDR S. Typhi Found in Pakistan

Sah R, Donovan S, Seth-Smith HMB, Bloemberg G, Wüthrich D, Stephan R, Kataria S, Kumar M, Singla S, Deswal V, Kaur A, Neumayr A, Hinic V, Egli A, Kuenzli E.

Clin Infect Dis. 2019 Dec 20:ciz1204. doi: 10.1093/cid/ciz1204.

Relative Bradycardia in Patients with COVID-19.

Capoferri G, Osthoff M, Egli A, Stoeckle M, and Bassetti S

Clinical Microbiology and Infection 27, no. 2 (February 2021): 295–96. https://doi.org/10.1016/j.cmi.2020.08.013

Identification of a Cluster of Extended-Spectrum Beta-Lactamase–Producing Klebsiella Pneumoniae Sequence Type 101 Isolated From Food and Humans.

Aguilar-Bultet L, Bagutti C, Egli A, Alt M, Maurer Pekerman L, Schindler R, Furger R, Eichenberger L, Roloff T, Steffen I, Huebner P, Stadler T, Tschudin-Sutter S

Clinical Infectious Diseases, no. ciaa1164 (August 10, 2020). https://doi.org/10.1093/cid/ciaa1164.

Burkholderia Cepacia Complex Outbreak Originating from Contaminated Wash Gloves

Lo Priore E, Bernasconi S, Schlotterbeck H, Seth-Smith HMB, Egli A, Martinetti G, and Balmelli C

Infection Prevention in Practice 2, no. 1 (March 1, 2020): 100039. https://doi.org/10.1016/j.infpip.2020.100039.

Quality assurance for genotyping and resistance testing of Clostridium (Clostridioides) difficile isolates - Experiences from the first inter-laboratory ring trial in four German speaking countries

Berger FK, Mellmann A, von Müller L, Bischoff M, Gärtner BC, Schneeberg A, Egli A, Maurischat S, Jazmati N, Malecki M, Nübel U, Junker V, Bettge-Weller G, Pranada F, Pranada A, Perrin M, Kolbe-Busch S, MacKenzie C, Groß U, Färber J, Gawlik D, Monecke S, Seyboldt C, Berger A, Tuschak C, Lâm TT, Hiergeist A, Reischl U, Adam M, Baumgartner S, Mantlik K

Anaerobe 61 (February 1, 2020): 102093. https://doi.org/10.1016/j.anaerobe.2019.102093.

Epidemiology and Precision of SARS-CoV-2 Detection Following Lockdown and Relaxation Measures.

Leuzinger K, Gosert R, Søgaard KK, Naegele K, Bielicki J, Roloff T, Bingisser R, Nickel CH, Khanna N, Tschudin-Sutter S, Widmer A, Rentsch K, Pargger H, Siegemund M, Stolz D, Tamm M, Bassetti S, Osthoff M, Battegay M, Egli A, Hirsch HH

Journal of Medical Virology 93, no. 4 (2021): 2374–84. https://doi.org/10.1002/jmv.26731.

First Case of IMP-15-Producing Pseudomonas Aeruginosa in Switzerland: Challenging Laboratory Diagnosis Using Whole Genome Sequencing (WGS).

Goldenberger D, Vuichard-Gysin D, Herzog K, Hinić V, Seth-Smith HMB, and Egli A.

IDCases 22 (January 1, 2020): e00933. https://doi.org/10.1016/j.idcr.2020.e00933.

SARS-CoV-2 scripts on Github

Influenza scripts on Github

Air-conditioner cooling towers as complex reservoirs and continuous source of Legionella pneumophila infection evidenced by a genomic analysis study in 2017, Switzerland

Wüthrich D, Gautsch S, Spieler-Denz R, Dubuis O, Gaia V, Moran-Gilad J, Hinic V, Seth-SmithHMB, Nickel CH, Tschudin-Sutter S, Bassett S, Haenggi M, Brodmann P, Fuchs S, Egli A

Euro Surveill. 2019;24(4):pii=1800192. https://doi.org/10.2807/1560-7917.ES.2019.24.4.1800192

Discovery and characterization of Mycobacterium basiliense sp. nov., a nontuberculous mycobacterium isolated from human lungs

Seth-Smith HM, Imkamp F, Tagini F, Cuenod A, Hoemke R, Jahn K, Tschacher A, Grendelmeier P, Baettig V, Erb S, Reinhard M, Ruettimann G, Borrell S, Gagneux S, Casanova C, Droz S, Osthoff M, Tamm M, Nübel U, Greub G, Keller P and Egli A

Frontiers Micro. 2018. doi: 10.3389/fmicb.2018.03184.

Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements- identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.

Stadler T, Meinel D, Aguilar-Bultet L, Huisman JS, Schindler R, Egli A, Seth-Smith HMB, Eichenberger L, Brodmann P, Hübner P, Bagutti C, Tschudin-Sutter S.

BMJ Open. 2018 Feb 17;8(2):e021823. doi: 10.1136/bmjopen-2018-021823.

Gut microbiota modulate T cell trafficking into human colorectal cancer

Cremonesi E, Governa V, Garzon JFG, Mele V, Amicarella F, Muraro MG, Trella E, Galati- Fournier V, Oertli D, Däster SR, Droeser RA, Weixler B, Bolli M, Rosso R, Nitsche U, Khanna N,Egli A, Keck S, Slotta-Huspenina J, Terracciano LM, Zajac P, Spagnoli GC, Eppenberger-Castori S, Janssen KP, Borsig L, Iezzi G.

Gut. 2018 Feb 6. pii. doi: 10.1136/gutjnl-2016-313498.

A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study

Walker TM, Merker M, Knoblauch AM, Helbling P, Schoch OD, van der Werf MJ, Kranzer K, Fiebig L, Kröger S, Haas W, Hoffmann H, Indra A, Egli A, Cirillo DM, Robert J, Rogers TR, Groenheit R, Mengshoel AT, Mathys V, Haanperä M, Soolingen DV, Niemann S, Böttger EC, Keller PM; MDR-TB Cluster Consortium.

Lancet Infect Dis. 2018 Jan 8. pii: S1473-3099(18)30004-5. doi: 10.1016/S1473-3099(18)30004-5.

Rare cases of Blastobotrys raffinosifermentans as cause of FEV1 decline in two CF patients - Whole genome sequencing to exclude transmission

Jahn K, Baettig V, Seth-Smith HMB, Egli A, Tamm M.

J Cyst Fibros. 2018 Mar;17(2):e17-e19. doi: 10.1016/j.jcf.2017.11.012.

Increasing prevalence of infectious diseases in asylum seekers at a tertiary care hospital in Switzerland.

Bloch-Infanger C, Bättig V, Kremo J, Widmer AF, Egli A, Bingisser R, Battegay M, Erb S.

PLoS One. 2017 Jun 15;12(6):e0179537. doi: 10.1371/journal.pone.0179537.

ESCMID postgraduate education course: applications of MALDI-TOF mass spectrometry in clinical microbiology.

Greub G, Moran-Gilad J, Rossen J, Egli A; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD).

Microbes Infect. 2017 Sep - Oct;19(9-10):433-442. doi: 10.1016/j.micinf.2017.06.004.

Respiratory Syncytial Virus Infection Control Challenges with a Novel Polymerase Chain Reaction Assay in a Tertiary Medical Center.

Sendi P, Egli A, Dangel M, Frei R, Tschudin-Sutter S, Widmer AF.

Infect Control Hosp Epidemiol. 2017 Nov;38(11):1291-1297. doi: 10.1017/ice.2017.213.

Evaluation of the rapid biochemical β-CARBATM test for detection of carbapenemase-producing Gram-negative bacteria.

Hinić V, Reist J, Egli A.

J Microbiol Methods. 2018 Jan;144:44-46. doi: 10.1016/j.mimet.2017.10.008.

Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates.

Allen RC, Pfrunder-Cardozo KR, Meinel D, Egli A, Hall AR.

MBio. 2017 Oct 31;8(5). pii: e01341-17. doi: 10.1128/mBio.01341-17.

Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016.

Sommerstein R, Führer U, Lo Priore E, Casanova C, Meinel DM, Seth-Smith HM, Kronenberg A, On Behalf Of Anresis, Koch D, Senn L, Widmer AF, Egli A, Marschall J, On Behalf Of Swissnoso.

Euro Surveill. 2017 Dec;22(49). doi: 10.2807/1560-7917.ES.2017.22.49.17-00213.

An Optimized Hemagglutination Inhibition (HI) Assay to Quantify Influenza-specific Antibody Titers.

Kaufmann L, Syedbasha M, Vogt D, Hollenstein Y, Hartmann J, Linnik JE, Egli A.

J Vis Exp. 2017 Dec 1;(130). doi: 10.3791/55833.

Concern regarding the alleged spread of the hypervirulent lymphogranuloma venereum chlamydia trachomatis strain in Europe.

Seth-Smith HM, Galán JC, Goldenberger D, Lewis DA, Peuchant O, Bébéar C, de Barbeyrac B, Bénard A, Carter I, Kok J, Bruisten SM, Versteeg B, Morré SA, Thomson NR, Egli A, de Vries HJ.

Euro Surveill. 2017;22(15):pii=30511. DOI: http://dx.doi.org/10.2807/1560- 7917.ES.2017.22.15.30511

When two and 1⁄2 men go camping...

von Rotz M, Dierig A, Heininger U, Chrobak C, Baettig V, Egli A.

BMC Infect Dis. 2017 Jan 30;17(1):102. doi: 10.1186/s12879-017-2213-3.

Evaluation of two novel chemiluminescence immunoassays for the detection of Clostridium difficile glutamate dehydrogenase and toxin A&B.

Blaich A, Frei R, Castellano C, Kiessling C, Geschke A, Rentsch KM, Egli A.

J Microbiol Methods. 2017 Apr;135:63-65. doi: 10.1016/j.mimet.2017.02.004.

Comparison of two rapid biochemical tests and four chromogenic selective media for detection of carbapenemase-producing Gram-negative bacteria.

Hinić V, Amrein I, Stammler S, Heckendorn J, Meinel D, Frei R, Egli A.

J Microbiol Methods. 2017 Jan 25. pii: S0167-7012(17)30022-2. doi: 10.1016/j.mimet.2017.01.012.

A novel method for detection of IFN-lambda 3 binding to cells for quantifying IFN-lambda 16. receptor expression.

Santer DM, Minty GE, Mohamed A, Baldwin L, Bhat R, Joyce M, Egli A, Tyrrell DL, Houghton M.

J Immunol Methods. 2017 Mar 6. pii: S0022-1759(17)30004-2. doi: 10.1016/j.jim.2017.03.001.

A Cross-Sectional Study of Colonization Rates with Methicillin-Resistant Staphylococcus aureus (MRSA) and Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase-Producing Enterobacteriaceae in Four Swiss Refugee Centres.

Piso RJ, Käch R, Pop R, Zillig D, Schibli U, Bassetti S, Meinel DM, Egli A.

PLoS One. 2017 Jan 13;12(1):e0170251. doi: 10.1371/journal.pone.0170251.

Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing.

Meinel DM, Kuehl R, Zbinden R, Boskova V, Garzoni C, Fadini D, Dolina M, Blümel B, Weibel T, Tschudin-Sutter S, Widmer AF, Bielicki JA, Dierig A, Heininger U, Konrad R, Berger A, Hinic V, Goldenberger D, Blaich A, Stadler T, Battegay M, Sing A, Egli A.

Clin Microbiol Infect. 2016 Dec;22(12):1003.e1-1003.e8. doi: 10.1016/j.cmi.2016.08.010.

The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study.

Oberle M, Wohlwend N, Jonas D, Maurer FP, Jost G, Tschudin-Sutter S, Vranckx K, Egli A.

PLoS One. 2016 Oct 31;11(10):e0164260. doi: 10.1371/journal.pone.0164260.

Association of daptomycin use with resistance development in Enterococcus faecium bacteraemia-a 7-year individual and population-based analysis.

Egli A, Schmid H, Kuenzli E, Widmer AF, Battegay M, Plagge H, Frei R, Achermann R, Weisser M.

Clin Microbiol Infect. 2017 Oct 13. pii: S1198-743X(16)30462-1. doi: 10.1016/j.cmi.2016.10.003.

Impact of MALDI-TOF-MS-based identification directly from positive blood cultures on patient management: a controlled clinical trial.

Osthoff M, Gürtler N, Bassetti S, Balestra G, Marsch S, Pargger H, Weisser M, Egli A.

Clin Microbiol Infect. 2016 Aug 26. pii: S1198-743X(16)30329-9. doi: 10.1016/j.cmi.2016.08.009.

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions.

Syedbasha M, Linnik J, Santer D, O'Shea D, Barakat K, Joyce M, Khanna N, Tyrrell DL, Houghton M, Egli A.

J Vis Exp. 2016 Mar 14;(109). doi: 10.3791/53575.

Prevention of hepatitis C virus infection using a broad cross-neutralizing monoclonal antibody (AR4A) and epigallocatechin gallate.

O'Shea D, Law J, Egli A, Douglas D, Lund G, Forester S, Lambert J, Law M, Burton DR, Tyrrell DL, Houghton M, Humar A, Kneteman N.

Liver Transpl. 2016 Mar;22(3):324-32. doi: 10.1002/lt.24344.

Complexity of Host Micro-RNA Response to Cytomegalovirus Reactivation After Organ Transplantation.

Egli A, Lisboa LF, O'Shea D, Asberg A, Mueller T, Emery V, Kumar D, Humar A.

Am J Transplant. 2016 Feb;16(2):650-60. doi: 10.1111/ajt.13464.

Influence of IFNL3/4 polymorphisms on the incidence of cytomegalovirus infection after solid- organ transplantation.

Manuel O, Wójtowicz A, Bibert S, Mueller NJ, van Delden C, Hirsch HH, Steiger J, Stern M, Egli A, Garzoni C, Binet I, Weisser M, Berger C, Cusini A, Meylan P, Pascual M, Bochud PY; Swiss Transplant Cohort Study.

J Infect Dis. 2015 Mar 15;211(6):906-14. doi: 10.1093/infdis/jiu557.

Louse-borne relapsing fever (Borrelia recurrentis) in an Eritrean refugee arriving in Switzerland, August 2015.

Goldenberger D, Claas GJ, Bloch-Infanger C, Breidthardt T, Suter B, Martínez M, Neumayr A, Blaich A, Egli A, Osthoff M.

Euro Surveill. 2015 Aug 13;20(32):2-5.

Ein nicht alltägliches türkisches Souvenir

Osthoff M, Egli A, Schürch N, Leib S, Mihatsch F, Frei R

Swiss Med Forum 2015;15(25):611-613

Hemolytic uremic syndrome in a 65 year-old male linked to a very unusual type of stx2e and eae harboring O51:H49 Shiga-toxin producing Escherichia coli.

Fasel D., Mellmann, A., Cernela, N. Hächler H. Fruth A., Khanna N., Egli A., Beckmann Ch., Hirsch H., Goldenberger D., Stephan R.

J Clin Microbiol. 2014 Apr;52(4):1301-3. doi: 10.1128/JCM.03459-13.

Mannose-binding lectin protein and its association to clinical outcomes in COPD: a longitudinal study.

Mandal J, Malla B, Steffensen R, Costa L, Egli A, Trendelenburg M, Blasi F, Kostikas K, Welte T, Torres A, Louis R, Boersma W, Milenkovic B, Aerts J, Rohde GG, Lacoma A, Rentsch K, Roth M, Tamm M, Stolz D.

Respir Res. 2015 Dec 18;16:150. doi: 10.1186/s12931-015-0306-3.

Hcmv-miR-UL22A-5p: A Biomarker in Transplantation With Broad Impact on Host Gene Expression and Potential Immunological Implications.

Lisboa LF, Egli A, O'Shea D, Åsberg A, Hartmann A, Rollag H, Pang XL, Tyrrell DL, Kumar D, Humar A.

Am J Transplant. 2015 Jul;15(7):1893-902. doi: 10.1111/ajt.13222. E

CCL8 and the Immune Control of Cytomegalovirus in Organ Transplant Recipients.

Lisboa LF, Egli A, Fairbanks J, O'Shea D, Manuel O, Husain S, Kumar D, Humar A.

Am J Transplant. 2015 Jul;15(7):1882-92. doi: 10.1111/ajt.13207.

T cells specific for different latent and lytic viral proteins efficiently control Epstein-Barr virus- transformed B cells.

Nowakowska J, Stuehler C, Egli A, Battegay M, Rauser G, Bantug GR, Brander C, Hess C, Khanna N.

Cytotherapy. 2015 Sep;17(9):1280-91. doi: 10.1016/j.jcyt.2015.06.003.

Effect of Immunosuppression on T-Helper 2 and B-Cell Responses to Influenza Vaccination.

Egli A, Humar A, Widmer LA, Lisboa LF, Santer DM, Mueller T, Stelling J, Baluch A, O'Shea D, Houghton M, Kumar D.

J Infect Dis. 2015 Jul 1;212(1):137-46. doi: 10.1093/infdis/jiv015.

The swiss transplant cohort study: lessons from the first 6 years.

Berger C, Bochud PY, Boggian K, Cusini A, Egli A, Garzoni C, Hirsch HH, Hoffmann M, Khanna N, Manuel O, Meylan P, Nadal D, van Delden C, Weisser M, Mueller NJ; Transplant Infectious Diseases Working Group, Swiss Transplant Cohort Study.

Curr Infect Dis Rep. 2015 Jun;17(6):486. doi: 10.1007/s11908-015-0486-5.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) directly from positive blood culture flasks allows rapid identification of bloodstream infections in immunosuppressed hosts.

Egli A, Osthoff M, Goldenberger D, Halter J, Schaub S, Steiger J, Weisser M, Frei R.

Transpl Infect Dis. 2015 Jun;17(3):481-7. doi: 10.1111/tid.12373.

Travelling activity and travel-related risks after allogeneic haematopoietic stem cell transplantation - a single centre survey.

Hollenstein Y, Elzi L, Hatz C, Passweg J, Weisser M, Stöckle M, Halter JP, Egli A.

Swiss Med Wkly. 2015 May 29;145:w14136. doi: 10.4414/smw.2015.14136.

Matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) based typing of extended-spectrum β-lactamase producing E. coli--a novel tool for real-time outbreak investigation.

Egli A, Tschudin-Sutter S, Oberle M, Goldenberger D, Frei R, Widmer AF.

PLoS One. 2015 Apr 10;10(4):e0120624. doi: 10.1371/journal.pone.0120624.

IL-28B is a key regulator of B- and T-cell vaccine responses against influenza.

Egli A, Santer DM, O'Shea D, Barakat K, Syedbasha M, Vollmer M, Baluch A, Bhat R, Groenendyk J, Joyce MA, Lisboa LF, Thomas BS, Battegay M, Khanna N, Mueller T, Tyrrell DL, Houghton M, Humar A, Kumar D.

PLoS Pathog. 2014 Dec 11;10(12):e1004556. doi: 10.1371/journal.ppat.1004556.

Immunomodulatory Function of Interleukin 28B during primary infection with cytomegalovirus.

Fischer KP, Houghton M, Tyrrell DL, Kumar D, Humar A.

J Infect Dis. 2014 Sep 1;210(5):717-27. doi: 10.1093/infdis/jiu144.

Seven hours to adequate antimicrobial therapy in urosepsis using isothermal microcalorimetry.

Braissant O, Müller G, Egli A, Widmer A, Frei R, Halla A, Wirz D, Gasser TC, Bachmann A, Wagenlehner F, Bonkat G.
J Clin Microbiol. 2014 Feb;52(2):624-6. doi: 10.1128/JCM.02374-13.

Low Levels of Mannan-Binding Lectin or Ficolins Are Not Associated with an Increased Risk of Cytomegalovirus Disease in HIV-Infected Patients.

Egli A, Schäfer J, Osthoff M, Thiel S, Mikkelsen C, Rauch A, Hirsch HH, Bucher HC, Young J, Jensenius JC, Battegay M, Trendelenburg M; Swiss HIV Cohort Study.

PLoS One. 2013;8(1):e51983. doi: 10.1371/journal.pone.0051983.

Comparison of the Effect of Standard and Novel Immunosuppressive Drugs on CMV-Specific T- Cell Cytokine Profiling.

Egli A, Kumar D, Broscheit C, O'Shea D, Humar A.
Transplantation. 2013 Feb 15;95(3):448-55. doi: 10.1097/TP.0b013e318276a19f.

Blockade of programmed death receptor-1 signaling restores expression of mostly proinflammatory cytokines in anergic cytomegalovirus-specific T cells.

Dirks J, Egli A (shared first co-author), Sester U, Sester M, Hirsch HH.
Transpl Infect Dis. 2013 Feb;15(1):79-89. doi: 10.1111/tid.12025.

JC and BK polyomavirus-specific immunoglobulin G responses in patients thymectomized in early childhood.

Prelog M, Egli A, Zlamy M, Hirsch HH
J Clin Virol. 2013 Nov;58(3):553-8. doi: 10.1016/j.jcv.2013.08.035.

Randomized Controlled Trial of High-Dose Intradermal Versus Standard-Dose Intramuscular Influenza Vaccine in Organ Transplant Recipients.

Baluch A, Humar A, Eurich D, Egli A, Liacini A, Hoschler K, Campbell P, Berka N, Urschel S, Wilson L, Kumar D.

Am J Transplant. 2013 Feb 13. doi: 10.1111/ajt.12149.

Late presentation of HIV despite earlier opportunities for detection, experience from an Irish Tertiary Referral Institution.

O’Shea D, Ebrahim M, Egli A, Redmond D, McConkey S.
Ir J Med Sci. 2013 Sep;182(3):389-94. doi: 10.1007/s11845-012-0898-2.

Book: Immunodiagnostics of CMV Infection After Transplantation

Egli A, Kumar D, Humar A

2012, Nova publisher, Editor: Lautenschlager I

Helanterä I, Egli A*, Koskinen P, Hirsch HH and Lautenschlager I

Impact of Polyomavirus BK and Cytomegalovirus on the Kidney Allograft
In: Kidney Transplantation: Challenging the Future, 2012, 273-288; Massimiliano Veroux and Pierfrancesco Veroux (Eds); 2012; Bentham Science Publishers *shared first co-author

Pharmacodynamic Analysis of Daptomycin-Treated Enterococcal Bacteremia: It Is Time to Change the Breakpoint.

Avery LM, Kuti JL, Weisser M, Egli A, Rybak MJ, Zasowski EJ, Arias CA, Contreras GA, Chong PP, Aitken SL, DiPippo AJ, Wang JT, Britt NS, Nicolau DP.

Clin Infect Dis. 2018 Sep 5. doi:10.1093/cid/ciy749.

First report of sexually transmitted multi-drug resistant Shigella sonnei infections in Switzerland, investigated by whole genome sequencing.

Hinic V, Seth-Smith H, Stöckle M, Goldenberger D, Egli A.

Swiss Med Wkly. 2018 Aug 22;148:w14645. doi: smw.2018.14645.

Self-associated molecular patterns mediate cancer immune evasion by engaging Siglecs on T cells.

Stanczak MA, Siddiqui SS, Trefny MP, Thommen DS, Boligan KF, von Gunten S, Tzankov A, Tietze L, Lardinois D, Heinzelmann-Schwarz V, von Bergwelt-Baidon M, Zhang W, Lenz HJ, Han Y, Amos CI, Syedbasha M, Egli A, Stenner F, Speiser DE, Varki A, Zippelius A, Läubli H.

J Clin Invest. 2018 Aug 21. pii:120612. doi: 10.1172/JCI120612.

Antibiotic resistance in Swiss nursing homes: analysis of National Surveillance Data over an 11-year period between 2007 and 2017.

Kohler P, Fulchini R, Albrich WC, Egli A, Balmelli C, Harbarth S, Héquet D, Kahlert CR, Kuster SP, Petignat C, Schlegel M, Kronenberg A.

Antimicrob Resist Infect Control. 2018 Jul 20;7:88. doi: 10.1186/s13756-018-0378-1.

Risk factors for colistin-resistant Enterobacteriaceae in a low-endemicity setting for carbapenem resistance - a matched case-control study.

Büchler AC, Gehringer C, Widmer AF, Egli A, Tschudin-Sutter S.

Euro Surveill. 2018 Jul;23(30). doi: 10.2807/1560-7917.ES.2018.23.30.1700777.

Outbreak of vancomycin-resistant Enterococcus faecium clone ST796, Switzerland, December 2017 to April 2018.

Wassilew N, Seth-Smith HM, Rolli E, Fietze Y, Casanova C, Führer U, Egli A, Marschall J, Buetti N.

Euro Surveill. 2018 Jul;23(29). doi: 10.2807/1560-7917.ES.2018.23.29.1800351.

Different Types of Heater-Cooler Units and Their Risk of Transmission of Mycobacterium chimaera During Open-Heart Surgery: Clues From Device Design.

Kuehl R, Banderet F, Egli A, Keller PM, Frei R, Döbele T, Eckstein F, Widmer AF.

Infect Control Hosp Epidemiol. 2018 Jul;39(7):834-840. doi: 10.1017/ice.2018.102.

Genetic characterization of Shiga toxin producing Escherichia coli belonging to the emerging hybrid pathotype O80:H2 isolated from humans 2010-2017 in Switzerland.

Nüesch-Inderbinen M, Cernela N, Wüthrich D, Egli A, Stephan R.

Int J Med Microbiol. 2018 Jul;308(5):534-538. doi: 10.1016/j.ijmm.2018.05.007.

Modulation of bacterial metabolism by the microenvironment controls MAIT cell stimulation.

Schmaler M, Colone A, Spagnuolo J, Zimmermann M, Lepore M, Kalinichenko A, Bhatia S, Cottier F, Rutishauser T, Pavelka N, Egli A, Azzali E, Pieroni M, Costantino G, Hruz P, Sauer U, Mori L, De Libero G.

Mucosal Immunol. 2018 Jul;11(4):1060-1070. doi: 10.1038/s41385-018-0020-9.

A contemporary case series of Fournier's gangrene at a Swiss tertiary care center-can scoring systems accurately predict mortality and morbidity?

Wetterauer C, Ebbing J, Halla A, Kuehl R, Erb S, Egli A, Schaefer DJ, Seifert HH.

World J Emerg Surg. 2018 Jun 22;13:25. doi: 10.1186/s13017-018-0187-0.

Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya.

Wambui J, Stevens M, Njage PMK, Wüthrich D, Egli A, Stephan R, Tasara T.

Genome Announc. 2018 May 24;6(21). pii: e00446-18. doi: 10.1128/genomeA.00446-18.

Influenza vaccination of cancer patients during PD-1 blockade induces serological protection but may raise the risk for immune-related adverse events.

Läubli H, Balmelli C, Kaufmann L, Stanczak M, Syedbasha M, Vogt D, Hertig A, Müller B, Gautschi O, Stenner F, Zippelius A, Egli A, Rothschild SI.

J Immunother Cancer. 2018 May 22;6(1):40. doi: 10.1186/s40425-018-0353-7.

Time-dependent differences in management and microbiology of orthopaedic internal fixation-associated infections: an observational prospective study with 229 patients.

Kuehl R, Tschudin-Sutter S, Morgenstern M, Dangel M, Egli A, Nowakowski A, Suhm N, Theilacker C, Widmer AF.

Clin Microbiol Infect. 2018 Apr 10. pii: S1198-743X(18)30318-5. doi: 10.1016/j.cmi.2018.03.040.

Impact of host genetic polymorphisms on vaccine induced antibody response.

Linnik JE, Egli A.

Hum Vaccin Immunother. 2016 Apr 2;12(4):907-15. doi: 10.1080/21645515.2015.1119345.

LILRB1 polymorphisms influence posttransplant HCMV susceptibility and ligand interactions.

Yu K, Davidson CL, Wójtowicz A, Lisboa L, Wang T, Airo AM, Villard J, Buratto J, Sandalova T, Achour A, Humar A, Boggian K, Cusini A, van Delden C, Egli A, Manuel O, Mueller N, Bochud PY; Swiss Transplant Cohort Study, Burshtyn DN.

J Clin Invest. 2018 Apr 2;128(4):1523-1537. doi: 10.1172/JCI96174.

IFNΛ3/4 locus polymorphisms and IFNΛ3 circulating levels are associated with COPD severity and outcomes.

Egli A, Mandal J, Schumann DM, Roth M, Thomas B, Lorne Tyrrell D, Blasi F, Kostikas K, Boersma W, Milenkovic B, Lacoma A, Rentsch K, Rohde GGU, Louis R, Aerts JG, Welte T, Torres A, Tamm M, Stolz D.

BMC Pulm Med. 2018 Mar 21;18(1):51. doi: 10.1186/s12890-018-0616-6.

Interferon Lambda: Modulating Immunity in Infectious Diseases.

Syedbasha M, Egli A.

Front Immunol. 2017 Feb 28;8:119. doi: 10.3389/fimmu.2017.00119.

Human MicroRNA Responses Predict Cytomegalovirus Replication Following Solid Organ Transplantation.

Han SH, Kumar D, Ferreira VH, Egli A, Hirsch HH, Weisser M, Garzoni C, van Delden C, Bochud PY, Manuel O, Meylan P, Boggian K, Husain S, Mueller NJ, Humar A; Swiss Transplant Cohort Study.

J Infect Dis. 2017 Dec 21. pii: jiw596. doi: 10.1093/infdis/jiw596.

The fast route to microbe identification: matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS).

Dierig A, Frei R, Egli A.

Pediatr Infect Dis J. 2015 Jan;34(1):97-9. doi:10.1097/INF.0000000000000601.

The impact of the interferon-lambda family on the innate and adaptive immune response to viral infections.

Egli A, Santer DM, O'Shea D, Tyrrell DL, Houghton M.

Emerg Microbes Infect. 2014 Jul;3(7):e51. doi: 10.1038/emi.2014.51.

Vaccine adjuvants--understanding molecular mechanisms to improve vaccines.

Egli A, Santer D, Barakat K, Zand M, Levin A, Vollmer M, Weisser M, Khanna N,
Kumar D, Tyrrell L, Houghton M, Battegay M, O'Shea D.

Swiss Med Wkly. 2014 May 20;144:w13940. doi: 10.4414/smw.2014.13940.

Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses

Wüthrich D, Lang D, Müller NF, Neher RA,Stadler T, Egli A

J Virol Methods. 2019 Jan 21;266:30-33. doi: 10.1016/j.jviromet.2019.01.009

Genomic characterization of inpatient evolution of MRSA resistant to daptomycin, vancomycin and ceftaroline

Wüthrich D, Cuénod A, Hinic V, Morgenstern M, Khanna N, Egli A, Kuehl R.

J Antimicrob Chemother, dkz003. https://doi.org/10.1093/jac/dkz003

ESBL-colonization at ICU admission: impact on subsequent infection, carbapenem-consumption, and outcome

Martinez A, Widmer A, Frei R, Pargger H, Tuchscherer D, Marsch S, Egli A, Tschudin-Sutter S.

Infect Control Hosp Epidemiol. 2019:1-6. doi: 10.1017/ice.2019.5

Clinical impact of the type VI secretion system on virulence of Campylobacter species during infection

Agnetti J, Seth-Smith HMB, Ursich S, Reist J, Basler M, Nickel C, Bassetti S, Ritz N, Tschudin-Sutter S, Egli A

BMC Infect Dis. 2019 Mar 7;19(1):237

Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains

Cunrath O, Meinel DM, Maturana P, Fanous J, Buyck JM, Saint Auguste P, Seth-Smith HMB, Körner J, Dehio C, Trebosc V, Kemmer C, Neher R, Egli A, Bumann D.

EBioMedicine. 2019 Mar 6. pii: S2352-3964(19)30140-9.

First clinical case of KPC-3–producing Klebsiella michiganensis in Europe

Seiffert SN, Wüthrich D, Gerth Y, Egli A, Kohler P, Nolte O

New Microbes and New Infections 29: 100516. https://doi.org/10.1016/j.nmni.2019.100516

High Mortality of Non-Fournier Necrotizing Fasciitis With Enterobacteriales: Time to Rethink Classification?

Kuehl R, Tschudin-Sutter S, Siegemund M, Marsch S, Battegay M, Wetterauer C, Seifert HH, Schaefer DJ, Erb S, Egli A.
Clin Infect Dis. 2019 Jun 18;69(1):147-150. doi: 10.1093/cid/ciy1011.

Antigen Extraction and B Cell Activation Enable Identification of Rare Membrane Antigen Specific Human B Cells

Zimmermann M, Rose N, Lindner JM, Kim H, Gonçalves AR, Callegari I, Syedbasha M, Kaufmann L, Egli A, Lindberg RLP, Kappos L, Traggiai E, Sanderson NSR, Derfuss T.
Front Immunol. 2019 Apr 16;10:829.

Phenotypic and Genomic Analyses of Burkholderia stabilis Clinical Contamination, Switzerland

Seth-Smith HMB, Casanova C, Sommerstein R, Meinel DM, Abdelbary MMH, Blanc DS, Droz S, Führer U, Lienhard R, Lang C, Dubuis O, Schlegel M, Widmer A, Keller PM, Marschall J, Egli A.
Emerg Infect Dis. 2019 Jun;25(6):1084-1092.

Influence of a resin-based blood culture medium on the time to clearance of methicillin-susceptible Staphylococcus aureus bloodstream infection - A retrospective cohort study

Gürtler N, Denz A, Egli A, Widmer AF, Osthoff M.
Diagn Microbiol Infect Dis. 2019 May 2. pii: S0732-8893(19)30083-5.

Prosthetic valve endocarditis caused by Pseudomonas aeruginosa with variable antibacterial resistance profiles: a diagnostic challenge

Gürtler N, Osthoff M, Rueter F, Wüthrich D, Zimmerli L, Egli A, Bassetti S.
BMC Infect Dis. 2019 Jun 17;19(1):530.

Pharmacodynamics of daptomycin when prescribed in combination with other antibiotics for treatment of enterococcal bacteremia

Avery LM, Kuti JL, Weisser M, Egli A, Rybak MJ, Zasowski EJ, Arias CA, Contreras GA, Chong PP, Aitken SL, DiPippo AJ, Wang JT, Britt NS, Nicolau DP.
Int J Antimicrob Agents. 2019 Jul 5. pii: S0924-8579(19)30182-7.

Complete Genome Assembly of an Auritidibacter ignavus Isolate Obtained from an Ear Infection in Switzerland and a Comparison to Global Isolates

Seth-Smith HMB, Goldenberger D, Bernard KA, Bernier AM, Egli A.
Microbiol Resour Announc. 2019 Jul 11;8(28). pii: e00291-19.

Emerging anaerobic and partially acid-fast Lawsonella clevelandensis: extended characterization by antimicrobial susceptibility testing and whole genome sequencing.

Goldenberger D, Naegele M, Steffens D, Eichenberger R, Egli A, Seth Smith HM.
Clin Microbiol Infect. 2019 Jul 12. pii: S1198-743X(19)30397-0.

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.

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Seth-Smith HMB, Egli A.

Frontiers in Public Health 2019;7:235 https://www.frontiersin.org/article/10.3389/fpubh.2019.00235

Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut

Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M, Egli A, Slack E, Sellin ME, Bonhoeffer S, Regoes RR, Diard M, Hardt WD.

Nature. 2019 Sep;573(7773):276-280. doi: 10.1038/s41586-019-1521-8

Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis.

Bernard KA, Pacheco AL, Burdz T, Wiebe D, Beniac DR, Hiebert SL, Booth TF, Jakopp B, Goldenberger D, Seth-Smith HMB, Egli A, Bernier AM.

Int J Syst Evol Microbiol. 2020 Jan;70(1):83-88. doi: 10.1099/ijsem.0.003719. PMID: 31596191

Siblings with typhoid fever: An investigation of intrafamilial transmission, clonality, and antibiotic susceptibility

Meyer Sauteur PM, Stevens MJA, Paioni P, Wüthrich D, Egli A, Stephan R, Berger C, Bloemberg GV.

Travel Med Infect Dis. 2020 Mar-Apr;34:101498. doi: 10.1016/j.tmaid.2019.101498. Epub 2019 Sep 30. PMID: 31580900

Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation

Seth-Smith HMB, Bonfiglio F, Cuénod A, Reist J, Egli A, Wüthrich D.

Front Public Health. 2019 Aug 27;7:241. doi:10.3389/fpubh.2019.00241

Impact of alcohol-based hand-gel sanitizer and hand hygiene advice on travellers' diarrhoea and colonization with extended-spectrum beta-lactamase-producing Enterobacteriaceae: A randomised, controlled trial

Kuenzli E, Jaeger VK, DeCrom S, Sydow V, Muigg V, Frei R, Egli A, Fehr J, Hatz C.

Travel Med Infect Dis. 2019 Sep 6:101475. doi: 10.1016/j.tmaid.2019.101475.

Antibiotic-resistant pathogens in different patient settings and identification of surveillance gaps in Switzerland - a systematic review

Fulchini R, Albrich WC, Kronenberg A, Egli A, Kahlert CR, Schlegel M, Kohler P.

Epidemiol Infect. 2019 Aug 30;147:e259. doi: 10.1017/S0950268819001523.

Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

Egli A, Saalfrank C, Goldman N, Brunner M, Hollenstein Y, Vogel T, Augustin N, Wüthrich D, Seth-Smith HMB, Roth E, Syedbasha M, Mueller NF, Vogt D, Bauer J, Amar-Sliwa N, Meinel DM, Dubuis O, Naegele M, Tschudin-Sutter S, Buser A, Nickel CH, Zeller A, Ritz N, Battegay M, Stadler T, Schneider-Sliwa R.

BMJ Open. 2019 Aug 20;9(8):e030913. doi: 10.1136/bmjopen-2019-030913.

Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing

Casanova C, Lo Priore E, Egli A, Seth-Smith HMB, Räber L, Ott D, Pflüger V, Droz S, Marschall J, Sommerstein R

Antimicrob Resist Infect Control. 2019 Nov 4;8:171. doi: 10.1186/s13756-019-0619-y.

Bloodstream infection with Candida kefyr / Kluyveromyces marxianus: case report and draft genome

Seth-Smith HMB, Büchler AC, Hinic V, Medinger M, Widmer AF, Egli A.

Clin Microbiol Infect. 2019 Nov 20. pii: S1198-743X(19)30613-5. doi: 10.1016/j.cmi.2019.11.014.

A novel lineage of ceftriaxone-resistant Salmonella Typhi from India that is closely related to XDR S. Typhi found in Pakistan.

Dissociations of oral foci of infections with infectious complications and survival after haematopoietic stem cell transplantation.

Mauramo M, Grolimund P, Egli A, Passweg J, Halter J, Waltimo T.

PLoS One. 2019 Dec 18;14(12):e0225099. doi: 10.1371/journal.pone.0225099. eCollection 2019. PMID: 31851665

Digital microbiology.

Egli A, Schrenzel J, Greub G.

Clin Microbiol Infect. 2020 Jun 27:S1198-743X(20)30367-0. doi: 10.1016/j.cmi.2020.06.023. PMID: 32603804

Reproductive number of the COVID-19 epidemic in Switzerland with a focus on the Cantons of Basel-Stadt and Basel-Landschaft.

Scire J, Nadeau S, Vaughan T, Brupbacher G, Fuchs S, Sommer J, Koch KN, Misteli R, Mundorff L, Götz T, Eichenberger T, Quinto C, Savic M, Meienberg A, Burkard T, Mayr M, Meier CA, Widmer A, Kuehl R, Egli A, Hirsch HH, Bassetti S, Nickel CH, Rentsch KS, Kübler W, Bingisser R, Battegay M, Tschudin-Sutter S, Stadler T.

Swiss Med Wkly. 2020 May 4;150:w20271. doi: 10.4414/smw.2020.20271. eCollection 2020 May 4. PMID: 32365217

Predictors of infectious meningitis or encephalitis: the yield of cerebrospinal fluid in a cross-sectional study.

Dittrich T, Marsch S, Egli A, Rüegg S, De Marchis GM, Tschudin-Sutter S, Sutter R.

BMC Infect Dis. 2020 Apr 23;20(1):304. doi: 10.1186/s12879-020-05022-6. PMID: 32326881

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra.

Weis C, Horn M, Rieck B, Cuénod A, Egli A, Borgwardt K.

Bioinformatics. 2020 Jul 1;36(Supplement_1):i30-i38. doi: 10.1093/bioinformatics/btaa429. PMID: 32657381

Effect of Systemic Inflammatory Response to SARS-CoV-2 on Lopinavir and Hydroxychloroquine Plasma Concentrations.

Marzolini C, Stader F, Stoeckle M, Franzeck F, Egli A, Bassetti S, Hollinger A, Osthoff M, Weisser M, Gebhard CE, Baettig V, Geenen J, Khanna N, Tschudin-Sutter S, Mueller D, Hirsch HH, Battegay M, Sendi P.

Antimicrob Agents Chemother. 2020 Jul 8:AAC.01177-20. doi: 10.1128/AAC.01177-20. PMID: 32641296

Independent, external validation of clinical prediction rules for the identification of extended-spectrum β-lactamase-producing Enterobacterales, University Hospital Basel, Switzerland, January 2010 to December 2016.

Vock I, Aguilar-Bultet L, Egli A, Tamma PD, Tschudin-Sutter S.

Euro Surveill. 2020 Jul;25(26). doi: 10.2807/1560-7917.ES.2020.25.26.1900317. PMID: 32643598

Digitalization, clinical microbiology and infectious diseases.

Egli A.

Clin Microbiol Infect. 2020 Jul 2:S1198-743X(20)30377-3. doi: 10.1016/j.cmi.2020.06.031. PMID: 32622954

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

Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay.

Goldenberger D, Leuzinger K, Sogaard KK, Gosert R, Roloff T, Naegele K, Cuénod A, Mari A, Seth-Smith H, Rentsch K, Hinić V, Hirsch HH, Egli A.

J Virol Methods. 2020 Jul 10:113925. doi: 10.1016/j.jviromet.2020.113925. PMID: 32659240

Cefiderocol for Extensively Drug-Resistant Gram-Negative Bacterial Infections: Real-world Experience From a Case Series and Review of the Literature

Zingg S, Nicoletti GJ, Kuster S, Junker M, Widmer A, Egli A, Hinic V, Sendi P, Battegay M, Bättig V, Khanna N, Tschudin-Sutter S.

Open Forum Infect Dis. 2020 May 21;7(6):ofaa185. doi: 10.1093/ofid/ofaa185. eCollection 2020 Jun. PMID: 32548207

Infections in Patients Colonized with Extended-Spectrum Beta-Lactamase-Producing Enterobacterales - a Retrospective Cohort Study.

Vock I, Aguilar-Bultet L, Egli A, Tamma PD, Tschudin-Sutter S.

Clin Infect Dis. 2020 Jul 30:ciaa895. doi: 10.1093/cid/ciaa895. PMID: 32604410

Bloodstream infection with Candida kefyr/Kluyveromyces marxianus: case report and draft genome.

Seth-Smith HMB, Büchler AC, Hinic V, Medinger M, Widmer AF, Egli A.

Clin Microbiol Infect. 2020 Apr;26(4):522-524. doi: 10.1016/j.cmi.2019.11.014. Epub 2019 Nov 20. PMID: 31759098

Identification of a cluster of Extended-Spectrum Beta-Lactamase producing Klebsiella pneumoniae sequence type 101 isolated from food and humans.

Campylobacter jejuni from Canine and Bovine Cases of Campylobacteriosis Express High Antimicrobial Resistance Rates against (Fluoro)quinolones and Tetracyclines.

Moser S, Seth-Smith H, Egli A, Kittl S, Overesch G.

Pathogens. 2020 Aug 23;9(9):E691. doi: 10.3390/pathogens9090691. PMID: 32842457

Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses.

Leuzinger K, Roloff T, Gosert R, Sogaard K, Naegele K, Rentsch K, Bingisser R, Nickel CH, Pargger H, Bassetti S, Bielicki J, Khanna N, Tschudin Sutter S, Widmer A, Hinic V, Battegay M, Egli A, Hirsch HH.

J Infect Dis. 2020 Sep 14;222(8):1270-1279. doi: 10.1093/infdis/jiaa464. PMID: 32726441

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 Aug 22:S1286-4579(20)30146-5. doi: 10.1016/j.micinf.2020.07.008. PMID: 32841729

Memory CD8 + T Cells Balance Pro- and Anti-inflammatory Activity by Reprogramming Cellular Acetate Handling at Sites of Infection.

Balmer ML, Ma EH, Thompson AJ, Epple R, Unterstab G, Lötscher J, Dehio P, Schürch CM, Warncke JD, Perrin G, Woischnig AK, Grählert J, Löliger J, Assmann N, Bantug GR, Schären OP, Khanna N, Egli A, Bubendorf L, Rentsch K, Hapfelmeier S, Jones RG, Hess C.

Cell Metab. 2020 Sep 1;32(3):457-467.e5. doi: 10.1016/j.cmet.2020.07.004. Epub 2020 Jul 31. PMID: 32738204

Two simultaneous cases of disseminated infections with Campylobacter fetus: clinical characteristics and molecular comparison.

Durovic A, Seth-Smith HMB, Hinic V, Kurz M, Khanna N, Egli A.

Clin Microbiol Infect. 2020 Jul 24:S1198-743X(20)30425-0. doi: 10.1016/j.cmi.2020.07.018. PMID: 32717414

Tick-Borne Relapsing Fever Caused by Borrelia persica in Traveler to Central Asia, 2019.

Muigg V, Seth-Smith HMB, Goldenberger D, Egli A, Nickel B, Dürig R, Kuenzli E, Hinic V, Neumayr A.

Emerg Infect Dis. 2020 Apr;26(4):824-826. doi: 10.3201/2604.191771. PMID: 32187006

Comorbidities, clinical signs and symptoms, laboratory findings, imaging features, treatment strategies, and outcomes in adult and pediatric patients with COVID-19: A systematic review and meta-analysis.

Jutzeler CR, Bourguignon L, Weis CV, Tong B, Wong C, Rieck B, Pargger H, Tschudin-Sutter S, Egli A, Borgwardt K, Walter M.

Travel Med Infect Dis. 2020 Aug 4;37:101825. doi: 10.1016/j.tmaid.2020.101825. PMID: 32763496

Successful Management of a Clostridioides difficile Ribotype 027 Outbreak with a Lean Intervention Bundle.

Kuenzli AB, Burri S, Casanova C, Sommerstein R, Buetti N, Seth-Smith HM, Bodmer T, Egli A, Marschall J.

J Hosp Infect. 2020 Jul 31:S0195-6701(20)30365-0. doi: 10.1016/j.jhin.2020.07.034. PMID: 32745592