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1. Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients

Author

Stéphanie Bibert, Nicolas Guex, Joao Lourenco, Thomas Brahier, Matthaios Papadimitriou-Olivgeris, Lauro Damonti, Oriol Manuel, Robin Liechti, Lou Götz, Jonathan Tschopp, Mathieu Quinodoz, Peter Vollenweider, Jean-Luc Pagani, Mauro Oddo, Olivier Hügli, Frédéric Lamoth, Véronique Erard, Cathy Voide, Mauro Delorenzi, Nathalie Rufer, Fabio Candotti, Carlo Rivolta, Noémie Boillat-Blanco, Pierre-Yves Bochud, the RegCOVID Study Group, Bochud Pierre-Yves, Desgranges Florian, Filippidis Paraskevas, Guéry Benoit, Haefliger David, Kampouri Eleftheria-Evdokia, Manuel Oriol, Munting Aline, Pagani Jean-Luc, Papadimitriou-Olivgeris Matthaios, Regina Jean, Rochat-Stettler Laurence, Suttels Veronique, Tadini Eliana, Tschopp Jonathan, Van Singer Mathias, Viala Benjamin, and Vollenweider Peter

Subjects
COVID-19, SARS-CoV-2, influenza, whole blood transcriptome, RNA-sequencing, immune profiling, Immunologic diseases. Allergy, RC581-607
Abstract

The reason why most individuals with COVID-19 have relatively limited symptoms while other develop respiratory distress with life-threatening complications remains unknown. Increasing evidence suggests that COVID-19 associated adverse outcomes mainly rely on dysregulated immunity. Here, we compared transcriptomic profiles of blood cells from 103 patients with different severity levels of COVID-19 with that of 27 healthy and 22 influenza-infected individuals. Data provided a complete overview of SARS-CoV-2-induced immune signature, including a dramatic defect in IFN responses, a reduction of toxicity-related molecules in NK cells, an increased degranulation of neutrophils, a dysregulation of T cells, a dramatic increase in B cell function and immunoglobulin production, as well as an important over-expression of genes involved in metabolism and cell cycle in patients infected with SARS-CoV-2 compared to those infected with influenza viruses. These features also differed according to COVID-19 severity. Overall and specific gene expression patterns across groups can be visualized on an interactive website (https://bix.unil.ch/covid/). Collectively, these transcriptomic host responses to SARS-CoV-2 infection are discussed in the context of current studies, thereby improving our understanding of COVID-19 pathogenesis and shaping the severity level of COVID-19.

Published
2021
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2. Point prevalence of healthcare-associated infections and antibiotic use in three large Swiss acute-care hospitals

Author

Aliki Metsini, Miriam Vazquez, Rami Sommerstein, Jonas Marschall, Cathy Voide, Nicolas Troillet, Céline Gardiol, Didier Pittet, Walter Zingg, and the Swissnoso network

Subjects
point prevalence survey, Switzerland, multicentre, healthcare-associated infection, antibiotic use, Medicine
Abstract

BACKGROUND The overall burden of healthcare-associated infections (HAIs) remains high, even in high-income countries. However, the current burden of HAI in Switzerland is unknown. Prevalence surveys have a long tradition in the field of infection prevention and control for measuring both HAI and antimicrobial use. The objective of this survey was to test the point prevalence survey (PPS) methodology of the European Centre for Disease Prevention and Control (ECDC) in acute-care hospitals in Switzerland. METHODS Two tertiary care hospitals and one secondary care hospital in central and western Switzerland participated in the survey. Patients from all wards except for emergency departments and psychiatric wards were included. Data were collected on a single day for every ward with a maximum time frame of 2 weeks for completing data collection. Methodology and definitions were based on the most recent ECDC PPS protocol. RESULTS Data on a total of 2421 patients were analysed. One hundred thirty-six patients had 153 HAIs, corresponding to a prevalence of 5.6% (95% confidence interval [CI] 4.7–6.5%). Rapidly fatal McCabe score, hospitalisation in the intensive care unit (ICU), and having a medical device in place were independent risk factors for HAI. Lower respiratory tract infection was the most frequent HAI type (24.8%), followed by surgical site infection (22.2%), bloodstream infection (17.0%) and urinary tract infection (13.7%). The highest HAI prevalence (26.2%) was observed in the ICU. In total, 60.8% of all HAIs were microbiologically confirmed. The most common microorganism was Escherichia coli (21.1%). Six hundred sixty-nine patients (27.6%, 95% CI 25.9–29.4%) received 893 antimicrobials for 705 indications. Community-acquired infections (39.0%) were the most common indication for antimicrobial use and amoxicillin-clavulanate was the most commonly prescribed antimicrobial (18.4%). CONCLUSIONS HAI prevalence and antimicrobial use in this survey were similar to findings of the past ECDC PPS. The ECDC methodology proved applicable to Swiss acute-care hospitals.

Published
2018
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3. Underreporting of needlestick and sharps injuries among healthcare workers in a Swiss University Hospital

Author

Cathy Voide, Katharine Elizabeth Darling, Alain Kenfak-Foguena, Véronique Erard, Matthias Cavassini, and Catherine Lazor-Blanchet

Subjects
blood-borne infections, healthcare workers, needlestick injuries, underreporting, Medicine
Abstract

OBJECTIVES: To determine 1) rates of needlestick and sharps injuries (NSSIs) not reported to occupational health services, 2) reasons for underreporting and 3) awareness of reporting procedures in a Swiss university hospital. MATERIALS AND METHODS: We surveyed 6,367 employees having close clinical contact with patients or patient specimens. The questionnaire covered age, sex, occupation, years spent in occupation, history of NSSI during the preceding twelve months, NSSI reporting, barriers to reporting and knowledge of reporting procedures. RESULTS: 2,778 questionnaires were returned (43.6%) of which 2,691 were suitable for analysis. 260/2,691 employees (9.7%) had sustained at least one NSSI during the preceding twelve months. NSSIs were more frequent among nurses (49.2%) and doctors performing invasive procedures (IPs) (36.9%). NSSI rate by occupation was 8.6% for nurses, 19% for doctors and 1.3% for domestic staff. Of the injured respondents, 73.1% reported all events, 12.3% some and 14.6% none. 42.7% of doctors performing invasive procedures (IPs) underreported NSSIs and represented 58.6% of underreported events. Estimation that transmission risk was low (87.1%) and perceived lack of time (34.3%) were the most common reasons for non-reporting. Regarding reporting procedures, 80.1% of respondents knew to contact occupational health services. CONCLUSION: Doctors performing IPs have high rates of NSSI and, through self-assessment that infection transmission risk is low or perceived lack of time, high rates of underreporting. If individual risk analyses underestimate the real risk, such underreporting represents a missed opportunity for post-exposure prophylaxis and identification of hazardous procedures. Doctors’ training in NSSI reporting merits re-evaluation.

Published
2012
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4. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Author

Matteo D’Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Agnieszka D’Antonio-Chronowska, Kelly A. Frazer, Benjamin M. Neale, Mark Daly, Andrea Ganna, Christine Stevens, Gita A. Pathak, Shea J. Andrews, Masahiro Kanai, Mattia Cordioli, Juha Karjalainen, Renato Polimanti, Matti Pirinen, Nadia Harerimana, Kumar Veerapen, Brooke Wolford, Huy Nguyen, Matthew Solomonson, Rachel G. Liao, Karolina Chwialkowska, Amy Trankiem, Mary K. Balaconis, Caroline Hayward, Anne Richmond, Archie Campbell, Marcela Morris, Chloe Fawns-Ritchie, Joseph T. Glessner, Douglas M. Shaw, Xiao Chang, Hannah Polikowski, Petty E. Lauren, Hung-Hsin Chen, Zhu Wanying, Hakon Hakonarson, David J. Porteous, Jennifer Below, Kari North, Joseph B. McCormick, Paul R.H.J. Timmers, James F. Wilson, Albert Tenesa, Kenton D’Mellow, Shona M. Kerr, Mari E.K. Niemi, Lindokuhle Nkambul, Kathrin Aprile von Hohenstaufen, Ali Sobh, Madonna M. Eltoukhy, Amr M. Yassen, Mohamed A.F. Hegazy, Kamal Okasha, Mohammed A. Eid, Hanteera S. Moahmed, Doaa Shahin, Yasser M. El-Sherbiny, Tamer A. Elhadidy, Mohamed S. Abd Elghafar, Jehan J. El-Jawhari, Attia A.S. Mohamed, Marwa H. Elnagdy, Amr Samir, Mahmoud Abdel-Aziz, Walid T. Khafaga, Walaa M. El-Lawaty, Mohamed S. Torky, Mohamed R. El-shanshory, Chiara Batini, Paul H. Lee, Nick Shrine, Alexander T. Williams, Martin D. Tobin, Anna L. Guyatt, Catherine John, Richard J. Packer, Altaf Ali, Robert C. Free, Xueyang Wang, Louise V. Wain, Edward J. Hollox, Laura D. Venn, Catherine E. Bee, Emma L. Adams, Ahmadreza Niavarani, Bahareh Sharififard, Rasoul Aliannejad, Ali Amirsavadkouhi, Zeinab Naderpour, Hengameh Ansari Tadi, Afshar Etemadi Aleagha, Saeideh Ahmadi, Seyed Behrooz Mohseni Moghaddam, Alireza Adamsara, Morteza Saeedi, Hamed Abdollahi, Abdolmajid Hosseini, Pajaree Chariyavilaskul, Monpat Chamnanphon, Thitima B. Suttichet, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Watsamon Jantarabenjakul, Opass Putchareon, Pattama Torvorapanit, Thanyawee Puthanakit, Pintip Suchartlikitwong, Nattiya Hirankarn, Voraphoj Nilaratanakul, Pimpayao Sodsai, Ben M. Brumpton, Kristian Hveem, Cristen Willer, Wei Zhou, Tormod Rogne, Erik Solligard, Bjørn Olav Åsvold, Malak Abedalthagafi, Manal Alaamery, Saleh Alqahtani, Dona Baraka, Fawz Al Harthi, Ebtehal Alsolm, Leen Abu Safieh, Albandary M. Alowayn, Fatimah Alqubaishi, Amal Al Mutairi, Serghei Mangul, Abdulraheem Alshareef, Mona Sawaji, Mansour Almutairi, Nora Aljawini, Nour Albesher, Yaseen M. Arabi, Ebrahim S. Mahmoud, Amin K. Khattab, Roaa T. Halawani, Ziab Z. Alahmadey, Jehad K. Albakri, Walaa A. Felemban, Bandar A. Suliman, Rana Hasanato, Laila Al-Awdah, Jahad Alghamdi, Deema AlZahrani, Sameera AlJohani, Hani Al-Afghani, May Alrashed, Nouf AlDhawi, Hadeel AlBardis, Sarah Alkwai, Moneera Alswailm, Faisal Almalki, Maha Albeladi, Iman Almohammed, Eman Barhoush, Anoud Albader, Salam Massadeh, Abdulaziz AlMalik, Sara Alotaibi, Bader Alghamdi, Junghyun Jung, Mohammad S. Fawzy, Yunsung Lee, Per Magnus, Lill-Iren S. Trogstad, Øyvind Helgeland, Jennifer R. Harris, Massimo Mangino, Tim D. Spector, Duncan Emma, Sandra P. Smieszek, Bartlomiej P. Przychodzen, Christos Polymeropoulos, Vasilios Polymeropoulos, Mihael H. Polymeropoulos, Israel Fernandez-Cadenas, Jordi Perez-Tur, Laia Llucià-Carol, Natalia Cullell, Elena Muiño, Jara Cárcel-Márquez, Marta L. DeDiego, Lara Lloret Iglesias, Anna M. Planas, Alex Soriano, Veronica Rico, Daiana Agüero, Josep L. Bedini, Francisco Lozano, Carlos Domingo, Veronica Robles, Francisca Ruiz-Jaén, Leonardo Márquez, Juan Gomez, Eliecer Coto, Guillermo M. Albaiceta, Marta García-Clemente, David Dalmau, Maria J. Arranz, Beatriz Dietl, Alex Serra-Llovich, Pere Soler, Roger Colobrán, Andrea Martín-Nalda, Alba Parra Martínez, David Bernardo, Silvia Rojo, Aida Fiz-López, Elisa Arribas, Paloma de la Cal-Sabater, Tomás Segura, Esther González-Villa, Gemma Serrano-Heras, Joan Martí-Fàbregas, Elena Jiménez-Xarrié, Alicia de Felipe Mimbrera, Jaime Masjuan, Sebastian García-Madrona, Anna Domínguez-Mayoral, Joan Montaner Villalonga, Paloma Menéndez-Valladares, Daniel I. Chasman, Julie E. Buring, Paul M. Ridker, Giulianini Franco, Howard D. Sesso, JoAnn E. Manson, Joseph R. Glessner, Carolina Medina-Gomez, Andre G. Uitterlinden, M. Arfan Ikram, Kati Kristiansson, Sami Koskelainen, Markus Perola, Kati Donner, Katja Kivinen, Aarno Palotie, Samuli Ripatti, Sanni Ruotsalainen, Mari Kaunisto, null FinnGen, Tomoko Nakanishi, Guillaume Butler-Laporte, Vincenzo Forgetta, David R. Morrison, Biswarup Ghosh, Laetitia Laurent, Alexandre Belisle, Danielle Henry, Tala Abdullah, Olumide Adeleye, Noor Mamlouk, Nofar Kimchi, Zaman Afrasiabi, Nardin Rezk Branka Vulesevic, Meriem Bouab, Charlotte Guzman, Louis Petitjean, Chris Tselios, Xiaoqing Xue, Erwin Schurr, Jonathan Afilalo, Marc Afilalo, Maureen Oliveira, Bluma Brenner, Pierre Lepage, Jiannis Ragoussis, Daniel Auld, Nathalie Brassard, Madeleine Durand, Michaël Chassé, Daniel E. Kaufmann, G. Mark Lathrop, Vincent Mooser, J. Brent Richards, Rui Li, Darin Adra, Souad Rahmouni, Michel Georges, Michel Moutschen, Benoit Misset, Gilles Darcis, Julien Guiot, Julien Guntz, Samira Azarzar, Stéphanie Gofflot, Yves Beguin, Sabine Claassen, Olivier Malaise, Pascale Huynen, Christelle Meuris, Marie Thys, Jessica Jacques, Philippe Léonard, Frederic Frippiat, Jean-Baptiste Giot, Anne-Sophie Sauvage, Christian Von Frenckell, Yasmine Belhaj, Bernard Lambermont, Sara Pigazzini, Lindokuhle Nkambule, Michelle Daya, Jonathan Shortt, Nicholas Rafaels, Stephen J. Wicks, Kristy Crooks, Kathleen C. Barnes, Christopher R. Gignoux, Sameer Chavan, Triin Laisk, Kristi Läll, Maarja Lepamets, Reedik Mägi, Tõnu Esko, Ene Reimann, Lili Milani, Helene Alavere, Kristjan Metsalu, Mairo Puusepp, Andres Metspalu, Paul Naaber, Edward Laane, Jaana Pesukova, Pärt Peterson, Kai Kisand, Jekaterina Tabri, Raili Allos, Kati Hensen, Joel Starkopf, Inge Ringmets, Anu Tamm, Anne Kallaste, Pierre-Yves Bochud, Carlo Rivolta, Stéphanie Bibert, Mathieu Quinodoz, Dhryata Kamdar, Noémie Boillat, Semira Gonseth Nussle, Werner Albrich, Noémie Suh, Dionysios Neofytos, Véronique Erard, Cathy Voide, null FHoGID, null RegCOVID, null P-PredictUs, null SeroCOVID, null CRiPSI, Rafael de Cid, Iván Galván-Femenía, Natalia Blay, Anna Carreras, Beatriz Cortés, Xavier Farré, Lauro Sumoy, Victor Moreno, Josep Maria Mercader, Marta Guindo-Martinez, David Torrents, Manolis Kogevinas, Judith Garcia-Aymerich, Gemma Castaño-Vinyals, Carlota Dobaño, Alessandra Renieri, Francesca Mari, Chiara Fallerini, Sergio Daga, Elisa Benetti, Margherita Baldassarri, Francesca Fava, Elisa Frullanti, Floriana Valentino, Gabriella Doddato, Annarita Giliberti, Rossella Tita, Sara Amitrano, Mirella Bruttini, Susanna Croci, Ilaria Meloni, Maria Antonietta Mencarelli, Caterina Lo Rizzo, Anna Maria Pinto, Giada Beligni, Andrea Tommasi, Laura Di Sarno, Maria Palmieri, Miriam Lucia Carriero, Diana Alaverdian, Stefano Busani, Raffaele Bruno, Marco Vecchia, Mary Ann Belli, Nicola Picchiotti, Maurizio Sanarico, Marco Gori, Simone Furini, Stefania Mantovani, Serena Ludovisi, Mario Umberto Mondelli, Francesco Castelli, Eugenia Quiros-Roldan, Melania Degli Antoni, Isabella Zanella, Massimo Vaghi, Stefano Rusconi, Matteo Siano, Francesca Montagnani, Arianna Emiliozzi, Massimiliano Fabbiani, Barbara Rossetti, Elena Bargagli, Laura Bergantini, Miriana D’Alessandro, Paolo Cameli, David Bennett, Federico Anedda, Simona Marcantonio, Sabino Scolletta, Federico Franchi, Maria Antonietta Mazzei, Susanna Guerrini, Edoardo Conticini, Luca Cantarini, Bruno Frediani, Danilo Tacconi, Chiara Spertilli, Marco Feri, Alice Donati, Raffaele Scala, Luca Guidelli, Genni Spargi, Marta Corridi, Cesira Nencioni, Leonardo Croci, Maria Bandini, Gian Piero Caldarelli, Paolo Piacentini, Elena Desanctis, Silvia Cappelli, Anna Canaccini, Agnese Verzuri, Valentina Anemoli, Agostino Ognibene, Alessandro Pancrazzi, Maria Lorubbio, Antonella D’Arminio Monforte, Federica Gaia Miraglia, Massimo Girardis, Sophie Venturelli, Andrea Cossarizza, Andrea Antinori, Alessandra Vergori, Arianna Gabrieli, Agostino Riva, Daniela Francisci, Elisabetta Schiaroli, Francesco Paciosi, Pier Giorgio Scotton, Francesca Andretta, Sandro Panese, Renzo Scaggiante, Francesca Gatti, Saverio Giuseppe Parisi, Stefano Baratti, Matteo Della Monica, Carmelo Piscopo, Mario Capasso, Roberta Russo, Immacolata Andolfo, Achille Iolascon, Giuseppe Fiorentino, Massimo Carella, Marco Castori, Giuseppe Merla, Gabriella Maria Squeo, Filippo Aucella, Pamela Raggi, Carmen Marciano, Rita Perna, Matteo Bassetti, Antonio Di Biagio, Maurizio Sanguinetti, Luca Masucci, Serafina Valente, Marco Mandalà, Alessia Giorli, Lorenzo Salerni, Patrizia Zucchi, Pierpaolo Parravicini, Elisabetta Menatti, Tullio Trotta, Ferdinando Giannattasio, Gabriella Coiro, Fabio Lena, Domenico A. Coviello, Cristina Mussini, Enrico Martinelli, Sandro Mancarella, Luisa Tavecchia, Lia Crotti, Chiara Gabbi, Marco Rizzi, Franco Maggiolo, Diego Ripamonti, Tiziana Bachetti, Maria Teresa La Rovere, Simona Sarzi-Braga, Maurizio Bussotti, Stefano Ceri, Pietro Pinoli, Francesco Raimondi, Filippo Biscarini, Alessandra Stella, Kristina Zguro, Katia Capitani, Claudia Suardi, Simona Dei, Gianfranco Parati, Sabrina Ravaglia, Rosangela Artuso, Giordano Bottà, Paolo Di Domenico, Ilaria Rancan, Antonio Perrella Francesco Bianchi, Davide Romani, Paola Bergomi, Emanuele Catena, Riccardo Colombo, Marco Tanfoni, Antonella Vincenti, Claudio Ferri, Davide Grassi, Gloria Pessina, Mario Tumbarello, Massimo Di Pietro, Ravaglia Sabrina, Sauro Luchi, Chiara Barbieri, Donatella Acquilini, Elena Andreucci, Francesco Vladimiro Segala, Giusy Tiseo, Marco Falcone, Mirjam Lista, Monica Poscente, Oreste De Vivo, Paola Petrocelli, Alessandra Guarnaccia, Silvia Baroni, Albert V. Smith, Andrew P. Boughton, Kevin W. Li, Jonathon LeFaive, Aubrey Annis, Anne E. Justice, Tooraj Mirshahi, Geetha Chittoor, Navya Shilpa Josyula, Jack A. Kosmicki, Manuel A.R. Ferreira, Joseph B. Leader, Dave J. Carey, Matthew C. Gass, Julie E. Horowitz, Michael N. Cantor, Ashish Yadav, Aris Baras, Goncalo R. Abecasis, David A. van Heel, Karen A. Hunt, Dan Mason, Qin Qin Huang, Sarah Finer, null Genes & Health Research Team, Bhavi Trivedi, Christopher J. Griffiths, Hilary C. Martin, John Wright, Richard C. Trembath, Nicole Soranzo, Jing Hua Zhao, Adam S. Butterworth, John Danesh, Emanuele Di Angelantonio, Lude Franke Marike Boezen, Patrick Deelen, Annique Claringbould, Esteban Lopera, Robert Warmerdam, Judith.M. Vonk, Irene van Blokland, Pauline Lanting, Anil P.S. Ori, Brooke Wolford Sebastian Zöllner, Jiongming Wang, Andrew Beck, Gina Peloso, Yuk-Lam Ho, Yan V. Sun, Jennifer E. Huffman, Christopher J. O’Donnell, Kelly Cho, Phil Tsao, J. Michael Gaziano, Michel (M.G.) Nivard, Eco (E.J.C.) de geus, Meike Bartels, Jouke Jan Hottenga, Scott T. Weiss, Elizabeth W. Karlson, Jordan W. Smoller, Robert C. Green, Yen-Chen Anne Feng, Josep Mercader, Shawn N. Murphy, James B. Meigs, Ann E. Woolley, Emma F. Perez, Daniel Rader, Anurag Verma, Marylyn D. Ritchie, Binglan Li, Shefali S. Verma, Anastasia Lucas, Yuki Bradford, Hugo Zeberg, Robert Frithiof, Michael Hultström, Miklos Lipcsey, Lindo Nkambul, Nicolas Tardif, Olav Rooyackers, Jonathan Grip, Tomislav Maricic, Konrad J. Karczewski, Elizabeth G. Atkinson, Kristin Tsuo, Nikolas Baya, Patrick Turley, Rahul Gupta, Shawneequa Callier, Raymond K. Walters, Duncan S. Palmer, Gopal Sarma, Nathan Cheng, Wenhan Lu, Sam Bryant, Claire Churchhouse, Caroline Cusick, Jacqueline I. Goldstein, Daniel King, Cotton Seed, Hilary Finucane, Alicia R. Martin, F. Kyle Satterstrom, Daniel J. Wilson, Jacob Armstrong, Justine K. Rudkin, Gavin Band, Sarah G. Earle, Shang-Kuan Lin, Nicolas Arning, Derrick W. Crook, David H. Wyllie, Anne Marie O’Connell, Chris C.A. Spencer, Nils Koelling, Mark J. Caulfield, Richard H. Scott, Tom Fowler, Loukas Moutsianas, Athanasios Kousathanas, Dorota Pasko, Susan Walker, Augusto Rendon, Alex Stuckey, Christopher A. Odhams, Daniel Rhodes, Georgia Chan, Prabhu Arumugam, Catherine A. Ball, Eurie L. Hong, Kristin Rand, Ahna Girshick, Harendra Guturu, Asher Haug Baltzell, Genevieve Roberts, Danny Park, Marie Coignet, Shannon McCurdy, Spencer Knight, Raghavendran Partha, Brooke Rhead, Miao Zhang, Nathan Berkowitz, Michael Gaddis, Keith Noto, Luong Ruiz, Milos Pavlovic, Laura G. Sloofman, Alexander W. Charney, Noam D. Beckmann, Eric E. Schadt, Daniel M. Jordan, Ryan C. Thompson, Kyle Gettler, Noura S. Abul-Husn, Steven Ascolillo, Joseph D. Buxbaum, Kumardeep Chaudhary, Judy H. Cho, Yuval Itan, Eimear E. Kenny, Gillian M. Belbin, Stuart C. Sealfon, Robert P. Sebra, Irene Salib, Brett L. Collins, Tess Levy, Bari Britvan, Katherine Keller, Lara Tang, Michael Peruggia, Liam L. Hiester, Kristi Niblo, Alexandra Aksentijevich, Alexander Labkowsky, Avromie Karp, Menachem Zlatopolsky, Michael Preuss, Ruth J.F. Loos, Girish N. Nadkarni, Ron Do, Clive Hoggart, Sam Choi, Slayton J. Underwood, Paul O’Reilly, Laura M. Huckins, Marissa Zyndorf, AII - Infectious diseases, Amsterdam Neuroscience - Neuroinfection & -inflammation, and Neurology

Subjects
Medical Physiology, Gene Expression, Genome-wide association study, Genome, Severity of Illness Index, colocalization, Gene expression, Databases, Genetic, Ethnicity, 2.1 Biological and endogenous factors, GWAS, Aetiology, Biology (General), Lung, Genetics, Chromosome Mapping, Single Nucleotide, Organ Specificity, Biotechnology, Cell type, QH301-705.5, Quantitative Trait Loci, Single-nucleotide polymorphism, Biology, eQTL, Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, Databases, Genetic, SNP, Humans, Genetic Predisposition to Disease, COVID-19 Host Genetics Initiative, Polymorphism, Gene, COVID-19, SARS-CoV-2, Gene Expression Profiling, Prevention, Human Genome, Computational Biology, Genetic Variation, Good Health and Well Being, Expression quantitative trait loci, Biochemistry and Cell Biology, Transcriptome, Genome-Wide Association Study
Abstract

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types., Graphical abstract, D’Antonio et al. characterize associations between GWAS signals for COVID-19 disease and eQTLs in 69 human tissues to identify causal variants and their underlying molecular mechanisms. They show that diverse symptoms and disease severity of COVID-19 are associated with variants affecting gene expression in a wide variety of tissues.

Published
2022
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5. Point prevalence of healthcare-associated infections and antibiotic use in three large Swiss acute-care hospitals

Author

Aliki, Metsini, Miriam, Vazquez, Rami, Sommerstein, Jonas, Marschall, Cathy, Voide, Nicolas, Troillet, Céline, Gardiol, Didier, Pittet, Walter, Zingg, and The Swissnoso Network

Subjects
0301 basic medicine, Cross Infection/epidemiology, Male, medicine.medical_specialty, animal structures, Cross-sectional study, 030106 microbiology, Anti-Infective Agents/therapeutic use, Prevalence, 610 Medicine & health, Respiratory Tract Infections/epidemiology, law.invention, 03 medical and health sciences, Switzerland/epidemiology, Anti-Infective Agents, law, Risk Factors, Acute care, Internal medicine, Lower respiratory tract infection, Surveys and Questionnaires, medicine, Infection control, Humans, Surgical Wound Infection, Respiratory Tract Infections, Surgical Wound Infection/epidemiology, Aged, ddc:616, Cross Infection, business.industry, virus diseases, Urinary Tract Infections/epidemiology, General Medicine, Hospitals/statistics & numerical data, Middle Aged, Antimicrobial, medicine.disease, Intensive care unit, Confidence interval, Hospitals, Intensive Care Units, Cross-Sectional Studies, Urinary Tract Infections, Female, business, Switzerland
Abstract

BACKGROUND The overall burden of healthcare-associated infections (HAIs) remains high, even in high-income countries. However, the current burden of HAI in Switzerland is unknown. Prevalence surveys have a long tradition in the field of infection prevention and control for measuring both HAI and antimicrobial use. The objective of this survey was to test the point prevalence survey (PPS) methodology of the European Centre for Disease Prevention and Control (ECDC) in acute-care hospitals in Switzerland. METHODS Two tertiary care hospitals and one secondary care hospital in central and western Switzerland participated in the survey. Patients from all wards except for emergency departments and psychiatric wards were included. Data were collected on a single day for every ward with a maximum time frame of 2 weeks for completing data collection. Methodology and definitions were based on the most recent ECDC PPS protocol. RESULTS Data on a total of 2421 patients were analysed. One hundred thirty-six patients had 153 HAIs, corresponding to a prevalence of 5.6% (95% confidence interval [CI] 4.7-6.5%). Rapidly fatal McCabe score, hospitalisation in the intensive care unit (ICU), and having a medical device in place were independent risk factors for HAI. Lower respiratory tract infection was the most frequent HAI type (24.8%), followed by surgical site infection (22.2%), bloodstream infection (17.0%) and urinary tract infection (13.7%). The highest HAI prevalence (26.2%) was observed in the ICU. In total, 60.8% of all HAIs were microbiologically confirmed. The most common microorganism was Escherichia coli (21.1%). Six hundred sixty-nine patients (27.6%, 95% CI 25.9-29.4%) received 893 antimicrobials for 705 indications. Community-acquired infections (39.0%) were the most common indication for antimicrobial use and amoxicillin-clavulanate was the most commonly prescribed antimicrobial (18.4%). CONCLUSIONS HAI prevalence and antimicrobial use in this survey were similar to findings of the past ECDC PPS. The ECDC methodology proved applicable to Swiss acute-care hospitals.

Published
2018
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6. Status febrilis und Hautausschlag

Author

Olivier Lamy, Cathy Voide, Christophe Kosinski, and Elena Garcia

Abstract

Ein 45-jahriger Patient mit ublicherweise gutem Gesundheitszustand konsultiert uns aufgrund eines seit 48 Stunden bestehenden Status febrilis von bis zu 39 °C ohne Schuttelfrost. Aufgrund einer Klopfdolenz im Bereich der rechten Nierenloge und eines pathologischen Urinstixbefundes wird eine empirische orale Antibiotikatherapie begonnen. Kurze Zeit spater entwickelt der Patient eine starke unblutige Diarrhoe und einen Hautausschlag.

Published
2016
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7. État fébrile et éruption cutanée

Author

Olivier Lamy, Cathy Voide, Christophe Kosinski, and Elena Garcia

Abstract

Un patient de 45 ans, en bonne sante habituelle, consulte pour un etat febrile jusqu’a 39°C depuis 48 heures, sans frissons.En raison d’une sensibilite a la percussion de la loge renale droite et d’un stix urinaire pathologique, une antibiotherapie empirique est debutee. Quelque temps plus tard, le patient presente des diarrhees non sanglantes et une eruption cutanee.

Published
2016
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8. Colonization With Vancomycin-Resistant Enterococci After Discharge From an Epidemic Ward: Results of Outpatient Contact Screening by Visiting Nurses

Author

Jean-Blaise Wasserfallen, Cathy Voide, Patrick Genoud, Giorgio Zanetti, Dominique S. Blanc, Christiane Petignat, and Laurence Senn

Subjects
0301 basic medicine, Microbiology (medical), Male, medicine.medical_specialty, Carrier State/diagnosis, Feces/microbiology, Female, Gram-Positive Bacterial Infections/diagnosis, Gram-Positive Bacterial Infections/epidemiology, Humans, Mass Screening/economics, Middle Aged, Nurses, Community Health, Outpatients/statistics & numerical data, Switzerland, Vancomycin Resistance, Vancomycin-Resistant Enterococci/isolation & purification, Epidemiology, 030106 microbiology, Visiting nurses, Vancomycin-Resistant Enterococci, 03 medical and health sciences, Feces, 0302 clinical medicine, Outpatients, Medicine, Mass Screening, Colonization, 030212 general & internal medicine, Intensive care medicine, Gram-Positive Bacterial Infections, business.industry, After discharge, Infectious Diseases, Emergency medicine, Carrier State, business
Published
2016

9. Outbreak of Mycobacterium haemophilum Infections after Permanent Makeup of the Eyebrows

Author

Raffaele Malinverni, Katia Jaton, Benoit Morisod, Stefano Giulieri, Cathy Voide, Timothy Edney, Enrico Musumeci, Eric Masserey, Matthias Cavassini, Catherine Hammann, Jacques Bille, Micaela Ödman, Gilbert Greub, and Daniel Genné

Subjects
Microbiology (medical), Pathology, medicine.medical_specialty, medicine.drug_class, Antibiotics, Eyebrow, Tuberculosis, Lymph Node, Disease Outbreaks, Lesion, Humans, Medicine, Mycobacterium Infections, Tattooing, biology, business.industry, Permanent makeup, Outbreak, Cervical lymphadenitis, Middle Aged, biology.organism_classification, Mycobacterium haemophilum, Infectious Diseases, medicine.anatomical_structure, Female, Eyebrows, medicine.symptom, business
Abstract

We report a Mycobacterium haemophilum outbreak after permanent make-up of the eyebrows performed by the same freelance artist. Twelve patients presented an eyebrow lesion and cervical lymphadenitis. All were treated with antibiotics. Surgery was required in 10 cases. M. haemophilum DNA was identified in the make-up ink.

Published
2011
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10. Drug-induced long QT syndrome in injection drug users receiving methadone: high frequency in hospitalized patients and risk factors

Author

Jocelyne Chabert, Thierry Musset, Valérie Piguet, Arnaud Perrier, Georg Ehret, Cathy Voide, Barbara Broers, Pierre Dayer, Jean-Michel Gaspoz, Dipen Shah, Marianne Gex-Fabry, and Jules Alexandre Desmeules

Subjects
Narcotics, Adult, Long QT Syndrome/chemically induced/epidemiology/physiopathology, Male, medicine.medical_specialty, Methadone maintenance, Adolescent, Long QT syndrome, Torsades de pointes, QT interval, ddc:616.89, Electrocardiography, Risk Factors, Internal medicine, Internal Medicine, medicine, Prevalence, Humans, Risk factor, Substance Abuse, Intravenous, ddc:613, Retrospective Studies, ddc:616, ddc:617, business.industry, Middle Aged, medicine.disease, Long QT Syndrome, Anesthesia, Female, Narcotics/adverse effects, Liver function, Methadone/adverse effects, business, Adverse drug reaction, Methadone, Substance Abuse, Intravenous/rehabilitation, medicine.drug, Follow-Up Studies
Abstract

Drug-induced long QT syndrome is a serious adverse drug reaction. Methadone prolongs the QT interval in vitro in a dose-dependent manner. In the inpatient setting, the frequency of QT interval prolongation with methadone treatment, its dose dependence, and the importance of cofactors such as drug-drug interactions remain unknown.We performed a systematic, retrospective study comparing active or former intravenous drug users receiving methadone and those not receiving methadone among all patients hospitalized over a 5-year period in a tertiary care hospital. A total of 167 patients receiving methadone fulfilled the inclusion criteria and were compared with a control group of 80 injection drug users not receiving methadone. In addition to methadone dose, 15 demographic, biological, and pharmacological variables were considered as potential risk factors for QT prolongation.Among 167 methadone maintenance patients, the prevalence of QTc prolongation to 0.50 second((1/2)) or longer was 16.2% compared with 0% in 80 control subjects. Six patients (3.6%) in the methadone group presented torsades de pointes. QTc length was weakly but significantly associated with methadone daily dose (Spearman rank correlation coefficient, 0.20; P.01). Multivariate regression analysis allowed attribution of 31.8% of QTc variability to methadone dose, cytochrome P-450 3A4 drug-drug interactions, hypokalemia, and altered liver function.QT interval prolongation in methadone maintenance patients hospitalized in a tertiary care center is a frequent finding. Methadone dose, presence of cytochrome P-450 3A4 inhibitors, potassium level, and liver function contribute to QT prolongation. Long QT syndrome can occur with low doses of methadone.

Published
2006

11. Cerebral Nocardiosis Mimicking Multiple Brain Metastases in a Patient with Locally Advanced Non–Small-Cell Lung Cancer

Author

Daniel Betticher, Solange Peters, Reto Meuli, Guy Prod'hom, Cathy Voide, Stefano Giulieri, Alex A. Adjei, and Stefan Zimmermann

Subjects
Male, Pulmonary and Respiratory Medicine, Pathology, medicine.medical_specialty, Lung Neoplasms, business.industry, Brain Neoplasms, Locally advanced, Cerebral Nocardiosis, Nocardia Infections, medicine.disease, Nocardia, Diagnosis, Differential, Fatal Outcome, Oncology, Carcinoma, Non-Small-Cell Lung, Antineoplastic Combined Chemotherapy Protocols, medicine, Humans, Non small cell, Lung cancer, business, Aged
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