1
|
Franz J, Scheier TC, Aerni M, Gubler A, Schreiber PW, Brugger SD, Schmidlin PR. Bacterial contamination of air and surfaces during dental procedures-An experimental pilot study using Staphylococcus aureus. Infect Control Hosp Epidemiol 2024; 45:658-663. [PMID: 38263751 PMCID: PMC11027080 DOI: 10.1017/ice.2023.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 01/25/2024]
Abstract
OBJECTIVE The oral cavity contains numerous microorganisms, including antimicrobial-resistant bacteria. These microorganisms can be transmitted via respiratory particles from patients to healthcare providers and vice versa during dental care. We evaluated the spread of Staphylococcus aureus during standardized dental procedures using different scaling devices and rinsing solutions. METHODS During systematic therapy for dental biofilm removal (guided biofilm therapy), using an airflow or ultrasound device to a model simulation head. Staphylococcus aureus suspension was injected into the mouth of the model to mimic saliva. Different suction devices (conventional saliva ejector or a prototype) and rising solutions (water or chlorhexidine) were used. To assess contamination with S. aureus, an air-sampling device was placed near the oral cavity and samples of surface areas were collected. RESULTS S. aureus was only detected by air sampling when the conventional saliva ejector with airflow was used. No growth was observed during treatments with the ultrasonic piezo instrument or the prototype suction device. Notably, a rinsing solution of chlorhexidine digluconate decreased the bacterial load compared to water. Surface contamination was rarely detected (1 of 120 samples). CONCLUSIONS Although our findings indicate potential airborne bacterial transmission during routine prophylactic procedures, specific treatment options during biofilm removal appear to reduce air contamination. These options include ultrasonic piezo devices or the prototype suction device. The use of chlorhexidine reduced the CFU counts of S. aureus detected by air sampling. Surface contamination during dental procedures was a rare occurrence.
Collapse
Affiliation(s)
- Jessica Franz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Maja Aerni
- Clinic of Conservative and Preventive Dentistry, Center for Dental and Oral Medicine and Maxillo-Facial Surgery, University of Zurich, Zurich, Switzerland
| | - Andrea Gubler
- Clinic of Conservative and Preventive Dentistry, Center for Dental and Oral Medicine and Maxillo-Facial Surgery, University of Zurich, Zurich, Switzerland
| | - Peter W. Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick R. Schmidlin
- Clinic of Conservative and Preventive Dentistry, Center for Dental and Oral Medicine and Maxillo-Facial Surgery, University of Zurich, Zurich, Switzerland
| |
Collapse
|
2
|
Obenhuber T, Scheier TC, Stutz T, Hug M, Fontein D, Kaiser A, Schoene S, Steiger P, Brugger SD, Zingg W, Schreiber PW. An outbreak of multi-drug-resistant Acinetobacter baumannii on a burns ICU and its control with multi-faceted containment measures. J Hosp Infect 2024; 146:102-108. [PMID: 38219836 DOI: 10.1016/j.jhin.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024]
Abstract
BACKGROUND Patients in burns centres are at high risk of acquiring multi-drug-resistant organisms (MDROs) due to the reduced skin barrier and long hospital stay. METHODS This study reports the investigation and control of an outbreak of MDR Acinetobacter baumannii in a burns centre. The 27 patients hospitalized in the centre during the outbreak were screened regularly, and a total of 132 environmental samples were analysed to identify a potential source. Fourier-transform infra-red (FT-IR) spectroscopy and multi-locus sequence typing were applied to characterize the outbreak strain. RESULTS Between August and November 2022, the outbreak affected eight patients, with 11 infections and three potentially related fatal outcomes. An interdisciplinary and multi-professional outbreak team implemented a bundle strategy with repetitive admission stops, isolation precaution measures, patient screenings, enhanced cleaning and disinfection, and staff education. FT-IR spectroscopy suggested that the outbreak started from a patient who had been repatriated 1 month previously from a country with high prevalence of MDR A. baumannii. Environmental sampling did not identify a common source. Acquisition of the outbreak strain was associated with a higher percentage of body surface area with burn lesions ≥2a [per percent increase: odds ratio (OR) 1.05, 95% confidence interval (CI) 0.99-1.12; P=0.09], and inversely associated with a higher nurse-to-patient ratio (per 0.1 increase: OR 0.34, 95% CI 0.10-1.12; P=0.06). CONCLUSIONS Burn patients with a higher percentage of body surface area with burn lesions ≥2a are at high risk of colonization and infection due to MDROs, particularly during periods of high workload. A multi-faceted containment strategy can successfully control outbreaks due to MDR A. baumannii in a burns centre.
Collapse
Affiliation(s)
- T Obenhuber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - T C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - T Stutz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - M Hug
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - D Fontein
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, Zurich, Switzerland
| | - A Kaiser
- Institute for Anaesthesiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - S Schoene
- Institute of Intensive Care Medicine, University Hospital of Zurich, Zurich, Switzerland
| | - P Steiger
- Institute of Intensive Care Medicine, University Hospital of Zurich, Zurich, Switzerland
| | - S D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - W Zingg
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - P W Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
| |
Collapse
|
3
|
Deplazes BC, Hofmaenner DA, Scheier TC, Epprecht J, Mayer M, Schweizer TA, Buehler PK, Frey PM, Brugger SD. Enzymatic debridement with bromelain and development of bacteremia in burn injuries: A retrospective cohort study. Burns 2024; 50:405-412. [PMID: 38182450 DOI: 10.1016/j.burns.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/12/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Debridement is crucial for effective wound management in patients with severe burn injuries, and bromelain, a proteolytic enzyme from pineapple stems, has emerged as a promising alternative for surgery. However, potential links of bromelain use to fever and sepsis have raised some concerns. Given the uncertainty as to whether this was caused by infection or other inflammatory sources, we aimed to investigate if the use of topical bromelain was associated with bacteremia. METHODS This single-centre retrospective cohort study included critically ill adult patients with severe burn injuries hospitalised at the Burn Center of the University Hospital Zurich between January 2017 and December 2021. Data were collected from two in-hospital electronic medical records databases. Our primary outcome, the association between topical bromelain treatment and the development of bacteremia, was investigated using a competing risk regression model, taking into account the competing risk of death. As a secondary outcome, the relationship between bromelain treatment and overall ICU mortality was examined using a Cox proportional hazards model. RESULTS The study included 269 patients with a median age of 50 years and median burnt total body surface area of 19%. A first bacteremia occurred in 61 patients (23%) after a median time of 6 days. Bromelain treatment was given to 83 (31%) of patients, with 22 (27%) of these developing bacteremia. In the fully adjusted competing risk regression model, no evidence for an association between bromelain treatment and bacteremia was found (SHR 0.79, 95%CI 0.42-1.48, p = 0.47). During hospital stay, 40 (15%) of patients died. There was no significant difference in mortality between patients treated with bromelain and those who were not (HR 0.55, 95%CI 0.26-1.20, p = 0.14). Among the five multidrug-resistant (MDR) pathogens identified, three were found in patients with bromelain treatment. CONCLUSION Our study did not confirm an association between topical bromelain and bacteremia in patients with severe burn injuries. This finding can inform evidence-based practices by addressing concerns about potential risks of bromelain use, contributing to the development of more effective and safe burn wound management strategies.
Collapse
Affiliation(s)
- Barla C Deplazes
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jana Epprecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michelle Mayer
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp K Buehler
- Department of Intensive Care Medicine, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Pascal M Frey
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of General Internal Medicine, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland.
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
4
|
Jünger C, Imkamp F, Balakrishna S, Gysin M, Haldimann K, Brugger SD, Scheier TC, Hampel B, Hobbie SN, Günthard HF, Braun DL. Phenotypic and genotypic characterization of Neisseria gonorrhoeae isolates among individuals at high risk for sexually transmitted diseases in Zurich, Switzerland. Int J STD AIDS 2024:9564624241230266. [PMID: 38297880 DOI: 10.1177/09564624241230266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
BACKGROUND While ceftriaxone resistance remains scarce in Switzerland, global Neisseria gonorrhoeae (NG) antimicrobial resistance poses an urgent threat. This study describes clinical characteristics in MSM (men who have sex with men) diagnosed with NG infection and analyses NG resistance by phenotypic and genotypic means. METHODS Data of MSM enrolled in three clinical cohorts with a positive polymerase chain reaction test (PCR) for NG were analysed between January 2019 and December 2021 and linked with antibiotic susceptibility testing. Bacterial isolates were subjected to whole genome sequencing (WGS). RESULTS Of 142 participants, 141 (99%) were MSM and 118 (84%) living with HIV. Participants were treated with ceftriaxone (N = 79), azithromycin (N = 2), or a combination of both (N = 61). No clinical or microbiological failures were observed. From 182 positive PCR samples taken, 23 were available for detailed analysis. Based on minimal inhibitory concentrations (MICs), all isolates were susceptible to ceftriaxone, gentamicin, cefixime, cefpodoxime, ertapenem, zoliflodacin, and spectinomycin. Resistance to azithromycin, tetracyclines and ciprofloxacin was observed in 10 (43%), 23 (100%) and 11 (48%) of the cases, respectively. Analysis of WGS data revealed combinations of resistance determinants that matched with the corresponding phenotypic resistance pattern of each isolate. CONCLUSION Among the MSM diagnosed with NG mainly acquired in Switzerland, ceftriaxone MICs were low for a subset of bacterial isolates studied and no treatment failures were observed. For azithromycin, high occurrences of in vitro resistance were found. Gentamicin, cefixime, cefpodoxime, ertapenem, spectinomycin, and zoliflodacin displayed excellent in vitro activity against the 23 isolates underscoring their potential as alternative agents to ceftriaxone.
Collapse
Affiliation(s)
- Christian Jünger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Suraj Balakrishna
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marina Gysin
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Klara Haldimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
5
|
Gebhard CE, Sütsch C, Gebert P, Gysi B, Bengs S, Todorov A, Deforth M, Buehler PK, Meisel A, Schuepbach RA, Zinkernagel AS, Brugger SD, Acevedo C, Patriki D, Wiggli B, Beer JH, Friedl A, Twerenbold R, Kuster GM, Pargger H, Tschudin-Sutter S, Schefold JC, Spinetti T, Henze C, Pasqualini M, Sager DF, Mayrhofer L, Grieder M, Tontsch J, Franzeck FC, Wendel Garcia PD, Hofmaenner DA, Scheier T, Bartussek J, Haider A, Grämer M, Mikail N, Rossi A, Zellweger N, Opić P, Portmann A, von Känel R, Pazhenkottil AP, Messerli M, Buechel RR, Kaufmann PA, Treyer V, Siegemund M, Held U, Regitz-Zagrosek V, Gebhard C. Impact of sex and gender on post-COVID-19 syndrome, Switzerland, 2020. Euro Surveill 2024; 29:2300200. [PMID: 38214079 PMCID: PMC10785203 DOI: 10.2807/1560-7917.es.2024.29.2.2300200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/04/2023] [Indexed: 01/13/2024] Open
Abstract
BackgroundWomen are overrepresented among individuals with post-acute sequelae of SARS-CoV-2 infection (PASC). Biological (sex) as well as sociocultural (gender) differences between women and men might account for this imbalance, yet their impact on PASC is unknown.AimWe assessed the impact of sex and gender on PASC in a Swiss population.MethodOur multicentre prospective cohort study included 2,856 (46% women, mean age 44.2 ± 16.8 years) outpatients and hospitalised patients with PCR-confirmed SARS-CoV-2 infection.ResultsAmong those who remained outpatients during their first infection, women reported persisting symptoms more often than men (40.5% vs 25.5% of men; p < 0.001). This sex difference was absent in hospitalised patients. In a crude analysis, both female biological sex (RR = 1.59; 95% CI: 1.41-1.79; p < 0.001) and a score summarising gendered sociocultural variables (RR = 1.05; 95% CI: 1.03-1.07; p < 0.001) were significantly associated with PASC. Following multivariable adjustment, biological female sex (RR = 0.96; 95% CI: 0.74-1.25; p = 0.763) was outperformed by feminine gender-related factors such as a higher stress level (RR = 1.04; 95% CI: 1.01-1.06; p = 0.003), lower education (RR = 1.16; 95% CI: 1.03-1.30; p = 0.011), being female and living alone (RR = 1.91; 95% CI: 1.29-2.83; p = 0.001) or being male and earning the highest income in the household (RR = 0.76; 95% CI: 0.60-0.97; p = 0.030).ConclusionSpecific sociocultural parameters that differ in prevalence between women and men, or imply a unique risk for women, are predictors of PASC and may explain, at least in part, the higher incidence of PASC in women. Once patients are hospitalised during acute infection, sex differences in PASC are no longer evident.
Collapse
Affiliation(s)
- Caroline E Gebhard
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
- These authors contributed equally
| | - Claudia Sütsch
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- These authors contributed equally
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Pimrapat Gebert
- Institute of Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Bianca Gysi
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Susan Bengs
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Atanas Todorov
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Manja Deforth
- Department of Biostatistics at Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Philipp K Buehler
- Institute of Intensive Care, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alexander Meisel
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Reto A Schuepbach
- Institute of Intensive Care, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dimitri Patriki
- Department of Cardiology, University Hospital Zurich, Zurich, Switzerland
| | - Benedikt Wiggli
- Department of Internal Medicine, Cantonal Hospital of Baden, Baden, Switzerland
| | - Jürg H Beer
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
- Department of Internal Medicine, Cantonal Hospital of Baden, Baden, Switzerland
| | - Andrée Friedl
- Department of Internal Medicine, Cantonal Hospital of Baden, Baden, Switzerland
| | - Raphael Twerenbold
- Department of Cardiology, University Hospital Basel, Basel, Switzerland
- Department of Cardiology and University Center of Cardiovascular Science, University Heart and Vascular Center Hamburg, Hamburg, Germany
| | - Gabriela M Kuster
- Department of Cardiology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Hans Pargger
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Joerg C Schefold
- Department of Intensive Care Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thibaud Spinetti
- Department of Intensive Care Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - Chiara Henze
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Mina Pasqualini
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Dominik F Sager
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Lilian Mayrhofer
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mirjam Grieder
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Janna Tontsch
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Fabian C Franzeck
- Department of Informatics, University Hospital Basel, Basel, Switzerland
| | - Pedro D Wendel Garcia
- Institute of Intensive Care, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jan Bartussek
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Intensive Care, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ahmed Haider
- Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, and Department of Radiology, Harvard Medical School, Boston, Massachusetts, United States
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Muriel Grämer
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Nidaa Mikail
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Alexia Rossi
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Núria Zellweger
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Petra Opić
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Angela Portmann
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Roland von Känel
- Department of Consultation-Liaison Psychiatry and Psychosomatic Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Aju P Pazhenkottil
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Messerli
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ronny R Buechel
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp A Kaufmann
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Valerie Treyer
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Martin Siegemund
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ulrike Held
- Department of Biostatistics at Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Vera Regitz-Zagrosek
- Institute of Gender in Medicine (GiM), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Catherine Gebhard
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| |
Collapse
|
6
|
Emmenegger M, Emmenegger V, Shambat SM, Scheier TC, Gomez-Mejia A, Chang CC, Wendel-Garcia PD, Buehler PK, Buettner T, Roggenbuck D, Brugger SD, Frauenknecht KBM. Antiphospholipid antibodies are enriched post-acute COVID-19 but do not modulate the thrombotic risk. Clin Immunol 2023; 257:109845. [PMID: 37995947 DOI: 10.1016/j.clim.2023.109845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/29/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND AND OBJECTIVES COVID-19-associated coagulopathy, shown to increase the risk for the occurrence of thromboses and microthromboses, displays phenotypic features of the antiphospholipid syndrome (APS), a prototype antibody-mediated autoimmune disease. Several groups have reported elevated levels of criteria and non-criteria antiphospholipid antibodies (aPL), assumed to cause APS, during acute or post-acute COVID-19. However, disease heterogeneity of COVID-19 is accompanied by heterogeneity in molecular signatures, including aberrant cytokine profiles and an increased occurrence of autoantibodies. Moreover, little is known about the association between autoantibodies and the clinical events. Here, we first aim to characterise the antiphospholipid antibody, anti-SARS-CoV-2 antibody, and the cytokine profiles in a diverse collective of COVID-19 patients (disease severity: asymptomatic to intensive care), using vaccinated individuals and influenza patients as comparisons. We then aim to assess whether the presence of aPL in COVID-19 is associated with an increased incidence of thrombotic events in COVID-19. METHODS AND RESULTS We conducted anti-SARS-CoV-2 IgG and IgA microELISA and IgG, IgA, and IgM antiphospholipid line immunoassay (LIA) against 10 criteria and non-criteria antigens in 155 plasma samples of 124 individuals, and we measured 16 cytokines and chemokines in 112 plasma samples. We additionally employed clinical and demographic parameters to conduct multivariable regression analyses within multiple paradigms. In line with recent results, we find that IgM autoantibodies against annexin V (AnV), β2-glycoprotein I (β2GPI), and prothrombin (PT) are enriched upon infection with SARS-CoV-2. There was no evidence for seroconversion from IgM to IgG or IgA. PT, β2GPI, and AnV IgM as well as cardiolipin (CL) IgG antiphospholipid levels were significantly elevated in the COVID-19 but not in the influenza or control groups. They were associated predominantly with the strength of the anti-SARS-CoV-2 antibody titres and the major correlate for thromboses was SARS-CoV-2 disease severity. CONCLUSION While we have recapitulated previous findings, we conclude that the presence of the aPL, most notably PT, β2GPI, AnV IgM, and CL IgG in COVID-19 are not associated with a higher incidence of thrombotic events.
Collapse
Affiliation(s)
- Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland; Division of Medical Immunology, Department of Laboratory Medicine, University Hospital Basel, 4031 Basel, Switzerland.
| | - Vishalini Emmenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gomez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Pedro D Wendel-Garcia
- Institute of Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Philipp K Buehler
- Institute of Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | | | - Dirk Roggenbuck
- GA Generic Assays GmbH, Dahlewitz, Germany; Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany; Faculty of Health Sciences Brandenburg, University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Katrin B M Frauenknecht
- Institute of Neuropathology, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany; National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Luxembourg Center of Neuropathology (LCNP), 3555 Dudelange, Luxembourg
| |
Collapse
|
7
|
Schärer V, Meier MT, Schuepbach RA, Zinkernagel AS, Boumasmoud M, Chakrakodi B, Brugger SD, Fröhlich MR, Wolfensberger A, Sax H, Kuster SP, Schreiber PW. An intensive care unit outbreak with multi-drug-resistant Pseudomonas aeruginosa - spotlight on sinks. J Hosp Infect 2023; 139:161-167. [PMID: 37343769 DOI: 10.1016/j.jhin.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa and other Gram-negative bacteria have the ability to persist in moist environments in healthcare settings, but their spread from these areas can result in outbreaks of healthcare-associated infections. METHODS This study reports the investigation and containment of a multi-drug-resistant P. aeruginosa outbreak in three intensive care units of a Swiss university hospital. In total, 255 patients and 276 environmental samples were screened for the multi-drug-resistant P. aeruginosa outbreak strain. The environmental sampling and molecular characterization of patient and environmental strains, and control strategies implemented, including waterless patient care, are described. RESULTS Between March and November 2019, the outbreak affected 29 patients. Environmental sampling detected the outbreak strain in nine samples of sink siphons of three different intensive care units with a common water sewage system, and on one gastroscope. Three weeks after replacement of the sink siphons, the outbreak strain re-grew in siphon-derived samples and newly affected patients were identified. The outbreak ceased after removal of all sinks in the proximity of patients and in medication preparation areas, and minimization of tap water use. Multi-locus sequence typing indicated clonality (sequence type 316) in 28/29 patient isolates and all 10 environmental samples. CONCLUSIONS Sink removal combined with the introduction of waterless patient care terminated the multi-drug-resistant P. aeruginosa outbreak. Sinks in intensive care units may pose a risk for point source outbreaks with P. aeruginosa and other bacteria persisting in moist environments.
Collapse
Affiliation(s)
- V Schärer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - M-T Meier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - R A Schuepbach
- Institute for Intensive Care Medicine, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - A S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - M Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - B Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - S D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - M R Fröhlich
- Institute for Intensive Care Medicine, University Hospital Zurich and University of Zurich, Zurich, Switzerland; Department of Perioperative Medicine, Kantonsspital Aarau, Aarau, Switzerland
| | - A Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - H Sax
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland; Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - S P Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - P W Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
| |
Collapse
|
8
|
Räz AK, Andreoni F, Boumasmoud M, Bergada-Pijuan J, Schweizer TA, Mairpady Shambat S, Hasse B, Zinkernagel AS, Brugger SD. Limited Adaptation of Staphylococcus aureus during Transition from Colonization to Invasive Infection. Microbiol Spectr 2023; 11:e0259021. [PMID: 37341598 PMCID: PMC10433843 DOI: 10.1128/spectrum.02590-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Staphylococcus aureus carriage is a risk factor for invasive infections. Unique genetic elements favoring the transition from colonizing to invasive phenotype have not yet been identified, and phenotypic adaptation traits are understudied. We therefore assessed phenotypic and genotypic profiles of 11 S. aureus isolate pairs sampled from colonized patients simultaneously suffering from invasive S. aureus infections. Ten out of 11 isolate pairs displayed the same spa and multilocus sequence type, suggesting colonization as an origin for the invasive infection. Systematic analysis of colonizing and invasive isolate pairs showed similar adherence, hemolysis, reproductive fitness properties, antibiotic tolerance, and virulence in a Galleria mellonella infection model, as well as minimal genetic differences. Our results provide insights into the similar phenotypes associated with limited adaptation between colonizing and invasive isolates. Disruption of the physical barriers of mucosa or skin was identified in the majority of patients, further emphasizing colonization as a major risk factor for invasive disease. IMPORTANCE S. aureus is a major pathogen of humans, causing a wide range of diseases. The difficulty to develop a vaccine and antibiotic treatment failure warrant the exploration of novel treatment strategies. Asymptomatic colonization of the human nasal passages is a major risk factor for invasive disease, and decolonization procedures have been effective in preventing invasive infections. However, the transition of S. aureus from a benign colonizer of the nasal passages to a major pathogen is not well understood, and both host and bacterial properties have been discussed as being relevant for this behavioral change. We conducted a thorough investigation of patient-derived strain pairs reflecting colonizing and invasive isolates in a given patient. Although we identified limited genetic adaptation in certain strains, as well as slight differences in adherence capacity among colonizing and invasive isolates, our work suggests that barrier breaches are a key event in the disease continuum of S. aureus.
Collapse
Affiliation(s)
- Anna K. Räz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
9
|
Reiber C, Bodendoerfer E, Brugger SD, Eberhard N, Hitz E, Hofmaenner DA, Herren S, Kolesnik-Goldmann N, Manicini S, Zbinden R, Zinkernagel AS, Hasse B. Rapid antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales: an implementation study. Swiss Med Wkly 2023; 153:40066. [PMID: 37190876 DOI: 10.57187/smw.2023.40066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
AIMS OF THE STUDY The goal of this descriptive study was to assess the performance as well as the extent of the clinical impact of rapid automated antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales. We also aimed to analyse how rapid automated antimicrobial susceptibility testing influences clinical decision-making. METHODS This single-centre study conducted at the University Hospital of Zurich included data from all consecutive patients with Enterobacterales bacteraemia from November 2019 to October 2020. There was no control group. The primary outcome was the effect of rapid automated antimicrobial susceptibility testing on antibiotic therapy (no adjustment, escalation to a broader-spectrum antibiotic or de-escalation to a narrower-spectrum antibiotic). Rapid automated antimicrobial susceptibility testing results were further compared to susceptibility tests using European Committee on Antimicrobial Susceptibility Testing (EUCAST) standard methods and erroneous results were noted. Additionally, we investigated turnaround times for rapid automated antimicrobial susceptibility testing and routine diagnostic testing. RESULTS We analysed 106 patients with 116 episodes of bacteraemia due to Enterobacterales, with Escherichia coli and Klebsiella pneumoniae being the most frequent isolates. Almost 8% of pathogens were multidrug resistant. Rapid automated antimicrobial susceptibility testing showed category agreement in 98.4% of all interpretable cases. A significant reduction of more than 20 h in turnaround times could be achieved with rapid automated antimicrobial susceptibility testing compared to the routine diagnostic workflow. In the majority of cases, rapid automated antimicrobial susceptibility testing had no effect, given that the empirical therapy was already correct or circumstances did not allow for de-escalation. In 38.8% of cases, antimicrobial therapy was adjusted, whereas eight cases were de-escalated based on rapid automated antimicrobial susceptibility testing alone. CONCLUSIONS Rapid automated antimicrobial susceptibility testing may be a valuable and safe way to accelerate diagnosis. In particular, time to suitable therapy can be shortened in cases of incorrect therapy. However, physicians are reluctant to de-escalate antibiotic therapy based on rapid automated antimicrobial susceptibility testing alone, limiting its impact in everyday clinics. To further explore the potential of rapid automated antimicrobial susceptibility testing, a stringent/compulsory antibiotic stewardship programme would be a valuable next step.
Collapse
Affiliation(s)
- Claudine Reiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Elias Bodendoerfer
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nadia Eberhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Eva Hitz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sebastian Herren
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | | | - Stefano Manicini
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
10
|
Naghavian R, Faigle W, Oldrati P, Wang J, Toussaint NC, Qiu Y, Medici G, Wacker M, Freudenmann LK, Bonté PE, Weller M, Regli L, Amigorena S, Rammensee HG, Walz JS, Brugger SD, Mohme M, Zhao Y, Sospedra M, Neidert MC, Martin R. Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma. Nature 2023; 617:807-817. [PMID: 37198490 PMCID: PMC10208956 DOI: 10.1038/s41586-023-06081-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Microbial organisms have key roles in numerous physiological processes in the human body and have recently been shown to modify the response to immune checkpoint inhibitors1,2. Here we aim to address the role of microbial organisms and their potential role in immune reactivity against glioblastoma. We demonstrate that HLA molecules of both glioblastoma tissues and tumour cell lines present bacteria-specific peptides. This finding prompted us to examine whether tumour-infiltrating lymphocytes (TILs) recognize tumour-derived bacterial peptides. Bacterial peptides eluted from HLA class II molecules are recognized by TILs, albeit very weakly. Using an unbiased antigen discovery approach to probe the specificity of a TIL CD4+ T cell clone, we show that it recognizes a broad spectrum of peptides from pathogenic bacteria, commensal gut microbiota and also glioblastoma-related tumour antigens. These peptides were also strongly stimulatory for bulk TILs and peripheral blood memory cells, which then respond to tumour-derived target peptides. Our data hint at how bacterial pathogens and bacterial gut microbiota can be involved in specific immune recognition of tumour antigens. The unbiased identification of microbial target antigens for TILs holds promise for future personalized tumour vaccination approaches.
Collapse
Affiliation(s)
- Reza Naghavian
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Cellerys AG, Schlieren, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Cellerys AG, Schlieren, Switzerland
- Immunity and Cancer, Institut Curie, PSL University, INSERM U932, Paris, France
| | - Pietro Oldrati
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Jian Wang
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Schlieren, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yuhan Qiu
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Gioele Medici
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marcel Wacker
- Department of Peptide-based Immunotherapy, University of Tübingen, University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Lena K Freudenmann
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | | | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology and Clinical Neuroscience, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luca Regli
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sebastian Amigorena
- Immunity and Cancer, Institut Curie, PSL University, INSERM U932, Paris, France
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University of Tübingen, University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Malte Mohme
- Department of Neurosurgery, University Hospital Hamburg Eppendorf, University of Hamburg, Hamburg, Germany
| | - Yingdong Zhao
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD, USA
| | - Mireia Sospedra
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Cellerys AG, Schlieren, Switzerland
| | - Marian C Neidert
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland.
- Cellerys AG, Schlieren, Switzerland.
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
- Therapeutic Immune Design Unit, Center for Molecular Medicine, Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
11
|
Sinnberg T, Lichtensteiger C, Ali OH, Pop OT, Jochum AK, Risch L, Brugger SD, Velic A, Bomze D, Kohler P, Vernazza P, Albrich WC, Kahlert CR, Abdou MT, Wyss N, Hofmeister K, Niessner H, Zinner C, Gilardi M, Tzankov A, Röcken M, Dulovic A, Shambat SM, Ruetalo N, Buehler PK, Scheier TC, Jochum W, Kern L, Henz S, Schneider T, Kuster GM, Lampart M, Siegemund M, Bingisser R, Schindler M, Schneiderhan-Marra N, Kalbacher H, McCoy KD, Spengler W, Brutsche MH, Maček B, Twerenbold R, Penninger JM, Matter MS, Flatz L. Pulmonary Surfactant Proteins Are Inhibited by Immunoglobulin A Autoantibodies in Severe COVID-19. Am J Respir Crit Care Med 2023; 207:38-49. [PMID: 35926164 PMCID: PMC9952873 DOI: 10.1164/rccm.202201-0011oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rationale: Coronavirus disease 2019 (COVID-19) can lead to acute respiratory distress syndrome with fatal outcomes. Evidence suggests that dysregulated immune responses, including autoimmunity, are key pathogenic factors. Objectives: To assess whether IgA autoantibodies target lung-specific proteins and contribute to disease severity. Methods: We collected 147 blood, 9 lung tissue, and 36 BAL fluid samples from three tertiary hospitals in Switzerland and one in Germany. Severe COVID-19 was defined by the need to administer oxygen. We investigated the presence of IgA autoantibodies and their effects on pulmonary surfactant in COVID-19 using the following methods: immunofluorescence on tissue samples, immunoprecipitations followed by mass spectrometry on BAL fluid samples, enzyme-linked immunosorbent assays on blood samples, and surface tension measurements with medical surfactant. Measurements and Main Results: IgA autoantibodies targeting pulmonary surfactant proteins B and C were elevated in patients with severe COVID-19 but not in patients with influenza or bacterial pneumonia. Notably, pulmonary surfactant failed to reduce surface tension after incubation with either plasma or purified IgA from patients with severe COVID-19. Conclusions: Our data suggest that patients with severe COVID-19 harbor IgA autoantibodies against pulmonary surfactant proteins B and C and that these autoantibodies block the function of lung surfactant, potentially contributing to alveolar collapse and poor oxygenation.
Collapse
Affiliation(s)
- Tobias Sinnberg
- Department of Dermatology,,Cluster of Excellence iFIT (EXC 2180) Image Guided and Functionally Instructed Tumor Therapies,,Department of Dermatology, Venereology and Allergology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany
| | | | - Omar Hasan Ali
- Institute of Immunobiology,,Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada;,Department of Dermatology
| | | | | | - Lorenz Risch
- Center of Laboratory Medicine, Vaduz, Liechtenstein;,Center of Laboratory Medicine, University Institute of Clinical Chemistry, University Hospital Bern, University of Bern, Bern, Switzerland;,Faculty of Medical Sciences, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | | | - Ana Velic
- Proteome Center Tübingen, Interfaculty Institute for Cell Biology
| | - David Bomze
- Institute of Immunobiology,,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Philipp Kohler
- Division of Infectious Diseases and Hospital Epidemiology
| | | | | | - Christian R. Kahlert
- Division of Infectious Diseases and Hospital Epidemiology,,Department of Infectious Diseases and Hospital Epidemiology, Children’s Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | | | | | | | - Heike Niessner
- Department of Dermatology,,Cluster of Excellence iFIT (EXC 2180) Image Guided and Functionally Instructed Tumor Therapies
| | - Carl Zinner
- Pathology, Institute of Medical Genetics and Pathology
| | - Mara Gilardi
- Pathology, Institute of Medical Genetics and Pathology
| | | | - Martin Röcken
- Department of Dermatology,,Cluster of Excellence iFIT (EXC 2180) Image Guided and Functionally Instructed Tumor Therapies
| | | | | | | | - Philipp K. Buehler
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | | | | | | | | | - Gabriela M. Kuster
- Department of Cardiology and Cardiovascular Research Institute Basel (CRIB)
| | - Maurin Lampart
- Department of Cardiology and Cardiovascular Research Institute Basel (CRIB)
| | - Martin Siegemund
- Intensive Care Unit, Department of Acute Medicine,,Department of Clinical Research, and
| | - Roland Bingisser
- Emergency Department, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | | | - Hubert Kalbacher
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
| | - Kathy D. McCoy
- Snyder Institute for Chronic Disease, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Werner Spengler
- Department of Medical Oncology and Pneumology, University Hospital Tübingen, Tübingen, Germany
| | - Martin H. Brutsche
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Boris Maček
- Proteome Center Tübingen, Interfaculty Institute for Cell Biology
| | - Raphael Twerenbold
- Division of Pneumology, and,University Center of Cardiovascular Science and Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Partner Site Hamburg-Kiel-Lübeck, Hamburg, Germany; and
| | - Josef M. Penninger
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada;,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | | | - Lukas Flatz
- Department of Dermatology,,Institute of Immunobiology,,Department of Dermatology, Venereology, and Allergology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland;,Department of Dermatology
| |
Collapse
|
12
|
Dähler R, Brugger SD, Frank M, Greutmann M, Sromicki J, Marques-Maggio E, Imkamp F, Bauernschmitt R, Carrel T, Zinkernagel AS, Hasse B. A retrospective analysis of blood culture-negative endocarditis at a tertiary care centre in Switzerland. Swiss Med Wkly 2022; 152:40012. [PMID: 36534966 DOI: 10.57187/smw.2022.40016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIMS OF THE STUDY Numerous studies from different countries have contributed to an improved understanding of blood culture-negative infective endocarditis. However, little is known about its epidemiology and microbiology in Switzerland. We aimed to assess the epidemiology and microbiology of blood culture-negative endocarditis at the University Hospital Zurich, Switzerland. METHODS We screened all patients hospitalised between 1997 and 2020 with possible or definite endocarditis at our institution. Thereof, we identified all cases with blood culture-negative endocarditis and retrospectively retrieved patient characteristics, microbiological, histopathological, radiographic and surgical data from medical records. RESULTS Among 861 patients screened, 66 (7.7%) cases of blood culture-negative endocarditis were identified. Thereof, 31 cases could be microbiologically documented or not documented (n = 30), and in five cases a non-infectious aetiology was confirmed. Endocarditis predominantly affected men (77%) and the left heart (79%); predisposing factors were prosthetic valves (42%), congenital heart disease (35%) and prior endocarditis (14%). The most common reasons for negative blood cultures were antibiotic treatment prior to blood culture sampling (35%), fastidious and slow growing microorganisms (30%) and definite non-infective endocarditis (8%). Coxiella burnetii and Bartonella spp. were the most common fastidious bacteria identified. In addition to serology, identification of causative microorganisms was possible by microbiological and/or histopathological analysis of tissue samples, of which polymerase chain reaction testing (PCR) of the 16S ribosomal RNA proved to be most successful. CONCLUSIONS The present study provides a detailed analysis of blood culture-negative endocarditis over a time span of more than 20 years in Zurich, Switzerland. Antibiotic treatment prior to blood collection, and fastidious and slow growing organisms were identified as main reasons for sterile blood cultures. Typical culture-negative bacteria were mainly found by PCR and/or culture of tissue samples.
Collapse
Affiliation(s)
- Roman Dähler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Silvio D Brugger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Michelle Frank
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Matthias Greutmann
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Juri Sromicki
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Switzerland
| | - Ewerton Marques-Maggio
- Department of Surgical Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Robert Bauernschmitt
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Switzerland
| | - Thierry Carrel
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| |
Collapse
|
13
|
Deforth M, Gebhard CE, Bengs S, Buehler PK, Schuepbach RA, Zinkernagel AS, Brugger SD, Acevedo CT, Patriki D, Wiggli B, Twerenbold R, Kuster GM, Pargger H, Schefold JC, Spinetti T, Wendel-Garcia PD, Hofmaenner DA, Gysi B, Siegemund M, Heinze G, Regitz-Zagrosek V, Gebhard C, Held U. Development and validation of a prognostic model for the early identification of COVID-19 patients at risk of developing common long COVID symptoms. Diagn Progn Res 2022; 6:22. [PMID: 36384641 PMCID: PMC9668400 DOI: 10.1186/s41512-022-00135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic demands reliable prognostic models for estimating the risk of long COVID. We developed and validated a prediction model to estimate the probability of known common long COVID symptoms at least 60 days after acute COVID-19. METHODS The prognostic model was built based on data from a multicentre prospective Swiss cohort study. Included were adult patients diagnosed with COVID-19 between February and December 2020 and treated as outpatients, at ward or intensive/intermediate care unit. Perceived long-term health impairments, including reduced exercise tolerance/reduced resilience, shortness of breath and/or tiredness (REST), were assessed after a follow-up time between 60 and 425 days. The data set was split into a derivation and a geographical validation cohort. Predictors were selected out of twelve candidate predictors based on three methods, namely the augmented backward elimination (ABE) method, the adaptive best-subset selection (ABESS) method and model-based recursive partitioning (MBRP) approach. Model performance was assessed with the scaled Brier score, concordance c statistic and calibration plot. The final prognostic model was determined based on best model performance. RESULTS In total, 2799 patients were included in the analysis, of which 1588 patients were in the derivation cohort and 1211 patients in the validation cohort. The REST prevalence was similar between the cohorts with 21.6% (n = 343) in the derivation cohort and 22.1% (n = 268) in the validation cohort. The same predictors were selected with the ABE and ABESS approach. The final prognostic model was based on the ABE and ABESS selected predictors. The corresponding scaled Brier score in the validation cohort was 18.74%, model discrimination was 0.78 (95% CI: 0.75 to 0.81), calibration slope was 0.92 (95% CI: 0.78 to 1.06) and calibration intercept was -0.06 (95% CI: -0.22 to 0.09). CONCLUSION The proposed model was validated to identify COVID-19-infected patients at high risk for REST symptoms. Before implementing the prognostic model in daily clinical practice, the conduct of an impact study is recommended.
Collapse
Affiliation(s)
- Manja Deforth
- Department of Biostatistics at Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland.
| | - Caroline E Gebhard
- Intensive Care Unit, Department of Acute Medicine, University Hospital Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Susan Bengs
- Department of Nuclear Medicine, University Hospital Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
| | - Philipp K Buehler
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Reto A Schuepbach
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Claudio T Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Dimitri Patriki
- Department of Internal Medicine, Cantonal Hospital Baden, Baden, Switzerland
| | - Benedikt Wiggli
- Department of Infectiology and Infection Control, Cantonal Hospital Baden, Baden, Switzerland
| | - Raphael Twerenbold
- Department of Cardiology, University Hospital Basel, Basel, Switzerland
- University Center of Cardiovascular Science & Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site Hamburg-Kiel-Lübeck, Berlin, Germany
| | - Gabriela M Kuster
- Department of Cardiology, University Hospital Basel, Basel, Switzerland
| | - Hans Pargger
- Intensive Care Unit, Department of Acute Medicine, University Hospital Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Joerg C Schefold
- Department of Intensive Care Medicine, University Hospital Bern, Bern, Switzerland
| | - Thibaud Spinetti
- Department of Intensive Care Medicine, University Hospital Bern, Bern, Switzerland
| | - Pedro D Wendel-Garcia
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Bianca Gysi
- Intensive Care Unit, Department of Acute Medicine, University Hospital Basel, Basel, Switzerland
| | - Martin Siegemund
- Intensive Care Unit, Department of Acute Medicine, University Hospital Basel, Basel, Switzerland
- Department Clinical Research, University of Basel, Basel, Switzerland
| | - Georg Heinze
- Center for Medical Statistics, Informatics and Intelligent Systems, Section for Clinical Biometrics, Medical University of Vienna, Vienna, Austria
| | - Vera Regitz-Zagrosek
- University of Zurich, Zurich, Switzerland
- Charité, University Medicine Berlin, Berlin, Germany
- Department of Cardiology, University Hospital Zurich, Zurich, Switzerland
| | - Catherine Gebhard
- Department of Nuclear Medicine, University Hospital Zurich, Zurich, Switzerland
- Center for Molecular Cardiology, University of Zurich, Schlieren, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Ulrike Held
- Department of Biostatistics at Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| |
Collapse
|
14
|
Gómez-Mejia A, Arnold K, Bär J, Singh KD, Scheier TC, Brugger SD, Zinkernagel AS, Sinues P. Rapid detection of Staphylococcus aureus and Streptococcus pneumoniae by real-time analysis of volatile metabolites. iScience 2022; 25:105080. [PMID: 36157573 PMCID: PMC9490032 DOI: 10.1016/j.isci.2022.105080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/06/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Early detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment of infections. In this study, we show that secondary electrospray ionization–high resolution mass spectrometry (SESI-HRMS) can be used as a diagnostic tool for rapid detection of bacterial infections as a supportive system for current state-of-the-art diagnostics. Volatile organic compounds (VOCs) produced by growing S. aureus or S. pneumoniae cultures on blood agar plates were detected within minutes and allowed for the distinction of these two bacteria on a species and even strain level within hours. Furthermore, we obtained a fingerprint of clinical patient samples within minutes of measurement and predominantly observed a separation of samples containing live bacteria compared to samples with no bacterial growth. Further development of this technique may reduce the time required for microbiological diagnosis and should help to improve patient’s tailored treatment. Real-time mass spectrometry shows potential as a tool for microbiological diagnosis Bacterial volatile metabolites from 1 × 103 CFUs are detected within minutes S. aureus and S. pneumoniae can be distinguished on species and even strain level Complex clinical samples cluster according to presence or absence of viable bacteria
Collapse
Affiliation(s)
- Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Kim Arnold
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Kapil Dev Singh
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Pablo Sinues
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| |
Collapse
|
15
|
Oyewole ORA, Latzin P, Brugger SD, Hilty M. Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants. Microbiome 2022; 10:152. [PMID: 36138483 PMCID: PMC9502908 DOI: 10.1186/s40168-022-01344-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of Streptococcus pneumoniae in a Swiss birth cohort by PacBio single-molecule real-time (SMRT) sequencing of the plyNCR marker. METHODS A total of 872 nasal swab (NS) samples were included from 47 healthy infants during the first year of life. Pneumococcal carriage was determined based on the quantitative real-time polymerase chain reaction (qPCR) targeting the lytA gene. The plyNCR marker was amplified from 214 samples having lytA-based carriage for pneumococcal strain resolution. Amplicons were sequenced using SMRT technology, and sequences were analyzed with the DADA2 pipeline. In addition, pneumococcal serotypes were determined using conventional, multiplex PCR (cPCR). RESULTS PCR-based plyNCR amplification demonstrated a 94.2% sensitivity and 100% specificity for Streptococcus pneumoniae if compared to lytA qPCR. The overall carriage prevalence was 63.8%, and pneumococcal co-colonization (≥ 2 plyNCR amplicon sequence variants (ASVs)) was detected in 38/213 (17.8%) sequenced samples with the relative proportion of the least abundant strain(s) ranging from 1.1 to 48.8% (median, 17.2%; IQR, 5.8-33.4%). The median age to first acquisition was 147 days, and having ≥ 2 siblings increased the risk of acquisition. CONCLUSION The plyNCR amplicon sequencing is species-specific and enables pneumococcal strain resolution. We therefore recommend its application for longitudinal strain-level carriage studies of Streptococcus pneumoniae. Video Abstract.
Collapse
Affiliation(s)
- Oluwaseun Rume-Abiola Oyewole
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland.
| |
Collapse
|
16
|
Schweizer TA, Andreoni F, Acevedo C, Scheier TC, Heggli I, Maggio EM, Eberhard N, Brugger SD, Dudli S, Zinkernagel AS. Intervertebral disc cell chondroptosis elicits neutrophil response in Staphylococcus aureus spondylodiscitis. Front Immunol 2022; 13:908211. [PMID: 35967370 PMCID: PMC9366608 DOI: 10.3389/fimmu.2022.908211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
To understand the pathophysiology of spondylodiscitis due to Staphylococcus aureus, an emerging infectious disease of the intervertebral disc (IVD) and vertebral body with a high complication rate, we combined clinical insights and experimental approaches. Clinical data and histological material of nine patients suffering from S. aureus spondylodiscitis were retrospectively collected at a single center. To mirror the clinical findings experimentally, we developed a novel porcine ex vivo model mimicking acute S. aureus spondylodiscitis and assessed the interaction between S. aureus and IVD cells within their native environment. In addition, the inflammatory features underlying this interaction were assessed in primary human IVD cells. Finally, mirroring the clinical findings, we assessed primary human neutrophils for their ability to respond to secreted inflammatory modulators of IVD cells upon the S. aureus challenge. Acute S. aureus spondylodiscitis in patients was characterized by tissue necrosis and neutrophil infiltration. Additionally, the presence of empty IVD cells’ lacunae was observed. This was mirrored in the ex vivo porcine model, where S. aureus induced extensive IVD cell death, leading to empty lacunae. Concomitant engagement of the apoptotic and pyroptotic cell death pathways was observed in primary human IVD cells, resulting in cytokine release. Among the released cytokines, functionally intact neutrophil-priming as well as broad pro- and anti-inflammatory cytokines which are known for their involvement in IVD degeneration were found. In patients as well as ex vivo in a novel porcine model, S. aureus IVD infection caused IVD cell death, resulting in empty lacunae, which was accompanied by the release of inflammatory markers and recruitment of neutrophils. These findings offer valuable insights into the important role of inflammatory IVD cell death during spondylodiscitis and potential future therapeutic approaches.
Collapse
Affiliation(s)
- Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Irina Heggli
- Center of Experimental Rheumatology, University Hospital Zurich and Balgrist University Hospital, University of Zurich, Zurich, Switzerland
- Department of Physical Medicine and Rheumatology, University Hospital Zurich and Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Ewerton Marques Maggio
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nadia Eberhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Stefan Dudli
- Center of Experimental Rheumatology, University Hospital Zurich and Balgrist University Hospital, University of Zurich, Zurich, Switzerland
- Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Zurich, Switzerland
- *Correspondence: Annelies S. Zinkernagel,
| |
Collapse
|
17
|
Maccio U, Zinkernagel AS, Schuepbach R, Probst-Mueller E, Frontzek K, Brugger SD, Hofmaenner DA, Moch H, Varga Z. Long-Term Persisting SARS-CoV-2 RNA and Pathological Findings: Lessons Learnt From a Series of 35 COVID-19 Autopsies. Front Med (Lausanne) 2022; 9:778489. [PMID: 35223894 PMCID: PMC8865372 DOI: 10.3389/fmed.2022.778489] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/04/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Long-term sequelae of coronavirus disease 2019 (COVID-19), including the interaction between persisting viral-RNA and specific tissue involvement, pose a challenging issue. In this study, we addressed the chronological correlation (after first clinical diagnosis and postmortem) between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and organ involvement. METHODS The presence of postmortem SARS-CoV-2 RNA from 35 complete COVID-19 autopsies was correlated with the time interval between the first diagnosis of COVID-19 and death and with its relationship to morphologic findings. RESULTS Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be evident up to 40 days after the first diagnosis and can persist to 94 hours after death. Postmortem SARS-CoV-2 RNA was mostly positive in lungs (70%) and trachea (69%), but all investigated organs were positive with variable frequency. Late-stage tissue damage was evident up to 65 days after initial diagnosis in several organs. Positivity for SARS-CoV-2 RNA in pulmonary swabs correlated with diffuse alveolar damage (p = 0.0009). No correlation between positive swabs and other morphologic findings was present. Cerebral (p = 0.0003) and systemic hemorrhages (p = 0.009), cardiac thrombi (p = 0.04), and ischemic events (p = 0.03) were more frequent in the first wave, whereas bacterial pneumonia (p = 0.03) was more prevalent in the second wave. No differences in biometric data, clinical comorbidities, and other autopsy findings were found. CONCLUSIONS Our data provide evidence not only of long-term postmortem persisting SARS-CoV-2 RNA but also of tissue damage several weeks after the first diagnosis of SARS-CoV-2 infection. Additional conditions, such as concomitant bacterial pulmonary superinfection, lung aspergillosis, thromboembolic phenomena, and hemorrhages can further worsen tissue damage.
Collapse
Affiliation(s)
- Umberto Maccio
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zürich, University of Zurich, Zurich, Switzerland
| | - Reto Schuepbach
- Institute of Intensive Care, University Hospital Zurich, University Hospital of Zürich, Zurich, Switzerland
| | | | - Karl Frontzek
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zürich, University of Zurich, Zurich, Switzerland
| | - Daniel Andrea Hofmaenner
- Institute of Intensive Care, University Hospital Zurich, University Hospital of Zürich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, University of Zurich, Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
18
|
Hofmaenner DA, Wendel Garcia PD, Blum MR, David S, Schuepbach RA, Buehler PK, Frey PM, Zinkernagel AS, Brugger SD. The importance of intravenous immunoglobulin treatment in critically ill patients with necrotizing soft tissue infection: a retrospective cohort study. BMC Infect Dis 2022; 22:168. [PMID: 35189821 PMCID: PMC8862556 DOI: 10.1186/s12879-022-07135-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Background Necrotizing soft-tissue infections are infections with high mortality. The use of immunoglobulins within a combination therapy including broad-spectrum antibiotics has been debated. We assessed potential benefits of immunoglobulins and hypothesized that they were associated with a treatment benefit in a high-resource setting. Methods Patients with necrotizing soft-tissue infection hospitalized in the tertiary intensive care unit of the University Hospital of Zurich, Switzerland, between 2008 and 2020 were included retrospectively. The association between immunoglobulin administration and in-hospital survival, intensive care unit length of stay, the incidences of acute renal failure, acute respiratory distress syndrome and septic shock were analyzed. Results After adjustment for confounders, no difference for in-hospital survival (hazard ratio 2.20, 95% confidence interval [CI] 0.24–20.20, p = 0.5), intensive care unit length of stay (subhazard ratio [SHR] 0.90, CI 0.41–1.98, p = 0.8) and the development of acute respiratory distress syndrome (SHR 1.2, CI 0.36–4.03, p = 0.77) was observed in patients with or without immunoglobulin treatment. The Simplified Acute Physiology Score II, the risk of developing acute renal failure (SHR 2.86, CI 1.33–6.15, p = 0.01) and septic shock (SHR 1.86, CI 1.02–3.40, p = 0.04) was higher in patients treated with immunoglobulins, possibly reflecting a higher disease severity beyond measured confounders. Conclusions No clear evidence for a benefit of immunoglobulins in our cohort with consistent antibiotic use was found. Patients receiving immunoglobulins appeared more severely ill. Complementary to high treatment standards and appropriate antibiotics including beta lactams and protein synthesis inhibitors, immunoglobulins should be administered on a case-to-case basis, at least while more evidence from larger randomized controlled trials is missing.
Collapse
Affiliation(s)
- Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Pedro David Wendel Garcia
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Manuel R Blum
- Department of General Internal Medicine, Bern University Hospital (Inselspital), University of Bern, Bern, Switzerland.,Institute for Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Sascha David
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Reto A Schuepbach
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Philipp K Buehler
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Pascal M Frey
- Department of General Internal Medicine, Bern University Hospital (Inselspital), University of Bern, Bern, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
19
|
Bär J, Boumasmoud M, Mairpady Shambat S, Vulin C, Huemer M, Schweizer TA, Gómez-Mejia A, Eberhard N, Achermann Y, Zingg PO, Mestres C, Brugger SD, Schuepbach RA, Kouyos RD, Hasse B, Zinkernagel AS. Quantification of within-patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations. Clin Microbiol Infect 2022; 28:1022.e1-1022.e7. [DOI: 10.1016/j.cmi.2022.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 12/21/2022]
|
20
|
Mairpady Shambat S, Gómez-Mejia A, Schweizer TA, Huemer M, Chang CC, Acevedo C, Bergada-Pijuan J, Vulin C, Hofmaenner DA, Scheier TC, Hertegonne S, Parietti E, Miroshnikova N, Wendel Garcia PD, Hilty MP, Buehler PK, Schuepbach RA, Brugger SD, Zinkernagel AS. Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19. PLoS Pathog 2022; 18:e1010176. [PMID: 35007290 PMCID: PMC8782468 DOI: 10.1371/journal.ppat.1010176] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/21/2022] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 displays diverse disease severities and symptoms including acute systemic inflammation and hypercytokinemia, with subsequent dysregulation of immune cells. Bacterial superinfections in COVID-19 can further complicate the disease course and are associated with increased mortality. However, there is limited understanding of how SARS-CoV-2 pathogenesis and hypercytokinemia impede the innate immune function against bacterial superinfections. We assessed the influence of COVID-19 plasma hypercytokinemia on the functional responses of myeloid immune cells upon bacterial challenges from acute-phase COVID-19 patients and their corresponding recovery-phase. We show that a severe hypercytokinemia status in COVID-19 patients correlates with the development of bacterial superinfections. Neutrophils and monocytes derived from COVID-19 patients in their acute-phase showed an impaired intracellular microbicidal capacity upon bacterial challenges. The impaired microbicidal capacity was reflected by abrogated MPO and reduced NETs production in neutrophils along with reduced ROS production in both neutrophils and monocytes. Moreover, we observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes, in line with suppressed autocrine and paracrine cytokine signaling. This phenotype was characterized by a high expression of CD66b, CXCR4 and low expression of CXCR1, CXCR2 and CD15 in neutrophils and low expression of HLA-DR, CD86 and high expression of CD163 and CD11b in monocytes. Furthermore, the impaired antibacterial effector function was mediated by synergistic effect of the cytokines TNF-α, IFN-γ and IL-4. COVID-19 patients receiving dexamethasone showed a significant reduction of overall inflammatory markers in the plasma as well as exhibited an enhanced immune response towards bacterial challenge ex vivo. Finally, broad anti-inflammatory treatment was associated with a reduction in CRP, IL-6 levels as well as length of ICU stay and ventilation-days in critically ill COVID-19 patients. Our data provides insights into the transient functional dysregulation of myeloid immune cells against subsequent bacterial infections in COVID-19 patients and describe a beneficial role for the use of dexamethasone in these patients.
Collapse
Affiliation(s)
- Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A. Hofmaenner
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Elena Parietti
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Nataliya Miroshnikova
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Pedro D. Wendel Garcia
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias P. Hilty
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Karl Buehler
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Reto A. Schuepbach
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
21
|
Schweizer TA, Mairpady Shambat S, Vulin C, Hoeller S, Acevedo C, Huemer M, Gomez‐Mejia A, Chang C, Baum J, Hertegonne S, Hitz E, Scheier TC, Hofmaenner DA, Buehler PK, Moch H, Schuepbach RA, Brugger SD, Zinkernagel AS. Blunted sFasL signalling exacerbates TNF-driven neutrophil necroptosis in critically ill COVID-19 patients. Clin Transl Immunology 2021; 10:e1357. [PMID: 34938538 PMCID: PMC8665925 DOI: 10.1002/cti2.1357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Critically ill coronavirus disease 2019 (COVID-19) patients are characterised by a severely dysregulated cytokine profile and elevated neutrophil counts, impacting disease severity. However, it remains unclear how neutrophils contribute to pathophysiology during COVID-19. Here, we assessed the impact of the dysregulated cytokine profile on the regulated cell death (RCD) programme of neutrophils. METHODS Regulated cell death phenotype of neutrophils isolated from critically ill COVID-19 patients or healthy donors and stimulated with COVID-19 or healthy plasma ex vivo was assessed by flow cytometry, time-lapse microscopy and cytokine multiplex analysis. Immunohistochemistry of COVID-19 patients and control biopsies were performed to assess the in situ neutrophil RCD phenotype. Plasma cytokine levels of COVID-19 patients and healthy donors were measured by multiplex analysis. Clinical parameters were correlated to cytokine levels of COVID-19 patients. RESULTS COVID-19 plasma induced a necroptosis-sensitive neutrophil phenotype, characterised by cell lysis, elevated release of damage-associated molecular patterns (DAMPs), increased receptor-interacting serine/threonine-protein kinase (RIPK) 1 levels and mixed lineage kinase domain-like pseudokinase (MLKL) involvement. The occurrence of neutrophil necroptosis MLKL axis was further confirmed in COVID-19 thrombus and lung biopsies. Necroptosis was induced by the tumor necrosis factor receptor 1 (TNFRI)/TNF-α axis. Moreover, reduction of soluble Fas ligand (sFasL) levels in COVID-19 patients and hence decreased signalling to Fas directly increased RIPK1 levels, exacerbated TNF-driven necroptosis and correlated with disease severity, which was abolished in patients treated with glucocorticoids. CONCLUSION Our results suggest a novel role for sFasL signalling in the TNF-α-induced RCD programme in neutrophils during COVID-19 and a potential therapeutic target to curb inflammation and thus influence disease severity and outcome.
Collapse
Affiliation(s)
- Tiziano A Schweizer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Clement Vulin
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Sylvia Hoeller
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Alejandro Gomez‐Mejia
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Chun‐Chi Chang
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Jeruscha Baum
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Eva Hitz
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Daniel A Hofmaenner
- Institute for Intensive Care MedicineUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Philipp K Buehler
- Institute for Intensive Care MedicineUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Holger Moch
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Reto A Schuepbach
- Institute for Intensive Care MedicineUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| |
Collapse
|
22
|
Hasan Ali O, Bomze D, Risch L, Brugger SD, Paprotny M, Weber M, Thiel S, Kern L, Albrich WC, Kohler P, Kahlert CR, Vernazza P, Bühler PK, Schüpbach RA, Gómez-Mejia A, Popa AM, Bergthaler A, Penninger JM, Flatz L. Erratum to: Severe Coronavirus Disease 2019 (COVID-19) is Associated With Elevated Serum Immunoglobulin (Ig) A and Antiphospholipid IgA Antibodies. Clin Infect Dis 2021; 73:1746. [PMID: 34550333 PMCID: PMC8787408 DOI: 10.1093/cid/ciab532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Omar Hasan Ali
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - David Bomze
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lorenz Risch
- Labormedizinisches Zentrum Dr. Risch, Vaduz, Liechtenstein
- Center of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, Bern, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Hygiene, University Hospital Zurich, Zurich, Switzerland
| | - Matthias Paprotny
- Department of General Internal Medicine, Landesspital Liechtenstein, Vaduz, Liechtenstein
| | - Myriam Weber
- Department of General Internal Medicine, Landesspital Liechtenstein, Vaduz, Liechtenstein
| | - Sarah Thiel
- Department of General Internal Medicine, Landesspital Liechtenstein, Vaduz, Liechtenstein
| | - Lukas Kern
- Department of Pulmonology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Werner C Albrich
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Philipp Kohler
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, Children’s Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Philipp K Bühler
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Reto A Schüpbach
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Hygiene, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra M Popa
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Bergthaler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Josef M Penninger
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Flatz
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Correspondence: L. Flatz, Kantonsspital St. Gallen, Institute of Immunobiology, Rorschacher Strasse 95, 9007 St. Gallen, Switzerland ()
| |
Collapse
|
23
|
Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. mSystems 2021; 6:e0042521. [PMID: 34546072 PMCID: PMC8547433 DOI: 10.1128/msystems.00425-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
Collapse
Affiliation(s)
| | - Silvio D. Brugger
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Isabel Fernandez Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sean L. Cotton
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Sara M. Eslami
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tommy H. Tran
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Dakota S. Jones
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel Minot
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christopher D. Johnston
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Section of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
24
|
Hofmaenner DA, Wendel Garcia PD, Ganter CC, Brugger SD, Buehler PK, David S. What every intensivist should know about Tocilizumab. Crit Care 2021; 25:262. [PMID: 34315504 PMCID: PMC8313874 DOI: 10.1186/s13054-021-03696-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel Andrea Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Pedro David Wendel Garcia
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Christoph Camille Ganter
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Karl Buehler
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Sascha David
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland.
| |
Collapse
|
25
|
Maibach MA, Allam A, Hilty MP, Perez Gonzalez NA, Buehler PK, Wendel Garcia PD, Brugger SD, Ganter CC, Krauthammer M, Schuepbach RA, Bartussek J. How to Synchronize Longitudinal Patient Data With the Underlying Disease Progression: A Pilot Study Using the Biomarker CRP for Timing COVID-19. Front Med (Lausanne) 2021; 8:607594. [PMID: 34307391 PMCID: PMC8295502 DOI: 10.3389/fmed.2021.607594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/07/2021] [Indexed: 01/29/2023] Open
Abstract
The continued digitalization of medicine has led to an increased availability of longitudinal patient data that allows the investigation of novel and known diseases in unprecedented detail. However, to accurately describe any underlying pathophysiology and allow inter-patient comparisons, individual patient trajectories have to be synchronized based on temporal markers. In this pilot study, we use longitudinal data from critically ill ICU COVID-19 patients to compare the commonly used alignment markers “onset of symptoms,” “hospital admission,” and “ICU admission” with a novel objective method based on the peak value of the inflammatory marker C-reactive protein (CRP). By applying our CRP-based method to align the progression of neutrophils and lymphocytes, we were able to define a pathophysiological window that improved mortality risk stratification in our COVID-19 patient cohort. Our data highlights that proper synchronization of longitudinal patient data is crucial for accurate interpatient comparisons and the definition of relevant subgroups. The use of objective temporal disease markers will facilitate both translational research efforts and multicenter trials.
Collapse
Affiliation(s)
- Martina A Maibach
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Ahmed Allam
- Department of Quantitative Biomedicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Matthias P Hilty
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Nicolas A Perez Gonzalez
- Department of Quantitative Biomedicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Philipp K Buehler
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Pedro D Wendel Garcia
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University and University Hospital Zurich, Zurich, Switzerland
| | - Christoph C Ganter
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | | | | | - Michael Krauthammer
- Department of Quantitative Biomedicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Reto A Schuepbach
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland
| | - Jan Bartussek
- Institute for Intensive Care Medicine, University and University Hospital Zurich, Zurich, Switzerland.,Department of Quantitative Biomedicine, University and University Hospital Zurich, Zurich, Switzerland
| |
Collapse
|
26
|
Wendel Garcia PD, Hofmaenner DA, Brugger SD, Acevedo CT, Bartussek J, Camen G, Bader PR, Bruellmann G, Kattner J, Ganter C, Schuepbach RA, Buehler PK. Closed-Loop Versus Conventional Mechanical Ventilation in COVID-19 ARDS. J Intensive Care Med 2021; 36:1184-1193. [PMID: 34098803 PMCID: PMC8442133 DOI: 10.1177/08850666211024139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Lung-protective ventilation is key in bridging patients suffering from
COVID-19 acute respiratory distress syndrome (ARDS) to recovery. However,
resource and personnel limitations during pandemics complicate the
implementation of lung-protective protocols. Automated ventilation modes may
prove decisive in these settings enabling higher degrees of lung-protective
ventilation than conventional modes. Method: Prospective study at a Swiss university hospital. Critically ill,
mechanically ventilated COVID-19 ARDS patients were allocated, by
study-blinded coordinating staff, to either closed-loop or conventional
mechanical ventilation, based on mechanical ventilator availability. Primary
outcome was the overall achieved percentage of lung-protective ventilation
in closed-loop versus conventional mechanical ventilation, assessed
minute-by-minute, during the initial 7 days and overall mechanical
ventilation time. Lung-protective ventilation was defined as the combined
target of tidal volume <8 ml per kg of ideal body weight, dynamic driving
pressure <15 cmH2O, peak pressure <30 cmH2O,
peripheral oxygen saturation ≥88% and dynamic mechanical power <17
J/min. Results: Forty COVID-19 ARDS patients, accounting for 1,048,630 minutes (728 days) of
cumulative mechanical ventilation, allocated to either closed-loop (n = 23)
or conventional ventilation (n = 17), presenting with a median
paO2/ FiO2 ratio of 92 [72-147] mmHg and a static
compliance of 18 [11-25] ml/cmH2O, were mechanically ventilated
for 11 [4-25] days and had a 28-day mortality rate of 20%. During the
initial 7 days of mechanical ventilation, patients in the closed-loop group
were ventilated lung-protectively for 65% of the time versus 38% in the
conventional group (Odds Ratio, 1.79; 95% CI, 1.76-1.82; P
< 0.001) and for 45% versus 33% of overall mechanical ventilation time
(Odds Ratio, 1.22; 95% CI, 1.21-1.23; P < 0.001). Conclusion: Among critically ill, mechanically ventilated COVID-19 ARDS patients during
an early highpoint of the pandemic, mechanical ventilation using a
closed-loop mode was associated with a higher degree of lung-protective
ventilation than was conventional mechanical ventilation.
Collapse
Affiliation(s)
| | | | - Silvio D Brugger
- Division of Infectious Diseases, 27243University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Claudio T Acevedo
- Division of Infectious Diseases, 27243University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Jan Bartussek
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Giovanni Camen
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Patrick Raphael Bader
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Gregor Bruellmann
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Johannes Kattner
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Christoph Ganter
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Reto Andreas Schuepbach
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| | - Philipp Karl Buehler
- Institute of Intensive Care Medicine, 27243University Hospital of Zurich, Zurich, Switzerland
| |
Collapse
|
27
|
Eshmuminov D, Mueller M, Brugger SD, Bautista Borrego L, Becker D, Hefti M, Hagedorn C, Duskabilova M, Tibbitt MW, Dutkowski P, Rudolf von Rohr P, Schuler MJ, Mueller NJ, Clavien PA. Sources and prevention of graft infection during long-term ex situ liver perfusion. Transpl Infect Dis 2021; 23:e13623. [PMID: 33887094 DOI: 10.1111/tid.13623] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 01/11/2023]
Abstract
INTRODUCTION The use of normothermic liver machine perfusion to repair injured grafts ex situ is an emerging topic of clinical importance. However, a major concern is the possibility of microbial contamination in the absence of a fully functional immune system. Here, we report a standardized approach to maintain sterility during normothermic liver machine perfusion of porcine livers for one week. METHODS Porcine livers (n = 42) were procured and perfused with blood at 34°C following aseptic technique and standard operating procedures. The antimicrobial prophylaxis was adapted and improved in a step-wise manner taking into account the pathogens that were detected during the development phase. Piperacillin-Tazobactam was applied as a single dose initially and modified to continuous application in the final protocol. In addition, the perfusion machine was improved to recapitulate partially the host's defense system. The final protocol was tested for infection prevention during one week of perfusion. RESULTS During the development phase, microbial contamination occurred in 27 out of 39 (69%) livers with a mean occurrence of growth on 4 ± 1.6 perfusion days. The recovered microorganisms suggested an exogenous source of microbial contamination. The antimicrobial agents (piperacillin/tazobactam) could be maintained above the targeted minimal inhibitory concentration (8-16 mg/L) only with continuous application. In addition to continuous application of piperacillin/tazobactam, partial recapitulation of the host immune system ex situ accompanied by strict preventive measures for contact and air contamination maintained sterility during one week of perfusion. CONCLUSION The work demonstrates feasibility of sterility maintenance for one week during ex situ normothermic liver perfusion.
Collapse
Affiliation(s)
- Dilmurodjon Eshmuminov
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | - Matteo Mueller
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Lucia Bautista Borrego
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | - Dustin Becker
- Wyss Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Max Hefti
- Wyss Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Catherine Hagedorn
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | - Muhayyo Duskabilova
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | - Mark W Tibbitt
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
| | - Philipp Dutkowski
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | - Philipp Rudolf von Rohr
- Transport Processes and Reactions Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
| | - Martin J Schuler
- Wyss Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Pierre-Alain Clavien
- Department of Surgery, Swiss Hepatopancreatobiliary and Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| |
Collapse
|
28
|
Leung YKS, Ledergerber B, Eberhard N, Mestres CA, Rancic Z, Zimmermann A, Zbinden R, Brugger SD, Zinkernagel AS, Hasse B. Open wounds and rifampicin therapy are associated with rifampicin resistance among staphylococcal vascular graft/endograft infections. JAC Antimicrob Resist 2021; 3:dlab041. [PMID: 34223108 PMCID: PMC8209986 DOI: 10.1093/jacamr/dlab041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/01/2021] [Indexed: 11/23/2022] Open
Abstract
Background Optimal timing for rifampicin combination therapy in patients with staphylococcal vascular graft/endograft infection (S-VGEI) is unknown. Experts recommend adding rifampicin after lowering bacterial load by surgery and wound closure. Objectives To assess predictors of rifampicin resistance among staphylococci isolated from patients in the Vascular Graft Infection Cohort Study. Methods We included prospective patients with S-VGEI diagnosis from 1 January 2002 to 30 June 2020. We retrospectively assessed determinants of rifampicin resistance using exact logistic regression and described survival with Kaplan–Meier curves. Results We analysed 513 Staphylococcus spp. among 143 predominantly male (82%) patients with a median age of 68 years (IQR 60–75). Thereof, 82 (57%) received a rifampicin combination therapy and 61 (43%) received an antimicrobial therapy without rifampicin. Among 82 patients with rifampicin, 26/26 patients with any rifampicin resistance had open wounds with a strong association of rifampicin resistance with rifampicin treatment while having open wounds (OR 37, 95% CI 6.1 to ∞). Among 75 patients with a rifampicin combination therapy and rifampicin-susceptible staphylococci at S-VGEI diagnosis, 12/12 patients with a secondary rifampicin-resistant isolate had an open wound (OR 14, 95% CI 2.1 to ∞). Conclusions Rifampicin should be started after wound closure due to increased risk of rifampicin resistance observed while having open wounds or second-look surgeries among patients with S-VGEI.
Collapse
Affiliation(s)
- Yau Kei Stefan Leung
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Nadia Eberhard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Carlos A Mestres
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Zoran Rancic
- Clinic for Vascular Surgery, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Alexander Zimmermann
- Clinic for Vascular Surgery, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28, Zurich, Switzerland
| | - Silvio D Brugger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, Zurich, Switzerland
| | | |
Collapse
|
29
|
Buehler PK, Zinkernagel AS, Hofmaenner DA, Wendel Garcia PD, Acevedo CT, Gómez-Mejia A, Mairpady Shambat S, Andreoni F, Maibach MA, Bartussek J, Hilty MP, Frey PM, Schuepbach RA, Brugger SD. Bacterial pulmonary superinfections are associated with longer duration of ventilation in critically ill COVID-19 patients. Cell Rep Med 2021; 2:100229. [PMID: 33748789 PMCID: PMC7955928 DOI: 10.1016/j.xcrm.2021.100229] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/29/2021] [Accepted: 03/09/2021] [Indexed: 01/02/2023]
Abstract
The impact of secondary bacterial infections (superinfections) in coronavirus disease 2019 (COVID-19) is not well understood. In this prospective, monocentric cohort study, we aim to investigate the impact of superinfections in COVID-19 patients with acute respiratory distress syndrome. Patients are assessed for concomitant microbial infections by longitudinal analysis of tracheobronchial secretions, bronchoalveolar lavages, and blood cultures. In 45 critically ill patients, we identify 19 patients with superinfections (42.2%). Superinfections are detected on day 10 after intensive care admission. The proportion of participants alive and off invasive mechanical ventilation at study day 28 (ventilator-free days [VFDs] at 28 days) is substantially lower in patients with superinfection (subhazard ratio 0.37; 95% confidence interval [CI] 0.15–0.90; p = 0.028). Patients with pulmonary superinfections have a higher incidence of bacteremia, virus reactivations, yeast colonization, and required intensive care treatment for a longer time. Superinfections are frequent and associated with reduced VFDs at 28 days despite a high rate of empirical antibiotic therapy. Secondary bacterial infections (superinfections) are found in 42% of patients Bacterial superinfections occur on day 10 after intensive care admission Bacterial superinfections are associated with longer duration of ventilation Bacterial superinfections are mostly caused by Gram-negative bacteria
Collapse
Affiliation(s)
- Philipp K Buehler
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Pedro David Wendel Garcia
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Claudio T Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Martina A Maibach
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Jan Bartussek
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.,Department of Quantitative Biomedicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Matthias P Hilty
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Pascal M Frey
- Department of General Internal Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Reto A Schuepbach
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| |
Collapse
|
30
|
Hofmaenner DA, Wendel Garcia PD, Duvnjak B, Chakrakodi B, Maier JD, Huber M, Huder J, Wolfensberger A, Schreiber PW, Schuepbach RA, Zinkernagel AS, Buehler PK, Brugger SD. Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients. Antimicrob Resist Infect Control 2021; 10:11. [PMID: 33436105 PMCID: PMC7802978 DOI: 10.1186/s13756-021-00885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/05/2021] [Indexed: 01/08/2023] Open
Abstract
Background In intensive care units (ICUs) treating patients with Coronavirus disease 2019 (COVID-19) invasive ventilation poses a high risk for aerosol and droplet formation. Surface contamination of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) or bacteria can result in nosocomial transmission.
Methods Two tertiary care COVID-19 intensive care units treating 53 patients for 870 patient days were sampled after terminal cleaning and preparation for regular use to treat non-COVID-19 patients. Results A total of 176 swabs were sampled of defined locations covering both ICUs. No SARS-CoV-2 ribonucleic acid (RNA) was detected. Gram-negative bacterial contamination was mainly linked to sinks and siphons. Skin flora was isolated from most swabbed areas and Enterococcus faecium was detected on two keyboards. Conclusions After basic cleaning with standard disinfection measures no remaining SARS-CoV-2 RNA was detected. Bacterial contamination was low and mainly localised in sinks and siphons.
Collapse
Affiliation(s)
- Daniel A Hofmaenner
- Institute of Intensive Care, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Pedro David Wendel Garcia
- Institute of Intensive Care, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Branko Duvnjak
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Bhavya Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Julian D Maier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jon Huder
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Aline Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Peter W Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Reto A Schuepbach
- Institute of Intensive Care, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Philipp K Buehler
- Institute of Intensive Care, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland.
| | | |
Collapse
|
31
|
Huemer M, Mairpady Shambat S, Brugger SD, Zinkernagel AS. Antibiotic resistance and persistence-Implications for human health and treatment perspectives. EMBO Rep 2020; 21:e51034. [PMID: 33400359 PMCID: PMC7726816 DOI: 10.15252/embr.202051034] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/13/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.
Collapse
Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| |
Collapse
|
32
|
Hasan Ali O, Bomze D, Risch L, Brugger SD, Paprotny M, Weber M, Thiel S, Kern L, Albrich WC, Kohler P, Kahlert CR, Vernazza P, Bühler PK, Schüpbach RA, Gómez-Mejia A, Popa AM, Bergthaler A, Penninger JM, Flatz L. Severe COVID-19 is associated with elevated serum IgA and antiphospholipid IgA-antibodies. Clin Infect Dis 2020; 73:e2869-e2874. [PMID: 32997739 PMCID: PMC7543315 DOI: 10.1093/cid/ciaa1496] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/29/2020] [Indexed: 01/15/2023] Open
Abstract
Background Severe coronavirus disease 2019 (COVID-19) frequently entails complications that bear similarities to autoimmune diseases. To date, there is little data on possible IgA-mediated autoimmune responses. Here, we aim to determine whether COVID-19 is associated with a vigorous total IgA response and if IgA antibodies are associated with complications of severe illness. Since thrombotic events are frequent in severe COVID-19 and resemble hypercoagulation of antiphospholipid syndrome (APS), our approach focused on antiphospholipid antibodies (aPL). Methods In this retrospective cohort study clinical data and aPL from 64 patients with COVID-19 were compared from three independent tertiary hospitals (one in Liechtenstein, two in Switzerland). Samples were collected from April 9 th to May 1 st, 2020. Results Clinical records of 64 patients with COVID-19 were reviewed and divided into a cohort with mild illness (mCOVID) (41%), a discovery cohort with severe illness (sdCOVID) (22%) and a confirmation cohort with severe illness (scCOVID) (38%). Total IgA, IgG and aPL were measured with clinical diagnostic kits. Severe illness was significantly associated with increased total IgA (sdCOVID, P=0.01; scCOVID, p-value<0.001), but not total IgG. Among aPL, both cohorts with severe illness significantly correlated with elevated anti-Cardiolipin IgA (sdCOVID and scCOVID, p-value<0.001), anti-Cardiolipin IgM (sdCOVID, P=0.003; scCOVID, P<0.001), and anti-Beta2 Glycoprotein-1 IgA (sdCOVID and scCOVID, P<0.001). Systemic lupus erythematosus was excluded from all patients as a potential confounder. Conclusions Higher total IgA and IgA-aPL were consistently associated with severe illness. These novel data strongly suggest that a vigorous antiviral IgA-response, possibly triggered in the bronchial mucosa, induces systemic autoimmunity.
Collapse
Affiliation(s)
- Omar Hasan Ali
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - David Bomze
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lorenz Risch
- Labormedizinisches Zentrum Dr. Risch, Vaduz, Liechtenstein.,Center of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, Bern, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Hygiene, University Hospital Zurich, Zurich, Switzerland
| | - Matthias Paprotny
- Department of General Internal Medicine, Landesspital Liechtenstein, Vaduz, Liechtenstein
| | - Myriam Weber
- Department of General Internal Medicine, Landesspital Liechtenstein, Vaduz, Liechtenstein
| | - Sarah Thiel
- Department of General Internal Medicine, Landesspital Liechtenstein, Vaduz, Liechtenstein
| | - Lukas Kern
- Department of Pulmonology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Werner C Albrich
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Philipp Kohler
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Philipp K Bühler
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Reto A Schüpbach
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Hygiene, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra M Popa
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Bergthaler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Josef M Penninger
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Flatz
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| |
Collapse
|
33
|
Braun DL, Turk T, Tschumi F, Grube C, Hampel B, Depmeier C, Schreiber PW, Brugger SD, Greiner M, Steffens D, De Torrenté-Bayard C, Courlet P, Neumann K, Kuster H, Flepp M, Bertisch B, Decosterd L, Böni J, Metzner KJ, Kouyos RD, Günthard HF. Noninferiority of Simplified Dolutegravir Monotherapy Compared to Continued Combination Antiretroviral Therapy That Was Initiated During Primary Human Immunodeficiency Virus Infection: A Randomized, Controlled, Multisite, Open-label, Noninferiority Trial. Clin Infect Dis 2020; 69:1489-1497. [PMID: 30601950 DOI: 10.1093/cid/ciy1131] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/28/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Patients who start combination antiretroviral therapy (cART) during primary human immunodeficiency virus type 1 (HIV-1) infection show a smaller HIV-1 latent reservoir, less immune activation, and less viral diversity compared to patients who start cART during chronic infection. We conducted a pilot study to determine whether these properties would allow sustained virological suppression after simplification of cART to dolutegravir monotherapy. METHODS EARLY-SIMPLIFIED is a randomized, open-label, noninferiority trial. Patients who started cART <180 days after a documented primary HIV-1 infection and had an HIV-1 RNA <50 copies/mL plasma for at least 48 weeks were randomized (2:1) to monotherapy with dolutegravir 50 mg once daily or to continuation of cART. The primary efficacy endpoint was the proportion of patients with <50 HIV-1 RNA copies/mL on or before week 48; noninferiority margin 10%. RESULTS Of the 101 patients randomized, 68 were assigned to simplification to dolutegravir monotherapy and 33 to continuation of cART. At week 48 in the per-protocol population, 67/67 (100%) had virological response in the dolutegravir monotherapy group vs 32/32 (100%) in the cART group (difference, 0.00%; 95% confidence interval, -100%, 4.76%). This showed noninferiority of the dolutegravir monotherapy at the prespecified level. CONCLUSION In this pilot study consisting of patients who initiated cART during primary HIV-1 infection and had <50 HIV-1 RNA copies/mL for at least 48 weeks, monotherapy with once-daily dolutegravir was noninferior to cART. Our results suggest that future simplification studies should use a stratification according to time of HIV infection and start of first cART. CLINICAL TRIALS REGISTRATION NCT02551523.
Collapse
Affiliation(s)
- Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Teja Turk
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Fabian Tschumi
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Christina Grube
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Benjamin Hampel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Carsten Depmeier
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Peter W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Silvio D Brugger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Michael Greiner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Daniela Steffens
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Cornelia De Torrenté-Bayard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Perrine Courlet
- Service of Clinical Pharmacology, University Hospital Center, University of Lausanne, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Markus Flepp
- Center of Infectious Diseases Zurich, Switzerland
| | - Barbara Bertisch
- Checkpoint Zurich, Switzerland.,Institute of Global Health, University of Geneva, Switzerland
| | - Laurent Decosterd
- Service of Clinical Pharmacology, University Hospital Center, University of Lausanne, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| |
Collapse
|
34
|
Troxler LJ, Werren JP, Schaffner TO, Mostacci N, Vermathen P, Vermathen M, Wüthrich D, Simillion C, Brugger SD, Bruggmann R, Hathaway LJ, Furrer J, Hilty M. Carbon source regulates polysaccharide capsule biosynthesis in Streptococcus pneumoniae. J Biol Chem 2019; 294:17224-17238. [PMID: 31594867 PMCID: PMC6873171 DOI: 10.1074/jbc.ra119.010764] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/02/2019] [Indexed: 11/06/2022] Open
Abstract
The exopolysaccharide capsule of Streptococcus pneumoniae is an important virulence factor, but the mechanisms that regulate capsule thickness are not fully understood. Here, we investigated the effects of various exogenously supplied carbohydrates on capsule production and gene expression in several pneumococcal serotypes. Microscopy analyses indicated a near absence of the capsular polysaccharide (CPS) when S. pneumoniae was grown on fructose. Moreover, serotype 7F pneumococci produced much less CPS than strains of other serotypes (6B, 6C, 9V, 15, and 23F) when grown on glucose or sucrose. RNA-sequencing revealed carbon source-dependent regulation of distinct genes of WT strains and capsule-switch mutants of serotypes 6B and 7F, but could not explain the mechanism of capsule thickness regulation. In contrast, 31P NMR of whole-cell extract from capsule-knockout strains (Δcps) clearly revealed the accumulation or absence of capsule precursor metabolites when cells were grown on glucose or fructose, respectively. This finding suggests that fructose uptake mainly results in intracellular fructose 1-phosphate, which is not converted to CPS precursors. In addition, serotype 7F strains accumulated more precursors than did 6B strains, indicating less efficient conversion of precursor metabolites into the CPS in 7F, in line with its thinner capsule. Finally, isotopologue sucrose labeling and NMR analyses revealed that the uptake of the labeled fructose subunit into the capsule is <10% that of glucose. Our findings on the effects of carbon sources on CPS production in different S. pneumoniae serotypes may contribute to a better understanding of pneumococcal diseases and could inform future therapeutic approaches.
Collapse
Affiliation(s)
- Lukas J Troxler
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, 3001 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Joel P Werren
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, 3001 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Thierry O Schaffner
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, 3001 Bern, Switzerland
| | - Nadezda Mostacci
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, 3001 Bern, Switzerland
| | - Peter Vermathen
- Department of BioMedical Research and Radiology, University of Bern and Inselspital, 3012 Bern, Switzerland
| | - Martina Vermathen
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, 3012 Bern, Switzerland.,Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Cedric Simillion
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, 3012 Bern, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.,The Forsyth Institute (Microbiology), Cambridge, Massachusetts 02142.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts 02142
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, 3012 Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, 3001 Bern, Switzerland
| | - Julien Furrer
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, 3001 Bern, Switzerland
| |
Collapse
|
35
|
Brugger SD, Kraemer JG, Qi W, Bomar L, Oppliger A, Hilty M. Age-Dependent Dissimilarity of the Nasopharyngeal and Middle Ear Microbiota in Children With Acute Otitis Media. Front Genet 2019; 10:555. [PMID: 31275355 PMCID: PMC6593076 DOI: 10.3389/fgene.2019.00555] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/24/2019] [Indexed: 12/16/2022] Open
Abstract
Acute bacterial otitis media is usually caused by otopathogens ascending to the middle ear from the nasopharynx (NP). However, it is unknown if the nasopharyngeal microbiota of children with acute otitis media (AOM) can serve as an age-dependent or independent proxy for the microbial communities of the middle ear fluid (MEF) as there is a lack of 16S rRNA amplicon sequencing studies simultaneously analyzing the microbial communities of the two sites. Within this study, we performed 16S rRNA next generation sequencing on a total of 286 nasopharyngeal swabs (NPSs) collected between 2004 and 2013 within a Swiss national AOM surveillance program from children (0-6 years) with AOM. In addition, 42/286 children had spontaneous tympanic membrane perforation and, therefore, those MEF could also be analyzed. We found that alpha [Richness, Shannon diversity index (SDI) and Evenness] and beta diversity measurements of the nasopharyngeal bacterial microbiota showed a clear dependency of the increasing age of the children. In more detail, bacterial richness and personalized profiles (measured by beta dispersion) were higher and more frequent in older children, respectively. Dissimilarity values based on the binary distance matrix of the microbiota patterns of the NP and the MEF also correlated with increasing age. In general, positive (PPV) and negative predictive values (NPV) of the most abundant operational taxonomic units (OTUs) in the NP were moderately and well predictive for their presence in the MEF, respectively. This data is crucial to better understand polymicrobial infections and therefore AOM pathogenesis.
Collapse
Affiliation(s)
- Silvio D Brugger
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich - University of Zurich, Zurich, Switzerland
| | - Julia G Kraemer
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Institute for Work and Health, University of Lausanne, University of Geneva, Épalinges, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology Zurich, University of Zurich, Zurich, Switzerland
| | - Lindsey Bomar
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States.,Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States
| | - Anne Oppliger
- Institute for Work and Health, University of Lausanne, University of Geneva, Épalinges, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| |
Collapse
|
36
|
Frey PM, Marti GR, Droz S, de Roche von Arx M, Suter-Riniker F, Aujesky D, Brugger SD. Bacterial colonization of handheld devices in a tertiary care setting: a hygiene intervention study. Antimicrob Resist Infect Control 2019; 8:97. [PMID: 31183077 PMCID: PMC6555736 DOI: 10.1186/s13756-019-0546-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/26/2019] [Indexed: 11/10/2022] Open
Abstract
Background Tablet computers are increasingly being used in hospital patient care and are often colonized with important human pathogens, while the impact of disinfection interventions remains controversial. Method In a prospective hygiene intervention study we consecutively sampled tablet computers exclusively used in a high-resource general internal medicine tertiary care setting with high routine hygiene measures. Our aim was to examine the change in colonizing bacteria on tablet computers before and after the introduction of a mandatory twice daily tablet disinfection intervention. Microbial identification was performed by conventional culture, and the association of bacterial colonization with the intervention was investigated using logistic regression. Results In a total of 168 samples we identified colonizing bacteria in 149 (89%) of samples. While the most commonly identified species were normal skin bacteria, Staphylococcus aureus found in 18 (11%) of samples was the most frequent potential pathogen. We did not detect any Enterococci or Enterobacteriaceae. The disinfection intervention was associated with substantially less overall bacterial colonization (odds ratio 0.16; 95%-CI 0.04–0.56), while specific colonization with Staphylococcus aureus was only slightly decreased (odds ratio 0.46; 95%-CI 0.16–1.29). Conclusion Our results indicate that a twice daily disinfection can still substantially reduce bacterial colonization of in-hospital tablet computers used in a high-resource and high hygiene setting.
Collapse
Affiliation(s)
- Pascal M Frey
- 1Department of General Internal Medicine, University Hospital Bern (Inselspital), University of Bern, 3010 Bern, Switzerland.,2Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Grischa R Marti
- 1Department of General Internal Medicine, University Hospital Bern (Inselspital), University of Bern, 3010 Bern, Switzerland
| | - Sara Droz
- 3Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | | | - Drahomir Aujesky
- 1Department of General Internal Medicine, University Hospital Bern (Inselspital), University of Bern, 3010 Bern, Switzerland
| | - Silvio D Brugger
- 1Department of General Internal Medicine, University Hospital Bern (Inselspital), University of Bern, 3010 Bern, Switzerland.,2Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| |
Collapse
|
37
|
Tschumi F, Brugger SD, Braun DL. [CME Answers: 'Dyslipidemia and Cardiovascular Risk in HIV Infected Patients', Praxis No. 7]. Praxis (Bern 1994) 2019; 108:566. [PMID: 31185847 DOI: 10.1024/1661-8157/a003248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Fabian Tschumi
- 1 Klinik für Infektionskrankheiten und Spitalhygiene, Universitätsspital Zürich
| | - Silvio D Brugger
- 1 Klinik für Infektionskrankheiten und Spitalhygiene, Universitätsspital Zürich
| | - Dominique L Braun
- 1 Klinik für Infektionskrankheiten und Spitalhygiene, Universitätsspital Zürich
| |
Collapse
|
38
|
Tschumi F, Brugger SD, Braun DL. [CME: Dyslipidemia and Cardiovascular Risk in HIV Infected Patients]. Praxis (Bern 1994) 2019; 108:451-458. [PMID: 31136273 DOI: 10.1024/1661-8157/a003247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
CME: Dyslipidemia and Cardiovascular Risk in HIV Infected Patients Abstract. Dyslipidemia is a common problem in HIV-infected patients and can contribute to an elevated cardiovascular risk among this patient group. An untreated HIV infection as well as certain antiretroviral drugs can lead to an unfavorable change of the lipid profile. This article describes the diagnosis, work up and treatment of dyslipidemia in HIV-infected patients.
Collapse
Affiliation(s)
- Fabian Tschumi
- 1 Klinik für Infektiologie und Spitalhygiene, Universitätsspital Zürich
| | - Silvio D Brugger
- 1 Klinik für Infektiologie und Spitalhygiene, Universitätsspital Zürich
| | - Dominique L Braun
- 1 Klinik für Infektiologie und Spitalhygiene, Universitätsspital Zürich
| |
Collapse
|
39
|
Bomar L, Brugger SD, Lemon KP. Bacterial microbiota of the nasal passages across the span of human life. Curr Opin Microbiol 2017; 41:8-14. [PMID: 29156371 DOI: 10.1016/j.mib.2017.10.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/15/2023]
Abstract
The human nasal passages host major human pathogens. Recent research suggests that the microbial communities inhabiting the epithelial surfaces of the nasal passages are a key factor in maintaining a healthy microenvironment by affecting both resistance to pathogens and immunological responses. The nasal bacterial microbiota shows distinct changes over the span of human life and disruption by environmental factors might be associated with both short- and long-term health consequences, such as susceptibility to viral and bacterial infections and disturbances of the immunological balance. Because infants and older adults experience a high burden of morbidity and mortality from respiratory tract infections, we review recent data on the bacterial nasal microbiota composition in health and acute respiratory infection in these age groups.
Collapse
Affiliation(s)
- Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, MA, United States; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Silvio D Brugger
- The Forsyth Institute (Microbiology), Cambridge, MA, United States; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Katherine P Lemon
- The Forsyth Institute (Microbiology), Cambridge, MA, United States; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.
| |
Collapse
|
40
|
Mika M, Maurer J, Korten I, Allemann A, Aebi S, Brugger SD, Qi W, Frey U, Latzin P, Hilty M. Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study. Microbiome 2017; 5:85. [PMID: 28738889 PMCID: PMC5525364 DOI: 10.1186/s40168-017-0302-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/06/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland. We compared pneumococcal carriage and the nasal microbiota within the first year of life of healthy infants vaccinated with either PCV7 (n = 20, born in 2010) or PCV13 (n = 21, born between 2011 and 2013). Nasal swabs were collected every second week (n = 763 in total). Pneumococcal carriage was analyzed by quantitative PCR of the pneumococcal-specific lytA gene. Analysis of the bacterial core microbiota was performed based on 16S rRNA sequencing and subsequent oligotyping. We exclusively performed oligotyping of the core microbiota members, which were defined as the five most abundant bacterial families (Moraxellaceae, Streptococcaceae, Staphylococcaceae, Corynebacteriaceae, and Pasteurellaceae). Linear mixed effect (LME) and negative binomial regression models were used for statistical analyses. RESULTS We found a higher number of samples positive for pneumococcal carriage in PCV7- compared to PCV13-vaccinated infants (LME model; P = 0.01). In contrast, infants vaccinated in the PCV13 era had an increased alpha diversity as measured by the richness and the Shannon Diversity Index (LME model; P = 0.003 and P = 0.01, respectively). Accordingly, the PCV13 era was associated with clusters of a higher diversity than PCV7-associated clusters. Furthermore, infants vaccinated with PCV13 had a higher binary-based within-subject microbiota similarity, as well as a decreased Jensen-Shannon distance over time as compared to PCV7-vaccinated infants, indicating a higher microbiota stability in the PCV13 era (LME model and t test; P = 0.06 and P = 0.03, respectively). CONCLUSIONS We hypothesize that the higher diversity and stability of the upper airway microbiota in the PCV13 era is the result of the lower pneumococcal carriage rate. This seems to indicate that the nasal bacterial microbiota of infants has changed in recent years as compared to the beginning of this study.
Collapse
Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Josua Maurer
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Silvio D Brugger
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich/University of Zurich, Zurich, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland.
- Department of Infectious Diseases, University Hospital, Bern, Switzerland.
| |
Collapse
|
41
|
Allemann A, Frey PM, Brugger SD, Hilty M. Pneumococcal carriage and serotype variation before and after introduction of pneumococcal conjugate vaccines in patients with acute otitis media in Switzerland. Vaccine 2017; 35:1946-1953. [PMID: 28279564 DOI: 10.1016/j.vaccine.2017.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/26/2017] [Accepted: 02/02/2017] [Indexed: 11/18/2022]
Abstract
BACKGROUND Acute otitis media (AOM) is an important cause for antibiotic prescription within the paediatric population and Streptococcus pneumoniae is a major pathogen associated with AOM episodes. This study aimed at analysing the influence of the heptavalent and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13) on pneumococcal carriage and serotype distribution in AOM. METHODS Nasopharyngeal swabs (NPS) and middle ear fluid (MEF) were collected within a Swiss surveillance study of outpatients from all ages with AOM between 2004 and 2015, covering three vaccination eras (pre-PCV7, PCV7 and PCV13). Samples were cultured for pneumococcal identification, and the association of vaccine era with pneumococcal carriage was investigated by logistic regression analysis adjusting for sociodemographic factors. FINDINGS In total, 3300 NPS and 620 MEF were included in this study. The number of samples from patients with AOM dropped over vaccination eras and S. pneumoniae was less frequently isolated in the PCV13 era as compared to the other two eras. The latest (PCV13) vaccination era was independently associated with a reduced pneumococcal carriage within NPS (adjusted odds ratio 0.65, 95%-CI 0.45-0.94). Investigating serotype epidemiology, vaccine serotypes decreased significantly after the conjugate vaccine introductions with the exception of serotype 3. Within the non-PCV13 serotypes, a particular increase of serogroups 11, 15 and 23 was observed in both NPS and MEF. CONCLUSION A substantial change in pneumococcal carriage and serotype epidemiology suggests an impact of the conjugate vaccines on pneumococcal AOM in Switzerland.
Collapse
Affiliation(s)
- Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Pascal M Frey
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA; Department of General Internal Medicine, Inselspital, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Silvio D Brugger
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Infectious Diseases, Inselspital, University Hospital Bern, University of Bern, Bern, Switzerland.
| |
Collapse
|
42
|
Affiliation(s)
- Silvio D. Brugger
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, United States of America
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Lindsey Bomar
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, United States of America
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Katherine P. Lemon
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
43
|
Garzoni C, Brugger SD, Qi W, Wasmer S, Cusini A, Dumont P, Gorgievski-Hrisoho M, Mühlemann K, von Garnier C, Hilty M. Microbial communities in the respiratory tract of patients with interstitial lung disease. Thorax 2013; 68:1150-6. [PMID: 23945167 PMCID: PMC3841796 DOI: 10.1136/thoraxjnl-2012-202917] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Molecular methods based on phylogenetic differences in the 16S rRNA gene are able to characterise the microbiota of the respiratory tract in health and disease. Objectives Our goals were (1) to characterise bacterial communities in lower and upper airways of patients with interstitial lung disease (ILD) and (2) to compare the results with the microbiota of patients with Pneumocystis pneumonia (PCP) and normal controls. Methods We examined the upper and lower respiratory tract of 18 patients with ILD of whom 5, 6, and 7 had idiopathic interstitial pneumonia (IIP), non-IIP and sarcoidosis, respectively. In addition, six immune-compromised patients with PCP and nine healthy subjects were included as controls. Exclusion criteria were recent bacterial/viral respiratory tract infection, HIV-positivity and subjects receiving antibiotic therapy. Bronchoalveolar lavage fluid and oropharyngeal swabs were simultaneously collected, and microbiota was characterised by ultra-deep 16S rRNA gene sequencing. Results The microbiota in lower airways of the majority of patients (30; 90%) primarily consisted of Prevotellaceae, Streptococcaceae and Acidaminococcaceae. α and β diversity measurements revealed no significant differences in airway microbiota composition between the five different groups of patients. Comparison of bacterial populations in upper and lower respiratory tract showed significant topographical discontinuities for 7 (23%) individuals. Conclusions IIP, non-IIP and sarcoidosis are not associated with disordered airway microbiota and a pathogenic role of commensals in the disease process is therefore unlikely. Nevertheless, molecular analysis of the topographical microbiota continuity along the respiratory tract may provide additional information to assist management of individual patients.
Collapse
Affiliation(s)
- Christian Garzoni
- Institute for Infectious Diseases, University of Bern, , Bern, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Brugger SD, Frei L, Frey PM, Aebi S, Mühlemann K, Hilty M. 16S rRNA terminal restriction fragment length polymorphism for the characterization of the nasopharyngeal microbiota. PLoS One 2012; 7:e52241. [PMID: 23284951 PMCID: PMC3527403 DOI: 10.1371/journal.pone.0052241] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 11/16/2012] [Indexed: 11/24/2022] Open
Abstract
A novel non-culture based 16S rRNA Terminal Restriction Fragment Length Polymorphism (T-RFLP) method using the restriction enzymes Tsp509I and Hpy166II was developed for the characterization of the nasopharyngeal microbiota and validated using recently published 454 pyrosequencing data. 16S rRNA gene T-RFLP for 153 clinical nasopharyngeal samples from infants with acute otitis media (AOM) revealed 5 Tsp509I and 6 Hpy166II terminal fragments (TFs) with a prevalence of >10%. Cloning and sequencing identified all TFs with a prevalence >6% allowing a sufficient description of bacterial community changes for the most important bacterial taxa. The conjugated 7-valent pneumococcal polysaccharide vaccine (PCV-7) and prior antibiotic exposure had significant effects on the bacterial composition in an additive main effects and multiplicative interaction model (AMMI) in concordance with the 16S rRNA 454 pyrosequencing data. In addition, the presented T-RFLP method is able to discriminate S. pneumoniae from other members of the Mitis group of streptococci, which therefore allows the identification of one of the most important human respiratory tract pathogens. This is usually not achieved by current high throughput sequencing protocols. In conclusion, the presented 16S rRNA gene T-RFLP method is a highly robust, easy to handle and a cheap alternative to the computationally demanding next-generation sequencing analysis. In case a lot of nasopharyngeal samples have to be characterized, it is suggested to first perform 16S rRNA T-RFLP and only use next generation sequencing if the T-RFLP nasopharyngeal patterns differ or show unknown TFs.
Collapse
Affiliation(s)
- Silvio D. Brugger
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of General Internal Medicine, University Hospital of Bern, Bern, Switzerland
| | - Laurence Frei
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pascal M. Frey
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Kathrin Mühlemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, University Hospital of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, University Hospital of Bern, Bern, Switzerland
| |
Collapse
|
45
|
Brugger SD, Baumberger C, Jost M, Jenni W, Brugger U, Mühlemann K. Automated counting of bacterial colony forming units on agar plates. PLoS One 2012; 7:e33695. [PMID: 22448267 PMCID: PMC3308999 DOI: 10.1371/journal.pone.0033695] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 02/20/2012] [Indexed: 11/30/2022] Open
Abstract
Manual counting of bacterial colony forming units (CFUs) on agar plates is laborious and error-prone. We therefore implemented a colony counting system with a novel segmentation algorithm to discriminate bacterial colonies from blood and other agar plates. A colony counter hardware was designed and a novel segmentation algorithm was written in MATLAB. In brief, pre-processing with Top-Hat-filtering to obtain a uniform background was followed by the segmentation step, during which the colony images were extracted from the blood agar and individual colonies were separated. A Bayes classifier was then applied to count the final number of bacterial colonies as some of the colonies could still be concatenated to form larger groups. To assess accuracy and performance of the colony counter, we tested automated colony counting of different agar plates with known CFU numbers of S. pneumoniae, P. aeruginosa and M. catarrhalis and showed excellent performance.
Collapse
Affiliation(s)
- Silvio D Brugger
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| | | | | | | | | | | |
Collapse
|
46
|
Hathaway LJ, Brugger SD, Morand B, Bangert M, Rotzetter JU, Hauser C, Graber WA, Gore S, Kadioglu A, Mühlemann K. Capsule type of Streptococcus pneumoniae determines growth phenotype. PLoS Pathog 2012; 8:e1002574. [PMID: 22412375 PMCID: PMC3297593 DOI: 10.1371/journal.ppat.1002574] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 01/26/2012] [Indexed: 11/19/2022] Open
Abstract
The polysaccharide capsule of Streptococcus pneumoniae defines over ninety serotypes, which differ in their carriage prevalence and invasiveness for poorly understood reasons. Recently, an inverse correlation between carriage prevalence and oligosaccharide structure of a given capsule has been described. Our previous work suggested a link between serotype and growth in vitro. Here we investigate whether capsule production interferes with growth in vitro and whether this predicts carriage prevalence in vivo. Eighty-one capsule switch mutants were constructed representing nine different serotypes, five of low (4, 7F, 14, 15, 18C) and four of high carriage prevalence (6B, 9V, 19F, 23F). Growth (length of lag phase, maximum optical density) of wildtype strains, nontypeable mutants and capsule switch mutants was studied in nutrient-restricted Lacks medium (MLM) and in rich undefined brain heart infusion broth supplemented with 5% foetal calf serum (BHI+FCS). In MLM growth phenotype depended on, and was transferred with, capsule operon type. Colonization efficiency of mouse nasopharynx also depended on, and was transferred with, capsule operon type. Capsule production interfered with growth, which correlated inversely with serotype-specific carriage prevalence. Serotypes with better growth and higher carriage prevalence produced thicker capsules (by electron microscopy, FITC-dextran exclusion assays and HPLC) than serotypes with delayed growth and low carriage prevalence. However, expression of cpsA, the first capsule gene, (by quantitative RT-PCR) correlated inversely with capsule thickness. Energy spent for capsule production (incorporation of H3-glucose) relative to amount of capsule produced was higher for serotypes with low carriage prevalence. Experiments in BHI+FCS showed overall better bacterial growth and more capsule production than growth in MLM and differences between serotypes were no longer apparent. Production of polysaccharide capsule in S. pneumoniae interferes with growth in nutrient-limiting conditions probably by competition for energy against the central metabolism. Serotype-specific nasopharyngeal carriage prevalence in vivo is predicted by the growth phenotype. Streptococcus pneumoniae bacteria are responsible for serious human infections including meningitis, pneumonia and bacteraemia and are a common cause of otitis media (ear infection) in children. However, they most often reside harmlessly in the infant nasopharynx. An association has long been observed between the type of polysaccharide capsule surrounding the bacteria and harmless colonization versus invasive disease. Here we suggest that capsule types that are costly for the bacteria to make are produced in lower quantities and their production limits the growth of the bacteria in nutrient-restricted conditions. In contrast, bacteria with capsules that require less energy can produce more capsule and grow more successfully. This may be an explanation for why S. pneumoniae with certain capsule types can be effective long-term colonizers of the nasopharynx while others need a richer nutritional environment to flourish and so are most often associated with invasive disease. This information may be of use when considering which capsules types to target in future vaccines.
Collapse
Affiliation(s)
- Lucy J. Hathaway
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Silvio D. Brugger
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Brigitte Morand
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Mathieu Bangert
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Christoph Hauser
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Suzanna Gore
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Aras Kadioglu
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Kathrin Mühlemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, University Hospital, Bern, Switzerland
- * E-mail:
| |
Collapse
|
47
|
Abstract
Background. Interspecies interactions of the nasopharyngeal microbiota are likely to be involved in the pathogenesis of acute otitis media (AOM). Capturing the breadth of microbial interactions requires a detailed description of the microbiota during health and AOM. Methods. The nasopharyngeal microbiota of 163 infants with (n = 153) or without (n = 10) AOM was characterized using nasopharyngeal swabs and multiplexed pyrosequencing of 16S rRNA. Nasopharyngeal swab specimens were collected during 4 winter seasons from 2004 through 2010 for infants with AOM and during 2010 for controls. Results. Fifty-eight bacterial families were identified, of which Moraxellaceae, Streptococcaceae, and Pasteurellaceae were the most frequent. Commensal families were less prevalent in infants with AOM than in controls. In infants with AOM, prior exposure to antimicrobials and administration of the heptavalent conjugated pneumococcal polysaccharide vaccine (PCV7) were also associated with reduced prevalence of distinct commensal families (Streptococcaceae and Corynebacteriaceae). In addition, antimicrobial exposure increased the prevalence of Enterobacteriaceae and the abundance of Pasteurellaceae. Other factors, such as age, sex, day care, and a history of recurrent AOM, did not influence the microbiota. Conclusions. Infants’ nasopharyngeal microbiota undergoes significant changes during AOM and after exposure to antimicrobials and PCV7, which is mainly attributable to reduced prevalence of commensal bacterial families.
Collapse
Affiliation(s)
- Markus Hilty
- Institute for Infectious Diseases, University of Berne, Berne, Switzerland.
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Valente C, Hinds J, Pinto F, Brugger SD, Gould K, Mühlemann K, de Lencastre H, Sá-Leão R. Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine. PLoS One 2012; 7:e30235. [PMID: 22253924 PMCID: PMC3257259 DOI: 10.1371/journal.pone.0030235] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 12/12/2011] [Indexed: 11/18/2022] Open
Abstract
Understanding the epidemiology of pneumococcal co-colonization is important for monitoring vaccine effectiveness and the occurrence of horizontal gene transfer between pneumococcal strains. In this study we aimed to evaluate the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal co-colonization among Portuguese children. Nasopharyngeal samples from children up to 6 years old yielding a pneumococcal culture were clustered into three groups: pre-vaccine era (n = 173), unvaccinated children of the vaccine era (n = 169), and fully vaccinated children (4 doses; n = 150). Co-colonization, serotype identification, and relative serotype abundance were detected by analysis of DNA of the total bacterial growth of the primary culture plate using the plyNCR-RFLP method and a molecular serotyping microarray-based strategy. The plyNCR-RFLP method detected an overall co-colonization rate of 20.1%. Microarray analysis confirmed the plyNCR-RFLP results. Vaccination status was the only factor found to be significantly associated with co-colonization: co-colonization rates were significantly lower (p = 0.004; Fisher's exact test) among fully vaccinated children (8.0%) than among children from the pre-PCV7 era (17.3%) or unvaccinated children of the PCV7 era (18.3%). In the PCV7 era there were significantly less non-vaccine type (NVT) co-colonization events than would be expected based on the NVT distribution observed in the pre-PCV7 era (p = 0.024). In conclusion, vaccination with PCV7 resulted in a lower co-colonization rate due to an asymmetric distribution between NVTs found in single and co-colonized samples. We propose that some NVTs prevalent in the PCV7 era are more competitive than others, hampering their co-existence in the same niche. This result may have important implications since a decrease in co-colonization events is expected to translate in decreased opportunities for horizontal gene transfer, hindering pneumococcal evolution events such as acquisition of antibiotic resistance determinants or capsular switch. This might represent a novel potential benefit of conjugate vaccines.
Collapse
Affiliation(s)
- Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jason Hinds
- Bacterial Microarray Group, St. George's, University of London, London, United Kingdom
| | - Francisco Pinto
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Silvio D. Brugger
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Katherine Gould
- Bacterial Microarray Group, St. George's, University of London, London, United Kingdom
| | - Kathrin Mühlemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
| |
Collapse
|
49
|
Brugger SD, Frey P, Aebi S, Hinds J, Mühlemann K. Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine. PLoS One 2010; 5:e11638. [PMID: 20661289 PMCID: PMC2905437 DOI: 10.1371/journal.pone.0011638] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 06/23/2010] [Indexed: 01/26/2023] Open
Abstract
Background Simultaneous carriage of more than one strain of Streptococcus pneumoniae promotes horizontal gene transfer events and may lead to capsule switch and acquisition of antibiotic resistance. We studied the epidemiology of cocolonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal vaccine (PCV7). Methodology Nasopharyngeal swabs (n 1120) were collected from outpatients between 2004 and 2009 within an ongoing nationwide surveillance program. Cocolonization was detected directly from swabs by restriction fragment length polymorphism (RFLP) analysis. Serotypes were identified by agglutination, multiplex PCR and microarray. Principal Findings Rate of multiple colonization remained stable up to three years after PCV7 introduction. Cocolonization was associated with serotypes of low carriage prevalence in the prevaccine era. Pneumococcal colonization density was higher in cocolonized samples and cocolonizing strains were present in a balanced ratio (median 1.38). Other characteristics of cocolonization were a higher frequency at young age, but no association with recurrent acute otitis media, recent antibiotic exposure, day care usage and PCV7 vaccination status. Conclusions Pneumococcal cocolonization is dominated by serotypes of low carriage prevalence in the prevaccine era, which coexist in the nasopharynx. Emergence of such previously rare serotypes under vaccine selection pressure may promote cocolonization in the future.
Collapse
Affiliation(s)
- Silvio D. Brugger
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pascal Frey
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jason Hinds
- Division of Cellular and Molecular Medicine, St. George's, University of London, London, United Kingdom
| | - Kathrin Mühlemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, University Hospital, Bern, Switzerland
- * E-mail:
| |
Collapse
|