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Turk T, Labarile M, Braun DL, Rauch A, Stöckle M, Cavassini M, Hoffmann M, Calmy A, Bernasconi E, Notter J, Pasin C, Günthard HF, Kouyos RD. Characterization and Determinants of Long-Term Immune Recovery Under Suppressive Antiretroviral Therapy. J Acquir Immune Defic Syndr 2024; 96:68-76. [PMID: 38301637 DOI: 10.1097/qai.0000000000003388] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
OBJECTIVE We developed a robust characterization of immune recovery trajectories in people living with HIV on antiretroviral treatment (ART) and relate our findings to epidemiological risk factors and bacterial pneumonia. METHODS Using data from the Swiss HIV Cohort Study and the Zurich Primary HIV Infection Cohort Study (n = 5907), we analyzed the long-term trajectories of CD4 cell and CD8 cell counts and their ratio in people living with HIV on ART for at least 8 years by fitting nonlinear mixed-effects models. The determinants of long-term immune recovery were investigated using generalized additive models. In addition, prediction accuracy of the modeled trajectories and their impact on the fit of a model for bacterial pneumonia was assessed. RESULTS Overall, our population showed good immune recovery (median plateau [interquartile range]-CD4: 718 [555-900] cells/μL, CD8: 709 [547-893] cells/μL, CD4/CD8: 1.01 [0.76-1.37]). The following factors were predictive of recovery: age, sex, nadir/zenith value, pre-ART HIV-1 viral load, hepatitis C, ethnicity, acquisition risk, and timing of ART initiation. The fitted models proved to be an accurate and efficient way of predicting future CD4 and CD8 cell recovery dynamics: Compared with carrying forward the last observation, mean squared errors of the fitted values were lower by 1.3%-18.3% across outcomes. When modeling future episodes of bacterial pneumonia, using predictors derived from the recovery dynamics improved most model fits. CONCLUSION We described and validated a method to characterize individual immune recovery trajectories of people living with HIV on suppressive ART. These trajectories accurately predict long-term immune recovery and the occurrence of bacterial pneumonia.
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Affiliation(s)
- Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marco Labarile
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Matthias Hoffmann
- Clinic for Infectious Diseases, Cantonal Hospital Olten, Olten, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, Geneva University Hospital, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Lugano, Switzerland
- University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland ; and
| | | | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Künzler-Heule P, Schmidt AJ, Fierz K, Battegay M, Engberg S, Kouyos RD, Nöstlinger C, Stöckle M, Béguelin C, Delaloye J, Schmid P, Rougemont M, Braun DL, Fehr JS, Nicca D. Exploring group differences in the response to a sexual risk reduction intervention to prevent hepatitis C virus reinfection in HIV-infected MSM: a mixed-methods study. AIDS Care 2024; 36:442-451. [PMID: 37182220 DOI: 10.1080/09540121.2023.2208318] [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: 05/05/2021] [Accepted: 04/21/2023] [Indexed: 05/16/2023]
Abstract
To prevent hepatitis C virus (HCV) reinfection, within the Swiss HCVree Trial, a preventive risk reduction intervention was implemented alongside curative treatment. Formative qualitative research identified three response patterns to the intervention. This mixed-methods study's aim was to cross-validate group differences in (a) the content of sexual risk reduction goals set during intervention and (b) the extent of their behavioural change in condomless anal intercourse with non-steady partners (nsCAI), sexualised and intravenous drug use at start and six-month post-intervention. Qualitative thematic analysis was used to summarise goal setting domains. Quantitative descriptive analysis was used to evaluate group differences based on assumptions of the group descriptions. Results largely confirmed assumptions on inter-group response differences in goal setting and behaviour: as expected group 1 Avoid risks showed the lowest HCV risk profile with changes in nsCAI. Group 2 Minimize-risks and Group 3 Accept-risks showed unchanged nsCAI. Group 3 had the highest HCV risk profile. Differences in their goal preferences (1: condom use; 2 reduction blood exposure; 3 safer dating) highlight diversity in attitudes to behavioural change. Our results improve understanding of variability in intervention responses such as changes in attitudes and behaviour. This provides evidence for intervention tailoring and outcome measurement.
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Affiliation(s)
- Patrizia Künzler-Heule
- Nursing Science, Department Public Health, Medical Faculty, University of Basel, Basel, Switzerland
- Department of Gastroenterology/Hepatology and Department of Nursing Development, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Axel J Schmidt
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Sigma Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Katharina Fierz
- Zurich University of Applied Sciences (ZUAS), Winterthur, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Medical Faculty, University of Basel, Basel, Switzerland
| | - Sandra Engberg
- Nursing Science, Department Public Health, Medical Faculty, University of Basel, Basel, Switzerland
- University of Pittsburgh, School of Nursing, Pittsburgh, PA, USA
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | | | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Medical Faculty, University of Basel, Basel, Switzerland
| | - Charles Béguelin
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Julie Delaloye
- Intensive Care Unit, Department of Intensive Care Medicine, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Mathieu Rougemont
- Primary Care Medicine Unit, University Hospital of Geneva, Geneva, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jan S Fehr
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Department of Public & Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Dunja Nicca
- Nursing Science, Department Public Health, Medical Faculty, University of Basel, Basel, Switzerland
- Department of Public & Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
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Zeeb M, Frischknecht P, Huber M, Schenkel CD, Neumann K, Leeman C, Notter J, Rauch A, Stöckle M, Cavassini M, Bernasconi E, Braun DL, Günthard HF, Metzner KJ, Kouyos RD. Genetic diversity from proviral DNA as a proxy for time since HIV-1 infection. J Infect Dis 2024:jiae149. [PMID: 38507572 DOI: 10.1093/infdis/jiae149] [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] [Received: 11/17/2023] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
HIV-1 RNA genetic diversity predicts time since infection which is important for clinical care and research. It's unclear, however, whether proviral DNA genetic diversity sampled under suppressive antiretroviral therapy can be used for this purpose. We tested whether proviral genetic diversity from NGS sequences predicts time since infection and recency in 221 people with HIV-1 with known infection time. Proviral diversity was significantly associated with time since infection (p<5*10-07, R2 up to 25%) and predictive of treatment initiation during recent infection (AUC-ROC up to 0.85). This shows the utility of proviral genetic diversity as a proxy for time since infection.
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Affiliation(s)
- Marius Zeeb
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Paul Frischknecht
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Corinne D Schenkel
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Kathrin Neumann
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Christine Leeman
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, 9007 St. Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
- Medical Faculty, University of Basel, 4031 Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, 1011 Lausanne, Switzerland
| | - Enos Bernasconi
- Division of infectious diseases, Ente Ospedaliero Cantonale, Lugano, University of Geneva and University of Southern Switzerland, 6900 Lugano, Switzerland
| | - Dominique L Braun
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Huldrych F Günthard
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Roger D Kouyos
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
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Tepekule Mueller B, Joerimann L, Schenkel CD, Opitz L, Tschumi J, Wolfensberger R, Neumann K, Kusejko K, Zeeb M, Boeck L, Kaelin M, Notter J, Furrer H, Hoffmann M, Hirsch HH, Calmy A, Cavassini M, Labhardt ND, Bernasconi E, Metzner KJ, Braun DL, Guenthard HF, Kouyos RD, Duffy F, Nemeth J. Mycobacterium tuberculosis infection associated immune perturbations correlate with antiretroviral immunity. bioRxiv 2024:2023.07.14.548872. [PMID: 37649906 PMCID: PMC10465018 DOI: 10.1101/2023.07.14.548872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Infection with Mycobacterium tuberculosis (MTB) remains one of the most important opportunistic infections in people with HIV-1 (PWH). While active Tuberculosis (TB) leads to rapid progression of immunodeficiency in PWH, the interaction between MTB and HIV-1 during the asymptomatic phase of both infections remains poorly understood. In a cohort of individuals with HIV (PWH) with and without suppressed HIV-1 viral load, the transcriptomic profiles of peripheral blood mononuclear cells (PBMC) clustered in individuals infected with Mycobacterium tuberculosis (MTB) compared to carefully matched controls. Subsequent functional annotation analysis disclosed alterations in the IL-6, TNF, and KRAS pathways. Notably, MTB-associated genes demonstrated an inverse correlation with HIV-1 viremia, evident at both on individual gene level and when employed as a gene score. In sum, our data show that MTB infection in PWH is associated with a shift in the activation state of the immune system, displaying an inverse relationship with HIV-1 viral load. These results could provide an explanation for the observed increased antiretroviral control associated with MTB infection in PWH.
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Kusejko K, Neofytos D, van Delden C, Hirsch HH, Meylan P, Boggian K, Hirzel C, Garzoni C, Sidler D, Schnyder A, Schaub S, Golshayan D, Haidar F, Bonani M, Kouyos RD, Mueller NJ, Schreiber PW. Do Infectious Diseases After Kidney Retransplantation Differ From Those After First Kidney Transplantation? Open Forum Infect Dis 2024; 11:ofae055. [PMID: 38464489 PMCID: PMC10923290 DOI: 10.1093/ofid/ofae055] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/29/2024] [Indexed: 03/12/2024] Open
Abstract
Background Infectious diseases (IDs) are highly relevant after solid organ transplantation in terms of morbidity and mortality, being among the most common causes of death. Patients undergoing kidney retransplantation (re-K-Tx) have been already receiving immunosuppressive therapy over a prolonged period, potentially facilitating subsequent infections. Comparing ID events after re-K-Tx and first kidney transplantation (f-K-Tx) can delineate patterns and risks of ID events associated with prolonged immunosuppression. Methods We included adult patients with records on f-K-Tx and re-K-Tx in the Swiss Transplant Cohort Study. We analyzed ID events after f-K-Tx and re-K-Tx within the same patients and compared infection rates, causative pathogens, and infection sites. Recurrent time-to-event analyses were performed for comparison of infection rates. Results A total of 59 patients with a median age of 47 years (range, 18-73) were included. Overall, 312 ID events in 52 patients occurred. In multivariable recurrent event modeling, the rate of ID events was significantly lower after re-K-Tx (hazard ratio, 0.70; P = .02). More bacterial (68.9% vs 60.4%) and fungal (4.0% vs 1.1%) infections were observed after f-K-Tx but fewer viral infections (27.0% vs 38.5%) as compared with re-K-Tx (P = .11). After f-K-Tx, urinary and gastrointestinal tract infections were more frequent; after re-K-Tx, respiratory tract and surgical site infections were more frequent (P < .001). Conclusions ID events were less frequent after re-K-Tx. Affected sites differed significantly after f-K-Tx vs re-K-Tx.
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Affiliation(s)
- Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Christian van Delden
- Division of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Hans H Hirsch
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Virology, Laboratory Medicine/Infectious Diseases, and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Pascal Meylan
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Katia Boggian
- Division of Infectious Diseases, Infection Prevention and Travel Medicine, Cantonal Hospital of St Gallen, St Gallen, Switzerland
| | - Cedric Hirzel
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christian Garzoni
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Internal Medicine, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Daniel Sidler
- Division of Nephrology and Hypertension, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Aurelia Schnyder
- Clinic for Nephrology, Cantonal Hospital of St Gallen, St Gallen, Switzerland
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Déla Golshayan
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Fadi Haidar
- Division of Nephrology, Department of Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Marco Bonani
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Peter W Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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Abela IA, Schwarzmüller M, Ulyte A, Radtke T, Haile SR, Ammann P, Raineri A, Rueegg S, Epp S, Berger C, Böni J, Manrique A, Audigé A, Huber M, Schreiber PW, Scheier T, Fehr J, Weber J, Rusert P, Günthard HF, Kouyos RD, Puhan MA, Kriemler S, Trkola A, Pasin C. Cross-protective HCoV immunity reduces symptom development during SARS-CoV-2 infection. mBio 2024; 15:e0272223. [PMID: 38270455 PMCID: PMC10865973 DOI: 10.1128/mbio.02722-23] [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: 10/05/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Numerous clinical parameters link to severe coronavirus disease 2019, but factors that prevent symptomatic disease remain unknown. We investigated the impact of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and endemic human coronavirus (HCoV) antibody responses on symptoms in a longitudinal children cohort (n = 2,917) and a cross-sectional cohort including children and adults (n = 882), all first exposed to SARS-CoV-2 (March 2020 to March 2021) in Switzerland. Saliva (n = 4,993) and plasma (n = 7,486) antibody reactivity to the four HCoVs (subunit S1 [S1]) and SARS-CoV-2 (S1, receptor binding domain, subunit S2 [S2], nucleocapsid protein) was determined along with neutralizing activity against SARS-CoV-2 Wuhan, Alpha, Delta, and Omicron (BA.2) in a subset of individuals. Inferred recent SARS-CoV-2 infection was associated with a strong correlation between mucosal and systemic SARS-CoV-2 anti-spike responses. Individuals with pre-existing HCoV-S1 reactivity exhibited significantly higher antibody responses to SARS-CoV-2 in both plasma (IgG regression coefficients = 0.20, 95% CI = [0.09, 0.32], P < 0.001) and saliva (IgG regression coefficient = 0.60, 95% CI = [0.088, 1.11], P = 0.025). Saliva neutralization activity was modest but surprisingly broad, retaining activity against Wuhan (median NT50 = 32.0, 1Q-3Q = [16.4, 50.2]), Alpha (median NT50 = 34.9, 1Q-3Q = [26.0, 46.6]), and Delta (median NT50 = 28.0, 1Q-3Q = [19.9, 41.7]). In line with a rapid mucosal defense triggered by cross-reactive HCoV immunity, asymptomatic individuals presented with higher pre-existing HCoV-S1 activity in plasma (IgG HKU1, odds ratio [OR] = 0.53, 95% CI = [0.29,0.97], P = 0.038) and saliva (total HCoV, OR = 0.55, 95% CI = [0.33, 0.91], P = 0.019) and higher SARS-CoV-2 reactivity in saliva (IgG S2 fold change = 1.26, 95% CI = [1.03, 1.54], P = 0.030). By investigating the systemic and mucosal immune responses to SARS-CoV-2 and HCoVs in a population without prior exposure to SARS-CoV-2 or vaccination, we identified specific antibody reactivities associated with lack of symptom development.IMPORTANCEKnowledge of the interplay between human coronavirus (HCoV) immunity and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection is critical to understanding the coexistence of current endemic coronaviruses and to building knowledge potential future zoonotic coronavirus transmissions. This study, which retrospectively analyzed a large cohort of individuals first exposed to SARS-CoV-2 in Switzerland in 2020-2021, revealed several key findings. Pre-existing HCoV immunity, particularly mucosal antibody responses, played a significant role in improving SARS-CoV-2 immune response upon infection and reducing symptoms development. Mucosal neutralizing activity against SARS-CoV-2, although low in magnitude, retained activity against SARS-CoV-2 variants underlining the importance of maintaining local mucosal immunity to SARS-CoV-2. While the cross-protective effect of HCoV immunity was not sufficient to block infection by SARS-CoV-2, the present study revealed a remarkable impact on limiting symptomatic disease. These findings support the feasibility of generating pan-protective coronavirus vaccines by inducing potent mucosal immune responses.
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Affiliation(s)
- Irene A. Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Agne Ulyte
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Thomas Radtke
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Sarah R. Haile
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Priska Ammann
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Alessia Raineri
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Sonja Rueegg
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Amapola Manrique
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Annette Audigé
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter W. Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, 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 Fehr
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Jacqueline Weber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F. Günthard
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Milo A. Puhan
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Susi Kriemler
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Collegium Helveticum, Zurich, Switzerland
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7
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Freind MC, Tallón de Lara C, Kouyos RD, Wimmersberger D, Kuster H, Aceto L, Kovari H, Flepp M, Schibli A, Hampel B, Grube C, Braun DL, Günthard HF. Cohort Profile: The Zurich Primary HIV Infection Study. Microorganisms 2024; 12:302. [PMID: 38399706 PMCID: PMC10893142 DOI: 10.3390/microorganisms12020302] [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] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The Zurich Primary HIV Infection (ZPHI) study is a longitudinal cohort study established in 2002, aiming to study the clinical, epidemiological, and biological characteristics of primary HIV infection. The ZPHI enrolls individuals with documented primary HIV-1 infection. At the baseline and thereafter, the socio-demographic, clinical, and laboratory data are systematically collected, and regular blood sampling is performed for biobanking. By the end of December 2022, 486 people were enrolled, of which 353 were still undergoing active follow-up. Of the 486 participants, 86% had an acute infection, and 14% a recent HIV-1 infection. Men who have sex with men accounted for 74% of the study population. The median time from the estimated date of infection to diagnosis was 32 days. The median time from diagnosis to the initiation of antiretroviral therapy was 11 days, and this has consistently decreased over the last two decades. During the seroconversion phase, 447 (92%) patients reported having symptoms, of which only 73% of the patients were classified as having typical acute retroviral syndrome. The ZPHI study is a well-characterized cohort belonging to the most extensively studied primary HIV infection cohort. Its findings contribute to advancing our understanding of the early stages of HIV infection and pathogenesis, and it is paving the way to further improve HIV translational research and HIV medicine.
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Affiliation(s)
- Matt C. Freind
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Carmen Tallón de Lara
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
| | - David Wimmersberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Hebert Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Leonardo Aceto
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Helen Kovari
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Markus Flepp
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Adrian Schibli
- Department of Infectious Diseases, Hospital Epidemiology and Occupational Health, City Hospital Zurich, 8091 Zurich, Switzerland;
| | | | | | - Dominique L. Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
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8
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Abela IA, Hauser A, Schwarzmüller M, Pasin C, Kusejko K, Epp S, Cavassini M, Battegay M, Rauch A, Calmy A, Notter J, Bernasconi E, Fux CA, Leuzinger K, Perreau M, Ramette A, Gottschalk J, Schindler E, Wepf A, Marconato M, Manz MG, Frey BM, Braun DL, Huber M, Günthard HF, Trkola A, Kouyos RD. Deciphering factors linked with reduced SARS-CoV-2 susceptibility in the Swiss HIV Cohort Study. J Infect Dis 2024:jiae002. [PMID: 38227786 DOI: 10.1093/infdis/jiae002] [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] [Received: 07/20/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Factors influencing susceptibility to SARS-CoV-2 remain to be resolved. Using data of the Swiss HIV Cohort Study (SHCS) on 6,270 people with HIV (PWH) and serologic assessment for SARS-CoV-2 and circulating-human-coronavirus (HCoV) antibodies, we investigated the association of HIV-related and general parameters with SARS-CoV-2 infection. METHODS We analyzed SARS-CoV-2 PCR-tests, COVID-19 related hospitalizations, and deaths reported to the SHCS between January 1, 2020 and December 31, 2021. Antibodies to SARS-CoV-2 and HCoVs were determined in pre-pandemic (2019) and pandemic (2020) bio-banked plasma and compared to HIV-negative individuals. We applied logistic regression, conditional logistic regression, and Bayesian multivariate regression to identify determinants of SARS-CoV-2 infection and Ab responses to SARS-CoV-2 in PWH. RESULTS No HIV-1-related factors were associated with SARS-CoV-2 acquisition. High pre-pandemic HCoV antibodies were associated with a lower risk of subsequent SARS-CoV-2 infection and with higher SARS-CoV-2 antibody responses upon infection. We observed a robust protective effect of smoking on SARS-CoV-2-infection risk (aOR= 0.46 [0.38,0.56], p=2.6*10-14), which occurred even in previous smokers, and was highest for heavy smokers. CONCLUSIONS Our findings of two independent protective factors, smoking and HCoV antibodies, both affecting the respiratory environment, underscore the importance of the local immune milieu in regulating susceptibility to SARS-CoV-2.
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Affiliation(s)
- Irene A Abela
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Anthony Hauser
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Chloé Pasin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Collegium Helveticum, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Christoph A Fux
- Department of Infectious Diseases, Kantonsspital Aarau, Aarau, Switzerland
| | | | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | | | - Alexander Wepf
- Institute of Laboratory Medicine, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Maddalena Marconato
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Beat M Frey
- Blood Transfusion Service Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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9
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Hovaguimian F, Kouyos RD, Kusejko K, Schmidt AJ, Tarr PE, Bernasconi E, Braun DL, Calmy A, Notter J, Stoeckle M, Surial B, Christinet V, Darling KEA, Depmeier C, Läuchli S, Reinacher M, Rasi M, Nicca D, Bruggmann P, Haerry D, Bize R, Low N, Vock F, El Amari EB, Böni J, Bosshard PP, Fehr JS, Hampel B. Incidence of sexually transmitted infections and association with behavioural factors: Time-to-event analysis of a large pre-exposure prophylaxis (PrEP) cohort. HIV Med 2024; 25:117-128. [PMID: 37771207 DOI: 10.1111/hiv.13543] [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: 03/24/2023] [Accepted: 09/01/2023] [Indexed: 09/30/2023]
Abstract
OBJECTIVES Our objective was to obtain long-term data on the incidence of sexually transmitted infections (STIs) and their association with behavioural factors after widespread pre-exposure prophylaxis (PrEP) implementation. METHODS This was a time-to-event analysis of a national PrEP cohort in Switzerland (SwissPrEPared study). Participants were people without HIV interested in taking PrEP with at least two STI screening visits. Primary outcomes were incidence rate of gonorrhoea, chlamydia, and syphilis. The association between behavioural factors and STI diagnosis was expressed using hazard ratios. We adjusted for testing frequency and calendar year. RESULTS This analysis included 3907 participants enrolled between April 2019 and April 2022, yielding 3815.7 person-years of follow-up for gonorrhoea (15 134 screenings), 3802.5 for chlamydia (15 141 screenings), and 3858.6 for syphilis (15 001 screenings). The median age was 39 years (interquartile range [IQR] 32-47), 93.8% (n = 3664) identified as men who have sex with men (MSM). The incidence was 22.8 (95% confidence interval [CI] 21.3-24.4) per 100 person-years for gonorrhoea, 26.3 (95% CI 24.7-28.0) for chlamydia, and 4.4 (95% CI 3.8-5.1) for syphilis. Yearly incidence rates decreased between 2019 (all bacterial STIs: 81.6; 95% CI 59.1-109.9) and 2022 (all bacterial STIs: 49.8; 95% CI 44.6-55.3). Participants reporting chemsex substance use were at higher risk of incident STIs, as were those reporting multiple sexual partners. Younger age was associated with a higher risk of gonorrhoea and chlamydia. CONCLUSIONS Incidence rates of bacterial STIs decreased over time. Young MSM, those with multiple partners, and those using chemsex substances were at increased risk of STIs.
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Affiliation(s)
- Frédérique Hovaguimian
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Axel J Schmidt
- Sigma Research, London School of Hygiene and Tropical Medicine, London, UK
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Philip E Tarr
- Kantonsspital Baselland, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedialiero Cantonale, Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Marcel Stoeckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Bernard Surial
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Katharine E A Darling
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Severin Läuchli
- Dermatologic Center Zurich, Zurich, Switzerland
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias Reinacher
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Manuela Rasi
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Dunja Nicca
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | | | | | - Raphaël Bize
- Department of Epidemiology and Health Systems, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Philipp P Bosshard
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jan S Fehr
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Benjamin Hampel
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
- Checkpoint Zurich, Zurich, Switzerland
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10
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Zeeb M, Tepekule B, Kusejko K, Reiber C, Kälin M, Bartl L, Notter J, Furrer H, Hoffmann M, Hirsch HH, Calmy A, Cavassini M, Labhardt ND, Bernasconi E, Braun DL, Günthard HF, Kouyos RD, Nemeth J. Understanding the Decline of Incident, Active Tuberculosis in People With Human Immunodeficiency Virus in Switzerland. Clin Infect Dis 2023; 77:1303-1311. [PMID: 37257071 PMCID: PMC10640694 DOI: 10.1093/cid/ciad330] [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: 01/25/2023] [Revised: 05/03/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND People with human immunodeficiency virus type 1 (HIV-1) (PWH) are frequently coinfected with Mycobacterium tuberculosis (MTB) and at risk for progressing from asymptomatic latent TB infection (LTBI) to active tuberculosis (TB). LTBI testing and preventive treatment (TB specific prevention) are recommended, but its efficacy in low transmission settings is unclear. METHODS We included PWH enrolled from 1988 to 2022 in the Swiss HIV Cohort study (SHCS). The outcome, incident TB, was defined as TB ≥6 months after SHCS inclusion. We assessed its risk factors using a time-updated hazard regression, modeled the potential impact of modifiable factors on TB incidence, performed mediation analysis to assess underlying causes of time trends, and evaluated preventive measures. RESULTS In 21 528 PWH, LTBI prevalence declined from 15.1% in 2001% to 4.6% in 2021. Incident TB declined from 90.8 cases/1000 person-years in 1989 to 0.1 in 2021. A positive LTBI test showed a higher risk for incident TB (hazard ratio [HR] 9.8, 5.8-16.5) but only 10.5% of PWH with incident TB were tested positive. Preventive treatment reduced the risk in LTBI test positive PWH for active TB (relative risk reduction, 28.1%, absolute risk reduction 0.9%). On population level, the increase of CD4 T-cells and reduction of HIV viral load were the main driver of TB decrease. CONCLUSIONS TB specific prevention is effective in selected patient groups. On a population level, control of HIV-1 remains the most important factor for incident TB reduction. Accurate identification of PWH at highest risk for TB is an unmet clinical need.
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Affiliation(s)
- Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Burcu Tepekule
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Claudine Reiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Marisa Kälin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Lena Bartl
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St. Gallen, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Hoffmann
- Clinic for Infectious Diseases, Cantonal Hospital Olten, Olten, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
- Department Biomedicine, Transplantation and Clinical Virology, University of Basel, Basel, Switzerland
| | - Alexandra Calmy
- HIV/AIDS Unit, Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Niklaus D Labhardt
- Division of Clinical Epidemiology, Department of Clinical Research, University Hospital Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Infectious Diseases, Ente Ospedaliero Cantonale Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Nemeth
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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11
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Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d'Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos RD. HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis. Lancet HIV 2023; 10:e733-e741. [PMID: 37832567 PMCID: PMC10913014 DOI: 10.1016/s2352-3018(23)00228-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir in first-line and second-line antiretroviral therapy (ART) might facilitate emerging resistance. The DTG RESIST study combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for dolutegravir resistance. METHODS We included cohorts with INSTI resistance data from two collaborations (ART Cohort Collaboration, International epidemiology Databases to Evaluate AIDS in Southern Africa), and the UK Collaborative HIV Cohort. Eight cohorts from Canada, France, Germany, Italy, the Netherlands, Switzerland, South Africa, and the UK contributed data on individuals who were viraemic on dolutegravir-based ART and underwent genotypic resistance testing. Individuals with unknown dolutegravir initiation date were excluded. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. FINDINGS We included 599 people with genotypic resistance testing on dolutegravir-based ART between May 22, 2013, and Dec 20, 2021. Most had HIV-1 subtype B (n=351, 59%), a third had been exposed to first-generation INSTIs (n=193, 32%), 70 (12%) were on dolutegravir dual therapy, and 18 (3%) were on dolutegravir monotherapy. INSTI DRMs were detected in 86 (14%) individuals; 20 (3%) had more than one mutation. Most (n=563, 94%) were susceptible to dolutegravir, seven (1%) had potential low, six (1%) low, 17 (3%) intermediate, and six (1%) high-level dolutegravir resistance. The risk of dolutegravir resistance was higher on dolutegravir monotherapy (adjusted odds ratio [aOR] 34·1, 95% CI 9·93-117) and dolutegravir plus lamivudine dual therapy (aOR 9·21, 2·20-38·6) compared with combination ART, and in the presence of potential low or low (aOR 5·23, 1·32-20·7) or intermediate or high-level (aOR 13·4, 4·55-39·7) nucleoside reverse transcriptase inhibitor (NRTI) resistance. INTERPRETATION Among people with viraemia on dolutegravir-based ART, INSTI DRMs and dolutegravir resistance were rare. NRTI resistance substantially increased the risk of dolutegravir resistance, which is of concern, notably in resource-limited settings. Monitoring is important to prevent resistance at the individual and population level and ensure the long-term sustainability of ART. FUNDING US National Institutes of Health, Swiss National Science Foundation.
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Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Suzanne M Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany; Department I of Internal Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - M John Gill
- Southern Alberta Clinic, Calgary, AB, Canada; Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jonathan A C Sterne
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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12
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Siedentop B, Kachalov VN, Witzany C, Egger M, Kouyos RD, Bonhoeffer S. The effect of combining antibiotics on resistance: A systematic review and meta-analysis. medRxiv 2023:2023.07.10.23292374. [PMID: 37503165 PMCID: PMC10370225 DOI: 10.1101/2023.07.10.23292374] [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] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
When and under which conditions antibiotic combination therapy decelerates rather than accelerates resistance evolution is not well understood. We examined the effect of combining antibiotics on within-patient resistance development across various bacterial pathogens and antibiotics. We searched CENTRAL, EMBASE and PubMed for (quasi)-randomised controlled trials (RCTs) published from database inception to November 24th, 2022. Trials comparing antibiotic treatments with different numbers of antibiotics were included. A patient was considered to have acquired resistance if, at the follow-up culture, a resistant bacterium was detected that had not been present in the baseline culture. We combined results using a random effects model and performed meta-regression and stratified analyses. The trials' risk of bias was assessed with the Cochrane tool. 42 trials were eligible and 29, including 5054 patients, were qualified for statistical analysis. In most trials, resistance development was not the primary outcome and studies lacked power. The combined odds ratio (OR) for the acquisition of resistance comparing the group with the higher number of antibiotics with the comparison group was 1.23 (95% CI 0.68-2.25), with substantial between-study heterogeneity (I2 =77%). We identified tentative evidence for potential beneficial or detrimental effects of antibiotic combination therapy for specific pathogens or medical conditions. The evidence for combining a higher number of antibiotics compared to fewer from RCTs is scarce and overall, is compatible with both benefit or harm. Trials powered to detect differences in resistance development or well-designed observational studies are required to clarify the impact of combination therapy on resistance.
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Affiliation(s)
- Berit Siedentop
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Viacheslav N. Kachalov
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christopher Witzany
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
- Population Health Sciences, University of Bristol, Bristol, UK
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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13
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Brown JA, Hauser A, Abela IA, Pasin C, Epp S, Mohloanyane T, Nsakala BL, Trkola A, Labhardt ND, Kouyos RD, Günthard HF. Seroprofiling of Antibodies Against Endemic Human Coronaviruses and Severe Acute Respiratory Syndrome Coronavirus 2 in a Human Immunodeficiency Virus Cohort in Lesotho: Correlates of Antibody Response and Seropositivity. J Infect Dis 2023; 228:1042-1054. [PMID: 37261930 PMCID: PMC10582919 DOI: 10.1093/infdis/jiad197] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Serological data on endemic human coronaviruses (HCoVs) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in southern Africa are scarce. Here, we report on (1) endemic HCoV seasonality, (2) SARS-CoV-2 seroprevalence, and (3) correlates of SARS-CoV-2 seropositivity and strength of SARS-CoV-2 and endemic HCoV serological responses among adults living with human immunodeficiency virus (HIV). METHODS Plasma samples were collected from February 2020 to July 2021 within an HIV cohort in Lesotho. We used the AntiBody CORonavirus Assay (ABCORA) multiplex immunoassay to measure antibody responses to endemic HCoV (OC43, HKU1, NL63, and 229E) and SARS-CoV-2 antigens. RESULTS Results for 3173 samples from 1403 adults were included. Serological responses against endemic HCoVs increased over time and peaked in winter and spring. SARS-CoV-2 seropositivity reached >35% among samples collected in early 2021 and was associated with female sex, obesity, working outside the home, and recent tiredness or fever. Positive correlations were observed between the strength of response to endemic HCoVs and to SARS-CoV-2 and between older age or obesity and the immunoglobulin G response to SARS-CoV-2. CONCLUSIONS These results add to our understanding of the impact of biological, clinical, and social/behavioral factors on serological responses to coronaviruses in southern Africa.
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Affiliation(s)
- Jennifer A Brown
- Division of Clinical Epidemiology, Department of Clinical Research, University Hospital Basel, Basel, Switzerland
- Division of Clinical Epidemiology, Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Anthony Hauser
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Irene A Abela
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | | | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niklaus D Labhardt
- Division of Clinical Epidemiology, Department of Clinical Research, University Hospital Basel, Basel, Switzerland
- Division of Clinical Epidemiology, Department of Clinical Research, University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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14
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West E, Zeeb M, Grube C, Kuster H, Wanner K, Scheier T, Neumann K, Jörimann L, Hampel B, Metzner KJ, Kouyos RD, Braun DL, Günthard HF. Sustained Viral Suppression With Dolutegravir Monotherapy Over 192 Weeks in Patients Starting Combination Antiretroviral Therapy During Primary Human Immunodeficiency Virus Infection (EARLY-SIMPLIFIED): A Randomized, Controlled, Multi-site, Noninferiority Trial. Clin Infect Dis 2023; 77:1012-1020. [PMID: 37338148 PMCID: PMC10552587 DOI: 10.1093/cid/ciad366] [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: 02/10/2023] [Revised: 05/01/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Starting combination antiretroviral therapy (cART) during primary human immunodeficiency virus type 1 (HIV-1) infection results in a smaller HIV-1 latent reservoir, reduced immune activation, and less viral diversity compared to starting cART during chronic infection. We report results of a 4-year study designed to determine whether these properties would allow sustained virological suppression after simplification of cART to dolutegravir (DTG) monotherapy. METHODS EARLY-SIMPLIFIED is a randomized, open-label, noninferiority trial. People with HIV (PWH) who started cART <180 days after a documented primary HIV-1 infection with suppressed viral load were randomized (2:1) to DTG monotherapy with 50 mg daily or continuation of cART. The primary endpoints were the proportion of PWH with viral failure at 48, 96, 144, and 192 weeks; noninferiority margin was 10%. After 96 weeks, randomization was lifted and patients were permitted to switch treatment groups as desired. RESULTS Of 101 PWH randomized, 68 were assigned to DTG monotherapy and 33 to cART. At week 96 in the per-protocol population, 64/64 (100%) showed virological response in the DTG monotherapy group versus 30/30 (100%) in the cART group (difference, 0.00%; upper bound of 95% confidence interval 6.22%). This demonstrated noninferiority of DTG monotherapy at the prespecified level. At week 192, the study end, no virological failure occurred in either group during 13 308 and 4897 person weeks of follow-up for the DTG monotherapy (n = 80) and cART groups, respectively. CONCLUSIONS This trial suggests that early cART initiation during primary HIV infection allows sustained virological suppression after switching to DTG monotherapy.
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Affiliation(s)
- Emily West
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christina Grube
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Herbert Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Katrin Wanner
- Department of Infectious Diseases and Hospital Epidemiology, 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
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lisa Jörimann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Benjamin Hampel
- Checkpoint Zurich, Zurich, Switzerland
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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15
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Maliqi L, Friedrich N, Glögl M, Schmutz S, Schmidt D, Rusert P, Schanz M, Zaheri M, Pasin C, Niklaus C, Foulkes C, Reinberg T, Dreier B, Abela I, Peterhoff D, Hauser A, Kouyos RD, Günthard HF, van Gils MJ, Sanders RW, Wagner R, Plückthun A, Trkola A. Assessing immunogenicity barriers of the HIV-1 envelope trimer. NPJ Vaccines 2023; 8:148. [PMID: 37777519 PMCID: PMC10542815 DOI: 10.1038/s41541-023-00746-3] [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] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
Understanding the balance between epitope shielding and accessibility on HIV-1 envelope (Env) trimers is essential to guide immunogen selection for broadly neutralizing antibody (bnAb) based vaccines. To investigate the antigenic space of Env immunogens, we created a strategy based on synthetic, high diversity, Designed Ankyrin Repeat Protein (DARPin) libraries. We show that DARPin Antigenicity Analysis (DANA), a purely in vitro screening tool, has the capability to extrapolate relevant information of antigenic properties of Env immunogens. DANA screens of stabilized, soluble Env trimers revealed that stronger trimer stabilization led to the selection of highly mutated DARPins with length variations and framework mutations mirroring observations made for bnAbs. By mimicking heterotypic prime-boost immunization regimens, DANA may be used to select immunogen combinations that favor the selection of trimer-reactive binders. This positions DANA as a versatile strategy for distilling fundamental antigenic features of immunogens, complementary to preclinical immunogenicity testing.
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Affiliation(s)
- Liridona Maliqi
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Nikolas Friedrich
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Matthias Glögl
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Daniel Schmidt
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Merle Schanz
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Cyrille Niklaus
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - David Peterhoff
- Institute of Clinical Microbiology and Hygiene, University Hospital, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Alexandra Hauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, USA
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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16
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Schwenke JM, Thorball CW, Schoepf IC, Ryom L, Hasse B, Lamy O, Calmy A, Wandeler G, Marzolini C, Kahlert CR, Bernasconi E, Kouyos RD, Günthard HF, Ledergerber B, Fellay J, Burkhalter F, Tarr PE. Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study. J Infect Dis 2023; 228:742-750. [PMID: 37225667 PMCID: PMC10503954 DOI: 10.1093/infdis/jiad179] [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: 02/10/2023] [Revised: 05/14/2023] [Accepted: 06/23/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Bone mineral density (BMD) loss may be accelerated in people with HIV (PLWH). It is unknown whether a polygenic risk score (PRS) is associated with low BMD in PLWH. METHODS Swiss HIV Cohort Study participants of self-reported European descent underwent ≥2 per-protocol dual x-ray absorptiometry (DXA) measurements ≥2 years apart (2011-2020). Univariable and multivariable odds ratios (ORs) for DXA-defined osteoporosis were based on traditional and HIV-related risk factors and a genome-wide PRS built from 9413 single-nucleotide polymorphisms associated with low BMD in the general population. Controls were free from osteoporosis/osteopenia on all DXA measurements. RESULTS We included 438 participants: 149 with osteoporosis and 289 controls (median age, 53 years; 82% male, 95% with suppressed HIV RNA). Participants with unfavorable osteoporosis PRS (top vs bottom quintile) had univariable and multivariable-adjusted osteoporosis ORs of 4.76 (95% CI, 2.34-9.67) and 4.13 (1.86-9.18), respectively. For comparison, hepatitis C seropositivity, 5-year tenofovir disoproxil fumarate exposure, and parent history of hip fracture yielded univariable osteoporosis ORs of 2.26 (1.37-3.74), 1.84 (1.40-2.43), and 1.54 (0.82-2.9). CONCLUSIONS In PLWH in Switzerland, osteoporosis was independently associated with a BMD-associated PRS after adjustment for established risk factors, including exposure to tenofovir disoproxil fumarate.
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Affiliation(s)
- Johannes M Schwenke
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz
| | - Christian W Thorball
- Precision Medicine Unit, Lausanne University Hospital, University of Lausanne
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne
| | - Isabella C Schoepf
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Switzerland
| | - Lene Ryom
- CHIP, Centre of Excellence for Health, Immunity and Infections, Rigshospitalet, University of Copenhagen
- Department of Infectious Diseases, Hvidovre University Hospital, Denmark
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich
| | - Olivier Lamy
- Bone Unit, Lausanne University Hospital, University of Lausanne
| | | | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Switzerland
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel
| | | | - Enos Bernasconi
- Division of Infectious Diseases, Ospedale Regionale Lugano, University of Geneva and Università della Svizzera italiana, Lugano
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich
- Institute of Medical Virology, University of Zurich
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich
- Institute of Medical Virology, University of Zurich
| | - Bruno Ledergerber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital, University of Lausanne
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne
| | - Felix Burkhalter
- University Department of Nephrology and Dialysis, Kantonsspital Baselland, University of Basel,Bruderholz, Switzerland
| | - Philip E Tarr
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz
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17
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Jaha B, Schenkel CD, Jörimann L, Huber M, Zaheri M, Neumann K, Leemann C, Calmy A, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018. J Antimicrob Chemother 2023; 78:2323-2334. [PMID: 37545164 PMCID: PMC10477134 DOI: 10.1093/jac/dkad240] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Genotypic resistance testing (GRT) is routinely performed upon diagnosis of HIV-1 infection or during virological failure using plasma viral RNA. An alternative source for GRT could be cellular HIV-1 DNA. OBJECTIVES A substantial number of participants in the Swiss HIV Cohort Study (SHCS) never received GRT. We applied a method that enables access to the near full-length proviral HIV-1 genome without requiring detectable viraemia. METHODS Nine hundred and sixty-two PBMC specimens were received. Our two-step nested PCR protocol was applied to generate two overlapping long-range amplicons of the HIV-1 genome, sequenced by next-generation sequencing (NGS) and analysed by MinVar, a pipeline to detect drug resistance mutations (DRMs). RESULTS Six hundred and eighty-one (70.8%) of the samples were successfully amplified, sequenced and analysed by MinVar. Only partial information of the pol gene was contained in 82/681 (12%), probably due to naturally occurring deletions in the proviral sequence. All common HIV-1 subtypes were successfully sequenced. We detected at least one major DRM at high frequency (≥15%) in 331/599 (55.3%) individuals. Excluding APOBEC-signature (G-to-A mutation) DRMs, 145/599 (24.2%) individuals carried at least one major DRM. RT-inhibitor DRMs were most prevalent. The experienced time on ART was significantly longer in DRM carriers (P = 0.001) independent of inclusion or exclusion of APOBEC-signature DRMs. CONCLUSIONS We successfully applied a reliable and efficient method to analyse near full-length HIV-1 proviral DNA and investigated DRMs in individuals with undetectable or low viraemia. Additionally, our data underscore the need for new computational tools to exclude APOBEC-related hypermutated NGS sequence reads for reporting DRMs.
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Affiliation(s)
- Bashkim Jaha
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Corinne D Schenkel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lisa Jörimann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Christine Leemann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
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18
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Inzaule SC, Siedner MJ, Little SJ, Avila-Rios S, Ayitewala A, Bosch RJ, Calvez V, Ceccherini-Silberstein F, Charpentier C, Descamps D, Eshleman SH, Fokam J, Frenkel LM, Gupta RK, Ioannidis JP, Kaleebu P, Kantor R, Kassaye SG, Kosakovsky Pond SL, Kouamou V, Kouyos RD, Kuritzkes DR, Lessells R, Marcelin AG, Mbuagbaw L, Minalga B, Ndembi N, Neher RA, Paredes R, Pillay D, Raizes EG, Rhee SY, Richman DD, Ruxrungtham K, Sabeti PC, Schapiro JM, Sirivichayakul S, Steegen K, Sugiura W, van Zyl GU, Vandamme AM, Wensing AM, Wertheim JO, Gunthard HF, Jordan MR, Shafer RW. Recommendations on data sharing in HIV drug resistance research. PLoS Med 2023; 20:e1004293. [PMID: 37738247 PMCID: PMC10558071 DOI: 10.1371/journal.pmed.1004293] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 10/06/2023] [Indexed: 09/24/2023] Open
Abstract
• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens. • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens. • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines. • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing. • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions. • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.
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Affiliation(s)
- Seth C. Inzaule
- Amsterdam Institute for Global Health and Development, and Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark J. Siedner
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan J. Little
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Alisen Ayitewala
- National Health Laboratories and Diagnostic Services, Ministries of Health, Kampala, Uganda
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | | | - Charlotte Charpentier
- Service de Virologie, Université Paris Cité, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Diane Descamps
- Service de Virologie, Université Paris Cité, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon, and Faculty of Health Sciences, University of Buea, Yaoundé, Cameroon
| | - Lisa M. Frenkel
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - John P.A. Ioannidis
- Department of Medicine, Department of Epidemiology and Population Health, and Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, United States of America
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Entebbe, Uganda
| | - Rami Kantor
- Department of Medicine, Brown University, The Miriam Hospital, Providence, Rhode Island, United States of America
| | - Seble G. Kassaye
- Department of Medicine, Division of Infectious Diseases, Georgetown University, Washington DC, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Vinie Kouamou
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Lessells
- Affiliation is KwaZulu-Natal Research Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière—Charles Foix, Laboratoire de Virologie, Paris, France
| | - Lawrence Mbuagbaw
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Brian Minalga
- Office of HIV/AIDS Network Coordination, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Herbert Macaulay Way, Abuja, Nigeria
| | | | - Roger Paredes
- Department of Infectious Diseases & irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Elliot G. Raizes
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Douglas D. Richman
- Center for AIDS Research, Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Kiat Ruxrungtham
- School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | | | - Kim Steegen
- Department of Molecular Medicine and Haematology, National Health Laboratory Service, Johannesburg, South Africa
| | - Wataru Sugiura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Gert U. van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service, Cape Town, South Africa
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health And Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Annemarie M.J. Wensing
- University Medical Center Utrecht, the Netherlands and Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, San Diego, La Jolla, California, United States of America
| | - Huldrych F. Gunthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael R. Jordan
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, United States of America
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19
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Hovaguimian F, Beeler PE, Müllhaupt B, Günthard HF, Maeschli B, Bruggmann P, Fehr JS, Kouyos RD. Mortality and morbidity related to hepatitis C virus infection in hospitalized adults-A propensity score matched analysis. J Viral Hepat 2023; 30:765-774. [PMID: 37309273 DOI: 10.1111/jvh.13861] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023]
Abstract
The World Health Organization (WHO) aims to reduce HCV mortality, but estimates are difficult to obtain. We aimed to identify electronic health records of individuals with HCV infection, and assess mortality and morbidity. We applied electronic phenotyping strategies on routinely collected data from patients hospitalized at a tertiary referral hospital in Switzerland between 2009 and 2017. Individuals with HCV infection were identified using International Classification of Disease (ICD)-10 codes, prescribed medications and laboratory results (antibody, PCR, antigen or genotype test). Controls were selected using propensity score methods (matching by age, sex, intravenous drug use, alcohol abuse and HIV co-infection). Main outcomes were in-hospital mortality and attributable mortality (in HCV cases and study population). The non-matched dataset included records from 165,972 individuals (287,255 hospital stays). Electronic phenotyping identified 2285 stays with evidence of HCV infection (1677 individuals). Propensity score matching yielded 6855 stays (2285 with HCV, 4570 controls). In-hospital mortality was higher in HCV cases (RR 2.10, 95%CI 1.64 to 2.70). Among those infected, 52.5% of the deaths were attributable to HCV (95%CI 38.9 to 63.1). When cases were matched, the fraction of deaths attributable to HCV was 26.9% (HCV prevalence: 33%), whilst in the non-matched dataset, it was 0.92% (HCV prevalence: 0.8%). In this study, HCV infection was strongly associated with increased mortality. Our methodology may be used to monitor the efforts towards meeting the WHO elimination targets and underline the importance of electronic cohorts as a basis for national longitudinal surveillance.
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Affiliation(s)
- Frédérique Hovaguimian
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Patrick E Beeler
- Division of Occupational and Environmental Medicine, Epidemiology, Biostatistics and Prevention Institute, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Center for Primary and Community Care, University of Lucerne, Lucerne, Switzerland
| | - Beat Müllhaupt
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Philip Bruggmann
- Swiss Hepatitis, Zurich, Switzerland
- Arud Centre for Addiction Medicine, Zurich, Switzerland
| | - Jan S Fehr
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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20
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Pasin C, Consiglio CR, Huisman J, de Lange AMG, Peckham H, Vallejo-Yagüe E, Abela IA, Islander U, Neuner-Jehle N, Pujantell M, Roth O, Schirmer M, Tepekule B, Zeeb M, Hachfeld A, Aebi-Popp K, Kouyos RD, Bonhoeffer S. Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications. R Soc Open Sci 2023; 10:221628. [PMID: 37416827 PMCID: PMC10320357 DOI: 10.1098/rsos.221628] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023]
Abstract
Although sex and gender are recognized as major determinants of health and immunity, their role is rarely considered in clinical practice and public health. We identified six bottlenecks preventing the inclusion of sex and gender considerations from basic science to clinical practice, precision medicine and public health policies. (i) A terminology-related bottleneck, linked to the definitions of sex and gender themselves, and the lack of consensus on how to evaluate gender. (ii) A data-related bottleneck, due to gaps in sex-disaggregated data, data on trans/non-binary people and gender identity. (iii) A translational bottleneck, limited by animal models and the underrepresentation of gender minorities in biomedical studies. (iv) A statistical bottleneck, with inappropriate statistical analyses and results interpretation. (v) An ethical bottleneck posed by the underrepresentation of pregnant people and gender minorities in clinical studies. (vi) A structural bottleneck, as systemic bias and discriminations affect not only academic research but also decision makers. We specify guidelines for researchers, scientific journals, funding agencies and academic institutions to address these bottlenecks. Following such guidelines will support the development of more efficient and equitable care strategies for all.
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Affiliation(s)
- Chloé Pasin
- Collegium Helveticum, 8092 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Camila R. Consiglio
- Department of Women's and Children's Health, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Jana S. Huisman
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ann-Marie G. de Lange
- Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
- Department of Psychology, University of Oslo, 0373 Oslo, Norway
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH and GOSH, London WC1E 6JF, UK
| | | | - Irene A. Abela
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Ulrika Islander
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 40530 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Nadia Neuner-Jehle
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Maria Pujantell
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Melanie Schirmer
- Emmy Noether Group for Computational Microbiome Research, ZIEL – Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Burcu Tepekule
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Marius Zeeb
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Anna Hachfeld
- Department of Infectious Diseases, University Hospital and University of Bern, 3012 Bern, Switzerland
| | - Karoline Aebi-Popp
- Department of Infectious Diseases, University Hospital and University of Bern, 3012 Bern, Switzerland
- Department of Obstetrics and Gynecology, Lindenhofspital, 3012 Bern, Switzerland
| | - Roger D. Kouyos
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sebastian Bonhoeffer
- Collegium Helveticum, 8092 Zurich, Switzerland
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
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21
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Avery EF, Kleynhans JN, Ledergerber B, Schoepf IC, Thorball CW, Kootstra NA, Reiss P, Ryom L, Braun DL, Thurnheer MC, Marzolini C, Seneghini M, Bernasconi E, Cavassini M, Buvelot H, Kouyos RD, Fellay J, Günthard HF, Tarr PE. Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study. Clin Infect Dis 2023; 76:1969-1979. [PMID: 36688465 PMCID: PMC10249993 DOI: 10.1093/cid/ciad033] [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: 08/26/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND People with human immunodeficiency virus (HIV; PWH) have increased cardiovascular risk. Higher leukocyte count has been associated with coronary artery disease (CAD) events in the general population. It is unknown whether the leukocyte-CAD association also applies to PWH. METHODS In a case-control study nested within the Swiss HIV Cohort Study, we obtained uni- and multivariable odds ratios (OR) for CAD events, based on traditional and HIV-related CAD risk factors, leukocyte count, and confounders previously associated with leukocyte count. RESULTS We included 536 cases with a first CAD event (2000-2021; median age, 56 years; 87% male; 84% with suppressed HIV RNA) and 1464 event-free controls. Cases had higher latest leukocyte count before CAD event than controls (median [interquartile range], 6495 [5300-7995] vs 5900 [4910-7200]; P < .01), but leukocytosis (>11 000/µL) was uncommon (4.3% vs 2.1%; P = .01). In the highest versus lowest leukocyte quintile at latest time point before CAD event, participants had univariable CAD-OR = 2.27 (95% confidence interval, 1.63-3.15) and multivariable adjusted CAD-OR = 1.59 (1.09-2.30). For comparison, univariable CAD-OR for dyslipidemia, diabetes, and recent abacavir exposure were 1.58 (1.29-1.93), 2.19 (1.59-3.03), and 1.73 (1.37-2.17), respectively. Smoking and, to a lesser degree, alcohol and ethnicity attenuated the leukocyte-CAD association. Leukocytes measured up to 8 years before the event were significantly associated with CAD events. CONCLUSIONS PWH in Switzerland with higher leukocyte counts have an independently increased risk of CAD events, to a degree similar to traditional and HIV-related risk factors.
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Affiliation(s)
- Emma F Avery
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
| | - Julia N Kleynhans
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Isabella C Schoepf
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
- Hepatology, Department for Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christian W Thorball
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Reiss
- Department of Global Health and Division of Infectious Disease, Amsterdam University Medical Centers, University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Lene Ryom
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maria C Thurnheer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Marco Seneghini
- Division of Infectious Diseases, Kantonsspital St Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ospedale Regionale Lugano, University of Geneva and Università della Svizzera italiana, Lugano, Switzerland
| | - Matthias Cavassini
- Infectious Diseases Service, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Hélène Buvelot
- Division of Infectious Disease, Geneva University Hospital, Geneva, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Philip E Tarr
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
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22
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Kusejko K, Smith D, Scherrer A, Paioni P, Kohns Vasconcelos M, Aebi-Popp K, Kouyos RD, Günthard HF, Kahlert CR. Migrating a Well-Established Longitudinal Cohort Database From Oracle SQL to Research Electronic Data Entry (REDCap): Data Management Research and Design Study. JMIR Form Res 2023; 7:e44567. [PMID: 37256686 DOI: 10.2196/44567] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/30/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Providing user-friendly electronic data collection tools for large multicenter studies is key for obtaining high-quality research data. Research Electronic Data Capture (REDCap) is a software solution developed for setting up research databases with integrated graphical user interfaces for electronic data entry. The Swiss Mother and Child HIV Cohort Study (MoCHiV) is a longitudinal cohort study with around 2 million data entries dating back to the early 1980s. Until 2022, data collection in MoCHiV was paper-based. OBJECTIVE The objective of this study was to provide a user-friendly graphical interface for electronic data entry for physicians and study nurses reporting MoCHiV data. METHODS MoCHiV collects information on obstetric events among women living with HIV and children born to mothers living with HIV. Until 2022, MoCHiV data were stored in an Oracle SQL relational database. In this project, R and REDCap were used to develop an electronic data entry platform for MoCHiV with migration of already collected data. RESULTS The key steps for providing an electronic data entry option for MoCHiV were (1) design, (2) data cleaning and formatting, (3) migration and compliance, and (4) add-on features. In the first step, the database structure was defined in REDCap, including the specification of primary and foreign keys, definition of study variables, and the hierarchy of questions (termed "branching logic"). In the second step, data stored in Oracle were cleaned and formatted to adhere to the defined database structure. Systematic data checks ensured compliance to all branching logic and levels of categorical variables. REDCap-specific variables and numbering of repeated events for enabling a relational data structure in REDCap were generated using R. In the third step, data were imported to REDCap and then systematically compared to the original data. In the last step, add-on features, such as data access groups, redirections, and summary reports, were integrated to facilitate data entry in the multicenter MoCHiV study. CONCLUSIONS By combining different software tools-Oracle SQL, R, and REDCap-and building a systematic pipeline for data cleaning, formatting, and comparing, we were able to migrate a multicenter longitudinal cohort study from Oracle SQL to REDCap. REDCap offers a flexible way for developing customized study designs, even in the case of longitudinal studies with different study arms (ie, obstetric events, women, and mother-child pairs). However, REDCap does not offer built-in tools for preprocessing large data sets before data import. Additional software is needed (eg, R) for data formatting and cleaning to achieve the predefined REDCap data structure.
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Affiliation(s)
- Katharina Kusejko
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Daniel Smith
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Paolo Paioni
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Malte Kohns Vasconcelos
- Department for Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland
| | - Karoline Aebi-Popp
- Department of Infectious Diseases, Inselspital Bern, University of Bern, Bern, Switzerland
- Department of Obstetrics and Gynecology, Lindenhofspital, Bern, Switzerland
| | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Christian R Kahlert
- Department of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St Gallen, Switzerland
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23
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Schoepf IC, Esteban-Cantos A, Thorball CW, Rodés B, Reiss P, Rodríguez-Centeno J, Riebensahm C, Braun DL, Marzolini C, Seneghini M, Bernasconi E, Cavassini M, Buvelot H, Thurnheer MC, Kouyos RD, Fellay J, Günthard HF, Arribas JR, Ledergerber B, Tarr PE. Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 years. Lancet Healthy Longev 2023; 4:e211-e218. [PMID: 37148893 DOI: 10.1016/s2666-7568(23)00037-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Accelerated epigenetic ageing can occur in untreated HIV infection and is partially reversible with effective antiretroviral therapy (ART). We aimed to make a long-term comparison of epigenetic ageing dynamics in people with HIV during untreated HIV infection and during suppressive ART. METHODS In this longitudinal study, conducted over 17 years in HIV outpatient clinics in Switzerland, we applied 5 established epigenetic age estimators (epigenetic clocks) in peripheral blood mononuclear cells (PBMCs) in Swiss HIV Cohort Study participants before or during suppressive ART. All participants had a longitudinal set of PBMC samples available at four timepoints (T1-T4). T1 and T2 had to be 3 years or longer apart, as did T3 and T4. We assessed epigenetic age acceleration (EAA) and a novel rate of epigenetic ageing. FINDINGS Between March 13, 1990, and Jan 18, 2018, we recruited 81 people with HIV from the Swiss HIV Cohort Study. We excluded one participant because a sample did not meet quality checks (transmission error). 52 (65%) of 80 patients were men, 76 (95%) were white, and the median patient age was 43 (IQR 37·5-47) years. Per year of untreated HIV infection (median observation 8·08 years, IQR 4·83-11·09), mean EAA was 0·47 years (95% CI 0·37 to 0·57) for Horvath's clock, 0·43 years (0·3 to 0·57) for Hannum's clock, 0·36 years (0·27 to 0·44) for SkinBlood clock, and 0·69 years (0·51 to 0·86) for PhenoAge. Per year of suppressive ART (median observation 9·8 years, IQR 7·2-11), mean EAA was -0·35 years (95% CI -0·44 to -0·27) for Horvath's clock, -0·39 years (-0·50 to -0·27) for Hannum's clock, -0·26 years (-0·33 to -0·18) for SkinBlood clock, and -0·49 years (-0·64 to -0·35) for PhenoAge. Our findings indicate that people with HIV epigenetically aged by a mean of 1·47 years for Horvath's clock, 1·43 years for Hannum's clock, 1·36 years for SkinBlood clock, and 1·69 years for PhenoAge per year of untreated HIV infection; and 0·65 years for Horvath's clock, 0·61 years for Hannum's clock, 0·74 years for SkinBlood clock, and 0·51 years for PhenoAge, per year of suppressive ART. GrimAge showed some change in the mean EAA during untreated HIV infection (0·10 years, 0·02 to 0·19) and suppressive ART (-0·05 years, -0·12 to 0·02). We obtained very similar results using the rate of epigenetic ageing. Contribution of multiple HIV-related, antiretroviral, and immunological variables, and of a DNA methylation-associated polygenic risk score to EAA was small. INTERPRETATION In a longitudinal study over more than 17 years, epigenetic ageing accelerated during untreated HIV infection and decelerated during suppressive ART, highlighting the importance of limiting the duration of untreated HIV infection. FUNDING Swiss HIV Cohort Study, Swiss National Science Foundation, and Gilead Sciences.
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Affiliation(s)
- Isabella C Schoepf
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland; University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
| | - Andrés Esteban-Cantos
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research, Madrid, Spain; CIBER of Infectious Diseases, Madrid, Spain
| | - Christian W Thorball
- Precision Medicine Unit, Centre hospitalier universitaire vaudois, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Berta Rodés
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research, Madrid, Spain; CIBER of Infectious Diseases, Madrid, Spain
| | - Peter Reiss
- Amsterdam UMC, location University of Amsterdam, Global Health, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Javier Rodríguez-Centeno
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research, Madrid, Spain; CIBER of Infectious Diseases, Madrid, Spain
| | - Carlotta Riebensahm
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland; Graduate School of Health Sciences, University of Bern, Bern, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Marco Seneghini
- Division of Infectious Diseases, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Matthias Cavassini
- Infectious Diseases Service, Lausanne University Hospital University of Lausanne, Switzerland
| | - Hélène Buvelot
- Division of Infectious Disease, Geneva University Hospital, Geneva, Switzerland
| | | | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Centre hospitalier universitaire vaudois, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - José R Arribas
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research, Madrid, Spain; CIBER of Infectious Diseases, Madrid, Spain
| | - Bruno Ledergerber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Philip E Tarr
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland.
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24
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Balakrishna S, Loosli T, Zaheri M, Frischknecht P, Huber M, Kusejko K, Yerly S, Leuzinger K, Perreau M, Ramette A, Wymant C, Fraser C, Kellam P, Gall A, Hirsch HH, Stoeckle M, Rauch A, Cavassini M, Bernasconi E, Notter J, Calmy A, Günthard HF, Metzner KJ, Kouyos RD. Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. J Antimicrob Chemother 2023; 78:656-664. [PMID: 36738248 DOI: 10.1093/jac/dkac430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is gradually replacing Sanger sequencing (SS) as the primary method for HIV genotypic resistance testing. However, there are limited systematic data on comparability of these methods in a clinical setting for the presence of low-abundance drug resistance mutations (DRMs) and their dependency on the variant-calling thresholds. METHODS To compare the HIV-DRMs detected by SS and NGS, we included participants enrolled in the Swiss HIV Cohort Study (SHCS) with SS and NGS sequences available with sample collection dates ≤7 days apart. We tested for the presence of HIV-DRMs and compared the agreement between SS and NGS at different variant-calling thresholds. RESULTS We included 594 pairs of SS and NGS from 527 SHCS participants. Males accounted for 80.5% of the participants, 76.3% were ART naive at sample collection and 78.1% of the sequences were subtype B. Overall, we observed a good agreement (Cohen's kappa >0.80) for HIV-DRMs for variant-calling thresholds ≥5%. We observed an increase in low-abundance HIV-DRMs detected at lower thresholds [28/417 (6.7%) at 10%-25% to 293/812 (36.1%) at 1%-2% threshold]. However, such low-abundance HIV-DRMs were overrepresented in ART-naive participants and were in most cases not detected in previously sampled sequences suggesting high sequencing error for thresholds <3%. CONCLUSIONS We found high concordance between SS and NGS but also a substantial number of low-abundance HIV-DRMs detected only by NGS at lower variant-calling thresholds. Our findings suggest that a substantial fraction of the low-abundance HIV-DRMs detected at thresholds <3% may represent sequencing errors and hence should not be overinterpreted in clinical practice.
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Affiliation(s)
- Suraj Balakrishna
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Karoline Leuzinger
- Clinical Virology Division, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Chris Wymant
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Astrid Gall
- Excellence in Life Sciences (EMBO), Heidelberg, Germany
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Marcel Stoeckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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25
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Labarile M, Loosli T, Zeeb M, Kusejko K, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Battegay M, Rauch A, Calmy A, Notter J, Bernasconi E, Fux C, Günthard HF, Pasin C, Kouyos RD, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Quantifying and Predicting Ongoing Human Immunodeficiency Virus Type 1 Transmission Dynamics in Switzerland Using a Distance-Based Clustering Approach. J Infect Dis 2023; 227:554-564. [PMID: 36433831 DOI: 10.1093/infdis/jiac457] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Despite effective prevention approaches, ongoing human immunodeficiency virus 1 (HIV-1) transmission remains a public health concern indicating a need for identifying its drivers. METHODS We combined a network-based clustering method using evolutionary distances between viral sequences with statistical learning approaches to investigate the dynamics of HIV transmission in the Swiss HIV Cohort Study and to predict the drivers of ongoing transmission. RESULTS We found that only a minority of clusters and patients acquired links to new infections between 2007 and 2020. While the growth of clusters and the probability of individual patients acquiring new links in the transmission network was associated with epidemiological, behavioral, and virological predictors, the strength of these associations decreased substantially when adjusting for network characteristics. Thus, these network characteristics can capture major heterogeneities beyond classical epidemiological parameters. When modeling the probability of a newly diagnosed patient being linked with future infections, we found that the best predictive performance (median area under the curve receiver operating characteristic AUCROC = 0.77) was achieved by models including characteristics of the network as predictors and that models excluding them performed substantially worse (median AUCROC = 0.54). CONCLUSIONS These results highlight the utility of molecular epidemiology-based network approaches for analyzing and predicting ongoing HIV transmission dynamics. This approach may serve for real-time prospective assessment of HIV transmission.
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Affiliation(s)
- Marco Labarile
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Manuel Battegay
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Christoph Fux
- Department of Infectious Diseases, Kantonsspital Aarau, Aarau, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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26
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Bergadà-Pijuan J, Frank M, Boroumand S, Hovaguimian F, Mestres CA, Bauernschmitt R, Carrel T, Stadlinger B, Ruschitzka F, Zinkernagel AS, Kouyos RD, Hasse B. Antibiotic prophylaxis before dental procedures to prevent infective endocarditis: a systematic review. Infection 2023; 51:47-59. [PMID: 35972680 PMCID: PMC9879842 DOI: 10.1007/s15010-022-01900-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/02/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE Infective endocarditis (IE) is a severe bacterial infection. As a measure of prevention, the administration of antibiotic prophylaxis (AP) prior to dental procedures was recommended in the past. However, between 2007 and 2009, guidelines for IE prophylaxis changed all around the word, limiting or supporting the complete cessation of AP. It remains unclear whether AP is effective or not against IE. METHODS We conducted a systematic review whether the administration of AP in adults before any dental procedure, compared to the non-administration of such drugs, has an effect on the risk of developing IE. We searched for studies in the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via OVID, and EMBASE. Two different authors filtered articles independently and data extraction was performed based on a pre-defined protocol. RESULTS The only cohort study meeting our criteria included patients at high-risk of IE. Analysis of the extracted data showed a non-significant decrease in the risk of IE when high-risk patients take AP prior to invasive dental procedures (RR 0.39, p-value 0.11). We did not find other studies including patients at low or moderate risk of IE. Qualitative evaluation of the excluded articles reveals diversity of results and suggests that most of the state-of-the-art articles are underpowered. CONCLUSIONS Evidence to support or discourage the use of AP prior to dental procedures as a prevention for IE is very low. New high-quality studies are needed, even though such studies would require big settings and might not be immediately feasible.
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Affiliation(s)
- Judith Bergadà-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091 Zurich, Switzerland
| | - Michelle Frank
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sara Boroumand
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Frédérique Hovaguimian
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091 Zurich, Switzerland ,Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Carlos A. Mestres
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Robert Bauernschmitt
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thierry Carrel
- Clinic for Cardiac Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bernd Stadlinger
- Center of Dental Medicine, University of Zurich, Zurich, Switzerland
| | - Frank Ruschitzka
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091 Zurich, Switzerland
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091 Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091 Zurich, Switzerland
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27
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Hamusonde K, Nicca D, Günthard HF, Stöckle M, Darling KEA, Calmy A, Bernasconi E, Haerry D, Schmid P, Kouyos RD, Rauch A, Salazar-Vizcaya L, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Jackson-Perry D, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Labhardt N, Leuzinger K, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Notter J, Paioni P, Pantaleo G, Perreau M, Rauch A, Salazar-Vizcaya L, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Weisser M, Yerly S. Triggers of Change in Sexual Behavior Among People With HIV: The Swiss U U Statement and COVID-19 Compared. J Infect Dis 2022; 227:407-411. [PMID: 36408629 PMCID: PMC9891402 DOI: 10.1093/infdis/jiac459] [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: 08/22/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
We assessed changes in sexual behavior among people with human immunodeficiency virus (HIV) over 20 years. Condom use with stable partners steadily declined from over 90 to 29 since the Swiss U U statement, with similar trajectories between men who have sex with men (MSM) and heterosexuals. Occasional partnership remained higher among MSM compared to heterosexuals even during coronavirus disease 2019 (COVID-19) social distancing.
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Affiliation(s)
- Kalongo Hamusonde
- Correspondence: K. Hamusonde, Msc, Bern University Hospital, Inselspital, Universitätsklinik für Infektiologie, Personalhaus 6, Bern 3010, Switzerland ()
| | - Dunja Nicca
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Katharine E A Darling
- Service of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, University of Southern Switzerland, Lugano, Switzerland
| | | | - Patrick Schmid
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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28
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Bosetti D, Mugglin C, Calmy A, Cavassini M, Stöckle M, Braun D, Notter J, Haerry D, Hampel B, Kovari H, Bernasconi E, Wandeler G, Rauch A, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Risk Factors and Incidence of Sexually Transmitted Infections in the Swiss HIV Cohort Study. Open Forum Infect Dis 2022; 9:ofac592. [PMID: 36504700 PMCID: PMC9728517 DOI: 10.1093/ofid/ofac592] [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: 07/01/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background Sexually transmitted infections (STIs) are common among people with human immunodeficiency virus (PWH), but there are limited data about risk factors and incidence of STIs in large, representative cohort studies. Methods We assessed incidence and risk factors of STIs reported by treating physicians within the Swiss HIV Cohort Study (SHCS). Sexually transmitted infections and demographic, clinical, and behavioral characteristics were prospectively collected at 6-month follow-up visits between October 2017 and November 2019. We used multilevel Poisson regression to assess incidence rate ratios of different STIs. Results Among 10 140 study participants, a total of 1634 STIs in 1029 SHCS participants were reported over 17 766 person-years of follow up (PYFUP). The overall incidence of any reported STI was 91.9 per 1000 PYFU (95% confidence interval [CI], 85.8 -98.5). Among the 1634 STI episodes, there were 573 (35.1%) incident cases of syphilis, 497 gonorrhea (30.4%), and 418 chlamydia (25.6%). Men who have sex with men (MSM) younger than 50 years represented 21% of the study population, but accounted for 61% of reported STIs. Male sex (adjusted incidence rate ratio [aIRR], 2.03; 95% CI, 1.36-3.02), MSM (aIRR, 3.62; 95% CI, 2.88-4.55), age group 18-34 years (aIRR, 1.78; 95% CI, 1.51-2.10), history of sexual relationships with occasional partners (aIRR, 6.87; 95% CI, 5.40-8.73), and reporting injecting drug use (aIRR, 2.48; 95% CI, 1.91-3.23) were associated with a higher risk of incident STIs. Conclusions Sexually transmitted infections were frequent among PWH and varied considerably between age and risk groups. Screening programs and recommendations for STI testing need to be adapted according to risk factors and demographic characteristics.
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Affiliation(s)
| | - Catrina Mugglin
- Correspondence: Catrina Mugglin, MSc, MD, PhD, Inselspital, Bern University Hospital, Freiburgstrasse, CH-3010 Bern, Switzerland ()
| | - Alexandra Calmy
- HIV/AIDS Unit, Department of Infectious Diseases, Geneva, Switzerland
| | - Matthias Cavassini
- University Hospital of Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Dominique Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, St. Gallen, Switzerland
| | | | - Benjamin Hampel
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland,Checkpoint Zurich, Zurich, Switzerland
| | - Helen Kovari
- Zentrum für Infektionskrankheiten, Klinik im Park, Zurich, Switzerland
| | - Enos Bernasconi
- Ente Ospedaliero Cantonale, Lugano, University of Geneva, and University of Southern Switzerland, Lugano, Switzerland
| | - Gilles Wandeler
- Department of Infectious Diseases, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
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29
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Zeeb M, Weissberg D, Rampini SK, Müller R, Scheier T, Zingg W, Kouyos RD, Wolfensberger A. Identifying Contact Risks for SARS-CoV-2 Transmission to Healthcare Workers during Outbreak on COVID-19 Ward. Emerg Infect Dis 2022; 28:2134-2137. [PMID: 36001791 PMCID: PMC9514331 DOI: 10.3201/eid2810.220266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We assessed the risk for different exposures to SARS-CoV-2 during a COVID-19 outbreak among healthcare workers on a hospital ward in late 2020. We found working with isolated COVID-19 patients did not increase the risk of COVID-19 among workers, but working shifts with presymptomatic healthcare coworkers did.
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30
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Chaudron SE, Leemann C, Kusejko K, Nguyen H, Tschumi N, Marzel A, Huber M, Böni J, Perreau M, Klimkait T, Yerly S, Ramette A, Hirsch HH, Rauch A, Calmy A, Vernazza P, Bernasconi E, Cavassini M, Metzner KJ, Kouyos RD, Günthard HF. A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study. J Infect Dis 2022; 226:1256-1266. [PMID: 35485458 DOI: 10.1093/infdis/jiac166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/10/2021] [Accepted: 04/27/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studying human immunodeficiency virus type 1 (HIV-1) superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies and insufficient longitudinal samples. METHODS Using the Swiss HIV Cohort Study (SHCS), we developed a molecular epidemiology screening for superinfections. A phylogeny built from 22 243 HIV-1 partial polymerase sequences was used to identify potential superinfections among 4575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples. RESULTS Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow confirming or rejecting superinfection because the sequenced samples did not include the relevant time points causing the superinfection signal in the original screen. Thus, NFVGS could support 52 of 67 adequately sampled potential superinfections. CONCLUSIONS This cohort-based molecular approach identified, to our knowledge, the largest population of confirmed superinfections, showing that, while rare with a prevalence of 1%-7%, superinfections are not negligible events.
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Affiliation(s)
- Sandra E Chaudron
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huyen Nguyen
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nadine Tschumi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Alex Marzel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Schulthess Klinik, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.,Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland.,Division of Infectious Diseases and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pietro Vernazza
- Clinic for Infectiology and Hospital Hygiene, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Service for Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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31
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Inderbitzin A, Loosli T, Kouyos RD, Metzner KJ. Quantification of transgene expression in GSH AAVS1 with a novel CRISPR/Cas9-based approach reveals high transcriptional variation. Mol Ther Methods Clin Dev 2022; 26:107-118. [PMID: 35795775 PMCID: PMC9234542 DOI: 10.1016/j.omtm.2022.06.003] [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: 01/07/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022]
Abstract
Genomic safe harbors (GSH) are defined as sites in the host genome that allow stable expression of inserted transgenes while having no adverse effects on the host cell, making them ideal for use in basic research and therapeutic applications. Silencing and fluctuations in transgene expression would be highly undesirable effects. We have previously shown that transgene expression in Jurkat T cells is not silenced for up to 160 days after CRISPR-Cas9-mediated insertion of reporter genes into the adeno-associated virus site 1 (AAVS1), a commonly used GSH. Here, we studied fluctuations in transgene expression upon targeted insertion into the GSH AAVS1. We have developed an efficient method to generate and validate highly complex barcoded plasmid libraries to study transgene expression on the single-cell level. Its applicability is demonstrated by inserting the barcoded transgene Cerulean into the AAVS1 locus in Jurkat T cells via the CRISPR-Cas9 technology followed by next-generation sequencing of the transcribed barcodes. We observed large transcriptional variations over two logs for transgene expression in the GSH AAVS1. This barcoded transgene insertion model is a powerful tool to investigate fluctuations in transgene expression at any GSH site.
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Affiliation(s)
- Anne Inderbitzin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Kusejko K, Tschumi N, Chaudron SE, Nguyen H, Battegay M, Bernasconi E, Böni J, Huber M, Calmy A, Cavassini M, Egle A, Grabmeier-Pfistershammer K, Haas B, Hirsch H, Klimkait T, Öllinger A, Perreau M, Ramette A, Flury BB, Sarcletti M, Scherrer A, Schmid P, Yerly S, Zangerle R, Günthard HF, Kouyos RD. Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics. J Acquir Immune Defic Syndr 2022; 90:e4-e12. [PMID: 35298446 PMCID: PMC9394492 DOI: 10.1097/qai.0000000000002949] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Phylogenetic analyses of 2 or more countries allow to detect differences in transmission dynamics of local HIV-1 epidemics beyond differences in demographic characteristics. METHODS A maximum-likelihood phylogenetic tree was built using pol -sequences of the Swiss HIV Cohort Study (SHCS) and the Austrian HIV Cohort Study (AHIVCOS), with international background sequences. Three types of phylogenetic cherries (clusters of size 2) were analyzed further: (1) domestic cherries; (2) international cherries; and (3) SHCS/AHIVCOS-cherries. Transmission group and ethnicities observed within the cherries were compared with the respective distribution expected from a random distribution of patients on the phylogeny. RESULTS The demographic characteristics of the AHIVCOS (included patients: 3'141) and the SHCS (included patients: 12'902) are very similar. In the AHIVCOS, 36.5% of the patients were in domestic cherries, 8.3% in international cherries, and 7.0% in SHCS/AHIVCOS cherries. Similarly, in the SHCS, 43.0% of the patients were in domestic cherries, 8.2% in international cherries, and 1.7% in SHCS/AHIVCOS cherries. Although international cherries in the SHCS were dominated by heterosexuals with men who have sex with men being underrepresented, the opposite was the case for the AHIVCOS. In both cohorts, cherries with one patient belonging to the transmission group intravenous drug user and the other one non-intravenous drug user were underrepresented. CONCLUSIONS In both cohorts, international HIV transmission plays a major role in the local epidemics, mostly driven by men who have sex with men in the AHIVOS, and by heterosexuals in the SHCS, highlighting the importance of international collaborations to understand global HIV transmission links on the way to eliminate HIV.
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Affiliation(s)
- Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nadine Tschumi
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Sandra E. Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexander Egle
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
| | | | - Bernhard Haas
- Institute of Hospital Hygiene and Microbiology, Styrian Hospital Corporation, The Styrian Healthcare Company, Graz, Austria
| | - Hans Hirsch
- Molecular Virology, Department of Biomedicine–Petersplatz, University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine–Petersplatz, University of Basel, Basel, Switzerland
| | - Angela Öllinger
- Department of Dermatology, Kepler University Hospital, Linz, Austria
| | - Matthieu Perreau
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Baharak Babouee Flury
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland; and
| | - Mario Sarcletti
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland; and
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Robert Zangerle
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Marconato M, Abela IA, Hauser A, Schwarzmüller M, Katzensteiner R, Braun DL, Epp S, Audigé A, Weber J, Rusert P, Schindler E, Pasin C, West E, Böni J, Kufner V, Huber M, Zaheri M, Schmutz S, Frey BM, Kouyos RD, Günthard HF, Manz MG, Trkola A. Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response. J Clin Invest 2022; 132:e158190. [PMID: 35482408 PMCID: PMC9197521 DOI: 10.1172/jci158190] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/26/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUNDNeutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The manner in which human infections respond to therapeutic SARS-CoV-2 antibodies, including convalescent plasma therapy, remains to be fully elucidated.METHODSWe conducted a proof-of-principle study of convalescent plasma therapy based on a phase I trial in 30 hospitalized COVID-19 patients with a median interval between onset of symptoms and first transfusion of 9 days (IQR, 7-11.8 days). Comprehensive longitudinal monitoring of the virological, serological, and disease status of recipients allowed deciphering of parameters on which plasma therapy efficacy depends.RESULTSIn this trial, convalescent plasma therapy was safe as evidenced by the absence of transfusion-related adverse events and low mortality (3.3%). Treatment with highly neutralizing plasma was significantly associated with faster virus clearance, as demonstrated by Kaplan-Meier analysis (P = 0.034) and confirmed in a parametric survival model including viral load and comorbidity (adjusted hazard ratio, 3.0; 95% CI, 1.1-8.1; P = 0.026). The onset of endogenous neutralization affected viral clearance, but even after adjustment for their pretransfusion endogenous neutralization status, recipients benefitted from plasma therapy with high neutralizing antibodies (hazard ratio, 3.5; 95% CI, 1.1-11; P = 0.034).CONCLUSIONOur data demonstrate a clear impact of exogenous antibody therapy on the rapid clearance of viremia before and after onset of the endogenous neutralizing response, and point beyond antibody-based interventions to critical laboratory parameters for improved evaluation of current and future SARS-CoV-2 therapies.TRIAL REGISTRATIONClinicalTrials.gov NCT04869072.FUNDINGThis study was funded via an Innovation Pool project by the University Hospital Zurich; the Swiss Red Cross Glückskette Corona Funding; Pandemiefonds of the UZH Foundation; and the Clinical Research Priority Program "Comprehensive Genomic Pathogen Detection" of the University of Zurich.
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Affiliation(s)
- Maddalena Marconato
- Department of Medical Oncology and Haematology; University Hospital Zurich and University of Zurich; Comprehensive Cancer Center Zurich; Switzerland
| | - Irene A. Abela
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Anthony Hauser
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | | | - Rheliana Katzensteiner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Dominique L. Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Annette Audigé
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacqueline Weber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Eméry Schindler
- Blood Transfusion Service Zurich, Swiss Red Cross, Zurich, Switzerland
| | - Chloé Pasin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Emily West
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Beat M. Frey
- Blood Transfusion Service Zurich, Swiss Red Cross, Zurich, Switzerland
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Markus G. Manz
- Department of Medical Oncology and Haematology; University Hospital Zurich and University of Zurich; Comprehensive Cancer Center Zurich; Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Salazar-Vizcaya L, Atkinson A, Kronenberg A, Plüss-Suard C, Kouyos RD, Kachalov V, Troillet N, Marschall J, Sommerstein R. The impact of public health interventions on the future prevalence of ESBL-producing Klebsiella pneumoniae: a population based mathematical modelling study. BMC Infect Dis 2022; 22:487. [PMID: 35606726 PMCID: PMC9125893 DOI: 10.1186/s12879-022-07441-z] [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: 06/09/2021] [Accepted: 05/03/2022] [Indexed: 11/22/2022] Open
Abstract
Background Future prevalence of colonization with extended-spectrum betalactamase (ESBL-) producing K. pneumoniae in humans and the potential of public health interventions against the spread of these resistant bacteria remain uncertain. Methods Based on antimicrobial consumption and susceptibility data recorded during > 13 years in a Swiss region, we developed a mathematical model to assess the comparative effect of different interventions on the prevalence of colonization. Results Simulated prevalence stabilized in the near future when rates of antimicrobial consumption and in-hospital transmission were assumed to remain stable (2025 prevalence: 6.8% (95CI%:5.4–8.8%) in hospitals, 3.5% (2.5–5.0%) in the community versus 6.1% (5.0–7.5%) and 3.2% (2.3–4.2%) in 2019, respectively). When overall antimicrobial consumption was set to decrease by 50%, 2025 prevalence declined by 75% in hospitals and by 64% in the community. A 50% decline in in-hospital transmission rate led to a reduction in 2025 prevalence of 31% in hospitals and no reduction in the community. The best model fit estimated that 49% (6–100%) of observed colonizations could be attributable to sources other than human-to-human transmission within the geographical setting. Conclusions Projections suggests that overall antimicrobial consumption will be, by far, the most powerful driver of prevalence and that a large fraction of colonizations could be attributed to non-local transmissions. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07441-z.
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Affiliation(s)
- Luisa Salazar-Vizcaya
- Department of Infectious Diseases, Bern University Hospital, Inselspital, University of Bern, University of Bern, Freiburgstrasse, 3010, Bern, Switzerland.
| | - Andrew Atkinson
- Department of Infectious Diseases, Bern University Hospital, Inselspital, University of Bern, University of Bern, Freiburgstrasse, 3010, Bern, Switzerland
| | - Andreas Kronenberg
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Viacheslav Kachalov
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nicolas Troillet
- Service of Infectious Diseases, Central Institute, Valais Hospitals, Sion, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital, Inselspital, University of Bern, University of Bern, Freiburgstrasse, 3010, Bern, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital, Inselspital, University of Bern, University of Bern, Freiburgstrasse, 3010, Bern, Switzerland.
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35
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Kachalov VN, Kuster SP, Balakrishna S, Schreiber PW, Jakob W, Sax H, Kouyos RD, Wolfensberger A. Modifiable and non-modifiable risk factors for non-ventilator-associated hospital-acquired pneumonia (nvHAP) identified in a retrospective cohort study. Clin Microbiol Infect 2022; 28:1451-1457. [PMID: 35597506 DOI: 10.1016/j.cmi.2022.05.011] [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] [Received: 11/15/2021] [Revised: 05/02/2022] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Hospital-acquired pneumonia in non-ventilated patients (nvHAP) belongs to the most common healthcare-associated infections. This study aimed to investigate risk factors for nvHAP in patients outside the intensive care unit, focusing on modifiable risk factors. METHODS All inpatients admitted to an academic teaching hospital in Switzerland between 2017 and 2018 were included. NvHAP was defined according to European Centre for Disease Prevention and Control criteria. Patient days during and after ICU stay were excluded. Candidate risk factors - both constant and time-varying - were included in uni- and multivariable Cox proportional hazards models. The decay ratio and the characteristic time of influence of HRs was estimated by adopting a linear decay in the Cox model. RESULTS A total of 66,001 hospitalizations with 314 (0.48%) nvHAP and 471,401 patient days were included. Median age was 57 years (interquartile range: 38-71 years) and 32,253 (48.9%) patients were male. Among non-modifiable risk factors, age (adjusted-HR 2.66 for age ≥60 years, 95%CI 1.59-4.45) and male sex (aHR 1.71, 95%CI 1.34-2.18) were independently associated with nvHAP. Time-varying exposures showing strongest independent association with nvHAP were tube feeding (aHR 3.24, 95%CI 2.17-4.83), impaired consciousness (aHR 2.32, 95%CI 1.63-3.31), and severely impaired activity and mobility (aHR 2.06, 95%CI 1.50-2.84). The association with nvHAP decayed within 7.1 - 13.2 days after these exposures ended. CONCLUSIONS The risk for nvHAP varies with time, depending on the patient's medical condition and medical interventions. Several risk factors for nvHAP represent potential targets for specific prevention measures.
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Affiliation(s)
- Viacheslav N Kachalov
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - Stefan P Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland; Cantonal Hospital St. Gallen, Division of Infectious Diseases and Hospital Epidemiology, St.Gallen, Switzerland
| | - Suraj Balakrishna
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - Peter W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - Werner Jakob
- Department of Medical Data Management Systems, ICT Directorate, University Hospital Zurich, Zurich, Switzerland
| | - Hugo Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland; Division of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - Aline Wolfensberger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland.
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Ring A, Balakrishna S, Imkamp F, Burkard S, Triet F, Brunschweiler F, Grube C, Bodmer R, Kouyos RD, Günthard HF, Braun DL. High rates of asymptomatic Mycoplasma genitalium infections with high proportion of genotypic resistance to first-line macrolide treatment among men enrolled in the Zurich primary HIV infection study. Open Forum Infect Dis 2022; 9:ofac217. [PMID: 35783686 PMCID: PMC9246285 DOI: 10.1093/ofid/ofac217] [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: 04/05/2022] [Accepted: 04/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background Mycoplasma genitalium (Mg) is an emerging sexually transmitted pathogen among men who have sex with men (MSM). Resistance to recommended antimicrobial agents are of public health concern. Few data exist on Mg infections in MSM diagnosed with human immunodeficiency virus (HIV) during primary HIV infection. Methods Participants of the Zurich Primary HIV Study (ClinicalTrials.gov Identifier NCT 00537966) were systematically offered screening for sexually transmitted infections (STIs) between April 2019 and September 2020. Screening was performed using an in-house polymerase chain reaction panel comprising Mg including genotypic resistance testing for macrolides and quinolones, Chlamydia trachomatis including serovars L1-L3, Neisseria gonorrhoeae, Treponema pallidum, and Hemophilus ducreyi. Results We screened 148 of 266 (55.6%) participants, with an overall total of 415 follow-up visits. Ninety-one percent were MSM. The incidence rate for all STIs was 47.0 (95% confidence interval [CI], 32.2–68.6) per 100 person-years. Mycoplasma genitalium was the most frequently detected pathogen: 30 participants (20%) presented with at least 1 Mg infection, corresponding to a period prevalence of 20.3% and incidence rate of 19.5 Mg infections (95% CI, 11.8–32.4). Most Mg infections (93%) were asymptomatic, and 9 (30%) participants showed spontaneous clearance. We detected high rates of antibiotic resistance: 73.3% to macrolides, 3.3% to quinolones, and 13.3% resistance to both antibiotics. Conclusions The high prevalence of mostly asymptomatic Mg infections and high rate of spontaneous clearance support cautious initiation for treatment. The high proportion of macrolide-resistant strains suggests that a genotypic determination of resistance should be standard of care. Moxifloxacin should be the preferred treatment option for symptomatic Mg infections among MSM if resistance testing is unavailable.
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Affiliation(s)
- Alexander Ring
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Suraj Balakrishna
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sara Burkard
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Flurina Triet
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Flurina Brunschweiler
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Christina Grube
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Rebecca Bodmer
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Dominique L. Braun
- Division of Infectious Disease and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Nguyen H, Hampel B, Nuñez DG, Battegay M, Hachfeld A, Bernasconi E, Calmy A, Cavassini M, Vernazza P, Fellay J, Rudolph H, Huber M, Leuzinger K, Perreau M, Scherrer A, Ramette AN, Yerly S, Günthard HF, Kouyos RD, Kusejko K. Correction to: Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. Clin Infect Dis 2022; 74:2266. [PMID: 35482552 DOI: 10.1093/cid/ciac242] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Benjamin Hampel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Department of Public Health, Epidemiology, Biostatistics, and Public Health Institute, University of Zurich, Zurich, Switzerland
| | - David Garcia Nuñez
- Centre for Gender Variance, University Hospital Basel, Basel, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Anna Hachfeld
- Department of Infectious Diseases, University of Bern, Bern, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hannes Rudolph
- Transgender Network Switzerland, Checkpoint Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karoline Leuzinger
- Clinical Virology Division, Laboratory Medicine, University Hospital Basel, Basel, Switzerlandand
| | - Matthieu Perreau
- Department of Immunology and Allergy, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | | | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Boumasmoud M, Dengler Haunreiter V, Schweizer TA, Meyer L, Chakrakodi B, Schreiber PW, Seidl K, Kühnert D, Kouyos RD, Zinkernagel AS. Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage. mBio 2022; 13:e0377121. [PMID: 35343787 PMCID: PMC9040824 DOI: 10.1128/mbio.03771-21] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of health care-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this time frame and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or wider transmission networks undetectable by routine surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N-acetyl-galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work highlights the potential of combining epidemiological, functional genomic, and evolutionary perspectives to unveil adaptation strategies of VREfm. IMPORTANCE Sequencing microbial pathogens causing outbreaks has become a common practice to characterize transmission networks. In addition to the signal provided by vertical evolution, bacterial genomes harbor mobile genetic elements shared horizontally between clones. While macroevolutionary studies have revealed an important role of plasmids and genes encoding carbohydrate utilization systems in the adaptation of Enterococcus faecium to the hospital environment, mechanisms of dissemination and the specific function of many of these genetic determinants remain to be elucidated. Here, we characterize a plasmid providing a nutrient utilization advantage and show evidence for its clonal and horizontal spread at a local scale. Further studies integrating epidemiological, functional genomics, and evolutionary perspectives will be critical to identify changes shaping the success of this pathogen.
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Affiliation(s)
- Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Vanina Dengler Haunreiter
- 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
| | - Lilly Meyer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bhavya Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter W. Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kati Seidl
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Denise Kühnert
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- 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
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Kusejko K, Salazar-Vizcaya L, Shah C, Stöckle M, Béguelin C, Schmid P, Ongaro M, Darling K, Bernasconi E, Rauch A, Kouyos RD, Günthard HF, Böni J, Fehr JS, Braun DL. Sustained effect on hepatitis C elimination among men who have sex with men in the Swiss HIV Cohort Study: A systematic re-screening for hepatitis C RNA two years following a nation-wide elimination program. Clin Infect Dis 2022; 75:1723-1731. [PMID: 35404384 DOI: 10.1093/cid/ciac273] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION The Swiss HCVree Trial (NCT02785666) was conducted in 2015-2017 with the goal of implementing a population-based systematic hepatitis C (HCV) micro-elimination program among men who have sex with men (MSM) living with HIV enrolled in the Swiss HIV Cohort Study (SHCS). The trial led to a 91% and 77% decline of HCV prevalence and incidence, respectively. The long-term effect of this HCV micro-elimination program is yet to be explored. METHODS All MSM enrolled in the SHCS were screened for HCV RNA using stored plasma samples obtained in 2019, termed "Swiss HCVree Post" screen. The incidence of HCV infection over time was assessed using additional information on HCV testing routinely collected in the SHCS. Characteristics of participants with replicating HCV infection were analyzed. RESULTS The point-prevalence of "Swiss HCVree Post" (N = 4641) was 0.6%, reflecting a decline of 48% compared to the end of the Swiss HCVree Trial where the prevalence was 1.2%. Further, the incidence of HCV among MSM in the SHCS declined from 0.31/100 person-years (py) (95%-confidence interval (CI) = [0.17,0.55]) in 2017 to 0.19/100 py (95%-CI = [0.09,0.39]) in 2019. CONCLUSION A systematic HCV RNA-based screening among MSM living with HIV conducted two years after the Swiss HCVree Trial revealed a sustained effect and further decline of the prevalence and incidence of replicating HCV infection. This indicates that the Swiss HCVree Trial was successful in curbing the HCV epidemic among MSM living with HIV in Switzerland.
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Affiliation(s)
- Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Luisa Salazar-Vizcaya
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cyril Shah
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Switzerland
| | - Charles Béguelin
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Marie Ongaro
- Division of Gastroenterology and Hepatology, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Katherine Darling
- Service of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, University of Geneva, Geneva, and University of Southern Switzerland, Lugano, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jan S Fehr
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Department Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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40
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Salazar-Vizcaya L, Kusejko K, Günthard HF, Böni J, Metzner KJ, Braun DL, Nicca D, Bernasconi E, Calmy A, Darling KEA, Wandeler G, Kouyos RD, Rauch A. An Approach to Quantifying the Interaction between Behavioral and Transmission Clusters. Viruses 2022; 14:v14040784. [PMID: 35458514 PMCID: PMC9032082 DOI: 10.3390/v14040784] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/04/2023] Open
Abstract
We hypothesize that patterns of sexual behavior play a role in the conformation of transmission networks, i.e., the way you behave might influence whom you have sex with. If that was the case, behavioral grouping might in turn correlate with, and potentially predict transmission networking, e.g., proximity in a viral phylogeny. We rigorously present an intuitive approach to address this hypothesis by quantifying mapped interactions between groups defined by similarities in sexual behavior along a virus phylogeny while discussing power and sample size considerations. Data from the Swiss HIV Cohort Study on condom use and hepatitis C virus (HCV) sequences served as proof-of-concept. In this case, a strict inclusion criteria contrasting with low HCV prevalence hindered our possibilities to identify significant relationships. This manuscript serves as guide for studies aimed at characterizing interactions between behavioral patterns and transmission networks. Large transmission networks such as those of HIV or COVID-19 are prime candidates for applying this methodological approach.
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Affiliation(s)
- Luisa Salazar-Vizcaya
- Department of Infectious Diseases, Bern University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; (G.W.); (A.R.)
- Correspondence:
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Karin J. Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Dominique L. Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Dunja Nicca
- Institute of Nursing Science, University of Basel, 4056 Basel, Switzerland;
- Department of Public Health, Epidemiology, Biostatistics and Public Health Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland;
- University of Southern Switzerland, 6928 Manno, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland;
| | - Alexandra Calmy
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland;
| | - Katharine E. A. Darling
- Infectious Diseases Service, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland;
- University of Lausanne, 1015 Lausanne, Switzerland
| | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; (G.W.); (A.R.)
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (K.K.); (H.F.G.); (K.J.M.); (D.L.B.); (R.D.K.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland;
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; (G.W.); (A.R.)
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41
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Rindler AE, Kusejko K, Kuster H, Neumann K, Leemann C, Zeeb M, Chaudron SE, Braun DL, Kouyos RD, Metzner KJ, Günthard HF. The interplay between replication capacity of HIV-1 and surrogate markers of disease. J Infect Dis 2022; 226:1057-1068. [PMID: 35299248 DOI: 10.1093/infdis/jiac100] [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] [Received: 01/05/2022] [Accepted: 03/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND HIV-1 replication capacity (RC) of transmitted/founder viruses may influence the further course of HIV-1 infection. METHODS Replication capacities (RCs) of 355 whole genome primary HIV-1 isolates derived from samples acquired during acute and recent primary HIV-1 infection (PHI) were determined using a novel high throughput infection assay in primary cells. The RCs were used to elucidate potential factors that could be associated with RC during PHI. RESULTS Increased RC was found to be associated with increased set point viral load (VL), and significant differences in RCs among 13 different HIV-1 subtypes were discerned. Notably, we observed an increase in RCs for primary HIV-1 isolates of HIV-1 subtype B over a 17-year period. Associations were not observed between RC and CD4 count at sample date of RC measurement, CD4 recovery after initiation of antiretroviral treatment (ART), CD4 decline in untreated individuals, and acute retroviral syndrome severity scores. DISCUSSION These findings highlight that RCs of primary HIV-1 isolates acquired during the acute and recent phase of infection are more associated with viral factors, i.e., set point VL, than with host factors. Furthermore, we observed a temporal increase in RC for HIV-1 subtype B viruses over a period of 17 years.
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Affiliation(s)
- Audrey E Rindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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42
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Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L. Phylogenetic Estimation of the Viral Fitness Landscape of HIV-1 Set-Point Viral Load. Virus Evol 2022; 8:veac022. [PMID: 35402002 PMCID: PMC8986633 DOI: 10.1093/ve/veac022] [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: 11/11/2021] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | | | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd, Cambridge, UK
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands
- Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Fournier AL, Hocqueloux L, Braun DL, Metzner KJ, Kouyos RD, Raffi F, Briant AR, Martinez E, De Lazzari E, Negredo E, Rijnders B, Rokx C, Günthard HF, Parienti JJ. Dolutegravir monotherapy as maintenance strategy: a meta-analysis of individual participant data from randomized controlled trials. Open Forum Infect Dis 2022; 9:ofac107. [PMID: 35615294 PMCID: PMC9125303 DOI: 10.1093/ofid/ofac107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/24/2021] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Background Dolutegravir monotherapy (DTG-m) results in virological failure (VF) in some people with human immunodeficiency virus (PWH). We sought to identify the independent factors associated with the risk of VF and to explore the effect size heterogeneity between subgroups of PWH enrolled in DTG-m trials. Methods We searched for randomized clinical trials (RCTs) evaluating DTG-m versus combined antiretroviral therapy (cART) among PWH virologically controlled for at least 6 months on cART. We performed an individual participant data meta-analysis of VF risk factors and quantified their explained heterogeneity in random-effect models. Definition of VF was a confirmed plasma human immunodeficiency virus (HIV)-1 ribonucleic acid (RNA) >50 copies/mL by week 48. Results Among 416 PWH from 4 RCTs, DTG-m significantly increased the risk of VF (16 of 227 [7%] versus 0 of 189 for cART; risk difference 7%; 95% confidence interval [CI], 1%–2%; P = .02; I2 = 51%). Among 272 participants exposed to DTG-m, VF were more likely in participants with the following: first cART initiated ≥90 days from HIV acute infection (adjusted hazard ratio [aHR], 5.16; 95% 95% CI, 1.60–16.65), CD4 T cells nadir <350/mm3 (aHR, 12.10; 95% CI, 3.92–37.40), HIV RNA signal at baseline (aHR, 4.84; 95% CI, 3.68–6.38), and HIV-deoxyribonucleic acid (DNA) copy number at baseline ≥2.7 log/106 peripheral blood mononuclear cells (aHR, 3.81; 95% CI, 1.99–7.30). Among these independent risk factors, the largest effect size heterogeneity was found between HIV DNA subgroups (I2 = 80.2%; P for interaction = .02). Conclusions Our study supports the importance of a large viral reservoir size for explaining DTG-m simplification strategy failure. Further studies are needed to link size and genetic diversity of the HIV-1 reservoir.
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Affiliation(s)
- Anna L Fournier
- INSERM U1311 DYNAMICURE, Université Caen Normandie, Caen, France Infectious Diseases, Department, UNICAEN, Normandie University Hospital, Caen, France
| | | | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 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, 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, Zurich, Switzerland
| | - François Raffi
- Infectious Diseases Department, Hotel-Dieu Hospital, INSERM CIC 1413, Nantes University Hospital, Nantes, France
| | - Anaïs R Briant
- Department of Biostatistic and Clinical Research, Caen University hospital, Caen, France
| | | | | | | | - Bart Rijnders
- Erasmus University Medical Center, Rotterdam, Netherlands. Departments of Internal Medicine and Department of Medical Microbiology and Infectious diseases
| | - Casper Rokx
- Erasmus University Medical Center, Rotterdam, Netherlands. Departments of Internal Medicine and Department of Medical Microbiology and Infectious diseases
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jean-Jacques Parienti
- INSERM U1311 DYNAMICURE, Université Caen Normandie, Caen, France Infectious Diseases, Department, UNICAEN, Normandie University Hospital, Caen, France
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44
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Tepekule B, Kusejko K, Zeeb M, Tarr PE, Calmy A, Battegay M, Furrer H, Cavassini M, Bernasconi E, Notter J, Günthard HF, Nemeth J, Kouyos RD. Impact of Latent Tuberculosis Infection on the Incidence of Type 2 Diabetes Mellitus in HIV-Infected Participants in the Swiss HIV Cohort Study. J Infect Dis 2022; 225:2229-2234. [PMID: 35172332 DOI: 10.1093/infdis/jiac054] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
While an increased risk of active and latent tuberculosis infection (LTBI) in people with type-2 diabetes (DM) has been demonstrated, it is less well characterized whether LTBI is associated with an increased risk of developing DM. We investigated the link between LTBI and DM in people living with HIV (PHIV) in the Swiss HIV Cohort Study via time-dependent cox proportional hazards models. We found that LTBI significantly increased the risk of developing DM (HR=1.47), which was robust across different adjustment and censoring techniques. Our results thus suggest that LTBI may be associated with an increased risk of developing DM.
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Affiliation(s)
- Burcu Tepekule
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Philip E Tarr
- Department of Medicine and Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases & Hospital Hygiene, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Julia Notter
- Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Johannes Nemeth
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 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
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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46
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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]
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Huang A, Cicin-Sain C, Pasin C, Epp S, Audigé A, Müller NJ, Nilsson J, Bankova A, Wolfensberger N, Vilinovszki O, Nair G, Hockl P, Schanz U, Kouyos RD, Hasse B, Zinkernagel AS, Trkola A, Manz MG, Abela IA, Müller AMS. Antibody Response to SARS-CoV-2 Vaccination in Patients Following Allogeneic Hematopoietic Cell Transplantation. Transplant Cell Ther 2022; 28:214.e1-214.e11. [PMID: 35092892 PMCID: PMC8802693 DOI: 10.1016/j.jtct.2022.01.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [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: 11/26/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/06/2023]
Abstract
Vaccines against SARS-CoV-2 have been rapidly approved. Although pivotal studies were conducted in healthy volunteers, little information is available on the safety and efficacy of mRNA vaccines in immunocompromised patients, including recipients of allogeneic hematopoietic cell transplantation (allo-HCT). Here we used a novel assay to analyze patient- and transplantation-related factors and their influence on immune responses to SARS-CoV-2 vaccination over an extended period (up to 6 months) in a large and homogenous group of allo-HCT recipients at a single center in Switzerland. We examined longitudinal antibody responses to SARS-CoV-2 vaccination with BNT162b2 (BioNTech/Pfizer) and mRNA-1273 (Moderna) in 110 allo-HCT recipients and 86 healthy controls. Seroprofiling recording IgG, IgA, and IgM reactivity against SARS-CoV-2 antigens (receptor-binding domain, spike glycoprotein subunits S1 and S2, and nucleocapsid protein) was performed before vaccination, before the second dose, and at 1, 3, and 6 months after the second dose. Patients were stratified to 3 groups: 3 to 6 months post-allo-HCT, 6 to 12 months post-allo-HCT, and >12 months post-allo-HCT. Patients in the 3 to 6 months and 6 to 12 months post-allo-HCT groups developed significantly lower antibody titers after vaccination compared with patients in the >12 months post-allo-HCT group and healthy controls (P < .001). Within the cohort of allo-HCT recipients, patients age >65 years (P = .030), those receiving immunosuppression for prevention or treatment of graft-versus-host disease (GVHD) (P = .033), and patients with relapsed disease (P = .014) displayed low humoral immune responses to the vaccine. In contrast, the intensity of the conditioning regimen, underlying disease (myeloid/lymphoid/other), and presence of chronic GVHD had no impact on antibody levels. Antibody titers achieved the highest levels at 1 month after the second dose of the vaccine but waned substantially in all transplantation groups and healthy controls over time. This analysis of long-term vaccine antibody response is of critical importance to allo-HCT recipients and transplant physicians to guide treatment decisions regarding revaccination and social behavior during the SARS-CoV-2 pandemic.
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Affiliation(s)
- Alice Huang
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Caroline Cicin-Sain
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Chloe Pasin
- Institute of Medical Virology, University of Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Annette Audigé
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Nicolas J Müller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Switzerland
| | - Andriyana Bankova
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Nathan Wolfensberger
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Oliver Vilinovszki
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Gayathri Nair
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Philipp Hockl
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Urs Schanz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Irene A Abela
- Institute of Medical Virology, University of Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Antonia M S Müller
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland.
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48
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Chok L, Kusejko K, Eberhard N, Chaudron SE, Saleschus D, Kocher C, Kouyos RD, Weber R, Kuster SP. Impact of an electronic alert on prescription patterns of meropenem, voriconazole and caspofungin. BMC Infect Dis 2021; 21:1263. [PMID: 34930162 PMCID: PMC8686259 DOI: 10.1186/s12879-021-06980-1] [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: 08/11/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antimicrobial stewardship programs promote the appropriate use of antimicrobial substances through the implementation of evidence-based, active and passive interventions. We analyzed the effect of a computer-assisted intervention on antimicrobial use in a tertiary care hospital. METHODS Between 2011 and 2016 we introduced an electronic alert for patients being prescribed meropenem, voriconazole and caspofungin. At prescription and at day 3 of treatment, physicians were informed about the risk related to these antimicrobial substances by an electronic alert in the medical records. Physicians were invited to revoke or confirm the prescription and to contact the infectious disease (ID) team. Using interrupted time series regression, the days of therapy (DOTs) and the number of prescriptions before and after the intervention were compared. RESULTS We counted 64,281 DOTs for 5549 prescriptions during 4100 hospital stays. Overall, the DOTs decreased continuously over time. An additional benefit of the alert could not be observed. Similarly, the number of prescriptions decreased over time, without significant effect of the intervention. When considering the three drugs separately, the alert impacted the duration (change in slope of DOTs/1000 bed days; P = 0.0017) as well as the number of prescriptions (change in slope of prescriptions/1000 bed days; P < 0.001) of voriconazole only. CONCLUSIONS The introduction of the alert lowered prescriptions of voriconazole only. Thus, self-stewardship alone seems to have a limited impact on electronic prescriptions of anti-infective substances. Additional measures such as face-to-face prompting with ID physicians or audit and feedback are indispensable to optimize antimicrobial use.
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Affiliation(s)
- Lionel Chok
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland.
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Nadia Eberhard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Dirk Saleschus
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Claudine Kocher
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Rainer Weber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
| | - Stefan P Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, Zurich, Switzerland
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49
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Schoepf IC, Thorball CW, Ledergerber B, Kootstra NA, Reiss P, Raffenberg M, Engel T, Braun DL, Hasse B, Thurnheer C, Marzolini C, Seneghini M, Bernasconi E, Cavassini M, Buvelot H, Arribas JR, Kouyos RD, Fellay J, Günthard HF, Tarr PE. Telomere Length Declines In Persons Living With HIV Before Antiretroviral Therapy Start But Not After Viral Suppression: A Longitudinal Study Over >17 Years. J Infect Dis 2021; 225:1581-1591. [PMID: 34910812 DOI: 10.1093/infdis/jiab603] [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] [Received: 09/15/2021] [Accepted: 12/13/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In people living with HIV (PWH), long-term telomere length (TL) change without/with suppressive antiretroviral therapy (ART) and the contribution of genetic background to TL are incompletely understood. METHODS We measured TL change in peripheral blood mononuclear cells by quantitative PCR in 107 Swiss HIV Cohort Study participants with longitudinal samples available both before and during suppressive ART. We applied mixed effects multi-level regression to obtain uni-/multivariable estimates for longitudinal TL dynamics including age, sex, and CD4:CD8 ratio. We assessed the effect of individual antiretrovirals and of an individual TL-polygenic risk score (TL-PRS; based on 239 single nucleotide polymorphisms) on TL in 798 additional participants from our previous longitudinal studies. RESULTS During untreated HIV infection (median observation, 7.7 [interquartile range, IQR, 4.7-11] years), TL declined significantly (median -2.12%/year; IQR, -3.48% to -0.76%/year; p=0.002). During suppressive ART (median observation, 9.8 [IQR, 7.1-11.1] years), there was no evidence of TL decline or increase (median +0.54%/year; IQR, -0.55% to +1.63%/year; p=0.329). TL-PRS contributed to TL change (global p=0.019) but particular antiretrovirals did not (all p>0.15). DISCUSSION In PWH, TL is associated with an individual polygenic risk score. TL declined significantly during untreated chronic HIV infection but no TL change occurred during suppressive ART.
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Affiliation(s)
- Isabella C Schoepf
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland.,Hepatology, Department for Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Switzerland
| | | | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Netherlands
| | - Peter Reiss
- Department of Global Health and Division of Infectious Disease, Amsterdam University Medical Centers, University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Marieke Raffenberg
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland.,Department of Intensive Care Medicine, Luzerner Kantonsspital, Luzern, Switzerland
| | - Tanja Engel
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland.,Department of Internal Medicine, Kantonsspital Uri, Altdorf, Switzerland
| | - Dominique L Braun
- 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
| | - Christine Thurnheer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Switzerland
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Switzerland
| | - Marco Seneghini
- Division of Infectious Diseases, Kantonsspital St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ospedale Regionale, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Matthias Cavassini
- Infectious Diseases Service, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Hélène Buvelot
- Division of Infectious Disease, Geneva University Hospital, Switzerland
| | - José R Arribas
- HIV/AIDS and Infectious Diseases Research Group , Department of Internal Medicine, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, CHUV, University of Lausanne, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 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, Zurich, Switzerland
| | - Philip E Tarr
- University Department of Medicine and Infectious Diseases Service, Kantonsspital Baselland, University of Basel, Bruderholz, Switzerland
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50
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Balakrishna S, Wolfensberger A, Kachalov V, Roth JA, Kusejko K, Scherrer AU, Furrer H, Hauser C, Calmy A, Cavassini M, Schmid P, Bernasconi E, Battegay M, Günthard HF, Kouyos RD. Decreasing incidence and determinants of Bacterial Pneumonia in people with HIV: The Swiss HIV Cohort Study. J Infect Dis 2021; 225:1592-1600. [PMID: 34792153 DOI: 10.1093/infdis/jiab573] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Bacterial pneumonia is one of the leading reasons for hospitalization among people with HIV (PWH), yet there is limited evidence regarding its drivers in the era of potent antiretroviral therapy. METHODS We assessed risk-factors for bacterial pneumonia in PWH enrolled in the Swiss HIV Cohort Study using univariable and multivariable marginal models. We further assessed the relationship between risk-factors and changes in bacterial pneumonia incidence using mediation analysis. RESULTS We included 12927 PWH with follow-ups between 2008 and 2018. These patients had 985 bacterial pneumonia events during a follow-up of 100779 person-years(py). bacterial pneumonia incidence significantly decreased from 13.2 cases/1000 py in 2008 to 6.8 cases/1000 py in 2018. Older age, lower education-level, intravenous drug use, smoking, lower CD4-cell-count, higher HIV-viral load, and prior pneumonia events were significantly associated with higher bacterial pneumonia incidence. Notably, even CD4-cell-counts 350-499 were significantly associated with an increased risk compared to CD4≥500 (adjusted HR,1.39; 95% CI,1.01-1.89). Finally, we found that the decreasing incidence over the last decade can be explained by decreasing proportion of patients with CD4<500, viral-RNA>200, and smoking>one cigarette/day. CONCLUSION Improvements in cascade of care of HIV and decrease in smoking may have mediated a substantial decrease in bacterial pneumonia incidence.
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Affiliation(s)
- Suraj Balakrishna
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Aline Wolfensberger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Viacheslav Kachalov
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jan A Roth
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital Basel, University of Basel, Basel, Switzerland.,Division of Research and Analytical Services, Department of Informatics, University Hospital Basel, Basel, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christoph Hauser
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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