Pub Date : 2022-07-31DOI: 10.1101/2022.07.28.22278048
C. Van Dijck, N. Hens, C. Kenyon, A. Tsoumanis
We used a network model to simulate a monkeypox epidemic among men who have sex with men. Our findings suggest that unrecognized infections have an important impact on the epidemic, and that vaccination of individuals at highest risk of infection reduces epidemic size more than post-exposure vaccination of sexual partners.
{"title":"The roles of unrecognized monkeypox cases, contact isolation and vaccination in determining epidemic size in Belgium. A modelling study","authors":"C. Van Dijck, N. Hens, C. Kenyon, A. Tsoumanis","doi":"10.1101/2022.07.28.22278048","DOIUrl":"https://doi.org/10.1101/2022.07.28.22278048","url":null,"abstract":"We used a network model to simulate a monkeypox epidemic among men who have sex with men. Our findings suggest that unrecognized infections have an important impact on the epidemic, and that vaccination of individuals at highest risk of infection reduces epidemic size more than post-exposure vaccination of sexual partners.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74308201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Reply to Author.","authors":"Lin Qiu, Lan Zhu","doi":"10.1093/cid/ciaa1610","DOIUrl":"10.1093/cid/ciaa1610","url":null,"abstract":"","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9258919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85035617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-05DOI: 10.1101/2022.03.13.22272267
Jonathan M Cohen, Michael Carter, C. Ronny Cheung, S. Ladhani
Abstract Little is known about the MIS-C risk with different SARS-CoV-2 variants. In Southeast England, MIS-C rates per confirmed SARS-CoV-2 infections in 0-16 years-olds were 56% lower (rate ratio, 0.34; 95%CI, 0.23-0.50) during pre-vaccine Delta, 66% lower (0.44; 0.28-0.69) during post-vaccine Delta and 95% lower (0.05; 0.02-0.10) during the Omicron period.
{"title":"Lower Risk of Multisystem Inflammatory Syndrome in Children (MIS-C) with the Delta and Omicron variants of SARS-CoV-2","authors":"Jonathan M Cohen, Michael Carter, C. Ronny Cheung, S. Ladhani","doi":"10.1101/2022.03.13.22272267","DOIUrl":"https://doi.org/10.1101/2022.03.13.22272267","url":null,"abstract":"Abstract Little is known about the MIS-C risk with different SARS-CoV-2 variants. In Southeast England, MIS-C rates per confirmed SARS-CoV-2 infections in 0-16 years-olds were 56% lower (rate ratio, 0.34; 95%CI, 0.23-0.50) during pre-vaccine Delta, 66% lower (0.44; 0.28-0.69) during post-vaccine Delta and 95% lower (0.05; 0.02-0.10) during the Omicron period.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78410595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Nasty Human Immunodeficiency Virus Type 1 (HIV-1) Variant.","authors":"S. Deresinski","doi":"10.1093/cid/ciac365","DOIUrl":"https://doi.org/10.1093/cid/ciac365","url":null,"abstract":"","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89321428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-16DOI: 10.1101/2022.06.14.22276401
Z. Swank, Y. Senussi, Z. Manickas-Hill, Xu G. Yu, Jonathan Z. Li, G. Alter, David R. Walt
The diagnosis and management of post-acute sequelae of COVID-19 (PASC) poses an ongoing medical challenge. Identifying biomarkers associated with PASC would immensely improve the classification of PASC patients and provide the means to evaluate treatment strategies. We analyzed plasma samples collected from a cohort of PASC and COVID-19 patients (n = 63) to quantify circulating viral antigens and inflammatory markers. Strikingly, we detect SARS-CoV-2 spike antigen in a majority of PASC patients up to 12 months post-diagnosis, suggesting the presence of an active persistent SARS-CoV-2 viral reservoir. Furthermore, temporal antigen profiles for many patients show the presence of spike at multiple time points over several months, highlighting the potential utility of the SARS-CoV-2 full spike protein as a biomarker for PASC.
{"title":"Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae","authors":"Z. Swank, Y. Senussi, Z. Manickas-Hill, Xu G. Yu, Jonathan Z. Li, G. Alter, David R. Walt","doi":"10.1101/2022.06.14.22276401","DOIUrl":"https://doi.org/10.1101/2022.06.14.22276401","url":null,"abstract":"The diagnosis and management of post-acute sequelae of COVID-19 (PASC) poses an ongoing medical challenge. Identifying biomarkers associated with PASC would immensely improve the classification of PASC patients and provide the means to evaluate treatment strategies. We analyzed plasma samples collected from a cohort of PASC and COVID-19 patients (n = 63) to quantify circulating viral antigens and inflammatory markers. Strikingly, we detect SARS-CoV-2 spike antigen in a majority of PASC patients up to 12 months post-diagnosis, suggesting the presence of an active persistent SARS-CoV-2 viral reservoir. Furthermore, temporal antigen profiles for many patients show the presence of spike at multiple time points over several months, highlighting the potential utility of the SARS-CoV-2 full spike protein as a biomarker for PASC.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76529618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A 58-Year-old Man With Multifocal Pulmonary Nodules.","authors":"Mitchell McClean, S. K. Gupta, R. Relich","doi":"10.1093/cid/ciab734","DOIUrl":"https://doi.org/10.1093/cid/ciab734","url":null,"abstract":"","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83032965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction to: A Rare Mutation in SPLUNC1 Affects Bacterial Adherence and Invasion in Meningococcal Disease","authors":"","doi":"10.1093/cid/ciac263","DOIUrl":"https://doi.org/10.1093/cid/ciac263","url":null,"abstract":"","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87586625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. de Castilhos, Eli Zamir, T. Hippchen, R. Rohrbach, Sabine Schmidt, Silvana Hengler, Hanna Schumacher, Melanie Neubauer, Sabrina Kunz, Tonia Müller-Esch, A. Hiergeist, A. Gessner, D. Khalid, R. Gaiser, N. Cullin, Stamatia M Papagiannarou, B. Beuthien-Baumann, A. Krämer, R. Bartenschlager, D. Jäger, Michael Müller, F. Herth, D. Duerschmied, J. Schneider, R. Schmid, Johann F Eberhardt, Y. Khodamoradi, M. Vehreschild, A. Teufel, M. Ebert, P. Hau, B. Salzberger, P. Schnitzler, Hendrik Poeck, E. Elinav, U. Merle, C. Stein-Thoeringer
{"title":"Correction to: Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients","authors":"J. de Castilhos, Eli Zamir, T. Hippchen, R. Rohrbach, Sabine Schmidt, Silvana Hengler, Hanna Schumacher, Melanie Neubauer, Sabrina Kunz, Tonia Müller-Esch, A. Hiergeist, A. Gessner, D. Khalid, R. Gaiser, N. Cullin, Stamatia M Papagiannarou, B. Beuthien-Baumann, A. Krämer, R. Bartenschlager, D. Jäger, Michael Müller, F. Herth, D. Duerschmied, J. Schneider, R. Schmid, Johann F Eberhardt, Y. Khodamoradi, M. Vehreschild, A. Teufel, M. Ebert, P. Hau, B. Salzberger, P. Schnitzler, Hendrik Poeck, E. Elinav, U. Merle, C. Stein-Thoeringer","doi":"10.1093/cid/ciac254","DOIUrl":"https://doi.org/10.1093/cid/ciac254","url":null,"abstract":"","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82426682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-03DOI: 10.1101/2022.05.02.22273921
B. Forde, H. Bergh, Thom Cuddihy, K. Hajkowicz, Trish Hurst, E. Playford, B. Henderson, N. Runnegar, J. Clark, A. Jennison, S. Moss, A. Hume, Hugo Leroux, S. Beatson, D. Paterson, P. Harris
Background: Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting. Materials/methods: We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MSLT) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams. Results: Over four years (April 2017 to July 2021) 2,660 isolates were sequenced. This included MDR gram-negative bacilli (n=293 CPE, n=1309 ESBL), MRSA (n=620) and VRE (n=433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the three target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community. In one hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy. Conclusions: Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.
{"title":"Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens","authors":"B. Forde, H. Bergh, Thom Cuddihy, K. Hajkowicz, Trish Hurst, E. Playford, B. Henderson, N. Runnegar, J. Clark, A. Jennison, S. Moss, A. Hume, Hugo Leroux, S. Beatson, D. Paterson, P. Harris","doi":"10.1101/2022.05.02.22273921","DOIUrl":"https://doi.org/10.1101/2022.05.02.22273921","url":null,"abstract":"Background: Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting. Materials/methods: We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MSLT) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams. Results: Over four years (April 2017 to July 2021) 2,660 isolates were sequenced. This included MDR gram-negative bacilli (n=293 CPE, n=1309 ESBL), MRSA (n=620) and VRE (n=433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the three target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community. In one hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy. Conclusions: Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83189101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-04-27DOI: 10.1101/2022.04.24.22274237
Tal Brosh-Nissimov, K. Hussein, Y. Wiener‐Well, E. Orenbuch-Harroch, Meital Elbaz, Shelly Lipman-Arens, Y. Maor, Y. Yagel, B. Chazan, M. Hershman-Sarafov, G. Rahav, O. Zimhony, Adi Zaidman Shimshovitz, M. Chowers
Importance: Waning immunity against COVID-19 in parallel with an increased incidence during the Omicron outbreak led the Israeli Ministry of Health to recommend a second booster dose of BNT162b2 (Pfizer) to high-risk individuals. Israel was the first country to recommend this, allowing evaluation of the added protection of a fourth vaccine dose to hospitalized patients with severe diseases. Objective: To assess the effect of a fourth dose for hospitalized patients with severe/critical breakthrough COVID-19. Design: A cohort study of hospitalized adults from 01/15/2022-01/31/2022. Settings: A multi center study of 14 medical centers in Israel. Participants: Hospitalized adult patients with PCR-confirmed severe/critical COVID-19. Excluded were patients lacking data on vaccination status. Exposure: Cases were divided according to the total number of vaccine doses received up to 7 days before diagnosis. Unvaccinated adults and single-dose recipients were grouped into an unvaccinated group. Main Outcome: A composite of mechanical ventilation or in-hospital death was defined as poor outcome. Outcomes were compared between 3- and 4-dose vaccinees. Results: Included were 1,049 patients with severe/critical COVID-19, median age 80 (IQR 69-87), 51% males. Among them, 360 unvaccinated, 34, 172, 386 and 88 were after 1, 2, 3 or 4 doses, respectively. Patients after 3 doses were older, had more males and immunosuppression, but with similar outcomes, 49% vs. 51% compared to unvaccinated patients (p=0.72). Patients after 4 doses were similarly older and immunosuppressed, but had improved outcomes compared to unvaccinated patients, 34% vs. 51% (p<0.01). We proceeded to examine independent predictors for poor outcome in fully-vaccinated patients with either 3 doses given a median of 161 (IQR 147-168) days earlier, or 4 doses given a median of 14 (IQR 10-18) days before diagnoses. Receipt of the fourth dose conferred significant protection: OR 0.51 (95%CI 0.30.87). Conclusion and Relevance: Within a population of hospitalized patients with severe/critical breakthrough COVID-19, a recent fourth dose was associated with significant protection against mechanical ventilation or death, compared to fully-vaccinated single boosted individuals.
{"title":"Hospitalized patients with severe COVID-19 during the Omicron wave in Israel – benefits of a fourth vaccine dose","authors":"Tal Brosh-Nissimov, K. Hussein, Y. Wiener‐Well, E. Orenbuch-Harroch, Meital Elbaz, Shelly Lipman-Arens, Y. Maor, Y. Yagel, B. Chazan, M. Hershman-Sarafov, G. Rahav, O. Zimhony, Adi Zaidman Shimshovitz, M. Chowers","doi":"10.1101/2022.04.24.22274237","DOIUrl":"https://doi.org/10.1101/2022.04.24.22274237","url":null,"abstract":"Importance: Waning immunity against COVID-19 in parallel with an increased incidence during the Omicron outbreak led the Israeli Ministry of Health to recommend a second booster dose of BNT162b2 (Pfizer) to high-risk individuals. Israel was the first country to recommend this, allowing evaluation of the added protection of a fourth vaccine dose to hospitalized patients with severe diseases. Objective: To assess the effect of a fourth dose for hospitalized patients with severe/critical breakthrough COVID-19. Design: A cohort study of hospitalized adults from 01/15/2022-01/31/2022. Settings: A multi center study of 14 medical centers in Israel. Participants: Hospitalized adult patients with PCR-confirmed severe/critical COVID-19. Excluded were patients lacking data on vaccination status. Exposure: Cases were divided according to the total number of vaccine doses received up to 7 days before diagnosis. Unvaccinated adults and single-dose recipients were grouped into an unvaccinated group. Main Outcome: A composite of mechanical ventilation or in-hospital death was defined as poor outcome. Outcomes were compared between 3- and 4-dose vaccinees. Results: Included were 1,049 patients with severe/critical COVID-19, median age 80 (IQR 69-87), 51% males. Among them, 360 unvaccinated, 34, 172, 386 and 88 were after 1, 2, 3 or 4 doses, respectively. Patients after 3 doses were older, had more males and immunosuppression, but with similar outcomes, 49% vs. 51% compared to unvaccinated patients (p=0.72). Patients after 4 doses were similarly older and immunosuppressed, but had improved outcomes compared to unvaccinated patients, 34% vs. 51% (p<0.01). We proceeded to examine independent predictors for poor outcome in fully-vaccinated patients with either 3 doses given a median of 161 (IQR 147-168) days earlier, or 4 doses given a median of 14 (IQR 10-18) days before diagnoses. Receipt of the fourth dose conferred significant protection: OR 0.51 (95%CI 0.30.87). Conclusion and Relevance: Within a population of hospitalized patients with severe/critical breakthrough COVID-19, a recent fourth dose was associated with significant protection against mechanical ventilation or death, compared to fully-vaccinated single boosted individuals.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90527902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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