T. Yip, G. Lui, Mandy Sze-Man Lai, V. Wong, Y. Tse, Bosco Ma, Elsie Hui, Maria Kw Leung, H. Chan, D. S. Hui, G. Wong
ABSTRACT Background We examined the effectiveness of molnupiravir and nirmatrelvir/ritonavir in reducing hospitalization and deaths in a real-world cohort of non-hospitalized COVID-19 patients. Methods This was a territory-wide retrospective cohort study in Hong Kong. Non-hospitalized COVID-19 patients who attended designated outpatient clinics between 16 February and 31 March 2022 were identified. Patients hospitalized on the day of the first clinic appointment or used both oral antivirals were excluded. The primary endpoint was hospitalization. The secondary endpoint was a composite of intensive care unit admission, invasive mechanical ventilation use, and/or death. Results Of 93,883 patients, 83,154 (88.6%), 5,808 (6.2%), and 4,921 (5.2%) were oral antiviral non-users, molnupiravir users, and nirmatrelvir/ritonavir users respectively. Compared to non-users, oral antiviral users were older and had more comorbidities, lower complete vaccination rate, and more hospitalizations in the previous year. Molnupiravir users were older, and had more comorbidities, lower complete vaccination rate, and more hospitalizations in the previous year than nirmatrelvir/ritonavir users. At a median follow-up of 30 days, 1,931 (2.1%) patients were hospitalized and 225 (0.2%) patients developed the secondary endpoint. After propensity score weighting, nirmatrelvir/ritonavir use (weighted hazard ratio 0.79, 95%CI 0.65-0.95, P = 0.011) but not molnupiravir use (weighted hazard ratio 1.17, 95%CI 0.99-1.39, P = 0.062) was associated with a reduced risk of hospitalization than non-users. The use of molnupiravir or nirmatrelvir/ritonavir was not associated with a lower risk of the secondary endpoint as compared to non-users. Conclusion Use of nirmatrelvir/ritonavir but not molnupiravir was associated with a reduced risk of hospitalization in real-world non-hospitalized COVID-19 patients.
背景:我们研究了莫努匹拉韦和尼马特利韦/利托那韦在现实世界非住院COVID-19患者队列中降低住院和死亡的有效性。方法:本研究是在香港进行的一项区域性回顾性队列研究。确定了2022年2月16日至3月31日期间在指定门诊就诊的非住院COVID-19患者。排除首次门诊预约当天住院或同时使用两种口服抗病毒药物的患者。主要终点是住院。次要终点是重症监护病房入住、有创机械通气使用和/或死亡的综合指标。结果93,883例患者中，83,154例(88.6%)、5,808例(6.2%)和4,921例(5.2%)分别为口服抗病毒药物非使用者、莫努匹拉韦使用者和尼马特利韦/利托那韦使用者。与非服用者相比，口服抗病毒药物服用者年龄更大，合并症更多，完全疫苗接种率更低，前一年住院次数更多。与尼马特里韦/利托那韦使用者相比，莫硝吡韦使用者年龄更大，合并症更多，完全疫苗接种率更低，前一年住院次数更多。中位随访时间为30天，1,931例(2.1%)患者住院，225例(0.2%)患者出现次要终点。在倾向评分加权后，尼马特利韦/利托那韦的使用(加权风险比0.79,95%CI 0.65-0.95, P = 0.011)与住院风险降低相关，而莫那匹拉韦的使用(加权风险比1.17,95%CI 0.99-1.39, P = 0.062)与住院风险降低无关。与非使用者相比，使用莫努匹拉韦或尼马特利韦/利托那韦与次要终点风险降低无关。结论:在现实世界的非住院COVID-19患者中，使用尼马特利韦/利托那韦而不使用莫努匹拉韦与住院风险降低相关。
{"title":"Impact of the use of oral antiviral agents on the risk of hospitalization in community COVID-19 patients","authors":"T. Yip, G. Lui, Mandy Sze-Man Lai, V. Wong, Y. Tse, Bosco Ma, Elsie Hui, Maria Kw Leung, H. Chan, D. S. Hui, G. Wong","doi":"10.2139/ssrn.4112160","DOIUrl":"https://doi.org/10.2139/ssrn.4112160","url":null,"abstract":"ABSTRACT Background We examined the effectiveness of molnupiravir and nirmatrelvir/ritonavir in reducing hospitalization and deaths in a real-world cohort of non-hospitalized COVID-19 patients. Methods This was a territory-wide retrospective cohort study in Hong Kong. Non-hospitalized COVID-19 patients who attended designated outpatient clinics between 16 February and 31 March 2022 were identified. Patients hospitalized on the day of the first clinic appointment or used both oral antivirals were excluded. The primary endpoint was hospitalization. The secondary endpoint was a composite of intensive care unit admission, invasive mechanical ventilation use, and/or death. Results Of 93,883 patients, 83,154 (88.6%), 5,808 (6.2%), and 4,921 (5.2%) were oral antiviral non-users, molnupiravir users, and nirmatrelvir/ritonavir users respectively. Compared to non-users, oral antiviral users were older and had more comorbidities, lower complete vaccination rate, and more hospitalizations in the previous year. Molnupiravir users were older, and had more comorbidities, lower complete vaccination rate, and more hospitalizations in the previous year than nirmatrelvir/ritonavir users. At a median follow-up of 30 days, 1,931 (2.1%) patients were hospitalized and 225 (0.2%) patients developed the secondary endpoint. After propensity score weighting, nirmatrelvir/ritonavir use (weighted hazard ratio 0.79, 95%CI 0.65-0.95, P = 0.011) but not molnupiravir use (weighted hazard ratio 1.17, 95%CI 0.99-1.39, P = 0.062) was associated with a reduced risk of hospitalization than non-users. The use of molnupiravir or nirmatrelvir/ritonavir was not associated with a lower risk of the secondary endpoint as compared to non-users. Conclusion Use of nirmatrelvir/ritonavir but not molnupiravir was associated with a reduced risk of hospitalization in real-world non-hospitalized COVID-19 patients.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90859247","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}
Ian W. Pray, B. Grajewski, Collin Morris, Komi Modji, P. DeJonge, Katherine McCoy, C. Tomasallo, Traci Desalvo, R. Westergaard, J. Meiman
Abstract Background Work-related exposures play an important role in SARS-CoV-2 transmission, yet few studies have measured the risk of COVID-19 across occupations and industries. Methods During September 2020 – May 2021, the Wisconsin Department of Health Services collected occupation and industry data as part of routine COVID-19 case investigations. Adults aged 18-64 years with confirmed or probable COVID-19 in Wisconsin were assigned standardized occupation and industry codes. Cumulative incidence rates were weighted for non-response and calculated using full-time equivalent (FTE) workforce denominators from the 2020 American Community Survey. Results An estimated 11.6% of workers (347,013 of 2.98 million) in Wisconsin, ages 18-64 years, had COVID-19 from September 2020 to May 2021. The highest incidence by occupation (per 100 full-time equivalents) occurred among personal care and services workers (22.4), healthcare practitioners and support staff (20.7), and protective services workers (20.7). High risk sub-groups included nursing assistants and personal care aides (28.8), childcare workers (25.8), food and beverage service workers (25.3), personal appearance workers (24.4), and law enforcement workers (24.1). By industry, incidence was highest in healthcare (18.6); the highest risk sub-sectors were nursing care facilities (30.5) and warehousing (28.5). Conclusions This analysis represents one of the most complete examinations to date of COVID-19 incidence by occupation and industry. Our approach demonstrates the value of standardized occupational data collection by public health, and may be a model for improved occupational surveillance elsewhere. Workers at higher risk of SARS-CoV-2 exposure may benefit from targeted workplace COVID-19 vaccination and mitigation efforts.
{"title":"Measuring work-related risk of COVID-19: comparison of COVID-19 incidence by occupation and industry – Wisconsin, September 2020-May 2021","authors":"Ian W. Pray, B. Grajewski, Collin Morris, Komi Modji, P. DeJonge, Katherine McCoy, C. Tomasallo, Traci Desalvo, R. Westergaard, J. Meiman","doi":"10.2139/ssrn.4081070","DOIUrl":"https://doi.org/10.2139/ssrn.4081070","url":null,"abstract":"Abstract Background Work-related exposures play an important role in SARS-CoV-2 transmission, yet few studies have measured the risk of COVID-19 across occupations and industries. Methods During September 2020 – May 2021, the Wisconsin Department of Health Services collected occupation and industry data as part of routine COVID-19 case investigations. Adults aged 18-64 years with confirmed or probable COVID-19 in Wisconsin were assigned standardized occupation and industry codes. Cumulative incidence rates were weighted for non-response and calculated using full-time equivalent (FTE) workforce denominators from the 2020 American Community Survey. Results An estimated 11.6% of workers (347,013 of 2.98 million) in Wisconsin, ages 18-64 years, had COVID-19 from September 2020 to May 2021. The highest incidence by occupation (per 100 full-time equivalents) occurred among personal care and services workers (22.4), healthcare practitioners and support staff (20.7), and protective services workers (20.7). High risk sub-groups included nursing assistants and personal care aides (28.8), childcare workers (25.8), food and beverage service workers (25.3), personal appearance workers (24.4), and law enforcement workers (24.1). By industry, incidence was highest in healthcare (18.6); the highest risk sub-sectors were nursing care facilities (30.5) and warehousing (28.5). Conclusions This analysis represents one of the most complete examinations to date of COVID-19 incidence by occupation and industry. Our approach demonstrates the value of standardized occupational data collection by public health, and may be a model for improved occupational surveillance elsewhere. Workers at higher risk of SARS-CoV-2 exposure may benefit from targeted workplace COVID-19 vaccination and mitigation efforts.","PeriodicalId":10421,"journal":{"name":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87932955","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 : 2022-07-31DOI: 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":"62 1","pages":""},"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}
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":"47 1","pages":""},"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":"1 1","pages":"i-ii"},"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":"57 1","pages":""},"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":"183 1","pages":"1879-1882"},"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":"30 1","pages":"184 - 184"},"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":"28 1","pages":""},"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":"103 1","pages":""},"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}
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