Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Abstract Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.

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The role of genomics in understanding COVID-19 outbreaks in long term care facilities

10.31219/osf.io/7y9rk ◽

2020 ◽

Author(s):

Dinesh Aggarwal ◽

Richard Myers ◽

William L. Hamilton ◽

Tehmina Bharucha ◽

Niamh Tumelty ◽

...

Keyword(s):

Long Term Care ◽

Control Measures ◽

Sequencing Data ◽

Term Care ◽

Genomic Epidemiology ◽

Infection Control Measures ◽

Care Facilities ◽

Epidemiology Studies

A review was undertaken of all genomic epidemiology studies on COVID-19 in long term care facilities (LTCF) that have been published to date. It was found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant lineage, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by spread rather than a series of seeding events from the community into LTCFs. Sequencing of samples taken consecutively from the same cases showed persistence of the same genome sequence indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics facilitated likely transmission sources to be better characterised. Transmission between LTCFs was detected in multiple studies. The mortality rate amongst residents was high in all cases, regardless of the lineage. Bioinformatics methods were inadequate in one third of the studies reviewed, and reproducing the analyses was difficult as sequencing data were not available in many cases.

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Innovate or perish: a new paradigm for academics in the biosciences?: Commercialization of academic research

The Biochemist ◽

10.1042/bio02606016 ◽

2004 ◽

Vol 26 (6) ◽

pp. 16-19

Author(s):

Christopher R. Lowe

Keyword(s):

Higher Education ◽

Cultural Change ◽

Academic Research ◽

New Paradigm ◽

Pure Science ◽

Knowledge Based ◽

University Of Cambridge ◽

Skilled Manpower ◽

Science Base ◽

The University

Europe is striving to become the world's most competitive knowledgebased economy by 2010. The higher education sector will play a key role by providing the ideas and skilled manpower to effect this transition, but will require organizational and cultural change to be truly effective. The Institute of Biotechnology at the University of Cambridge is used as an example of how these issues can be addressed in a single organization that is able to provide a seamless mechanism to exploit its pure science base to create knowledge-based business spin-offs.

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Interventions to control nosocomial transmission of SARS-CoV-2: a modelling study

BMC Medicine ◽

10.1186/s12916-021-02060-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Thi Mui Pham ◽

Hannan Tahir ◽

Janneke H. H. M. van de Wijgert ◽

Bastiaan R. Van der Roest ◽

Pauline Ellerbroek ◽

...

Keyword(s):

Control Measures ◽

Nosocomial Transmission ◽

Sensitivity Analyses ◽

Contact Tracing ◽

Hospital Data ◽

Agent Based ◽

Effective Interventions ◽

Maximum Test ◽

Hospital Wards ◽

The Impact

Abstract Background Emergence of more transmissible SARS-CoV-2 variants requires more efficient control measures to limit nosocomial transmission and maintain healthcare capacities during pandemic waves. Yet the relative importance of different strategies is unknown. Methods We developed an agent-based model and compared the impact of personal protective equipment (PPE), screening of healthcare workers (HCWs), contact tracing of symptomatic HCWs and restricting HCWs from working in multiple units (HCW cohorting) on nosocomial SARS-CoV-2 transmission. The model was fit on hospital data from the first wave in the Netherlands (February until August 2020) and assumed that HCWs used 90% effective PPE in COVID-19 wards and self-isolated at home for 7 days immediately upon symptom onset. Intervention effects on the effective reproduction number (RE), HCW absenteeism and the proportion of infected individuals among tested individuals (positivity rate) were estimated for a more transmissible variant. Results Introduction of a variant with 56% higher transmissibility increased — all other variables kept constant — RE from 0.4 to 0.65 (+ 63%) and nosocomial transmissions by 303%, mainly because of more transmissions caused by pre-symptomatic patients and HCWs. Compared to baseline, PPE use in all hospital wards (assuming 90% effectiveness) reduced RE by 85% and absenteeism by 57%. Screening HCWs every 3 days with perfect test sensitivity reduced RE by 67%, yielding a maximum test positivity rate of 5%. Screening HCWs every 3 or 7 days assuming time-varying test sensitivities reduced RE by 9% and 3%, respectively. Contact tracing reduced RE by at least 32% and achieved higher test positivity rates than screening interventions. HCW cohorting reduced RE by 5%. Sensitivity analyses show that our findings do not change significantly for 70% PPE effectiveness. For low PPE effectiveness of 50%, PPE use in all wards is less effective than screening every 3 days with perfect sensitivity but still more effective than all other interventions. Conclusions In response to the emergence of more transmissible SARS-CoV-2 variants, PPE use in all hospital wards might still be most effective in preventing nosocomial transmission. Regular screening and contact tracing of HCWs are also effective interventions but critically depend on the sensitivity of the diagnostic test used.

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Creating a Community of Data Champions

International Journal of Digital Curation ◽

10.2218/ijdc.v12i2.562 ◽

2018 ◽

Vol 12 (2) ◽

pp. 96-106 ◽

Cited By ~ 3

Author(s):

Rosie Higman ◽

Marta Teperek ◽

Danny Kingsley

Keyword(s):

Higher Education ◽

Community Of Practice ◽

Service Providers ◽

Research Data ◽

Research Career ◽

Specific Training ◽

Practice Model ◽

University Of Cambridge ◽

Data Team ◽

The University

Research Data Management (RDM) presents an unusual challenge for service providers in Higher Education. There is increased awareness of the need for training in this area but the nature of the discipline-specific practices involved make it difficult to provide training across a multi-disciplinary organisation. Whilst most UK universities now have a research data team of some description, they are often small and rarely have the resources necessary to provide targeted training to the different disciplines and research career stages that they are increasingly expected to support. This practice paper describes the approach taken at the University of Cambridge to address this problem by creating a community of Data Champions. This collaborative initiative, working with researchers to provide training and advocacy for good RDM practice, allows for more discipline-specific training to be given, researchers to be credited for their expertise and creates an opportunity for those interested in RDM to exchange knowledge with others. The ‘community of practice’ model has been used in many sectors, including Higher Education, to facilitate collaboration across organisational units and this initiative will adopt some of the same principles to improve communication across a decentralised institution. The Data Champions initiative at Cambridge was launched in September 2016 and this paper reports on the early months, plans for building the community in the future and the possible risks associated with this approach to providing RDM services.

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Creating a Community of Data Champions

10.1101/104661 ◽

2017 ◽

Cited By ~ 2

Author(s):

Rosie Higman ◽

Marta Teperek ◽

Danny Kingsley

Keyword(s):

Higher Education ◽

Community Of Practice ◽

Service Providers ◽

Research Data ◽

Research Career ◽

Specific Training ◽

Practice Model ◽

University Of Cambridge ◽

Data Team ◽

The University

AbstractResearch Data Management (RDM) presents an unusual challenge for service providers in Higher Education. There is increased awareness of the need for training in this area but the nature of discipline-specific practices involved make it difficult to provide training across a multi-disciplinary organisation. Whilst most UK universities now have a research data team of some description, they are often small and rarely have the resources necessary to provide targeted training to the different disciplines and research career stages that they are increasingly expected to support.This practice paper describes the approach taken at the University of Cambridge to address this problem by creating a community of Data Champions. This collaborative initiative, working with researchers to provide training and advocacy for good RDM practice, allows for more discipline-specific training to be given, researchers to be credited for their expertise and an opportunity for those interested in RDM to exchange knowledge with others. The ‘community of practice’ model has been used in many sectors, including Higher Education, to facilitate collaboration across organisational units and this initiative will adopt some of the same principles to improve communication across a decentralised institution. The Data Champions initiative at Cambridge was launched in September 2016 and this paper reports on the early months, plans for building the community in the future and the possible risks associated with this approach to providing RDM services.

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Interventions to control nosocomial transmission of SARS-CoV-2: a modelling study

10.1101/2021.02.26.21252327 ◽

2021 ◽

Author(s):

Thi Mui Pham ◽

Hannan Tahir ◽

Janneke H.H.M. van de Wijgert ◽

Bastiaan Van der Roest ◽

Pauline Ellerbroek ◽

...

Keyword(s):

Control Measures ◽

Nosocomial Transmission ◽

Sensitivity Analyses ◽

Contact Tracing ◽

Hospital Data ◽

Agent Based ◽

Effective Interventions ◽

Maximum Test ◽

Hospital Wards ◽

The Impact

AbstractBackgroundEmergence of more transmissible SARS-CoV-2 variants requires more efficient control measures to limit nosocomial transmission and maintain healthcare capacities during pandemic waves. Yet, the relative importance of different strategies is unknown.MethodsWe developed an agent-based model and compared the impact of personal protective equipment (PPE), screening of healthcare workers (HCWs), contact tracing of symptomatic HCWs, and restricting HCWs from working in multiple units (HCW cohorting) on nosocomial SARS-CoV-2 transmission. The model was fit on hospital data from the first wave in the Netherlands (February until August 2020) and assumed that HCWs used 90% effective PPE in COVID-19 wards and self-isolated at home for seven days immediately upon symptom onset. Intervention effects on the effective reproduction number (RE), HCW absenteeism and the proportion of infected individuals among tested individuals (positivity rate) were estimated for a more transmissible variant.ResultsIntroduction of a variant with 56% higher transmissibility increased – all other variables kept constant – RE from 0.4 to 0.65 (+63%) and nosocomial transmissions by 303%, mainly because of more transmissions caused by pre-symptomatic patients and HCWs. Compared to baseline, PPE use in all hospital wards (assuming 90% effectiveness) reduced RE by 85% and absenteeism by 57%. Screening HCWs every three days with perfect test sensitivity reduced RE by 67%, yielding a maximum test positivity rate of 5%. Screening HCWs every three or seven days assuming time-varying test sensitivities reduced RE by 9% and 3%, respectively. Contact tracing reduced RE by at least 32% and achieved higher test positivity rates than screening interventions. HCW cohorting reduced RE by 5%. Sensitivity analyses for 50% and 70% effectiveness of PPE use did not change interpretation.ConclusionsIn response to the emergence of more transmissible SARS-CoV-2 variants, PPE use in all hospital wards might still be most effective in preventing nosocomial transmission. Regular screening and contact tracing of HCWs are also effective interventions, but critically depend on the sensitivity of the diagnostic test used.

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Multidrug-resistant organisms detected in refugee patients admitted to a University Hospital, Germany June‒December 2015

Eurosurveillance ◽

10.2807/1560-7917.es.2016.21.2.30110 ◽

2016 ◽

Vol 21 (2) ◽

Cited By ~ 48

Author(s):

Claudia Reinheimer ◽

Volkhard A. J. Kempf ◽

Stephan Göttig ◽

Michael Hogardt ◽

Thomas A. Wichelhaus ◽

...

Keyword(s):

Confidence Interval ◽

Multidrug Resistant ◽

Control Measures ◽

University Hospital ◽

Healthcare Personnel ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Infection Control Measures ◽

Multidrug Resistant Organisms ◽

The University

Multidrug-resistant Gram-negative bacteria (MDR GNB) were found to colonise 60.8% (95% confidence interval: 52.3–68.9) of 143 refugee patients mainly from Syria (47), Afghanistan (29), and Somalia (14) admitted to the University Hospital Frankfurt, Germany, between June and December 2015. This percentage exceeds the prevalence of MDR GNB in resident patients four–fold. Healthcare personnel should be aware of this and the need to implement or adapt adequate infection control measures.

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Surgical site infections in an abdominal surgical ward at Kosovo Teaching Hospital

The Journal of Infection in Developing Countries ◽

10.3855/jidc.375 ◽

2007 ◽

Vol 1 (03) ◽

pp. 337-341 ◽

Cited By ~ 3

Author(s):

Lul Raka ◽

Avdyl Krasniqi ◽

Faton Hoxha ◽

Ruustem Musa ◽

Gjyle Mulliqi ◽

...

Keyword(s):

Abdominal Surgery ◽

Infection Control ◽

Surgical Site Infections ◽

Control Measures ◽

Surgical Interventions ◽

Infection Control Measures ◽

Duration Of Hospitalization ◽

System Risk ◽

Considerable Morbidity ◽

The University

Background: Abdominal surgical site infections (SSI) cause substantial morbidity and mortality for patients undergoing operative procedures. We determined the incidence of and risk factors for SSI after abdominal surgery in the Department of Abdominal Surgery at the University Clinical Centre of Kosovo (UCCK). Methodology: Prospective surveillance of patients undergoing abdominal surgery was performed between December 2005 and June 2006. CDC definitions were followed to detect SSI and study forms were based on Europe Link for Infection Control through Surveillance (HELICS) protocol. Results: A total of 253 surgical interventions in 225 patients were evaluated. The median age of patients was 42 years and 55.1% of them were male. The overall incidence rate of SSI was 12%. Follow-up was achieved for 84.1% of the procedures. For patients with an SSI, the median duration of hospitalization was 9 days compared with 4 days for those without an SSI (p2, use of antibiotic prophylaxis and NNIS class of >2 were all significant at p < .001. The SSI rates for the NNIS System risk classes 0, 1 and 2-3 were 4.2%, 46.7% and 100%, respectively. Conclusions: SSI caused considerable morbidity among surgical patients in UCCK. Appropriate active surveillance and infection control measures should be introduced during preoperative, intra-operative, and postoperative care to reduce infection rates.

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Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

Microorganisms ◽

10.3390/microorganisms8121986 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1986

Author(s):

João Perdigão ◽

Cátia Caneiras ◽

Rita Elias ◽

Ana Modesto ◽

Anton Spadar ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bioinformatic Analysis ◽

Multidrug Resistant ◽

Control Measures ◽

Whole Genome ◽

Genomic Epidemiology ◽

Infection Control Measures ◽

Carbapenemase Gene

The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.

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A Comparison of Dental Education Between University of Toronto and Zhejiang University During COVID-19 Pandemic

10.21203/rs.3.rs-112022/v1 ◽

2020 ◽

Author(s):

Juan Zhao ◽

Xiaomin Zhao ◽

Na Zhou ◽

Sijie Wang ◽

Guanchen Ye ◽

...

Keyword(s):

Online Survey ◽

Dental Education ◽

Dental Students ◽

Control Measures ◽

Small Scale ◽

University Of Toronto ◽

Online Mode ◽

Infection Control Measures ◽

Research Activities ◽

The University

Abstract Background: To compare the contingency modifications to the dental education between the University of Toronto Faculty of Dentistry and the Zhejiang University School of Stomatology during COVID-19 pandemic, and to share experiences in keeping the dental academic continuity, resuming practicing activities and preparing the faculty and students for a new normality. Three approaches were adopted to collect information and data: online interviews and email-contact with the instructors and the deans, a small-scale online survey of dental students, and official online announcements of various authorities. Results: The two universities shared similarity in changing trends, while differed in details. The delivery of lectures, seminars and exams was transitioned from in-person mode to online mode and has proceeded effectively and efficiently. The pre-clinical lab training and clinical rotation were the most retarded parts and will not be resumed until the settle-down of the pandemic. Research activities have been kept on at the best possible level. Since the Zhejiang University reopened the campus in May 2020, clinical activities and research works were in recovery with a cautiously-planned and gradual phased approach. Conclusion: Both universities have been trying their best to meet the academic needs of students while protect their health, and to keep alert to the real time epidemic situation in preparation for resumption. Dental institutions could take the COVID-19 pandemic as an opportunity to armor dental students with infection control measures prior to their reengagement into clinical practice. There is a need of a new normality for global dental education that spans time and space.

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