Improving the management of sepsis through rapid pathogen and antibiotic resistance detection in blood
Lead Research Organisation:
University of East Anglia
Department Name: Norwich Medical School
Abstract
It is widely recognised that rapid diagnostics are crucial (1) in the fight against antimicrobial resistance (AMR), allowing earlier and more precise targeting of pathogens with narrow-spectrum antibiotics, and (2) for improving the management of life threatening infections such as sepsis. Current methods - blood culture and PCR based molecular tests - are not fit-for-purpose in this context. Blood culture methods have long turn-around times and offer poor clinical sensitivity; PCR based methods are not sufficiently comprehensive, detecting only selected pathogens and/or resistance markers. A paradigm shift in diagnostic microbiology is urgently required.
Next generation sequencing (NGS) based diagnosis has the potential to deliver this step change, being potentially as swift as PCR and as comprehensive as culture. However, sequencing-based pathogen identification in bloodstream infection diagnosis is very challenging owing to the vast amount of human DNA present compared with pathogen DNA (the ratio can be as high as 10^9:1). Therefore, pathogen DNA enrichment is crucial and we are developing novel strategies to achieve this, removing the vast majority of the human DNA from blood (without any significant loss of pathogen DNA) and reducing the ratio of human:pathogen DNA from 10^9:1 to < 10:1. We have proof-of-concept data to demonstrate that our approach, combined with MinION nanopore sequencing technology, can be used successfully to identify pathogens and their resistance genes in blood samples from patients with sepsis within 8h.
With this approach, if it can be introduced to the clinic, patients need receive only one dose of empirical broad-spectrum antibiotics before treatment can be tailored for the pathogen/patient - a true 'precision medicine' approach to antibiotic treatment. This dramatic improvement to the 'Start Smart - then Focus' approach to antimicrobial stewardship (Public Health England) will lead to a reduction in the use of broad-spectrum antibiotics, mitigating selection pressure for antibiotic resistance. It will also reduce the number of patients who receive inappropriate antibiotics for their infections, with contingent decreases in morbidity and mortality.
We propose to:
- Further develop and optimise our current pathogen DNA enrichment strategy and to test two new enrichment strategies
- Test a number of NGS technologies/platforms to determine the most suitable in terms of analysis time, flexibility, complexity of bioinformatics analysis, cost and comprehensiveness of sequencing results
- Run a clinical diagnostics evaluation, testing 50 well-phenotyped, biobanked human blood samples from sepsis patients and controls to validate the performance of the optimised NGS based method.
This project, combining our novel pathogen DNA enrichment strategies with NGS, represents the cutting edge of clinical microbiology and genomics, and will ensure the UK and the NHS are among the global leaders in genomics-based stratified and precision medicine.
The pathogen DNA enrichment and NGS workflows will be applicable to diagnostic samples from other life-threatening infections e.g. healthcare-associated pneumonia and complicated urinary tract infections. Comprehensive sequencing-based diagnostics will enable not only the wider use, but also the clinical development of narrow spectrum antibiotics. Lastly, they will identify bacterial strains and their variants, providing information that can be used for infection control and for both local and national epidemiology purposes. The preliminary work that I have performed, along with my expertise and that of my collaborators, make me uniquely positioned to deliver this cutting edge, ambitious, high impact translational research project.
Next generation sequencing (NGS) based diagnosis has the potential to deliver this step change, being potentially as swift as PCR and as comprehensive as culture. However, sequencing-based pathogen identification in bloodstream infection diagnosis is very challenging owing to the vast amount of human DNA present compared with pathogen DNA (the ratio can be as high as 10^9:1). Therefore, pathogen DNA enrichment is crucial and we are developing novel strategies to achieve this, removing the vast majority of the human DNA from blood (without any significant loss of pathogen DNA) and reducing the ratio of human:pathogen DNA from 10^9:1 to < 10:1. We have proof-of-concept data to demonstrate that our approach, combined with MinION nanopore sequencing technology, can be used successfully to identify pathogens and their resistance genes in blood samples from patients with sepsis within 8h.
With this approach, if it can be introduced to the clinic, patients need receive only one dose of empirical broad-spectrum antibiotics before treatment can be tailored for the pathogen/patient - a true 'precision medicine' approach to antibiotic treatment. This dramatic improvement to the 'Start Smart - then Focus' approach to antimicrobial stewardship (Public Health England) will lead to a reduction in the use of broad-spectrum antibiotics, mitigating selection pressure for antibiotic resistance. It will also reduce the number of patients who receive inappropriate antibiotics for their infections, with contingent decreases in morbidity and mortality.
We propose to:
- Further develop and optimise our current pathogen DNA enrichment strategy and to test two new enrichment strategies
- Test a number of NGS technologies/platforms to determine the most suitable in terms of analysis time, flexibility, complexity of bioinformatics analysis, cost and comprehensiveness of sequencing results
- Run a clinical diagnostics evaluation, testing 50 well-phenotyped, biobanked human blood samples from sepsis patients and controls to validate the performance of the optimised NGS based method.
This project, combining our novel pathogen DNA enrichment strategies with NGS, represents the cutting edge of clinical microbiology and genomics, and will ensure the UK and the NHS are among the global leaders in genomics-based stratified and precision medicine.
The pathogen DNA enrichment and NGS workflows will be applicable to diagnostic samples from other life-threatening infections e.g. healthcare-associated pneumonia and complicated urinary tract infections. Comprehensive sequencing-based diagnostics will enable not only the wider use, but also the clinical development of narrow spectrum antibiotics. Lastly, they will identify bacterial strains and their variants, providing information that can be used for infection control and for both local and national epidemiology purposes. The preliminary work that I have performed, along with my expertise and that of my collaborators, make me uniquely positioned to deliver this cutting edge, ambitious, high impact translational research project.
Technical Summary
Next generation sequencing (NGS) based pathogen identification in bloodstream infection is very challenging owing to the vast amount of human DNA present compared with pathogen DNA (the ratio can be as high as 10^9:1). Therefore, pathogen DNA enrichment is crucial and we are developing novel strategies to achieve this, removing the vast majority of the human DNA from blood and reducing the ratio of human:pathogen DNA < 10:1. This will enable us to develop sequencing based workflows for the rapid and accurate diagnosis of sepsis which will result in reduced patient morbidity and mortality.
Objectives:
(1) Further develop and optimise our current pathogen DNA enrichment strategy and to test two new enrichment strategies
(2) Test a number of NGS technologies/platforms to determine the most suitable in terms of analysis time, flexibility, complexity of bioinformatics analysis, cost and comprehensiveness of sequencing results
(3) Run a clinical diagnostics evaluation study of an optimised NGS based diagnostic method
Objective 1:
Method 1 (current method): We will continue to develop the current method and determine the limit of detection of this method.
Method 2: We have devised a second novel approach to pathogen DNA enrichment involving the removal of human DNA using nucleic acid capture.
Method 3: This approach is designed to ensure detection of both intracellular/phagocytosed pathogens and cell free pathogen DNA while readily removing human DNA.
Objective 2:
Short read (Illumina MiSeq) sequencing technology will be compared to nanopore (MinION and PromethION) sequencing technology to determine which is best suited to infectious diseases diagnostics.
Objective 3:
The performance of the optimised sepsis diagnostic workflow will be tested on 50 biobanked blood samples from sepsis patients and controls. The arising NGS results will be compared to blood culture, PCR (Septifast) and the clinical gold standard diagnosis.
Objectives:
(1) Further develop and optimise our current pathogen DNA enrichment strategy and to test two new enrichment strategies
(2) Test a number of NGS technologies/platforms to determine the most suitable in terms of analysis time, flexibility, complexity of bioinformatics analysis, cost and comprehensiveness of sequencing results
(3) Run a clinical diagnostics evaluation study of an optimised NGS based diagnostic method
Objective 1:
Method 1 (current method): We will continue to develop the current method and determine the limit of detection of this method.
Method 2: We have devised a second novel approach to pathogen DNA enrichment involving the removal of human DNA using nucleic acid capture.
Method 3: This approach is designed to ensure detection of both intracellular/phagocytosed pathogens and cell free pathogen DNA while readily removing human DNA.
Objective 2:
Short read (Illumina MiSeq) sequencing technology will be compared to nanopore (MinION and PromethION) sequencing technology to determine which is best suited to infectious diseases diagnostics.
Objective 3:
The performance of the optimised sepsis diagnostic workflow will be tested on 50 biobanked blood samples from sepsis patients and controls. The arising NGS results will be compared to blood culture, PCR (Septifast) and the clinical gold standard diagnosis.
Planned Impact
Industry, the NHS, society and academia will benefit from this research as follows:
Industry: Once we secure IP on our novel methods we plan to partner with industry to (1) enable better diagnostics for sepsis and other serious infections (2) enable narrow spectrum antibiotics development through better patient selection in clinical trials and (3) open up new potential markets and collaboration opportunities with the genomics industry. The translation of our research through industry will lead to significant economic and social impact including: (1) enhancing the research capacity of diagnostics, pharmaceutical and genomics businesses; (2) contributing toward wealth creation and economic prosperity by creating jobs and enhancing business revenue (3) attracting R&D investment from global business and (4) commercialisation and exploitation of scientific knowledge by creating new diagnostics products and possibly leading to a spin out company.
The NHS and society: We are working closely with the Norfolk and Norwich University Hospital Microbiology and Critical Care departments providing expertise and evidence to support the future implementation of sequencing based diagnostics methods. These methods have the potential to have a big impact on the NHS and society in general. By providing rapid and accurate diagnostics, clinicians will be able to make better informed treatment decisions faster. This will lead to a precision medicine approach to antibiotic treatment with improved antimicrobial stewardship and reduced patient morbidity and mortality. Sequencing based diagnostics will also improve infection control and epidemiology in hospitals and nationally. These benefits will enhance the health and well-being of the nation and lead to health policy changes at national and possibly international levels.
Academia: I am developing novel sample preparation based 'enabling technologies' that have wide potential diagnostic applications and can be used with any sequencing platform. Our methods can be used by academics involved in drug development and clinical trials, medical microbiology, veterinary and marine microbiology and cancer research (sequencing of exosomes and cell free DNA). Hence, we have the potential to make a large academic impact and enhance the knowledge economy by developing and utilising our new and innovative techniques and technologies.
Industry: Once we secure IP on our novel methods we plan to partner with industry to (1) enable better diagnostics for sepsis and other serious infections (2) enable narrow spectrum antibiotics development through better patient selection in clinical trials and (3) open up new potential markets and collaboration opportunities with the genomics industry. The translation of our research through industry will lead to significant economic and social impact including: (1) enhancing the research capacity of diagnostics, pharmaceutical and genomics businesses; (2) contributing toward wealth creation and economic prosperity by creating jobs and enhancing business revenue (3) attracting R&D investment from global business and (4) commercialisation and exploitation of scientific knowledge by creating new diagnostics products and possibly leading to a spin out company.
The NHS and society: We are working closely with the Norfolk and Norwich University Hospital Microbiology and Critical Care departments providing expertise and evidence to support the future implementation of sequencing based diagnostics methods. These methods have the potential to have a big impact on the NHS and society in general. By providing rapid and accurate diagnostics, clinicians will be able to make better informed treatment decisions faster. This will lead to a precision medicine approach to antibiotic treatment with improved antimicrobial stewardship and reduced patient morbidity and mortality. Sequencing based diagnostics will also improve infection control and epidemiology in hospitals and nationally. These benefits will enhance the health and well-being of the nation and lead to health policy changes at national and possibly international levels.
Academia: I am developing novel sample preparation based 'enabling technologies' that have wide potential diagnostic applications and can be used with any sequencing platform. Our methods can be used by academics involved in drug development and clinical trials, medical microbiology, veterinary and marine microbiology and cancer research (sequencing of exosomes and cell free DNA). Hence, we have the potential to make a large academic impact and enhance the knowledge economy by developing and utilising our new and innovative techniques and technologies.
Organisations
- University of East Anglia (Lead Research Organisation)
- HARVARD UNIVERSITY (Collaboration)
- Mayo Clinic (Collaboration)
- University of Bergen (Collaboration)
- Grifols (Collaboration)
- Simcere Diagnostics (Collaboration)
- OXFORD NANOPORE TECHNOLOGIES (Collaboration)
- University of Pittsburgh (Collaboration)
People |
ORCID iD |
Justin O'Grady (Principal Investigator) |
Publications
Bates M
(2016)
Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection.
in International journal of mycobacteriology
Brinda K
(2020)
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.
in Nature microbiology
Burnham CD
(2017)
Diagnosing antimicrobial resistance.
in Nature reviews. Microbiology
Charalampous T
(2019)
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.
in Nature biotechnology
Jain M
(2017)
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
in F1000Research
Jain M
(2018)
Nanopore sequencing and assembly of a human genome with ultra-long reads.
in Nature biotechnology
Jeanes C
(2016)
Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution?
in International journal of mycobacteriology
O'Grady J
(2019)
A powerful, non-invasive test to rule out infection.
in Nature microbiology
O'Grady Justin
(2017)
Improving the diagnosis and management of serious infection using rapid point-of-care metagenomic sequencing
in INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
Phelan J
(2016)
The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs.
in Genome medicine
Description | CRITICAL ASSESSMENT OF THE USE OF NGS FOR THE MONITORING OF AMR ACROSS DIFFERENT ECOLOGICAL COMPARTMENTS |
Geographic Reach | Europe |
Policy Influence Type | Participation in a guidance/advisory committee |
URL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039958/ |
Description | China-UK AMR workshop 2019 run by UKRI, Department of Health and Chinese partners - Beijing China, Dec 2019 |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | Contributions to SAGE on transmission of SARS-CoV-2 in care homes during pandemic |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | Work on genomics of COVID-19 outbreaks in care facilities in Norfolk highlighted that transmission was likely caused by movement of staff between facilities and not movement of patients between hospitals and care facilities was less important. This information was reported to Dr Meera Chand at PHE discussed at SAGE (points 50 and 51 in the PDF associated with the URL below). |
URL | https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/9311... |
Description | The role and implementation of next generation sequencing technologies in the coordinated action plan against antimicrobial resistance |
Geographic Reach | Europe |
Policy Influence Type | Participation in a guidance/advisory committee |
URL | https://ec.europa.eu/jrc/en/publication/role-and-implementation-next-generation-sequencing-technolog... |
Description | The use of NGS to monitor antimicrobial resostance - European Commission Joint Research Centre (JRC) |
Geographic Reach | Europe |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | Analysis of lung microbiome profiles in ventilated patients to identify prognostic markers of infection |
Amount | £45,000 (GBP) |
Funding ID | M468-F1 |
Organisation | Rosetrees Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2021 |
End | 12/2023 |
Description | Development of Key Technologies for Real-Time Diagnosis, Surveillance and Intervention of Resistant-Bacterial Infections Based on Nanopore Sequencing |
Amount | £730,000 (GBP) |
Funding ID | 104991 |
Organisation | Innovate UK |
Sector | Public |
Country | United Kingdom |
Start | 04/2019 |
End | 04/2022 |
Description | Grifols collaboration on detection of pathogens in blood |
Amount | £150,000 (GBP) |
Organisation | Grifols |
Sector | Private |
Country | Global |
Start | 03/2017 |
End | 09/2017 |
Description | MRC iCASE programme |
Amount | £400,000 (GBP) |
Funding ID | MR/R015937/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2018 |
End | 03/2022 |
Description | Prostate Cancer UK grant |
Amount | £208,610 (GBP) |
Organisation | Prostate Cancer UK |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 11/2016 |
End | 10/2018 |
Title | CoronaHiT - a high throughput method for sequencing SARS-CoV-2 genomes |
Description | CoronaHiT is a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (= 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, = 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally. |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Several sites in UK and globally are using CoronaHiT to sequence SARS-CoV-2 genomes. The Crick, The University of Northumbria, Child Health Research Foundation, Dakah, Bangladesh (to name but a few - other sites will be using without our knowledge). |
URL | https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00839-5 |
Title | Method for depleting host nucleic acid from urine for the rapid metagenomic diagnosis of urinary tract infections |
Description | The method is based on a combination of differential centrifugation and differential lysis to remove human DNA from infected urine before applying rapid MinION metagenomic sequencing to identify the pathogen and associated antimicrobial resistance genes. |
Type Of Material | Technology assay or reagent |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Successful application of metagenomics for acute infectious diseases diagnostics requires short turnaround time. The time required to complete a metagenomic sequencing based test is related to sample preparation and depth of sequencing required. The proportion of host compared to pathogen nucleic acid in a clinical sample can be very high and increases to time and cost of metagenomic pathogen detection. We demonstrated a sample-to-result turnaround time for the diagnosis of pathogens and associated antimicrobial resistance in urine of 4 hours, including host depletion, library preparation and sequencing. Our research is being used by Oxford Nanopore Technologies as evidence to secure UK Government funding to trial MinION technology for pathogen and AMR diagnosis. |
Title | Saponin based host DNA depletion |
Description | We developed a rapid and highly efficient method for removing host DNA (eg human, chicken, salmon etc) from samples when analysing the microbial content of a sample by metagenomics. This method was published in Nature Biotechnology in 2019 and is being used by multiple labs in multiple sectors (food, vererinary, human clinical). Organisations I am aware that are using our methods include: Public Health England, Harvard, University of Cambridge, University of Liverpool, University of Oxford, University of Birmingham, University of Bergen, Statens Serum Institute, Quadram Institute Bioscience (outside of my group), Guy's and St Thomas' Hospital, DSTL. |
Type Of Material | Technology assay or reagent |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | This tool led to a major collaboration with Simcere Diagnostics in China and has led to follow on funding from Innovate UK. It has now also led to a new patent application (see patent section) and several collaborative scientific papers. |
Title | Rapid lineage calling |
Description | Our metagenomics data from respiratory samples and our understanding of diagnostics and AMR resistance and susceptibility prediction was influential in the development and optimisation of the RASE tool developed in collaboration with Harvard and published in Nature Microbiology in 2020.This tool is capable of determining whether selected pathogens are resistance or susceptible to antibiotics using metagenomics data within 5 minutes of testing. |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Several laboratories globally are starting to use the approach including University of Oxford and University of Bergen |
URL | https://github.com/c2-d2/rase |
Description | Applying clinical metagenomics for the diagnosis of pneumonia |
Organisation | University of Pittsburgh |
Department | Department of Medicine |
Country | United States |
Sector | Academic/University |
PI Contribution | I transferred out methods for performing clinical metagenomics on respiratory samples to my collaborator at Pittsburgh Medical School (Georgios Kitsios). He is now applying these methods to patient samples in Pittsburgh and achieving excellent results. |
Collaborator Contribution | Georgios Kitsios is now applying our respiratory metagenomics methods in Pittsburgh, currently in a research context, to diagnose hospital acquired and ventillator associated pneumonia. We have submitted an conference abstract together on his study and a journal publication will follow later this year. |
Impact | Metagenomic DNA sequencing of respiratory microbial communities for detection of etiologic pathogens of pneumonia in mechanically-ventilated adult patients - American Thoracic Society abstract |
Start Year | 2018 |
Description | Bioinformatic tool development for the rapid analysis of clinical metagenomics data |
Organisation | Harvard University |
Department | Harvard T.H. Chan School of Public Health |
Country | United States |
Sector | Academic/University |
PI Contribution | We transferred out respiratory clinical metagenomics data to Harvard (William Hanage) for bioinformatic tool development and analysis. Nobody else in the world had nanopore respiratory metagenomics data. |
Collaborator Contribution | Bill Hanage and colleagues developed a bioinformatic tool to rapidly genotype respiratory pathogens. He tested this on bacterial isolated, which worked well. Then he heard we had respiratory metagenomes and he applied his tools on our data. It was then possible to predict antimicrobial resistance/susceptability directly from metagenomics data within 5 mins. |
Impact | Lineage calling can identify antibiotic resistant clones within minutes - BioXriv preprint currently under review in Nature Biotechnology. |
Start Year | 2018 |
Description | Evaluation of respiratory metagenomics for diagnosing pneumonia in Norway |
Organisation | University of Bergen |
Country | Norway |
Sector | Academic/University |
PI Contribution | We are working with partners at the University of Bergen to evaluate the performance of clinical metagenomics for the diagnosis of pneumonia in the RESPNOR study |
Collaborator Contribution | I am working closely with Bergen to dveelop the clinical evaluation protocols, share our most recent clinical metagenomics methods and advise on their implementation. |
Impact | It is multi-disciplinary - clinical microbiologists, ICU phisicians, medical microbiologists, bioinformaticians |
Start Year | 2019 |
Description | Grifols collaboration |
Organisation | Grifols |
Country | Global |
Sector | Private |
PI Contribution | A collaboration on the metagenomic sequencing based detection of pathogens in blood. We provide the knowhow and the background intellectual property. |
Collaborator Contribution | Grifols will provide the pathogens and fund some of the research. |
Impact | No outputs to date as the collaboration has just begun. |
Start Year | 2017 |
Description | Mayo Clinic |
Organisation | Mayo Clinic |
Country | United States |
Sector | Charity/Non Profit |
PI Contribution | We have provided our human DNA depletion methods to Professor Robin Patel at the Mayo Clinic (under NDA) for use in clinical metagenomics with a particular focus on prosthetic joint infection. I will give a Grand Round at the Mayo Clinic in May 2018 and will provide some training on the method while there. |
Collaborator Contribution | Prof Patel will test clinical samples using our methods with an eye on future clinical implementation and publication. |
Impact | No outputs yet. The collaboration is multidisciplinary including clinicians, microbiologists biomedical scientists and bioinformaticians. |
Start Year | 2017 |
Description | Oxford Nanopore Technologies collaboration |
Organisation | Oxford Nanopore Technologies |
Country | United Kingdom |
Sector | Private |
PI Contribution | We are working closely with ONT to develop clinical metagenomics applications in diseases such as UTIs, pneumonia and meningitis. |
Collaborator Contribution | ONT have co-funded a PhD student in my lab, are an iCASE partner and have provided financial and in-kind contributions to a number of my research projects. They have hosted one PhD student and will host another next year at ONT for 3 months where they have been trained in bioinformatics and library preparation techniques. |
Impact | 1. ASHTON, P. M., NAIR, S., DALLMAN, T., RUBINO, S., RABSCH, W., MWAIGWISYA, S., WAIN, J. & O'GRADY, J. 2015. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol, 33, 296-300. 2. BRINDA, K., CALLENDRELLO, A., COWLEY, L., CHARALAMPOUS, T., LEE, R. S., MACFADDEN, D. R., KUCHEROV, G., O'GRADY, J., BAYM, M. & HANAGE, W. P. 2018. Lineage calling can identify antibiotic resistant clones within minutes. bioRxiv. 3. CHARALAMPOUS, T., RICHARDSON, H., KAY, G. L., BALDAN, R., JEANES, C., RAE, D., GRUNDY, S., TURNER, D. J., WAIN, J., LEGGETT, R. M., LIVERMORE, D. M. & O'GRADY, J. 2018. Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics. bioRxiv, 387548. 4. IP, C. L. C., LOOSE, M., TYSON, J. R., DE CESARE, M., BROWN, B. L., JAIN, M., LEGGETT, R. M., ECCLES, D. A., ZALUNIN, V., URBAN, J. M., PIAZZA, P., BOWDEN, R. J., PATEN, B., MWAIGWISYA, S., BATTY, E. M., SIMPSON, J. T., SNUTCH, T. P., BIRNEY, E., BUCK, D., GOODWIN, S., JANSEN, H. J., O'GRADY, J., OLSEN, H. E., MIN, I. O. N. A. & REFERENCE, C. 2015. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res, 4, 1075. 5. JAIN, M., KOREN, S., MIGA, K. H., QUICK, J., RAND, A. C., SASANI, T. A., TYSON, J. R., BEGGS, A. D., DILTHEY, A. T., FIDDES, I. T., MALLA, S., MARRIOTT, H., NIETO, T., O'GRADY, J., OLSEN, H. E., PEDERSEN, B. S., RHIE, A., RICHARDSON, H., QUINLAN, A. R., SNUTCH, T. P., TEE, L., PATEN, B., PHILLIPPY, A. M., SIMPSON, J. T., LOMAN, N. J. & LOOSE, M. 2018. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol, 36, 338-345. 6. JAIN, M., TYSON, J. R., LOOSE, M., IP, C. L. C., ECCLES, D. A., O'GRADY, J., MALLA, S., LEGGETT, R. M., WALLERMAN, O., JANSEN, H. J., ZALUNIN, V., BIRNEY, E., BROWN, B. L., SNUTCH, T. P., OLSEN, H. E., MIN, I. O. N. A. & REFERENCE, C. 2017. MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. F1000Res, 6, 760. 7. SCHMIDT, K., MWAIGWISYA, S., CROSSMAN, L. C., DOUMITH, M., MUNROE, D., PIRES, C., KHAN, A. M., WOODFORD, N., SAUNDERS, N. J., WAIN, J., O'GRADY, J. & LIVERMORE, D. M. 2017. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother, 72, 104-114. |
Start Year | 2014 |
Description | Simcere Diagnostics |
Organisation | Simcere Diagnostics |
Country | China |
Sector | Private |
PI Contribution | We are in the late stages of negotiating a collaboration agreement and possible patent licence with Simcere Diagnostics. We plan to co-develop a 'laboratory developed test' (LDT) for nosocomial pneumonia to be offered as a service in hospitals in China. The agreement will likely involve funding for my laboratory for a Post-doc plus consumables and a potential licence agreement for the human DNA depletion patent developed during this MRC Innovation Award. We have intellectual property and knowhow in the metagenomics infection diagnostics space that Simcere want access to. This IP and knowhow has been developed through funding from MRC (human DNA depletion patent), Rosetrees Trust (human DNA depletion patent) and NIHR (INHALE trial on nosocomial pneumonia diagnosis). |
Collaborator Contribution | I was introduced to Simcere (a large Chinese pharmaceutical company with a diagnostics division that invest in Oxford Nanopore Technologies, ONT) by the CEO of ONT at the Nanopore Community Meeting in New York in Dec 2017. Simcere were very interested in my presentation on metagenomics based diagnosis of nosocomial pneumonia and were interested in collaboration. I visited their headquarters in Nanjing in late January 2018 and return in late March 2018 to complete the collaboration agreement. Simcere have an extensive network of customers/collaborators in hospitals throughout China, expertise in nanopore sequencing based metagenomics and a track record in LDT development. They will provide the expertise to drive our diagnostics tests from the research lab to the bedside, through the difficult regulatory landscape, and can access the huge healthcare market in China. |
Impact | No outputs from this project yet. The collaboration is multidisciplinary, including industry, academia, genomics, bioinformatics, rapid diagnostics, clinical microbiology, intensive care medicine, sample preparation, molecular biology. |
Start Year | 2017 |
Description | Simcere collaboration |
Organisation | Simcere Diagnostics |
Country | China |
Sector | Private |
PI Contribution | We have transferred methods to Simcere and will continue to work with them as part of a new grant (Innovate UK UK-China AMR grant) to develop these methods for clinical implementation. |
Collaborator Contribution | Simcere are further developing our methods to clinical standards for future implementation. |
Impact | Follow on funding - an Innovate UK grant |
Start Year | 2018 |
Title | METHOD FOR NUCLEIC ACID DEPLETION |
Description | Provided is a method for depleting host nucleic acid in a biological sample, said sample having been previously obtained from an animal host, said method comprising the steps of (a) adding a cytolysin, or an active variant thereof, to said sample; and (b) carrying-out a process to physically deplete nucleic acid released from host cells within said sample or otherwise render such nucleic acid unidentifiable. |
IP Reference | WO2018109454 |
Protection | Patent application published |
Year Protection Granted | 2018 |
Licensed | Yes |
Impact | No notable impact to date, this will develop over the coming years |
Title | Rapid metagenomics based diagnosis of nosocomial pneumonia |
Description | We have developed a rapid (6hr) metagenomics sequencing method for diagnosis of nosocomial pneumonia. This method is currently being evaluated in comparison with PCR tests in the INHALE trial (NIHR, £2.5M). |
Type | Diagnostic Tool - Non-Imaging |
Current Stage Of Development | Early clinical assessment |
Year Development Stage Completed | 2018 |
Development Status | Under active development/distribution |
Clinical Trial? | Yes |
Impact | This method has generated a lot of interest and is being used by a lot researchers around the world. The ones that I am aware of, as I am directly collaborating with them, are: Pittsburgh Medical School, University of Bergen, PHE, University of Oxford, University of Cambridge, Harvard and one large Chinese multinational company. |
URL | https://www.biorxiv.org/content/10.1101/387548v1 |
Title | Simcere respiratory metagenomics products |
Description | Simcere Diagnostics, a division of Simcere Pharmaceuticals (top 100 Chinese pharma company with >5000 employees), have developed a nanopore sequencing based respiratory metagenomics test in collaboration with O'Grady (and incorporates O'Grady's host depletion technology). This test is being used in multiple hospitals across China (currently selling approx 100 tests per week). This collaboration is the basis of an Impact Case for REF 2021. |
Type | Diagnostic Tool - Non-Imaging |
Current Stage Of Development | Early clinical assessment |
Year Development Stage Completed | 2019 |
Development Status | Under active development/distribution |
Impact | Development of this product led to further funding from Innovate UK (UK-China AMR grant >£1million between UK and Chinese partners). It has also led to clinical evaluation study on ~300 patients - the paper on this study was submitted in March 2020. Creation of 80 jobs. Impact Case for REF 2021. |
Description | BBC television interview with Richard Westcott |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | On two occasions, once in the summer and once in December, Richard Westcott (BBC Science Correspondent) filmed at QIB to describing our SARS-CoV-2 sequencing work and its use for tracking and controlling outbreaks (summer) and identifying and controlling variants of concern (December). |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.youtube.com/watch?v=q0O0nzbaHQc |
Description | Cambridge PHE talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | I was invited to give a talk at Public Health England, Addenbrookes on my metagenomics sequencing based infection diagnostics work. Clinicians and scientists attended and there was lively discussion afterward. PHE Addenbrookes are interested in applying the MinION in research and potentially for certain services in the future. |
Year(s) Of Engagement Activity | 2017 |
Description | FIS/HIS talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presentation at FIS / HIS International Nov 2020 on clinical metagenomics |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.his.org.uk/training-events/fis-his-2020/ |
Description | Press release on rapid MinION sequencing based diagnosis of urinary tract infection |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | We reported our work on rapid UTI diagnosis using MinION metagenomic sequencing at an international conference in the US. This was accompanied by a press release by UEA and the conference (ICAAC 2015) and was reported widely, including an article on the BBC News website. |
Year(s) Of Engagement Activity | 2015,2016 |
URL | http://www.bbc.co.uk/news/health-34295481 |
Description | Press release on respiratory metagenomics Nature paper |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | We wrote and shared a press relaese on our Nature Biotechnology paper published in June 2019. It was covered by several print and online media outlets, leading to a high Altmetric score (260). |
Year(s) Of Engagement Activity | 2019 |
URL | https://quadram.ac.uk/new-rapid-test-lower-respiratory-infections/ |
Description | Royal Norfolk Show - AMR research tent and Superbugs panel |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Demonstrating MinION naopore sequencing to school kids and the general public and explaining how we use it for the detection on pathogens and antimicrobial resistance. Also on a discussion panel re superbugs and how to control them. Both activities led to multiple questions on the nanopore technology and how we can use this British technology to control superbugs and fight AMR. |
Year(s) Of Engagement Activity | 2018 |
URL | https://royalnorfolkshow.rnaa.org.uk/discovery-zone/ |
Description | SAW Trust school visit |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Schools |
Results and Impact | I, together with post-docs from my lab an artist and a writer, ran a SAW (Science, art and writing) day for year 6 students at my children's primary school. The focus was on antibiotic resistance and the role rapid diagnostics can play in the fight against AMR. A description of the science and example poems and art created by the students formed part of a book, SAW Antibiotics, published by the SAW trust. Professor Dame Sally Davies is quoted in the book stating: "I thoroughly enjoyed this stunning book. Educating children in such an interactive way is so important. I am passionate about addressing AMR, as are the researchers, and I hope this can help inspire future generations to engage in the efforts to save modern medicine". SAW now runs in a number of countries and the book is sold globally. |
Year(s) Of Engagement Activity | 2016,2017 |
URL | http://www.sawtrust.org/buy-the-books/saw-antibiotics/ |
Description | Science Museum Lates - Superbugs |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Interactive presentation on the rapid diagnosis of infection and antimicrobial resistance using metagenomics performed multiple times over the evening. 50-100 people were present for each presentation. Several people asked questions afterwards about the technology and the importance of diagnostics in the fight against AMR. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.sciencemuseum.org.uk/see-and-do/lates |
Description | Wall Street Journal interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | I spoke to WSJ about the SARS-CoV-2 sequencing we are doing as part of COG-UK, the value of sequencing and some of our findings |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.wsj.com/articles/new-playbook-for-covid-19-protection-emerges-after-year-of-study-misste... |