The UK s National Collection of Type Cultures: Answers to 21 st century public health questions

Transcription

1 The UK s National Collection of Type Cultures: Answers to 21 st century public health questions Julie E. Russell Head of Culture Collections 28 th September 2016

2 Public Health England (PHE) Executive agency of UK government s Department of Health Established on 1 st April 2013 Previous organisations date back to 1940 Remit: Protecting the public s health from infectious diseases and other hazards to health Improving the public s health and wellbeing and reducing health inequalities ~5000 employees including scientists, researchers and public health professionals 2 Culture Collections ~ a Public Health England Biological Resource

3 Culture Collections National Collection of Type Cultures (NCTC) established in 1920 (MRC grant) National Collection of Pathogenic Fungi (NCPF) established in 1947 after NCTC focus was changed to bacteria of medical and veterinary importance European Collection of Authenticated Cell Cultures (ECACC) established in 1985 funded by UK s Department of Trade and Industry National Collection of Pathogenic Viruses (NCPV) established in 1999 (Wellcome Trust grant) 3 Culture Collections ~ a Public Health England Biological Resource

4 National Collection of Type Cultures Established in 1920 now ~ 5100 strains of bacteria available (on-line catalogue) Historical strains and recent deposits valuable for microbial evolutionary studies Type strains - the type strain is the strain on which the description of a species is based NCTC holds ~900 type strains together with > 4000 strains 4 Culture Collections ~ a Public Health England Biological Resource

5 Where do NCTC strains come from? Individual collections of scientific value - Sir Frederick William Andrewes (medical doctor collected Shigella strains during World War 1) High profile depositors: Alexander Fleming, Theodore Escherich Wide range of geographical locations Isolates sent to PHE reference laboratories newly emerging strains of clinical and public health importance (such as multi-resistant bacteria, MRSA, carbapenamase-producers) New species/new type strains global research community Strains deposited in other collections such as in Belgium, France, Germany, Japan, Spain, Sweden (with reference to ISO methods and WDCM) 5 Culture Collections ~ a Public Health England Biological Resource

6 What are NCTC strains used for? Controls for clinical diagnostic tests (eg antimicrobial susceptibility testing) Controls for culture media Controls for food, water and environmental microbiology Veterinary microbiology Standardisation of methods Research projects Understanding microbial evolution and bacterial pathogenicity Identifying targets for developing new antibiotics and vaccines Strains selected by the user with reference to metadata: species/strain name, clinical site, date of isolation, phenotypic or genotypic characteristics 6 Culture Collections ~ a Public Health England Biological Resource

7 The challenge of technology changes New and emerging technology/methods will be adopted at different rates by different market sectors Newer technologies will not necessarily replace more traditional methods but may be used alongside them Are we ready? 7

8 Proteomic technology The structural and functional proteins present in an organism are known collectively as the proteome - proteomics is the study of the proteome Mass spectrometry (MS) underpins proteomics in clinical microbiology MALDI-TOF* MS instruments used routinely in numerous PHE and NHS diagnostic testing laboratories for the rapid identification of microorganisms Used for authentication of NCTC strains Protein profiling for NCTC cultures to complement genome data for characterisation and to help understand virulence mechanisms *MALDI-TOF matrix-assisted laser desorption/ionisation - time of flight 8 Culture Collections ~ a Public Health England Biological Resource

9 Whole Genome Sequencing technology Whole genome sequencing (WGS) identifies the sequences of bases that make up the DNA; sequencing the genome helps to decode the genes Of particular interest in public health are those genes responsible for virulence WGS shows promise as a routine epidemiological typing tool Short or long read technology? Long reads: greater accuracy, quicker, delivers closed (complete) bacterial genomes, more expensive, provides methylation data Short read technology: adopted routinely in some PHE Reference Laboratories 9 Culture Collections ~ a Public Health England Biological Resource

10 Gastrointestinal Bacteria Reference Unit 1. Salmonella Reference Service 2. Shigella, E.coli, Vibrio and Yersinia Reference Service 3. Foodborne Pathogen Reference Service Listeria monocytogenes, Bacillus cereus, Clostridium botulinum and C.perfringens, Staphylococcus aureus 4. Campylobacter and Helicobacter Reference Service National surveillance, outbreak detection and investigation 10 Culture Collections ~ a Public Health England Biological Resource

11 Salmonella identification and typing Genus Species Subspecies Salmonella serovars: 2610 Slide acknowledgment: Kathie Grant and Satheesh Nair

12 Salmonella identification and subtyping Sub-speciation Identification RT-PCR Phenotypic microarray Serotyping Sub typing AMR Phage Typing MLVA PFGE Slide Salmonella acknowledgement: NGS at PHE Dr Kathy Grant

13 DNA Extraction Salmonella WGS workflow Sequencing Reads Bioinformatics IDENTIFICATION CHARACTERISATION TYPING Serotyping PCR Omnilog Speciate/Clone Detecting genetic diversity Surveillance Outbreaks Phage typing MLVA PFGE R-Typing Antimicrobial resistance Virulence factors 16 Slide acknowledgement: Kathie Grant and Satheesh Nair

14 Automated report for Salmonella ID 17 Slide acknowledgement: Kathie Grant and Satheesh Nair

15 Preparing for quality and consistency in WGS methods 2013: Wellcome Trust grant awarded to PHE and Wellcome Trust Sanger Institute (WTSI) Remit: generate reference genomes for 3000 NCTC bacteria and 500 NCPV viruses and: Embed those genomes in an accessible electronic resource to enhance the scientific value of the collection. All data must easily accessible to everyone via the E-resource (web-site) 15 Culture Collections ~ a Public Health England Biological Resource

16 NCTC 3000 ~2000 NCTC organisms already have raw sequence data and many have annotated genomes available via links on the NCTC website, ENA/NCBI databases, and Sanger Institute website Currently prioritising type strains Providing more information for microbiologists selecting which strains they require Allowing bioinformaticians to mine the raw data for specific genes We are designing a new e-resource that will link the data associated with each NCTC strain Follow 16 Culture Collections ~ a Public Health England Biological Resource

17 17 Culture Collections ~ a Public Health England Biological Resource

18 Planning the eresource: user stories The Scientist I want to see the annotated sequence to see if the strain has x, y, or z genes I want to know whether the strain is endemic or imported I want to know if a recently isolated strain has new antigenic properties I would like have a feature "Scientist who viewed his item also viewed " so that I can see related and popular strains I want to find plasmids to see if a particular strain is resistant to antibiotics I would like facets to sort my results so that I can quickly pick strain according to my preferred facets I would like to see the methylation data for a particular pathogen 18 Culture Collections ~ a Public Health England Biological Resource

19 E-resource: user stories The Bioinformatician I want access to the assembled genome so that I can use it as a reference genome I want access to raw data so that I can assess new annotation and assembly technology I want to see indicators of the availability of WGS data on the search result Miscellaneous I want access to integrated PubMed searching and referencing I would like to link to NCTC strain from ENA so that I can look at the sequence data and order it quickly via NCTC I want to find the history of nomenclature and taxonomic information to ensure the strain is suitable for my study 19 Culture Collections ~ a Public Health England Biological Resource

20 NCTC in recent research (2016) Enterococcus faecium: study revealed the evolution and dissemination of hospital-associated infection in the UK & Ireland, providing evidence for WGS as an instrument for infection control Raven et al Shigella dysenteriae type 1: Analysis of 330 genome sequences demonstrated that Europe was probably the geographical origin of modern Asian and African epidemics of dysentery. This study also charts the development of the pathogen s resistance to antibiotics F-X Weill Enterococcus faecalis: WGS-based characterisation of historical (including NCTC) and current strains of enterococcus help to reveal hospital-adapted lineages Raven et al Culture Collections ~ a Public Health England Biological Resource

21 Challenges: Quality and consistency of WGS and associated data Role of WGS in strain authentication cost effectiveness? Demonstrating equivalence across different Culture Collections to underpin WDCM listings Acceptance of WDCM strain equivalence across the different sectors Linking genome sequence data to proteomic data Making the proteomic data useful and accessible 21 Culture Collections ~ a Public Health England Biological Resource

22 Acknowledgements Entire Culture Collections Team >70 people: Kathy Grant Satheesh Nair Sarah Alexander Ana Deheer-Graham Ed Burnett Mohammed Abbas Fazal Ayuen Lual Hannah McGregor Trisha Rawat Heena Shah Jake Turnbull Julian Parkhill and WTSI team Pacific Biosciences @ECACC Stuart Yeates 22 Culture Collections ~ a Public Health England Biological Resource