the uk’s national collection of type cultures julie e. russell wdcm... · culture collections •...
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The UK’s National Collection of
Type Cultures:
Answers to 21st century
public health questions
Julie E. Russell Head of Culture Collections 28th September 2016
Public Health England (PHE) • Executive agency of UK government’s Department of Health
• Established on 1st 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
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Culture Collections ~ a Public Health England Biological Resource
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)
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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
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Culture Collections ~ a Public Health England Biological Resource
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
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
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The challenge of technology changes
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• 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?
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
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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
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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
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Slide acknowledgment: Kathie Grant and Satheesh Nair
Genus
Species
Subspecies
Salmonella serovars:
2610
Salmonella identification and typing
Salmonella identification and subtyping
12 Salmonella NGS at PHE 12 Slide acknowledgement: Dr Kathy Grant
RT-PCR Phenotypic
microarray
Sub-speciation Identification
Sub typing
Serotyping
Phage Typing MLVA PFGE
AMR
16 Slide acknowledgement: Kathie Grant and Satheesh Nair
DNA Extraction
Sequencing Reads
Bioinformatics
IDENTIFICATION
CHARACTERISATION
Speciate/Clone
Antimicrobial resistance
Virulence factors
TYPING
Detecting genetic diversity
Surveillance
Outbreaks
Salmonella WGS workflow
Serotyping
PCR
Omnilog
R-Typing
Phage typing
MLVA
PFGE
Automated report for Salmonella ID
17 Slide acknowledgement: Kathie Grant and Satheesh Nair
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)
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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 us:
@NCTC_3000
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www.phe-culturecollections.org.uk/
17 Culture Collections ~ a Public Health England Biological Resource
Planning the eResource: user stories
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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
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
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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
http://m.genome.cshlp.org/content/early/2016/08/15/gr.204024.116.full.pdf
http://www.nature.com/articles/nmicrobiol201627
http://www.nature.com/articles/nmicrobiol201533
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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
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Acknowledgements Entire Culture Collections Team
>70 people:
Sarah Alexander
Ana Deheer-Graham
Ed Burnett
Mohammed Abbas Fazal
Ayuen Lual
Hannah McGregor
Trisha Rawat
Heena Shah
Jake Turnbull
Stuart Yeates
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Kathy Grant
Satheesh Nair
Julian Parkhill and WTSI team
Pacific Biosciences
Follow us:
@NCTC_3000
@NCPV
@ECACC