The UK’s National Collection of Type Cultures Julie E. Russell WDCM... · Culture Collections •...

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)

3 Culture Collections ~ a Public Health England Biological Resource

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)


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


The challenge of technology changes

7

• 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


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


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


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)


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


www.phe-culturecollections.org.uk/


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

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


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











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


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


Kathy Grant

Satheesh Nair

Julian Parkhill and WTSI team

Pacific Biosciences

Follow us:

@NCTC_3000

@NCPV

@ECACC

The UK’s National Collection of Type Cultures Julie E. Russell WDCM... · Culture Collections •...

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