nsw public health pathogen genomics partnerships

The University of Sydney

NSW Public Health

Pathogen Genomics

Partnerships

Vitali Sintchenko

Centre for Infectious Diseases and Microbiology-Public Health

Marie Bashir Institute for Infectious Diseases and Biosecurity


Augmenting NSW infrastructure for

pathogen genomics

Partnership between CIDM-PH, NSW Health Pathology,

and MBI, University of Sydney

Supported by NSW Health

High-throughput Illumina NGS

NECTAR-enabled PHLN endorsed informatics pipeline

Cumulative numbers of sequenced genomes

Bordetella holmesii

Bordetella pertussis

Burkholderia cenocepacia

Candida glabrate

Candida parapsilosis

Chlamydia trachomatis

Corynebacterium diphtheriae

Enterococcus species

Enteroviruses

Escherichia coli

Hepatitis C virus

Human papilloma virus

Francisella tularensis

Klebsiella species

Legionella pneumophila

Mycobacterium abscessus

Mycobacterium bovis BCG

Mycobacterium chimaera

Mycobacterium tuberculosis

Neisseria gonorrhoeae

Neisseria meningitidis

Salmonella species

Shigella species

Staphylococcus aureus

Staphylococcus epidermidis

Streptococcus agalactiae

Streptococcus pneumoniae

Species sequenced


Enhancing public health capability:

outbreak investigations

All isolates from the outbreak were ST211



High-resolution surveillance

Shifts in diversity of dominant Salmonella Typhimurium clones in NSW



High-resolution surveillance

Local endemicity and independent introductions of MDR

Salmonella Typhimurium ST34



Deciphering contaminations of instruments

Williamson D et al NEJM 2017; 376:600

Comparative genomics of clinical and

environmental isolates of Mycobacterium chimaera


Clinical infectious disease genomics

Subspeciation of pathogens

and pathogen discovery

Hospital infection control and

HAI transmission

Resistome testing (AMR)

NSW Health Pathology

Pathogen Genomics Working

Group


Promoting new research partnerships

Project title Principal

investigator

Leading institution Network partners

VanA VRE: emergence of new

threat

A/Prof Sebastian van

Hal

RPAH Network of nine NSW

hospitals

Diversity of viral quasi-species

and HIV-1 drug resistance

Dr Shailendra

Sawleshwalkar

Western Sydney

Sexual Health

RPAH and Western

Sydney LHD

MRSA acquisition and

transmission in the ICU and Burns

Unit

Dr Genevieve McKew Concord Hospital Sydney LHD, Sydney

South West Pathology

Service

Sources of Salmonella Wangata

in NE NSW

Dr Julie Collins Hunter NE Population

Health

MBI, USyd Vet Sciences,

ANU

Respiratory virome in lung

transplant patients

Prof Alan Glanville &

Alicia Mitchell

Woolcock Institute St Vincent’s Hospital,

UTS

Human norovirus diversity in

NSW

Prof Peter White University of New

South Wales

NSW Health Pathology

Pathogenesis of Enterovirus 71 Prof W Rawlinson Prince of Wales

Hospital and SEALS

Sydney Children’s

Hospital, UNSW


Enabling competitive translational research

Research themes

• Genomics surveillance of emerging pathogens of public health concern (bacterial, viral,

fungal and protozoan)

• Reconstructing transmission pathways of significant community and hospital outbreaks

• Genomic mechanisms of pathogen adaptation to public health interventions

• NSW Translational Research Grants

• Translating Pathogen Genomics into Improved Public Health Outcomes: Evaluation

of the effectiveness of genome sequencing-guided investigation of outbreaks (Iredell

& Sintchenko)

• State-wide typing network for rapid detection of outbreaks of healthcare

associated infection (O’Sullivan)

NHMRC Centres for Research Excellence in Emerging infectious Diseases

(Prof Sorrell), Tuberculosis Control (Prof Britton) and Digital Health (Prof

Coiera) and HMRC project grants

The University of Sydney 8

Opponent of Koch’s monocausalistic

views. By a self-test with cholera

bacteria he proved that the germs

alone were not sufficient for infection.

Max von Pettenkofer

1818-1901

Robert Koch

1843-1910

Germ theory/

Monocausalism

versus

Hygiene

Historical battle for supremacy


Epidemiological and microbial genomics

approaches

8

Drivers- Urbanisation and census data

- Advances in statistics

Advantages

• Independence of lab

confirmation

Disadvantages

• Low resolution/subjectivity

• Recall bias

Drivers- Globalisation and data sharing

- Advances in phylogenomics

Advantages

• High resolution/objectivity

• International context

Disadvantages

• Depends of lab confirmed

cases


Epidemiological and microbial genomics

approaches

8

Drivers- Urbanisation and census data

- Advances in statistics

Advantages

• Independence of lab

confirmation

Disadvantages

• Low resolution/subjectivity

• Recall bias

Drivers- Globalisation and data sharing

- Advances in phylogenomics

Advantages

• High resolution/objectivity

• International context

Disadvantages

• Depends of lab confirmed

cases

Opportunity for convergence:

Synthesis of two lines of evidence and application of methods of

analytic microbiology to data generated by genomics


Acknowledgements

• CIDM• Jon Iredell

• Sharon Chen

• Matthew O’Sullivan

• Peter Howard

• Peter Jelfs

• Taryn Crighton

• University of Sydney/MBI• Eddie Holmes

• John-Sebastian Eden

• Ranjeeta Menon

• University of NSW• Ruiting Lan

• Sophie Octavia

• Mark Tanaka

• CIDM-PH• Lyn Gilbert

• Lou Orszulak

• Elena Martinez

• Rebecca Rockett

• Rosemarie Sadsad

• Verlaine Timms

• Qinning Wang

• Chayanika Biswas

• Rajat Dhakal

• NSW Ministry of Health• Vicky Sheppeard

• Kirsty Hope

• Kira Galsgow

• Brett Reed


THANK YOU!

First announcement

nsw public health pathogen genomics partnerships

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