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The University of Sydney Page 1
NSW Public Health
Pathogen Genomics
Partnerships
Vitali Sintchenko
Centre for Infectious Diseases and Microbiology-Public Health
Marie Bashir Institute for Infectious Diseases and Biosecurity
The University of Sydney Page 2
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
The University of Sydney Page 3
Enhancing public health capability:
outbreak investigations
All isolates from the outbreak were ST211
The University of Sydney Page 4
Enhancing public health capability:
High-resolution surveillance
Shifts in diversity of dominant Salmonella Typhimurium clones in NSW
The University of Sydney Page 5
Enhancing public health capability:
High-resolution surveillance
Local endemicity and independent introductions of MDR
Salmonella Typhimurium ST34
The University of Sydney Page 6
Enhancing public health capability:
Deciphering contaminations of instruments
Williamson D et al NEJM 2017; 376:600
Comparative genomics of clinical and
environmental isolates of Mycobacterium chimaera
The University of Sydney Page 7
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
The University of Sydney Page 8
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
The University of Sydney Page 9
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 Page 108
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
The University of Sydney Page 11
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
The University of Sydney Page 12
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
The University of Sydney Page 13
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
The University of Sydney Page 14
THANK YOU!
First announcement