Activities

Pathogen Genomics Implementation Program

In 2018, the Victorian Department of Health funded MDU PHL to undertake a large-scale pathogen genomics project focusing on transitioning traditional laboratory processes to whole-genome sequences for a range of state and national notifiable pathogens. The project aims to embed pathogen genomics into standard practices and maintains the collaborative relationship with the department which is critical in harnessing the full benefits of the technology and to date has yielded significant public health benefit to the state. The investment in MDU PHL provided critical preparedness capacity, enabling MDU PHL to be one of the first laboratories in Australia to develop SARS-CoV-2 sequencing capacity very early in the pandemic which has now been scaled up to rapid whole-genome sequencing of all Victorian cases. This project has significantly enhanced Victoria’s capacity to provide a safe and accurate public health microbiology service, enabling MDU PHL to support other jurisdictions and countries in their implementation of pathogen genomics for public health.

Innovative Testing Program

The COVID-19 Innovative Testing Program is a Victorian Department of Health funded initiative in collaboration with MDU PHL and the Victorian Infection Diseases Reference Laboratory (VIDRL) at the Doherty Institute. This program aims to rapidly explore and scale novel testing modalities that are clinically and operationally appropriate to support the Victorian testing strategy and comprises two key domains:

1. Optimising the ‘gold-standard PCR’ using methods such as saliva sampling and pooling
2. Validating and pilot testing near point of care rapid molecular and antigen tests

Victorian Department of Health Partnership Grant

Funded by the Commonwealth National Health and Medical Research Council (NHMRC) Partnership Grant, ‘An evidence based framework for Establishing Microbial Public Health Genomics in Australia’ (2018 -2022) is a collaborative translational research project led by MDU PHL, implemented in partnership with the Victorian Department of Health and industry partner, Illumina Pty Ltd. The project aims to define the genomic characteristics and population structure of pathogens, and develop species-specific analytical pipelines for pathogens falling into four major communicable diseases themes:

1. Antimicrobial resistance and invasive bacterial pathogens
2. Sexually transmitted infections
3. Foodborne disease
4. Environmental pathogens

The project is also supported by an Evaluation Team to evaluate the utility and benefits in using genomics to track communicable diseases, and an Informatics and Platforms team to support development and implementation of bioinformatics tools.

Communicable Diseases Genomics Network (CDGN)

The Communicable Diseases Genomics Network (CDGN) was established in 2015 and is a Commonwealth funded network of genomics-enabled public health laboratories coordinated by MDU PHL, and includes all states and territories in Australia and New Zealand. The CDGN aims to ensure rapid translation of pathogen genomics into public health through the facilitation of genomic sequencing data and knowledge, including antimicrobial resistance pathogens and other pathogens of outbreak significance, in a collaborative and responsible manner to improve public health activities nationally.

AusTrakka

AusTrakka is a Commonwealth-funded central, secure, and private online location to share, analyse and view aggregated national pathogen genomic data from Australia and New Zealand. Public health laboratories across all states and territories have access to AusTrakka and are routinely uploading genomic sequences for nationally notifiable pathogens for real-time surveillance and tracking of transmission between jurisdictions. The platform was developed by A/Prof Torsten Seemann and Dr Anders Goncalves da Silva, MDU PHL, and is Australia’s first real-time national genomics surveillance platform.

Australian Pathogen Genomics Program

The Australian Pathogen Genomics (AusPathoGen) Program is a large scale integrated public health pathogen genomics research program funded by the Commonwealth Medical Research Future Fund (MRFF) that will demonstrate the utility, cost-effectiveness, and capacity for translation of genomics into public health nationally. The program will deploy the national genomic platform (AusTrakka), for consistent analysis and reporting, and will collaborate with health departments and public health laboratories to implement national genomics-based responses to major infectious diseases, focusing on respiratory and vaccine preventable diseases, foodborne diseases, sexually transmitted infections and antimicrobial resistance.

MRFF COVID-19 Genomics Grant

The Tracking COVID-19 in Australia using Genomics Grant is a research program funded by the Commonwealth Medical Research Future Fund (MRFF) to address the urgent need for national implementation of SARS-CoV-2 genomics in Australia, to better understand the behaviour, spread and evolution of the virus using next-generation sequencing technology

COMBAT-AMR

COMBAT-AMR works in partnership with government, National AMR Committees and public health counterparts in Fiji, Samoa, Solomon Islands and Papua New Guinea, to implement capacity building and training activities to support the prevention, diagnosis, surveillance and management of AMR pathogens, under the framework of National AMR Action Plans and priorities. COMBAT-AMR is supported by the Department of Foreign Affairs and Trade’s Indo-Pacific Centre for Health Security.

Fleming Fund

The Fleming Fund is a £265 million UK aid investment to tackle antimicrobial resistance in low- and middle-income countries around the world. The program is managed by the UK Department of Health and Social Care, in partnership with Mott MacDonald, the Fleming Fund Grants Management Agent. As a host institution under the Fleming Fund Scheme, the Doherty Institute Fleming Fund Fellowships offer a program of on-the-job training, mentoring and professional development to improve the capability and capacity of in-country institutions and staff to respond to the threat of antimicrobial resistance across human and animal health. The Doherty Institute is currently running programs in Bhutan, Nepal, Papua New Guinea and Timor-Leste.

WHO Collaborating Centre for Antimicrobial Resistance

The WHO Collaborating Centre for Antimicrobial Resistance works under the leadership of the WHO, particularly the Western Pacific Regional Office, to strengthen and build antimicrobial stewardship and laboratory capacity for diagnosis and surveillance of antimicrobial resistance (AMR). Based at the Doherty Institute, in Melbourne, Australia, the Centre is one of 30 designated AMR Collaborating Centres worldwide in place to support the WHO with activities to prevent, detect and monitor, and respond to AMR.