Issue #4

Tuesday, 17 October 2023

Dear Stakeholder,

Welcome to the quarterly issue of the Australian Pathogen Genomics (AusPathoGen/APG) Program newsletter. As a reminder, our team will use these communications to keep you up to date on the latest news, as well as any events and opportunities that may be of interest to this community.

This edition of the newsletter will highlight several updates across the Program's activities, most notably the Annual Symposium which took place at the State Library Victoria in Melbourne on Thrusday 17th August. Additional updates have been summarised below. 

• Pathogen updates
  • Mycobacterium tuberculosis deep dive
  • Candida auris Working Group
  • Invasive Pneumococcal Disease Working Group
• AusPathoGen presentations
• Evaluation of Whole Genome Sequencing Utility and Cost-Effectiveness
  • Paper published
• Cross-cutting theme update
  • Teaching and Training webinar

We hope you will find this newsletter informative, and if you have any colleagues that may be interested in receiving this too, please feel free to put them in touch with our team.

AusPathoGen Annual Symposium

This year’s symposium highlighted the incredible amount of work, time and effort dedicated to progressing our collaborative activities. AusPathoGen brought together over 100 public health experts, policymakers, scientists, and researchers who are passionate in developing, exploring and evaluating best-practice approaches for implementing pathogen genomics into the Australian public health system. 

The article will take you through the key takeaways from the day and is available on the AusPathoGen website via the below link:

In-person attendees at State Library Victoria

Pathogen Updates

This quarterly update will go in-depth on the recent progress for the Mycobacterium tuberculosis project, specifically with regards to the prospective snapshot and subsequent analysis. We would like to thank the Tuberculosis Working Group (WG) members for their collaboration on the project thus far and for their contribution to this issue of the newsletter.  

Prospective Snapshot

The 12-month national snapshot where Mycobacterium tuberculosis (Mtb) across the majority of jurisdictions were sequenced and uploaded to AusTrakka is due to conclude in October. This snapshot is the first of its kind conducted on Mtb in Australia and is critical for providing important insights into Mtb drug resistance trends, case clusters and informing public health surveillance of Mtb in Australia.

Analysis

First stages of analysis have been undertaken on the retrospective (2015-2021) and prospective datasets by the national network of bioinformaticians using the AusPathoGen dedicated server. Results from the preliminary analysis were presented by Dr Eby Sim, Research Fellow, NSW, and Dr Jessica Webb, Research Fellow, VIC, on behalf of the Tuberculosis WG at the AusPathoGen symposium. Preliminary results touched on antimicrobial resistance trends across the clinically-significant drugs and revealed that pathogen genomics is critical to detecting cross-jurisdictional Mtb case clusters. This analysis is being refined by the bioinformaticians, with results to be published in three separate research publications currently being drafted and discussed in working group meetings.

Candida auris Working Group

An AusPathoGen Working Group (WG) has been established for Candida auris (C. auris), a pathogen of increasing clinical importance due to widespread multi-drug resistance with a recent multi-country study revealing over 40% of strains exhibiting combined resistance to two or more classes of antifungals.

The aims of the AusPathoGen C. auris WG are: to implement harmonised national analysis methodologies in AusTrakka; to undertake retrospective whole genome sequence analysis of all isolates archived and implement a 12-month prospective collection from all jurisdictions to identify the strains and clades present and highlight local transmission/importation events; and to develop a guidance document on C. auris genomic surveillance for public health laboratories and integrate with public health agencies.

Given the global increase in C. auris in recent years, it is important to initiate national surveillance to inform public health measures.  The first Australian case was identified in Perth in 2015, which was isolated from an overseas visitor. There is currently limited national genomic data available, with only 13 other Australian isolates publicly available. Further reflecting the increasing awareness of this pathogen of concern, C. auris is a notifiable disease in Victoria, South Australia, and New South Wales, with Queensland and Western Australia requesting notifications for any identification. C. auris is not currently a notifiable pathogen in New Zealand, where the first C. auris was identified in 2023.

Invasive Pneuomococcal Disease WG

An AusPathoGen WG has been established for Invasive Pneumococcal Disease (IPD) and will meet for the first time toward the end of October. The WG is looking to develop a framework to inform the best strategy for national genomic surveillance of IPD and integration into AusTrakka. This will provide high-resolution information to inform and evaluate public health interventions, including the National Immunisation Program.

The WG are specifically aiming to: implement harmonised national analysis methodologies in AusTrakka; to undertake a national comprehensive snapshot over a 12-month period to define the genomic epidemiology of IPD and contextualisation of Australian cases globally; and to explore integration models with existing national epidemiological surveillance systems.

IPD has been nationally notifiable since 2001 and is monitored through the Enhanced Invasive Pneumococcal Disease Surveillance Program (EIPDSP), part of the National Notifiable Diseases Surveillance System. National genomic analysis of IPD cases is an opportunity to further enhance and strengthen this program. Whole genome sequencing has the capability of providing high-resolution information on the phylogenetic relationship of isolates to contextualise serotype data and unravel the evolutionary dynamics of pneumococcal populations, while simultaneously providing a comprehensive genome-wide view of AMR determinants. Full realisation of the value of a genomics informed surveillance system for IPD would be through integration with key epidemiological data sources, such the Australian Immunisation Registry (AIR), NINDSS and electronic medical records.

AusPathoGen presentations

Several members of AusPathoGen recently attended the launch of the Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food and Environment (CRC SAAFE), with Dr Patiyan Andersson, Research Fellow, VIC, presenting an overview of the program thus far. The $150M CRC is led by Prof. Erica Donner (Research Director), Co-Lead of the One Health theme in AusPathoGen, and Mr Alex Lloyd (CEO), with the aim to understand and mitigate the threat of AMR and translate Australia's National One Health AMR action plan into practice. The team was in attendance to showcase relevant AusPathoGen and AusTrakka activities to underpin future collaborative efforts.

AusPathoGen was also presented by program partners on the following occasions:

• Doherty Institute Public Health Laboratory Seminar - Prof Ben Howden, VIC
• Australian Society of Infectious Diseases (ASID) Bug Club SA Branch - Dr Lex Leong, SA 
• Public Health Laboratory Network - A/Prof Amy Jennison, QLD
• Global Microbial Identifier (GMI) 13 - Prof Ben Howden, VIC

Evaluation of Whole Genome Sequencing Utility and Cost-Effectiveness

This was published in The Lancet Microbe and is available via DOI:https://doi.org/10.1016/S2666-5247(23)00180-5

Teaching and Training Webinar

The fourth and final instalment of our "Introduction to Pathogen Genomics for Public Health" series, co-hosted with CDGN. 

AusPathoGen Working Groups

Established working groups under the program are listed below. If you wish to join a working group or would like further information, please email the AusPathoGen Secretariat.

AusPathoGen Progam Partners

All previous newsletters are available to browse via the archive on our website.