September report for Infectious Disease Epidemiology and Modelling

1 September 2020

Keynote and invited presentations

Danielle Ingle was invited to talk on “Multidrug resistant Shigella circulating in Australia” at the Australian Society of Microbiology Hour on the 4th of August

Outreach and engagement

Danielle Ingle is a member of the organising committee for an annual introductory course in applied microbial genomics for public health at MDU. They have an upcoming workshop in December that may be of interest to IDEM members – more information is available at

Tambri Housen, Martyn Kirk, Polly Wallace and Anna Rafferty have conducted contact tracing training for ACT Health and the Commonwealth National Incident room, whom are assisting the Department of Health and Human Services in Victoria with the COVID-19 response. A total of 64 contact tracers and case interviewers have been trained. The training materials have been requested by and shared with public health departments throughout Australia, and were recently requested by the Pacific. These training materials focus on the epidemiology of SARS-Cov-2, an introduction to contact tracing for COVID-19, interview techniques for contact tracing and cognitive interview techniques for case interviews, mental health and wellbeing for cases, contacts and contact tracing teams, introduction to standard operating procedures, data quality, reporting and the ACT electronic data collection tools.

Tambri Housen was invited to facilitate a TEPHINET Global COVID-19 Teleconference on Contact Tracing with presentations from the Global Task Force at CDC in the USA, and Field Epidemiology Training Programs from India, Uganda and Belize on Wednesday 19th August. Over 50 global Field Epidemiology Training programs were present on the call. This was a great opportunity for countries to hear the diversity of approaches to contact tracing and e-tools being used.

Tambri Housen and Ben Polkinghorne worked with RSPHs Society, Culture and Health team and the Public Health Agency of Canada to produce three e-learning modules on contact tracing which are hosted on the World Health Organisations, Global Outbreak Alert and Response Networks Training Hub and are open access. These modules focus on an introduction to contact tracing, social determinants culture and contact tracing, and mental health and contact tracing.

Papers accepted/published:

  1. Parisi A, Phuong TLT, Mather A, Jombart T, Tuyen HT, Lan NPH, Trang NHT, Carrique-Mas J, Campbell JI, Glass K, Kirk MD, Baker S. (2020) Differential antimicrobial susceptibility profiles between symptomatic and asymptomatic non-typhoidal Salmonella infections in Vietnamese children. Epidemiology and Infection 148, e144, 1–3.

Wan Y, Wick RR, Zobel J, Ingle DJ, Inouye M, Holt KE. (2020). GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. bioRxiv 2020.02.29.970970; doi: