Infectious disease epidemiology and modelling

Infectious disease epidemiology and modelling


This theme applies multidisciplinary approaches to emerging issues in communicable diseases. We combine strengths in research, education and the disciplines of field-based epidemiology, health services research and mathematical modeling to translate research findings into policy and practice.


External members


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Project Status
A Revisit to On the Mode of Communication of Cholera by John Snow: A Systematic Review and Meta-Analysis Completed
Assessing the risk of Salmonella associated with importation of beef Completed
Assessment of potential risks to human health posed by Cypranid herpesvirus 3 Completed
Australian Pathogen Genomics Program: evaluation and cost-effectiveness of pathogen genomics Current
Burden and costs of gastroenteritis Completed
Clinical outcomes of Campylobacter in Australia Current
Critical review of major Australian outbreaks of infectious diseases 1991-2015 Current
Estimating the global risk of the emergence, transmission, and spread of novel diseases Current
Evaluation of the outputs of the MAE program: reviewing 25 years of operation Completed
Gastroenteritis and foodborne disease in older adults Completed
Mathematical modelling of Clostridium difficile Current
Mathematical modelling of diseases at low prevalence Potential
Mathematical modelling of respiratory pathogens Current
Measuring the financial burden of tuberculosis in the Asia-Pacific region Current
Modelling spatial sampling strategies for eliminating infectious diseases Potential
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)and Long COVID Current
Optimal design of surveillance of vector-borne diseases Current
Planning for an influenza pandemic and responding to the COVID-19 pandemic Current
Quality and Efficiency in Laboratory Medicine and Pathology Current
Sources and transmission zoonotic enteric pathogens: A One Health approach to the analysis of exposure and genomic data Current
Supervisory models for outbreak investigation training in FETP in Asia-Pacific Current
Surveillance and modelling of diseases at low prevalence Current
The Australian tuberculosis risk factor survey Current
Tracking outbreaks of foodborne disease internationally through Whole Genome Sequencing Current
Understanding information needs about COVID-19 vaccines and the vaccination program among migrants in Australia Completed
Understanding the sources of Campylobacter in Australia Current
Using new point-of-care tests to improve outbreak response to epidemic and emerging pandemic influenza Current
What immunisation data matters most in the Pacific? Current
Whole genome sequencing in Salmonella surveillance and control Completed


Recent publications

Applied epidemiology

  • Davis S, Fearnley E, Viney K, Patel M, Kirk M.  The Australian Master of Applied Epidemiology Program:  Looking back, moving forward.  Communicable Diseases Intelligence, 2016; (in press).
  • Kirk MD, Davis S, Viney K  Ebola outbreak in West Africa: considerations for strengthening Australia’s international health emergency response, MJA, 2016;  205(5):236-7.
  • Guthrie J, Dance PR, Kelly PM, Lokuge K, McPherson M, Faulkner S Public health capacity development through Indigenous involvement in the master of applied epidemiology program - celebrations and commiserations. Australian Aboriginal Studies, 2011; 2:102-110.
  • Foxwell AR, Roberts L, Lokuge K, Kelly PM Transmission of influenza on international flights,Emerg. Infect. Dis. 2009; 17:1188-1194.
  • Jardine A, Menzies RI, Deeks SL, Patel MS, McIntyre PB  The impact of pneumococcal conjugate vaccine on rates of myringotomy with ventilation tube insertion in Australia. Pediatr. Infect. Dis. J. 2009; 28:761-765.
  • McPherson ME, Kelly H, Patel MS, Leslie D. Persistent risk of tuberculosis in migrants a decade after arrival in Australia. MJA 2008;188(9):528-531.
  • Franklin LJ, Fielding JE, Gregory J, Gullan I, Lightfoot D, Poznanski SY, Vally H  ‘An outbreak of Salmonella Typhimurium 9 at a school camp linked to contamination of rainwater tanks’, Epidemiology and Infection, 2008; 137(3), pp. 434–440.
  • Webby RJ, Carville KS, Kirk MD, Greening G, Ratcliff RM, Crerar SK, Dempsey K, Sarna M, Stafford R, Patel M, Hall G Internationally Distributed Frozen Oyster Meat Causing Multiple Outbreaks of Norovirus Infection in Australia Clin Infect Dis. 2008; 44 (8): 1026-1031.

Infectious disease modelling

  • Hogan AB, Anderssen RS, Davis S, Moore HC, Lim FJ, Fathima P, Glass K. Time series analysis of RSV and bronchiolitis seasonality in temperate and tropical Western Australia. Epidemics 2016;16 49-55.
  • Sharmin S, Glass K, Viennet E, Harley D. Interaction of mean temperature and daily fluctuation influences dengue incidence in Dhaka, Bangladesh. PLOS Neglected Tropical Diseases, 2015; 9(7):e0003901.
  • Aditama TY, Samaan G, Kusriastuti R, Sampurno OD, Purba M, Santoso H, Bratasena A, Marruf A, Sariwati E, Setiawaty V, Glass K, Lokuge K, Kelly PM, Kandu IN. Avian influenza H5N1 transmission in households, Indonesia. PLOS One, 2013; 7(1):e29971
  • Fielding J, Kelly HA, Mercer GN, Glass K,  Systematic review of influenza A(H1N1)pdm09 virus shedding: duration is affected by severity but not age. Influenza and other respiratory viruses, 2013; 8(2):142-150.
  • Hickson RI, Mercer GN, Lokuge KM.  A metapopulation model of tuberculosis transmission with a case study from high to low burden areas. PLOS One, 2012; 7(4):e34411.
  • Mercer GN, Glass K, Becker NG. Effective reproduction numbers are commonly overestimated early in a disease outbreak. Statistics in Medicine, 2011; 30:984-994
  • Caley P, Philp DJ, McCracken K. Quantifying social distancing arising from pandemic influenza. J Roy Soc. Interface, 2008; 5(23):631-639.
  • Park AW, Glass K.Dynamic patterns of avian and human influenza in east and southeast Asia. Lancet: Infectious Diseases, 2007; 7: 543-548.
  • Caley P, Becker NG, Philp DJ  The waiting time from inter-country spread of pandemic influenza. PLOS One, 2007; 2(1):e143.
  • Glass K, Barnes B. How much would closing schools reduce transmission during an Influenza pandemic? Epidemiology, 2007; 18: 623-628.

Foodborne diseases

  • Kirk MD, Pires SM, Black RE, Caipo M, Crump JA, Devleesschauwer, Dopfer D, Fazil A, Fischer-Walker CL, Hald T, Hall AJ, Keddy KH, Lake RJ, Lanata CF, Togerson PR, Havelaar AH, Angulo FJ (2015) World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal and viral diseases,  a data synthesis. PLOS Medicine, 2010; 12(12):e1001940
  • Lal A, Cornish LM, Fearnley E, Glass K, Kirk M. Cryptosporidiosis: a disease of tropical and remote areas in Australia. PLOS Neglected Tropical Diseases, 2015; 9(9):e0004078.
  • Kirk M, Ford L, Glass K, Hall G. Foodborne illness, Australia, circa 2000 and circa 2010.Emerging Infectious Diseases, 2014; 20(11):1857-64.
  • Ford L, Kirk MD, Glass K, Hall G. Sequelae of foodborne illness caused by 5 pathogens, Australia, Circa 2010. Emerging Infectious Diseases, 2014; 20(11):1865-1871.
  • Chen Y, Kirk MD Incidence of acute respiratory infections in Australia. Epidemiology and Infection, 2014; 142(7):1355-1361.
  • Fearnley E, Raupach J, Lagala F, Cameron S (2011) Salmonella  in chicken meat, eggs and humans; Adelaide, South Australia, Int. J. Food Microbiology, 2008; 146:219-227.
  • Kirk MD, Fullerton KE, Hall GV, Gregory J, Stafford R, Veitch MG, Becker N.Surveillance for outbreaks of gastroenteritis in long-term care facilities, Australia, 2002-2008. Clinical Infectious Diseases. 2010; 51:907-14.
  • Kirk MD, McKay I, Hall GV, Dalton CB, Stafford R, Unicomb L, Gregory J. Foodborne disease in Australia: the OzFoodNet experience,2008.
  • D’Souza RM, Hall G, Becker NG Climatic factors associated with hospitalizations for rotavirus diarrhoea in children under 5 years of age. Epidemiology and Infection 2008;136:56-64.
  • Hall G, Yohannes K, Raupach J, Becker N, Kirk M. Estimating community incidence of Salmonella, Campylobacter, and Shiga toxin-producing Escherichia coli infections, Australia. Emerg Infect Dis. 2008; Oct;14(10):1601-9