ODeSI – Operational Research and Decision Support for Prevention, Control and Elimination of Infectious Diseases

The poolTestR R package, developed by Angus McLure, lets you easily analyse your data on pooled  samples, such as a tube of mosquitoes, to estimate the prevalence of a disease in your overall sample. With just a few lines of R code you can estimate infection prevalence in vectors, even from large and complex molecular xeno monitoring surveys across many sampling sites and vector species, split by however many levels you like. This means you can quickly compare the results between sites, villages, regions, time, or species. You can read more about how and why the software was developed on this COR-NTD blog post.

Related publications

McLure, A., O'Neill, B., Mayfield, H., Lau, C. & McPherson, B. PoolTestR: An R package for estimating prevalence and regression modelling for molecular xenomonitoring and other applications with pooled samples. Environmental Modelling & Software 145, 105158, doi:https://doi.org/10.1016/j.envsoft.2021.105158 (2021).

The CoRiCAL COVID-19 vaccine risk-benefit calculator, hosted by the Immunisation Coalition, combines the latest evidence on the benefits of being vaccinated against COVID-19 compared to the risks from vaccines. The webpage is powered by a Bayesian Network model than combines results from published studies with Government published reports and knowledge from medical experts. CoRiCAL is the result of a dedicated team of academics and medical practitioners who collate and present the evidence into a user-friendly format to help people make an informed choice on vaccination.  It’s updated regularly to account for new evidence, vaccines and COVID-19 variants and is feely available from the IC website.

Related publications

Lau, C. L. et al. Risk-benefit analysis of the AstraZeneca COVID-19 vaccine in Australia using a Bayesian network modelling framework. Vaccine, doi: https://doi.org/10.1016/j.vaccine.2021.10.079 (2021).

Sinclair, J. E. et al. Quantifying the risks versus benefits of the Pfizer COVID-19 vaccine in Australia: a Bayesian network analysis. medRxiv, 2022.2002.2007.22270637, doi:10.1101/2022.02.07.22270637 (2022).

Mayfield, H. J. et al. Designing an evidence-based Bayesian network for estimating the risk versus benefits of AstraZeneca COVID-19 vaccine. Vaccine 40, 3072-3084, doi: https://doi.org/10.1016/j.vaccine.2022.04.004 (2022).

CRISPER is an interactive dashboard that provides accurate and spatially explicit real-time information for COVID-19 cases, deaths, testing and contact tracing locations in Australia. Developed based on feedback from key users and stakeholders, the system comprises three main components: (1) a data engine; (2) data visualization and interactive mapping tools; and (3) an automated alert system. The system provides integrated data from multiple sources in one platform which optimizes information sharing with public health responders, primary health care practitioners and the general public.

Related publications

Field E, Dyda A, Hewett M, Weng H, Shi J, Curtis S, Law C, McHugh L, Sheel M, Moore J, Furuya-Kanamori L, Pillai P, Konings P, Purcell M, Stocks N, Williams G, Lau CL. Development of the COVID-19 Real-time Information System for Preparedness and Epidemic Response (CRISPER), Australia. https://doi.org/10.3389/fpubh.2021.753493 (2021).

Field E, Dyda A, Lau CL. COVID‐19 Real‐time Information System for Preparedness and Epidemic Response (CRISPER). doi: 10.5694/mja2.51019 (2021).

Dyda A, Purcell M, Curtis S, Field E, Pillai P, Ricardo K, Weng H, Moore JC, Hewett M, Williams G, Lau CL. Differential privacy for public health data: An innovative tool to optimize information sharing while protecting data confidentiality. doi: 10.1016/j.patter.2021.100366 (2021).

Martin, B.M., Cadavid Restrepo, A. M., Mayfield, H., Lau, C.L. Towards Global Elimination of Lymphatic Filariasis – A Systematic Review of the Applications of Spatial Epidemiological Methods to Enhance Surveillance and Support Elimination Programs. BML Public Health, 2024.

Heryanto, B., Prasettya Japri, A., Craig, A.T. Community-based surveillance (CBS) review in Indonesia. 2024. Australia Indonesia Health Security Partnership: Jakarta, Indonesia.

Sartorius B, Gray AP, Weaver ND, Aguilar GR, Swetschinski LR, Ikuta KS, Mestrovic T, Chung E, Wool EE, Han C, Hayoon AG. The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis. The Lancet Global Health. 2023 Dec 19. DOI: https://doi.org/10.1016/S2214-109X(23)00539-9.

Sartorius K, Sartorius B, Winkler C, Chuturgoon A, Shen TW, Zhao Y, An P. Serum microRNA Profiles and Pathways in Hepatitis B-Associated Hepatocellular Carcinoma: A South African Study. International Journal of Molecular Sciences. 2024 Jan 12;25(2):975. DOI: https://doi.org/10.3390/ijms25020975.

Munazza Fatima, Ibtisam Butt, Neda Firouraghi, Maria Khalil, Behzad Kiani. Space-time analysis of tuberculosis (2016-2020) in South Punjab, Pakistan,  GeoJournal, 2024; http://dx.doi.org/10.1007/s10708-024-11020-x

Dove, G.; Kelly-Hanku, A.; Usurup, J.; O’Keeffe, A.; Scahill, G.; Craig, A. Collaboration in a partnership for primary health care: a case study from Papua New Guinea. Global Health: Science and Practice, (in press), 2023.

Sarah L. McGuinness, Colleen Lau, Karin Leder, The evolving Japanese encephalitis situation in Australia and implications for travel medicine, Journal of Travel Medicine, 2023

Nilles E, de St. Aubin M, Dumas D, Duke W, Etienne MC, Abdalla G, et al. Monitoring Temporal Changes in SARS-CoV-2 Spike Antibody Levels and Variant-Specific Risk for Infection, Dominican Republic, March 2021–August 2022. Emerging Infectious Disease journal. 2023;29(4).

Assoum, M.; Lau, C.L.; Thai, P.K.; Ahmed, W.; Mueller, J.F.; Thomas, K.V.; Choi, P.M.; Jackson, G.; Selvey, L.A. Wastewater Surveillance Can Function as an Early Warning System for COVID-19 in Low-Incidence Settings. Trop. Med. Infect. Dis. 2023, 8, 211. https://doi.org/10.3390/tropicalmed8040211

Lau CL, Mills DJ, Mayfield H, Gyawali N, Johnson BJ, Lu H, et al. A decision support tool for risk–benefit analysis of Japanese encephalitis vaccine in travellers. Journal of Travel Medicine. 2023.

Cavany S, Nanyonga S, Hauk C, Lim C, Tarning J, Sartorius B, Dolecek C, Caillet C, Newton PN, Cooper BS. The uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance. Nature Communications. 2023 Oct 3;14(1):6153.

Rees EM, Lau CL, Kama M, Reid S, Lowe R, Kucharski AJ. Estimating the duration of antibody positivity and likely time of Leptospira infection using data from a cross-sectional serological study in Fiji. PLOS Neglected Tropical Diseases. 2022. 

Bragazzi Nicola Luigi, Woldegerima Woldegebriel Assefa, Iyaniwura Sarafa Adewale, Han Qing, Wang Xiaoying, Shausan Aminath, e tal. Knowing the unknown: The underestimation of monkeypox cases. Insights and implications from an integrative review of the literature. Frontiers in Microbiology, 2022. https://doi.org/10.3389/fmicb.2022.1011049 

Nilles, E. J., Paulino, C. T., de St. Aubin, M., Restrepo, A. C., Mayfield, H., Dumas, D., . . . Lau, C. L. (2022). SARS-CoV-2 seroprevalence, cumulative infections, and immunity to symptomatic infection – A multistage national household survey and modelling study, Dominican Republic, June–October 2021. The Lancet Regional Health - Americas, 16, 100390. doi:https://doi.org/10.1016/j.lana.2022.100390

Nilles, E. J., Aubin, M. D. S., Dumas, D., Duke, W., Etienne, M. C., Abdalla, G., . . . Paulino, C. T. (2022). Integrated SARS-CoV-2 serological and virological screening across an acute fever surveillance platform to monitor temporal changes in anti-spike antibody levels and risk of infection during sequential waves of variant transmission — Dominican Republic, March 2021 to August 2022. medRxiv. doi:10.1101/2022.10.24.22281399

Stanhope J*, Mayfield HJ*, Guillaume JHA, Sahin O, Weinstein P, Lau CL. Synergising decision making and interventions across human health and environment: concepts for designing ana model for infectious disease transmission modeldiseases.  Socio-Environmental Systems Modelling, 3, 18126. https://doi.org/10.18174/sesmo.18126

Field E., Dyda, A. Lau CL.,The Medical Journal of Australia ; 214 (8): 386-386.e1.  doi: 10.5694/mja2.51019

Curtis SJ, Cutcher Z, Brett JA, Burrell S, Richards MJ, Hennessy D, Gang RF, Lau CL, Rowe SL. An evaluation of enhanced surveillance of hospitalised COVID-19 patients to inform the public health response in Victoria. Communicable Disease Intellgence 2021. doi: https://doi.org/10.33321/cdi.2020.44.98

McLure A, Lau CL, Furuya-Kanamori L. Has the effectiveness of Australia’s travel bans against China on the importation of COVID-19 been overestimated? Journal of Travel Medicine. 2020;28(2). doi: 10.1093/jtm/taaa191.

Cadavid Restrepo A, Furuya-Kanamori L, Mayfield H, Nilles E, Lau CL. Implications of a travel connectivity-based approach for infectious disease transmission risks in Oceania. BMJ Open. 2021;11(8):e046206. doi: 10.1136/bmjopen-2020-046206.

Dyda A, Fahim M, Fraser J, Kirrane M, Wong I, McNeil K, Ruge M, Lau CL, Sullivan C. Managing the Digital Disruption Associated with COVID-19-Driven Rapid Digital Transformation in Brisbane, Australia. Applied clinical informatics. 2021;12(5):1135-43. Epub 2021/12/02. doi: 10.1055/s-0041-1740190. PubMed PMID: 34852391; PubMed Central PMCID: PMCPMC8636016.

Field E, Dyda A, Hewett M, Weng H, Shi J, Curtis S, Law C, McHugh L, Sheel M, Moore J, Furuya-Kanamori L, Pillai P, Konings P, Purcell M, Stocks N, Williams G, Lau CL. Development of the COVID-19 Real-Time Information System for Preparedness and Epidemic Response (CRISPER), Australia. Front Public Health. 2021;9:753493. Epub 2021/12/04. doi: 10.3389/fpubh.2021.753493. PubMed PMID: 34858930; PubMed Central PMCID: PMCPMC8631999.

Lau CL, Mayfield HJ, Sinclair JE, Brown SJ, Waller M, Enjeti AK, Baird A, Short K, Mengersen K, Litt J. Risk-benefit analysis of the AstraZeneca COVID-19 vaccine in Australia using a Bayesian network modelling framework. Vaccine. 2021. doi: https://doi.org/10.1016/j.vaccine.2021.10.079.

Lau CL, Galea I. Risk–benefit analysis of COVID-19 vaccines — a neurological perspective. Nature Reviews Neurology. 2022;18(2):69-70. doi: 10.1038/s41582-021-00606-5.

Mayfield HJ, Lau CL, Sinclair JE, Brown SJ, Baird A, Litt J, Vuorinen A, Short KR, Waller M, Mengersen K. Designing an evidence-based Bayesian network for estimating the risk versus benefits of AstraZeneca COVID-19 vaccine. medRxiv. 2021:2021.10.28.21265588. doi: 10.1101/2021.10.28.21265588.

Gilmour B, Wangdi K, Restrepo AC, Tsheten T, Kelly M, Clements A, Gray D, Lau C, et al. Protocol for spatial prediction of soil transmitted helminth prevalence in the Western Pacific region using a meta-analytical approach. Systematic Reviews. 2024;13(1)

Adam Craig, Nixon Panda, Rudgard Palapu, Geoffrey Oku, Clement Lifoia, Joanna Tatalu, Nigel Beebe, Gerard Kelly, Nathan Kama Jr, Charlie Iro’ofa, Hugo Bugoro. Citizen Science for Enhanced Dengue Vector Surveillance in Solomon Islands: A Methods Paper. Cit Sci Theory & Prac.

Sohail A, Barry A, Auburn S, Cheng Q, Lau CL, Lee R, et al. Imported malaria into Australia: surveillance insights and opportunities. Journal of Travel Medicine. 2023. https://academic.oup.com/jtm/advance-article/doi/10.1093/jtm/taad164/7486528?login=true

Dove G, Kelly-Hanku A, Usurup J, O’Keeffe, Scahill G, Craig A. Collaboration in a partnership for primary health care: a case study from Papua New Guinea. Glob Health Sci Pract. 2024;12(1):e2300040. https://doi.org/10.9745/GHSP-D-23-00040

McLure A, Graves PM, Lau C, Shaw C, Glass K. Modelling lymphatic filariasis elimination in American Samoa: GEOFIL predicts need for new targets and six rounds of mass drug administration. Epidemics. 2022:100591.

Dickson, B.F.R.; Masson, J.J.R.; Mayfield, H.J.; Aye, K.S.; Htwe, K.M.; Roineau, M.; Andreosso, A.; Ryan, S.; Becker, L.; Douglass, J.; Graves, P.M. Bayesian Network Analysis of Lymphatic Filariasis Serology from Myanmar Shows Benefit of Adding Antibody Testing to Post-MDA Surveillance. Trop. Med. Infect. Dis. 2022, 7, 113. https://doi.org/10.3390/tropicalmed7070113

McPherson, B.; Mayfield, H.J.; McLure, A.; Gass, K.; Naseri, T.; Thomsen, R.; Williams, S.A.; Pilotte, N.; Kearns, T.; Graves, P.M.; Lau, C.L. Evaluating Molecular Xenomonitoring as a Tool for Lymphatic Filariasis Surveillance in Samoa, 2018–2019. Trop. Med. Infect. Dis. 2022, 7, 203. https://doi.org/10.3390/tropicalmed7080203. 

Assoum, M.; Ortu, G.; Basáñez, M.-G.; Lau, C.; Clements, A.C.A.; Halton, K.; Fenwick, A.; Magalhães, R.J.S. Impact of a 5-Year Mass Drug Administration Programme for Soil-Transmitted Helminthiases on the Spatial Distribution of Childhood Anaemia in Burundi from 2007 to 2011. Trop. Med. Infect. Dis. 2022, 7, 307. https://doi.org/10.3390/tropicalmed7100307

Lemin, M.E.; Cadavid Restrepo, A.; Mayfield, H.J.; Lau, C.L. Spatially Explicit Environmental Factors Associated with Lymphatic Filariasis Infection in American Samoa. Trop. Med. Infect. Dis. 2022, 7, 295. https://doi.org/10.3390/tropicalmed7100295

Wangdi K, Sheel M, Fuimaono S, Graves PM, Lau CL. Lymphatic filariasis in 2016 in American Samoa: Identifying clustering and hotspots using non-spatial and three spatial analytical methods. PLoS Negl Trop Dis. 2022;16(3):e0010262.

McPherson B,  Mayfield HJ, McLure A, Gass K,  Naseri T, Thomsen R,  Williams S, Pilotte R, Kearns T, Graves PM, Lau CL. Molecular xenomonitoring as a complement to human antigen seroprevalence for lymphatic filariasis surveillance in Samoa. Research Square 2022.  10.21203/rs.3.rs-1294399/v1

Sheel M, Lau CL, Sheridan S, Fuimaono S, Graves PM. Comparison of Immunochromatographic Test (ICT) and Filariasis Test Strip (FTS) for Detecting Lymphatic Filariasis Antigen in American Samoa, 2016. Tropical Medicine and Infectious Disease. 2021;6(3):132. PubMed PMID: doi:10.3390/tropicalmed6030132.

Graves PM, Sheridan S, Scott J, Amosa-Lei Sam F, Naseri T, Thomsen R, King CL, Lau CL. Triple-Drug Treatment Is Effective for Lymphatic Filariasis Microfilaria Clearance in Samoa. Tropical Medicine and Infectious Disease. 2021;6(2):44. PubMed PMID: doi: 10.3390/tropicalmed6020044.

Graves PM, Joseph H, Coutts SP, Mayfield HJ, Maiava F, Ah Leong-Lui TA, Tupuimatagi Toelupe P, Toeaso Iosia V, Loau S, Pemita P, Naseri T, Thomsen R, Berg Soto A, Burkot TR, Wood P, Melrose W, Aratchige P, Capuano C, Kim SH, Ozaki M, et al. Control and elimination of lymphatic filariasis in Oceania: Prevalence, geographical distribution, mass drug administration, and surveillance in Samoa, 1998-2017. Advances in parasitology. 2021;114:27-73. Epub 2021/10/27. doi: 10.1016/bs.apar.2021.03.002. PubMed PMID: 34696844.

Henderson AD, Kama M, Aubry M, Hue S, Teissier A, Naivalu T, Bechu VD, Kailawadoko J, Rabukawaqa I, Sahukhan A, Hibberd ML, Nilles EJ, Funk S, Whitworth J, Watson CH, Lau CL, Edmunds WJ, Cao-Lormeau V-M, Kucharski AJ. Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji. Nature Communications. 2021;12(1):1671. doi: 10.1038/s41467-021-21788-y.

Aw JYH, Clarke NE, Mayfield HJ, Lau CL, Richardson A, Vaz Nery S. Novel statistical approaches to identify risk factors for soil-transmitted helminth infection in Timor-Leste. International Journal for Parasitology. 2021;51(9):729-39. doi: https://doi.org/10.1016/j.ijpara.2021.01.005.

Hedtke SM, Zendejas-Heredia PA, Graves PM, Sheridan S, Sheel M, Fuimaono SD, Lau CL, Grant WN. Genetic epidemiology of lymphatic filariasis in American Samoa after mass drug administration. International Journal for Parasitology. 2021;51(2):137-47. doi: https://doi.org/10.1016/j.ijpara.2020.08.009.

Suwannatrai AT, Thinkhamrop K, Suwannatrai K, Pratumchart K, Wangdi K, Kelly M, Cadavid Restrepo, A, Gray DJ, Clements ACA, Tangkawattana S. Opisthorchis viverrini and Strongyloides stercoralis mono-and co-infections: Bayesian geostatistical analysis in an endemic area, Thailand. Acta tropica. 2021;223:106079. doi: https://doi.org/10.1016/j.actatropica.2021.106079

Cadavid Restrepo A, Gass K, Won KY, Sheel M, Robinson K, Graves PM, Fuimaono S, Lau CL. Potential use of antibodies to provide an earlier indication of lymphatic filariasis resurgence in post-mass drug administration surveillance, American Samoa. MedRxiv. 2021. doi: doi.org/10.1101/2021.11.29.21267031 

McPherson B,  Mayfield HJ, McLure A, Gass K,  Naseri T, Thomsen R,  Williams S, Pilotte R, Kearns T, Graves PM, Lau CL. Molecular xenomonitoring as a complement to human antigen seroprevalence for lymphatic filariasis surveillance in Samoa. Research Square 2022.  doi: 10.21203/rs.3.rs-1294399/v1

Muttucumaru R, Lau CL, Leeb A, Mills DJ, Wood N, Furuya-Kanamori L. Post-marketing surveillance of 10,392 herpes zoster vaccines doses in Australia. Vaccine [accepted]

Hasan, M., Talukder, S., Mandal, A.K., Tasmim, S.T., Parvin, S., Ali, Y., Sikder, M.H., Callaghan, T.J., Soares Magalhães, R.J., Islam, T., 2024. Antimicrobial Resistance Profiles of Campylobacter spp. Recovered from Chicken Farms in Two Districts of Bangladesh. Foodborne Pathogens and Disease.. https://doi.org/10.1089/fpd.2023.0079

Nasser A, de Zwart BJ, Stewart DJ, Zielke AM, Blazek K, Heywood AE, Craig AT. Risk factors predicting the need for intensive care unit admission within forty-eight hours of emergency department presentation: A case-control study. Aust Crit Care. 2024 Apr 6:S1036-7314(24)00028-6. doi: 10.1016/j.aucc.2024.01.012. Epub ahead of print. PMID: 38584063

Mathoma A, Sartorius B, Mahomed S. The Trends and Risk Factors of AIDS-Defining Cancers and Non-AIDS-Defining Cancers in Adults Living with and without HIV: A Narrative Review. Journal of Cancer Epidemiology. 2024 Mar 21;2024. https://doi.org/10.1155/2024/7588928. 

Mathoma A, Sartorius B, Mahomed S (2024). The trends and risk factors of AIDS Defining Cancers and non-AIDS Defining Cancers in adults living with and without HIV: A narrative review. Accepted: Journal of Cancer Epidemiology.

Tadese, M., Endale, A., Asegidew, W., Tessema, S. D., & Shiferaw, W. S. (2024). Nursing patient record practice and associated factors among nurses working in North Shewa Zone public hospitals, Ethiopia. Frontiers in Health Services, 4, 1340252. https://doi.org/10.3389/frhs.2024.1340252

Behzad Kiani, Benn Sartorius, Colleen L Lau, Robert Bergquist. Mastering Geographically Weighted Regression: Key Considerations for Building a Robust Model, Geospatial Health Journal, 2024.

Browne A,…[62 authors], Sartorius B, Dolecek C. Estimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990–2019: a modelling study. The Lancet Global Health, 2024; 12: e406–18.

Dove, G.; Kelly-Hanku, A.; Usurup, J.; O’Keeffe, A.; Scahill, G.; Craig, A. Collaboration in a partnership for primary health care: a case study from Papua New Guinea. Global Health: Science and Practice, 2023.

Gilmour B, Wangdi K, Restrepo AC, Tsheten T, Kelly M, Clements A, Gray D, Lau C et al. Protocol for spatial prediction of soil transmitted helminth prevalence in the Western Pacific region using a meta-analytical approach. Systematic Reviews. 2024;13(1).

Ahmad Nasser, Blake de Zwart, Anne Zielke, Katrina Blazek, Anita Heywood, Adam Craig. Risk Factors Predicting the Need for Intensive Care Unit Admission within Forty-Eight Hours of Emergency Department Presentation. Aust Crit Care,