Journal Articles

Profiling Mycobacterium tuberculosis transmission and the resulting disease burden in the five highest tuberculosis burden countries: a modelling study.

Ragonnet R, Trauer JM, Geard N, Scott N, McBryde, ES. BMC Medicine (accepted 25 October 2019). Accepted 25th October, 2019

What can urban mobility data reveal about the spatial distribution of infection in a single city?

Moss R, Naghizade E, Tomko M, Geard N BMC Public Health 19: 656, May 2019; What can urban mobility data reveal about the spatial distribution of infection in a single city? Background Infectious diseases spread through inherently spatial processes. Road and air traffic data have been used to model these processes at national and global…

Longitudinal analysis of group A Streptococcus emm types and emm clusters in a high prevalence setting reveals past infection does not prevent future infection

Campbell PT, Tong SYC, Geard N, Davies MR, Worthing KA, Lacey JA, Smeesters PR, Batzloff MR, Kado J, Jenney AWJ, McVernon J, Steer AC. Journal of Infectious Diseases, accepted for publication 9th October 2019  

Inhibition of influenza A virus by human infant saliva

Gilbertson B, Edenborough K, McVernon J, Brown LE. Viruses, 2019 Aug 20;11(8). pii: E766.  DOI: 10.3390/v11080766 Innate antiviral factors in saliva play a role in protection against respiratory infections. We tested the anti-influenza virus activities of saliva samples taken from human infants, 1-12 months old, with no history of prior exposure to influenza. In contrast to the inhibitory activity we observed in mouse and…

Perinatal risk factors associated with skin infection hospitalization in Western Australian Aboriginal and Non-Aboriginal children

Barnes R, Bowen AC, Walker R, Tong SYC, McVernon J, Campbell PT, Fathima P, de Klerk NH, Wu Y, Blyth CC, Carapetis JR, Moore HC. Paediatric and Perinatal Epidemiology, 2019 Sep;33(5):374-383. Epub 2019 Sep 12, 10.1111/ppe.12573 BACKGROUND: Hospitalisation with skin infection in Western Australian (WA) Aboriginal children is common, with the highest rates in infants and children from remote WA. OBJECTIVE: We aimed to quantify infant,…

Optimal Timing of Influenza Vaccine during Pregnancy: a Systematic Review and Meta-Analysis

Cuningham W, Geard N, Fielding JE, Braat S, Madhi SA, Nunes MC, Christian LM, Lin S-Y, Lee C-N, Yamaguchi K, Bisgaard H, Chawes B, Chao A-S, Blanchard-Rohner G, Schlaudecker EP, Fisher BM, McVernon J, Moss R. Influenza and other Respiratory Viruses, 2019 Sep;13(5):438-452. Epub 2019 Jun 5; 10.1111/irv.12649 BACKGROUND: Pregnant women have an elevated risk…

Prior exposure to immunogenic peptides found in human influenza A viruses may influence the age distribution of cases with avian influenza H5N1 and H7N9 virus infections.

Komadina N, Sullivan SG, Kedzierska K, Quinones-Parra SM, Leder K, McVernon J. Epidemiology and Infection, 2019: Jan147:e213; 10.1017/S095026881900102X The epidemiology of H5N1 and H7N9 avian viruses of humans infected in China differs despite both viruses being avian reassortants that have inherited six internal genes from a common ancestor, H9N2. The median age of infected populations is substantially younger for H5N1 virus (26 years) compared with H7N9 virus (63 years). Population susceptibility to infection…

High burden of infectious disease and antibiotic use in early life in Australian Aboriginal communities

Cuningham W, McVernon J, Lydeamore MJ, Andrews RM, Carapaetis J, Kearns T, Clucas D, Dhurrkay RG, Tong SYC, Campbell PT. Australia and New Zealand Journal of Public Health, 2019; 43(2):149-155; 10.1111/1753-6405.12876 OBJECTIVE: To quantify the childhood infectious disease burden and antibiotic use in the Northern Territory’s East Arnhem region through synthesis and analysis of historical data resources. METHODS: We combined primary…

Advancing the ethical use of digital data in research: challenges and strategies to promote ethical practice

Clark K, Duckham, M, Guillemin M, Hunter A, McVernon J, OKeefe C, Pitkin C, Prawer S, Sinnott R, Warr D and Waycott J. Ethics and Information Technology 2019: 21(1): 59-73; https://doi.org/10.1007/s10676-018-9490-4 The proliferation of digital data and internet-based research technologies is transforming the research landscape, and researchers and research ethics communities are struggling to respond…

Quantity or quality? Assessing relationships between perceived social connectedness and recorded encounters

Dias AE, Geard N, Campbell PT, Warr D, McVernon J. PLoS ONE, 2018; 13(11):e0208083; 0.1371/journal.pone.0208083 INTRODUCTION: Higher levels of social connectedness are associated with better physical and mental health outcomes, but measures of connectedness are often study specific. Prior research has distinguished between perceived and received (quantifiable) measures of social connectedness, with differing impacts on health, sometimes mediated by place of residence. This analysis…

Treatment outcomes of patients with multidrug-resistant and extensively drug resistant tuberculosis in Hunan Province, China.

Alene KA, Yi H, Viney K, McBryde ES, Yang K, Bai L, Gray DJ, Clements AC, Xu Z. 2017; 17: 675. https://doi.org/10.1186/s12879-017-2662-8 BACKGROUND: The worldwide emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug–resistant tuberculosis (XDR-TB) has posed additional challenges for global tuberculosis (TB) control efforts, as limited treatment options are available and treatment outcomes are often sub-optimal. This study determined treatment outcomes among a cohort of MDR-TB and XDR-TB patients in Hunan Province, China, and identified factors…

Spatial clustering of notified tuberculosis in Ethiopia: A nationwide study

Alene KA, Clements ACA PLoS ONE. 2019; 14(8): e0221027. https://doi.org/10.1371/journal.pone.0221027 BACKGROUND: Tuberculosis (TB) remains a major health problem worldwide and in Ethiopia. This study aimed to investigate the spatial distributions of notified TB over the whole territory of Ethiopia and to quantify the role of health care access, environmental, socio-demographic, and behavioural factors associated with the clustering of TB. METHODS: A spatial analysis was conducted using national TB data…

Increasing incidence of nontyphoidal Salmonella infections in Queensland, Australia, 2007-2016

Parisi A, Crump JA, Stafford R, Glass K, Howden BP, Kirk MD PLOS Neglected Tropical Diseases (2019) 13(3): e0007187; 10.1371/journal.pntd.0007187 Nontyphoidal Salmonella is a major contributor to the global burden of foodborne disease, with invasive infections contributing substantially to illnesses and deaths. We analyzed notifiable disease surveillance data for invasive nontyphoidal Salmonella disease (iNTS) in Queensland, Australia. We used Poisson regression to estimate incidence rate ratios…

Modelling the impact of biosecurity practices on the risk of high pathogenic avian influenza outbreaks in Australian commercial chicken farms

Glass K, Barnes B, Scott A, Toribio J-A, Moloney B, Singh M, Hernandez-Jover M Prev Vet Med (2019) 165:8-14; 10.1016/j.prevetmed.2019.02.002 As of 2018, Australia has experienced seven outbreaks of highly pathogenic avian influenza (HPAI) in poultry since 1976, all of which involved chickens. There is concern that increases in free-range farming could heighten HPAI outbreak risk due to the potential for greater contact…

Modelling diverse sources of Clostridium difficile in the community: importance of animals, infants and asymptomatic carriers

McLure A, Clements ACA, Kirk MD, Glass K Epidemiol Infect (2019) e152, 1–9; 10.1017/S0950268819000384 Clostridium difficile infections (CDIs) affect patients in hospitals and in the community, but the relative importance of transmission in each setting is unknown. We developed a mathematical model of C. difficile transmission in a hospital and surrounding community that included infants, adults and transmission from animal reservoirs. We assessed the role…

Modelling high pathogenic avian influenza outbreaks in the commercial poultry industry.

Barnes B, Scott A, Hernandez-Jover M, Toribio J-A, Moloney B, Glass K Theoretical Population Biology (2019) 126:59-71; 10.1016/j.tpb.2019.02.004 Highly pathogenic avian influenza (HPAI) outbreaks are devastating to poultry industries and pose a risk to human health. There is concern that demand for free-range poultry products could increase the number of HPAI outbreaks by increasing the potential for low pathogenic avian influenza (LPAI) introduction to commercial flocks. We formulate stochastic mathematical models…

Seasonality and community interventions in a mathematical model of Clostridium difficile

McLure A, Clements ACA, Kirk MD, Glass K J. Hospital Infection. doi: 10.1016/j.jhin.2019.03.001 (2019); 10.1016/j.jhin.2019.03.001 BACKGROUND: Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhoea with peak incidence in late winter or early autumn. Although CDI is commonly associated with hospitals, community transmission is important. AIM: To explore potential drivers of CDI seasonality and the effect of community-based interventions to reduce transmission….

Routine and pulse vaccination for Lassa virus could reduce high levels of endemic disease: a mathematical modelling study

Davies J, Lokuge K, Glass K Vaccine 37(26):3451-3456, 2019; 10.1016/j.vaccine.2019.05.010 Lassa fever is an acute viral illness caused by Lassa virus (LASV), a rodent-borne pathogen. LASV is endemic to much of Sub-Saharan West Africa, where seasonal outbreaks cause significant morbidity and mortality. Increased global awareness of LASV has led to development of improved diagnostic tests, treatments and vaccines. As vaccine candidates…

Source attribution of Salmonella in macadamia nuts to animal and environmental reservoirs in Queensland, Australia

Munck N, Smith J, Bates J, Glass K, Hald T, Kirk MD Foodborne Pathogens and Disease (in press)

Infection-acquired versus vaccine-acquired immunity in an SIRWS model

Leung T, Campbell PT, Hughes BD, Frascoli F, McCaw JM Infectious Disease Modelling 3: 118–135 (2018) [doi] In some disease systems, the process of waning immunity can be subtle, involving a complex relationship between the duration of immunity—acquired either through natural infection or vaccination—and subsequent boosting of immunity through asymptomatic re-exposure. We present and analyse…

Within-host modelling of blood-stage malaria

Khoury DS, Aogo R, Randriafanomezantsoa-Radohery G, McCaw JM, Simpson JA, McCarthy JS, Haque A, Cromer D, Davenport MP Immunological Reviews 285: 168–193 (2018) [doi] Malaria infection continues to be a major health problem worldwide and drug resistance in the major human parasite species, Plasmodium falciparum, is increasing in South East Asia. Control measures including novel drugs…

Accounting for healthcare-seeking behaviours and testing practices in real-time influenza forecasts

Moss R, Zarebski AE, Carlson SJ, McCaw JM Tropical Medicine and Infectious Disease 4(1): 12 (2019) [doi] For diseases such as influenza, where the majority of infected persons experience mild (if any) symptoms, surveillance systems are sensitive to changes in healthcare-seeking and clinical decision-making behaviours. This presents a challenge when trying to interpret surveillance data in near-real-time (e.g., to provide…

Anatomy of a seasonal influenza epidemic forecast

Moss R, Zarebski AE, Dawson P, Franklin LJ, Birrell FA, McCaw JM Communicable Diseases Intelligence 43: 1–14 (2019)[doi] Bayesian methods have been used to predict the timing of infectious disease epidemics in various settings and for many infectious diseases, including seasonal influenza. But integrating these techniques into public health practice remains an ongoing challenge, and requires close…

Modelling the dynamics of Plasmodium falciparum gametocytes in humans during malaria infection

Pengxing Cao, Katharine A Collins, Sophie Zaloumis, Thanaporn Wattanakul, Joel Tarning, Julie A Simpson, James S McCarthy, James M McCaw Accepted in eLife on Oct 15, 2019. Pre-publication.  

Mathematical analysis of a Wolbachia invasive model with imperfect maternal transmission and loss of Wolbachia infection

Adeshina I. Adekunle, Michael T. Meehan, Emma S. McBryde Infectious Disease Modelling, https://doi.org/10.1016/j.idm.2019.10.001. Arboviral infections, especially dengue, continue to cause significant health burden in their endemic regions. One of the strategies to tackle these infections is to replace the main vector agent, Ae. aegypti, with the ones incapable of transmitting the virus. Wolbachia, an intracellular…

Profiles of tuberculosis disease activation among contacts of patients with tuberculosis

Yayehirad A Melsew, Allen C Cheng, Emma S McBryde, Justin T Denholm, EeLaine Tay, Romain Ragonnet, James M Trauer European Respiratory Journal 2019; Profiles of tuberculosis disease activation among contacts of patients with tuberculosis The risk of a person progressing to TB disease after infection with Mycobacterium tuberculosis (Mtb) remains poorly understood, with some contacts developing TB in the…

Revisiting the Natural History of Pulmonary Tuberculosis: a Bayesian Estimation of Natural Recovery and Mortality rates

Romain Ragonnet, Jennifer A Flegg, Samuel L Brilleman, Edine Tiemersma, Yayehirad A Melsew, Emma S McBryde, James M Trauer BioRxiv, 729426, 2019/1/1; Revisiting the Natural History of Pulmonary Tuberculosis: a Bayesian Estimation of Natural Recovery and Mortality rates   Background Tuberculosis (TB) natural history remains poorly characterised and new investigations are impossible as it would be…

Molecular Evidence of Drug-Resistant Tuberculosis in the Balimo Region of Papua New Guinea

Tanya Diefenbach-Elstob, Vanina Guernier, Graham Burgess, Daniel Pelowa, Robert Dowi, Bisato Gula, Munish Puri, William Pomat, Emma McBryde, David Plummer, Catherine Rush, Jeffrey Warner Tropical medicine and infectious disease 4 (1), 33; Molecular Evidence of Drug-Resistant Tuberculosis in the Balimo Region of Papua New Guinea Papua New Guinea (PNG) has a high burden of tuberculosis…

Cross-Border Movement of Highly Drug-Resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010–2015

Arnold Bainomugisa, Sushil Pandey, Ellen Donnan, Graham Simpson, J’Belle Foster, Evelyn Lavu, Stenard Hiasihri, Emma S McBryde, Rendi Moke, Steven Vincent, Vitali Sintchenko, Ben J Marais, Lachlan JM Coin, Christopher Coulter Emerging infectious diseases 25 (3), 406; Cross-Border Movement of Highly Drug-Resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone,…

Risk factors for multidrug‐resistant tuberculosis in northwest Ethiopia: A case–control study

Kefyalew Addis Alene, Kerri Viney, Emma S McBryde, Darren J Gray, Mulugeta Melku, Archie CA Clements Transbound Emerg Dis. 2019 Jul;66(4):1611-1618. doi: 10.1111/tbed.13188. Epub 2019 Apr 15; Risk factors for multidrug‐resistant tuberculosis in northwest Ethiopia: A case–control study Ethiopia is one of 30-high burden multidrug-resistant tuberculosis (MDR-TB) countries globally. The aim of this study was to describe the characteristics of…

Community-based hepatitis C treatment of people who inject drugs and their injecting network is feasible and effective: Results from the TAP (Treatment And Prevention) study

Joseph Doyle, Paul Dietze, Mark Stoove, Peter Higgs, Paul Desmond, David Iser, Emma Mcbryde, Brendan Harney, Alisa Pedrana, Tim Spelman, Sally Von Bibra, Janine Roney, Alexander Thompson, Margaret Hellard JOURNAL OF HEPATOLOGY 70, E495-E495; Community-based hepatitis C treatment of people who inject drugs and their injecting network is feasible and effective: Results from the TAP…

Global stability properties of a class of renewal epidemic models

Michael T Meehan, Daniel G Cocks, Johannes Müller, Emma S McBryde Journal of mathematical biology 78 (6), 1713-1725; Global stability properties of a class of renewal epidemic models   We investigate the global dynamics of a general Kermack–McKendrick-type epidemic model formulated in terms of a system of renewal equations. Specifically, we consider a renewal model…

Treatment access is only the first step to hepatitis C elimination: experience of universal anti‐viral treatment access in Australia

Joseph S Doyle, Nick Scott, Rachel Sacks‐Davis, Alisa E Pedrana, Alexander J Thompson, Margaret E Hellard, Eliminate Hepatitis C Partnership, Margaret Hellard, Alex Thompson, Joseph Doyle, Paul Dietze, Emma McBryde, William Sievert, Mark Stoove, Peter Higgs, Denis Petrie, Peter Vickerman Alimentary pharmacology & therapeutics 49 (9), 1223-1229; Treatment access is only the first step to…

Health system preparedness for emerging infectious diseases: A synthesis of the literature

Anna Palagyi, Ben J Marais, Seye Abimbola, Stephanie M Topp, Emma S McBryde, Joel Negin Global public health, 1-22; Health system preparedness for emerging infectious diseases: A synthesis of the literature This review reflects on what the literature to date has taught us about how health systems of low- and middle-income countries (LMICs) respond to emerging infectious disease (EID) outbreaks. These findings…

Strategic Planning for Tuberculosis Control in the Republic of Fiji

Romain Ragonnet, Frank Underwood, Tan Doan, Eric Rafai, James Trauer, Emma McBryde Tropical medicine and infectious disease 4 (2), 71; Strategic Planning for Tuberculosis Control in the Republic of Fiji The tuberculosis (TB) health burden in Fiji has been declining in recent years, although challenges remain in improving control of the diabetes co-epidemic and achieving…

On the probability of strain invasion in endemic settings: accounting for individual heterogeneity and control in multi-strain dynamics

Michael T Meehan, Robert C Cope, Emma S McBryde arXiv preprint arXiv:1907.05010; On the probability of strain invasion in endemic settings: accounting for individual heterogeneity and control in multi-strain dynamics The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological…

Mathematical analysis of a two-strain disease model with amplification

Md Abdul Kuddus, Michael T Meehan, Adeshina I Adekunle, Lisa J White, Emma S McBryde arXiv preprint arXiv:1908.07837; Mathematical analysis of a two-strain disease model with amplification We investigate a two-strain disease model with amplification to simulate the prevalence of drug-susceptible (s) and drug-resistant (m) disease strains. We model the emergence of drug resistance as…

Delay effect and burden of weather-related tuberculosis cases in Rajshahi province, Bangladesh, 2007–2012

Md Abdul Kuddus, Emma S McBryde, Oyelola A Adegboye Scientific reports 9 (1), 1-13; Delay effect and burden of weather-related tuberculosis cases in Rajshahi province, Bangladesh, 2007–2012 Tuberculosis (TB) is a potentially fatal infectious disease that continues to be a public health problem in Bangladesh. Each year in Bangladesh an estimated 70,000 people die of TB and 300,000 new cases are…

Modelling tuberculosis control priorities: more of the same will not do

C Wejse, R Ragonnet, ES McBryde, JM Trauer The Lancet Global Health 7 (10), e1319; Modelling tuberculosis control priorities: more of the same will not do In The Lancet Global Health, Juan F Vesga and colleagues1 reported on their assessment of tuberculosis control priorities in high-burden settings using a robust and well accepted modelling approach…

Epidemiological analysis of association between lagged meteorological variables and pneumonia in wet-dry tropical North Australia, 2006–2016

Oyelola A Adegboye, Emma S McBryde, Damon P Eisen Journal of exposure science & environmental epidemiology, 1-11; Epidemiological analysis of association between lagged meteorological variables and pneumonia in wet-dry tropical North Australia, 2006–2016 Pneumonia accounts for 1.5% of all overnight hospital admission in Australia. We investigated the nonlinear and delay effect of weather (temperature and rainfall) on pneumonia….

The role of super-spreading events in Mycobacterium tuberculosis transmission: evidence from contact tracing

Yayehirad A Melsew, Manoj Gambhir, Allen C Cheng, Emma S McBryde, Justin T Denholm, Ee Laine Tay, James M Trauer BMC infectious diseases 19 (1), 244; The role of super-spreading events in Mycobacterium tuberculosis transmission: evidence from contact tracing In current epidemiology of tuberculosis (TB), heterogeneity in infectiousness among TB patients is a challenge, which is not…

Mapping tuberculosis treatment outcomes in Ethiopia

KA Alene, K Viney, DJ Gray, ES McBryde, M Wagnew, ACA Clements BMC infectious diseases 19 (1), 474; Mapping tuberculosis treatment outcomes in Ethiopia Tuberculosis (TB) is the leading cause of death from an infectious disease in Ethiopia, killing more than 30 thousand people every year. This study aimed to determine whether the rates of…

High burden of infectious disease and antibiotic use in early life in Australian Aboriginal communities

Will Cuningham  Jodie McVernon  Michael J. Lydeamore  Ross M. Andrews  Jonathan Carapetis  Therese Kearns  Danielle Clucas  Roslyn Gundjirryirr Dhurrkay  Steven Y.C. Tong  Patricia T. Campbell. High burden of infectious disease and antibiotic use in early life in Australian Aboriginal communities. First published: 06 February 2019 https://doi.org/10.1111/1753-6405.12876 Abstract Objective: To quantify the childhood infectious disease burden…

Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection

Ada W. C. Yan, Sophie G. Zaloumis, Julie A. Simpson, James M. McCaw. Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection. arXiv:1709.02145 

Investigation of group A Streptococcus immune responses in an endemic setting, with a particular focus on J8

Patricia Campbell, Hannah Frost, Pierre R. Smeesters, Joseph Kado, Michael F.Good, Michael Batzloff, Nicholas Geard, Jodie McVernon, Andrew Steer. Investigation of group A Streptococcus immune responses in an endemic setting, with a particular focus on J8. Volume 36, Issue 50, 29 November 2018, Pages 7618-7624. https://doi.org/10.1016/j.vaccine.2018.10.091

Mental health disorders, social stressors, and health-related quality of life in patients with multidrug-resistant tuberculosis: A systematic review and meta-analysis

Kefyalew Addis Alene, Archie C A Clements, Emma S McBryde, Ernesto Jaramillo, Knut Lönnroth, Debebe Shaweno, Amelia Gullivera Kerri Viney. Mental health disorders, social stressors, and health-related quality of life in patients with multidrug-resistant tuberculosis: A systematic review and meta-analysis. Journal of Infection, Volume 77, Issue 5, November 2018, Pages 357-367, https://doi.org/10.1016/j.jinf.2018.07.007

Geostatistical mapping of the seasonal spread of under-reported dengue cases in Bangladesh

Sharmin S, Glass K, Viennet E, Harley D. Geostatistical mapping of the seasonal spread of under-reported dengue cases in Bangladesh. PLoS Neglected Tropical Diseases, November 15, 2018. https://doi.org/10.1371/journal.pntd.0006947.

The Importance of Heterogeneity to the Epidemiology of Tuberculosis

James M Trauer, Peter J Dodd, M Gabriela M Gomes, Gabriela B Gomez, Rein MGJ Houben, Emma S McBryde, Yayehirad A Melsew, Nicolas A Menzies, Nimalan Arinaminpathy, Sourya Shrestha, David W Dowdy. The Importance of Heterogeneity to the Epidemiology of Tuberculosis. Clinical infectious diseases https://doi.org/10.1186/s12879-018-3388-y

Treatment for pharyngeal gonorrhoea under threat

David G Regan, Ben B Hui, James G Wood, Helen Fifer, Monica M Lahra, David M Whiley. Treatment for pharyngeal gonorrhoea under threat. Lancet,Volume 18, Issue 11, P1175-1177, November 01, 2018. https://doi.org/10.1016/S1473-3099(18)30610-8

Investigating the efficacy of triple artemisinin-based combination therapies (TACTs) for treating Plasmodium falciparum malaria patients using mathematical modelling

Saber Dini, Sophie Zaloumis, Pengxing Cao, Ric N. Price, Freya J. I. Fowkes, Rob W. van der Pluijm, James M. McCaw, Julie A. Simpson. Investigating the efficacy of triple artemisinin-based combination therapies (TACTs) for treating Plasmodium falciparum malaria patients using mathematical modelling. Antimicrobial Agents and Chemotherapy doi: 10.1128/aac.01068-18

Designing group dose-response studies in the presence of transmission

David J.Price ^a,b , Nigel G. Bean ^c,d , Joshua V. Ross ^c,d , Jonathan Tuke ^c,d. Designing group dose-response studies in the presence of transmission. Mathematical Biosciences, Volume 304,October 2018, Pages 62-78. https://doi.org/10.1016/j.mbs.2018.07.007 .

An induced natural selection heuristic for finding optimal Bayesian experimental designs

David J.Price ^a,b , Nigel G. Bean ^c,d , Joshua V. Ross ^c,d , Jonathan Tuke ^c,d. An induced natural selection heuristic for finding optimal Bayesian experimental designs. Computational Statistics & Data Analysis, Volume 126,October 2018, Pages 112-124. https://doi.org/10.1016/j.csda.2018.04.011

Global stability of the multi-strain Kermack-McKendrick epidemic model

Michael T. Meehan^a, Daniel G. Cocks^b, Emma S. McBryde^a. Global stability of the multi-strain Kermack-McKendrick epidemic model. 19 October 2018. https://arxiv.org/pdf/1710.06984.pdf

Mathematical modelling of vancomycin-resistant enterococci transmission during passive surveillance and active surveillance with contact isolation highlights the need to identify and address the source of acquisition

Agnes Loo Yee Cheah, Allen C. Cheng, Denis Spelman, Roger L. Nation, David C. M. Kong and Emma S. McBryde. Mathematical modelling of vancomycin-resistant enterococci transmission during passive surveillance and active surveillance with contact isolation highlights the need to identify and address the source of acquisition. BMC Infectious Diseases 201818:511 https://doi.org/10.1186/s12879-018-3388-y

Methods used in the spatial analysis of tuberculosis epidemiology: a systematic review

Debebe Shaweno, Malancha Karmakar, Kefyalew Addis Alene, Romain Ragonnet, Archie CA Clements, James M. Trauer, Justin T. Denholm and Emma S. McBryde. Methods used in the spatial analysis of tuberculosis epidemiology: a systematic review. BMC Medicine 2018 16:193. https://doi.org/10.1186/s12916-018-1178-4

Modelling the decline and future of hepatitis A transmission in Australia

Jayasundara, D. , Hui, B. B., Regan, D. G., Heywood, A. E., MacIntyre, C. R. and Wood, J. G. Modelling the decline and future of hepatitis A transmission in Australia. J Viral Hepat. 13 October 2018. doi:10.1111/jvh.13018

Retrospective cost-effectiveness of the 23-valent pneumococcal polysaccharide vaccination program in Australia

C.Chen ^a, P. Beutels ^b, J. Wood ^a, R. Menzies ^a, C.R. MacIntyre ^a, P. McIntyre ^c, A.T. Newall ^a. Retrospective cost-effectiveness of the 23-valent pneumococcal polysaccharide vaccination program in Australia. Vaccine,Volume 36, Issue 42, 8 October 2018, Pages 6307-6313. https://doi.org/10.1016/j.vaccine.2018.08.084.

Cost-effectiveness of 3 months of weekly rifapentine and isoniazid compared with other standard treatment regimens for latent tuberculosis infection: a decision analysis study

Tan N Doan,  Greg J Fox,  Michael T Meehan,  Nick Scott,  Romain Ragonnet,  Kerri Viney,  James M Trauer, Emma S McBryde. Cost-effectiveness of 3 months of weekly rifapentine and isoniazid compared with other standard treatment regimens for latent tuberculosis infection: a decision analysis study. Journal of Antimicrobial Chemotherapy, dky403, https://doi.org/10.1093/jac/dky403

Predicting the Outcomes of New Short-Course Regimens for Multi-Drug Resistant Tuberculosis Using Intrahost and Pharmacokinetic-Pharmacodynamic Modelling

Tan N Doan, Pengxing Cao, Theophilus I Emeto, James M McCaw, Emma S McBryde. Predicting the Outcomes of New Short-Course Regimens for Multi-Drug Resistant Tuberculosis Using Intrahost and Pharmacokinetic-Pharmacodynamic Modelling. American Society for Microbiology Journals,September 24, 2018, https://doi.org/10.1128/AAC.01487-18.

In silico investigation of the decline in clinical efficacy of artemisinin combination therapies due to increasing artemisinin and partner drug resistance

Sophie G. Zaloumis, Pengxing Cao, Saber Dini, Miles P. Davenport, Deborah Cromer, David S. Khoury, Freya J.I. Fowkes, James M. McCaw,Julie A. Simpson. In silico investigation of the decline in clinical efficacy of artemisinin combination therapies due to increasing artemisinin and partner drug resistance. Antimicrobial Agents and Chemotherapy Sep 2018, AAC.01292-18; DOI: 10.1128/AAC.01292-18

The distribution of the time taken for an epidemic to spread between two communities

Ada W.C.Yan ^a,b , Andrew J. Black ^c , James M. McCaw ^b,d,e , Nicolas Rebuli ^c , Joshua V. Ross ^c , Annalisa J. Swan ^a , Roslyn I. Hickson ^a. The distribution of the time taken for an epidemic to spread between two communities. Mathematical Biosciences, Volume 303, September 2018, Pages 139-147. https://doi.org/10.1016/j.mbs.2018.07.004

The role of geospatial hotspots in the spatial spread of tuberculosis in rural Ethiopia: a mathematical model

Debebe Shaweno, James M. Trauer, Justin T. Denholm, Emma S. McBryde. The role of geospatial hotspots in the spatial spread of tuberculosis in rural Ethiopia: a mathematical model. R. Soc. open sci. 5: 180887. http://dx.doi.org/10.1098/rsos.180887

Within-season influenza vaccine waning suggests potential net benefits to delayed vaccination in older adults in the United States

A.T. Newall ^a, C. Chen ^a, J.G. Wood ^a, M.S. Stockwell ^b. Within-season influenza vaccine waning suggests potential net benefits to delayed vaccination in older adults in the United States. Vaccine,Volume 36, Issue 39, 18 September 2018, Pages 5910-5915. https://doi.org/10.1016/j.vaccine.2018.08.007

Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility

R. Farrukee, A. E. Zarebski, J. M. McCaw, J. D. Bloom, P. C. Reading, A. C. Hurt. Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Antimicrobial Agents and Chemotherapy Oct 2018, 62 (11) e01081-18; DOI: 10.1128/AAC.01081-18

Description of social contacts among student cases of pandemic influenza during the containment phase, Melbourne, Australia, 2009

Caroline van Gemert, Emma S McBryde, Isabel Bergeri, Rachel Sacks-Davis, Hassan Vally, Tim Spelman, Brett Sutton, Margaret Hellard. Description of social contacts among student cases of pandemic influenza during the containment phase, Melbourne, Australia, 2009.Western Pac Surveill Response J. 2018 Sep;9(5). doi:10.5365/wpsar.2018.9.5.003

Cytokine biomarkers for the diagnosis of tuberculosis infection and disease in adults in a low prevalence setting

Vanessa Clifford, Marc Tebruegge, Christel Zufferey, Susie Germano, Ben Forbes, Lucy Cosentino, Elizabeth Matchett, Emma McBryde, Damon Eisen, Roy Robins-Browne, Alan Street, Justin Denholm, Nigel Curtis. Cytokine biomarkers for the diagnosis of tuberculosis infection and disease in adults in a low prevalence setting. Tuberculosis, 25 August 2018. https://doi.org/10.1016/j.tube.2018.08.011

A simple influenza model with complicated dynamics

Roberts, M.G., Hickson, R.I., McCaw, J.M. et al. A simple influenza model with complicated dynamics. J. Math. Biol. (2018). https://doi.org/10.1007/s00285-018-1285-z

A biological model of scabies infection dynamics and treatment informs mass drug administration strategies to increase the likelihood of elimination

M.J. Lydeamore, P.T. Campbell, D.G. Regan, S.Y.C. Tong, R.M. Andrews, A.C. Steer, L. Romani, J.M. Kaldor, J. McVernon, J.M. McCaw,
A biological model of scabies infection dynamics and treatment informs mass drug administration strategies to increase the likelihood of elimination. Mathematical Biosciences, 2018, ISSN 0025-5564. https://doi.org/10.1016/j.mbs.2018.08.007.

Salmonella source attribution in a subtropical state of Australia: capturing environmental reservoirs of infection

Fearnley E, Lal A, Bates J, Stafford R, Kirk M, Glass K. Salmonella source attribution in a subtropical state of Australia: capturing environmental reservoirs of infection. Epidemiology & Infection, 146(15):1903-1908. https://doi.org/10.1017/S0950268818002224

The Indo‐Papuan conduit: a biosecurity challenge for Northern Australia

Paul F. Horwood , Emma S. McBryde , Dunstan Peniyamina , Scott A. Ritchie. The Indo‐Papuan conduit: a biosecurity challenge for Northern Australia. Australian and New Zealand Journal of Public Health, 42: 434-436. doi:10.1111/1753-6405.12808

Scabies and risk of skin sores in remote Australian Aboriginal communities: A self-controlled case series study

Phyo Thu Zar Aung¹ , Will Cuningham^1,2, Kerry Hwang³ , Ross M. Andrews^2,4, Jonathan R. Carpetis⁵ , Therese Kearns² , Danielle Clucas⁶ , Jodie McVernon^1,3,7, Julie Ann Simpson³ , Steven Y.C. Tong^2,8, Patricia Therese Campbell^1,7. Scabies and risk of skin sores in remote Australian Aboriginal communities: A self-controlled case series study. PLoS Neglected Tropical Diseases, 2018, 12(7):e0006668.

Measles control in Australia – threats, opportunities and future needs

C. Raina MacIntyre, Elizabeth Kpozehouen, Mohana Kunasekaran, Kathleen Harriman, Stephen Conaty, Alexander Rosewell, Julian Druce, Nicolee Martin, Anita E. Heywood, Heather F. Gidding, James Wood, Sonya Nicholl. Measles control in Australia – threats, opportunities and future needs. Vaccine,Volume 36, Issue 30, 16 July 2018, Pages 4393-4398.. https://doi.org/10.1016/j.vaccine.2018.06.022

Appropriate comparisons of tuberculosis latency structures with empiric data

Denholm JT, McBryde ES, Eisen D, Street A, Matchett E, Chen C, Shultz TR, Biggs B, Leder K. Appropriate comparisons of tuberculosis latency structures with empiric data. The Lancet, VOLUME 18, ISSUE 7, P720-721, JULY 01, 2018, https://doi.org/10.1016/S1473-3099(18)30339-6

Health Outcomes from Multidrug-Resistant Salmonella Infections in High-Income Countries: A Systematic Review and Meta-Analysis

Parisi A, Crump JA,Glass K, Howden B, Furuya-Kanamori L, Vilkins S, Kirk MD. Health outcomes from multi-drug resistant Salmonella infections in high-income countries: A systematic review and meta-analysis. Foodborne Pathogens and Disease 15(7):1-9. https://doi.org/10.1089/fpd.2017.2403

The epidemiology of tuberculosis in the rural Balimo region of Papua New Guinea

Tanya Diefenbach-Elstob, Patricia Graves, Robert Dowi, Bisato Gula, David Plummer, Emma McBryde, Daniel Pelowa, Peter Siba, William Pomat and Jeffrey Warner. The epidemiology of tuberculosis in the rural Balimo region of Papua New Guinea. 19 June 2018. https://doi.org/10.1111/tmi.13118

Australian rubella serosurvey 2012–2013: On track for elimination?

Edirisuriya, C., Beard, F.H., Hendry, A.J., Dey, A., Gidding, H.F., Hueston, L., Dwyer, D.E., Wood, J.G., Macartney, K.K., McIntyre, P.B. Australian rubella serosurvey 2012–2013: On track for elimination? (2018) Vaccine, 36 (20), pp. 2794-2798.  DOI: 10.1016/j.vaccine.2018.03.086

Comparison of the validity of smear and culture conversion as a prognostic marker of treatment outcome in patients with multidrug-resistant tuberculosis

Kefyalew Addis Alene , Kerri Viney, Hengzhong Yi, Emma S. McBryde, Kunyun Yang, Liqiong Bai, Darren J. Gray, Zuhui Xu, Archie C. A. Clements. Comparison of the validity of smear and culture conversion as a prognostic marker of treatment outcome in patients with multidrug-resistant tuberculosis. Plos One, May 2018. https://doi.org/10.1371/journal.pone.0197880

The influence of incomplete case ascertainment on measures of vaccine efficacy

YueWu ^a, Julie A. Marsh ^a,b , Emma S. McBryde ^c , Thomas L. Snelling ^a,d,e,f. The influence of incomplete case ascertainment on measures of vaccine efficacy. Vaccine, Volume 36, Issue 21, 17 May 2018, Pages 2946-2952, https://doi.org/10.1016/j.vaccine.2018.04.046

Calculation of the age of the first infection for skin sores and scabies in five remote communities in northern Australia

Lydeamore MJ^1,2, Campbell PT^2,3, Cuningham W³, Andrews RM^4,5, Kearns T⁴, Clucas D⁶, Gundjirryirr Dhurrkay R⁴, Carapetis J⁷, Tong SYC ^5,8, McCaw JM¹, McVernon J^2,3,9. Calculation of the age of the first infection for skin sores and scabies in five remote communities in northern Australia. Epidemiol Infect. 2018 May 8:1-8. https://doi.org/10.1017/S0950268818001061

Investigating Viral Interference Between Influenza A Virus and Human Respiratory Syncytial Virus in a Ferret Model of Infection

Chan KF, Carolan LA, Korenkov D, Druce J, McCaw JM, Reading PC, Barr IG, Laurie KL. Investigating viral interference between influenza A virus and human respiratory syncytial virus in a ferret model of infection. Journal of Infectious Diseases, published 8 May 2018. https://doi.org/10.1093/infdis/jiy184

Steps to solving the infant biometric problem with ridge-based biometrics

Johannes Kotzerke¹ , Stephen A. Davis¹, Jodie McVernon², Kathy J. Horadam¹ . Steps to solving the infant biometric problem with ridge-based biometrics. (February 2018) IET Biometrics. doi: 10.1049/iet-bmt.2017.0282.

Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units

Kinyanjui T, Middleton J, Guttel S, Cassell J, Ross J, House T (2018) Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units. PLoS Comput Biol 14(3): e1006046. https://doi.org/10.1371/journal.pcbi.1006046

Modelling low pathogenic avian influenza introduction into the commercial poultry industry

Barnes, B & Glass, K. Modelling low pathogenic avian influenza introduction into the commercial poultry industry, Mathematical Biosciences. vol. 300, pp. 112-121, 2018.  https://doi.org/10.1016/j.mbs.2018.03.021

Successful Control of Ebola Virus Disease: Analysis of Service Based Data from Rural Sierra Leone

Kamalini Lokuge , Grazia Caleo, Jane Greig, Jennifer Duncombe, Nicholas McWilliam, James Squire, Manjo Lamin, Emily Veltus, Anja Wolz, Gary Kobinger, Marc-Antoine de la Vega, Osman Gbabai, Sao Nabieu, Mohammed Lamin, Ronald Kremer, Kostas Danis, Emily Banks, Kathryn Glass. Successful Control of Ebola Virus Disease: Analysis of Service Based Data from Rural Sierra Leone. PLoS Neglected Tropical Diseases, vol. 10, no. 3, pp. 13 pp. https://doi.org/10.1371/journal.pntd.0004498

Reducing length of stay to improve Clostridium difficile-related health outcomes

Brain D.C., Barnett A.G., Yakob L., Clements A., Riley T.V., Halton K., Graves N. (2018) Reducing length of stay to improve Clostridium difficile-related health outcomes. Infection, Disease and Health. Published online ahead of print: DOI: 1016/j.idh.2018.01.001

Prolonged persistence of clonally diverse CD38+HLA-DR+CD8+ T cells during fatal H7N9 disease

Wang Z, Zhu L, Nguyen THO, Wan Y, Sant S, Quinones-Parra SM, Crawford J, Eltahla AA, Rizzetto S, Bull RA, Qiu C, Koutsakos M, Bridie Clemens E, Loh L, Zhu L, Chen T, Liu L, Cao P, Ren Y, Kedzierski L, Kotsimbos TC, McCaw JM, La Gruta NL, Turner SJ, Cheng AC, Luciani F, Zhang X, Doherty PC, Thomas PG, Xu J, Kedzierska K, Prolonged persistence of clonally diverse CD38⁺HLA-DR⁺CD8⁺ T cells during fatal H7N9 disease, Nature Communications 9: 824 (2018).  doi:10.1038/s41467-018-03243-7

Spatiotemporal patterns and environmental drivers of human echinococcoses over a twenty-year period in Ningxia Hui Autonomous Region, China.

Cadavid Restrepo A.M., Yang Y., McManus D.P., Gray D.J., Barnes T.S., Williams G.M., Soares Magalhães R.J., Hamm N.A.S., Clements A.C.A. (2018). Spatiotemporal patterns and environmental drivers of human echinococcoses over a twenty-year period in Ningxia Hui Autonomous Region, China. Parasites and Vectors. 11:108. https://doi.org/10.1186/s13071-018-2693-z.

Coupled, multi-strain epidemic models of mutating pathogens

Meehan M, Cocks D, Trauer J and McBryde E (2018) Coupled, multi-strain epidemic models of mutating pathogens. Mathematical Biosciences, 296. pp. 82-92. https://doi.org/10.1016/j.mbs.2017.12.006

Implications of asymptomatic carriers for infectious disease transmission and control

Chisholm RH, Campbell PT, Wu Y, Tong SYC, McVernon J, Geard N (2018) Implications of asymptomatic carriers for infectious disease transmission and control. Royal Society Open Science 5:172341. DOI: 10.1098/rsos.172341

Evidence for Viral Interference and Cross-reactive Protective Immunity Between Influenza B Virus Lineages

Laurie KL, Horman W, Carolan LA, Chan KF, Layton D, Bean A, Vijaykrishna D, Reading P, McCaw JM, Barr IG , Evidence for viral interference and cross-reactive protective immunity between influenza B virus lineages, Journal of Infectious Diseases 217(4): 548–559 (2018). https://doi.org/10.1093/infdis/jix509

Risk factors for infectiousness of patients with tuberculosis: a systematic review and meta-analysis

Y.A. Melsew ^(a1) (a2), T.N. Doan ^(a3) (a4), M. Gambhir ^(a1), A.C. Cheng ^(a1) (a5), E. McBryde ^(a3) (a4) and J.M. Trauer ^(a1). Risk factors for infectiousness of patients with tuberculosis: a systematic review and meta-analysis. Epidemiology and Infection, 146(3), 345-353. doi:10.1017/S0950268817003041.

Spatial and temporal patterns of dengue infections in Timor-Leste, 2005–2013

Wangdi K., Clements A.C.A, Du T., Nery S.V. (2018) Spatial and temporal patterns of dengue infections in Timor-Leste, 2005-2013. Parasites and Vectors. 11:9. https://doi.org/10.1186/s13071-017-2588-4.

Economic evaluation of interventions designed to reduce Clostridium difficile infection

Brain D., Yakob L., Barnett A., Riley T., Clements A., Halton K., Graves N. (2018) Economic evaluation of interventions designed to reduced Clostridium difficile infection.  PLoS One. 13:e0190093. https://doi.org/10.1371/journal.pone.0190093.

Optimally capturing latency dynamics in models of tuberculosis transmission

Romain Ragonnet, James M.Trauer, Nick Scott, Michael T.Meehan, Justin T.Denholm, Emma S.McBryde. Optimally capturing latency dynamics in models of tuberculosis transmission. Epidemics,Volume 21, December 2017, Pages 39-47. https://doi.org/10.1016/j.epidem.2017.06.002

Epidemic forecasts as a tool for public health: interpretation and (re)calibration

Robert Moss,¹ James E. Fielding,² Lucinda J. Franklin,³ Nicola Stephens,³ Jodie McVernon,^1,2,4 Peter Dawson,⁵ James M. McCaw^1,4,6. Epidemic forecasts as a tool for public health: interpretation and (re)calibration. Australian and New Zealand Journal of Public Health 2018 vol. 42 no. 1. https://doi.org/10.1111/1753-6405.12750

Molecular diagnosis of suspected tuberculosis from archived smear slides from the Balimo region, Papua New Guinea

Guernier V, Diefenbach-Elstob T, Pelowa D, Pollard S, Burgess G, McBryde E and Warner J (2018) Molecular diagnosis of suspected tuberculosis from archived smear slides from the Balimo region, Papua New Guinea. International Journal of Infectious Diseases, 67. pp. 75-81.

Clostridium difficile classification overestimates hospital-acquired infections

McLure, A., Clements, A.C.A., Kirk, M. et al. Clostridium difficile classification overestimates hospital-acquired infections. Journal of Hospital Infection, 16 December 2017.  https://doi.org/10.1016/j.jhin.2017.12.014

SIRCLE: a randomised controlled cost comparison of self-administered short-course isoniazid and rifapentine for cost-effective latent tuberculosis eradication.

Denholm JT ^1,2,3, McBryde ES ⁴, Eisen D ^4,5, Street A ², Matchett E ², Chen C ⁶, Shultz TR ², Biggs B ², Leder K ^2,7. SIRCLE: a randomised controlled cost comparison of self‐administered short‐course isoniazid and rifapentine for cost‐effective latent tuberculosis eradication. Intern Med J. 2017 Dec;47(12):1433-1436. doi: 10.1111/imj.13601.

A Synthetic Population for Modelling the Dynamics of Infectious Disease Transmission in American Samoa

Xu Z, Glass K, Lau C, Geard N, Graves P, Clements A (2017) A synthetic population for modelling the dynamics of infectious disease transmission in American Samoa. Scientific Reports 7:16725.   doi:10.1038/s41598-017-17093-8

Interferon-gamma release assay for the diagnosis of latent tuberculosis infection: A latent-class analysis

Tan N. Doan, Damon P. Eisen, Morgan T. Rose,Andrew Slack, Grace Stearnes, Emma S. McBryde. Interferon-gamma release assay for the diagnosis of latent tuberculosis infection: A latent-class analysis. PlosOne November 28, 2017. https://doi.org/10.1371/journal.pone.0188631

Spatiotemporal transmission and socio-climatic factors related to paediatric tuberculosis in north-western Ethiopia

Alene, K. A., Viney, K., McBryde, E., & Clements, A. (2017). Spatiotemporal transmission and socio-climatic factors related to paediatric tuberculosis in north-western Ethiopia. Geospatial Health, 12(2). https://doi.org/10.4081/gh.2017.575

Sequelae of multidrug-resistant tuberculosis: protocol for a systematic review and meta-analysis

Alene K.A., Clements A.C.A., McBryde E.S., Jaramillo E., Lonnroth K., Shaweno D., Viney K. (2018) Sequelae of multidrug resistant tuberculosis: protocol for a systematic review and meta-analysis. BMJ Open. 8: http://dx.doi.org/10.1136/bmjopen-2017-019593.

Estimating the basic reproductive number during the early stages of an emerging epidemic

Nicolas P. Rebuli, N.G. Bean, J.V. Ross. Estimating the basic reproductive number during the early stages of an emerging epidemic. Theoretical Population Biology, Volume 119, 2018, Pages 26-36, https://doi.org/10.1016/j.tpb.2017.10.004

Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases

Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases. Thiripura Vino ¹ , Gurmeet R. Singh ^2,3 , Belinda Davison ² , Patricia T. Campbell ^4,5 , Michael J. Lydeamore ^4,5 , Andrew Robinson ^1,6,7 , Jodie McVernon ⁵ , Steven Y.C. Tong ^2,8 and Nicholas Geard^9,10 . PeerJ October 2017 5:e3958; DOI 10.7717/peerj.3958

Inference of epidemiological parameters from household stratified data

Inference of epidemiological parameters from household stratified data. James N. Walker, Joshua V. Ross, Andrew J. Black. PLOS One October 2017.  https://doi.org/10.1371/journal.pone.0185910

The Impact of Antimalarial Use on the Emergence and Transmission of Plasmodium falciparum Resistance: A Scoping Review of Mathematical Models

The Impact of Antimalarial Use on the Emergence and Transmission of Plasmodium falciparum Resistance: A Scoping Review of Mathematical Models . Aleisha R. Brock¹, Carole A. Gibbs², Joshua V. Ross ³ and Adrian Esterman ^4,5 Trop. Med. Infect. Dis. 2017, 2(4), 54; doi:10.3390/tropicalmed2040054

A Dynamic Stress Model Explains the Delayed Drug Effect in Artemisinin Treatment of Plasmodium falciparum

Cao P, Klonis N, Zaloumis S, Dogovski C, Xie SC, Saralamba S, White LJ, Fowkes FJI, Tilley L, Simpson JA, McCaw JM, A dynamic stress model explains the delayed drug effect in artemisinin treatment of Plasmodium falciparum, Antimicrobial Agents and Chemotherapy 61(12): e00618–17 (2017). doi:10.1128/AAC.00618-17

A novel Bayesian geospatial method for estimating tuberculosis incidence reveals many missed TB cases in Ethiopia

Debebe Shaweno, James M Trauer, Justin T Denholm, Emma S McBryde. A novel Bayesian geospatial method for estimating tuberculosis incidence reveals many missed TB cases in Ethiopia. BMC Infectious DiseasesBMC series – open, inclusive and trusted 2017, 17:662. https://doi.org/10.1186/s12879-017-2759-0

Who’s holding the baby? A prospective diary study of the contact patterns of mothers with an infant

Who’s holding the baby? A prospective diary study of the contact patterns of mothers with an infant. Patricia Therese Campbell, Jodie McVernon, Niraj Shrestha, Paula M. Nathan and Nicholas Geard. BMC Infectious Diseases September 2017. https://doi.org/10.1186/s12879-017-2735-8.

Potential impact of a maternal vaccine for RSV: A mathematical modelling study

Alexandra B.Hogan^a, Patricia T.Campbell ^{b c} , Christopher C. Blyth^def, Faye J. Lim^e, Parveen Fathim^ae,  Stephanie Davis^a, Hannah C. Moore^e, Kathryn Glass^a. Potential impact of a maternal vaccine for RSV: A mathematical modelling study. Vaccine. 2017 Oct 27;35(45):6172-6179. doi: 10.1016/j.vaccine.2017.09.043. Epub 2017 Sep 28.

Hybrid Markov chain models of S–I–R disease dynamics

Hybrid Markov chain models of S–I–R disease dynamics. Nicholas P. Rebuli, N.G.Beanm J.V.Ross. Journal of Mathematical Biology September 2017, Volume 75 Issue 3, pp 52. https://doi.org/10.1186/s12879-017-2735-8.

Vaccine efficacy against Indonesian Highly Pathogenic Avian Influenza H5N1: systematic review and meta-analysis.

Vaccine efficacy against Indonesian Highly Pathogenic Avian Influenza H5N1: systematic review and meta-analysis. Villanueva-Cabezas JP, Coppo MJC, Durr PA, McVernon J. Vaccine September 2017 DOI: 10.1016/j.vaccine.2017.07.059

Predicting the Risk of Biological Invasions Using Environmental Similarity and Transport Network Connectedness

Predicting the Risk of Biological Invasions Using Environmental Similarity and Transport Network Connectedness. Robert C. Cope, Joshua V. Ross, Talia A. Wittmann, Michael J. Watts, Phillip Cassey. Risk Analysis Aug 2017. DOI: 10.1111/risa.12870.

Modular programming for tuberculosis control, the “AuTuMN” platform

James Trauer, Romain Ragonnet, Tan Nhut Doan and Emma McBryde. Modular programming for tuberculosis control, the “AuTuMN” platform. BMC Infectious Diseases BMC series 2017, 17:546. 7 August 2017. https://doi.org/10.1186/s12879-017-2648-6

Healthcare-Associated Clostridium difficile Infections are Sustained by Disease from the Community

McLure, A., Clements, A.C.A., Kirk, M. et al. Healthcare-Associated Clostridium difficile Infections are Sustained by Disease from the Community. Bull Math Biol (2017) 79: 2242. https://doi.org/10.1007/s11538-017-0328-8.

The Mechanisms for Within-Host Influenza Virus Control Affect Model-Based Assessment and Prediction of Antiviral Treatment

The Mechanisms for Within-Host Influenza Virus Control Affect Model-Based Assessment and Prediction of Antiviral Treatment. Pengxing Cao ¹ and James M. McCaw ^1,2,3 .Viruses 2017, 9(8), 197; doi:10.3390/v9080197

A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection

A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection. Pengxing Cao^a, Nectarios Klonis^b, Sophie Zaloumis^c, David S. Khoury^d, Deborah Cromer^d, Miles P. Davenport^d, Leann Tilley^b, Julie A. Simpson^c, James M. McCaw ^a, c, e,. https://doi.org/10.1016/j.jtbi.2017.07.017

Influenza as a trigger for cardiovascular disease: An investigation of serotype, subtype and geographic location

Influenza as a trigger for cardiovascular disease: An investigation of serotype, subtype and geographic location. D.C.Pearce ^ab, J.M.McCaw ^acd, J.McVernon ^ac ,  J.D.Mathews ^a. Environmental Research Volume 156 July 2017, pages 688-696.  https://doi.org/10.1016/j.envres.2017.04.024

A user-friendly mathematical modelling web interface to assist local decision making in the fight against drug-resistant tuberculosis

Romain Ragonnet, James M. Trauer, Justin T. Denholm, Ben J. Marais and Emma S. McBryde. A user-friendly mathematical modelling web interface to assist local decision making in the fight against drug-resistant tuberculosis. BMC Infectious Diseases BMC series 2017, 17:374 https://doi.org/10.1186/s12879-017-2478-6

Modelling the impact of antimalarial quality on the transmission of sulfadoxine-pyrimethamine resistance in Plasmodium falciparum

Modelling the impact of antimalarial quality on the transmission of sulfadoxine-pyrimethamine resistance in Plasmodium falciparum. Aleisha R.Brock ^a , Joshua V. Ross ^b , Scott Greenhalgh ^c , David P.Durham ^d , Alison Galvani ^d , Sunil Parikh ^e , Adrian Esterman ^{f g} . Infectious Disease Modelling 2 (2017) 161e187. https://doi.org/10.1016/j.idm.2017.04.001

Determining the Best Strategies for Maternally Targeted Pertussis Vaccination Using an Individual-Based Model

Determining best strategies for maternally-targeted pertussis vaccination using an individual based model. Campbell PT, McVernon J, Geard N. American Journal of Epidemiology 186 (1):109-117. https://doi.org/10.1093/aje/kwx002.

Complex demodulation: a novel time series method for analysing seasonal infectious diseases

HOGAN, A., GLASS, K., & ANDERSSEN, R. (2017). Complex demodulation: a novel time series method for analysing seasonal infectious diseases. The ANZIAM Journal, 59(1), 51-60. doi:10.1017/S1446181116000377

Is Australia prepared for the next pandemic?

Is Australia prepared for the next pandemic? Jodie McVernon, Tania C Sorrell, Jenny Firman, Brendan Murphy and Sharon R Lewin. Med J Aust 2017; 206 (7): 284-286. || doi: 10.5694/mja16.01451

High rates of latent TB infection in contacts and the wider community in South India

High rates of latent tuberculosis infection in contacts and the wider community in South India. P Narasimhan, CR MacIntyre, D Mathai, JG Wood. Transactions of the Royal Society of Tropical Medicine and Hygiene (accepted, Feb 2017).

Measuring Transitions in Sexual Risk Among Men Who Have Sex With Men: The Novel Use of Latent Class and Latent Transition Analysis in HIV Sentinel Surveillance

Measuring Transitions in Sexual Risk Among Men Who Have Sex With Men: The Novel Use of Latent Class and Latent Transition Analysis in HIV Sentinel Surveillance. Wilkinson AL, El-Hayek C, Fairley CK, Roth N, Tee BK, McBryde E, Hellard M, Stoové M. Am J Epidemiol (2017) 185 (8): 627-635, Mar 10:1-9. doi: 10.1093/aje/kww239.

Wilkinson et al. Respond to “Latent Transition Analyses in Clinical Cohorts”

Wilkinson et al. Respond to “Latent Transition Analyses in Clinical Cohorts”. Wilkinson AL, El-Hayek C, Fairley CK, Roth N, Tee BK, McBryde E, Hellard M, Stoové M. Am J Epidemiol. 2017 Mar 10:1-2. doi: 10.1093/aje/kww238.

Treatment outcomes in patients with multidrug-resistant tuberculosis in north-west Ethiopia

Treatment outcomes in patients with multidrug-resistant tuberculosis in north-west Ethiopia. Kefyalew Addis Alene, Kerri Viney, Emma S. McBryde, Adino Tesfahun Tsegaye, Archie C. A. Clements. Tropical Medicine and International Health. First published: 6 January 2017. Volume 22, Issue 3 March 2017, pages 351–362. doi: 10.1111/tmi.12826

Mycobacteria-specific IL-1RA response as a potential correlate of treatment success in active and latent tuberculosis infection

Mycobacteria-specific IL-1RA response as a potential correlate of treatment success in active and latent tuberculosis infection. Vanessa Clifford, Marc Tebruegge, Christel Zufferey, Susie Germano, Ben Forbes, Lucy Cosentino, Elizabeth Matchett, Emma McBryde, Damon Eisen, Roy Robins-Browne, Alan Street, Justin Denholm, Nigel Curtis.  Pathology 49 (Feb 2017): S59.

Spatial patterns of multidrug resistant tuberculosis and relationships to socio-economic, demographic and household factors in northwest Ethiopia

Spatial patterns of multidrug resistant tuberculosis and relationships to socio-economic, demographic and household factors in northwest Ethiopia. Kefyalew Addis Alene , Kerri Viney, Emma S. McBryde, Archie C. A. Clements.Published: February 9, doi.org/10.1371/journal.pone.0171800

The risk of global epidemic replacement with drug-resistant Mycobacterium tuberculosis strains

The risk of global epidemic replacement with drug-resistant Mycobacterium tuberculosis strains. Emma S. McBryde, Michael T. Meehan, Tan N. Doan, Romain Ragonnet, Ben J. Marais, Vanina Guernier, James M. Trauer. International Journal of Infectious Diseases Vol 56, P 14-20. doi: http://dx.doi.org/10.1016/j.ijid.2017.01.031

Characterising pandemic severity and transmissibility from data collected during first few hundred studies

Andrew J. Black^a , Nicholas Geard^{b, c}, James M. McCaw^{b, d, e}, Jodie McVernon^{b, e, f}, Joshua V. Ross^{a .} Characterising pandemic severity and transmissibility from data collected during first few hundred studies. | Epidemics, 19th January 2017 doi: 10.3389/fimmu.2016.00611.

Characterizing the risk of respiratory syncytial virus in infants with older siblings: a population-based birth cohort study

Jacoby P, Glass K, Moore HC. Characterizing the risk of respiratory syncytial virus in infants with older siblings: a population-based birth cohort study.  Epidemiology and Infection 145(2):266-271. https://doi.org/10.1017/S0950268816002545

Model selection for seasonal influenza forecasting

Model selection for seasonal influenza forecasting. Zarebski AE, Dawson P, McCaw JM, Moss R, Infectious Disease Modelling. (accepted 16 December 2016) doi.org/10.1016/j.idm.2016.12.004

High rates of multidrug-resistant and rifampicin-resistant tuberculosis among re-treatment cases: where do they come from?

High rates of multidrug-resistant and rifampicin-resistant tuberculosis among re-treatment cases: where do they come from? Romain Ragonnet, James M. Trauer, Justin T. Denholm, Ben J. Marais and Emma S. McBryde. BMC Infectious Diseases:36, doi: 10.1186/s12879-016-2171-1 Published: 6 January 2017

Is IPT more effective in high-burden settings? Modelling the effect of tuberculosis incidence on IPT impact

Is IPT more effective in high-burden settings? Modelling the effect of tuberculosis incidence on IPT impact. Ragonnet, R, Trauer J,  McBryde E,  Houben R. M. G. J, Denholm, J, Handel A, Sumner, T. The International Journal of Tuberculosis and Lung Disease, Volume 21, Nr 1, 1 January 2017, pp. 60-66(7). doi:10.5588/ijtld.16.0297

Heterogeneity of distribution of tuberculosis in Sheka Zone, Ethiopia: drivers and temporal trends

Heterogeneity of distribution of tuberculosis in Sheka Zone, Ethiopia: drivers and temporal trends. Shaweno, D, Shaweno, T, Trauer J.M, Denholm J, McBryde, E. The International Journal of Tuberculosis and Lung Disease, Volume 21, Number 1, 1 January 2017, pp. 79-85(7)

On the role of CD8+ T cells in determining recovery time from influenza virus infection

Pengxing Cao¹,  Zhongfang Wang ^{2, 3},  Ada W. Yan¹, Jodie McVernon ^{4, 6}, Jianqing Xu²,  Jane M. Heffernan⁵,  Katherine Kedzierska³ and  James M. McCaw^{1, 4, 6*,} 

On the role of CD8+ T cells in determining recovery time from influenza virus infection. Front. Immunol. | doi: 10.3389/fimmu.2016.00611.

Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models

Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models. Nicolas A Menzies, Gabriela B Gomez, , Emma S McBryde, James M Trauer, et al. The Lancet Global Health Volume 4, Issue 11, November 2016, Pages e816–e826. doi.org/10.1016/S2214-109X(16)30265-0

Modelling the effect of short-course multidrug-resistant tuberculosis treatment in Karakalpakstan, Uzbekistan

Modelling the effect of short-course multidrug-resistant tuberculosis treatment in Karakalpakstan, Uzbekistan. James M. Trauer, Jay Achar, Nargiza Parpieva, Atadjan Khamraev, Justin T. Denholm, Dennis Falzon, Ernesto Jaramillo, Anita Mesic, Philipp du Cros and Emma S. McBryde BMC Medicine2016 14:187. doi: 10.1186/s12916-016-0723-2. Published: 18 November 2016

Influence of Population Demography and Immunization History on the Impact of an Antenatal Pertussis Program

Patricia Therese Campbell^1,2, Jodie McVernon^1,2,3, Peter McIntyre⁴, and Nicholas Geard¹,Influence of Population Demography and Immunization History on the Impact of an Antenatal Pertussis Program. Clinical Infectious Diseases Volume 63, Issue suppl 4Pp. S213-S220, doi: 10.1093/cid/ciw520.

Modelling cross-reactivity and memory in the cellular adaptive immune response to influenza infection in the host

Ada W. C. Yan^a , Pengxing Cao^a , Jane M. Heffernan ^b,c, Jodie McVernon^d,e,f, Kylie M. Quinn ^g,h, Nicole L. L^a Grutag,^h, Karen L. Laurie ^i,j,g, James M. McCaw ^a,e,f.Modelling cross-reactivity and memory in the cellular adaptive immune response to influenza infection in the host. Journal of Theoretical Biology. Accepted 2016 Nov 8.

A comparison of Clostridium difficile ribotypes circulating in Australian hospitals and communities

Furuya-Kanamori L¹, Riley TV^2,3, Paterson DL⁴, Foster NF^2,3, Huber CA⁴, Hong S², Harris-Brown T⁴, Robson J⁵, Clements AC⁶. A comparison of Clostridium difficile ribotypes circulating in Australian hospitals and communities. J Clin Microbiol 2016; Epub ahead of print. doi:10.1128/JCM.01779-16

The impact of active surveillance and health education on an Ebola virus disease cluster — Kono District, Sierra Leone, 2014–2015

The impact of active surveillance and health education on an Ebola virus disease cluster – Kono District, Sierra Leone, 2014-2015. Stehling-Ariza T, Wood JG, Manso D et. al. BMC Infectious Diseases, Oct 2016(1). doi:10.1186/s12879-016-1941-0

A data-driven model for influenza transmission incorporating media effects

A data-driven model for influenza transmission incorporating media effects. Mitchell L, Ross JV. 2016 A R. Soc. open sci.3: 160481..doi.org/10.1098/rsos.160481

Reducing disease burden in an influenza pandemic by targeted delivery of neuraminidase inhibitors: mathematical models in the Australian context

Robert Moss,¹ James M. McCaw,^1,2,3 Allen C. Cheng,^4,5 Aeron C. Hurt,⁶ and Jodie McVernon^1,3.Reducing disease burden in an influenza pandemic by targeted delivery of neuraminidase inhibitors: mathematical models in the Australian context.Published online 2016 Oct 10, BMC Infectious Diseases.doi:10.1186/s12879-016-1866-7

Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models

Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models. Rein M G J Houben, Nicolas A Menzies, Tom Sumner, Grace H Huynh, Nimalan Arinaminpathy, Jeremy D Goldhaber-Fiebert, James M Trauer, Justin T Denholm, Emma S McBryde, Anna Vassall, Richard G White, et al. Lancet Glob Health 2016;4: e806–15 Published Online October 6, 2016. doi.org/10.1016/ S2214-109X(16)30199-1

Retrospective forecasting of the 2010–2014 Melbourne influenza seasons using multiple surveillance systems

R. MOSS ^(a1), A. ZAREBSKI ^(a2), P. DAWSON ^(a3) and J. M. McCAW ^{(a1) (a2) (a4).}Retrospective forecasting of the 2010–2014 Melbourne influenza seasons using multiple surveillance systems. Epidemiology and Infection, 145(1), 156-169. doi:10.1017/S0950268816002053. Published online: 27 September 2016

Model-Informed Risk Assessment and Decision Making for an Emerging Infectious Disease in the Asia-Pacific Region

Robert Moss, Roslyn I. Hickson, Jodie McVernon, James M. McCaw, Krishna Hort, Jim Black, John R. Madden, Nhi H. Tran, Emma S. McBryde, Nicholas Geard. Model-Informed Risk Assessment and Decision Making for an Emerging Infectious Disease in the Asia-Pacific Region. PLOS Neglected Tropical Diseases. 2016 Sep 23;DOI:10.1371/journal.pntd.0005018

Community-Acquired Clostridium difficile Infection, Queensland, Australia

   Furuya-Kanamori L, Yakob L, Riley TV, Paterson DL, Baker P, McKenzie SJ, Robson J, Clements AC. Community-acquired Clostridium difficile infections in Queensland, Australia. Emerg Infect Dis 2016; 22(9):1659-61.DOI: http://dx.doi.org/10.3201/eid2209.151115

Asymptomatic Clostridium difficile colonisation in two Australian tertiary hospitals, 2012-2014: A prospective, repeated cross-sectional study

Furuya-Kanamori L¹, Clements AC², Foster NF³, Huber CA⁴, Hong S⁵, Harris-Brown T⁴, Yakob L⁶, Paterson DL⁴, Riley TV³.Asymptomatic Clostridium difficile colonisation in two Australian tertiary hospitals, 2012-2014: A prospective, repeated cross-sectional study. Clin Microb Infect 2016. doi: 10.1016/j.cmi.2016.08.030

Problematic Dichotomization of Risk for Intensive Care Unit (ICU)–Acquired Invasive Candidiasis: Results Using a Risk-Predictive Model to Categorize 3 Levels of Risk From a Multicenter Prospective Cohort of Australian ICU Patients

Problematic Dichotomization of Risk for Intensive Care Unit (ICU)–Acquired Invasive Candidiasis: Results Using a Risk-Predictive Model to Categorize 3 Levels of Risk From a Multicenter Prospective Cohort of Australian ICU Patients. E. Geoffrey Playford  Jeffrey Lipman  Michael Jones  Anna F. Lau  Masrura Kabir Sharon C.-A. Chen  Deborah J. Marriott  Ian Seppelt  Thomas Gottlieb  Winston Cheung Jonathan R. Iredell  Emma S. McBryde, Tania C. Sorrell.  Clin Infect Dis (2016) 63 (11): 1463-1469. doi.org/10.1093/cid/ciw610 .Published: 06 September 2016

Periodic solutions in an SIRWS model with immune boosting and cross-immunity

Tiffany Leung ^a, Barry D. Hughes ^a, Federico Frascoli ^b, James M. McCaw ^{a, c, d,}Periodic solutions in an SIRWS model with immune boosting and cross-immunity. Journal of Theoretical Biology 410, December 2016, 55-64.http://dx.doi.org/10.1016/j.jtbi.2016.08.034

Efficacy of a trivalent influenza vaccine against seasonal strains and against 2009 pandemic H1N1: A randomized, placebo-controlled trial.

McBride WJH, Abhayaratna WP, Barr I, Booy R, Carapetis J, Carson S, De Looze F, Ellis-Pegler R, Heron L, Karrasch J, Marshall H, McVernon J, Nolan T, Rawlinson W, Reid J, Richmond P, Shakib S, Basser RL, Hartel GF, Lai MH, Rockman S, Greenberg ME. Efficacy of a trivalent influenza vaccine against seasonal strains and against 2009 pandemic H1N1: a randomized placebo-controlled trial. Vaccine 34 (2016) 4991–4997. http://dx.doi.org/10.1016/j.vaccine.2016.08.038. 

Managing the risk of wildlife disease introduction: pathway-level biosecurity for preventing the introduction of alien ranaviruses

Managing the risk of wildlife disease introduction: pathway-level biosecurity for preventing the introduction of alien ranaviruses. Pablo García-Díaz, Joshua V. Ross, Andrew P. Woolnough, Phillip Cassey. Vol54, Issue 1 Feb 2017 P 234–241. First published: 9 August 2016. doi: 10.1111/1365-2664.12749

Comparison of the Exposure Time Dependence of the Activities of Synthetic Ozonide Antimalarials and Dihydroartemisinin against K13 Wild-Type and Mutant Plasmodium falciparum Strains

Yang T, Xie SC, Cao P, Giannangelo C, McCaw J, Creek DJ, Charman SA, Klonis N, Tilley L. Comparison of the Exposure Time Dependence of the Activities of Synthetic Ozonide Antimalarials and Dihydroartemisinin against K13 Wild-Type and Mutant Plasmodium falciparum Strains. Antimicrobial Agents and Chemotherapy. 2016 Jul 22;60(8):4501-10.2016 Aug; 60(8): 4501–4510. DOI:10.1128/AAC.00574-16

Turnover of Village Chickens Undermines Vaccine Coverage to Control HPAI H5N1

Villanueva-Cabezas JP^1,2, Campbell PT^1,3, McCaw JM^1,3,4, Durr PA², McVernon J^1,3. Turnover of Village Chickens Undermines Vaccine Coverage to Control HPAI H5N1.Zoonoses and Public Health.2016 Jun 30. doi: 10.1111/zph.12282.

A role of influenza exposure history in determining pandemic susceptibility and CD8+ T cell responses

Quinones-Parra S, Clemens B, Wang Z, Croom H, Kedzierski L, McVernon J, Vijaykrishna D, Kedzierska K. A role of influenza exposure history in determining pandemic susceptibility and CD8+ T cell responses. Journal of Virology, August 2016 vol. 90 no. 15 6936-6947. doi:10.1128/JVI.00349-16 Abstract Novel influenza viruses often cause differential infection patterns across different age groups, an effect…

Time series analysis of RSV and bronchiolitis seasonality in temperate and tropical Western Australia

Alexandra B. Hogan a, Robert S. Anderssen b, Stephanie Davis a, Hannah C. Moore c, Faye J. Lim c, Parveen Fathima c, Kathryn Glass a.Time series analysis of RSV and bronchiolitis seasonality in temperate and tropical Western Australia. Epidemics 16 (2016) 49–55. http://dx.doi.org/10.1016/j.epidem.2016.05.001 Abstract Respiratory syncytial virus (RSV) causes respiratory illness in young children and is…

The Potential Impact of a Hepatitis C Vaccine for People Who Inject Drugs: Is a Vaccine Needed in the Age of Direct-Acting Antivirals?

The Potential Impact of a Hepatitis C Vaccine for People Who Inject Drugs: Is a Vaccine Needed in the Age of Direct-Acting Antivirals?  Jack Stone , Natasha K. Martin, Matthew Hickman, Margaret Hellard, Nick Scott, Emma McBryde, Heidi Drummer, Peter Vickerman. PLOS one.Published: May 25, 2016. http://dx.doi.org/10.1371/journal.pone.0156213

On the efficient determination of optimal Bayesian experimental designs using ABC: A case study in optimal observation of epidemics

On the efficient determination of optimal Bayesian experimental designs using ABC: A case study in optimal observation of epidemics. David J. Price, Nigel G. Bean, Joshua V. Ross, Jonathan Tuke. Journal of Statistical Planning and Inference.Vol 172, May 2016, Pages 1–15. doi.org/10.1016/j.jspi.2015.12.008

Scenario Analysis for Programmatic Tuberculosis Control in Western Province, Papua New Guinea

Scenario Analysis for Programmatic Tuberculosis Control in Western Province, Papua New Guinea. James M. Trauer  Justin T. Denholm  Saba Waseem, Romain Ragonnet, Emma S. McBryde. Am J Epidemiol (2016) 183 (12): 1138-1148. doi.org/10.1093/aje/kwv323. Published: 19 May 2016

Exploring the dynamics of respiratory syncytial virus (RSV) transmission in children

Alexandra B. Hogan , Kathryn Glass, Hannah C. Moore, Robert S. Anderssen. Exploring the dynamics of respiratory syncytial virus (RSV) transmission in children. Theoretical Population Biology, May 2016. doi:10.1016/j.tpb.2016.04.003

Feasibiliy of Recruiting People who Inject Drugs into a Nurse-Led Model of Care Trial: The Tap Study

Feasibiliy of Recruiting People who Inject Drugs into a Nurse-Led Model of Care Trial: The Tap Study. S. von Bibra, J.S. Doyle, P. Higgs, P. Dietze, P. Desmond, M. Stoove, E. McBryde, L. Burke, J. Lupi, M. Bryant, A.J. Thompson, M.E. Hellard. Journal of Hepatology Vol 64-2. doi: 10.1016/S0168-8278(16)01598-1

Hepatic Fibrosis Measured by Elastography among People who Inject Drugs with Chronic HCV in Community Settings: The Tap Study

Hepatic Fibrosis Measured by Elastography among People who Inject Drugs with Chronic HCV in Community Settings: The Tap Study. J.S. Doyle, P. Dietze, P. Desmond, D.M. Iser, M. Stoove, E. McBryde, P. Higgs, M.E. Hellard, A.J. Thompson. 16 April 2016: Viral hepatitis: Hepatitis C – Clinical (therapy). Journal of Hepatology, 2016 Vol 64-2. doi: 10.1016/S0168-8278(16)01526-9

Treatment scale-up to achieve global HCV incidence and mortality elimination targets: a cost-effectiveness model

Treatment scale-up to achieve global HCV incidence and mortality elimination targets: a cost-effectiveness model. Nick Scott, Emma S McBryde, Alexander Thompson, Joseph S Doyle, Margaret E Hellard. BMJ Journal.doi.org/10.1136/gutjnl-2016-311504

The effect of Wolbachia on dengue dynamics in the presence of two serotypes of dengue: symmetric and asymmetric epidemiological characteristics

Ndii MZ, Allingham D, Hickson RI, Glass K. (2016) The effect of Wolbachia on dengue dynamics in the presence of two serotypes of dengue: symmetric and asymmetric epidemiological characteristics. Epidemiology & Infection March2016. doi:10.1017/S0950268816000753

High conservation level of CD8+ T cell immunogenic regions within an unusual H1N2 human influenza variant

Komadina N, Quinones-Parra SM, Kedzierska K, McCaw JM, Kelso A, Leder K, McVernon J. High conservation level of CD8+ T cell immunogenic regions within an unusual H1N2 human influenza variant. Journal Med Virol Mar 2016. DOI: 10.1002/jmv.24516

The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography

The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography. P.G. Ballard, N.G. Bean, J.V. Ross. Journal of Theoretical Biology. Volume 393, 2016, Pages 170–178 doi/10.1016/j.jtbi.2016.01.012

The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography

Ballard, P.G., Bean, N.G. and Ross, J.V. (2016) The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography. Journal of Theoretical Biology 393, 170-178. doi:10.1016/j.jtbi.2016.01.012

Simulation-based Bayesian inference for epidemic models

McKinley, T.J., Ross, J.V., Deardon, R. and Cook, A.R. (2014) Simulation-based Bayesian inference for epidemic models. Computational Statistics and Data Analysis 71, 434-447. doi:10.1016/j.csda.2012.12.012

Upper Versus Lower Gastrointestinal Delivery for Transplantation of Fecal Microbiota in Recurrent or Refractory Clostridium difficile Infection: A Collaborative Analysis of Individual Patient Data From 14 Studies

Furuya-Kanamori L, Doi SA, Paterson DL, Helms SK, Yakob L, McKenzie SJ, Garborg K, Emanuelsson F, Stollman N, Kronman MP, Clark J, Huber CA, Riley TV, Clements AC. Upper versus lower-gastrointestinal delivery for transplantation of fecal microbiota in recurrent or refractory Clostridium difficile infection – A collaborative analysis of individual patient data from 14 studies. J Clin Gastroenterol 2016; Epub ahead of print.DOI:10.1097/MCG.0000000000000511

Successful control of Ebola Virus Disease: analysis of service based data from rural Sierra Leone

Lokuge K, Caleo G, Greig J, Duncombe J, McWilliam N, Squire J, Lamin M, Wolz A, Kobinger G,de la Vega M-A, Gbabai O, Nabieu S, Lamin M, Kremer R, Danis K, Banks E, Glass K. (2016) Successful control of Ebola Virus Disease: analysis of service based data from rural Sierra Leone. Plos Neglected Tropical Diseases 10(3):e0004498. doi: 10.1371/journal.pntd.0004498

Economic Evaluation of Vaccination Programmes in Older Adults and the Elderly: Important Issues and Challenges

Dirmesropian S; Wood JG; MacIntyre CR; Beutels P; Newall AT, 2016, ‘Economic Evaluation of Vaccination Programmes in Older Adults and the Elderly: Important Issues and Challenges.’,PharmacoEconomics, http://dx.doi.org/10.1007/s40273-016-0393-0

Choice of Antiviral Allocation Scheme for Pandemic Influenza Depends on Strain Transmissibility, Delivery Delay and Stockpile Size

Choice of Antiviral Allocation Scheme for Pandemic Influenza Depends on Strain Transmissibility, Delivery Delay and Stockpile Size. Lydeamore, M., Bean, N., Black, A.J., Ross J.V. Bull Math Biol (2016) 78: 293. doi:10.1007/s11538-016-0144-6

Risk of Active Tuberculosis in the Five Years Following Infection . . . 15%?

Risk of Active Tuberculosis in the Five Years Following Infection . . . 15%? James M. Trauer, Nompilo Moyo, Ee-Laine Tay, Katie Dale, Romain Ragonnet, Emma S. McBryde, Justin T. Denholm. Chest. 2016;149(2):516-525. doi:10.1016/j.chest.2015.11.017

Modeling the impact of interventions against Acinetobacter baumannii transmission in intensive care units

Doan TN, Kong DC, Marshall C, Kirkpatrick CM, McBryde ES. Modeling the impact of interventions against Acinetobacter baumannii transmission in intensive care units. Virulence.2015:112. doi:10.1080/21505594.2015.1076615

Choice of Antiviral Allocation Scheme for Pandemic Influenza Depends on Strain Transmissibility, Delivery Delay and Stockpile Size

Lydeamore, M., Bean, N., Black, A.J. and Ross, J.V. (2016) Choice of antiviral allocation scheme for pandemic influenza depends on strain transmissibility, delivery delay and stockpile size. Bulletin of Mathematical Biology 78, 293-321. DOI 10.1007/s11538-016-0144-6

Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities

Bowen AC, Harris T, Holt DC, Giffard PM, Carapetis JR, Campbell PT, McVernon J, Tong SYC. Whole genomesequencing reveals extensive community-level transmission of Group AStreptococcus in remote communities. Epidemiol Infect.doi.org/10.1017/S095026881500326X

Integrative analysis of the physical transport network into Australia.

Cope, R.C., Ross, J.V., Wittmann, T.A. and Cassey, P. (2016) Integrative analysis of the physical transport network into Australia. PLOS ONE 11, e0148831.  http://dx.doi.org/10.1371/journal.pone.0148831

Forecasting influenza outbreak dynamics in Melbourne from Internet search query surveillance data

Robert Moss, Alexander Zarebski, Peter Dawson, James M. McCaw. Forecasting influenza outbreak dynamics in Melbourne from Internet search query surveillance data. Influenza and other respiratory viruses 7 MAR 2016. DOI:10.1111/irv.12376

A ‘test and treat’ prevention strategy in Australia requires innovative HIV testing models: a cohort study of repeat testing among ‘high-risk’ men who have sex with men

Wilkinson AL, El-Hayek C, Spelman T, Fairley CK, Leslie D, McBryde ES, et al. A ‘test and treat’ prevention strategy in Australia requires innovative HIV testing models: a cohort study of repeat testing among ‘high-risk’ men who have sex with men. Sex Transm Infect. 2016.  doi:10.1136/sextrans-2015-052421

Retrospective economic evaluation of childhood 7-valent pneumococcal conjugate vaccination in Australia: Uncertain herd impact on pneumonia critical

Newall AT, Reyes JF, McIntyre P., Menzies R, Beutels P, & Wood, JG (2016). Retrospective economic evaluation of childhood 7-valent pneumococcal conjugate vaccination in Australia: Uncertain herd impact on pneumonia critical. Vaccine, 34(3), 320-327. doi:10.1016/j.vaccine.2015.11.053

On the extinction probability in models of within-host infection: the role of latency and immunity

Yan AWC, Cao P, McCaw JM, On the extinction probability in models of within-host infection: the role of latency and immunity, Journal of Mathematical Biology 9 Jan 2016 doi:10.​1007/​s00285-015-0961-5

25-Hydroxyvitamin D Concentrations and Clostridium difficile Infection: A Meta-Analysis.

Furuya-Kanamori L, Wangdi K, Yakob L, McKenzie SJ, Doi SA, Clark J, Paterson DL, Riley TV, Clements AC. 25-Hydroxyvitamin D concentrations and Clostridium difficile infection – A meta-analysis. JPEN Parenter Enter 2015; Epub ahead of print.DOI:10.1177/0148607115623457

Heightened self-reactivity associated with selective survival, but not expansion, of naïve virus-specific CD8+ T cells in aged mice

Quinn KM, Zaloumis SG, Cukalac T, Kan W-T, Sng X, Mirams M, Watson K, McCaw JM, Doherty PC, Thomas PG, Handel A, La Gruta NL, Heightened self-reactivity associated with selective survival, but not expansion, of naïve virus-specific CD8+ T cells in aged mice, PNAS January 19, 2016, doi: 10.1073/pnas.1525167113 

Transmission of the First Influenza A(H1N1)pdm09 Pandemic Wave in Australia Was Driven by Undetected Infections: Pandemic Response Implications

Fielding JE, Kelly HA, Glass K (2015) Transmission of the first influenza A(H1N1)pdm09 pandemic wave in Australia was driven by undetected infections: pandemic response implications. PLoS One 10(12): e0144331.http://dx.doi.org/10.1371/journal.pone.0144331

Deep sequence characterisation of a divergent HPIV-4a from an adult with prolonged influenza-like illness

Arden KE, Beatson SA, Lambert SB, Wang CYT, McVernon J, Nissen MD, Nolan T, Sloots TP, Mackay IM. Deep sequence characterization of a divergent HPIV-4a from an adult with prolonged influenza-like illness. Virology Reports, 2015 February 18. doi:10.1016/j.virep.2015.02.001

Modelling the Impact of Condom Distribution on the Incidence and Prevalence of Sexually Transmitted Infections in an Adult Male Prison System

Scott N, McBryde E, Kirwan A, Stoove M. Modelling the Impact of Condom Distribution on the Incidence and Prevalence of Sexually Transmitted Infections in an Adult Male Prison System. PLoS One. 2015;10(12):e0144869. DOI: 10.1371/journal.pone.0144869

The effects of demographic change on disease transmission and vaccine impact in a household structured population

Geard N, Glass K, McCaw JM, McBryde E, Korb, K, Keeling MJ, McVernon J (2015) The effects of demographic change on disease transmission and vaccine impact in a household structured population. Epidemics, 13:56-64. doi:10.1016/j.epidem.2015.08.002

Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications

Furuya-Kanamori L, Marquess J, Yakob L, Riley TV, Paterson DL, Foster NF, Huber C, Clements AC. Asymptomatic Clostridium difficile colonization – Epidemiology and Clinical Implications. BMC Infect Dis2015; 15:516.DOI:10.1186/s12879-015-1258-4

Estimating the critical immunity threshold for preventing hepatitis A outbreaks in men who have sex with men

Regan DG, Wood JG, Benevent C. et. al. (2016). Estimating the critical immunity threshold for preventing hepatitis A outbreaks in men who have sex with men. Epidemiology and Infection. 144(7):1528-37.http://dx.doi.org/10.1017/S0950268815002605

A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models

Rolls DA, Wang P, McBryde E, Pattison P, Robins G. A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models. PLoS One. 2015;10(11):e0142181. DOI: 10.1371/journal.pone.0142181

Social encounter profiles of greater Melbourne residents, by location – a telephone survey

Rolls D, Geard N, Warr DJ, Nathan PM, Robins GL, Pattison PE, McCaw JM, McVernon J (2015) Social encounter profiles of greater Melbourne residents, by location – a telephone survey.BMC Infectious Diseases, 15:494. doi:10.1186/s12879-015-1237-9

Defining long-term drivers of pertussis resurgence, and optimal vaccine control strategies

Patricia Campbell, James McCaw, Peter McIntyre , Jodie McVernon. Defining long-term drivers of pertussis resurgence, and optimal vaccine control strategies. Vaccine, 19 September 2015. doi:10.1016/j.vaccine.2015.09.025

Vaccination Programs for Endemic Infections: Modelling Real versus Apparent Impacts of Vaccine and Infection Characteristics

Ragonnet R, Trauer JM, Denholm JT, Geard N, Hellard M, McBryde ES (2015) Vaccination programs for endemic infections: modelling real versus apparent impacts of vaccine and infection characteristics. Scientific Reports, 15:15468. doi:10.1038/srep15468

Immune responses to a recombinant, four-component, meningococcal serogroup B vaccine (4CMenB) in adolescents: a phase III, randomized, multicentre, lot-to-lot consistency study.

Perrett, K.P., McVernon, J., Richmond, P.C., Marshall, H., Nissen, M., August, A., Percell, S., Toneatto, D., Nolan, T.: Immune responses to a recombinant, four-component, meningococcal serogroup B vaccine (4CMenB) in adolescents: a phase III, randomized, multicentre, lot-to-lot consistency study.Vaccine, 2015; 33(39):5217-24. doi:10.1016/j.vaccine.2015.06.103

Contact tracing and antiviral prophylaxis in the early stages of a pandemic: the probability of a major outbreak

Ross, J.V. and Black, A.J. (2015) Contact tracing and antiviral prophylaxis in the early stages of a pandemic: The probability of a major outbreak. Mathematical Medicine and Biology 32, 331-343. doi: 10.1093/imammb/dqu014

“Seek, Test, Treat” Lessons From Australia: A Study of HIV Testing Patterns From a Cohort of Men Who Have Sex With Men

Wilkinson AL, El-Hayek C, Spelman T, Fairley C, Leslie D, McBryde E, et al. “Seek, Test, Treat” Lessons From Australia: A Study of HIV Testing Patterns From a Cohort of Men Who Have Sex With Men. J Acquir Immune Defic Syndr. 2015;69(4):460-5. doi: 10.1097/QAI.0000000000000613.

The emergence of dengue in Bangladesh: epidemiology, challenges and future disease risk

Sharmin S, Viennet E, Glass K, Harley D. (2015) The emergence and decline of dengue in Bangladesh: Epidemiology, challenges, and future disease risk. Trans. Roy. Soc. Trop. Med. Hyg. 109(10):619-627. doi: 10.1093/trstmh/trv067

Modeling hepatitis C virus transmission among people who inject drugs: Assumptions, limitations and future challenges

Scott N, Hellard M, McBryde E. Modelling hepatitis C virus transmission among people who inject drugs: assumptions, limitations and future challenges. Virulence. 2015.  doi:10.1080/21505594.2015.1085151

Innate immunity and the inter-exposure interval determine the dynamics of secondary influenza virus infection and explain observed viral hierarchies

Cao P, Yan AWC, Heffernan JM, Petrie S, Moss RG, Carolan LA, Guarnaccia TA, Kelso A, Barr IG, McVernon J, Laurie KL, McCaw JM, Innate immunity and the inter-exposure interval determine the dynamics of secondary influenza virus infection and explain observed viral hierarchies, PLoS Computational Biology 11(8): e1004334 (2015). doi:10.1371/journal.pcbi.1004334.

Factors associated with transmission of influenza-like illness in a cohort of households containing multiple children

Brown CR, McCaw JM, Fairmaid EJ, Brown LE, Leder K, Sinclair M, McVernon J, Factors associated with transmission of influenza-like illness in a cohort of households containing multiple children, Influenza Other Respi Viruses 9(5): 247-254 (2015). doi:10.1111/irv.12331.

The role of a hepatitis C virus vaccine: modelling the benefits alongside direct-acting antiviral treatments

Scott N, McBryde E, Vickerman P, Martin NK, Stone J, Drummer H, et al. The role of a hepatitis C virus vaccine: modelling the benefits alongside direct-acting antiviral treatments. BMC medicine. 2015;13(1):198. DOI: 10.1186/s12916-015-0440-2

Modelled mechanisms of hypervirulent Clostridium difficile ribotype 027 displacement of endemic strains

Yakob L., Riley T.V., Paterson D.L., Marquess J., Soares Magalhaes R., Furuya Kanamori L.,Clements A.C.A. (2015) Modelled mechanisms of hypervirulent Clostridium difficile ribotype 027 displacement of endemic strains. Scientific Reports. 5:12666. doi:  10.1038/srep12666

On binomial observations of continuous-time Markovian population models

Bean, N.G., Elliott, R.J., Eshragh, A. and Ross, J.V. On binomial observations of continuous-time Markovian population models. Journal of Applied Probability 52, 457-472. doi:10.1239/jap/1437658609

Quantifying relative within-host replication fitness in influenza virus competition experiments

Petrie SM, Butler J, Bar IG, McVernon J, Hurt AC, McCaw JM, Quantifying relative within-host replication fitness in influenza virus competition experiments, Journal of Theoretical Biology 382: 259-271 (2015). doi:10.1016/j.jtbi.2015.07.003

Interaction of Mean Temperature and Daily Fluctuation Influences Dengue Incidence in Dhaka, Bangladesh

Sharmin S, Glass K, Viennet E, Harley D. (2015) Interaction of mean temperature and daily fluctuation influences dengue incidence in Dhaka, Bangladesh. PLOS Neglected Tropical Diseases 9(7):e0003901.http://dx.doi.org/10.1371/journal.pntd.0003901

Characterising the Transmission Dynamics of Acinetobacter baumannii in Intensive Care Units Using Hidden Markov Models

Doan TN, Kong DC, Marshall C, Kirkpatrick CM, McBryde ES. Characterising the Transmission Dynamics of Acinetobacter baumannii in Intensive Care Units Using Hidden Markov Models. PLoS One. 2015;10(7):e0132037. DOI: 10.1371/journal.pone.0132037

Optimal prophylactic vaccination in segregated populations: When can we improve on the equalising strategy?

Keeling, M.J. and Ross, J.V. (2015) Optimal prophylactic vaccination in segregated populations: When can we improve on the equalising strategy? Epidemics 11, 7-13.doi:10.1016/j.epidem.2015.01.002

The time-interval between infections and viral hierarchies are determinants of viral interference following influenza virus infection in a ferret model

Laurie KL, Guarnaccia TA, Carolan LA, Yan AWC, Aban M, Petrie S, Cao P, Heffernan JM, McVernon J, Mosse J, Kelso A, McCaw JM, Barr IG, The time-interval between infections and viral hierarchies are determinants of viral interference following influenza virus infection in a ferret model, Journal of Infectious Diseases (accepted 24th March 2015). doi:10.1093/infdis/jiv260

Estimating vaccine coverage from serial trivariate serologic data in the presence of waning immunity.

Wood JG; Goeyvaerts N; Raina MacIntyre C; Menzies RI; McIntyre PB; Hens N, 2015. Estimating vaccine coverage from serial trivariate serologic data in the presence of waning immunity. Epidemiology. vol. 26, no. 3, pp. 381 – 389, http://dx.doi.org/10.1097/eDe.0000000000000278

Hepatitis C transmission and treatment as prevention – The role of the injecting network

Hellard M, McBryde E, Sacks Davis R, Rolls DA, Higgs P, Aitken C, et al. Hepatitis C transmission and treatment as prevention – The role of the injecting network. Int J Drug Policy. 2015. doi.org/10.1016/j.drugpo.2015.05.006

A review of economic evaluations of 13-valent pneumococcal conjugate vaccine (PCV13) in adults and the elderly

Dirmesropian S; Wood JG; Macintyre CR; Newall AT, 2015, ‘A review of economic evaluations of 13-valent pneumococcal conjugate vaccine (PCV13) in adults and the elderly‘, Human Vaccines and Immunotherapeutics, vol. 11, no. 4, pp. 818 – 825, http://dx.doi.org/10.1080/21645515.2015.1011954

Targeting the Cell Stress Response of Plasmodium falciparum to Overcome Artemisinin Resistance

Dogovski C, Xie SC, Burgio G, Bridgford J, Mok S, McCaw JM, Chotivanich K, Kenny S, Gnadig N, Straimer J, Bozdech Z, Fidock DA, Simpson JA, Dondorp AM, Foote S, Klonis N, Tilley L, Targeting the cell stress response of plasmodium falciparum to overcome artemisinin resistance, PLoS Biology 13(4): e1002132 (2015). doi:10.1371/journal.pbio.1002132

Periodicity of varicella-zoster virus in the presence of immune boosting and clinical reinfection with varicella

Korostil, I. A., Wood, J. G., & Regan, D. G. (2015). Periodicity of varicella-zoster virus in the presence of immune boosting and clinical reinfection with varicella. Theoretical Biology and Medical Modelling, 12(1).DOI: 10.1186/s12976-015-0002-5

Prior population immunity reduces the expected impact of CTL-inducing vaccines for pandemic influenza control

Bolton KJ, McCaw JM, Brown L, Jackson D, Kedzierska K, McVernon J, Prior population immunity reduces the expected impact of CTL-inducing vaccines for pandemic influenza control, PLoS ONE 10(3): e0120138 (2015). doi:10.1371/journal.pone.0120138

Antibody persistence in Australian adolescents following meningococcal C conjugate vaccination.

Perrett K, Richmond P, Borrow R, Nolan T, McVernon J. Antibody persistence in Australian adolescents following meningococcal C conjugate vaccination. Pediatric Infect Dis J 2015; 34(3):279-85. doi: 10.1097/INF.0000000000000541

Clostridium difficile infection seasonality: Patterns across hemispheres and continents

Furuya-Kanamori L., McKenzie S.J., Yakob L., Clark J., Paterson D.L., Riley T.V., Clements A.C. (2015) Clostridium difficile infection seasonality: Patterns across hemispheres and continents. PLoS One. doi: 10.1371/journal.pone.0120730

Pertussis models to inform vaccine policy

Campbell PT, McCaw JM, McVernon J, Pertussis models to inform vaccine policy, Human Vaccines and Immunotherapeutics 11(3): 669-678 (2015). doi:10.1080/21645515.2015.1011575.

Computation of epidemic final size distributions

Black, A.J. and Ross, J.V. (2015)Computation of epidemic final size distributions.Journal of Theoretical Biology 367, 159-165.  doi:10.1016/j.jtbi.2014.11.029

Impact of high coverage of monovalent human rotavirus vaccine on Emergency Department presentations for rotavirus gastroenteritis.

Davey, H. M., Muscatello, D. J., Wood, J. G., Snelling, T. L., Ferson, M. J., & Macartney, K. K. (2015). Impact of high coverage of monovalent human rotavirus vaccine on Emergency Department presentations for rotavirus gastroenteritis. Vaccine, 33(14), 1726-1730. doi: 10.1016/j.vaccine.2015.01.082

Predicting localised measles outbreak potential in Australia

Wood, J. G., Heywood, A. E., Menzies, R. I., McIntyre, P. B., & MacIntyre, C. R. (2015). Predicting localised measles outbreak potential in Australia. Vaccine, 33(9), 1176-1181. doi: 10.1016/j.vaccine.2014.12.071

Optimizing Hospital Infection Control: The Role of Mathematical Modeling

Doan, Tan N, Kong, David, Kirkpatrick, Carl MJ, McBryde, Emma S. Optimizing Hospital Infection Control: The Role of Mathematical Modeling. Infection Control & Hospital Epidemiology / Volume 35 / Issue 12 / December 2014, pp 1521-1530. dx.doi.org/10.1086/678596

A new approach to estimating trends in chlamydia incidence

Ali H, Cameron E, Drovandi CC, McCaw JM, Guy RJ, Middleton M, El -Hayek C, Hocking JS, Kaldor JM, Donovan B, Wilson DP, on behalf of the Australian chlamydia incidence estimation group, A new approach to estimating trends in chlamydia incidence,Sexually Transmitted InfectionsSexually Transmitted Infections 91: 513-519 (2015).doi:10.1136/sextrans-2014-051631

Comorbidities, Exposure to Medications, and the Risk of Community-Acquired Clostridium difficile Infection: A Systematic Review and Meta-analysis

Furuya-Kanamori L., Stone J.C., Clark J., McKenzie S.J., Yakob L., Paterson D.L., Riley T.V., Doi S.A.R., Clements A.C. (2015) Comorbidities, exposure to medications and the risk of community-acquired Clostridium difficile infection – A systematic review and meta-analysis. Infection Control and Hospital Epidemiology. 36:132–141. doi: 10.1017/ice.2014.39

Assessment of the Risk of Ebola Importation to Australia

Cope, R.C., Cassey, P., Hugo, G.J. and Ross, J.V. (2014) Assessment of the Risk of Ebola Importation to Australia. PLoS Curents Outbreaks 2014 Dec 10. Edition 1. doi:10.1371/currents.outbreaks.aa0375fd48a92c7c9422aa543a88711f.

Many hepatitis C reinfections that spontaneously clear may be undetected: Markov-chain Monte Carlo analysis of observational study data

Sacks-Davis R, McBryde E, Grebely J, Hellard M, Vickerman P. Many hepatitis C reinfections that spontaneously clear may be undetected: Markov-chain Monte Carlo analysis of observational study data. J R Soc Interface. 2015;12(104):20141197. doi: 10.1098/rsif.2014.1197.

The dynamical consequences of seasonal forcing, immune boosting and demographic change in a model of disease transmission

Dafilis MP, Frascoli F, McVernon J, Heffernan JM, McCaw JM, The dynamical consequences of seasonal forcing, immune boosting and demographic change in a model of disease transmission, J Theor Biol 361: 124-132 (2014). doi:10.1016/j.jtbi.2014.07.028

The impact of injecting networks on hepatitis C transmission and treatment in people who inject drugs

Hellard, Margaret; Rolls, David A; Sacks-Davis, Rachel; Robins, Garry; Pattison, Philippa; Higgs, Peter; Aitken, Campbell; McBryde, Emma; The impact of injecting networks on hepatitis C transmission and treatment in people who inject drugs, Hepatology Vol 60, 1861-1870 (2014).

The effect of clumped population structure on the variability of spreading dynamics

Black, A.J., House, T., Keeling, M.J. and Ross, J.V. (2014) The effect of clumped population structure on the variability of spreading dynamics. Journal of Theoretical Biology359, 45-53. doi:10.1016/j.jtbi.2014.05.042

Construction of a mathematical model for tuberculosis transmission in highly endemic regions of the Asia-Pacific

Trauer JM, Denholm JT, McBryde ES. Construction of a mathematical model for tuberculosis transmission in highly endemic regions of the Asia-pacific. J Theor Biol. 2014;358(7 October 2014):74–84. doi:10.1016/j.jtbi.2014.05.023

Dynamical crises, multistability and the influence of the duration of immunity in a seasonally-forced model of disease transmission

Dafilis MP, Frascoli F, McVernon J, Heffernan JM, McCaw JM, Dynamical crises, multistability and the influence of the duration of immunity in a seasonally-forced model of disease transmission, Theoretical Biology and Medical Modelling 11:43 (2014). doi:10.1186/1742-4682-11-43

Revisiting Styblo’s law: Could mathematical models aid in estimating incidence from prevalence data?

Begun M; Newall AT; Marks GB; Wood JG, 2015, ‘Revisiting Styblo’s law: Could mathematical models aid in estimating incidence from prevalence data?‘, Epidemiology and Infection, vol. 143, no. 7, pp. 1556 – 1565, http://dx.doi.org/10.1017/S0950268814002428

Control of varicella in the post-vaccination era in Australia: a model-based assessment of catch-up and infant vaccination strategies for the future

Gao, Z., Wood, J. G., Gidding, H. F., Newall, A. T., Menzies, R. I., Wang, H., . . . MacIntyre, C. R. (2015). Control of varicella in the post-vaccination era in Australia: A model-based assessment of catch-up and infant vaccination strategies for the future. Epidemiology and Infection, 143(7), 1467-1476. http://dx.doi.org/10.1017/S0950268814002222

Interpreting scratch assays using pair density dynamics and approximate Bayesian computation

Johnston, S.T., Simpson, M.J., McElwain, D.L.S., Binder, B.J. and Ross, J.V. (2014)Interpreting scratch assays using pair density dynamics and approximate Bayesian computation. Open Biology 4: 140097. DOI: 10.1098/rsob.140097

Making the Most of Clinical Data: Reviewing the Role of Pharmacokinetic-Pharmacodynamic Models of Anti-malarial Drugs

Simpson JA, Zaloumis S, DelIvera AM, Price RN, McCaw JM, Making the most of clinical data: reviewing the role of pharmacokinetic-pharmacodynamic models of anti-malarial drugs, AAPS Journal 16(5): 962-974 (2014) doi: 10.1208/s12248-014-9647-y

On the derivation of approximations to cellular automata models and the assumption of independence

Davies, K.J., Green, J.E.F., Bean, N.G., Binder, B.J. and Ross, J.V. (2014) On the derivation of approximations to cellular automata models and the assumption of independence. Mathematical Biosciences 253, 63-71.doi:10.1016/j.mbs.2014.04.004

A scenario-based evaluation of the Middle East respiratory syndrome coronavirus and the Hajj

Gardner LM; Rey D; Heywood AE; Toms R; Wood J; Travis Waller S; Raina MacIntyre C, 2014, ‘A scenario-based evaluation of the Middle East respiratory syndrome coronavirus and the Hajj’, Risk Analysis: an international journal, vol. 34, no. 8, pp. 1391 – 1400, http://dx.doi.org/10.1111/risa.12253

A population-based spatio-temporal analysis of Clostridium difficile infection in Queensland, Australia over a 10-year period

Furuya-Kanamori L., Robson J., Soares Magalhaes R.J., Yakob L., McKenzie S., Paterson D.L., Riley T.V., Clements A.C. (2014) A population-based spatio-temporal analysis of Clostridium difficile infection in Queensland, Australia over a 10-year period. Journal of Infection. 69:447–455. doi:10.1016/j.jinf.2014.06.014

Modelling the seasonal epidemics of respiratory syncytial virus in young children

Moore HC, Jacoby P, Hogan AB, Blyth CC, Mercer GN (2014) Modelling the seasonal epidemics of respiratory syncytial virus in young children.(2014) PLOS One 9(6):e100422.

Assessing control bundles for Clostridium difficile: a review and mathematical model

Yakob L., Riley T.V., Paterson D.L., Marquess J., Clements A.C.A.(2014) Assessing control bundles for Clostridium difficile: a review and mathematical model. Emerging Microbes and Infections. doi: 10.1038/emi.2014.43

Approximating spatially exclusive invasion processes

Ross, J.V. and Binder, B.J. (2014) Approximating spatially-exclusive invasion processes.Physical Review E 89, 052709.   http://dx.doi.org/10.1103/PhysRevE.89.052709

Quantifying differences in the epidemic curves from three influenza surveillance systems: a nonlinear regression analysis

Thomas EG, McCaw JM, Kelly H, Grant K, McVernon J, Quantifying differences in the epidemic curves from three influenza surveillance systems: a nonlinear regression analysis, Epidemiology and Infection 43(2): 427-439 (2015). doi:10.1017/S0950268814000764

Seroprevalence of antibody to influenza A(H1N1)pdm09 attributed to vaccination or infection, before and after the second (2010) pandemic wave in Australia

McVernon J,Laurie K, Faddy H, Irving D, Nolan T, Barr I, Kelso A, Seroprevalence of antibody to influenza A(H1N1)pdm09 attributed to vaccination or infection, before and after the second (2010) pandemic wave in Australia, Influenza Other Resp Vir 8(2): 194-200 (2014). doi:10.1111/irv.12225

Eradication of hepatitis C infection: the importance of targeting people who inject drugs

Hellard, Margaret, Doyle, Joseph S, Sacks-Davis, Rachel, Thompson, Alexander J,McBryde, Emma. Eradication of hepatitis C infection: the importance of targeting people who inject drugs. Hepatology 2014 Vol 59 nr 2. 366-369, DOI: 10.1002/hep.26623

Estimating the measles effective reproduction number in Australia from routine notification data

Chiew M; Gidding HF; Dey A; Wood J; Martin N; Davis S; McIntyre P, 2014, ‘Estimating the measles effective reproduction number in Australia from routine notification data.’, Bulletin of the World Health Organization, vol. 92, no. 3, pp. 171 – 177, http://dx.doi.org/10.2471/BLT.13.125724

Economic evaluations of implemented vaccination programmes: key methodological challenges in retrospective analyses

Newall, A. T., Reyes, J. F., Wood, J. G., Beutels, P., McIntyre, P., & Menzies, R. (2014). Economic evaluations of implemented vaccination programmes: key methodological challenges in retrospective analyses. Vaccine. 32(7):759-65. doi: 10.1016/j.vaccine.2013.11.067

Systematic review of influenza A (H1N1)pdm09 virus shedding: duration is affected by severity but not age

Fielding JE, Kelly HA, Mercer GN, Glass K (2014) Systematic review of influenza A (H1N1)pdm09 virus shedding: duration is affected by severity but not age. Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12216.

Clostridium difficile exposure as an insidious source of infection in healthcare settings: an epidemiological model

Yakob L., Riley T.V., Paterson D.L., Clements A.C.A. (2013) Clostridium difficile exposure as an insidious source of infection in healthcare settings: An epidemiologic model. BMC Infectious Diseases. 13:376. doi:10.1186/1471-2334-13-376

The influence of increasing life expectancy on the dynamics of SIRS systems with immune boosting

Dafilis MP, Frascoli F, Wood JG, McCaw JM, The influence of increasing life expectancy on the dynamics of SIRS systems with immune boosting, Australian New Zealand Industrial and Applied Mathematics Journal 54:50-63 (2012). doi:10.1017/S1446181113000023.

Increased population prevalence of low pertussis toxin antibody levels preceding a record epidemic in Australia

Campbell P, McIntyre P, Quinn H, Hueston L, Gilbert GL, McVernon J, Increased population prevalence of low pertussis toxin antibody levels preceding a record epidemic in Australia. PLoS ONE 7(4): e35874 (2012). doi:10.1371/journal.pone.0035874.