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A new approach to estimating trends in chlamydia incidence
  1. Hammad Ali1,
  2. Ewan Cameron2,3,
  3. Christopher C Drovandi2,
  4. James M McCaw4,
  5. Rebecca J Guy1,
  6. Melanie Middleton1,
  7. Carol El-Hayek5,
  8. Jane S Hocking4,
  9. John M Kaldor1,
  10. Basil Donovan1,6,
  11. David P Wilson1
  12. on behalf of the Australian chlamydia incidence estimation group
    1. 1The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia
    2. 2School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
    3. 3Spatial Ecology & Epidemiology Group, University of Oxford, Oxford, United Kingdom
    4. 4Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
    5. 5Centre for Population Health, Burnet Institute, Melbourne, Australia
    6. 6Sydney Sexual Health Centre, Sydney Hospital, Sydney, Australia
    1. Correspondence to Dr Hammad Ali, The Kirby Institute, UNSW Australia, UNSW, Sydney, NSW 2052, Australia; hali{at}


    Objectives Directly measuring disease incidence in a population is difficult and not feasible to do routinely. We describe the development and application of a new method for estimating at a population level the number of incident genital chlamydia infections, and the corresponding incidence rates, by age and sex using routine surveillance data.

    Methods A Bayesian statistical approach was developed to calibrate the parameters of a decision-pathway tree against national data on numbers of notifications and tests conducted (2001–2013). Independent beta probability density functions were adopted for priors on the time-independent parameters; the shapes of these beta parameters were chosen to match prior estimates sourced from peer-reviewed literature or expert opinion. To best facilitate the calibration, multivariate Gaussian priors on (the logistic transforms of) the time-dependent parameters were adopted, using the Matérn covariance function to favour small changes over consecutive years and across adjacent age cohorts. The model outcomes were validated by comparing them with other independent empirical epidemiological measures, that is, prevalence and incidence as reported by other studies.

    Results Model-based estimates suggest that the total number of people acquiring chlamydia per year in Australia has increased by ∼120% over 12 years. Nationally, an estimated 356 000 people acquired chlamydia in 2013, which is 4.3 times the number of reported diagnoses. This corresponded to a chlamydia annual incidence estimate of 1.54% in 2013, increased from 0.81% in 2001 (∼90% increase).

    Conclusions We developed a statistical method which uses routine surveillance (notifications and testing) data to produce estimates of the extent and trends in chlamydia incidence.

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