title: A new approach to estimating trends in chlamydia incidence.
abstract: OBJECTIVE
  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.
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia.
authors.forename: Hammad
authors.initials: H
authors.lastname: Ali
authors.affiliation: School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia Spatial Ecology & Epidemiology Group, University of Oxford, Oxford, United Kingdom.
authors.forename: Ewan
authors.initials: E
authors.lastname: Cameron
authors.affiliation: School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Drovandi
authors.affiliation: Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia.
authors.forename: James M
authors.initials: JM
authors.lastname: McCaw
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Guy
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia.
authors.forename: Melanie
authors.initials: M
authors.lastname: Middleton
authors.affiliation: Centre for Population Health, Burnet Institute, Melbourne, Australia.
authors.forename: Carol
authors.initials: C
authors.lastname: El-Hayek
authors.affiliation: Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia.
authors.forename: Jane S
authors.initials: JS
authors.lastname: Hocking
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia.
authors.forename: John M
authors.initials: JM
authors.lastname: Kaldor
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia Sydney Sexual Health Centre, Sydney Hospital, Sydney, Australia.
authors.forename: Basil
authors.initials: B
authors.lastname: Donovan
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia.
authors.forename: David P
authors.initials: DP
authors.lastname: Wilson
mesh_terms: D000293:Adolescent; D000328:Adult; D000367:Age Factors; D001315:Australia / Q000453:epidemiology; D056808:Biostatistics / Q000379:methods*; D002689:Chlamydia / Q000302:isolation & purification*; D002690:Chlamydia Infections / Q000453:epidemiology*; D004812:Epidemiologic Methods; D006801:Humans; D015994:Incidence; D060737:Reproductive Tract Infections / Q000453:epidemiology*; D012737:Sex Factors; D055815:Young Adult