Developing noninvasive methodologies to assess koala population health through detecting Chlamydia from scats

Mol Ecol Resour. 2019 Jul;19(4):957-969. doi: 10.1111/1755-0998.12999. Epub 2019 May 5.


Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Noninvasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Here, we use the known threat of Chlamydia disease to the iconic, yet vulnerable, koala Phascolarctos cinereus to compare three methods for Chlamydia detection in scats: multiplex quantitative PCR, next generation sequencing, and a detection dog specifically trained on scats from Chlamydia-infected koalas. All three methods demonstrated 100% specificity, while sensitivity was variable. Of particular interest is the variable sensitivity of these diagnostic tests to detect sick individuals (i.e., not only infection as confirmed by Chlamydia-positive swabs, but with observable clinical signs of the disease); for koalas with urogenital tract disease signs, sensitivity was 78% with quantitative PCR, 50% with next generation genotyping and 100% with the detection dog method. This may be due to molecular methods having to rely on high-quality DNA whereas the dog most likely detects volatile organic compounds. The most appropriate diagnostic test will vary with disease prevalence and the specific aims of disease surveillance. Acknowledging that detection dogs might not be easily accessible to all, the future development of affordable and portable "artificial noses" to detect diseases from scats in the field might enable cost-effective, rapid and large-scale disease surveillance.

Keywords: Phascolarctos cinereus; detection dog; next generation genotyping; noninvasive diagnostic methods; quantitative PCR; sensitivity; specificity.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Animals
  • Biological Assay / methods*
  • Chlamydia / genetics
  • Chlamydia / isolation & purification*
  • Chlamydia Infections / veterinary*
  • Feces / microbiology*
  • High-Throughput Nucleotide Sequencing / methods*
  • Multiplex Polymerase Chain Reaction / methods*
  • Phascolarctidae*
  • Population Health
  • Real-Time Polymerase Chain Reaction / methods
  • Sensitivity and Specificity