Chlamydial disease
Of the two species of chlamydia that infect koalas (Chlamydia pecorum and C. pneumoniae), C. pecorum is consistently more prevalent (i.e., higher percentage individuals infected) and more pathogenic . C. pecorum is therefore the chlamydia species that researchers and veterinarians focus on . At each veterinary examination, koalas were (1) tested for the presence of C. pecorum , and (2) assessed for clinical signs of chlamydial disease. Tests for C. pecorum were conducted using either quantitative real-time PCR (qPCR) targeting a fragment of the C. pecorum 16s rRNA gene , or using the Clearview® Chlamydia MF test kit, which has a 60% sensitivity (Inverness Medical, Unipath Ltd). Clinical signs of chlamydial disease are mostly found in the ocular and urogenital regions. The ocular form of the disease varies from inflammation of the mucosal surfaces of the eye, or conjunctival hyperplasia, to the complete opacification and scarring of the cornea, which can cause blindness . In urinary disease, inflammation of the bladder (cystitis) leads to incontinence and staining of the fur around the cloaca, which is also coupled with alopecia and ulceration in severe cases . Finally, infection of the reproductive tract in females causes bursal cysts surrounding the ovary and upper reproductive tract pathology, while in males orchitis and epididymitis can occur . In this study, veterinary diagnostic techniques for assessing the presence of chlamydial disease involved observation of external signs of disease, cystocentesis with observation of the urine sediment, and ultrasound examination of the kidneys, reproductive tract, and bladder (as described in ). We initially aimed to independently analyse whether koalas tested positive for the presence of C. pecorum , and whether koalas were diagnosed with clinical signs of disease. However, in our data, the majority of individuals that tested positive also displayed clinical signs of disease (87%). We therefore opted to use whether koalas tested positive (‘chlamydia status’) as our response variable in all analyses.
Although individuals were monitored for multiple years (average = 1.2 years, max = 4 years) and had repeated measures of disease status gathered at scheduled veterinary exams (N = 1182 observations of N = 342 koalas, average = 3 observations per koala), we selected to only use chlamydia status at their first capture. This was because during the project individual koalas were treated for any illness or injury they presented at veterinary examinations (including chlamydial disease), and some individuals were also included in a chlamydia vaccination trial . Individual disease status at subsequent veterinary examinations could therefore have been affected by the veterinary treatment, vaccine trial and management of the population.