Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: Identification and modelling of a population free from infection

Abstract

Chlamydia pecorum is an established and prevalent infection that produces severe clinical disease in many koala populations, contributing to dramatic population declines. In wild South Australian koala populations, C. pecorum occurrence and distribution is unknown. Here, C. pecorum-specific real-time quantitative PCR (qPCR) was applied to ocular and urogenital swabs from targeted surveys of wild koalas from the mainland Mount Lofty Ranges (MLR) (n = 75) and Kangaroo Island (KI) (n = 170) populations. Historical data from 13,081 KI koalas (1997-2018) provided additional evidence for assessing the absence of C. pecorum infection. In the MLR population, 46.7% (CI: 35.1-58.6%) of koalas were C. pecorum positive by qPCR but only 4% had grade 3 clinical disease. MLR koala fertility was significantly reduced by C. pecorum infection; all reproductively active females (n = 16) were C. pecorum negative, whereas 85.2% of inactive females (n = 23) were positive (P < 0.001). KI koalas were C. pecorum negative and the population was demonstrated to be free of C. pecorum infection with 95% confidence. C. pecorum is a real threat for the sustainability of the koala and KI is possibly the last isolated, large C. pecorum-free population remaining in Australia. These koalas could provide a safeguard against this serious disease threat to an iconic Australian species.

Figure 1

Geographical range of the Mount Lofty Ranges (dark grey) and the Kangaroo Island (light grey) koala populations, South Australia, Australia.

Figure 2

Conjunctival changes in koalas from the Mount Lofty Ranges, South Australia. (a) Female koala with unilateral grade 3 severe conjunctivitis, positive for Chlamydia pecorum. (b) Female koala with grade 1 reddened conjunctiva, negative for C. pecorum infection.

Figure 3

Reproductively active (orange) and inactive (blue) female koalas across age classes (TWC II (lightest) to VI (darkest)) from the Mount Lofty Ranges (inner circle) and Kangaroo Island (outer circle) populations.

Figure 4

Demonstration of freedom from Chlamydia pecorum infection in the KI koala population. Mean estimates for surveillance sensitivity (SSe) and probability of freedom, P(free)_i from C. pecorum between 1997 and 2018. The mean P(free) (solid, dark green line) with 95% CI as lower (shorted, dashed, dark green line) and upper (long, dashed, dark green line) confidence limits and SSe (long, dashed, light blue line) with a probability of introduction, P(intro) of 7% (solid double red line) and a design prevalence (P*) of 2%, concluded in 2018 above the 95% limit (solid double yellow line).

Figure 5

Structure of scenario trees used to estimate the Component Unit Sensitivity to detect Chlamydia pecorum infection in individual koalas during the DEW Koala Program or C. pecorum Targeted Survey, respectively.