These datasets are associated with the NSW Koala Research Plan project 2019_10: Impacts and drivers of chlamydial disease in the koala – relationships between the host, pathogen and environment. They comprise urogenital and ocular swab samples collected from koalas in the Liverpool Plains, Southern Highlands and Port Macquarie regions of New South Wales, together with associated clinical and health data. The datasets include molecular characterisation of Chlamydia pecorum infections using genotyping of key virulence markers (incA, ORF663 and plasmid presence) and Multi‑Locus Sequence Typing (MLST) to assess strain diversity and emergence. In addition, immunological data are provided to investigate variation in koala immune responses in relation to chlamydial infection, co‑infection, and environmental stressors. Further details on the datasets, analytical methods, and data access arrangements are available in the associated peer‑reviewed publications:

• Fernandez et al. (2023). Genetic markers of Chlamydia pecorum virulence in ruminants support host–pathogen relationships in koalas. Infection, Genetics and Evolution, 116, 105527.
• Fernandez et al. (2024). Novel typing scheme reveals emergence and genetic diversity of Chlamydia pecorum. Veterinary Microbiology, 293, 110085.
• Kidd et al. (2024). Koala MHCII association with chlamydia infertility remains equivocal. Scientific Reports, 14, 31074.
• Fernandez et al. (2024). A novel multivariate immunological approach reveals immune variation associated with environmental conditions and co‑infection in the koala (Phascolarctos cinereus). Scientific Reports, 14, 7260. https://doi.org/10.1038/s41598-024-07260-x