Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety of C. pecorum molecular studies, to date, only four complete and 16 draft genomes have been published. Of those, only five draft genomes are from koalas. Here, using whole-genome sequencing and a comparative genomics approach, we describe the first two complete C. pecorum genomes collected from diseased koalas. A de novo assembly of DBDeUG_2018 and MC/MarsBar_2018 resolved the chromosomes and chlamydial plasmids each as single, circular contigs. Robust phylogenomic analyses indicate biogeographical separation between strains from northern and southern koala populations, and between strains infecting koala and livestock hosts. Comparative genomics between koala strains identified new, unique, and shared loci that accumulate single-nucleotide polymorphisms and separate between northern and southern, and within northern koala strains. Furthermore, we predicted novel type III secretion system effectors. This investigation constitutes a comprehensive genome-wide comparison between C. pecorum from koalas and provides improvements to annotations of a C. pecorum reference genome. These findings lay the foundations for identifying and understanding host specificity and adaptation behind chlamydial infections affecting koalas.
Cryptococcosis, caused by environmental fungi in the Cryptococcus neoformans and Cryptococcus gattii species complexes, affects a variety of hosts, including koalas (Phascolarctos cinereus). Cryptococcal antigenemia and nasal colonization are well characterized in captive koalas, but free-ranging populations have not been studied systematically. Free-ranging koalas (181) from the Liverpool Plains region of New South Wales, Australia, were tested for cryptococcal antigenemia (lateral flow immunoassay) and nasal colonization (bird seed agar culture). Results were related to environmental and individual koala characteristics. Eucalypt trees (14) were also randomly tested for the presence of Cryptococcus spp. by bird seed agar culture. In sum, 5.5% (10/181) and 6.6% (12/181) of koalas were positive for antigenemia and nasal colonization, respectively, on at least one occasion. And 64.3% (9/14) of eucalypts were culture-positive for Cryptococcus spp. URA5 restriction fragment length polymorphism analysis identified most isolates as C. gattii VGI, while C. neoformans VNI was only found in one koala and one tree. Colonized koalas were significantly more likely to test positive for antigenemia. No associations between antigenemia or colonization, and external environmental characteristics (the relative abundance of Eucalyptus camaldulensis and season), or individual koala characteristics (body condition, sex, and age), could be established, suggesting that antigenemia and colonization are random outcomes of host-pathogen-environment interactions. The relationship between positive antigenemia status and a relatively high abundance of E. camaldulensis requires further investigation. This study characterizes cryptococcosis in a free-ranging koala population, expands the ecological niche of the C. gattii/C. neoformans species complexes and highlights free-ranging koalas as important sentinels for this disease.
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