Understanding the zoonotic pathogen, Coxiella burnetii in Australian fur seal breeding colonies through environmental DNA and genotyping

Abstract

Context Coxiella burnetii is suspected as a novel pathogen contributing to decreased pup production in Australian fur seals (Arctocephalus pusillus doriferus). It has recently been described from a single breeding colony in Bass Strait, has previously been associated with two decreasing populations of northern hemisphere pinnipeds and is a known reproductive pathogen. Data around its disease ecology in marine mammals are sparse. Aims To determine whether environmental DNA (eDNA) can be used to survey for C. burnetii in Australian fur seal breeding colonies. To determine whether C. burnetii in Australian fur seals is the same genotype as terrestrial Australian C. burnetii. Methods Soil samples were collected from Kanowna Island and Seal Rocks. Placental samples were collected from Kanowna Island. Soil was evaluated for eDNA using a quantitative polymerase chain reaction (qPCR) for com1 gene. Placental samples were evaluated with com1, htpAB and IS1111 markers. Multiple-locus variable number of tandem repeats analysis for three microsatellite loci (ms-24, ms-28 and ms-33) was used to determine relatedness to Australian C. burnetii genotypes. Key results eDNA results varied between pre-and post-pupping at Seal Rocks. When targeting the com1 gene, the post-pupping prevalence at Kanowna Island and Seal Rocks was 59.6% and 90%, respectively. eDNA PCR inhibition of samples was low at 1.9%. There was very poor, sporadic to absent IS1111 amplification in placental samples. The com1 and htpAB qPCRs had an overall prevalence across placental samples of 39.2% and 56.7% respectively. In 90.1% of placental samples (n = 11), the ms-28 locus amplified. Neither ms-24 nor ms-33 amplified. Conclusions eDNA is an effective tool to survey Australian fur seal breeding colonies in the post-pupping period for C. burnetii. The prevalence appears to be much higher in the Seal Rocks colony than in the Kanowna Island colony. It appears that this is not a terrestrial Australian genotype but rather closely related to genotypes detected in marine mammals in the northern hemisphere. Implications This research significantly expands our ability to survey for C. burnetii in Australian fur seals and other marine mammals. It highlights knowledge gaps in our understanding of the disease ecology and phylogeny of C. burnetii in marine mammals.