The Australian fur seal (Arctocephalus pusillus doriferus) has experienced a slower than expected population recovery since the end of the commercial sealing era, with a high third trimester abortion rate. There is currently no known proximate cause. Coxiella burnetii (Cb) is a well-known cause of abortion in domestic and wildlife species and an important zoonotic pathogen. It has been recorded from a small number of northern hemisphere marine mammals and may be a potential contributory factor to decreasing populations of northern fur seals (Callorhinus ursinus) and Steller sealions (Eumetopias jubatus). It has not been recorded from marine mammals in the southern hemisphere but is well documented in ruminants and wildlife in Australia as a cause of reproductive failure. Third trimester aborted fetuses (n = 46) and full-term placentas (n = 66) from Australian fur seals, were collected on Kanowna Island and Seal Rocks in Bass Strait, south-eastern Australia. Utilizing routine hematoxylin and eosin histopathology, Cb immunohistochemistry and two different qPCR targets–htpAB and com1, Cb was identified. Routine histopathology and immunohistochemistry were insensitive for the detection of Cb. The detected Cb prevalence ranged from 10.6% for com1 up to 40.9% with htpAB. Coxiella burnetti was readily detected in full-term placentas but in aborted fetal material only in a single placenta associated with a still birth. The exact significance is currently unclear, but this highlights that Cb is present in Australian fur seals, breeding in Bass Strait. Bass Strait is in one of the world’s fastest warming oceanic regions and marine mammals breeding in the area are likely to be key indicators of marine ecosystem stressors. This first description of Cb in a marine mammal from the southern hemisphere, highlights the need to further investigate the potential risks this pathogen poses to Australian fur seals and sympatric marine mammals. Additionally, it is important to determine the zoonotic risk of this pathogen to persons working with, and in proximity of, Australian fur seal breeding colonies.

The obligate intracellular bacterial pathogen Coxiella burnetii has been identified in a few species of marine mammals, some of which are showing population declines. It has been hypothesized that C. burnetii in marine mammals is a distinct genotype that varies significantly from the typical terrestrial genotypes. It appears to lack an IS1111. Isolates originating from Australian marine animals have a distinctly non-Australian profile of multiple-locus variable-number tandem-repeat analysis (MLVA). Extracted Coxiella DNA of Australian fur seal placental origin was sequenced using the Novaseq platform. Illumina 150 bp paired-end reads were filtered and trimmed with Trimgalore. The microbial community present in the sequenced genome was evaluated with Kraken and Bracken software using the NCBI database. A phylogenetic analysis was performed using 1131 core genes. Core genes were identified using Panaroo and inputted into Iqtree to determine the maximum-likelihood tree. A second phylogenetic tree was created using Rickettsiella grylii and using seven housekeeping genes. Results were compared with the C. burnetii Nine Mile RSA439 virulent genome. This new Australian marine mammal isolate of Coxiella (PG457) appears to be a novel genotype that lacks IS1111 and has a distinct MLVA signature (ms26, ms27, ms28, ms30, and ms31). The presence of genes for multiple virulence factors appears to give this genotype sufficient pathogenicity for it to be considered a possible causative agent of abortion in Australian fur seals as well as a potential zoonotic risk.

Recently, Coxiella burnetii has been described as a novel pathogen potentially contributing to decreased pup production in Australian fur seals (AusFS, Arctocephalus pusillus doriferus). Pacific gulls (PGs, Larus pacificus) are known to scavenge AusFS placental material during the fur seal breeding season. It is hypothesized that PGs may act as vectors for this pathogen. In the present study, cloacal swabs, oral swabs and serum were collected from PGs on Kanowna Island (KI, an AusFS breeding colony) and a nearby island, Seal Island (SI), not occupied by pinnipeds. All sample sets were evaluated with qPCR for the com1, htpAB and IS1111 markers. Most oral and cloacal swabs from KI tested positive on both the com1 (94.1%; 88.2%) and htpAB targets (76.5%; 76.5%). Amplification was very low from the SI oral swabs and cloacal swabs. Only the KI serum samples had amplification (17.7% for both com1 and htpAB). There was no IS1111 amplification in either colony. The results demonstrate that PGs can potentially act as vectors for the spread of C. burnetii. In some birds, C. burnetii was detectable in the serum, indicating that gulls can experience bacteraemia. It appears that different feeding strategies in the same species within the same ecosystem can have profound effects on the prevalence of pathogens. Further studies are required to better understand the epidemiology and potential risks of this organism.

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.

Anaesthesia in pinnipeds is considered a much higher risk than in most terrestrial mammals because of their frequent proximity to water and physiological and anatomical adaptations related to diving, which also influence their anaesthesia management. Anaesthetising and immobilising entangled seals does not allow for selection of animals that are at a safe distance from the water’s edge. Medetomidine-midazolam-butorphanol (MMB) sedation was trialled on eight entangled Cape fur seals (CFS) (Arctocephalus pusillus pusillus) to determine if it was safe to use on animals that entered the water post-darting. The MMB was given at an estimated dose of 0.03 mg/kg, 0.2 mg/kg and 0.2 mg/kg, respectively, via remote darting. Sedation was reversed with intramuscular atipamezole (0.15 mg/kg) and naltrexone (0.4 mg/kg) to antagonise the effects of medetomidine and butorphanol, respectively. Moderate sedation was achieved in six animals. Six of the animals entered the water after being darted. There was a single mortality and a single animal that was too lightly sedated for capture. The preliminary results indicate that MMB produces suitable sedation for disentanglement of CFS. Additionally, MMB might be suitable for application to field-based biological research.