The virulence of chlamydial infection in wild koalas is highly variable between individuals. Some koalas can be infected (PCR positive) with Chlamydia for long periods but remain asymptomatic, whereas others develop clinical disease. Chlamydia in the koala has traditionally been studied without regard to coinfection with other pathogens, although koalas are usually subject to infection with koala retrovirus (KoRV). Retroviruses can be immunosuppressive, and there is evidence of an immunosuppressive effect of KoRV in vitro. Originally thought to be a single endogenous strain, a new, potentially more virulent exogenous variant (KoRV-B) was recently reported. We hypothesized that KoRV-B might significantly alter chlamydial disease outcomes in koalas, presumably via immunosuppression. By studying sub-groups of Chlamydia and KoRV infected koalas in the wild, we found that neither total KoRV load (either viraemia or proviral copies per genome), nor chlamydial infection level or strain type, was significantly associated with chlamydial disease risk. However, PCR positivity with KoRV-B was significantly associated with chlamydial disease in koalas (p = 0.02961). This represents an example of a recently evolved virus variant that may be predisposing its host (the koala) to overt clinical disease when co-infected with an otherwise asymptomatic bacterial pathogen (Chlamydia).

Diseases associated with Chlamydia pecorum infection are a major cause of decline in koala populations in Australia. While koalas in care can generally be treated, a vaccine is considered the only option to effectively reduce the threat of infection and disease at the population level. In the current study, we vaccinated 30 free-ranging koalas with a prototype Chlamydia pecorum vaccine consisting of a recombinant chlamydial MOMP adjuvanted with an immune stimulating complex. An additional cohort of 30 animals did not receive any vaccine and acted as comparison controls. Animals accepted into this study were either uninfected (Chlamydia PCR negative) at time of initial vaccination, or infected (C. pecorum positive) at either urogenital (UGT) and/or ocular sites (Oc), but with no clinical signs of chlamydial disease. All koalas were vaccinated / sampled and then re-released into their natural habitat before re-capturing and re-sampling at 6 and 12 months. All vaccinated koalas produced a strong immune response to the vaccine, as indicated by high titres of specific plasma antibodies. The incidence of new infections in vaccinated koalas over the 12-month period post-vaccination was slightly less than koalas in the control group, however, this was not statistically significant. Importantly though, the vaccine was able to significantly reduce the infectious load in animals that were Chlamydia positive at the time of vaccination. This effect was evident at both the Oc and UGT sites and was stronger at 6 months than at 12 months post-vaccination. Finally, the vaccine was also able to reduce the number of animals that progressed to disease during the 12-month period. While the sample sizes were small (statistically speaking), results were nonetheless striking. This study highlights the potential for successful development of a Chlamydia vaccine for koalas in a wild setting.

Chlamydial disease continues to be one of the main factors threatening the long-term survival of the koala (Phascolarctos cinereus). Despite this, large epidemiological studies of chlamydial infection and disease in wild koala populations are lacking. A better understanding of the prevalence, transmission and pathogenesis is needed to improve control measures, such as the development of vaccines. We investigated the prevalence of Chlamydia pecorum infection and disease in 160 koalas in a peri-urban wild population in Queensland, Australia and found that 31% of koalas were Chlamydia PCR positive and 28% had clinically detectable chlamydial disease. Most infections were at the urogenital site (27%; both males and females) with only 14% at the ocular site. Interestingly, we found that 27% (4/15) of koalas considered to be sexually immature (9–13 months) were already infected with C. pecorum, suggesting that a significant percentage of animals are infected directly from their mother. Ocular infection levels were less prevalent with increasing age (8% in koalas older than 4 years), whereas the prevalence of urogenital tract infections remained high into older age (26% in koalas older than 4 years), suggesting that, after mother-to-young transmission, C. pecorum is predominantly a sexually transmitted infection. While 28% of koalas in this population had clinically detectable chlamydial disease (primarily urogenital tract disease), many PCR positive koalas had no detectable disease and importantly, not all diseased animals were PCR positive. We also observed higher chlamydial loads in koalas who were C. pecorum infected without clinical disease than in koalas who were C. pecorum infected with clinical disease. These results shed light on the potential mechanisms of transmission of C. pecorum in koalas and also guide future control measures, such as vaccination.

Southern hemisphere humpback whales undertake the longest migrations and associated periods of fasting of any mammal. Fluctuations in lipid energy stores are known to profoundly affect the toxicokinetics of lipophilic organochlorine compound (OC) burdens. Results from blubber biopsy sampling of adult, male humpback whales at two time points of the annual migration journey revealed dramatic concentration effects for the majority of OC compounds. The observed concentration effect was, however, not linear with measured average blubber lipid loss indicating significant redistribution of OCs and hence the importance of alternate lipid depots for meeting the energetic demands of the migration journey. Applying lipophilic OC burdens as novel tracers of whole-body lipid dynamics, the observed average concentration index suggests an average individual weight loss of 13% over 4 months of the migration journey. This value is based upon lipid derived energy and is in good agreement with previous weight prediction formulas. Notably, however, these estimates may greatly underestimate individual weight loss if significant protein catabolism occurs. Biomagnification factors between migrating southern hemisphere humpback whales and their principal prey item, Antarctic krill, closely resembled those of baleen whales feeding on herbivorous zooplankton in the Arctic. This study emphasizes the importance of considering prolonged periods of food deprivation when assessing chemical risks posed to wildlife. This is of particular importance for Polar biota adapted to extremes in ecosystem productivity.

BackgroundChlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics of C. pecorum strains from sheep, cattle and koalas has revealed that only single nucleotide polymorphisms (SNPs) and a limited number of pseudogenes appear to contribute to the genetic diversity of this pathogen. No chlamydial plasmid has been detected in these strains despite its ubiquitous presence in almost all other chlamydial species. Genomic analyses have not previously included C. pecorum from porcine hosts. We sequenced the genome of three C. pecorum isolates from pigs with differing pathologies in order to re-evaluate the genetic differences and to update the phylogenetic relationships between C. pecorum from each of the hosts.MethodsWhole genome sequences for the three porcine C. pecorum isolates (L1, L17 and L71) were acquired using C. pecorum-specific sequence capture probes with culture-independent methods, and assembled in CLC Genomics Workbench. The pairwise comparative genomic analyses of 16 pig, sheep, cattle and koala C. pecorum genomes were performed using several bioinformatics platforms, while the phylogenetic analyses of the core C. pecorum genomes were performed with predicted recombination regions removed. Following the detection of a C. pecorum plasmid, a newly developed C. pecorum-specific plasmid PCR screening assay was used to evaluate the plasmid distribution in 227 C. pecorum samples from pig, sheep, cattle and koala hosts.ResultsThree porcine C. pecorum genomes were sequenced using C. pecorum-specific sequence capture probes with culture-independent methods. Comparative genomics of the newly sequenced porcine C. pecorum genomes revealed an increased average number of SNP differences (~11 500) between porcine and sheep, cattle, and koala C. pecorum strains, compared to previous C. pecorum genome analyses. We also identified a third copy of the chlamydial cytotoxin gene, found only in porcine C. pecorum isolates. Phylogenetic analyses clustered porcine isolates into a distinct clade, highlighting the polyphyletic origin of C. pecorum in livestock.Most surprising, we also discovered a plasmid in the porcine C. pecorum genome. Using this novel C. pecorum plasmid (pCpec) sequence, a) we developed a pCpec screening assay to evaluate the plasmid distribution in C. pecorum from different hosts; and b) to characterise the pCpec sequences from available previously sequenced C. pecorum genome data. pCpec screening showed that the pCpec is common in all hosts of C. pecorum, however not all C. pecorum strains carry pCpec.ConclusionsThis study provides further insight into the complexity of C. pecorum epidemiology and novel genomic regions that may be linked to host specificity. C. pecorum plasmid characterisation may aid in improving our understanding of C. pecorum pathogenesis across the variety of host species this animal pathogen infects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2053-8) contains supplementary material, which is...

Southern hemisphere humpback whales (Megaptera novaeangliae) rely on summer prey abundance of Antarctic krill (Euphausia superba) to fuel one of the longest‐known mammalian migrations on the planet. It is hypothesized that this species, already adapted to endure metabolic extremes, will be one of the first Antarctic consumers to show measurable physiological change in response to fluctuating prey availability in a changing climate; and as such, a powerful sentinel candidate for the Antarctic sea‐ice ecosystem. Here, we targeted the sentinel parameters of humpback whale adiposity and diet, using novel, as well as established, chemical and biochemical markers, and assembled a time trend spanning 8 years. We show the synchronous, inter‐annual oscillation of two measures of humpback whale adiposity with Southern Ocean environmental variables and climate indices. Furthermore, bulk stable isotope signatures provide clear indication of dietary compensation strategies, or a lower trophic level isotopic change, following years indicated as leaner years for the whales. The observed synchronicity of humpback whale adiposity and dietary markers, with climate patterns in the Southern Ocean, lends strength to the role of humpback whales as powerful Antarctic sea‐ice ecosystem sentinels. The work carries significant potential to reform current ecosystem surveillance in the Antarctic region.

The lipid and fatty acid (FA) composition of the outer blubber layer was characterized in 46 east Australian migrating humpback whales Megaptera novaeangliae. Samples were obtained at 2 time points of the annual migration, which occurs between Antarctic feeding grounds and low-latitude breeding grounds and is associated with a prolonged period of fasting. Blubber lipid composition was dominated by triacylglycerols in all individuals, and the FA profiles of both migration cohorts and sexes were dominated by monounsaturated fatty acids (MUFA). Results indicate that males primarily mobilise polyunsaturated fatty acids in response to migration and fasting, favouring the most readily utilisable FA as governed by their physicochemical properties. In comparison, females appear to initially mobilise short-chain (<18 carbons) MUFA stores, potentially to attend to dependent calves' thermoregulatory needs. Feeding ecology investigations suggested that humpback whales have a species-specific FA composition of their blubber, including a detectable influence of their diet. This study provides the first insight into lipid and FA profiles of Southern Hemisphere humpback whales. A comprehensive understanding of FA dynamics, especially during times of energy deficit, is essential for understanding the nutritional status of Southern Hemisphere humpback whales and thereby the risks posed by growing environmental threats including toxic and persistent lipophilic pollutants. KEY WORDS: Humpback whale · Megaptera novaeangliae · Biopsy sampling · Blubber · Fatty acid Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 471: [271][272][273][274][275][276][277][278][279][280][281] 2012 files can provide further information regarding thermoregulatory and insulating properties of the tissue as well as complement toxicokinetic investigations of lipophilic pollutants, the movement of which are governed by lipid dynamics (Strandberg et al. 2008(Strandberg et al. , 2011. Most recently, FA regression models have been employed as a novel non-lethal method of age estimation in certain populations of large biopsied cetaceans (Herman et al. 2008(Herman et al. , 2009.Marine mammal blubber is dynamic in nature and significantly influenced by nutritional condition (Budge et al. 2006). In times of low food availability, animals mobilise stored blubber FA to provide metabolic fuel. Conversely, animals deposit FA when energy intake exceeds demands. FA metabolism at times of energy deficit is not well understood in marine mammals, especially in large baleen whales, although there is evidence to suggest that in some species it is a selective and/or temporal process (Raclot 2003, Wheatley et al. 2008). To better understand the lipid dynamics of Southern Hemisphere humpback whales Megaptera novaeangliae, we focused this study on the east Australian migrating population (E1, as designated by the International Whaling Commission, 1999).Southern Hemisphere humpback whales have adapted to the productivity e...

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