Microbiota composition of the koala (Phascolarctos cinereus) ocular and urogenital sites, and their association with Chlamydia infection and disease

Carriage of antibiotic resistance genes to treatments for chlamydial disease in koalas (Phascolarctos cinereus): A comparison of occurrence before and during catastrophic wildfires

Growing reports of diverse antibiotic resistance genes in wildlife species around the world symbolises the extent of this global One Health issue. The health of wildlife is threatened by antimicrobial resistance in situations where wildlife species develop disease and require antibiotics. Chlamydial disease is a key threat for koalas in Australia, with infected koalas frequently entering wildlife hospitals and requiring antibiotic therapy, typically with chloramphenicol or doxycycline. This study investigated the occurrence and diversity of target chloramphenicol and doxycycline resistance genes (cat and tet respectively) in koala urogenital and faecal microbiomes. DNA was extracted from 394 urogenital swabs and 91 faecal swabs collected from koalas in mainland Australia and on Kangaroo Island (KI) located 14 km off the mainland, before (n = 145) and during (n = 340) the 2019-2020 wildfires. PCR screening and DNA sequencing determined 9.9% of samples (95%CI: 7.5% to 12.9%) carried cat and/or tet genes, with the highest frequency in fire-affected KI koalas (16.8%) and the lowest in wild KI koalas sampled prior to fires (6.5%). The diversity of cat and tet was greater in fire-affected koalas (seven variants detected), compared to pre-fire koalas (two variants detected). Fire-affected koalas in care that received antibiotics had a significantly higher proportion (p < 0.05) of cat and/or tet genes (37.5%) compared to koalas that did not receive antibiotics (9.8%). Of the cat and/or tet positive mainland koalas, 50.0% were Chlamydia-positive by qPCR test. Chloramphenicol and doxycycline resistance genes in koala microbiomes may contribute to negative treatment outcomes for koalas receiving anti-chlamydial antibiotics. Thus a secondary outcome of wildfires is increased risk of acquisition of cat and tet genes in fire-affected koalas that enter care, potentially exacerbating the already significant threat of chlamydial disease on Australia's koalas. This study highlights the importance of considering impacts to wildlife health within the One Health approach to AMR and identifies a need for greater understanding of AMR ecology in wildlife.

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality

BACKGROUND

Captive koala breeding programmes are essential for long-term species management. However, breeding efficacy is frequently impacted by high neonatal mortality rates in otherwise healthy females. Loss of pouch young typically occurs during early lactation without prior complications during parturition and is often attributed to bacterial infection. While these infections are thought to originate from the maternal pouch, little is known about the microbial composition of koala pouches. As such, we characterised the koala pouch microbiome across the reproductive cycle and identified bacteria associated with mortality in a cohort of 39 captive animals housed at two facilities.

RESULTS

Using 16S rRNA gene amplicon sequencing, we observed significant changes in pouch bacterial composition and diversity between reproductive time points, with the lowest diversity observed following parturition (Shannon entropy - 2.46). Of the 39 koalas initially sampled, 17 were successfully bred, after which seven animals lost pouch young (overall mortality rate - 41.18%). Compared to successful breeder pouches, which were largely dominated by Muribaculaceae (phylum - Bacteroidetes), unsuccessful breeder pouches exhibited persistent Enterobacteriaceae (phylum - Proteobacteria) dominance from early lactation until mortality occurred. We identified two species, Pluralibacter gergoviae and Klebsiella pneumoniae, which were associated with poor reproductive outcomes. In vitro antibiotic susceptibility testing identified resistance in both isolates to several antibiotics commonly used in koalas, with the former being multidrug resistant.

CONCLUSIONS

This study represents the first cultivation-independent characterisation of the koala pouch microbiota, and the first such investigation in marsupials associated with reproductive outcomes. Overall, our findings provide evidence that overgrowth of pathogenic organisms in the pouch during early development is associated with neonatal mortality in captive koalas. Our identification of previously unreported, multidrug resistant P. gergoviae strains linked to mortality also underscores the need for improved screening and monitoring procedures aimed at minimising neonatal mortality in future. Video Abstract.

How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore

BACKGROUND

The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing.

RESULTS

Across the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives.

CONCLUSIONS

Our data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.

Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities

Enthusiasm for research describing microbial communities using next-generation sequencing (NGS) has outpaced efforts to standardize methodology. Without consistency in the way research is carried out in this field, the comparison of data between studies is near impossible and the utility of results remains limited. This holds true for bacterial microbiome research of the ocular surface, and other sites, in both humans and animals. In addition, the ocular surface remains under-explored when compared to other mucosal sites. Low bacterial biomass samples from the ocular surface lead to further technical challenges. Taken together, two major problems were identified: (1) Normalization of the workflow in studies utilizing NGS to investigate the ocular surface bacteriome is necessary in order to propel the field forward and improve research impact through cross-study comparisons. (2) Current microbiome profiling technology was developed for high bacterial biomass samples (such as feces or soil), posing a challenge for analyses of samples with low bacterial load such as the ocular surface. This article reviews the challenges and limitations currently facing ocular microbiome research and provides recommendations for minimum reporting standards for veterinary ophthalmologists and clinician scientists to limit inter-study variation, improve reproducibility, and ultimately render results from these studies more impactful. The move toward normalization of methodology will expedite and maximize the potential for microbiome research to translate into meaningful discovery and tangible clinical applications.

A 29-year retrospective analysis of koala rescues in New South Wales, Australia

The koala (Phascolarctos cinereus) is currently listed by both the IUCN and the Australian Governments' Threatened Species Scientific Committee as vulnerable to extinction with an overall decreasing population trend. It is unknown exactly how many koalas remain in the wild, but it is known that habitat fragmentation and bushfires have ultimately contributed to the decline of the koala all over Australia. This novel study is a retrospective analysis of data over a 29-year period (1989-2018) using records for 12,543 sightings and clinical care admissions for wild koalas from the major koala hot-spots (Port Stephens, port Macquarie and Lismore) in New South Wales, Australia. This study aims to understand the long-term patterns and trends of key stressors that are contributing to the decline of koalas in New South Wales, and the synergic interactions of factors such as rescue location, sex and age of the koala, and if their decline is influenced progressively by year. The main findings of this retrospective analysis indicated that between all 3 rescue sites, the most common prognosis was disease, the most common disease was signs of chlamydia, and the most common outcome was release. The location where the highest number of koalas were found prior to being reported as sighted or admitted into clinical care was within the regional area of Lismore. Furthermore, sex was not a discriminating factor when it came to prognosis or outcome, but age was significant. Finally, incidents of disease were found to increase over long-term, whereas release decreased over time and euthanasia increased. The wealth of data available to us and the retrospective analysis enabled us in a way to 'zoom out' and reveal how the key environmental stressors have fluctuated spatially and temporally. In conclusion, our data provides strong evidence of added pressures of increased human population growth in metropolitan zones, which increases risks of acute environmental trauma and proximate stressors such as vehicle collisions and dog-attacks as well as increased sightings of virtually healthy koalas found in exposed environments. Thus our 'zoom out' approach provides support that there is an urgent need to strengthen on-ground management, bushfire control regimes, environmental planning and governmental policy actions that should hopefully reduce the proximate environmental stressors in a step wise approach. This will ensure that in the next decade (beyond 2020), NSW koalas will hopefully start to show reversed trends and patterns in exposure to environmental trauma and disease, and population numbers will return towards recovery and stability.

Polyphasic Characterisation of Cedecea colo sp. nov., a New Enteric Bacterium Isolated from the Koala Hindgut

The Cedecea genus is comprised of six rarely isolated species within the Enterobacteriaceae family. Representatives are Gram-negative motile bacilli, and are typically oxidase-negative, lipase-positive and resistant to colistin and cephalothin. In this study, a putative novel Cedecea species (designated strain ZA_0188T), isolated from the koala hindgut, was characterised using a polyphasic taxonomic approach. Maximum average nucleotide identity (ANI) and 16S ribosomal RNA (rRNA) similarity scores well below thresholds of species demarcation were reported, at 81.1% and 97.9%, respectively. Multilocus phylogenetic analysis indicated strain ZA_0188T was most similar to but divergent from recognised Cedecea species. The isolate's genomic G+C content was determined as 53.0 mol%, >1% lower than previously reported in Cedecea. Phenotypically, strain ZA_0188T was distinct from recognised Cedecea species such as colistin- and cephalothin-sensitive, lipase-, sorbitol-, sucrose-, and Voges-Proskauer-negative, and melibiose-, arabinose-, arginine-, and rhamnose-positive. In preliminary experiments, strain ZA_0188T exhibited cellulase activity and high-level tolerance to eucalyptus oil compared to other enteric species surveyed. Collectively, these findings suggest that strain ZA_0188T represents a novel enteric species, for which the name Cedecea colo is proposed.

Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: Identification and modelling of a population free from infection

Chlamydia pecorum is an established and prevalent infection that produces severe clinical disease in many koala populations, contributing to dramatic population declines. In wild South Australian koala populations, C. pecorum occurrence and distribution is unknown. Here, C. pecorum-specific real-time quantitative PCR (qPCR) was applied to ocular and urogenital swabs from targeted surveys of wild koalas from the mainland Mount Lofty Ranges (MLR) (n = 75) and Kangaroo Island (KI) (n = 170) populations. Historical data from 13,081 KI koalas (1997–2018) provided additional evidence for assessing the absence of C. pecorum infection. In the MLR population, 46.7% (CI: 35.1–58.6%) of koalas were C. pecorum positive by qPCR but only 4% had grade 3 clinical disease. MLR koala fertility was significantly reduced by C. pecorum infection; all reproductively active females (n = 16) were C. pecorum negative, whereas 85.2% of inactive females (n = 23) were positive (P < 0.001). KI koalas were C. pecorum negative and the population was demonstrated to be free of C. pecorum infection with 95% confidence. C. pecorum is a real threat for the sustainability of the koala and KI is possibly the last isolated, large C. pecorum-free population remaining in Australia. These koalas could provide a safeguard against this serious disease threat to an iconic Australian species.

Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population

OBJECTIVE

To characterize the bacterial community residing on the conjunctiva of clinically healthy dogs.

METHODS

Bacterial DNA from conjunctival swabs of 10 dogs with normal ocular examinations (both OD and OS, n = 20) was extracted, and 16S rRNA amplicons were sequenced using Illumina MiSeq 600. Resulting data were subjected to quality control steps, and analyzed for bacterial community richness and diversity, within- and between-group dissimilarity, and relative taxonomic composition.

RESULTS

High-quality reads (2.22 million bp) resulted in a mean of 159 068 sequences per sample. Bacterial community evenness and diversity was high when compared to other species, and did not significantly differ when samples were grouped by dogs or eyes. As expected, within-dog samples were more similar than between-dog samples. Taxonomic classification revealed that >95% of the community consisted of Firmicutes (34.9 ± 8.8%), Actinobacteria (26.3 ± 7.1%), Proteobacteria (26.2 ± 6.6%), and Bacteroidetes (9.4 ± 2.4%). Key members of the dog ocular surface microbiome, found in all dogs and corresponding to >25% of all identified OTUs (operational taxonomic units), were part of the Bifidobacteriaceae, Lachnospiraceae, Moraxellaceae, Corynebacteriaceae families. Genera previously thought to account for the majority of the core ocular surface microbiome in the dog (Staphylococcus sp., Streptococcus sp., and Bacillus sp.) were associated with only 2.63% of overall reads.

CONCLUSIONS

This study shows the feasibility of conjunctival swabs and high-throughput sequencing to profile the bacterial community structure of the canine ocular surface. A core ocular surface microbiome was identified for this canine population.

Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll

The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal.

The relative contribution of causal factors in the transition from infection to clinical chlamydial disease

Chlamydia is a major bacterial pathogen in humans and animals globally. Yet 80% of infections never progress to clinical disease. Decades of research have generated an interconnected network linking pathogen, host, and environmental factors to disease expression, but the relative importance of these and whether they account for disease progression remains unknown. To address this, we used structural equation modeling to evaluate putative factors likely to contribute to urogenital and ocular chlamydial disease in the koala (Phascolarctos cinereus). These factors include Chlamydia detection, load, and ompA genotype; urogenital and ocular microbiomes; host sex, age, weight, body condition; breading season, time of year; location; retrovirus co-infection; and major histocompatibility complex class II (MHCII) alleles. We show different microbiological processes underpin disease progression at urogenital and ocular sites. From each category of factors, urogenital disease was most strongly predicted by chlamydial PCR detection and load, koala body condition and environmental location. In contrast, ocular disease was most strongly predicted by phylum-level Chlamydiae microbiome proportions, sampling during breeding season and co-infection with koala retrovirus subtype B. Host MHCII alleles also contributed predictive power to both disease models. Our results also show considerable uncertainty remains, suggesting major causal mechanisms are yet to be discovered.

Detection of Chlamydiaceae and Chlamydia-like organisms on the ocular surface of children and adults from a trachoma-endemic region

Trachoma, the leading infectious cause of blindness, is caused by Chlamydia trachomatis (Ct), a bacterium of the phylum Chlamydiae. Recent investigations revealed the existence of additional families within the phylum Chlamydiae, also termed Chlamydia-like organisms (CLOs). In this study, the frequency of Ct and CLOs was examined in the eyes of healthy Sudanese (control) participants and those with trachoma (case). We tested 96 children (54 cases and 42 controls) and 93 adults (51 cases and 42 controls) using broad-range Chlamydiae and Ct-specific (omcB) real-time PCR. Samples positive by broad-range Chlamydiae testing were subjected to DNA sequencing. Overall Chlamydiae prevalence was 36%. Sequences corresponded to unclassified and classified Chlamydiae. Ct infection rate was significantly higher in children (31.5%) compared to adults (0%) with trachoma (p < 0.0001). In general, 21.5% of adults and 4.2% of children tested positive for CLOs (p = 0.0003). Our findings are consistent with previous investigations describing the central role of Ct in trachoma among children. This is the first study examining human eyes for the presence of CLOs. We found an age-dependent distribution of CLO DNA in human eyes with significantly higher positivity in adults. Further studies are needed to understand the impact of CLOs in trachoma pathogenicity and/or protection.

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without 'wet bottom'

Koalas (Phascolarctos cinereus) are iconic Australian marsupials currently threatened by several processes, including infectious diseases and ecological disruption. Infection with Chlamydia pecorum, is considered a key driver of population decline. The clinical sign of 'wet bottom', a staining of the rump associated with urinary incontinence, is often caused by chlamydial urinary tract infections. However, wet bottom has been recorded in koalas free of C. pecorum, suggesting other causative agents in those individuals. We used 16S rRNA diversity profiling to investigate the microbiome of the urogenital tract of ten female koalas in order to identify potential causative agents of wet bottom, other than C. pecorum. Five urogenital samples were processed from koalas presenting with wet bottom and five were clinically normal. All koalas were negative for C. pecorum infection. We detected thirteen phyla across the ten samples, with Firmicutes occurring at the highest relative abundance (77.6%). The order Lactobacillales, within the Firmicutes, comprised 70.3% of the reads from all samples. After normalising reads using DESeq2 and testing for significant differences (P < 0.05), there were 25 operational taxonomic units (OTUs) more commonly found in one group over the other. The families Aerococcaceae and Tissierellaceae both had four significantly differentially abundant OTUs. These four Tissierellaceae OTUs were all significantly more abundant in koalas with wet bottom. This study provides the foundation for future investigations of causes of koala wet bottom, other than C. pecorum infection. This is of clinical relevance as wet bottom is often assumed to be caused by C. pecorum and treated accordingly. Our research highlights that other organisms may be causing wet bottom, and these potential aetiological agents need to be further investigated to fully address the problems this species faces.