Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum

Molecular detection of Chlamydia psittaci in birds: a systematic review

Molecular methods are currently the most sensitive for detecting Chlamydia psittaci in birds. Most laboratories have developed their own molecular assays or adapted published protocols, often making slight modifications to fit their specific study purposes. The sensitivity and specificity of a molecular test depend on the target gene, primer sequences, types of molecular test, DNA extraction method, and sampling methods. We reviewed 120 articles published between 2000 and 2020 to compile information on the molecular detection of C. psittaci in birds. Of the ten genomic targets currently available to detect C. psittaci in birds, the ompA gene was the most widely used. In published surveillance studies, of the fourteen molecular test types, conventional PCR and quantitative PCR were applied the most. A testing strategy using a hierarchical approach that includes molecular tests of genus- and species-specific targets is recommended to detect other avian chlamydial species besides the well-recognized C. psittaci. Samples should be sourced from both the respiratory and gastrointestinal tracts whenever possible for better accuracy. High-quality DNA can be obtained when the sample is preserved in optimal medium and temperature, and an optimized DNA extraction protocol is applied. Standardization and validation of molecular Chlamydia tests are needed to enhance the comparability and reliability of assays to detect C. psittaci and other chlamydiae species in birds.RESEARCH HIGHLIGHTSHierarchical molecular testing is recommended for the detection of avian C. psittaci.Key molecular tests for surveillance were conventional PCR and quantitative PCR.The most used genomic target to detect C. psittaci in birds was the ompA gene.

Chlamydia psittaci: A zoonotic pathogen causing avian chlamydiosis and psittacosis

Chlamydia psittaci is an obligate intracellular gram-negative bacterium with a unique biphasic developmental cycle. It is a zoonotic pathogen with a wide range of hosts and can cause avian chlamydiosis in birds and psittacosis in humans. The pathogen is transmitted mainly through horizontal transmission between birds. Cross-species transmission sometimes occurs and human-to-human transmission has recently been confirmed. This review provides an updated overview of C. psittaci from the perspective of both avian chlamydiosis and psittacosis. We include the aspects of genotype, host-pathogen interaction, transmission, epidemiology, detection and diagnosis, clinical manifestation, management, and prevention, aiming to provide a basic understanding of C. psittaci and offer fresh insights focused on zoonosis and cross-species transmission.

Koala ocular disease grades are defined by chlamydial load changes and increases in Th2 immune responses

Introduction

This study employs bulk RNA sequencing, PCR, and ELISA assays to analyze the pathological factors affecting the outcomes of C. pecorum ocular infections in koalas. It investigates the immune responses and gene expression profiles associated with various stages of koala ocular chlamydiosis.

Methods

A cohort of 114 koalas from Queensland, Australia were assessed, with 47% displaying clinical signs of ocular disease. Animals were classified into three cohorts: acute active disease (G1), chronic active disease (G2), and chronic inactive disease (G3), along with subclinical Chlamydia pecorum positive (H2) and healthy (H1) cohorts.

Results

Analysis of clinical, microbiological, humoral immune and cellular immune biomarkers revealed varying chlamydial loads and anti-chlamydial IgG levels across disease grades, with a negative correlation observed between ocular chlamydial load and anti-chlamydial IgG. Koala ocular mucosa gene expression analysis from 27 koalas identified shared expression pathways across disease cohorts, with a significant upregulation of IFNγ expression and tryptophan metabolism in all disease stages.

Discussion

These findings help elucidate immune response dynamics and molecular pathways underlying koala ocular chlamydiosis, providing insights crucial for disease management strategies.

The Utility of the Koala Scat: A Scoping Review

The use of samples or scats to provide important ecological, genetic, disease and physiology details on free-range populations is gaining popularity as an alternative non-invasive methodology. Koala populations in SE Queensland and NSW have recently been listed as endangered and continue to face anthropomorphic and stochastic environmental impacts that could potentially lead to their extinction. This scoping review examines the current and potential utility of the koala scat to contribute data relevant to the assessment of koala conservation status and decision making. Although we demonstrate that there is great potential for this methodology in providing details for both individual wild animal and population biology (distribution, abundance, sex ratio, immigration/emigration, genetic diversity, evolutionary significant unit, disease epidemiology, nutrition, reproductive status and stress physiology), the calibre of this information is likely to be a function of the quality of the scat that is sampled.

Rapid visual detection of the allergen Dermatophagoides farinae in house dust by loop-mediated isothermal amplification

Dermatophagoides farinae is considered to be an important factor causing some allergic diseases, such as urticaria, allergic rhinitis, asthma, and other interrelated diseases. Avoiding exposure to allergens is the most effective way to reduce allergic reactions. In this study, we successfully established a loop-mediated isothermal amplification (LAMP) method for the detection of D. farinae DNA target internal transcribed spacer (ITS) and D. farinae 1 allergen (Der f 1) genes. The turbidity-monitoring system and visual fluorescent reagents were used to verify the test results of LAMP assay. Following optimization of the primers and reaction temperatures, the amplification sensitivity, specificity, and efficiency of the method for detecting D. farinae were assessed. There was no cross-reaction with other arthropod species that are commonly found in indoor environmental dust, such as Dermatophagoides pteronyssinus, Alophagoides ovatus, Periplaneta americana, Anopheles sinensis, and Musca domestica. Furthermore, the sensitivity of LAMP assay for detecting D. farinae DNA was 10 times greater than that of conventional PCR. The positive detection rate by the LAMP method was greater than the conventional PCR for both single D. farinae mites and D. farinae mites in indoor dust. A new type of LAMP method for D. farinae based on the Der f 1 and ITS genes was, therefore, successfully established. This study is the first time to detect the D. farinae allergen using LAMP assay. This assay could be useful as a model for the rapid detection of allergens produced by other house dust mites in the future.

Development of diagnostic and point of care assays for a gammaherpesvirus infecting koalas

The recent listing of koala populations as endangered across much of their range has highlighted the need for better management interventions. Disease is a key threat to koala populations but currently there is no information across the threatened populations on the distribution or impact of a gammaherpesvirus, phascolarctid gammaherpesvirus 1 (PhaHV-1). PhaHV-1 is known to infect koalas in southern populations which are, at present, not threatened. Current testing for PhaHV-1 involves lengthy laboratory techniques that do not permit quantification of viral load. In order to better understand distribution, prevalence and impacts of PhaHV-1 infections across koala populations, diagnostic and rapid point of care tests are required. We have developed two novel assays, a qPCR assay and an isothermal assay, that will enable researchers, clinicians and wildlife managers to reliably and rapidly test for PhaHV-1 in koalas. The ability to rapidly diagnose and quantify viral load will aid quarantine practices, inform translocation management and guide research into the clinical significance and impacts of PhaHV-1 infection in koalas.

A targeted approach to investigating immune genes of an iconic Australian marsupial

Disease is a contributing factor to the decline of wildlife populations across the globe. Koalas, iconic yet declining Australian marsupials, are predominantly impacted by two pathogens, Chlamydia and koala retrovirus. Chlamydia is an obligate intracellular bacterium and one of the most widespread sexually transmitted infections in humans worldwide. In koalas, Chlamydia infections can present as asymptomatic or can cause a range of ocular and urogenital disease signs, such as conjunctivitis, cystitis and infertility. In this study, we looked at differences in response to Chlamydia in two northern populations of koalas using a targeted gene sequencing of 1209 immune genes in addition to genome‐wide reduced representation data. We identified two MHC Class I genes associated with Chlamydia disease progression as well as 25 single nucleotide polymorphisms across 17 genes that were associated with resolution of Chlamydia infection. These genes are involved in the innate immune response (TLR5) and defence (TLR5, IFNγ, SERPINE1, STAT2 and STX4). This study deepens our understanding of the role that genetics plays in disease progression in koalas and leads into future work that will use whole genome resequencing of a larger sample set to investigate in greater detail regions identified in this study. Elucidation of the role of host genetics in disease progression and resolution in koalas will directly contribute to better design of Chlamydia vaccines and management of koala populations which have recently been listed as “endangered.”

Real-Time Fluorometric Isothermal LAMP Assay for Detection of Chlamydia pecorum in Rapidly Processed Ovine Abortion Samples: A Veterinary Practitioner's Perspective

Traditional methods of detecting Chlamydia pecorum in tissue samples such as polymerase chain reaction or cell culture are laborious and costly. We evaluated the use of a previously developed C. pecorum LAMP assay using minimally processed ovine samples. Cotyledon (n = 16), foetal liver (n = 22), foetal lung (n = 2), and vaginal (n = 6) swabs, in addition to cotyledon (n = 6) and foetal liver (n = 8) tissue samples, were rapidly processed and used for LAMP testing without DNA extraction. Overall, LAMP test results were highly congruent with the in-house reference qPCR, with 80.43% (37/46; 72.73% positive agreement (PA); 84.75% negative agreement (NA)) overall agreeance for swab samples, and 85.71% (12/14; 80% PA; 88.89% NA) overall agreeance for tissue samples. Out of the 11 total discrepant results, discrepancy was mainly observed in samples (n = 10) with less than 100 copies/µL C. pecorum DNA. While sensitivity could be improved, the simplicity, low cost, and accuracy of detection makes this test amenable for use at point-of-care for detecting C. pecorum in sheep.

Real-time fluorometric and end-point colorimetric isothermal assays for detection of equine pathogens C. psittaci and equine herpes virus 1: validation, comparison and application at the point of care

Background

C. psittaci has recently emerged as an equine abortigenic pathogen causing significant losses to the Australian Thoroughbred industry, while Equine herpesvirus-1 (EHV-1) is a well-recognized abortigenic agent. Diagnosis of these agents is based on molecular assays in diagnostic laboratories.

In this study, we validated C. psittaci and newly developed EHV-1 Loop Mediated Isothermal Amplification (LAMP) assays performed in a real-time fluorometer (rtLAMP) against the reference diagnostic assays. We also evaluated isothermal amplification using commercially available colorimetric mix (cLAMP), and SYBR Green DNA binding dye (sgLAMP) for “naked eye” end-point detection when testing ‘real-world’ clinical samples. Finally, we applied the C. psittaci LAMP assays in two pilot Point-of-Care (POC) studies in an equine hospital.

Results

The analytical sensitivity of C. psittaci and EHV-1 rt-, and colorimetric LAMPs was determined as one and 10 genome equivalents per reaction, respectively. Compared to reference diagnostic qPCR assays, the C. psittaci rtLAMP showed sensitivity of 100%, specificity of 97.5, and 98.86% agreement, while EHV-1 rtLAMP showed 86.96% sensitivity, 100% specificity, and 91.43% agreement.

When testing rapidly processed clinical samples, all three C. psittaci rt-, c-, sg-LAMP assays were highly congruent with each other, with Kappa values of 0. 906 for sgLAMP and 0. 821 for cLAMP when compared to rtLAMP. EHV-1 testing also revealed high congruence between the assays, with Kappa values of 0.784 for cLAMP and 0.638 for sgLAMP when compared to rtLAMP. The congruence between LAMP assays and the C. psittaci or EHV-1 qPCR assays was high, with agreements ranging from 94.12 to 100% for C. psittaci, and 88.24 to 94.12% for EHV-1, respectively.

At the POC, the C. psittaci rt- and c-LAMP assays using rapidly processed swabs were performed by technicians with no prior molecular experience, and the overall congruence between the POC C. psittaci LAMPs and the qPCR assays ranged between 90.91–100%.

Conclusions

This study describes reliable POC options for the detection of the equine pathogens: C. psittaci and EHV-1. Testing ‘real-world’ samples in equine clinical setting, represents a proof-of-concept that POC isothermal diagnostics can be applied to rapid disease screening in the equine industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02986-8.

Chlamydia Psittaci ST24: Clonal Strains of One Health Importance Dominate in Australian Horse, Bird and Human Infections

Chlamydia psittaci is traditionally regarded as a globally distributed avian pathogen that can cause zoonotic spill-over. Molecular research has identified an extended global host range and significant genetic diversity. However, Australia has reported a reduced host range (avian, horse, and human) with a dominance of clonal strains, denoted ST24. To better understand the widespread of this strain type in Australia, multilocus sequence typing (MLST) and ompA genotyping were applied on samples from a range of hosts (avian, equine, marsupial, and bovine) from Australia. MLST confirms that clonal ST24 strains dominate infections of Australian psittacine and equine hosts (82/88; 93.18%). However, this study also found novel hosts (Australian white ibis, King parrots, racing pigeon, bovine, and a wallaby) and demonstrated that strain diversity does exist in Australia. The discovery of a C. psittaci novel strain (ST306) in a novel host, the Western brush wallaby, is the first detection in a marsupial. Analysis of the results of this study applied a multidisciplinary approach regarding Chlamydia infections, equine infectious disease, ecology, and One Health. Recommendations include an update for the descriptive framework of C. psittaci disease and cell biology work to inform pathogenicity and complement molecular epidemiology.

Undiagnosed Cases of Human Pneumonia Following Exposure to Chlamydia psittaci from an Infected Rosella Parrot

This report describes two cases of occupational exposure to Chlamydia psittaci following dissection of an infected Rosella (Platycercus elegans). The C. psittaci infections (with one of them resulting in diagnosed pneumonia and hospitalisation) were undiagnosed during routine medical investigations but later established due to epidemiological and clinical evidence, and molecular testing of the archived Rosella’ specimens. This case report stresses the importance of correct application and interpretation of diagnostic tests and the need to raise awareness about this zoonotic pathogen among medical practitioners and people exposed to potential animal carriers. Our findings suggest other infected individuals might be misdiagnosed and that C. psittaci (psittacosis) is likely to be underreported in Australia. This case highlights the need to operationalise the One Health concept. We call for improved communication between human and animal health service providers to allow accurate and rapid diagnosis of this zoonotic disease and raised awareness among medical practitioners. Further targeted surveys of wild birds (and other animals) should be conducted to improve assessment of risks to the general population and people working with or exposed to wild birds.

Epidemiology of Chlamydia psittaci infections in pregnant Thoroughbred mares and foals

Late-term foal loss due to the traditional avian pathogen Chlamydia psittaci recently emerged as a threat to the Australian Thoroughbred industry. A longitudinal study of 14 stud farms was undertaken to better understand C. psittaci infection in pregnant mares and their foals by evaluating C. psittaci prevalence, equine herpesvirus-1 (EHV-1) co-infection, avian reservoirs, and potential risk factors. Mucosal swabs taken from 228 healthy pregnant mares and their foals were tested for C. psittaci and EHV-1 using species-specific qPCR assays. No foal loss was recorded due to either pathogen, and no mare tested positive to either C. psittaci or EHV-1. However, healthy newborn foals tested positive to both pathogens, at low levels, with 13.2% (n = 30/228) and 14.5% (n = 33/228) prevalence for C. psittaci and EHV-1, respectively. Co-infection occurred in 1.3% (n = 3/228) of foals. In avian environmental faecal samples collected from the same studs, C. psittaci was detected at 5.3% (n = 5/94). Multiple logistic regression modelling found that foals born in winter were more likely to be infected with C. psittaci (adjusted odds ratio = 15.83; P < 0.001; Confidence Interval 5.12-48.49). Being a maiden mare, absence of prophylactic vaginal suture, interventions in the last trimester and residing on a farm with prior history of C. psittaci abortion posed no higher risk to infection in the newborn. Analysis of all reported C. psittaci abortion cases (Hunter Valley, 2016-2019) revealed a dominant C. psittaci sequence type (denoted ST24) and a significant correlation with frost events (Spearmans' rho = 0.44; P = 0.002).

A 25-year retrospective study of Chlamydia psittaci in association with equine reproductive loss in Australia

Introduction. Chlamydia psittaci is primarily a pathogen of birds but can also cause disease in other species. Equine reproductive loss caused by C. psittaci has recently been identified in Australia where cases of human disease were also reported in individuals exposed to foetal membranes from an ill neonatal foal in New South Wales.Hypothesis/Gap Statement. The prevalence of C. psittaci in association with equine reproductive over time and in different regions of Australia is not known.Aim. This study was conducted to detect C. psittaci in equine abortion cases in Australia using archived samples spanning 25 years.Methodology. We tested for C. psittaci in 600 equine abortion cases reported in Australia between 1994 to 2019 using a Chlamydiaceae real-time quantitative PCR assay targeting the 16S rRNA gene followed by high-resolution melt curve analysis. Genotyping and phylogenetic analysis was performed on positive samples.Results. The overall prevalence of C. psittaci in material from equine abortion cases was 6.5 %. C. psittaci-positive cases were detected in most years that were represented in this study and occurred in Victoria (prevalence of 7.6 %), New South Wales (prevalence of 3.9 %) and South Australia (prevalence of 15.4 %). Genotyping and phylogenetic analysis showed that the C. psittaci detected in the equine abortion cases clustered with the parrot-associated 6BC clade (genotype A/ST24), indicating that infection of horses may be due to spillover from native Australian parrots.Conclusion. This work suggests that C. psittaci has been a significant agent of equine abortion in Australia for several decades and underscores the importance of taking appropriate protective measures to avoid infection when handling equine aborted material.

Species, sex and geographic variation in chlamydial prevalence in abundant wild Australian parrots

Chlamydia psittaci (order: Chlamydiales) is a globally distributed zoonotic bacterium that can cause potentially fatal disease in birds and humans. Parrots are a major host, yet prevalence and risk factors for infection in wild parrots are largely unknown. Additionally, recent research suggests there is a diverse range of novel Chlamydiales circulating in wildlife. We therefore sampled seven abundant parrot species in south-eastern Australia, taking cloacal swabs and serum from n = 132 wild adults. We determined C. psittaci and Chlamydiales prevalence and seroprevalence, and tested for host species, sex, geographical and seasonal differences, and temporal changes in individual infection status. Across all species, Chlamydiales prevalence was 39.8% (95% CI 31.6, 48.7), C. psittaci prevalence was 9.8% (95% CI 5.7, 16.3) and C. gallinacea prevalence was 0.8% (95% CI 0.1, 4.5). Other Chlamydiales species were not identified to species level. We identified two C. psittaci strains within the 6BC clade, which is highly virulent in humans. Seroprevalence was 37.0% (95% CI 28.5, 46.4). Host species (including crimson rosellas, galahs, sulphur-crested cockatoos and blue-winged parrots) differed in seroprevalence and Chlamydiales prevalence. Galahs had both highest Chlamydiales prevalence (54.8%) and seroprevalence (74.1%). Seroprevalence differed between sites, with a larger difference in males (range 20–63%) than females (29–44%). We reveal a higher chlamydial prevalence than previously reported in many wild parrots, with implications for potential reservoirs, and transmission risks to humans and other avian hosts.

Chlamydia pecorum-Induced Arthritis in Experimentally and Naturally Infected Sheep

Chlamydia pecorum is an obligate intracellular pathogen with a wide host range including livestock such as sheep, cattle, goats, and pigs as well as wildlife species such as koalas. Chlamydial polyarthritis is an economically important disease resulting in swollen joints, lameness, stiffness, and weight loss in young sheep. In the present study, tissues from sheep experimentally or naturally infected with Chlamydia pecorum were assessed by histopathology and immunohistochemistry. Carpal, hock, and stifle joints as well as spleen, liver, kidney, lymph nodes, lung, and brain of 35 sheep from different inoculation groups were available. Two different C. pecorum strains (IPA and E58), different routes of administration (intraarticular or intravenous), UVA-irradiated IPA strain, and corresponding noninfected control groups were investigated. Similar investigations on tissues from 5 naturally infected sheep were performed. The most obvious inflammatory lesions were observed in synovial tissues and, notably, in the renal pelvis from the experimentally infected group and naturally infected animals. This resulted in chronic or chronic-active arthritis and pyelitis. Intralesional chlamydial inclusions could be demonstrated by immunohistochemistry in both tissues. Immunohistochemical evaluation of the presence and distribution of macrophages, T and B cells in synovial tissues revealed macrophages as the most prevalent inflammatory cell population. Previous observations indicated that C. pecorum isolates can infect circulating monocytes. Together with the finding of the histological lesions in synovial tissues and internal organs alongside the presence of C. pecorum DNA, these observations suggest chlamydial arthritis in lambs is the result of hematogeneous spread of C. pecorum.

Koala immunogenetics and chlamydial strain type are more directly involved in chlamydial disease progression in koalas from two south east Queensland koala populations than koala retrovirus subtypes

Chlamydial disease control is increasingly utilised as a management tool to stabilise declining koala populations, and yet we have a limited understanding of the factors that contribute to disease progression. To examine the impact of host and pathogen genetics, we selected two geographically separated south east Queensland koala populations, differentially affected by chlamydial disease, and analysed koala major histocompatibility complex (MHC) genes, circulating strains of Chlamydia pecorum and koala retrovirus (KoRV) subtypes in longitudinally sampled, well-defined clinical groups. We found that koala immunogenetics and chlamydial genotypes differed between the populations. Disease progression was associated with specific MHC alleles, and we identified two putative susceptibility (DCb 03, DBb 04) and protective (DAb 10, UC 01:01) variants. Chlamydial genotypes belonging to both Multi-Locus Sequence Typing sequence type (ST) 69 and ompA genotype F were associated with disease progression, whereas ST 281 was associated with the absence of disease. We also detected different ompA genotypes, but not different STs, when long-term infections were monitored over time. By comparison, KoRV profiles were not significantly associated with disease progression. These findings suggest that chlamydial genotypes vary in pathogenicity and that koala immunogenetics and chlamydial strains are more directly involved in disease progression than KoRV subtypes.

Helping koalas battle disease - Recent advances in Chlamydia and koala retrovirus (KoRV) disease understanding and treatment in koalas

The iconic Australian marsupial, the koala (Phascolarctos cinereus), has suffered dramatic population declines as a result of habitat loss and fragmentation, disease, vehicle collision mortality, dog attacks, bushfires and climate change. In 2012, koalas were officially declared vulnerable by the Australian government and listed as a threatened species. In response, research into diseases affecting koalas has expanded rapidly. The two major pathogens affecting koalas are Chlamydia pecorum, leading to chlamydial disease and koala retrovirus (KoRV). In the last eight years, these pathogens and their diseases have received focused study regarding their sources, genetics, prevalence, disease presentation and transmission. This has led to vast improvements in pathogen detection and treatment, including the ongoing development of vaccines for each as a management and control strategy. This review will summarize and highlight the important advances made in understanding and combating C. pecorum and KoRV in koalas, since they were declared a threatened species. With complementary advances having also been made from the koala genome sequence and in our understanding of the koala immune system, we are primed to make a significant positive impact on koala health into the future.

Chlamydial diversity and predictors of infection in a wild Australian parrot, the Crimson Rosella (Platycercus elegans)

Members of the Chlamydia genus are known to cause disease in both humans and animals. A variety of other species in the order Chlamydiales are increasingly being discovered and emerging as potential pathogens, yet there are scarce data on the diversity, prevalence and impacts of these pathogens in wild birds. To address this gap, we investigated which Chlamydiales species are present in a wild population of a common Australian parrot, the Crimson Rosella (Platycercus elegans). We collected cloacal swabs and serum from 136 individuals in south-eastern Australia, over two years, and tested several predictors of prevalence: age, sex, season and breeding status. We used multiple PCR assays to determine bacterial prevalence in cloacal swabs and a solid-phase ELISA to determine seroprevalence. We found Chlamydiales PCR prevalence of 27.7% (95% CI 20.2, 36.2) and identified at least two families (Chlamydiaceae and Parachlamydiaceae). Regarding known chlamydial avian pathogens, we found C. psittaci at 6.2% (95% CI 2.7, 11.8) and C. gallinacea at 4.6% (95% CI 1.7, 9.8) prevalence. We also identified at least two potentially novel Chlamydiales species, of unknown pathogenicity. Sex and breeding status predicted Chlamydiales PCR prevalence, with females more likely to be infected than males, and non-breeding birds more likely to be infected than breeding birds. Seroprevalence was 16% (95% CI 8.8, 25.9). Season and breeding status were strong predictors of seroprevalence, with highest seroprevalence in autumn and in non-breeding birds. Our results reveal a diversity of Chlamydiales species in this abundant wild host, and indicate that host-specific and temporal factors are associated with infection risk. Our findings suggest that wild parrots are a reservoir of both known and novel Chlamydiales lineages, of zoonotic and pathogenic potential.

Common bacterial, viral, and parasitic diseases in pigeons (Columba livia): A review of diagnostic and treatment strategies

Pigeons (Columba livia) have been associated with humans for a long time now. They are raised for sport (pigeon race), exhibition (display of fancy breeds), food, and research. Most of the pigeons kept are Racing Homers, trained to compete in the pigeon race. Other breeds, such as Rollers, Nose Divers, Doneks are bred for their aerial abilities. Incorporation of a good preventive medicine program is one of the most critical factors in averting infectious diseases in pigeon flocks. This review summarizes the common bacterial, viral, and parasitic infections in pigeons. The different clinical signs, symptoms, diagnostic strategies, prevention, and treatments were described in this review. Current researches, molecular diagnostic assays, and treatment strategies such as vaccines and drug candidates were included. The information found in this review can provide insights for veterinarians and researchers studying pigeons to develop effective and efficient immunoprophylactic and diagnostic tools for pigeon diagnosis and therapeutics.

Diagnostic accuracy of LAMP assay for HBV infection

Background

Detection of hepatitis B virus (HBV) is vital for the diagnosis of hepatitis B infection. A novel test loop‐mediated isothermal amplification (LAMP) has been successfully applied to detect various pathogens. However, the accuracy of LAMP in diagnosing HBV remains unclear. Therefore, in the present study, the accuracy of LAMP for HBV detection was evaluated systematically.

Methods

Embase, Cochrane Library, and PubMed databases were searched for studies using LAMP to detect HBV. Then, two researchers extracted data and assessed the quality of literature using the QUADAS‐2 tool independently. I² statistic and chi‐square test were analyzed to investigate the heterogeneity, and Deek's funnel plot assessed the publication bias. The pooled sensitivity (SEN), specificity (SPE), positive LR (PLR), negative LR (NLR), diagnostic odds ratio (DOR), and 95% confidence intervals were displayed in forest plots. We calculated the area under the curve (AUC) to assess the overall efficiency of LAMP for HBV detection.

Results

A total of nine studies with 1298 samples were finally included in this evaluation. The pooled sensitivity and specificity of HBV detection were 0.91 (95% CI: 0.89 ~ 0.92) and 0.97 (95% CI: 0.94 ~ 0.99), respectively. The PLR, NLR, and DOR were 16.93 (95% CI: 6.15 ~ 46.55), 0.08 (95% CI: 0.05 ~ 0.14), and 397.57 (95% CI: 145.41 ~ 1087.07). Besides, the AUC was 0.9872, and Deek's plot suggested that there existed publication bias in the studies.

Conclusion

Compared with PCR, LAMP is a simple, rapid, and effective assay to diagnose HBV. However, additional evidence is essential to confirm that LAMP can replace other methods in diagnosing HBV infection.

An advanced loop-mediated isothermal amplification assay for the rapid detection of beak and feather disease virus in psittacine birds

Swarm primer-applied loop-mediated isothermal amplification (sLAMP) assay was developed for the rapid and specific detection of the ORF V1 gene of beak and feather disease virus (BFDV). The amplification can be completed in 40 min at 62 °C, and the results can be visually detected by the naked eye. The assay specifically amplified BFDV DNA and not amplified other viral nucleic acids. The limit of detection of the assay was 5 × 10² DNA copies/reaction, which was lower than that of the previously described LAMP (preLAMP) assay and comparable to that of a previously reported real time quantitative PCR (qPCR) assay. The detection rates of BFDV from psittacine clinical samples by the sLAMP, qPCR and preLAMP assays were 36.0 %, 36.0 % and 25.6 %, respectively, and the sLAMP results showed 100.0 % concordance with the qPCR results with a kappa value of 1.0. On the other hand, the preLAMP assay did not detect nine out of the 31 samples that were positive by sLAMP and qPCR assays, probably due to low sensitivity of the assay. These data suggest that the newly developed sLAMP assay will be a valuable tool for the rapid, sensitive, specific and reliable detection of BFDV in suspected psittacine birds, even in resource-limited laboratories.

Chlamydial infection and on-farm risk factors in dairy cattle herds in South East Queensland

Chlamydial infections in dairy cattle are common and have been sporadically associated with reduced performance and severe disease manifestations. While chlamydial infections are well described in sheep, very little is known about the epidemiology of these infections in dairy cattle in Australia. In this study, we screened for chlamydial infections and assessed on-farm risks in dairy cattle herds from Southeast Queensland (SE Qld) region of Australia. In total, 228 paired vaginal and rectal swabs were collected from 114 visually healthy dairy cows from four farms in SE Qld. Risk factors were rated by observational study and included: hygiene and cleanliness of cows, walkway and parlour, incidence of perinatal mortality, external replacements, mode of breeding, calving pen management, heat reduction strategies, and feed ration usage. Testing for chlamydial pathogens (Chlamydia pecorum, Chlamydia psittaci and Chlamydia abortus) was done using species-specific quantitative polymerase chain reaction (qPCR) assays. Detected rates of chlamydial infection were evaluated against the on-farm risk factors. C. pecorum infection was widespread in all four farms, with 56.1% (64/114) of individual animals shedding this organism from vaginal and rectal, or both sites. C. abortus and C. psittaci were not detected in any animals. No association was found to exist with risk factors and C. pecorum infection rates in our study, however the number of Chlamydia positive animals was statistically different between the herds. This study suggests that subclinical chlamydial infections may impact on dairy herd health at the production level rather than affecting individual animal.

Longitudinal study of wild koalas (Phascolarctos cinereus) reveals chlamydial disease progression in two thirds of infected animals

Chlamydial disease threatens many of Australia’s koala populations, and yet our understanding of chlamydial epidemiology and disease dynamics in koalas is limited by a lack of comprehensive, longitudinal population studies. To address this, we utilised longitudinal samples from a large-scale population study of wild koalas in south-east Queensland, to follow chlamydial infections over time and to investigate some of the drivers of disease progression. Our findings show, firstly, that almost two thirds of chlamydial infections progressed to disease, challenging the notion that chlamydial infections in koalas commonly remain chronic and asymptomatic. Secondly, disease progression at the urogenital tract site was associated with infection load, and urogenital tract shedding was significantly higher when koalas acquired a new infection. Thirdly, chronic chlamydial exposure was not necessary for pathogenic sequelae to develop, such as infertility and mortality. Fourthly, ompA-characterised strain sub-types may reflect tissue tropisms and pathogenicity, and the chlamydial status of some chronically infected koalas may be explained by reinfections with novel genotypes. Finally, successful antimicrobial treatment provided only short-term protection against reinfection and disease progression in susceptible koalas. These findings highlight the importance of identifying and preventing chlamydial infections in koalas, informing new population management strategies and research priorities.

Changes in Endogenous and Exogenous Koala Retrovirus Subtype Expression over Time Reflect Koala Health Outcomes

Koala retrovirus (KoRV) is unique in that it exists as both an exogenous and actively endogenizing gamma retrovirus of koalas. While nine subtypes of KoRV have been recognized, focused study of these subtypes in koalas over time and with different health outcomes has been lacking. Therefore, in this study, three wild koala cohorts were established and monitored to examine KoRV proviral and expression data from koalas that either remained healthy over time, began healthy before developing chlamydial cystitis, or presented with chlamydial cystitis and were treated with antibiotics. Deep sequencing of the proviral KoRV envelope gene revealed KoRV-A, -B, -D, and -F to be the major subtypes in this population and allowed for subtype-specific assays to be created. Quantification of KoRV transcripts revealed that KoRV-D expression mirrored the total KoRV expression levels (10⁶ copies/ml of plasma), with KoRV-A and KoRV-F expression being ∼10-fold less and KoRV-B expression being ∼100-fold less, when detected. Strikingly, there was significantly higher expression of KoRV-D in healthy koalas than in koalas that developed chlamydial cystitis, with healthy koalas expressing a major KoRV-D/minor KoRV-A profile, whereas koalas that developed cystitis had variable KoRV expression profiles. Total anti-KoRV IgG antibody levels were found not to correlate with the expression of total KoRV or any individual KoRV subtype. Finally, KoRV expression was consistent between systemic and mucosal body sites and during antibiotic treatment. Collectively, this gives a comprehensive picture of KoRV dynamics during several important koala health states.IMPORTANCE The long-term survival of the koala is under serious threat, with this iconic marsupial being declared "vulnerable" by the Australian Government and officially listed as a threatened species. KoRV is clearly contributing to the overall health status of koalas, and research into this virus has been lacking detailed study of the multiple subtypes at both the proviral and expressed viral levels over time. By designing new subtype-specific assays and following well-defined koala cohorts over time, this study has generated a new more complete picture of KoRV and its relationship to koala health outcomes in the wild. Only by building a comprehensive picture of KoRV during both koala health and disease can we bring meaningful koala health interventions into better focus.

Rapid point-of-care diagnostics for the detection of Chlamydia pecorum in koalas (Phascolarctos cinereus) using loop-mediated isothermal amplification without nucleic acid purification

Infectious disease, predominately chlamydiosis, contributes significantly to the decline in health of wild koala (Phascolarctos cinereus) populations in some regions of Australia. In this study, we describe the development and evaluation of a simple, sensitive, and specific loop‐mediated isothermal amplification (LAMP) assay for the detection of Chlamydia pecorum in koalas as a point‐of‐care diagnostic tool that can be used in any wildlife hospital and in the field on specialized instrumentation. A set of primers targeting a 188‐bp region of the C. pecorum genome was designed. 100% specificity of the LAMP assay was revealed by demonstrating no cross‐reactivity with 33 nontarget pathogens, and complete correlation with qPCR results for 43 clinical swabs collected opportunistically from wildlife hospitals. In sensitivity evaluations, the technique successfully detected serial dilutions of extracted C. pecorum DNA with a detection limit of 44 IFU/ml.

Antibiotic treatment of Chlamydia-induced cystitis in the koala is linked to expression of key inflammatory genes in reactive oxygen pathways

Chlamydial-induced cystitis in the koala (Phascolarctos cinereus) is currently treated by antibiotics. However, while reducing the chlamydial load, this treatment can also lead to gastrointestinal complications and death. Development of alternative treatments, such as a therapeutic chlamydial vaccine, are hindered by the lack of detailed understanding of the innate immune response to chlamydial clearance and disease regression during antibiotic treatment. Through clinical, microbiological and transcriptomic approaches, disease regression, bacterial clearance and innate immune responses were mapped in koalas with signs of chlamydial-induced cystitis while receiving anti-chlamydial antibiotics. Significant reduction in the signs of cystitis were observed during and post antibiotic treatment. This was observed as a thinning of the bladder wall and complete reversal of urinary incontinence. Transcriptomic analysis before treatment, at the end of treatment and prior to release identified significant down-regulation of specific genes involved in 21 biological pathways. Of these, the chemokine receptor signalling and NOD-like receptor signalling pathways where identified as important markers of inflammation. Specific genes within these pathways (NCF1 and NOX2) were significantly down-regulated, suggesting a decrease in reactive oxygen species production. Through the monitoring of specific clinical and transcriptomic markers, these findings allow detailed profiling of the clinical response to therapeutic vaccination in koalas with current signs of disease. This also adds to our understanding of innate immune responses to chlamydial infections and indicates that chlamydial-induced cystitis in the koala is linked to the regulation of reactive oxygen pathways.

Detection of Chlamydiaceae in ocular swabs from Australian pre-export feedlot sheep

Infectious Ovine Keratoconjunctivitis (IOK) is a contagious ocular disease of sheep. A range of organisms have been observed as the aetiological agents of IOK. In this study, the presence of chlamydial pathogens (C. pecorum, C. abortus, C. psittaci) in conjunctival swabs was tested for. The swabs were collected from sheep with varying grades of IOK in an Australian pre-export feedlot. The sheep had been rejected from a shipment because of the eye disease. The relative contribution of chlamydial pathogens to IOK and the rejection of animals was evaluated. In total, 149 conjunctival swabs were taken from rejected sheep (IOK Grades 1 to 6; n = 126) as well as those with healthy eyes (Grade 0; n = 23). Screening for chlamydial pathogens was done using species-specific qPCR assays. Chlamydial DNA was detected in 35.6% (53/149) of conjunctival samples. C. pecorum was the most predominant species with an overall prevalence of 28.9% (43/149). C. psittaci prevalence was 6.7% (10/149). Both organisms were detected in healthy as well as IOK-affected eyes. All swabs tested negative for C. abortus. The results from this study demonstrate that Chlamydia spp can be readily detected in sheep presenting with IOK. The zoonotic C. abortus was not detected in any of the samples in this study, providing further evidence to the suggestion that this pathogen remains absent from Australia. Although the exact contribution of Chlamydia spp in the IOK pathogenesis is unclear, such studies are anticipated to be of benefit to Australian domestic and live export production systems.

Development of a colorimetric loop-mediated isothermal amplification assay for rapid and specific detection of Aves polyomavirus 1 from psittacine birds

A colorimetric loop-mediated isothermal amplification (LAMP) assay was developed for the rapid and specific detection of the T gene of Aves polyomavirus 1 (APyV), a causative agent of budgerigar fledgling disease (BFD) in psittacine birds. The amplification can be completed in 40 min at 60 °C, and the results can be visually detected by the naked eye using hydroxyl naphthol blue as a colorimetric indicator. The assay specifically amplified APyV DNA but not other viral and bacterial nucleic acids. The limit of detection of the assay was 5 × 10² DNA copies/reaction, which was comparable to those of previously reported conventional polymerase chain reaction assays. In the clinical evaluation, the LAMP results showed 100% concordance with those of the previously reported PCR assays with regard to specificity, sensitivity, and percentage of overall agreement, with a kappa value of 1.0. These results indicate that the developed LAMP assay will be a valuable tool for the rapid, sensitive and specific detection of APyV from BFD-suspected psittacine bird samples even in resource-limited laboratories.

Prevalence and clinical significance of koala retrovirus in two South Australian koala (Phascolarctos cinereus) populations

PURPOSE

Koala retrovirus (KoRV-A) is 100  % prevalent in northern Australian (Queensland and New South Wales) koala populations, where KoRV-B has been associated with Chlamydia pecorum disease and the development of lymphosarcoma. In southern populations (Victoria and South Australia), KoRV-A is less prevalent and KoRV-B has not been detected in Victoria, while the current prevalence in South Australian populations is unknown but is thought to be low. This study aimed to determine (i) the prevalence of KoRV in the two largest South Australian koala populations [Kangaroo Island (KI) and Mount Lofty Ranges (MLR)], (ii) KoRV subtype and (iii) if an association between KoRV and C. pecorum exists.

METHODOLOGY

Wild koalas were sampled in KI ( n =170) between 2014 and 2017 and in MLR ( n =75) in 2016. Clinical examinations were performed, with blood collected for KoRV detection and typing by PCR.

RESULTS

KoRV prevalence was 42.4  % [72/170, 95 % confidence interval (CI): 34.9-49.8  %] in KI and 65.3  % (49/75, 95 % CI: 54.6-76.1  %) in MLR. Only KoRV-A, and not KoRV-B, was detected in both populations. In MLR, there was no statistical association between KoRV and C. pecorum infection (P =0.740), or KoRV and C. pecorum disease status ( P=0.274), although KoRV-infected koalas were more likely to present with overt C. pecorum disease than subclinical infection (odds ratio: 3.15, 95 % CI: 0.91-5.39).

CONCLUSION

KoRV-A is a prevalent pathogen in wild South Australian koala populations. Future studies should continue to investigate KoRV and C. pecorum associations, as the relationship is likely to be complex and to differ between the northern and southern populations.

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.

Detection of a range of genetically diverse chlamydiae in Australian domesticated and wild ungulates

Chlamydiae are globally widespread obligate intracellular bacteria, which several species are a well-recognized threat to human and animal health. In Australia, the most successful chlamydial species are the infamous koala pathogen C. pecorum, and C. psittaci, an emerging pathogen associated with zoonotic events. Little is known about infections caused by other chlamydial organisms in Australian livestock or wildlife. Considering that these hosts can be encountered by humans at the animal/human interface, in this study, we investigated genetic diversity of chlamydial organisms infecting Australian domesticated and wild ungulates. A total of 185 samples from 129 domesticated (cattle, horses, sheep, and pigs) and 29 wild (deer) ungulate hosts were screened with C. pecorum and C. psittaci species-specific assays, followed by a screen with pan-Chlamydiales assay. Overall, chlamydial DNA was detected in 120/185 (65%) samples, including all ungulate hosts. Species-specific assays further revealed that C. pecorum and C. psittaci DNA were detected in 27% (50/185) and 6% (11/185) of the samples, respectively, however from domesticated hosts only. A total of 46 "signature" 16S rRNA sequences were successfully resolved by sequencing and were used for phylogenetic analyses. Sequence analyses revealed that genetically diverse novel as well as traditional chlamydial organisms infect an expanded range of ungulate hosts in Australia. Detection of the C. psittaci and C. pecorum in livestock, and novel taxa infecting horses and deer raises questions about the genetic make-up and pathogenic potential of these organisms, but also concerns about risks of spill-over between livestock, humans, and native wildlife.

Identification of A Novel Picorna-Like Virus, Burpengary Virus, that is Negatively Associated with Chlamydial Disease in the Koala

Koalas (Phascolarctos cinereus) are native Australian marsupials whose populations are in decline from a range of threats. Infectious diseases caused by the bacterium Chlamydia pecorum and other pathogens are of particular concern. We analysed 26 poly-A selected RNA-sequencing libraries from a data set designed to study the immune response of koalas to ocular chlamydial infection. Using virus discovery techniques, we identified the coding-complete genome sequence of a novel picorna-like virus, denoted Burpengary virus, that was most common in south-east Queensland. Notably, abundance measurements of the virus across all 26 libraries revealed an inverse relationship between abundance and ocular disease in koalas, suggesting that the co-infection of Burpengary virus and Chlamydia pecorum is inhibited.

Optimising the short and long-term clinical outcomes for koalas (Phascolarctos cinereus) during treatment for chlamydial infection and disease

Koalas (Phascolarctos cinereus) have suffered severe declines in the northern extent of their range due to a variety of threats, including habitat destruction, trauma from cars and dogs, climate change and importantly, disease. The most significant pathogen in koalas is Chlamydia pecorum, which causes inflammation and fibrosis at mucosal sites, resulting in blindness, infertility and death in severe cases. Chlamydia treatment can be problematic in koalas as the response to treatment is often poor in chronic cases and antimicrobial choice is limited. Thus, chlamydial disease is a severely threatening process for koala conservation. We investigated the short and long-term clinical outcomes for 167 koalas with Chlamydia that underwent capture, telemetric monitoring and intensive veterinary management as part of a large-scale population management program in South East Queensland. Chlamydia treatments included the standard regimen of daily subcutaneous chloramphenicol injections (60mg/kg) for 14 to 28-days, and a variety of non-standard regimens such as topical antimicrobials only (for ocular disease), surgical treatment only (for bilateral reproductive tract disease), and other antimicrobials/treatment lengths. To assess these regimens we analysed clinical records, field monitoring data and swab samples collected from the urogenital tract and ocular conjunctiva. Overall, in contrast to other studies, treatment was generally successful with 86.3% of treated koalas released back into the wild. The success of treatment rose to 94.8% however, when the standard treatment regimen was employed. Further, 100% of koalas that were also treated with surgical ovariohysterectomy (n = 12) remained healthy for a median of 466 days of post-treatment monitoring, demonstrating the benefits of surgical treatment. Previous studies reported 45-day chloramphenicol regimens, but the shorter standard regimen still achieved microbiological cure and reduces the risk of negative sequelae associated with treatment and/or captivity and treatment costs. Despite these positive clinical outcomes, alternatives to chloramphenicol are warranted due to its decreasing availability.

Real-time loop-mediated isothermal amplification for rapid detection of Enterocytozoon hepatopenaei

Background

Enterocytozoon hepatopenaei (EHP) is a newly emerged microsporidian parasite that causes retarded shrimp growth in many countries. But there are no effective approaches to control this disease to date. The EHP could be an immune risk factor for increased dissemination of other diseases. Further, EHP infection involves the absence of obvious clinical signs and it is difficult to identify the pathogen through visual examination, increasing the risk of disease dissemination. It is urgent and necessary to develop a specific, rapid and sensitive EHP-infected shrimp diagnostic method to detect this parasite. In the present study, we developed and evaluated a rapid real-time loop-mediated isothermal amplification (real-time LAMP) for detection of EHP.

Methods

A rapid and efficient real-time LAMP method for the detection of EHP has been developed. Newly emerged EHP pathogens in China were collected and used as the sample, and three sets of specificity and sensitivity primers were designed. Three other aquatic pathogens were used as templates to test the specificity of the real-time LAMP assay. Also, we compared the real-time LAMP with the conventional LAMP by the serial dilutions of EHP DNA and their amplification curves. Application of real-time LAMP was carried out with clinical samples.

Results

Positive products were amplified only from EHP, but not from other tested species, EHP was detected from the clinical samples, suggesting a high specificity of this method. The final results of this assay were available within less than 45 min, and the initial amplification curve was observed at about 6 min. We found that the amplification with an exponential of sixfold dilutions of EHP DNA demonstrated a specific positive signal by the real-time LAMP, but not for the LAMP amplicons from the visual inspection. The real-time LAMP amplification curves demonstrated a higher slope than the conventional LAMP.

Discussion

In this study, pathogen virulence impacts have been increased in aquaculture and continuous observation was predominantly focused on EHP. The present study confirmed that the real-time LAMP assay is a promising and convenient method for the rapid identification of EHP in less time and cost. Its application greatly aids in the detection, surveillance, and prevention of EHP.

Chlamydia pecorum gastrointestinal tract infection associations with urogenital tract infections in the koala (Phascolarctos cinereus)

Background

Chlamydia infects multiple sites within hosts, including the gastrointestinal tract (GIT). In certain hosts, gastrointestinal infection is linked to treatment avoidance and self-infection at disease susceptible sites. GIT C. pecorum has been detected in livestock and koalas, however GIT prevalence rates within the koala are yet to be established.

Methods

Paired conjunctival, urogenital and rectal samples from 33 koalas were screened for C. pecorum and C. pecorum plasmid using 16S rRNA and CDS5-specific quantitative PCR assays, respectively. Amplicon sequencing of 359 bp ompA fragment was used to identify site-specific genotypes.

Results

The overall C. pecorum prevalence collectively (healthy and clinically diseased koalas) was 51.5%, 57.6% and 42.4% in urogenital, conjunctival and gastrointestinal sites, respectively. Concurrent urogenital and rectal Chlamydia was identified in 14 koalas, with no cases of GIT only Chlamydia shedding. The ompA genotype G dominated the GIT positive samples, and genotypes A and E’ were dominant in urogenital tract (UGT) positive samples. Increases in C. pecorum plasmid per C. pecorum load (detected by PCR) showed clustering in the clinically diseased koala group (as assessed by scatter plot analysis). There was also a low correlation between plasmid positivity and C. pecorum infected animals at any site, with a prevalence of 47% UGT, 36% rectum and 40% faecal pellet.

Conclusions

GIT C. pecorum PCR positivity suggests that koala GIT C. pecorum infections are common and occur regularly in animals with concurrent genital tract infections. GIT dominant genotypes were identified and do not appear to be related to plasmid positivity. Preliminary results indicated a possible association between C. pecorum plasmid load and clinical UGT disease.

Review of Diagnostic Procedures and Approaches to Infectious Causes of Reproductive Failures of Cattle in Australia and New Zealand

Infectious causes of reproductive failure in cattle are important in Australia and New Zealand, where strict biosecurity protocols are in place to prevent the introduction and spread of new diseases. Neospora caninum ranks highly as an important cause of reproductive wastage along with fungal and bacterial infections. Brucella, a leading cause of abortion elsewhere in the world, is foreign, following successful programs to control and eradicate the disease. Leptospirosis in cattle is largely controlled by vaccination, while Campylobacter and Tritrichomonas infections occur at low rates. In both countries, Bovine Viral Diarrhea virus (BVDV) infection rates as the second most economically important disease of cattle and one that also has an effect on reproduction. Effective disease control strategies require rapid diagnoses at diagnostic laboratories. To facilitate this process, this review will discuss the infectious causes of reproductive losses present in both countries, their clinical presentation and an effective pathway to a diagnosis.

A Sarcoptes scabiei specific isothermal amplification assay for detection of this important ectoparasite of wombats and other animals

Background

The globally distributed epidermal ectoparasite, Sarcoptes scabiei, is a serious health and welfare burden to at-risk human and animal populations. Rapid and sensitive detection of S. scabiei infestation is critical for intervention strategies. While direct microscopy of skin scrapings is a widely utilised diagnostic method, it has low sensitivity. PCR, alternatively, has been shown to readily detect mite DNA even in microscopy-negative skin scrapings. However, a limitation to the latter method is the requirements for specialised equipment and reagents. Such resources may not be readily available in regional or remote clinical settings and are an important consideration in diagnosis of this parasitic disease.

Methodology

A Loop Mediated Isothermal Amplification (LAMP) assay targeting the ITS-2 gene for S. scabiei was developed and evaluated on clinical samples from various hosts, previously screened with conventional S. scabies-specific PCR. Species specificity of the newly developed LAMP assay was tested against a range of DNA samples from other arthropods. The LAMP assays were performed on a real-time fluorometer as well as thermal cycler to evaluate an end-point of detection. Using skin scrapings, a rapid sample processing method was assessed to eliminate extensive processing times involved with DNA extractions prior to diagnostic assays, including LAMP.

Results

The S. scabiei LAMP assay was demonstrated to be species-specific and able to detect DNA extracted from a single mite within a skin scraping in under 30 minutes. Application of this assay to DNA extracts from skin scrapings taken from a range of hosts revealed 92.3% congruence (with 92.50% specificity and 100% sensitivity) to the conventional PCR detection of S. scabiei. Preliminary results have indicated that diagnostic outcome from rapidly processed dry skin scrapings using our newly developed LAMP is possible in approximately 40 minutes.

Discussion

We have developed a novel, rapid and robust molecular assay for detecting S. scabiei infesting humans and animals. Based on these findings, we anticipate that this assay will serve an important role as an ancillary diagnostic tool at the point-of-care, complementing existing diagnostic protocols for S. scabiei.

Development and application of two multiplex real-time PCR assays for detection and speciation of bacterial pathogens in the koala

Infectious diseases have contributed to the decline in the health of koala ( Phascolarctos cinereus) populations in the wild in some regions of Australia. Herein we report the development and validation of 2 multiplex real-time PCR (rtPCR) panels for the simultaneous detection of Mycoplasma spp., Ureaplasma spp., Bordetella bronchiseptica, and Chlamydia, including speciation and quantification of Chlamydia, in ocular, reproductive, and nasal swab samples in addition to semen and male urogenital and reproductive tissues, from koalas. Each rtPCR panel was developed for use as a single-tube reaction using pathogen-specific primers and fluorescently labeled probe sets. DNA extracted from reference strains and isolates was used for validation of sequence gene targets for the multiplex rtPCR panels. Each panel was shown to be sensitive and specific in detecting and differentiating the bacterial pathogens. The multiplex rtPCR panels were used to screen clinical samples from free-ranging and hospitalized koalas for multiple pathogens simultaneously. The multiplex rtPCR will improve turnaround time compared to individual-pathogen rtPCR methods used, to date, for confirmation of diagnosis and will provide the wildlife clinician with the ability to make treatment decisions more rapidly.

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

Chlamydia psittaci is an avian pathogen capable of spill-over infections to humans. A parrot C. psittaci strain was recently detected in an equine reproductive loss case associated with a subsequent cluster of human C. psittaci infections. In this study, we screened for C. psittaci in cases of equine reproductive loss reported in regional New South Wales, Australia during the 2016 foaling season. C. psittaci specific-PCR screening of foetal and placental tissue samples from cases of equine abortion (n = 161) and foals with compromised health status (n = 38) revealed C. psittaci positivity of 21.1% and 23.7%, respectively. There was a statistically significant geographical clustering of cases ~170 km inland from the mid-coast of NSW (P < 0.001). Genomic analysis and molecular typing of C. psittaci positive samples from this study and the previous Australian equine index case revealed that the equine strains from different studs in regional NSW were clonal, while the phylogenetic analysis revealed that the C. psittaci strains from both Australian equine disease clusters belong to the parrot-associated 6BC clade, again indicative of spill-over of C. psittaci infections from native Australian parrots. The results of this work suggest that C. psittaci may be a more significant agent of equine reproductive loss than thought. A range of studies are now required to evaluate (a) the exact role that C. psittaci plays in equine reproductive loss; (b) the range of potential avian reservoirs and factors influencing infection spill-over; and (c) the risk that these equine infections pose to human health.

Evaluation of fluorimetry and direct visualization to interpret results of a loop-mediated isothermal amplification kit to detect Leishmania DNA

Background

Nucleic acid amplification tests (NAATs) have proven to be advantageous in the diagnosis of leishmaniases, allowing sensitive diagnosis of: (i) cutaneous leishmaniasis in long duration lesions and (ii) visceral leishmaniasis using a less-invasive sample like peripheral blood, in opposition to tissue aspiration required for parasite demonstration by microscopy. Despite their benefits, the implementation of NAATs for leishmaniasis diagnosis at the point-of-care has not been achieved yet, mostly due to the complexity and logistical issues associated with PCR-based methods.

Methods

In this work, we have evaluated the performance of a ready-to-use loop-mediated isothermal amplification (LAMP) kit using two real time fluorimeters to amplify leishmanial DNA obtained by silica column-based and Boil & Spin protocols.

Results

The different approaches used to run and interpret the LAMP reactions showed a performance equivalent to PCR and real-time PCR, using spiked and clinical samples. The time to positivity obtained with real-time fluorimetry showed an excellent correlation with both Ct values and parasite load from real-time quantitative PCR.

Conclusions

The results obtained open the possibility of using a highly stable, ready-to-use LAMP kit for the accurate diagnosis of leishmaniasis at the point-of-care. Furthermore, the feasibility of relating time to positivity, determined with a portable real-time fluorimeter, with the parasite burden could have a wider application in the management of leishmaniasis, such as in treatment efficacy monitoring or as a pharmacodynamics tool in clinical trials.

Molecular and serological dynamics of Chlamydia pecorum infection in a longitudinal study of prime lamb production

BACKGROUND

Chlamydia pecorum is a globally significant livestock pathogen causing pathology and production losses. The on-farm infection and serological dynamics and the relevance of existing diagnostic tools for diagnosing C. pecorum in livestock remains poorly characterized. In this study, we characterized the antigen and antibody dynamics of this pathogen in a longitudinal study of prime lamb production, utilizing the infection focused C. pecorum-specific 16S rRNA qPCR assay and serology based chlamydial Complement fixation Test (CFT).

METHODS

The study consisted of 76 Border Leicester mixed sex lambs (39 females and 37 males) that were sampled bimonthly from 2-10 months of age in a commercial farm operating in Central NSW, Australia. Blood/plasma was analysed for CFT antibodies, and swabs from conjunctival, rectal and vaginal sites were analysed for C. pecorum shedding using qPCR. We assessed the temporal and overall dynamics of C. pecorum in lambs, including detailed description and comparison of qPCR and CFT, the timing of first detection by either diagnostic method, the lag between infection and antibody response; and the distribution of qPCR load and CFT antibody titre over time.

RESULTS

Over the study period, C. pecorum was highly prevalent (71.0% by qPCR, 92.1% by CFT, 96.0% by both), with 21.1% (16/76) lambs shedding ≥1, 000 qPCR copies/µl (denoted as high shedders). C. pecorum shedding (as evidence of infection) were first observed at two months of age (14.4%) with a significant peak of infection occurring at six months of age (34.2%), whereas seroconversions peaked at eight months of age (81.5%). 52.6% of C. pecorum qPCR and CFT positive lambs became qPCR negative by 10 months of age, indicating clearance of chlamydial infection. Although CFT is utilised for on-farm detection of active infection, we confirm that it lagged behind qPCR detection (average lag 1.7 ± 2.1 months) and that the proportion of qPCR positives simultaneously identified by CFT was low with 2/11 (18.1%), 0/13, 17/25 (68.0%), 5/7 (71.4%) and 1/10 (10.0%) concurrent seroconversions occurring at two, four, six, eight and 10 months of age, respectively.

DISCUSSION

This work reveals rapid rates of C. pecorum infection and widespread exposure during lamb production. The comparison of molecular and serological diagnostic agreement longitudinally, supports the use of qPCR as an important ancillary tool for the detection of active infections in conjunction with chlamydial CFT for routine veterinary diagnostics. Development of rapid Point-of-Care (POC) tools for diagnosing active infection would be valuable for producers and veterinarians.