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Fernandez CM, Krockenberger MB, Ho SYW, Crowther MS, Mella VSA, Jelocnik M, Wilmott L, Higgins DP. Novel typing scheme reveals emergence and genetic diversity of Chlamydia pecorum at the local management scale across two koala populations. Vet Microbiol 2024; 293:110085. [PMID: 38581768 DOI: 10.1016/j.vetmic.2024.110085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Australia: the Liverpool Plains and the Southern Highlands to South-west Sydney (SHSWS). Our method provides greater resolution than traditional multi-locus sequence typing, and can be used to monitor strain emergence, movement, and divergence across a range of fragmented habitats. Within the Liverpool Plains population, suspected recent introduction of a novel strain was confirmed by an absence of genetic diversity at the earliest sampling events and limited diversity at recent sampling events. Across the partially fragmented agricultural landscape of the Liverpool Plains, diversity within a widespread sequence type suggests that this degree of fragmentation may hinder but not prevent spread. In the SHSWS population, our results suggest movement of a strain from the south, where diverse strains exist, into a previously Chlamydia-free area in the north, indicating the risk of expansion towards an adjacent Chlamydia-negative koala population in South-west Sydney. In the south of the SHSWS where koala subpopulations appear segregated, we found evidence of divergent strain evolution. Our tool can be used to infer the risks of strain introduction across fragmented habitats in population management, particularly through practices such as wildlife corridor constructions and translocations.
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Affiliation(s)
- Cristina M Fernandez
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark B Krockenberger
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; Sydney Infectious Diseases, The University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mathew S Crowther
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Valentina S A Mella
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Martina Jelocnik
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia; Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Lachlan Wilmott
- NSW Department of Planning and Environment, Wollongong, NSW 2005, Australia
| | - Damien P Higgins
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia.
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2
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Hagenbuch F, Loehrer S, Marti H, Kasimov V, Jelocnik M, Borel N. Investigation of Chlamydia pecorum in livestock from Switzerland reveals a high degree of diversity in bovine strains. Vet Microbiol 2024; 292:110057. [PMID: 38502978 DOI: 10.1016/j.vetmic.2024.110057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Chlamydia pecorum is a widespread veterinary chlamydial species causing endemic infections in livestock, such as ruminants and pigs, globally. However, there is limited contemporary knowledge on infecting strain diversity in various hosts. This study aimed to evaluate the genetic diversity of C. pecorum strains infecting Swiss livestock through C. pecorum genotyping and phylogenetic analyses in comparison to the global population, while also assessing chlamydial strains for plasmid carriage. A total of 263 C. pecorum positive samples from clinically healthy ruminant and pig herds (Bovines = 216, sheep = 25, pigs = 14) as well as placentae from eight C. pecorum positive ruminant abortion cases from other Swiss herds were investigated. The ompA and Multi-Locus sequence typing revealed novel C. pecorum genotypes, and bovine strains exhibited considerable genetic diversity, contrasting with lower diversity in sheep and pig strains. C. pecorum plasmid was detected in 100.0% of sheep (41/41) and pig (255/255) samples, and in 69.4% of bovine samples (150/216). In contrast, no plasmid was detected in the eight C. pecorum-positive ruminant abortion cases either representing plasmid-less strains or possibly escaping PCR detection due to autolysis of the placenta. This study supports the genetic diversity of C. pecorum strains, particularly in bovines, and identifies novel sequence types in Swiss livestock.
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Affiliation(s)
- Fabian Hagenbuch
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Samuel Loehrer
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Vasilli Kasimov
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia; Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, 4556, Australia
| | - Martina Jelocnik
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia; Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, 4556, Australia
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland.
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3
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Casteriano A, Van Aggelen AR, Fischer S, Flanagan C, Marschner C, Nugent H, Huston W, Higgins DP. Evaluation of a biosecurity survey approach for contamination by Chlamydia pecorum in koala rehabilitation, field capture, and captive settings. PeerJ 2023; 11:e15842. [PMID: 37601255 PMCID: PMC10437030 DOI: 10.7717/peerj.15842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Transmission of Chlamydia pecorum between koalas is a potential risk in field capture or rehabilitation settings, where koalas are held in proximity to each other, or equipment is shared between animals. Given the impact of C. pecorum on koala welfare and population viability it is surprising that quarantine and disinfection protocols in a koala rehabilitation facility or capture settings have not previously been evaluated. This study aimed to evaluate an approach, based on the detection of chlamydial DNA and cell viability, to determine the degree of environmental contamination within a koala care facility. Various fomite sites associated with koala care at a koala rehabilitation facility in New South Wales, Australia were identified as potential sources of chlamydial contamination, following exposure to koalas known to be infected with C. pecorum. Fomite sites were swabbed following exposure, and again after decontamination procedures were carried out. Samples were tested for the presence of chlamydial DNA using qPCR and viability using both RT-qPCR and cell culture. From a total of 239 sampling events, 30 tested qPCR positive for chlamydial DNA, with 19 and 11 samples corresponding to pre-decontamination and post-decontamination events respectively. Detection of chlamydial DNA appeared to be most common in the examination room, especially on fomite sites in direct contact with koalas. Physical removal of chlamydial DNA, or its degradation by the elements, appeared to be more common on outdoor enclosures, clothing, and hands. Based on the cell culture assay, of the pre-decontamination samples with chlamydial DNA, eight had viable chlamydial cells, two of these at low levels. Of the post-decontamination samples with chlamydial DNA, one had a moderate number, and one had a very low number of viable chlamydial cells. RT-qPCR was unsuccessful in determining cell viability due to low yields of RNA and high levels of contaminants from the environmental samples. The outcomes of this study provide a knowledge base for the design of future biosecurity evaluation guidelines in captive and koala rehabilitation facilities. The higher incidence of chlamydial DNA detection by qPCR than viable organism highlights the need to use viability assays in similar studies. However, further investment is still needed to optimise these methods and improve sensitivity for complex environmental samples.
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Affiliation(s)
- Andrea Casteriano
- Faculty of Science/Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Astrid Robin Van Aggelen
- Koala Hospital Port Macquarie, Koala Conservation Australia, Port Macquarie, New South Wales, Australia
| | - Shali Fischer
- Koala Hospital Port Macquarie, Koala Conservation Australia, Port Macquarie, New South Wales, Australia
| | - Cheyne Flanagan
- Koala Hospital Port Macquarie, Koala Conservation Australia, Port Macquarie, New South Wales, Australia
| | - Caroline Marschner
- Faculty of Science/Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Hannah Nugent
- Faculty of Science/School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Wilhelmina Huston
- Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Damien P. Higgins
- Faculty of Science/Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
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Cristescu RH, Strickland K, Schultz AJ, Kruuk LEB, de Villiers D, Frère CH. Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression. Mol Ecol 2022; 31:5455-5467. [PMID: 36043238 PMCID: PMC9826501 DOI: 10.1111/mec.16676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/11/2023]
Abstract
The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and, to date, we know little about the determinants of individual susceptibility to disease. Here, we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95% CI: 0.06-0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.
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Affiliation(s)
- Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Kasha Strickland
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Anthony J. Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia,Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Loeske E. B. Kruuk
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK,Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - Céline H. Frère
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
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Rigamonti S, Floriano AM, Scaltriti E, Longbottom D, Livingstone M, Comandatore F, Pongolini S, Capucci L, Mandola ML, Bazzucchi M, Prati P, Vicari N. Comparative analysis of two genomes of Chlamydia pecorum isolates from an Alpine chamois and a water buffalo. BMC Genomics 2022; 23:645. [PMID: 36088280 PMCID: PMC9464383 DOI: 10.1186/s12864-022-08860-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
To date, whole genome sequencing has been performed mainly for isolates of Chlamydia trachomatis, C. pneumoniae, C. psittaci and C. abortus, but only a few isolates of C. pecorum have been entirely sequenced and this makes it difficult to understand its diversity and population structure. In this study the genome of two C. pecorum strains isolated from the lung of an Alpine chamois affected with pneumonia (isolate PV7855) and the brain of a water buffalo affected with meningoencephalomyelitis (isolate PV6959), were completely sequenced with MiSeq system (Illumina) and analyzed in their most polymorphic regions.
Results
The genome length and GC content of the two isolates were found to be consistent with other C. pecorum isolates and the gene content of polymorphic membrane proteins and plasticity zone was found to be very similar. Some differences were observed in the phospholipase genes for both isolates and in the number of genes in the plasticity zone, such as the presence of some hypothetical proteins in PV6959, not present in any other genomes analyzed in this study. Interestingly, PV6959 possesses an extra pmp and has an incomplete tryptophan biosynthesis operon. Plasmids were detected in both isolates.
Conclusions
Genome sequencing of the two C. pecorum strains did not reveal differences in length and GC content despite the origin from different animal species with different clinical disease. In the plasticity zone, the differences in the genes pattern might be related to the onset of specific symptoms or infection of specific hosts. The absence of a tryptophan biosynthesis pathway in PV6959 may suggest a strict relationship between C. pecorum and its host.
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White RT, Legione AR, Taylor-Brown A, Fernandez CM, Higgins DP, Timms P, Jelocnik M. Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala ( Phascolarctos cinereus) Pathogen. Pathogens 2021; 10:1543. [PMID: 34959498 PMCID: PMC8703710 DOI: 10.3390/pathogens10121543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety of C. pecorum molecular studies, to date, only four complete and 16 draft genomes have been published. Of those, only five draft genomes are from koalas. Here, using whole-genome sequencing and a comparative genomics approach, we describe the first two complete C. pecorum genomes collected from diseased koalas. A de novo assembly of DBDeUG_2018 and MC/MarsBar_2018 resolved the chromosomes and chlamydial plasmids each as single, circular contigs. Robust phylogenomic analyses indicate biogeographical separation between strains from northern and southern koala populations, and between strains infecting koala and livestock hosts. Comparative genomics between koala strains identified new, unique, and shared loci that accumulate single-nucleotide polymorphisms and separate between northern and southern, and within northern koala strains. Furthermore, we predicted novel type III secretion system effectors. This investigation constitutes a comprehensive genome-wide comparison between C. pecorum from koalas and provides improvements to annotations of a C. pecorum reference genome. These findings lay the foundations for identifying and understanding host specificity and adaptation behind chlamydial infections affecting koalas.
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Affiliation(s)
- Rhys T. White
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
| | - Alistair R. Legione
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Alyce Taylor-Brown
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Cristina M. Fernandez
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; (C.M.F.); (D.P.H.)
| | - Damien P. Higgins
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; (C.M.F.); (D.P.H.)
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
| | - Martina Jelocnik
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
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TESTIS ABNORMALITIES IN A POPULATION OF SOUTH AUSTRALIAN KOALAS (PHASCOLARCTOS CINEREUS). J Wildl Dis 2021; 58:158-167. [PMID: 34797903 DOI: 10.7589/jwd-d-21-00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/20/2021] [Indexed: 11/20/2022]
Abstract
Testis asymmetry, in which the testes in an individual differ in size, has recently been reported in koalas (Phascolarctos cinereus) in the Mount Lofty Ranges population of South Australia. We describe the morphology and histology of both testes from affected individuals in this population (n=56) and the parameters of koalas with normal-sized testes based on age and breeding season (n=56). Morphologic measurements included testis weight, length, width, and volume; histologic parameters included seminiferous tubule diameter, seminiferous epithelial height, and seminiferous tubule (interstitial tissue ratio and presence or absence of spermatozoa). Of the 56 koalas with intraindividual variation in testes size, 47 were classified as asymmetric and nine as microtestes. For koalas with asymmetric testes, all morphologic parameters were significantly decreased in the smaller testes compared with normal-sized testes, but for the histologic parameters, only seminiferous tubule diameter was significantly less. Histopathologic examination of the asymmetric testes showed 38 with normal parenchyma histologically indistinguishable between intraindividual testes, four with degeneration and atrophy, and three with hypoplasia, whereas examination of microtestes showed degeneration and atrophy in seven, hypoplasia in one, and aplasia in one. No association of testis size difference with Chlamydia pecorum infection was found in a subset of animals. For the 56 koalas with normal-sized testes, morphologic parameters were found to increase with age, and juvenile and young adults were found to have smaller seminiferous tubule diameters than adults. No differences were found between testes of koalas in the breeding and nonbreeding season. Overall, these findings indicate that testis asymmetry in koalas from the Mount Lofty Ranges population is common but not associated with decreased function, except where testis malformations such as hypoplasia or aplasia occur or when parenchyma has been disrupted by acquired disease.
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Robbins A, Hanger J, Jelocnik M, Quigley BL, Timms P. 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. Sci Rep 2020; 10:15013. [PMID: 32929174 PMCID: PMC7490398 DOI: 10.1038/s41598-020-72050-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/18/2020] [Indexed: 02/02/2023] Open
Abstract
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.
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Affiliation(s)
- Amy Robbins
- Genecology Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, 4556, Australia.,Endeavour Veterinary Ecology Pty Ltd, 1695 Pumicestone Road, Toorbul, QLD, 4510, Australia
| | - Jonathan Hanger
- Endeavour Veterinary Ecology Pty Ltd, 1695 Pumicestone Road, Toorbul, QLD, 4510, Australia
| | - Martina Jelocnik
- Genecology Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, 4556, Australia
| | - Bonnie L Quigley
- Genecology Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, 4556, Australia
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, 4556, Australia.
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Quigley BL, Timms P. Helping koalas battle disease - Recent advances in Chlamydia and koala retrovirus (KoRV) disease understanding and treatment in koalas. FEMS Microbiol Rev 2020; 44:583-605. [PMID: 32556174 PMCID: PMC8600735 DOI: 10.1093/femsre/fuaa024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/14/2020] [Indexed: 12/31/2022] Open
Abstract
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.
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Affiliation(s)
- Bonnie L Quigley
- Genecology Research Centre, University of the Sunshine Coast,
90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast,
90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia
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10
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Schultz AJ, Cristescu RH, Hanger J, Loader J, de Villiers D, Frère CH. Inbreeding and disease avoidance in a free-ranging koala population. Mol Ecol 2020; 29:2416-2430. [PMID: 32470998 DOI: 10.1111/mec.15488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 05/11/2020] [Indexed: 11/30/2022]
Abstract
Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free-ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.
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Affiliation(s)
- Anthony J Schultz
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Romane H Cristescu
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | - Jo Loader
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | | | - Celine H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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11
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Fabijan J, Sarker N, Speight N, Owen H, Meers J, Simmons G, Seddon J, Emes RD, Tarlinton R, Hemmatzadeh F, Woolford L, Trott DJ. Pathological Findings in Koala Retrovirus-positive Koalas (Phascolarctos cinereus) from Northern and Southern Australia. J Comp Pathol 2020; 176:50-66. [PMID: 32359636 DOI: 10.1016/j.jcpa.2020.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 01/05/2023]
Abstract
Koala retrovirus (KoRV) infection shows differences in prevalence and load between northern and southern Australian koala populations; however, the effect of this on diseases such as lymphoma and chlamydial disease is unclear. This study compared clinicopathological findings, haematology and splenic lymphoid area of KoRV-positive koalas from northern (Queensland [Qld], n = 67) and southern (South Australia [SA], n = 92) populations in order to provide further insight into KoRV pathogenesis. Blood was collected for routine haematology and for measurement of KoRV proviral load by quantitative polymerase chain reaction (qPCR). Plasma samples were assessed for KoRV viral load by reverse transcriptase qPCR and conjunctival and cloacal swabs were collected for measurement of the load of Chlamydia pecorum (qPCR). During necropsy examination, spleen was collected for lymphoid area analysis. Lymphoma was morphologically similar between the populations and occurred in koalas with the highest KoRV proviral and viral loads. Severe ocular chlamydial disease was observed in both populations, but urinary tract disease was more severe in Qld, despite similar C. pecorum loads. No associations between KoRV and chlamydial disease severity or load were observed, except in SA where viral load correlated positively with chlamydial disease severity. In both populations, proviral and viral loads correlated positively with lymphocyte and metarubricyte counts and correlated negatively with erythrocyte and neutrophil counts. Splenic lymphoid area was correlated positively with viral load. This study has shown further evidence for KoRV-induced oncogenesis and highlighted that lymphocytes and splenic lymphoid tissue may be key sites for KoRV replication. However, KoRV infection appears to be highly complex and continued investigation is required to fully understand its pathogenesis.
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Affiliation(s)
- J Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia.
| | - N Sarker
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - H Owen
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - J Meers
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - G Simmons
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - J Seddon
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - R Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - F Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
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12
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Waugh CA, Timms P. A proposed roadmap for the control of infections in wildlife using Chlamydia vaccine development in koalas Phascolarctos cinereus as a template. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Courtney A. Waugh
- C. Waugh ✉ , Faculty of Bioscience and Aquaculture, Nord Univ., Steinkjer, Norway
| | - Peter Timms
- P. Timms, Univ. of the Sunshine Coast, Sippy Downs, Queensland, Australia
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13
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Hulse LS, McDonald S, Johnston SD, Beagley KW. Rapid point-of-care diagnostics for the detection of Chlamydia pecorum in koalas (Phascolarctos cinereus) using loop-mediated isothermal amplification without nucleic acid purification. Microbiologyopen 2019; 8:e916. [PMID: 31419041 PMCID: PMC6925175 DOI: 10.1002/mbo3.916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
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.
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Affiliation(s)
- Lyndal S Hulse
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD, Australia
| | | | - Stephen D Johnston
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD, Australia
| | - Kenneth W Beagley
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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14
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Phillips S, Quigley BL, Aziz A, Bergen W, Booth R, Pyne M, Timms P. Antibiotic treatment of Chlamydia-induced cystitis in the koala is linked to expression of key inflammatory genes in reactive oxygen pathways. PLoS One 2019; 14:e0221109. [PMID: 31415633 PMCID: PMC6695219 DOI: 10.1371/journal.pone.0221109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/30/2019] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Samuel Phillips
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
- * E-mail:
| | - Bonnie L. Quigley
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - Ammar Aziz
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Wendy Bergen
- Australia Zoo Wildlife Hospital, Steve Irwin Way, Queensland, Australia
| | - Rosemary Booth
- Australia Zoo Wildlife Hospital, Steve Irwin Way, Queensland, Australia
| | - Michael Pyne
- Currumbin Wildlife Hospital, Currumbin, Queensland, Australia
| | - Peter Timms
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia
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15
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Bommana S, Jelocnik M, Borel N, Marsh I, Carver S, Polkinghorne A. The limitations of commercial serological assays for detection of chlamydial infections in Australian livestock. J Med Microbiol 2019; 68:627-632. [PMID: 30839254 DOI: 10.1099/jmm.0.000951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chlamydia pecorum and Chlamydia abortus are related ruminant pathogens endemic to different global regions. Potential co-infections combined with the lack of species-specific serological assays challenge accurate diagnosis. Serological screening revealed low C. abortus seropositivity with the peptide-based ELISA (1/84; 1.2%) in Australian sheep yet moderate seropositivity in a Swiss flock with history of C. abortus-associated abortions (17/63; 26.9%). By whole cell antigen complement fixation tests (CFT) and ELISA, chlamydial seropositivity was significantly higher in all groups, suggesting cross-reactivity between these two chlamydial species and non-specificity of the tests. However, only C. pecorum DNA could be detected by qPCR in Chlamydia seropositive Australian animals screened, suggesting chlamydial seropositivity was due to cross-reactivity with endemic C. pecorum infections. These results suggest ascribing Chlamydia seropositivity to chlamydial species in livestock using whole-cell antigen CFT or ELISA should be treated with caution; and that peptide-based ELISA and qPCR provide greater chlamydial species-specificity.
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Affiliation(s)
- Sankhya Bommana
- Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Martina Jelocnik
- Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Nicole Borel
- Institute of Veterinary Pathology, Department of Pathobiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Ian Marsh
- Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Adam Polkinghorne
- Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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16
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Fernandez CM, Schmertmann LJ, Higgins DP, Casteriano A, Irinyi L, Mella VSA, Crowther MS, Meyer W, Krockenberger MB. Genetic differences in Chlamydia pecorum between neighbouring sub-populations of koalas (Phascolarctos cinereus). Vet Microbiol 2019; 231:264-270. [PMID: 30853132 DOI: 10.1016/j.vetmic.2019.02.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 01/09/2023]
Abstract
Chlamydiosis, caused by Chlamydia pecorum, is regarded as an important threat to koala populations. Across the koala's geographical range, disease severity associated with C. pecorum infection varies, with pathogen diversity and strain pathogenicity being likely important factors. To examine C. pecorum diversity on a sub-population level a Multi-Locus Sequence Typing (MLST) scheme, containing the housekeeping genes; gatA, oppA_3, hflX, gidA, enoA, hemN and fumC, was used to type strains from two sub-populations of koalas from the Liverpool Plains, NSW, Australia, with different disease expressions. Typing of samples from 2015 to 2017, revealed a significant association between sequence type ST 69 and clinical disease and a significant difference in sequence type frequencies between sub-populations. Sequence type ST 69 has previously been identified in both subclinical and clinically diseased koalas indicating that these markers alone are not illustrative of pathogenicity. However, recent emergence of this sequence type in a naïve population may explain the differing disease expressions. Sequence types ST 73 and ST 69 have been described in koalas across a broad geographic range, indicating multiple introduction events and/or a limited veracity of the MLST loci to explore fine scale epidemiological investigations, particularly those examining the interface between pathogenic strain and disease outcome.
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Affiliation(s)
- Cristina M Fernandez
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia; The Westmead Institute for Medical Research, 176 Hawkesbury Road, 2145, Westmead, NSW, Australia; Sydney School of Veterinary Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Laura J Schmertmann
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia; The Westmead Institute for Medical Research, 176 Hawkesbury Road, 2145, Westmead, NSW, Australia; Sydney School of Veterinary Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Damien P Higgins
- Sydney School of Veterinary Science, The University of Sydney, Sydney, 2006, NSW, Australia; Marie Bashir Institute for Emerging Infectious diseases and Biosecurity, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia
| | - Andrea Casteriano
- Sydney School of Veterinary Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia; The Westmead Institute for Medical Research, 176 Hawkesbury Road, 2145, Westmead, NSW, Australia
| | - Valentina S A Mella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Mathew S Crowther
- School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia; The Westmead Institute for Medical Research, 176 Hawkesbury Road, 2145, Westmead, NSW, Australia; Marie Bashir Institute for Emerging Infectious diseases and Biosecurity, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia
| | - Mark B Krockenberger
- Sydney School of Veterinary Science, The University of Sydney, Sydney, 2006, NSW, Australia; Marie Bashir Institute for Emerging Infectious diseases and Biosecurity, The University of Sydney, 176 Hawkesbury road, 2145, Westmead, NSW, Australia.
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17
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Phillips S, Robbins A, Loader J, Hanger J, Booth R, Jelocnik M, Polkinghorne A, Timms P. Chlamydia pecorum gastrointestinal tract infection associations with urogenital tract infections in the koala (Phascolarctos cinereus). PLoS One 2018; 13:e0206471. [PMID: 30383822 PMCID: PMC6211709 DOI: 10.1371/journal.pone.0206471] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
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.
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Affiliation(s)
- Samuel Phillips
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
- * E-mail:
| | - Amy Robbins
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Australia
| | - Joanne Loader
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Australia
| | | | | | - Martina Jelocnik
- Animal Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
| | - Adam Polkinghorne
- Animal Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
| | - Peter Timms
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
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18
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Characterization of the In Vitro Chlamydia pecorum Response to Gamma Interferon. Infect Immun 2018; 86:IAI.00714-17. [PMID: 29358337 DOI: 10.1128/iai.00714-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/14/2018] [Indexed: 12/12/2022] Open
Abstract
Chlamydia pecorum is an important intracellular bacterium that causes a range of diseases in animals, including a native Australian marsupial, the koala. In humans and animals, a gamma interferon (IFN-γ)-mediated immune response is important for the control of intracellular bacteria. The present study tested the hypotheses that C. pecorum can escape IFN-γ-mediated depletion of host cell tryptophan pools. In doing so, we demonstrated that, unlike Chlamydia trachomatis, C. pecorum is completely resistant to IFN-γ in human epithelial cells. While the growth of C. pecorum was inhibited in tryptophan-deficient medium, it could be restored by the addition of kynurenine, anthranilic acid, and indole, metabolites that could be exploited by the gene products of the C. pecorum tryptophan biosynthesis operon. We also found that expression of trp genes was detectable only when C. pecorum was grown in tryptophan-free medium, with gene repression occurring in response to the addition of kynurenine, anthranilic acid, and indole. When grown in bovine kidney epithelial cells, bovine IFN-γ also failed to restrict the growth of C. pecorum, while C. trachomatis was inhibited, suggesting that C. pecorum could use the same mechanisms to evade the immune response in vivo in its natural host. Highlighting the different mechanisms triggered by IFN-γ, however, both species failed to grow in murine McCoy cells treated with murine IFN-γ. This work confirms previous hypotheses about the potential survival of C. pecorum after IFN-γ-mediated host cell tryptophan depletion and raises questions about the immune pathways used by the natural hosts of C. pecorum to control the widespread pathogen.
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19
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Bommana S, Walker E, Desclozeaux M, Jelocnik M, Timms P, Polkinghorne A, Carver S. Molecular and serological dynamics of Chlamydia pecorum infection in a longitudinal study of prime lamb production. PeerJ 2018; 6:e4296. [PMID: 29379689 PMCID: PMC5787346 DOI: 10.7717/peerj.4296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/06/2018] [Indexed: 01/25/2023] Open
Abstract
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.
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Affiliation(s)
- Sankhya Bommana
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | | | - Marion Desclozeaux
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Martina Jelocnik
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Peter Timms
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
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20
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Nyari S, Waugh CA, Dong J, Quigley BL, Hanger J, Loader J, Polkinghorne A, Timms P. Epidemiology of chlamydial infection and disease in a free-ranging koala (Phascolarctos cinereus) population. PLoS One 2017; 12:e0190114. [PMID: 29281731 PMCID: PMC5744985 DOI: 10.1371/journal.pone.0190114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/10/2017] [Indexed: 12/01/2022] Open
Abstract
Chlamydial disease continues to be one of the main factors threatening the long-term survival of the koala (Phascolarctos cinereus). Despite this, large epidemiological studies of chlamydial infection and disease in wild koala populations are lacking. A better understanding of the prevalence, transmission and pathogenesis is needed to improve control measures, such as the development of vaccines. We investigated the prevalence of Chlamydia pecorum infection and disease in 160 koalas in a peri-urban wild population in Queensland, Australia and found that 31% of koalas were Chlamydia PCR positive and 28% had clinically detectable chlamydial disease. Most infections were at the urogenital site (27%; both males and females) with only 14% at the ocular site. Interestingly, we found that 27% (4/15) of koalas considered to be sexually immature (9–13 months) were already infected with C. pecorum, suggesting that a significant percentage of animals are infected directly from their mother. Ocular infection levels were less prevalent with increasing age (8% in koalas older than 4 years), whereas the prevalence of urogenital tract infections remained high into older age (26% in koalas older than 4 years), suggesting that, after mother-to-young transmission, C. pecorum is predominantly a sexually transmitted infection. While 28% of koalas in this population had clinically detectable chlamydial disease (primarily urogenital tract disease), many PCR positive koalas had no detectable disease and importantly, not all diseased animals were PCR positive. We also observed higher chlamydial loads in koalas who were C. pecorum infected without clinical disease than in koalas who were C. pecorum infected with clinical disease. These results shed light on the potential mechanisms of transmission of C. pecorum in koalas and also guide future control measures, such as vaccination.
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Affiliation(s)
- Sharon Nyari
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Courtney A. Waugh
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Jianbao Dong
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Bonnie L. Quigley
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Jonathan Hanger
- Endeavour Veterinary Ecology, Toorbul, Queensland, Australia
| | - Joanne Loader
- Endeavour Veterinary Ecology, Toorbul, Queensland, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Peter Timms
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- * E-mail:
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21
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Molecular Dynamics and Mode of Transmission of Koala Retrovirus as It Invades and Spreads through a Wild Queensland Koala Population. J Virol 2017; 92:JVI.01871-17. [PMID: 29237837 DOI: 10.1128/jvi.01871-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/02/2017] [Indexed: 12/31/2022] Open
Abstract
The recent acquisition of a novel retrovirus (KoRV) by koalas (Phascolarctos cinereus) has created new opportunities for retroviral research and new challenges for koala conservation. There are currently two major subtypes of KoRV: KoRV-A, which is believed to be endogenous only in koalas from the northern part of Australia, and KoRV-B, which appears to be exogenous. Understanding and management of these subtypes require population level studies of their prevalence and diversity, especially when coinfected in the same population, and investigations of their modes of transmission in the wild. Toward this end, we studied a wild Queensland koala population of 290 animals over a 5-year period and investigated the prevalence, diversity and mode of transmission of KoRV-A and KoRV-B. We found KoRV-A to have an infection level of 100% in the population, with all animals sharing the same dominant envelope protein sequence. In contrast, the KoRV-B infection prevalence was only 24%, with 21 different envelope protein sequence variants found in the 83 KoRV-B-positive animals. Linked to severe disease outcomes, a significant association between KoRV-B positivity and both chlamydial disease and neoplasia was found in the population. Transmission of KoRV-B was found at a rate of 3% via adult-to-adult contact per year, while there was a 100% rate of KoRV-B-positive mothers transmitting the virus to their joeys. Collectively, these findings demonstrate KoRV-B as the pathogenic subtype in this wild koala population and inform future intervention strategies with subtype variation and transmission data.
IMPORTANCE KoRV represents a unique opportunity to study a relatively young retrovirus as it goes through its molecular evolution in both an endogenous form and a more recently evolved exogenous form. The endogenous form, KoRV-A, now appears to have stably and completely established itself in Northern Australian koala populations and is progressing south. Conversely, the exogenous form, KoRV-B, is undergoing continuous mutation and spread in the north and, as yet, has not reached all southern koala populations. We can now link KoRV-B to neoplasia and chlamydial disease in both wild and captive koalas, making it an imminent threat to this already vulnerable species. This work represents the largest study of koalas in a wild population with respect to KoRV-A/KoRV-B-infected/coinfected animals and the linkage of this infection to chlamydial disease, neoplasia, viral evolution, and spread.
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22
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Molecular evidence of Chlamydia pecorum and arthropod-associated Chlamydiae in an expanded range of marsupials. Sci Rep 2017; 7:12844. [PMID: 28993660 PMCID: PMC5634461 DOI: 10.1038/s41598-017-13164-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/19/2017] [Indexed: 11/21/2022] Open
Abstract
The order Chlamydiales are biphasic intracellular bacterial pathogens infecting humans and domesticated animals. Wildlife infections have also been reported, with the most studied example being Chlamydia pecorum infections in the koala, an iconic Australian marsupial. In koalas, molecular evidence suggests that spill-over from C. pecorum infected livestock imported into Australia may have had a historical or contemporary role. Despite preliminary evidence that other native Australian marsupials also carry C. pecorum, their potential as reservoirs of this pathogen and other Chlamydia-related bacteria (CRBs) has been understudied. Mucosal epithelial samples collected from over 200 native Australian marsupials of different species and geographic regions across Australia were PCR screened for Chlamydiales. Previously described and genetically distinct C. pecorum genotypes and a range of 16S rRNA genotypes sharing similarity to different CRBs in the broader Chlamydiales order were present. One 16S rRNA Chlamydiales genotype recently described in Australian ticks that parasitise native Australian marsupials was also identified. This study provides further evidence that chlamydial infections are widespread in native fauna and that detailed investigations are required to understand the influence these infections have on host species conservation, but also whether infection spill-over plays a role in their epidemiology.
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Jelocnik M, Islam MM, Madden D, Jenkins C, Branley J, Carver S, Polkinghorne A. Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum. PeerJ 2017; 5:e3799. [PMID: 28929022 PMCID: PMC5592900 DOI: 10.7717/peerj.3799] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022] Open
Abstract
Background Chlamydia psittaci and Chlamydia pecorum are important veterinary pathogens, with the former also being responsible for zoonoses, and the latter adversely affecting koala populations in Australia and livestock globally. The rapid detection of these organisms is still challenging, particularly at the point-of-care (POC). In the present study, we developed and evaluated rapid, sensitive and robust C. psittaci-specific and C. pecorum-specific Loop Mediated Isothermal Amplification (LAMP) assays for detection of these pathogens. Methods and Materials The LAMP assays, performed in a Genie III real-time fluorometer, targeted a 263 bp region of the C. psittaci-specific Cps_0607 gene or a 209 bp region of a C. pecorum-specific conserved gene CpecG_0573, and were evaluated using a range of samples previously screened using species-specific quantitative PCRs (qPCRs). Species-specificity for C. psittaci and C. pecorum LAMP targets was tested against DNA samples from related chlamydial species and a range of other bacteria. In order to evaluate pathogen detection in clinical samples, C. psittaci LAMP was evaluated using a total of 26 DNA extracts from clinical samples from equine and avian hosts, while for C. pecorum LAMP, we tested a total of 63 DNA extracts from clinical samples from koala, sheep and cattle hosts. A subset of 36 C. pecorum samples was also tested in a thermal cycler (instead of a real-time fluorometer) using newly developed LAMP and results were determined as an end point detection. We also evaluated rapid swab processing (without DNA extraction) to assess the robustness of these assays. Results Both LAMP assays were demonstrated to species-specific, highly reproducible and to be able to detect as little as 10 genome copy number/reaction, with a mean amplification time of 14 and 24 min for C. psittaci and C. pecorum, respectively. When testing clinical samples, the overall congruence between the newly developed LAMP assays and qPCR was 92.3% for C. psittaci (91.7% sensitivity and 92.9% specificity); and 84.1% for C. pecorum (90.6% sensitivity and 77.4% specificity). For a subset of 36 C. pecorum samples tested in a thermal cycler using newly developed LAMP, we observed 34/36 (94.4%) samples result being congruent between LAMP performed in fluorometer and in thermal cycler. Rapid swab processing method evaluated in this study also allows for chlamydial DNA detection using LAMP. Discussion In this study, we describe the development of novel, rapid and robust C. psittaci-specific and C. pecorum-specific LAMP assays that are able to detect these bacteria in clinical samples in either the laboratory or POC settings. With further development and a focus on the preparation of these assays at the POC, it is anticipated that both tests may fill an important niche in the repertoire of ancillary diagnostic tools available to clinicians.
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Affiliation(s)
- Martina Jelocnik
- Centre for Animal Health Innovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Md Mominul Islam
- Centre for Animal Health Innovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Danielle Madden
- Centre for Animal Health Innovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - James Branley
- Nepean Hospital, Penrith, New South Wales, Australia
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
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Lymphoma, Koala Retrovirus Infection and Reproductive Chlamydiosis in a Koala (Phascolarctos cinereus). J Comp Pathol 2017; 157:188-192. [PMID: 28942303 DOI: 10.1016/j.jcpa.2017.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/17/2017] [Accepted: 07/29/2017] [Indexed: 11/20/2022]
Abstract
Koala retrovirus (KoRV) infection, thought to be associated with lymphoid neoplasia, and Chlamydia pecorum-related ocular and urogenital disease are both highly prevalent in eastern Australian koala (Phascolarctos cinereus) populations. However, in South Australian koalas, little is known about KoRV infection and C. pecorum-associated disease. We report the first South Australian case of lymphoma in a KoRV-A-positive female koala also affected by severe reproductive chlamydiosis. The koala was from the Mount Lofty Ranges population and was presented with hindlimb lameness. Clinical examination identified right stifle crepitus, enlarged superficial lymph nodes and paraovarian cysts. Necropsy examination revealed extensive cartilage degeneration and loss over the medial femoral condyle, solid femoral bone marrow, mesenteric and ovarian tumours, paraovarian cysts and purulent metritis. Histopathology confirmed lymphoma in the bone marrow, mesenteric lymph nodes and ovary, with infiltration and parenchymal effacement in the pancreas, adrenal glands and other tissues. Lymphoma, KoRV and chlamydiosis are being investigated further in this population.
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Vidgen ME, Hanger J, Timms P. Microbiota composition of the koala (Phascolarctos cinereus) ocular and urogenital sites, and their association with Chlamydia infection and disease. Sci Rep 2017; 7:5239. [PMID: 28701755 PMCID: PMC5507983 DOI: 10.1038/s41598-017-05454-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/24/2017] [Indexed: 12/14/2022] Open
Abstract
Disease caused by Chlamydia pecorum is characterised by ocular and urogenital infections that can lead to blindness and infertility in koalas. However, koalas that are infected with C. pecorum do not always progress to disease. In other host systems, the influence of the microbiota has been implicated in either accelerating or preventing infections progressing to disease. This study investigates the contribution of koala urogenital and ocular microbiota to Chlamydia infection and disease in a free ranging koala population. Using univariate and multivariate analysis, it was found that reproductive status in females and sexual maturation in males, were defining features in the koala urogenital microbiota. Changes in the urogenital microbiota of koalas is correlated with infection by the common pathogen, C. pecorum. The correlation of microbiota composition and C. pecorum infection is suggestive of members of the microbiota being involved in the acceleration or prevention of infections progressing to disease. The analysis also suggests that multiple microbes are likely to be associated with this process of disease progression, rather than a single organism. While other Chlamydia-like organisms were also detected, they are unlikely to contribute to chlamydial disease as they are rare members of the urogenital and ocular microbiota communities.
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Affiliation(s)
- Miranda E Vidgen
- University of the Sunshine Coast, Faculty of Science, Health, Education & Engineering, Centre for Animal Health Innovation, Locked Bag 4, Maroochydore, Qld 4558, Australia
| | - Jonathan Hanger
- Endeavour Veterinary Ecology Pty Ltd., 1695 Pumicestone Rd., Toorbul, Qld 4510, Australia
| | - Peter Timms
- University of the Sunshine Coast, Faculty of Science, Health, Education & Engineering, Centre for Animal Health Innovation, Locked Bag 4, Maroochydore, Qld 4558, Australia.
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Immunization of a wild koala population with a recombinant Chlamydia pecorum Major Outer Membrane Protein (MOMP) or Polymorphic Membrane Protein (PMP) based vaccine: New insights into immune response, protection and clearance. PLoS One 2017; 12:e0178786. [PMID: 28575080 PMCID: PMC5456371 DOI: 10.1371/journal.pone.0178786] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/18/2017] [Indexed: 12/11/2022] Open
Abstract
We assessed the effects of two different single-dose anti-Chlamydia pecorum (C. pecorum) vaccines (containing either Major Outer Membrane Protein (3MOMP) or Polymorphic Membrane Protein (Pmp) as antigens) on the immune response of a group of wild koalas. Both vaccines elicited a systemic humoral response as seen by the production of anti-chlamydial IgG antibodies in more than 90% of vaccinated koalas. A mucosal immune response was also observed, with an increase in Chlamydia-specific mucosal IgG and/or IgA antibodies in some koalas post-vaccination. Both vaccines elicited a cell-mediated immune response as measured by the production of the cytokines IFN-γ and IL-17 post-vaccination. To determine the level of protection provided by the vaccines under natural conditions we assessed C. pecorum infection loads and chlamydial disease status of all vaccinated koalas pre- and post-vaccination, compared to a non-vaccinated cohort from the same habitat. The MOMP vaccinated koalas that were infected on the day of vaccination showed significant clearance of their infection at 6 months post-vaccination. In contrast, the number of new infections in the PMP vaccine was similar to the control group, with some koalas progressing to disease. Genotyping of the ompA gene from the C. pecorum strains infecting the vaccinated animals, identified genetic variants of ompA-F genotype and a new genotype ompA-O. We found that those animals that were the least well protected became infected with strains of C. pecorum not covered by the vaccine. In conclusion, a single dose vaccine formulated with either recombinant PmpG or MOMP can elicit both cell-mediated and humoral (systemic and mucosal) immune responses, with the MOMP vaccine showing clearance of infection in all infected koalas. Although the capability of our vaccines to stimulate an adaptive response and be protective needs to be fully evaluated, this work illustrates the necessity to combine epitopes most relevant to a large panel of variable strains with an efficient adjuvant.
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Waugh CA, Hanger J, Loader J, King A, Hobbs M, Johnson R, Timms P. Infection with koala retrovirus subgroup B (KoRV-B), but not KoRV-A, is associated with chlamydial disease in free-ranging koalas (Phascolarctos cinereus). Sci Rep 2017; 7:134. [PMID: 28273935 PMCID: PMC5427818 DOI: 10.1038/s41598-017-00137-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/09/2017] [Indexed: 02/02/2023] Open
Abstract
The virulence of chlamydial infection in wild koalas is highly variable between individuals. Some koalas can be infected (PCR positive) with Chlamydia for long periods but remain asymptomatic, whereas others develop clinical disease. Chlamydia in the koala has traditionally been studied without regard to coinfection with other pathogens, although koalas are usually subject to infection with koala retrovirus (KoRV). Retroviruses can be immunosuppressive, and there is evidence of an immunosuppressive effect of KoRV in vitro. Originally thought to be a single endogenous strain, a new, potentially more virulent exogenous variant (KoRV-B) was recently reported. We hypothesized that KoRV-B might significantly alter chlamydial disease outcomes in koalas, presumably via immunosuppression. By studying sub-groups of Chlamydia and KoRV infected koalas in the wild, we found that neither total KoRV load (either viraemia or proviral copies per genome), nor chlamydial infection level or strain type, was significantly associated with chlamydial disease risk. However, PCR positivity with KoRV-B was significantly associated with chlamydial disease in koalas (p = 0.02961). This represents an example of a recently evolved virus variant that may be predisposing its host (the koala) to overt clinical disease when co-infected with an otherwise asymptomatic bacterial pathogen (Chlamydia).
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Affiliation(s)
- Courtney A Waugh
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, 4558, Queensland, Australia.,Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Jonathan Hanger
- Endeavour Veterinary Ecology, 1695 Pumicestone Rd, Toorbul, 4510, Queensland, Australia
| | - Joanne Loader
- Endeavour Veterinary Ecology, 1695 Pumicestone Rd, Toorbul, 4510, Queensland, Australia
| | - Andrew King
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Matthew Hobbs
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Rebecca Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, 4558, Queensland, Australia.
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Jelocnik M, Polkinghorne A. Chlamydia pecorum: successful pathogen of koalas or Australian livestock? MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In Australia, the obligate intracellular bacterium Chlamydia pecorum is best known as the notorious koala pathogen that causes debilitating ocular and urogenital tract disease. While globally published data suggests that this species is essentially ubiquitous in livestock, little is known about the epidemiology of livestock C. pecorum infections here in Australia. My research is focused on investigating the genetic diversity and transmission patterns of C. pecorum, and why it causes disease. Using our newly developed C. pecorum-specific molecular epidemiology typing scheme we provided the first epidemiological data on infections in sheep and cattle in Australia, identifying strains associated with a range of diseases in livestock, and uncovering an unexpected level of diversity for this pathogen. Most importantly, we observed that the same strain can infect koala and sheep, indicating on ongoing cross-host transmission and ‘spill-over' risks to wildlife. Further, by dissecting koala, sheep, cattle and pig C. pecorum strains genomes, we have also identified novel virulence-associated factors that could be explored as vaccine candidates for both livestock and koala infections.
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29
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Waugh C, Austin R, Polkinghorne A, Timms P. Treatment of Chlamydia-associated ocular disease via a recombinant protein based vaccine in the koala (Phascolarctos cinereus). Biologicals 2016; 44:588-590. [PMID: 27707559 DOI: 10.1016/j.biologicals.2016.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/23/2016] [Accepted: 09/13/2016] [Indexed: 10/20/2022] Open
Abstract
Koalas (Phascolarctos cinereus) are affected by debilitating chlamydial disease that can lead to blindness, infertility, and death. The causative agent is the intracellular bacterium Chlamydia pecorum. While antibiotics can be used to treat koala chlamydial infection, they are often ineffective or cause severe dysbiosis to the animal's unique gut flora. Recent work has progressed on the development of a protective vaccine for Chlamydia in the koala. This study demonstrates that the use of a vaccine can have a positive effect in koalas already with clinical signs of ocular disease, suggesting a possible therapeutic effect and an alternative to antibiotic therapy.
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Affiliation(s)
- Courtney Waugh
- Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia.
| | - Ray Austin
- Keen Street Veterinary Clinic, Lismore, New South Wales, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia.
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia.
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30
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Narayan EJ, Williams M. Understanding the dynamics of physiological impacts of environmental stressors on Australian marsupials, focus on the koala (Phascolarctos cinereus). BMC ZOOL 2016. [DOI: 10.1186/s40850-016-0004-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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31
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Legione AR, Patterson JLS, Whiteley PL, Amery-Gale J, Lynch M, Haynes L, Gilkerson JR, Polkinghorne A, Devlin JM, Sansom FM. Identification of unusual Chlamydia pecorum genotypes in Victorian koalas (Phascolarctos cinereus) and clinical variables associated with infection. J Med Microbiol 2016; 65:420-428. [PMID: 26932792 DOI: 10.1099/jmm.0.000241] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlamydia pecorum infection is a threat to the health of free-ranging koalas (Phascolarctos cinereus) in Australia. Utilizing an extensive sample archive we determined the prevalence of C. pecorum in koalas within six regions of Victoria, Australia. The ompA genotypes of the detected C. pecorum were characterized to better understand the epidemiology of this pathogen in Victorian koalas. Despite many studies in northern Australia (i.e. Queensland and New South Wales), prior Chlamydia studies in Victorian koalas are limited. We detected C. pecorum in 125/820 (15 %) urogenital swabs, but in only one ocular swab. Nucleotide sequencing of the molecular marker C. pecorum ompA revealed that the majority (90/114) of C. pecorum samples typed were genotype B. This genotype has not been reported in northern koalas. In general, Chlamydia infection in Victorian koalas is associated with milder clinical signs compared with infection in koalas in northern populations. Although disease pathogenesis is likely to be multifactorial, the high prevalence of genotype B in Victoria may suggest it is less pathogenic. All but three koalas had C. pecorum genotypes unique to southern koala populations (i.e. Victoria and South Australia). These included a novel C. pecorum ompA genotype and two genotypes associated with livestock. Regression analysis determined that significant factors for the presence of C. pecorum infection were sex and geographical location. The presence of 'wet bottom' in males and the presence of reproductive tract pathology in females were significantly associated with C. pecorum infection, suggesting variation in clinical disease manifestations between sexes.
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Affiliation(s)
- Alistair R Legione
- Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia
| | - Jade L S Patterson
- Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia.,Veterinary Department, Melbourne Zoo,Parkville, Victoria,Australia
| | - Pam L Whiteley
- Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia.,Wildlife Health Surveillance Victoria, The University of Melbourne,Werribee, Victoria,Australia
| | - Jemima Amery-Gale
- Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia.,Australian Wildlife Health Centre, Healesville Sanctuary, Healesville,Victoria,Australia
| | - Michael Lynch
- Veterinary Department, Melbourne Zoo,Parkville, Victoria,Australia
| | - Leesa Haynes
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Werribee, Victoria,Australia
| | - James R Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs,Queensland,Australia
| | - Joanne M Devlin
- Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia
| | - Fiona M Sansom
- Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne,Parkville, Victoria,Australia
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Waugh C, Khan SA, Carver S, Hanger J, Loader J, Polkinghorne A, Beagley K, Timms P. A Prototype Recombinant-Protein Based Chlamydia pecorum Vaccine Results in Reduced Chlamydial Burden and Less Clinical Disease in Free-Ranging Koalas (Phascolarctos cinereus). PLoS One 2016; 11:e0146934. [PMID: 26756624 PMCID: PMC4710501 DOI: 10.1371/journal.pone.0146934] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/23/2015] [Indexed: 11/19/2022] Open
Abstract
Diseases associated with Chlamydia pecorum infection are a major cause of decline in koala populations in Australia. While koalas in care can generally be treated, a vaccine is considered the only option to effectively reduce the threat of infection and disease at the population level. In the current study, we vaccinated 30 free-ranging koalas with a prototype Chlamydia pecorum vaccine consisting of a recombinant chlamydial MOMP adjuvanted with an immune stimulating complex. An additional cohort of 30 animals did not receive any vaccine and acted as comparison controls. Animals accepted into this study were either uninfected (Chlamydia PCR negative) at time of initial vaccination, or infected (C. pecorum positive) at either urogenital (UGT) and/or ocular sites (Oc), but with no clinical signs of chlamydial disease. All koalas were vaccinated / sampled and then re-released into their natural habitat before re-capturing and re-sampling at 6 and 12 months. All vaccinated koalas produced a strong immune response to the vaccine, as indicated by high titres of specific plasma antibodies. The incidence of new infections in vaccinated koalas over the 12-month period post-vaccination was slightly less than koalas in the control group, however, this was not statistically significant. Importantly though, the vaccine was able to significantly reduce the infectious load in animals that were Chlamydia positive at the time of vaccination. This effect was evident at both the Oc and UGT sites and was stronger at 6 months than at 12 months post-vaccination. Finally, the vaccine was also able to reduce the number of animals that progressed to disease during the 12-month period. While the sample sizes were small (statistically speaking), results were nonetheless striking. This study highlights the potential for successful development of a Chlamydia vaccine for koalas in a wild setting.
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Affiliation(s)
- Courtney Waugh
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs, 4558, Queensland, Australia
| | - Shahneaz Ali Khan
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059, Queensland, Australia
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - Jonathan Hanger
- Endeavour Veterinary Ecology, 1695 Pumicestone Rd, Toorbul, 4510, Queensland, Australia
| | - Joanne Loader
- Endeavour Veterinary Ecology, 1695 Pumicestone Rd, Toorbul, 4510, Queensland, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs, 4558, Queensland, Australia
| | - Kenneth Beagley
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059, Queensland, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs, 4558, Queensland, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059, Queensland, Australia
- * E-mail:
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Khan SA, Polkinghorne A, Waugh C, Hanger J, Loader J, Beagley K, Timms P. Humoral immune responses in koalas (Phascolarctos cinereus) either naturally infected with Chlamydia pecorum or following administration of a recombinant chlamydial major outer membrane protein vaccine. Vaccine 2015; 34:775-82. [PMID: 26747718 DOI: 10.1016/j.vaccine.2015.12.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 11/15/2022]
Abstract
The development of a vaccine is a key strategy to combat the widespread and debilitating effects of chlamydial infection in koalas. One such vaccine in development uses recombinant chlamydial major outer membrane protein (rMOMP) as an antigen and has shown promising results in several koala trials. Previous chlamydial vaccine studies, primarily in the mouse model, suggest that both cell-mediated and antibody responses will be required for adequate protection. Recently, the important protective role of antibodies has been highlighted. In our current study, we conducted a detailed analysis of the antibody-mediated immune response in koalas that are either (a) naturally-infected, and/or (b) had received an rMOMP vaccine. Firstly, we observed that naturally-infected koalas had very low levels of Chlamydia pecorum-specific neutralising antibodies. A strong correlation between low IgG total titers/neutralising antibody levels, and higher C. pecorum infection load was also observed in these naturally-infected animals. In vaccinated koalas, we showed that the vaccine was able to boost the humoral immune response by inducing strong levels of C. pecorum-specific neutralising antibodies. A detailed characterisation of the MOMP epitope response was also performed in naturally-infected and vaccinated koalas using a PepScan epitope approach. This analysis identified unique sets of MOMP epitope antibodies between naturally-infected non-protected and diseased koalas, versus vaccinated koalas, with the latter group of animals producing a unique set of specific epitope-directed antibodies that we demonstrated were responsible for the in vitro neutralisation activity. Together, these results show the importance of antibodies in chlamydial infection and immunity following vaccination in the koala.
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Affiliation(s)
- Shahneaz Ali Khan
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University, Khulshi, Chittagong 4202, Bangladesh.
| | - Adam Polkinghorne
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD 4558, Australia.
| | - Courtney Waugh
- Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD 4558, Australia.
| | - Jon Hanger
- Endeavour Veterinary Ecology Pty Ltd, 1695 Pumicestone Road, Toorbul, QLD 4510, Australia.
| | - Jo Loader
- Endeavour Veterinary Ecology Pty Ltd, 1695 Pumicestone Road, Toorbul, QLD 4510, Australia.
| | - Kenneth Beagley
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia.
| | - Peter Timms
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD 4558, Australia.
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Jelocnik M, Bachmann NL, Kaltenboeck B, Waugh C, Woolford L, Speight KN, Gillett A, Higgins DP, Flanagan C, Myers GSA, Timms P, Polkinghorne A. Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas. BMC Genomics 2015; 16:893. [PMID: 26531162 PMCID: PMC4632680 DOI: 10.1186/s12864-015-2053-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/08/2015] [Indexed: 12/22/2022] Open
Abstract
Background Chlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics of C. pecorum strains from sheep, cattle and koalas has revealed that only single nucleotide polymorphisms (SNPs) and a limited number of pseudogenes appear to contribute to the genetic diversity of this pathogen. No chlamydial plasmid has been detected in these strains despite its ubiquitous presence in almost all other chlamydial species. Genomic analyses have not previously included C. pecorum from porcine hosts. We sequenced the genome of three C. pecorum isolates from pigs with differing pathologies in order to re-evaluate the genetic differences and to update the phylogenetic relationships between C. pecorum from each of the hosts. Methods Whole genome sequences for the three porcine C. pecorum isolates (L1, L17 and L71) were acquired using C. pecorum-specific sequence capture probes with culture-independent methods, and assembled in CLC Genomics Workbench. The pairwise comparative genomic analyses of 16 pig, sheep, cattle and koala C. pecorum genomes were performed using several bioinformatics platforms, while the phylogenetic analyses of the core C. pecorum genomes were performed with predicted recombination regions removed. Following the detection of a C. pecorum plasmid, a newly developed C. pecorum-specific plasmid PCR screening assay was used to evaluate the plasmid distribution in 227 C. pecorum samples from pig, sheep, cattle and koala hosts. Results Three porcine C. pecorum genomes were sequenced using C. pecorum-specific sequence capture probes with culture-independent methods. Comparative genomics of the newly sequenced porcine C. pecorum genomes revealed an increased average number of SNP differences (~11 500) between porcine and sheep, cattle, and koala C. pecorum strains, compared to previous C. pecorum genome analyses. We also identified a third copy of the chlamydial cytotoxin gene, found only in porcine C. pecorum isolates. Phylogenetic analyses clustered porcine isolates into a distinct clade, highlighting the polyphyletic origin of C. pecorum in livestock. Most surprising, we also discovered a plasmid in the porcine C. pecorum genome. Using this novel C. pecorum plasmid (pCpec) sequence, a) we developed a pCpec screening assay to evaluate the plasmid distribution in C. pecorum from different hosts; and b) to characterise the pCpec sequences from available previously sequenced C. pecorum genome data. pCpec screening showed that the pCpec is common in all hosts of C. pecorum, however not all C. pecorum strains carry pCpec. Conclusions This study provides further insight into the complexity of C. pecorum epidemiology and novel genomic regions that may be linked to host specificity. C. pecorum plasmid characterisation may aid in improving our understanding of C. pecorum pathogenesis across the variety of host species this animal pathogen infects. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2053-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martina Jelocnik
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Nathan L Bachmann
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | | | - Courtney Waugh
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - K Natasha Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, QLD, 4519, Australia
| | - Damien P Higgins
- Faculty of Veterinary Science, The University of Sydney, New South Wales, 2006, Australia
| | - Cheyne Flanagan
- Port Macquarie Koala Hospital, Port Macquarie, NSW, 2444, Australia
| | - Garry S A Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia.
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Black LA, Higgins DP, Govendir M. In vitro activity of chloramphenicol, florfenicol and enrofloxacin against Chlamydia pecorum isolated from koalas (Phascolarctos cinereus). Aust Vet J 2015; 93:420-3. [PMID: 26412342 DOI: 10.1111/avj.12364] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 04/12/2015] [Accepted: 05/04/2015] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To determine the in vitro susceptibilities of koala isolates of Chlamydia pecorum to enrofloxacin and chloramphenicol, which are frequently used to treat koalas with chlamydiosis, and florfenicol, a derivative of chloramphenicol. METHODS The in vitro susceptibilities were determined by culturing three stored isolates and seven clinical swabs of C. pecorum. Susceptibility testing was undertaken using cycloheximide-treated buffalo green monkey kidney cells in 96 well microtitre plates. RESULTS The minimum inhibitory concentrations (MICs) for all isolates were 0.25-0.50 µg/mL (enrofloxacin), 1-2 µg/mL (chloramphenicol), and 1-2 µg/mL (florfenicol). Minimum bactericidal concentration (MBC) values for five isolates were also determined and were within one two-fold dilution of MICs. The MICs and MBCs of these antimicrobials were within ranges previously reported for other chlamydial species. CONCLUSION When combined with previously published pharmacokinetic data, the in vitro susceptibility results support chloramphenicol as a more appropriate treatment option than enrofloxacin for koalas with chlamydiosis. The susceptibility results also indicate florfenicol may be an appropriate treatment option for koalas with chlamydiosis, warranting further investigation.
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Affiliation(s)
- L A Black
- McMaster Building B14, Faculty of Veterinary Science, The University of Sydney, New South Wales, Australia
| | - D P Higgins
- McMaster Building B14, Faculty of Veterinary Science, The University of Sydney, New South Wales, Australia
| | - M Govendir
- McMaster Building B14, Faculty of Veterinary Science, The University of Sydney, New South Wales, Australia.
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Culture-independent genome sequencing of clinical samples reveals an unexpected heterogeneity of infections by Chlamydia pecorum. J Clin Microbiol 2015; 53:1573-81. [PMID: 25740768 DOI: 10.1128/jcm.03534-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
Chlamydia pecorum is an important global pathogen of livestock, and it is also a significant threat to the long-term survival of Australia's koala populations. This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single-nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate C. pecorum strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct C. pecorum isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole-genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala C. pecorum strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two minor strains assembled from the koala swab samples clustered with livestock strains rather than koala strains. Culture-independent probe-based genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that naturally occurring chlamydial infections are comprised of multiple genetically distinct strains.
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Novel sequence types of Chlamydia pecorum infect free-ranging Alpine ibex (Capra ibex) and red deer (Cervus elaphus) in Switzerland. J Wildl Dis 2015; 51:479-83. [PMID: 25647593 DOI: 10.7589/2014-08-220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chlamydia pecorum, a recognized pathogen of domesticated ruminants and koalas (Phascolarctos cinereus), has been recently reported in a broad range of other wildlife species including water buffalo (Bubalus bubalis), ibex (Capra ibex), chamois (Rupicapra rupicapra), red deer (Cervus elaphus), and birds. This identification raises questions as to whether cross-host transmission may be a factor in the epidemiology of infections in these species. To begin to address this question, we employed a C. pecorum species-specific multi-locus sequence typing (MLST) scheme to characterize a small collection of C. pecorum-positive samples from wild, free-range ibex, a chamois, and a red deer from Grison, Switzerland, a canton where domesticated and wild ruminants graze in close proximity during the summer. Screening by PCR confirmed low to moderate levels of Chlamydia pecorum DNA in the eyes of healthy ibex (n = 4) and in the deer fecal sample (n = 1). The MLST analysis revealed three novel sequence types (STs; 88, 90, and 89) in these samples. On phylogenetic analysis, the ibex and deer sequences clustered by host species in their own well-supported clades and away from C. pecorum STs found in other hosts. Even though the analyzed sample size was small, the identification of unique C. pecorum STs infecting free-ranging Alpine ibex and red deer provides useful information for further C. pecorum epidemiologic studies.
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Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST). Vet Microbiol 2014; 174:214-22. [PMID: 25223647 DOI: 10.1016/j.vetmic.2014.08.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/28/2014] [Accepted: 08/14/2014] [Indexed: 11/22/2022]
Abstract
Chlamydia pecorum is globally associated with several ovine diseases including keratoconjunctivitis and polyarthritis. The exact relationship between the variety of C. pecorum strains reported and the diseases described in sheep remains unclear, challenging efforts to accurately diagnose and manage infected flocks. In the present study, we applied C. pecorum multi-locus sequence typing (MLST) to C. pecorum positive samples collected from sympatric flocks of Australian sheep presenting with conjunctivitis, conjunctivitis with polyarthritis, or polyarthritis only and with no clinical disease (NCD) in order to elucidate the exact relationships between the infecting strains and the range of diseases. Using Bayesian phylogenetic and cluster analyses on 62 C. pecorum positive ocular, vaginal and rectal swab samples from sheep presenting with a range of diseases and in a comparison to C. pecorum sequence types (STs) from other hosts, one ST (ST 23) was recognised as a globally distributed strain associated with ovine and bovine diseases such as polyarthritis and encephalomyelitis. A second ST (ST 69) presently only described in Australian animals, was detected in association with ovine as well as koala chlamydial infections. The majority of vaginal and rectal C. pecorum STs from animals with NCD and/or anatomical sites with no clinical signs of disease in diseased animals, clustered together in a separate group, by both analyses. Furthermore, 8/13 detected STs were novel. This study provides a platform for strain selection for further research into the pathogenic potential of C. pecorum in animals and highlights targets for potential strain-specific diagnostic test development.
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Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GSA, Timms P, Polkinghorne A. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum. BMC Genomics 2014; 15:667. [PMID: 25106440 PMCID: PMC4137089 DOI: 10.1186/1471-2164-15-667] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced. RESULTS Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations. CONCLUSIONS The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4558, Queensland, Australia.
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Host adaptation of Chlamydia pecorum towards low virulence evident in co-evolution of the ompA, incA, and ORF663 Loci. PLoS One 2014; 9:e103615. [PMID: 25084532 PMCID: PMC4118914 DOI: 10.1371/journal.pone.0103615] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 07/03/2014] [Indexed: 11/19/2022] Open
Abstract
Chlamydia (C.) pecorum, an obligate intracellular bacterium, may cause severe diseases in ruminants, swine and koalas, although asymptomatic infections are the norm. Recently, we identified genetic polymorphisms in the ompA, incA and ORF663 genes that potentially differentiate between high-virulence C. pecorum isolates from diseased animals and low-virulence isolates from asymptomatic animals. Here, we expand these findings by including additional ruminant, swine, and koala strains. Coding tandem repeats (CTRs) at the incA locus encoded a variable number of repeats of APA or AGA amino acid motifs. Addition of any non-APA/AGA repeat motif, such as APEVPA, APAVPA, APE, or APAPE, associated with low virulence (P<10−4), as did a high number of amino acids in all incA CTRs (P = 0.0028). In ORF663, high numbers of 15-mer CTRs correlated with low virulence (P = 0.0001). Correction for ompA phylogram position in ORF663 and incA abolished the correlation between genetic changes and virulence, demonstrating co-evolution of ompA, incA, and ORF663 towards low virulence. Pairwise divergence of ompA, incA, and ORF663 among isolates from healthy animals was significantly higher than among strains isolated from diseased animals (P≤10−5), confirming the longer evolutionary path traversed by low-virulence strains. All three markers combined identified 43 unique strains and 4 pairs of identical strains among all 57 isolates tested, demonstrating the suitability of these markers for epidemiological investigations.
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Kollipara A, Polkinghorne A, Wan C, Kanyoka P, Hanger J, Loader J, Callaghan J, Bell A, Ellis W, Fitzgibbon S, Melzer A, Beagley K, Timms P. Genetic diversity of Chlamydia pecorum strains in wild koala locations across Australia and the implications for a recombinant C. pecorum major outer membrane protein based vaccine. Vet Microbiol 2013; 167:513-22. [DOI: 10.1016/j.vetmic.2013.08.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 11/29/2022]
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Multilocus sequence analysis provides insights into molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle, and koalas. J Clin Microbiol 2013; 51:2625-32. [PMID: 23740730 DOI: 10.1128/jcm.00992-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlamydia pecorum is a significant pathogen of domestic livestock and wildlife. We have developed a C. pecorum-specific multilocus sequence analysis (MLSA) scheme to examine the genetic diversity of and relationships between Australian sheep, cattle, and koala isolates. An MLSA of seven concatenated housekeeping gene fragments was performed using 35 isolates, including 18 livestock isolates (11 Australian sheep, one Australian cow, and six U.S. livestock isolates) and 17 Australian koala isolates. Phylogenetic analyses showed that the koala isolates formed a distinct clade, with limited clustering with C. pecorum isolates from Australian sheep. We identified 11 MLSA sequence types (STs) among Australian C. pecorum isolates, 10 of them novel, with koala and sheep sharing at least one identical ST (designated ST2013Aa). ST23, previously identified in global C. pecorum livestock isolates, was observed here in a subset of Australian bovine and sheep isolates. Most notably, ST23 was found in association with multiple disease states and hosts, providing insights into the transmission of this pathogen between livestock hosts. The complexity of the epidemiology of this disease was further highlighted by the observation that at least two examples of sheep were infected with different C. pecorum STs in the eyes and gastrointestinal tract. We have demonstrated the feasibility of our MLSA scheme for understanding the host relationship that exists between Australian C. pecorum strains and provide the first molecular epidemiological data on infections in Australian livestock hosts.
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Preliminary characterisation of tumor necrosis factor alpha and interleukin-10 responses to Chlamydia pecorum infection in the koala (Phascolarctos cinereus). PLoS One 2013; 8:e59958. [PMID: 23527290 PMCID: PMC3602058 DOI: 10.1371/journal.pone.0059958] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/20/2013] [Indexed: 01/16/2023] Open
Abstract
Debilitating infectious diseases caused by Chlamydia are major contributors to the decline of Australia's iconic native marsupial species, the koala (Phascolarctos cinereus). An understanding of koala chlamydial disease pathogenesis and the development of effective strategies to control infections continue to be hindered by an almost complete lack of species-specific immunological reagents. The cell-mediated immune response has been shown to play an influential role in the response to chlamydial infection in other hosts. The objective of this study, hence, was to provide preliminary data on the role of two key cytokines, pro-inflammatory tumour necrosis factor alpha (TNFα) and anti-inflammatory interleukin 10 (IL10), in the koala Chlamydia pecorum response. Utilising sequence homology between the cytokine sequences obtained from several recently sequenced marsupial genomes, this report describes the first mRNA sequences of any koala cytokine and the development of koala specific TNFα and IL10 real-time PCR assays to measure the expression of these genes from koala samples. In preliminary studies comparing wild koalas with overt chlamydial disease, previous evidence of C. pecorum infection or no signs of C. pecorum infection, we revealed strong but variable expression of TNFα and IL10 in wild koalas with current signs of chlamydiosis. The description of these assays and the preliminary data on the cell-mediated immune response of koalas to chlamydial infection paves the way for future studies characterising the koala immune response to a range of its pathogens while providing reagents to assist with measuring the efficacy of ongoing attempts to develop a koala chlamydial vaccine.
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Polkinghorne A, Hanger J, Timms P. Recent advances in understanding the biology, epidemiology and control of chlamydial infections in koalas. Vet Microbiol 2013; 165:214-23. [PMID: 23523170 DOI: 10.1016/j.vetmic.2013.02.026] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 02/24/2013] [Indexed: 11/16/2022]
Abstract
The koala (Phascolarctos cinereus) is recognised as a threatened wildlife species in various parts of Australia. A major contributing factor to the decline and long-term viability of affected populations is disease caused by the obligate intracellular bacteria, Chlamydia. Two chlamydial species infect the koala, Chlamydia pecorum and Chlamydia pneumoniae, and have been reported in nearly all mainland koala populations. Chlamydial infections of koalas are associated with ocular infections leading to blindness and genital tract infections linked to infertility, among other serious clinical manifestations. Diagnosis can be based on clinical presentation alone, however, it is complicated by the observation that many koala chlamydial infections occur with no overt signs of clinical disease. Instead, accurate diagnosis requires detailed clinical assessment and confirmatory testing by a range of PCR-based assays. Antibiotic treatment for koala chlamydial infection is possible, however, results on its success are mixed. A more practical solution for the protection of diseased populations is the application of a koala Chlamydia vaccine, with recent trials indicating promising results. Interestingly, molecular epidemiology studies of koala C. pecorum infections and recent comparative genomic analyses of koala C. pneumoniae have revealed potential differences in their origin that will have wider ramifications for our understanding of human chlamydial infections and host adaptation of the chlamydiae. This review summarises changes to the taxonomy of koala chlamydial infections and recent advances in our understanding of the epidemiology, diagnosis, treatment, control and evolution of Chlamydia infections in this iconic wildlife species.
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Affiliation(s)
- Adam Polkinghorne
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Brisbane 4059, Australia.
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A testing time for koalas. Vet J 2013; 195:273-4. [DOI: 10.1016/j.tvjl.2012.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
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46
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Kollipara A, Wan C, Rawlinson G, Brumm J, Nilsson K, Polkinghorne A, Beagley K, Timms P. Antigenic specificity of a monovalent versus polyvalent MOMP based Chlamydia pecorum vaccine in koalas (Phascolarctos cinereus). Vaccine 2013; 31:1217-23. [DOI: 10.1016/j.vaccine.2012.12.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
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Characterisation of four major histocompatibility complex class II genes of the koala (Phascolarctos cinereus). Immunogenetics 2012; 65:37-46. [PMID: 23089959 DOI: 10.1007/s00251-012-0658-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 10/08/2012] [Indexed: 12/12/2022]
Abstract
Major histocompatibility complex (MHC) class II molecules have an integral role in the adaptive immune response, as they bind and present antigenic peptides to T helper lymphocytes. In this study of koalas, species-specific primers were designed to amplify exon 2 of the MHC class II DA and DB genes, which contain much of the peptide-binding regions of the α and β chains. A total of two DA α1 domain variants and eight DA β1 (DAB), three DB α1 and five DB β1 variants were amplified from 20 koalas from two free-living populations from South East Queensland and the Port Macquarie region in northern New South Wales. We detected greater variation in the β1 than in the α1 domains as well as evidence of positive selection in DAB. The present study provides a springboard to future investigation of the role of MHC in disease susceptibility in koalas.
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Hanger J, Loader J, Wan C, Beagley KW, Timms P, Polkinghorne A. Comparison of antigen detection and quantitative PCR in the detection of chlamydial infection in koalas (Phascolarctos cinereus). Vet J 2012; 195:391-3. [PMID: 22944246 DOI: 10.1016/j.tvjl.2012.07.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 06/26/2012] [Accepted: 07/12/2012] [Indexed: 11/25/2022]
Abstract
The gold standard method for detecting chlamydial infection in domestic and wild animals is PCR, but the technique is not suited to testing animals in the field when a rapid diagnosis is frequently required. The objective of this study was to compare the results of a commercially available enzyme immunoassay test for Chlamydia against a quantitative Chlamydia pecorum-specific PCR performed on swabs collected from the conjunctival sac, nasal cavity and urogenital sinuses of naturally infected koalas (Phascolarctos cinereus). The level of agreement for positive results between the two assays was low (43.2%). The immunoassay detection cut-off was determined as approximately 400 C. pecorum copies, indicating that the test was sufficiently sensitive to be used for the rapid diagnosis of active chlamydial infections.
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Affiliation(s)
- Jon Hanger
- Endeavour Veterinary Ecology, Toorbul, Queensland, Australia; Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
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Kollipara A, George C, Hanger J, Loader J, Polkinghorne A, Beagley K, Timms P. Vaccination of healthy and diseased koalas (Phascolarctos cinereus) with a Chlamydia pecorum multi-subunit vaccine: Evaluation of immunity and pathology. Vaccine 2012; 30:1875-85. [DOI: 10.1016/j.vaccine.2011.12.125] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 01/08/2023]
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