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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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Fernandez CM, Krockenberger MB, Crowther MS, Mella VSA, Wilmott L, Higgins DP. Genetic markers of Chlamydia pecorum virulence in ruminants support short term host-pathogen evolutionary relationships in the koala, Phascolarctos cinereus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105527. [PMID: 37977420 DOI: 10.1016/j.meegid.2023.105527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
In ruminants infected with Chlamydia pecorum, shorter lengths of coding tandem repeats (CTR) within two genes, the inclusion membrane protein (incA) and Type III secretor protein (ORF663), have been previously associated with pathogenic outcomes. In other chlamydial species, the presence of a chlamydial plasmid has been linked to heightened virulence, and the plasmid is not ubiquitous in C. pecorum across the koala's range. We therefore investigated these three markers: incA, ORF663 and C. pecorum plasmid, as potential indicators of virulence in two koala populations in New South Wales with differing expression of urogenital chlamydiosis; the Liverpool Plains and one across the Southern Highlands and South-west Sydney (SHSWS). We also investigated the diversity of these loci within strains characterised by the national multi-locus sequence typing (MLST) scheme. Although CTR lengths of incA and ORF663 varied across the populations, they occurred only within previously described pathogenic ranges for ruminants. This suggests a relatively short-term host-pathogen co-evolution within koalas and limits the utility of CTR lengths for incA and ORF663 as virulence markers in the species. However, in contrast to reports of evolution of C. pecorum towards lower virulence, as indicated by longer CTR lengths in ruminants and swine, CTR lengths for ORF663 appeared to be diverging towards less common shorter CTR lengths within strains recently introduced to koalas in the Liverpool Plains. We detected the plasmid across 90% and 92% of samples in the Liverpool Plains and SHSWS respectively, limiting its utility as an indicator of virulence. It would be valuable to examine the CTR lengths of these loci across koala populations nationally. Investigation of other hypervariable loci may elucidate the evolutionary trajectory of virulence in C. pecorum induced disease in koalas. Profiling of virulent strains will be important in risk assessments for strain movement to naïve or susceptible populations through translocations and wildlife corridor construction.
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Affiliation(s)
- Cristina M Fernandez
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camperdown, Sydney 2006, NSW, Australia
| | - Mark B Krockenberger
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camperdown, Sydney 2006, NSW, Australia; Sydney Infectious diseases, The University of Sydney, Camperdown, Sydney 2006, NSW, Australia
| | - Mathew S Crowther
- Faculty of Science, School of Life and Environmental Science, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Valentina S A Mella
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camperdown, Sydney 2006, NSW, Australia; Faculty of Science, School of Life and Environmental Science, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Lachlan Wilmott
- NSW Department of Planning and Environment, Wollongong 2005, New South Wales, Australia
| | - Damien P Higgins
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camperdown, Sydney 2006, NSW, Australia.
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Sachse K, Hölzer M, Vorimore F, Barf LM, Sachse C, Laroucau K, Marz M, Lamkiewicz K. Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference. BMC Genomics 2023; 24:288. [PMID: 37248517 DOI: 10.1186/s12864-023-09370-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid. RESULTS Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2- 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps). CONCLUSIONS Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.
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Affiliation(s)
- Konrad Sachse
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany.
| | - Martin Hölzer
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353, Berlin, Germany
| | - Fabien Vorimore
- Laboratory for Animal Health, Identypath, ANSES Maisons-Alfort, Paris-Est University, 94706, Paris, France
| | - Lisa-Marie Barf
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre 3 / Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- Institute for Biological Information Processing 6 / Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Karine Laroucau
- Laboratory for Animal Health, Bacterial Zoonosis Unit, ANSES Maisons-Alfort, Paris-Est University, 94706, Paris, France
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- JRG Analytical MicroBioinformatics, Friedrich Schiller University Jena, 07743, Jena, Germany
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Cheong HC, Sulaiman S, Looi CY, Chang LY, Wong WF. Chlamydia Infection Remodels Host Cell Mitochondria to Alter Energy Metabolism and Subvert Apoptosis. Microorganisms 2023; 11:1382. [PMID: 37374883 DOI: 10.3390/microorganisms11061382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Chlamydia infection represents an important cause for concern for public health worldwide. Chlamydial infection of the genital tract in females is mostly asymptomatic at the early stage, often manifesting as mucopurulent cervicitis, urethritis, and salpingitis at the later stage; it has been associated with female infertility, spontaneous abortion, ectopic pregnancy, and cervical cancer. As an obligate intracellular bacterium, Chlamydia depends heavily on host cells for nutrient acquisition, energy production, and cell propagation. The current review discusses various strategies utilized by Chlamydia in manipulating the cell metabolism to benefit bacterial propagation and survival through close interaction with the host cell mitochondrial and apoptotic pathway molecules.
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Affiliation(s)
- Heng Choon Cheong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Sofiah Sulaiman
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chung Yeng Looi
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya 47500, Selangor, Malaysia
| | - Li-Yen Chang
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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Luu LDW, Kasimov V, Phillips S, Myers GSA, Jelocnik M. Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny. Front Cell Infect Microbiol 2023; 13:1178736. [PMID: 37287464 PMCID: PMC10242142 DOI: 10.3389/fcimb.2023.1178736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis and C. pneumoniae. Since 1998, when the first Chlamydia genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in Chlamydia genomics and how whole genome sequencing has revolutionised our understanding of Chlamydia virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Vasilli Kasimov
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Samuel Phillips
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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7
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Cheong HC, Cheok YY, Chan YT, Tang TF, Sulaiman S, Looi CY, Gupta R, Arulanandam B, Chang LY, Wong WF. Chlamydia trachomatis plasmid-encoding Pgp3 protein induces secretion of distinct inflammatory signatures from HeLa cervical epithelial cells. BMC Microbiol 2023; 23:58. [PMID: 36870960 PMCID: PMC9985209 DOI: 10.1186/s12866-023-02802-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Genital Chlamydia trachomatis infection is the most common bacterial sexual transmitted disease that causes severe complications including pelvic inflammatory disease, ectopic pregnancy, and infertility in females. The Pgp3 protein encoded by C. trachomatis plasmid has been speculated to be an important player in chlamydial pathogenesis. However, the precise function of this protein is unknown and thus remains to be thoroughly investigated. METHODS In this study, we synthesized Pgp3 protein for in vitro stimulation in the Hela cervical carcinoma cells. RESULTS AND CONCLUSION We showed that Pgp3 induced prominent expression of host inflammatory cytokine genes including interleukin-6 (IL-6), IL-8, tumor necrosis factor alpha-induced protein 3 (TNFAIP3), and chemokine C-X-C motif ligand 1 (CXCL1), implying a possible role of Pgp3 in modulating the inflammatory reaction in the host.
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Affiliation(s)
- Heng Choon Cheong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yi Ying Cheok
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yee Teng Chan
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ting Fang Tang
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sofiah Sulaiman
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Chung Yeng Looi
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Rishein Gupta
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Bernard Arulanandam
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA.,Department of Immunology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Li-Yen Chang
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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8
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Cheng A, Wan D, Ghatak A, Wang C, Feng D, Fondell JD, Ebright RH, Fan H. Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria. mBio 2023; 14:e0349922. [PMID: 36719197 PMCID: PMC9973325 DOI: 10.1128/mbio.03499-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Gene transcription in bacteria is carried out by the multisubunit RNA polymerase (RNAP), which is composed of a catalytic core enzyme and a promoter-recognizing σ factor. The core enzyme comprises two α subunits, one β subunit, one β' subunit, and one ω subunit. The ω subunit plays critical roles in the assembly of the core enzyme and other cellular functions, including the regulation of bacterial growth, the stress response, and biofilm formation. However, the identity of an ω subunit for the obligate intracellular bacterium Chlamydia has not previously been determined. Here, we report the identification of the hypothetical protein CTL0286 as the probable chlamydial ω subunit based on sequence, synteny, and AlphaFold and AlphaFold-Multimer three-dimensional-structure predictions. Our findings indicate that CTL0286 functions as the missing ω subunit of chlamydial RNAP. Our extended analysis also indicates that all obligate intracellular bacteria have ω orthologs. IMPORTANCE Chlamydiae are obligate intracellular bacteria that replicate only inside eukaryotic cells. Previously, it has not been possible to identify a candidate gene encoding the chlamydial RNA polymerase ω subunit, and it has been hypothesized that the chlamydial RNA polymerase ω subunit was lost in the evolutionary process through which Chlamydiae reduced their genome size and proteome sizes to adapt to an obligate intracellular lifestyle. Here, we report the identification of the chlamydial RNA polymerase ω subunit, based on conserved sequence, conserved synteny, AlphaFold-predicted conserved three-dimensional structure, and AlfaFold-Multimer-predicted conserved interactions. Our identification of the previously elusive chlamydial RNA polymerase ω subunit sets the stage for investigation of its roles in regulation of gene expression during chlamydial growth, development, and stress responses, and sets the stage for preparation and study of the intact chlamydial RNA polymerase and its interactions with inhibitors.
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Affiliation(s)
- Andrew Cheng
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Danny Wan
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
- Graduate Program in Physiology and Integrative Biology, Rutgers School of Graduate Studies, Piscataway, New Jersey, USA
| | - Arkaprabha Ghatak
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Chengyuan Wang
- Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Deyu Feng
- Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Joseph D. Fondell
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Richard H. Ebright
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Huizhou Fan
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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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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10
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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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11
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Zaręba-Marchewka K, Szymańska-Czerwińska M, Livingstone M, Longbottom D, Niemczuk K. Whole Genome Sequencing and Comparative Genome Analyses of Chlamydia abortus Strains of Avian Origin Suggests That Chlamydia abortus Species Should Be Expanded to Include Avian and Mammalian Subgroups. Pathogens 2021; 10:1405. [PMID: 34832561 PMCID: PMC8623937 DOI: 10.3390/pathogens10111405] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
A variety of Chlamydia species belonging to the Chlamydiaceae family have been reported in birds. Until recently, C. psittaci was considered to be the most common avian species, although found in both birds and mammals, while C. abortus has only been found in mammals. Recently, a new group of avian C. abortus strains with worldwide distribution in various wild bird families has been described. In this study, whole genome sequencing (WGS) of three of these strains (15-70d24, 15-49d3 and 15-58d44, representing genotypes G1, G2 and 1V, respectively) that were isolated from wild birds were analysed. Genome assemblies based on both short-read Illumina and long-read Nanopore data indicate that these avian C. abortus strains show features characteristic of both C. abortus and C. psittaci species, although phylogenetic analyses demonstrate a closer relationship with classical C. abortus strains. Currently, species classification established by the ICSP Subcommittee on the taxonomy of Chlamydiae, determines that these avian C. abortus strains 15-70d24, 15-49d3 and 15-58d44 should be classified as C. abortus. However, the authors of this study conclude that the current taxonomic definition of C. abortus is outdated and should be amended to include two subgroups, mammalian and avian, the latter of which would include all isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.
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Affiliation(s)
- Kinga Zaręba-Marchewka
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland; (M.S.-C.); (K.N.)
| | - Monika Szymańska-Czerwińska
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland; (M.S.-C.); (K.N.)
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
| | - Morag Livingstone
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK; (M.L.); (D.L.)
| | - David Longbottom
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK; (M.L.); (D.L.)
| | - Krzysztof Niemczuk
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland; (M.S.-C.); (K.N.)
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
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12
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Chlamydia pecorum Ovine Abortion: Associations between Maternal Infection and Perinatal Mortality. Pathogens 2021; 10:pathogens10111367. [PMID: 34832523 PMCID: PMC8618313 DOI: 10.3390/pathogens10111367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/29/2022] Open
Abstract
Chlamydia pecorum is a common gastrointestinal inhabitant of livestock but infections can manifest in a broad array of clinical presentations and in a range of host species. While C. pecorum is a known cause of ovine abortion, clinical cases have only recently been described in detail. Here, the prevalence and sequence types (STs) of C. pecorum in ewes from a property experiencing high levels of perinatal mortality (PNM) in New South Wales (NSW), Australia, were investigated using serological and molecular methods. Ewes that were PNM+ were statistically more likely to test seropositive compared to PNM− ewes and displayed higher antibody titres; however, an increase in chlamydial shedding from either the rectum, vagina or conjunctiva of PNM+ ewes was not observed. Multilocus sequence typing (MLST) indicated that C. pecorum ST23 was the major ST shed by ewes in the flock, was the only ST identified from the vaginal site, and was the same ST detected within aborted foetal tissues. Whole genome sequencing of C. pecorum isolated from one abortion case revealed that the C. pecorum plasmid (pCpec) contained a unique deletion in coding sequence 1 (CDS1) that was also present in C. pecorum ST23 shed from the ewes. A further unique deletion was noted in a polymorphic membrane protein gene (pmpG) of the C. pecorum chromosome, which warrants further investigation given the role of PmpG in host cell adherence and tissue tropism.This study describes novel infection parameters in a sheep flock experiencing C. pecorum-associated perinatal mortality, provides the first genomic data from an abortigenic C. pecorum strain, and raises questions about possible links between unique genetic features of this strain and C. pecorum abortion.
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13
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Peel E, Cheng Y, Djordjevic JT, O’Meally D, Thomas M, Kuhn M, Sorrell TC, Huston WM, Belov K. Koala cathelicidin PhciCath5 has antimicrobial activity, including against Chlamydia pecorum. PLoS One 2021; 16:e0249658. [PMID: 33852625 PMCID: PMC8046226 DOI: 10.1371/journal.pone.0249658] [Citation(s) in RCA: 3] [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: 10/23/2020] [Accepted: 03/22/2021] [Indexed: 11/18/2022] Open
Abstract
Devastating fires in Australia over 2019-20 decimated native fauna and flora, including koalas. The resulting population bottleneck, combined with significant loss of habitat, increases the vulnerability of remaining koala populations to threats which include disease. Chlamydia is one disease which causes significant morbidity and mortality in koalas. The predominant pathogenic species, Chlamydia pecorum, causes severe ocular, urogenital and reproductive tract disease. In marsupials, including the koala, gene expansions of an antimicrobial peptide family known as cathelicidins have enabled protection of immunologically naïve pouch young during early development. We propose that koala cathelicidins are active against Chlamydia and other bacteria and fungi. Here we describe ten koala cathelicidins, five of which contained full length coding sequences that were widely expressed in tissues throughout the body. Focusing on these five, we investigate their antimicrobial activity against two koala C. pecorum isolates from distinct serovars; MarsBar and IPTaLE, as well as other bacteria and fungi. One cathelicidin, PhciCath5, inactivated C. pecorum IPTaLE and MarsBar elementary bodies and significantly reduced the number of inclusions compared to the control (p<0.0001). Despite evidence of cathelicidin expression within tissues known to be infected by Chlamydia, natural PhciCath5 concentrations may be inadequate in vivo to prevent or control C. pecorum infections in koalas. PhciCath5 also displayed antimicrobial activity against fungi and Gram negative and positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Electrostatic interactions likely drive PhciCath5 adherence to the pathogen cell membrane, followed by membrane permeabilisation leading to cell death. Activity against E. coli was reduced in the presence of 10% serum and 20% whole blood. Future modification of the PhciCath5 peptide to enhance activity, including in the presence of serum/blood, may provide a novel solution to Chlamydia infection in koalas and other species.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Julianne T. Djordjevic
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, New South Wales, Australia
| | - Denis O’Meally
- Center for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Mark Thomas
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Michael Kuhn
- Zoetis, Veterinary Medicine Research and Development, Kalamazoo, Michigan, United States of America
| | - Tania C. Sorrell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, New South Wales, Australia
| | - Wilhelmina M. Huston
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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14
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Rohner L, Marti H, Torgerson P, Hoffmann K, Jelocnik M, Borel N. Prevalence and molecular characterization of C. pecorum detected in Swiss fattening pigs. Vet Microbiol 2021; 256:109062. [PMID: 33848714 DOI: 10.1016/j.vetmic.2021.109062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/24/2021] [Indexed: 11/25/2022]
Abstract
Chlamydia (C.) pecorum, an obligate intracellular bacterial species commonly found in ruminants, can also occur in pigs. However, its significance as a potential porcine pathogen, or commensal, is still unclear. In a previous study (Hoffmann et al. 2015), mixed infections of C. suis and C. pecorum were detected in 14 Swiss fattening pig farms. Using these samples, we aimed to investigate the infection dynamics of C. suis and C. pecorum mixed infections in these farms. In addition, we analyzed the genetic diversity of Swiss porcine C. pecorum strains in relation to globally circulating strains. In total, 1284 conjunctival and rectal swabs from 391 pigs, collected at the beginning and end of the fattening period, were tested during the course of this study. We determined the bacterial loads of C. suis and C. pecorum using species-specific real-time PCR (qPCR) and compared these results to already existing DNA-microarray and Chlamydiaceae qPCR data. Overall, C. suis and Chlamydiaceae copy numbers decreased in the course of the fattening period, whereas C. pecorum copy numbers increased. No association was found between clinical signs (conjunctivitis, lameness and diarrhea) and the bacterial loads. Preventive antibiotic treatment at the beginning of the fattening period significantly lowered the chlamydial load and outdoor access was associated with higher loads. Proximity to the nearest ruminants correlated with increased C. pecorum loads, indicating that C. pecorum could be transmitted from ruminants to pigs. Multi-locus sequence typing (MLST) and major outer membrane protein (ompA) genotyping revealed two novel sequence types (STs) (301, 302) and seven unique ompA genotypes (1-7) that appear to form a specific clade separate from other European C. pecorum strains.
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Affiliation(s)
- Lea Rohner
- Institute of Veterinary Pathology, Vetsuisse-Faculty University Zurich, Zurich, 8057, Switzerland; Center for Clinical Studies, Vetsuisse-Faculty, University of Zurich, Zurich, 8057, Switzerland
| | - Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty University Zurich, Zurich, 8057, Switzerland; Center for Clinical Studies, Vetsuisse-Faculty, University of Zurich, Zurich, 8057, Switzerland.
| | - Paul Torgerson
- Section of Veterinary Epidemiology, Vetsuisse-Faculty, University of Zurich, Zurich, 8057, Switzerland
| | - Karolin Hoffmann
- Institute of Veterinary Pathology, Vetsuisse-Faculty University Zurich, Zurich, 8057, Switzerland; Center for Clinical Studies, Vetsuisse-Faculty, University of Zurich, Zurich, 8057, Switzerland
| | - Martina Jelocnik
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, 4556, Queensland, Australia
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse-Faculty University Zurich, Zurich, 8057, Switzerland; Center for Clinical Studies, Vetsuisse-Faculty, University of Zurich, Zurich, 8057, Switzerland
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15
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Ostfeld N, Islam MM, Jelocnik M, Hilbe M, Sydler T, Hartnack S, Jacobson C, Clune T, Marsh I, Sales N, Polkinghorne A, Borel N. Chlamydia pecorum-Induced Arthritis in Experimentally and Naturally Infected Sheep. Vet Pathol 2020; 58:346-360. [PMID: 33208021 DOI: 10.1177/0300985820973461] [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] [Indexed: 12/25/2022]
Abstract
Chlamydia pecorum is an obligate intracellular pathogen with a wide host range including livestock such as sheep, cattle, goats, and pigs as well as wildlife species such as koalas. Chlamydial polyarthritis is an economically important disease resulting in swollen joints, lameness, stiffness, and weight loss in young sheep. In the present study, tissues from sheep experimentally or naturally infected with Chlamydia pecorum were assessed by histopathology and immunohistochemistry. Carpal, hock, and stifle joints as well as spleen, liver, kidney, lymph nodes, lung, and brain of 35 sheep from different inoculation groups were available. Two different C. pecorum strains (IPA and E58), different routes of administration (intraarticular or intravenous), UVA-irradiated IPA strain, and corresponding noninfected control groups were investigated. Similar investigations on tissues from 5 naturally infected sheep were performed. The most obvious inflammatory lesions were observed in synovial tissues and, notably, in the renal pelvis from the experimentally infected group and naturally infected animals. This resulted in chronic or chronic-active arthritis and pyelitis. Intralesional chlamydial inclusions could be demonstrated by immunohistochemistry in both tissues. Immunohistochemical evaluation of the presence and distribution of macrophages, T and B cells in synovial tissues revealed macrophages as the most prevalent inflammatory cell population. Previous observations indicated that C. pecorum isolates can infect circulating monocytes. Together with the finding of the histological lesions in synovial tissues and internal organs alongside the presence of C. pecorum DNA, these observations suggest chlamydial arthritis in lambs is the result of hematogeneous spread of C. pecorum.
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Affiliation(s)
| | - Mominul M Islam
- 5333University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Martina Jelocnik
- 5333University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | | | | | | | | | - Tom Clune
- 5673Murdoch University, Perth, Western Australia, Australia
| | - Ian Marsh
- NSW Department of Primary Industries, 153388Elizabeth Macarthur Agricultural Institut, Menangle, New South Wales, Australia
| | - Narelle Sales
- NSW Department of Primary Industries, 153388Elizabeth Macarthur Agricultural Institut, Menangle, New South Wales, Australia
| | - Adam Polkinghorne
- 6488Nepean Hospital, NSW Health Pathology, Penrith, New South Wales, Australia.,University of Sydney, Sydney, New South Wales, Australia
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16
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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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17
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Dimond ZE, Hefty PS. Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors. Pathog Dis 2020; 79:5868767. [PMID: 32639528 DOI: 10.1093/femspd/ftaa035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Chlamydia suis, a ubiquitous swine pathogen, has the potential for zoonotic transmission to humans and often encodes for resistance to the primary treatment antibiotic, tetracycline. Because of this emerging threat, comparative genomics for swine isolate R19 with inter- and intra-species genomes was performed. A 1.094 Mb genome was determined through de novo assembly of Illumina high throughput sequencing reads. Annotation and subsystem analyses were conducted, revealing 986 putative genes (Chls_###) that are predominantly orthologs to other known Chlamydia genes. Subsequent comparative genomics revealed a high level of genomic synteny and overall sequence identity with other Chlamydia while 92 unique C. suis open reading frames were annotated. Direct comparison of Chlamydia-specific gene families that included the plasticity zone, inclusion membrane proteins, polymorphic membrane proteins and the major outer membrane protein, demonstrated high gene content identity with C. trachomatis and C. muridarum. These comparisons also identified diverse components that potentially could contribute to host-specificity. This study constitutes the first genome-wide comparative analysis for C. suis, generating a fully annotated reference genome. These studies will enable focused efforts on factors that provide key species specificity and adaptation to cognate hosts that are attributed to chlamydial infections, including humans.
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Affiliation(s)
- Zoe E Dimond
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave. Lawrence KS 66044
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave. Lawrence KS 66044
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18
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Szabo KV, O’Neill CE, Clarke IN. Diversity in Chlamydial plasmids. PLoS One 2020; 15:e0233298. [PMID: 32469898 PMCID: PMC7259575 DOI: 10.1371/journal.pone.0233298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/01/2020] [Indexed: 11/30/2022] Open
Abstract
Background Evolutionary studies have been conducted that have investigated the chromosomal variance in the genus of Chlamydia. However, no all-encompassing genus-wide comparison has been performed on the plasmid. Therefore, there is a gap in the current knowledge on Chlamydia plasmid diversity. Aims This project is aimed to investigate and establish the nature and extent of diversity across the entire genus of Chlamydia, by comparing the sequences of all currently available plasmid carrying strains. Methods The PUBMED database was used to identify plasmid sequences from all available strains that met the set quality criteria for their inclusion in the study. Alignments were performed on the 51 strains that fulfilled the criteria using MEGA X software. Following that Maximum Likelihood estimation was used to construct 11 phylogenetic trees of the whole plasmid sequence, the individual 8 coding sequences, the iteron and a chromosomal gene ompA as a comparator. Results The genus-wide plasmid phylogeny produced three distinct lineages labelled as alpha, beta and gamma. Nineteen genotypes were found in the initial whole plasmid analysis. Their distribution was allocated as six C. pecorum, two C. pneumoniae, one C. gallinacea, one C. avium, one C. caviae, one C. felis, two C. psittaci, one C. trachomatis, one C. muridarum, and two C. suis. The chromosomal comparative gene ompA supported this distribution, with the same number of primary clades with the same species distribution. However, ompA sequence comparison resulted in fewer genotypes due to a reduced amount of available sequences (33 out of 51). All results were statistically significant. Conclusion The results of this study indicate that the common bacterial ancestor of all the species had a plasmid, which has diverged over time. Moreover, it suggests that there is a strong evolutionary selection towards these species retaining their plasmids due to its high level of conservation across the genus, with the notable exception of C. pneumoniae. Furthermore, the evolutionary analysis showed that the plasmid and the chromosome have co-evolved.
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Affiliation(s)
- Kolos V. Szabo
- Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom
- * E-mail:
| | - Colette E. O’Neill
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Ian N. Clarke
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
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19
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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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20
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Jelocnik M. Chlamydiae from Down Under: The Curious Cases of Chlamydial Infections in Australia. Microorganisms 2019; 7:microorganisms7120602. [PMID: 31766703 PMCID: PMC6955670 DOI: 10.3390/microorganisms7120602] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
In Australia, the most researched and perhaps the most successful chlamydial species are the human pathogen Chlamydia trachomatis, animal pathogens Chlamydia pecorum and Chlamydia psittaci. C. trachomatis remains the leading cause of sexually transmitted infections in Australians and trachoma in Australian Indigenous populations. C. pecorum is globally recognised as the infamous koala and widespread livestock pathogen, whilst the avian C. psittaci is emerging as a horse pathogen posing zoonotic risks to humans. Certainly not innocuous, the human infections with Chlamydia pneumoniae seem to be less prevalent that other human chlamydial pathogens (namely C. trachomatis). Interestingly, the complete host range for C. pecorum and C. psittaci remains unknown, and infections by other chlamydial organisms in Australian domesticated and wildlife animals are understudied. Considering that chlamydial organisms can be encountered by either host at the human/animal interface, I review the most recent findings of chlamydial organisms infecting Australians, domesticated animals and native wildlife. Furthermore, I also provide commentary from leading Australian Chlamydia experts on challenges and future directions in the Chlamydia research field.
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Affiliation(s)
- Martina Jelocnik
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs 4557, Australia
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21
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Fabijan J, Caraguel C, Jelocnik M, Polkinghorne A, Boardman WSJ, Nishimoto E, Johnsson G, Molsher R, Woolford L, Timms P, Simmons G, Hemmatzadeh F, Trott DJ, Speight N. Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: Identification and modelling of a population free from infection. Sci Rep 2019; 9:6261. [PMID: 31000763 PMCID: PMC6472425 DOI: 10.1038/s41598-019-42702-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/02/2019] [Indexed: 11/21/2022] Open
Abstract
Chlamydia pecorum is an established and prevalent infection that produces severe clinical disease in many koala populations, contributing to dramatic population declines. In wild South Australian koala populations, C. pecorum occurrence and distribution is unknown. Here, C. pecorum-specific real-time quantitative PCR (qPCR) was applied to ocular and urogenital swabs from targeted surveys of wild koalas from the mainland Mount Lofty Ranges (MLR) (n = 75) and Kangaroo Island (KI) (n = 170) populations. Historical data from 13,081 KI koalas (1997–2018) provided additional evidence for assessing the absence of C. pecorum infection. In the MLR population, 46.7% (CI: 35.1–58.6%) of koalas were C. pecorum positive by qPCR but only 4% had grade 3 clinical disease. MLR koala fertility was significantly reduced by C. pecorum infection; all reproductively active females (n = 16) were C. pecorum negative, whereas 85.2% of inactive females (n = 23) were positive (P < 0.001). KI koalas were C. pecorum negative and the population was demonstrated to be free of C. pecorum infection with 95% confidence. C. pecorum is a real threat for the sustainability of the koala and KI is possibly the last isolated, large C. pecorum-free population remaining in Australia. These koalas could provide a safeguard against this serious disease threat to an iconic Australian species.
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Affiliation(s)
- Jessica Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia.
| | - Charles Caraguel
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Martina Jelocnik
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, 4558, Queensland, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, 4558, Queensland, Australia
| | - Wayne S J Boardman
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Elisa Nishimoto
- Kangaroo Island Veterinary Clinic, Kingscote, 5223, South Australia, Australia
| | - Greg Johnsson
- Kangaroo Island Veterinary Clinic, Kingscote, 5223, South Australia, Australia
| | - Robyn Molsher
- Department for Environment and Water, Adelaide, 5000, South Australia, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, 4558, Queensland, Australia
| | - Greg Simmons
- School of Veterinary Sciences, The University of Queensland, Gatton, 4343, Queensland, Australia
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Darren J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
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22
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In vitro analysis of genetically distinct Chlamydia pecorum isolates reveals key growth differences in mammalian epithelial and immune cells. Vet Microbiol 2019; 232:22-29. [PMID: 31030841 DOI: 10.1016/j.vetmic.2019.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/21/2019] [Accepted: 03/21/2019] [Indexed: 11/23/2022]
Abstract
Chlamydia (C.) pecorum is an obligate intracellular bacterium that infects and causes disease in a broad range of animal hosts. Molecular studies have revealed that this pathogen is genetically diverse with certain isolates linked to different disease outcomes. Limited in vitro or in vivo data exist to support these observations, further hampering efforts to improve our understanding of C. pecorum pathogenesis. In this study, we evaluated whether genetically distinct C. pecorum isolates (IPA, E58, 1710S, W73, JP-1-751) display different in vitro growth phenotypes in different mammalian epithelial and immune cells. In McCoy cells, shorter lag phases were observed for W73 and JP-1-751 isolates. Significantly smaller inclusions were observed for the naturally plasmid-free E58 isolate. C. pecorum isolates of bovine (E58) and ovine origin (IPA, W73, JP-1-751) grew faster in bovine cells compared to a porcine isolate (1710S). C. pecorum isolates could infect but appear not able to complete their developmental cycle in bovine peripheral neutrophil granulocytes. All isolates, except 1710S, could multiply in bovine monocyte-derived macrophages. These results reveal potentially important phenotypic differences that will help to understand the pathogenesis of C. pecorum in vivo and to identify C. pecorum virulence factors.
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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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Speight KN, Hicks P, Graham C, Boardman W, Breed WG, Manthorpe E, Funnell O, Woolford L. Necropsy findings of koalas from the Mount Lofty Ranges population in South Australia. Aust Vet J 2018; 96:188-192. [PMID: 29691854 DOI: 10.1111/avj.12690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/03/2017] [Accepted: 08/22/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This study reports necropsy findings of koalas from the Mount Lofty Ranges region in order to identify health threats to this mainland South Australian population. METHODS Koalas from the Mount Lofty Ranges region (n = 85) that had died or been euthanased on welfare grounds were examined at necropsy during 2012-13 at the School of Animal and Veterinary Sciences, University of Adelaide. Disease findings, approximate age, sex and body condition of koalas were recorded. Histopathological examination was undertaken on gross lesions and in suspect cases, skin scrapings taken for microscopy and PCR performed for Chlamydia pecorum detection. RESULTS Traumatic injury was the most common necropsy finding (48/85; 57%), caused by motor vehicle accidents (35/48; 73%), canine attacks (11/48; 23%) or bushfire burns (2/48; 4%). Oxalate nephrosis (27/85; 32%) was also more common than other conditions. Infectious diseases included chlamydiosis (10/85; 12%) and sarcoptic mange (7/85; 8%). Marked testis asymmetry was evident in 11% (6/56) of males, with histopathology suggestive of atrophic change in four animals. Other pathological conditions included gastrointestinal disease (7/85; 8%) and respiratory disease (3/85; 4%). Almost half of the koalas (38/85; 45%) were found to have two or more abnormalities at necropsy. CONCLUSION This study found trauma, mainly from motor vehicle accidents, and oxalate nephrosis to be the predominant causes of death and/or disease in koalas from the Mount Lofty Ranges region. Recent emergence of both clinical chlamydiosis and sarcoptic mange has also occurred, providing insight into the health status and causes of disease or injury in this South Australian mainland koala population.
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Affiliation(s)
- K N Speight
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
| | - P Hicks
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
| | - C Graham
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
| | - W Boardman
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
| | - W G Breed
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia
| | - E Manthorpe
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
| | - O Funnell
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy campus, Roseworthy, South, Australia 5371, Australia
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Shima K, Wanker M, Skilton RJ, Cutcliffe LT, Schnee C, Kohl TA, Niemann S, Geijo J, Klinger M, Timms P, Rattei T, Sachse K, Clarke IN, Rupp J. The Genetic Transformation of Chlamydia pneumoniae. mSphere 2018; 3:e00412-18. [PMID: 30305318 PMCID: PMC6180227 DOI: 10.1128/msphere.00412-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/11/2018] [Indexed: 11/26/2022] Open
Abstract
We demonstrate the genetic transformation of Chlamydia pneumoniae using a plasmid shuttle vector system which generates stable transformants. The equine C. pneumoniae N16 isolate harbors the 7.5-kb plasmid pCpnE1. We constructed the plasmid vector pRSGFPCAT-Cpn containing a pCpnE1 backbone, plus the red-shifted green fluorescent protein (RSGFP), as well as the chloramphenicol acetyltransferase (CAT) gene used for the selection of plasmid shuttle vector-bearing C. pneumoniae transformants. Using the pRSGFPCAT-Cpn plasmid construct, expression of RSGFP in koala isolate C. pneumoniae LPCoLN was demonstrated. Furthermore, we discovered that the human cardiovascular isolate C. pneumoniae CV-6 and the human community-acquired pneumonia-associated C. pneumoniae IOL-207 could also be transformed with pRSGFPCAT-Cpn. In previous studies, it was shown that Chlamydia spp. cannot be transformed when the plasmid shuttle vector is constructed from a different plasmid backbone to the homologous species. Accordingly, we confirmed that pRSGFPCAT-Cpn could not cross the species barrier in plasmid-bearing and plasmid-free C. trachomatis, C. muridarum, C. caviae, C. pecorum, and C. abortus However, contrary to our expectation, pRSGFPCAT-Cpn did transform C. felis Furthermore, pRSGFPCAT-Cpn did not recombine with the wild-type plasmid of C. felis Taken together, we provide for the first time an easy-to-handle transformation protocol for C. pneumoniae that results in stable transformants. In addition, the vector can cross the species barrier to C. felis, indicating the potential of horizontal pathogenic gene transfer via a plasmid.IMPORTANCE The absence of tools for the genetic manipulation of C. pneumoniae has hampered research into all aspects of its biology. In this study, we established a novel reproducible method for C. pneumoniae transformation based on a plasmid shuttle vector system. We constructed a C. pneumoniae plasmid backbone shuttle vector, pRSGFPCAT-Cpn. The construct expresses the red-shifted green fluorescent protein (RSGFP) fused to chloramphenicol acetyltransferase in C. pneumoniaeC. pneumoniae transformants stably retained pRSGFPCAT-Cpn and expressed RSGFP in epithelial cells, even in the absence of chloramphenicol. The successful transformation in C. pneumoniae using pRSGFPCAT-Cpn will advance the field of chlamydial genetics and is a promising new approach to investigate gene functions in C. pneumoniae biology. In addition, we demonstrated that pRSGFPCAT-Cpn overcame the plasmid species barrier without the need for recombination with an endogenous plasmid, indicating the potential probability of horizontal chlamydial pathogenic gene transfer by plasmids between chlamydial species.
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Affiliation(s)
- Kensuke Shima
- Department of Infectious Diseases and Microbiology, University of Luebeck, Luebeck, Germany
| | - Maximilian Wanker
- Department of Infectious Diseases and Microbiology, University of Luebeck, Luebeck, Germany
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Luebeck-Borstel-Riems, Germany
| | - Rachel J Skilton
- Molecular Microbiology Group, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Lesley T Cutcliffe
- Molecular Microbiology Group, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitute (Federal Research Institute for Animal Health), Jena, Germany
| | - Thomas A Kohl
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Luebeck-Borstel-Riems, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Luebeck-Borstel-Riems, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Javier Geijo
- Division of Computational Systems Biology, University Vienna, Vienna, Austria
| | | | - Peter Timms
- University of Sunshine Coast, Maroochydore, Australia
| | - Thomas Rattei
- Division of Computational Systems Biology, University Vienna, Vienna, Austria
| | - Konrad Sachse
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Ian N Clarke
- Molecular Microbiology Group, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Luebeck, Luebeck, Germany
- German Center for Infection Research (DZIF), Partner Site, Hamburg-Luebeck-Borstel-Riems, Germany
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Kim H, Kwak W, Yoon SH, Kang DK, Kim H. Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation. PLoS One 2018; 13:e0195139. [PMID: 29621277 PMCID: PMC5886423 DOI: 10.1371/journal.pone.0195139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/16/2018] [Indexed: 01/07/2023] Open
Abstract
Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree database constructed in our recent study. Tree reconciliation method was applied in order to calculate feasible HGT events. Following initial detection and an evaluation procedure, evidence of the HGT was identified in 548 gene families including 42 gene families transferred from outside of Chlamydiae phylum with high reliability. The donor species of inter-phylum HGT consists of 12 different bacterial and archaeal phyla, suggesting that Chlamydia might have even more various host range than in previous reports. In addition, each species of Chlamydia showed varying preference towards HGT, and genes engaged in HGT within Chlamydia and between other species showed different functional distribution. Also, examination of individual gene flows of niche-specific genes suggested that many of such genes are transferred mainly within Chlamydia genus. Our results uncovered novel features of HGT acting on Chlamydia genome evolution, and it would be also strong evidence that HGT is an ongoing process for intracellular pathogens. We expect that the results provide more insight into lineage- and niche-specific adaptations regarding their infectivity and pathogenicity.
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Affiliation(s)
- Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woori Kwak
- C&K genomics, Seoul National University Research Park, Seoul, Republic of Korea
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- C&K genomics, Seoul National University Research Park, Seoul, Republic of Korea
- * E-mail:
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27
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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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Abstract
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement. To circumvent these challenges, researchers have developed culture-independent sample preparation methods that can be applied to the sample directly or to genomic material extracted from the sample. These methods, which encompass both targeted [immunomagnetic separation-multiple displacement amplification (IMS-MDA) and sequence capture] and non-targeted approaches (host methylated DNA depletion-microbial DNA enrichment and cell-sorting-MDA), have been applied to a range of clinical and environmental samples to generate whole genomes of novel chlamydial species and strains. This review aims to provide an overview of the application, advantages and limitations of these targeted and non-targeted approaches in the chlamydial context. The methods discussed also have broad application to other obligate intracellular bacteria or clinical and environmental samples.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Danielle Madden
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
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Guo W, Jelocnik M, Li J, Sachse K, Polkinghorne A, Pannekoek Y, Kaltenboeck B, Gong J, You J, Wang C. From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen. BMC Genomics 2017; 18:949. [PMID: 29212448 PMCID: PMC5717833 DOI: 10.1186/s12864-017-4343-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of C. psittaci, but genetic and genomic research on C. gallinacea is still at the beginning. In this study, we conducted whole-genome sequencing of C. gallinacea strain JX-1 isolated from an asymptomatic chicken, and comparative genomic analysis between C. gallinacea strains and related chlamydial species. RESULTS The genome of C. gallinacea JX-1 was sequenced by single-molecule, real-time technology and is comprised of a 1,059,522-bp circular chromosome with an overall G + C content of 37.93% and sequence similarity of 99.4% to type strain 08-1274/3. In addition, a plasmid designated pJX-1, almost identical to p1274 of the type strain, except for two point mutations, was only found in field strains from chicken, but not in other hosts. In contrast to chlamydial species with notably variable polymorphic membrane protein (pmp) genes and plasticity zone (PZ), these regions were conserved in both C. gallinacea strains. There were 15 predicted pmp genes, but only B, A, E1, H, G1 and G2 were apparently intact in both strains. In comparison to chlamydial species where the PZ may be up to 50 kbp, C. gallinacea strains displayed gene content reduction in the PZ (14 kbp), with strain JX-1 having a premature STOP codon in the cytotoxin (tox) gene, while tox gene is intact in the type strain. In multilocus sequence typing (MLST), 15 C. gallinacea STs were identified among 25 strains based on cognate MLST allelic profiles of the concatenated sequences. The type strain and all Chinese strains belong to two distinct phylogenetic clades. Clade of the Chinese strains separated into 14 genetically distinct lineages, thus revealing considerable genetic diversity of C. gallinacea strains in China. CONCLUSIONS In this first detailed comparative genomic analysis of C. gallinacea, we have provided evidence for substantial genetic diversity among C. gallinacea strains. How these genetic polymorphisms affect C. gallinacea biology and pathogenicity should be addressed in future studies that focus on phylogenetics and host adaption of this enigmatic bacterial agent.
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Affiliation(s)
- Weina Guo
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu 225009 People’s Republic of China
- College of Animal Science, Anhui Science and Technology University, Maanshan, Anhui China
| | - Martina Jelocnik
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD Australia
| | - Jing Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu 225009 People’s Republic of China
| | - Konrad Sachse
- Institute of Bioinformatics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD Australia
| | - Yvonne Pannekoek
- Department of Microbiology, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu China
| | - Jinfeng You
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu 225009 People’s Republic of China
| | - Chengming Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu 225009 People’s Republic of China
- College of Veterinary Medicine, Auburn University, Auburn, AL USA
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30
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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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Taylor-Brown A, Spang L, Borel N, Polkinghorne A. Culture-independent metagenomics supports discovery of uncultivable bacteria within the genus Chlamydia. Sci Rep 2017; 7:10661. [PMID: 28878306 PMCID: PMC5587560 DOI: 10.1038/s41598-017-10757-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/14/2017] [Indexed: 12/02/2022] Open
Abstract
Advances in culture-independent methods have meant that we can more readily detect and diagnose emerging infectious disease threats in humans and animals. Metagenomics is fast becoming a popular tool for detection and characterisation of novel bacterial pathogens in their environment, and is particularly useful for obligate intracellular bacteria such as Chlamydiae that require labour-intensive culturing. We have used this tool to investigate the microbial metagenomes of Chlamydia-positive cloaca and choana samples from snakes. The microbial complexity within these anatomical sites meant that despite previous detection of chlamydial 16S rRNA sequences by single-gene broad-range PCR, only a chlamydial plasmid could be detected in all samples, and a chlamydial chromosome in one sample. Comparative genomic analysis of the latter revealed it represented a novel taxon, Ca. Chlamydia corallus, with genetic differences in regards to purine and pyrimidine metabolism. Utilising statistical methods to relate plasmid phylogeny to the phylogeny of chromosomal sequences showed that the samples also contain additional novel strains of Ca. C. corallus and two putative novel species in the genus Chlamydia. This study highlights the value of metagenomics methods for rapid novel bacterial discovery and the insights it can provide into the biology of uncultivable intracellular bacteria such as Chlamydiae.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Health, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Labolina Spang
- Centre for Animal Health Innovation, Faculty of Science, Health, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Nicole Borel
- Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 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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33
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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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35
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Burnard D, Polkinghorne A. Chlamydial infections in wildlife-conservation threats and/or reservoirs of 'spill-over' infections? Vet Microbiol 2016; 196:78-84. [PMID: 27939160 DOI: 10.1016/j.vetmic.2016.10.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 12/25/2022]
Abstract
Members of the order Chlamydiales are biphasic intracellular pathogens known to cause disease in both humans and animals. As we learn more about the genetic diversity of this group of pathogens, evidence is growing that these bacteria infect a broader range of animal hosts than previously thought. Over 400 host species are now documented globally with the majority of these being wild animals. Given the impact of chlamydial infections on humans and domesticated animals, the identification of members of the order Chlamydiales in wildlife raises significant questions over a) their impact on animal health and b) the relationships to those strains also found in humans and domestic animals. In some species such as the iconic marsupial, the koala, the conservation impact is known with chlamydial infections associated with debilitating disease, however, in general, little is known about the pathogenic potential of Chlamydiae infecting most wildlife hosts. Accumulating evidence suggests contact with wild animals is a risk factor for infections in domestic animals and/or humans. Beyond the well-recognised zoonotic pathogen, Chlamydia psittaci, a range of studies have now reported traditional pathogens in the family Chlamydiaceae such as Chlamydia pecorum, Chlamydia suis, Chlamydia pneumoniae and Chlamydia abortus in wild animals. The spectre of cross-host transmission 'spill-over' and 'spill-back' in the epidemiology of infections is of potential concern, however, comprehensive epidemiological studies are lacking for most of these. Accurate evaluation of the significance of chlamydial infections in wildlife is otherwise hampered by i) the cross-sectional nature of most impact studies, ii) a lack of standardised diagnostic approaches, iii) limited study sizes, and iv) biases associated with opportunistic sampling.
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Affiliation(s)
- Delaney Burnard
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia.
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36
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Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes. BMC Genomics 2016; 17:710. [PMID: 27595750 PMCID: PMC5011893 DOI: 10.1186/s12864-016-3055-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement for culturing. We recently identified a range of novel uncultured chlamydiae in captive snakes in Switzerland, however, nothing is known about their biology. Using a metagenomics approach, the aim of this study was to characterise the genome of a novel chlamydial taxon from the choana of a captive snake. In doing so, we propose a new candidate species in the genus Chlamydia (Candidatus Chlamydia sanzinia) and reveal new information about the biological diversity of this important group of pathogens. RESULTS We identified two chlamydial genomic contigs: a 1,113,073 bp contig, and a 7,504 bp contig, representing the chromosome and plasmid of Ca. Chlamydia sanzinia strain 2742-308, respectively. The 998 predicted coding regions include an expanded repertoire of outer membrane proteins (Pmps and Omps), some of which exhibited frameshift mutations, as well as several chlamydial virulence factors such as the translocating actin-recruitment phosphoprotein (Tarp) and macrophage inhibition potentiator (Mip). A suite of putative inclusion membrane proteins were also predicted. Notably, no evidence of a traditional chlamydial plasticity zone was identified. Phylogenetically, Ca. Chlamydia sanzinia forms a clade with C. pneumoniae and C. pecorum, distinct from former "Chlamydophila" species. CONCLUSIONS Genomic characterisation of a novel uncultured chlamydiae from the first reptilian host has expanded our understanding of the diversity and biology of a genus that was thought to be the most well-characterised in this unique phylum. It is anticipated that this method will be suitable for characterisation of other novel chlamydiae.
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37
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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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Penicillin G-Induced Chlamydial Stress Response in a Porcine Strain of Chlamydia pecorum. Int J Microbiol 2016; 2016:3832917. [PMID: 26997956 PMCID: PMC4779511 DOI: 10.1155/2016/3832917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/26/2016] [Indexed: 01/14/2023] Open
Abstract
Chlamydia pecorum causes asymptomatic infection and pathology in ruminants, pigs, and koalas. We characterized the antichlamydial effect of the beta lactam penicillin G on Chlamydia pecorum strain 1710S (porcine abortion isolate). Penicillin-exposed and mock-exposed infected host cells showed equivalent inclusions numbers. Penicillin-exposed inclusions contained aberrant bacterial forms and exhibited reduced infectivity, while mock-exposed inclusions contained normal bacterial forms and exhibited robust infectivity. Infectious bacteria production increased upon discontinuation of penicillin exposure, compared to continued exposure. Chlamydia-induced cell death occurred in mock-exposed controls; cell survival was improved in penicillin-exposed infected groups. Similar results were obtained both in the presence and in the absence of the eukaryotic protein translation inhibitor cycloheximide and at different times of initiation of penicillin exposure. These data demonstrate that penicillin G induces the chlamydial stress response (persistence) and is not bactericidal, for this chlamydial species/strain in vitro, regardless of host cell de novo protein synthesis.
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Jelocnik M, Bachmann NL, Seth-Smith H, Thomson NR, Timms P, Polkinghorne AM. Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution. PeerJ 2016; 4:e1661. [PMID: 26870613 PMCID: PMC4748734 DOI: 10.7717/peerj.1661] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/14/2016] [Indexed: 01/07/2023] Open
Abstract
Background. Highly stable, evolutionarily conserved, small, non-integrative plasmids are commonly found in members of the Chlamydiaceae and, in some species, these plasmids have been strongly linked to virulence. To date, evidence for such a plasmid in Chlamydia pecorum has been ambiguous. In a recent comparative genomic study of porcine, ovine, bovine, and koala C. pecorum isolates, we identified plasmids (pCpec) in a pig and three koala strains, respectively. Screening of further porcine, ovine, bovine, and koala C. pecorum isolates for pCpec showed that pCpec is common, but not ubiquitous in C. pecorum from all of the infected hosts. Methods. We used a combination of (i) bioinformatic mining of previously sequenced C. pecorum genome data sets and (ii) pCpec PCR-amplicon sequencing to characterise a further 17 novel pCpecs in C. pecorum isolates obtained from livestock, including pigs, sheep, and cattle, as well as those from koala. Results and Discussion. This analysis revealed that pCpec is conserved with all eight coding domain sequences (CDSs) present in isolates from each of the hosts studied. Sequence alignments revealed that the 21 pCpecs show 99% nucleotide sequence identity, with 83 single nucleotide polymorphisms (SNPs) shown to differentiate all of the plasmids analysed in this study. SNPs were found to be mostly synonymous and were distributed evenly across all eight pCpec CDSs as well as in the intergenic regions. Although conserved, analyses of the 21 pCpec sequences resolved plasmids into 12 distinct genotypes, with five shared between pCpecs from different isolates, and the remaining seven genotypes being unique to a single pCpec. Phylogenetic analysis revealed congruency and co-evolution of pCpecs with their cognate chromosome, further supporting polyphyletic origin of the koala C. pecorum. This study provides further understanding of the complex epidemiology of this pathogen in livestock and koala hosts and paves the way for studies to evaluate the function of this putative C. pecorum virulence factor.
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Affiliation(s)
- Martina Jelocnik
- Centre for Animal Health Innovation, University of the Sunshine Coast , Sippy Downs, Queensland , Australia
| | - Nathan L Bachmann
- Centre for Animal Health Innovation, University of the Sunshine Coast , Sippy Downs, Queensland , Australia
| | - Helena Seth-Smith
- Functional Genomics Center Zurich, University of Zurich , Zurich , Switzerland
| | - Nicholas R Thomson
- Infection Genomics, The Wellcome Trust Sanger Institute , Cambridge , United Kingdom
| | - Peter Timms
- Centre for Animal Health Innovation, University of the Sunshine Coast , Sippy Downs, Queensland , Australia
| | - Adam M Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast , Sippy Downs, Queensland , Australia
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