1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Kasimov V, White RT, Foxwell J, Jenkins C, Gedye K, Pannekoek Y, Jelocnik M. Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers. Microb Genom 2023; 9:mgen001072. [PMID: 37486739 PMCID: PMC10438822 DOI: 10.1099/mgen.0.001072] [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: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes from Australia and New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing to expand the global C. psittaci genome catalogue. Here, we provide new C. psittaci genomes from two pigeons, six psittacines, and novel hosts such as the Australian bustard (Ardeotis australis) and sooty shearwater (Ardenna grisea) from Australia and New Zealand. We also evaluated C. psittaci genetic diversity using multilocus sequence typing (MLST) and major outer membrane protein (ompA) genotyping on additional C. psittaci-positive samples from various captive avian hosts and field isolates from Australasia. We showed that the first C. psittaci genomes sequenced from New Zealand parrots and pigeons belong to the clonal sequence type (ST)24 and diverse 'pigeon-type' ST27 clade, respectively. Australian parrot-derived strains also clustered in the ST24 group, whereas the novel ST332 strain from the Australian bustard clustered in a genetically diverse clade of strains from a fulmar, parrot, and livestock. MLST and ompA genotyping revealed ST24/ompA genotype A in wild and captive parrots and a sooty shearwater, whilst 'pigeon-types' (ST27/35 and ompA genotypes B/E) were found in pigeons and other atypical hosts, such as captive parrots, a little blue penguin/Kororā (Eudyptula minor) and a zebra finch (Taeniopygia guttata castanotis) from Australia and New Zealand. This study provides new insights into the global phylogenomic diversity of C. psittaci and further demonstrates the multi-host generalist capacity of this pathogen.
Collapse
Affiliation(s)
- Vasilli Kasimov
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
| | - Rhys T. White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia
- The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Upper Hutt 5018, New Zealand
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Kristene Gedye
- Massey University, School of Veterinary Science, Palmerston North 4442, New Zealand
| | - Yvonne Pannekoek
- University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, Netherlands
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Jelocnik M, White RT, Clune T, O'Connell J, Foxwell J, Hair S, Besier S, Tom L, Phillips N, Robbins A, Bogema D, Vaz PK, Legione AR, Jenkins C, Jacobson C. Molecular characterisation of the Australian and New Zealand livestock Chlamydia pecorum strains confirms novel but clonal ST23 in association with ovine foetal loss. Vet Microbiol 2023; 283:109774. [PMID: 37216721 DOI: 10.1016/j.vetmic.2023.109774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]
Abstract
Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs. Presently, there is limited genotypic information on C. pecorum strains associated with reproductive disease, although whole genome sequencing (WGS) of one abortigenic ST23 C. pecorum strain identified unique features, including a deletion in the CDS1 locus of the chlamydial plasmid. We applied WGS on two ST23 strains detected in aborted and stillborn lambs from Australia and used phylogenetic and comparative analyses to compare these to the other available C. pecorum genomes. To re-evaluate the genetic diversity of contemporary strains, we applied C. pecorum genotyping, and chlamydial plasmid sequencing to a range of C. pecorum positive samples and isolates from ewes, aborted foetuses and stillborn lambs, cattle and a goat from diverse geographical regions across Australia and New Zealand.The two new C. pecorum genomes are nearly identical to the genome of the Australian abortigenic strain including the unique deletion in the chlamydial plasmid. Genotyping revealed that these novel C. pecorum ST23 strains are widespread and associated with sheep abortions on Australian and New Zealand farms. In addition, a goat C. pecorum strain (denoted ST 304) from New Zealand was also characterised. This study expands the C. pecorum genome catalogue and describes a comprehensive molecular characterisation of the novel livestock ST23 strains associated with foetal and lamb mortality.
Collapse
Affiliation(s)
- Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia.
| | - Rhys T White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia; The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia; The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia.
| | - Tom Clune
- Murdoch University, Centre for Animal Production and Health, Perth, Western Australia 6150, Australia.
| | - John O'Connell
- Ministry for Primary Industries, Diagnostic and Surveillance Services Directorate, Upper Hutt 5140, New Zealand. john.o'
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Upper Hutt 5018, New Zealand.
| | - Sam Hair
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| | - Shane Besier
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| | - La Tom
- Murdoch University, Centre for Animal Production and Health, Perth, Western Australia 6150, Australia.
| | - Nyree Phillips
- Murdoch University, Centre for Animal Production and Health, Perth, Western Australia 6150, Australia.
| | - Amy Robbins
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia.
| | - Daniel Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia.
| | - Paola K Vaz
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia.
| | - Alistair R Legione
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia.
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia.
| | - Caroline Jacobson
- Murdoch University, Centre for Animal Production and Health, Perth, Western Australia 6150, Australia.
| |
Collapse
|
6
|
White RT, Anstey SI, Kasimov V, Jenkins C, Devlin J, El-Hage C, Pannekoek Y, Legione AR, Jelocnik M. One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia. Microb Genom 2022; 8. [PMID: 36269227 PMCID: PMC9676050 DOI: 10.1099/mgen.0.000888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24 strains in horse, psittacine, and human infections. We sought to assess the clonality between ST24 strains and the emergence of equine ST24 with a comprehensive genomics approach. We used culture-independent probe-based and metagenomic whole-genome sequencing to investigate 13 C. psittaci genomes from horses, psittacines, and a pigeon from Australia. Published genomes of 36 C. psittaci strains were also used to contextualise our Australian dataset and investigate lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach. C. psittaci has four major phylogenetic groups (PG1-4) based on core-genome SNP-based phylogeny. PG1 contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. PG2, PG3, and PG4 had greater genomic diversity, including diverse STs collected from birds, livestock, human, and horse hosts from Europe and North America and a racing pigeon from Australia. We show that the clustering of C. psittaci by MLST was congruent with SNP-based phylogeny. The monophyletic ST24 clade has four major sub-lineages. The genomes of 17 Australian human, equine, and psittacine strains collected between 2008 and 2021 formed the predominant ST24 sub-lineage 1 (emerged circa 1979). Despite a temporal distribution of 13 years, the genomes within sub-lineage 1 had a median pairwise SNP distance of 32 SNPs, suggesting a recent population expansion or potential cross-host transmission. However, two C. psittaci genomes collected in 2015 from Victorian parrots clustered into distinct ST24 sub-lineage 4 (emerged circa 1965) with ovine strain C19/98 from Germany. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird-to-equine spillover events.
Collapse
Affiliation(s)
- Rhys T White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia.,The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia
| | - Susan I Anstey
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia
| | - Vasilli Kasimov
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Joanne Devlin
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia
| | - Charles El-Hage
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia
| | - Yvonne Pannekoek
- University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, The Netherlands
| | - Alistair R Legione
- The University of Melbourne, Melbourne Veterinary School, Asia Pacific Centre for Animal Health, Parkville, Victoria 3010, Australia
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia
| |
Collapse
|
7
|
Marti H, Jelocnik M. Animal Chlamydiae: A Concern for Human and Veterinary Medicine. Pathogens 2022; 11:pathogens11030364. [PMID: 35335688 PMCID: PMC8951289 DOI: 10.3390/pathogens11030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty University of Zurich, 8057 Zurich, Switzerland
- Correspondence: (H.M.); (M.J.)
| | - Martina Jelocnik
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs 4556, Australia
- Correspondence: (H.M.); (M.J.)
| |
Collapse
|