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Chaiwattanarungruengpaisan S, Thongdee M, Arya N, Paungpin W, Sirimanapong W, Sariya L. Diversity and genetic characterization of Chlamydia isolated from Siamese crocodiles (Crocodylus siamensis). Acta Trop 2024; 253:107183. [PMID: 38479468 DOI: 10.1016/j.actatropica.2024.107183] [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: 12/20/2023] [Revised: 02/25/2024] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
Chlamydiosis, an infection caused by several Chlamydia species, has been reported in Nile, saltwater, and Siamese crocodiles. Despite its widespread reports in various countries, including Thailand, genetic information on Chlamydia species remains limited. This study presents a whole-genome-based characterization of Siamese crocodile-isolated Chlamydia. The results showed that Siamese crocodile Chlamydia contained a single circular chromosome with a size of 1.22-1.23 Mbp and a plasmid with a size of 7.7-8.0 kbp. A plasmid containing eight coding sequences (CDSs) was grouped in a β lineage. A chromosome sequence had approximately 1,018-1,031 CDSs. Chlamydial factors involving virulence were documented in terms of the presence of cytotoxins and several virulence factors in the chromosomes of Siamese crocodile Chlamydia. The analysis of antimicrobial resistance genes in the Chlamydia genome revealed that the most common resistance genes were associated with aminoglycosides, fluoroquinolones, macrolides, tetracyclines, and cephalosporins, with loose matching (identities between 21.12 % and 74.65 %). Phylogenetic analyses, encompassing the assessments of both whole proteome and nine taxonomic markers, revealed that Siamese crocodile Chlamydia was separated into three lineages (lineages I-III) with high bootstrapping statistic support. Interestingly, isolate 12-01 differed genetically from the others, suggesting that it is a new member of Chlamydia. The study findings indicate that Siamese crocodiles are susceptible hosts to Chlamydia, involving more than one species. This study is the first employing the highest number of whole-genome data on Siamese crocodile Chlamydia and provides better insights into pathogen genetics.
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Affiliation(s)
- Somjit Chaiwattanarungruengpaisan
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Metawee Thongdee
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Nlin Arya
- Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Weena Paungpin
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Wanna Sirimanapong
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Ladawan Sariya
- Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand.
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Yang J, Chen S, Quan M, Li L, Shang L, Fan Z, Hu S. Seroprevalence and Risk Factors of Chlamydia Infection in Pigs in Hunan Province, Southern China, 2017-2018. Vector Borne Zoonotic Dis 2024; 24:214-218. [PMID: 38422215 PMCID: PMC11035838 DOI: 10.1089/vbz.2023.0064] [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] [Indexed: 03/02/2024] Open
Abstract
Background: Chlamydia is a Gram-negative obligate intracellular bacterium that is pathogenic for humans and a large variety of veterinary animal species. However, there is no continuous monitoring of chlamydia infection data in pigs in Hunan province, southern China. Therefore, in order to evaluate the seroprevalence and identify risk factors associated with Chlamydia infection in pigs within this region, a comprehensive study was conducted. Methods: A total of 3848 serum samples were collected from pigs (from farmers and companies) between May 2017 and August 2018. The presence of specific antibodies against Chlamydia was determined through the employment of the indirect hemagglutination assay (IHA). Results: The overall seroprevalence of Chlamydia was determined to be 26.90% (1038/3848, 95% confidence interval: 25.60-28.40). By employing statistical analysis using SPSS software (p < 0.05), factors such as altitude, sampling regions, and rearing systems of pigs were identified as potential risk factors for Chlamydia infection. Conclusion: These findings elucidate a substantial prevalence of Chlamydia in pigs within the mountainous region of Hunan province, southern China, thereby highlighting a potential risk to human health. These results underscore the need for proactive measures and targeted interventions to mitigate the transmission of Chlamydia in porcine populations, safeguarding both animal welfare and public health.
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Affiliation(s)
- Junkun Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, PR China
- Central South University of Forestry and Technology, Changsha, PR China
| | - Shilin Chen
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, PR China
- Wanning Animal Disease Prevention and Control Center of Hainan Province, Wanning, PR China
| | - Minxiu Quan
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, PR China
| | - Leqin Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, PR China
| | - Ling Shang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, PR China
| | - Zhongxin Fan
- Animal Disease Prevention and Control Center of Hunan Province, Changsha, PR China
| | - Shifeng Hu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, PR China
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Szymańska-Czerwińska M, Zaręba-Marchewka K, Niemczuk K. New insight on chlamydiae. J Vet Res 2023; 67:559-565. [PMID: 38130448 PMCID: PMC10730554 DOI: 10.2478/jvetres-2023-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
This article provides an overview of the current knowledge on chlamydiae, which are intracellular bacteria belonging to the Chlamydiaceae family. Whole-genome sequencing leads to great increases in the available data about Chlamydia spp. Recently, novel chlamydial taxons in various hosts living in different environments have been recognised. New species and taxons with Candidatus status have been recorded mainly in birds and reptiles. Chlamydia gallinacea is an emerging infectious agent in poultry with indirectly confirmed zoonotic potential. Recently, a new group of avian C. abortus strains with worldwide distribution in various wild bird families has been described. The definition of C. abortus species became outdated with the discovery of these strains and has been amended. It now includes two subgroups, mammalian and avian, the latter including all isolates hitherto referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.
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Affiliation(s)
- Monika Szymańska-Czerwińska
- Department of Cattle and Sheep Diseases, Puławy, Poland
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, 24-100Puławy, Poland
| | | | - Krzysztof Niemczuk
- Department of Cattle and Sheep Diseases, Puławy, Poland
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, 24-100Puławy, Poland
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Greub G, Pillonel T, Bavoil PM, Borel N, Campbell LA, Dean D, Hefty S, Horn M, Morré SA, Ouellette SP, Pannekoek Y, Puolakkainen M, Timms P, Valdivia R, Vanrompay D. Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae. New Microbes New Infect 2023; 54:101158. [PMID: 37416863 PMCID: PMC10320375 DOI: 10.1016/j.nmni.2023.101158] [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: 10/06/2021] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The International Committee on Systematics of Prokaryotes (ICSP) discussed and rejected in 2020 a proposal to modify the International Code of Nomenclature of Prokaryotes to allow the use of gene sequences as type for naming prokaryotes. An alternative nomenclatural code, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which considers genome sequences as type material for naming species, was published in 2022. Members of the ICSP subcommittee for the taxonomy of the phylum Chlamydiae (Chlamydiota) consider that the use of gene sequences as type would benefit the taxonomy of microorganisms that are difficult to culture such as the chlamydiae and other strictly intracellular bacteria. We recommend the registration of new names of uncultured prokaryotes in the SeqCode registry.
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Affiliation(s)
- Gilbert Greub
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland
| | - Trestan Pillonel
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland
| | - Patrik M. Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Nicole Borel
- Department of Pathobiology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, CH-8057, Zurich, Switzerland
| | - Lee Ann Campbell
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Deborah Dean
- Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, Oakland, CA, USA
| | - Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090, Vienna, Austria
| | - Servaas A. Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Developmental Biology), Faculty of Health, Medicine & Life Sciences, University of Maastricht, Maastricht, the Netherlands
- Dutch Chlamydia Trachomatis Reference Laboratory, Department of Medical Microbiology & Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Scot P. Ouellette
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mirja Puolakkainen
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peter Timms
- Genecology Research Center, University of Sunshine Coast, Queensland, Australia
| | - Raphael Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710, USA
| | - Daisy Vanrompay
- Department of Animal Science and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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Zaręba-Marchewka K, Bomba A, Scharf S, Niemczuk K, Schnee C, Szymańska-Czerwińska M. Whole Genome Sequencing and Comparative Genomic Analysis of Chlamydia gallinacea Field Strains Isolated from Poultry in Poland. Pathogens 2023; 12:891. [PMID: 37513738 PMCID: PMC10384503 DOI: 10.3390/pathogens12070891] [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: 05/30/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Chlamydia gallinacea is an intracellular bacterium belonging to the Chlamydiaceae family. Poultry is considered to be the major reservoir of this agent, which has worldwide distribution and a particularly consistent worldwide occurrence in chicken flocks. The bacterium has been linked to respiratory disease in humans but without definitive confirmation; nevertheless, while it has not been proved to be the cause of human respiratory disease, a recent report from Italy verified its bird-to-human transmission. This aspect being significant for public health, more research is needed to gain insight into the infection biology of C. gallinacea. In this study, the genomes of eleven novel C. gallinacea field strains from different regions of Poland were analyzed comparatively. It was confirmed that C. gallinacea strains are closely related, with at least 99.46% sequence identity. They possess a conservative genome structure involving the plasticity zone with a complete cytotoxin, the type three secretion system, inclusion membrane proteins, polymorphic membrane proteins, hctA and hctB histone-like proteins, and the chlamydial protease-like activating factor exoenzyme, as well as plasmids. Genetic diversity seems to be restricted. However, some genetic loci, such as ompA and multi-locus sequence typing target genes, are diverse enough to enable high-resolution genotyping and epidemiological tracing.
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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
| | - Arkadiusz Bomba
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
| | - Sabine Scharf
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96 a, D-07743 Jena, Germany
| | - Krzysztof Niemczuk
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96 a, D-07743 Jena, Germany
| | - Monika Szymańska-Czerwińska
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland
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Benamri I, Azzouzi M, Moussa A, Radouani F. An in silico analysis of rpoB mutations to affect Chlamydia trachomatis sensitivity to rifamycin. J Genet Eng Biotechnol 2022; 20:146. [DOI: 10.1186/s43141-022-00428-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/08/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Chlamydia trachomatis is an obligate intracellular gram-negative pathogen, responsible for diverse affections, mainly trachoma and sexually transmitted diseases. Antibiotics are the commonly used drugs to tackle chlamydiae infections. However, when overused or wrongly used this may lead to strains’ resistance to antibiotics, this phenomenon represents a real health problem worldwide. Numerous studies showed the association of Chlamydia trachomatis resistance with mutations in different genes; these mutations could have a deleterious or neutral impacts on the encoded proteins. The aim of this study is to perform an in silico analysis of C. trachomatis rpoB-encoded proteins using numerous bioinformatics tools and to identify the functional and structural-related effects of the mutations and consequently their impact on the bacteria sensitivity to antibiotics.
Results
The analysis revealed that the prediction of the damaging impact related to the mutations in rpoB-encoded proteins showed eight mutations: V136F, Q458K, V466A, A467T, H471N, H471Y, H471L, and I517M with big deleterious effects. Among them, six mutations, V136F, Q458K, V466A, A467T, H471N, and I517M, are located in a highly conserved regions decreasing the protein’s stability. Furthermore, the structures analysis showed that the mutations A467T, H471N, I517M, and V136F models had a high deviation compared to the wild type. Moreover, the prediction of protein-protein network indicated that rpoB wild type interacts strongly with 10 proteins of C. trachomatis, which are playing different roles at different levels.
Conclusion
As conclusion, the present study revealed that the changes observed in the encoded proteins can affect their functions and structures, in addition to their interactions with other proteins which impact the bacteria sensitivity to antibiotics. Consequently, the information revealed through this in silico analysis would be useful for deeper exploration to understand the mechanisms of C. trachomatis resistance and enable managing the infection to avoid its complications. We recommend further investigations and perform deeper experimental analysis with collaboration between bioinformaticians, physicians, biologists, pharmacists, and chemistry and biochemistry scientists.
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Aaziz R, Laroucau K, Gobbo F, Salvatore D, Schnee C, Terregino C, Lupini C, Di Francesco A. Occurrence of Chlamydiae in Corvids in Northeast Italy. Animals (Basel) 2022; 12:ani12101226. [PMID: 35625072 PMCID: PMC9137748 DOI: 10.3390/ani12101226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The continuous improvement of next-generation sequencing techniques has led to an expansion of the number of Chlamydia species, as well as their host range. Recent studies performed on wild birds have detected Chlamydia strains with characteristics intermediate between Chlamydia psittaci and Chlamydia abortus. In this study, 12/108 corvids tested positive for Chlamydia by real-time PCR. Molecular characterisation at the species level was possible for eight samples, with one positive for C. psittaci and seven for C. abortus. Considering the well-known zoonotic role of C. psittaci and that a potential zoonotic role of avian C. abortus strains cannot be excluded, people who may have professional or other contact with wild birds should take appropriate preventive measures. Abstract Chlamydiaceae occurrence has been largely evaluated in wildlife, showing that wild birds are efficient reservoirs for avian chlamydiosis. In this study, DNA extracted from cloacal swabs of 108 corvids from Northeast Italy was screened for Chlamydiaceae by 23S real-time (rt)PCR. The positive samples were characterised by specific rtPCRs for Chlamydia psittaci, Chlamydia abortus, Chlamydia gallinacea, Chlamydia avium, Chlamydia pecorum and Chlamydia suis. Cloacal shedding of Chlamydiaceae was detected in 12 out of 108 (11.1%, 5.9%–18.6% 95% CI) corvids sampled. Molecular characterisation at the species level was possible in 8/12 samples, showing C. psittaci positivity in only one sample from a hooded crow and C. abortus positivity in seven samples, two from Eurasian magpies and five from hooded crows. Genotyping of the C. psittaci-positive sample was undertaken via PCR/high-resolution melting, clustering it in group III_pigeon, corresponding to the B genotype based on former ompA analysis. For C. abortus genotyping, multilocus sequence typing was successfully performed on the two samples with high DNA load from Eurasian magpies, highlighting 100% identity with the recently reported Polish avian C. abortus genotype 1V strain 15-58d44. To confirm the intermediate characteristics between C. psittaci and C. abortus, both samples, as well as two samples from hooded crows, showed the chlamydial plasmid inherent in most C. psittaci and avian C. abortus, but not in ruminant C. abortus strains. The plasmid sequences were highly similar (≥99%) to those of the Polish avian C. abortus genotype 1V strain 15-58d44. To our knowledge, this is the first report of avian C. abortus strains in Italy, specifically genotype 1V, confirming that they are actively circulating in corvids in the Italian region tested.
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Affiliation(s)
- Rachid Aaziz
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, 94700 Maisons-Alfort, France; (R.A.); (K.L.)
| | - Karine Laroucau
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, 94700 Maisons-Alfort, France; (R.A.); (K.L.)
| | - Federica Gobbo
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, PD, Italy; (F.G.); (C.T.)
| | - Daniela Salvatore
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (D.S.); (C.L.)
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), D-07743 Jena, Germany;
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, PD, Italy; (F.G.); (C.T.)
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (D.S.); (C.L.)
| | - Antonietta Di Francesco
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (D.S.); (C.L.)
- Correspondence:
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Carossino M, Nevarez JG, Sakaguchi K, Paulsen DB, Langohr IM, Strother K, Ferracone J, Roy A, Crossland NA, Del Piero F. An outbreak of systemic chlamydiosis in farmed American alligators ( Alligator mississippiensis). Vet Pathol 2022; 59:860-868. [PMID: 35502797 DOI: 10.1177/03009858221095269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Chlamydia spp are reported to causes systemic disease in a variety of hosts worldwide including few reports in crocodilians. Disease presentations vary from asymptomatic to fulminant disease, some of which are zoonotic. The aim of this study was to describe the pathological, immunohistochemical, and molecular findings associated with the occurrence of a previously unreported Chlamydia sp infection causing a major mortality event in farmed American alligators (Alligator mississippiensis). The outbreak presented with sudden death in juvenile alligators mainly associated with necrotizing hepatitis and myocarditis, followed by the occurrence of conjunctivitis after the initial high mortality event. The widespread inflammatory lesions in multiple organs correlated with intralesional chlamydial organisms identified via immunohistochemistry and confirmed by 23S rRNA-specific real-time quantitative polymerase chain reaction (qPCR) for Chlamydiaceae bacteria. By sequencing and phylogenetic analysis of the OmpA gene, this uncultured Chlamydia sp grouped closely with Chlamydia poikilothermis recently described in snakes. This study highlights the significance of such outbreaks in farmed populations. Enhanced epidemiological monitoring is needed to gain further insight into the biology of Chlamydia sp in alligators, disease dynamics, risk factors, and role of carrier animals.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Javier G Nevarez
- Veterinary Teaching Hospital & Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | | | - Daniel B Paulsen
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Ingeborg M Langohr
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Keith Strother
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | | | - Alma Roy
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Nicholas A Crossland
- Department of Pathology & National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA
| | - Fabio Del Piero
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
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Bellinati L, Pesaro S, Marcer F, Danesi P, Natale A, Ceglie L. Detection of a Novel Chlamydia Species in Invasive Turtles. Animals (Basel) 2022; 12:ani12060784. [PMID: 35327181 PMCID: PMC8944456 DOI: 10.3390/ani12060784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary The pond slider (Trachemys scripta) is a turtle species native to Central America. Pond sliders have been commercialized as pets since the 1950s, but often ended up being released or escaping into an environment to which they are allochthonous. Trachemys scripta is presently classified as an invasive alien species in Europe and other countries. The introduction of pond sliders in foreign ecosystems has had a deep environmental and ecological impact. Moreover, freed or escaped captive turtles could be carriers of pathogens, such as Chlamydiaceae. In this study, we report the identification of a Chlamydia spp. in two pond sliders found dead after the hibernation period. Further molecular characterization revealed that this Chlamydia is identical to a strain reported in Poland in 2017, found in both captive and free-living freshwater turtles, and has a close phylogenetic relationship to Chlamydia pneumoniae, a species infectious to humans, and to chlamydial strains found in other reptiles. This first finding evidences the presence of this novel Chlamydia in Italian turtles, but further studies will be necessary to evaluate the prevalence in the local turtles’ population and the strain pathogenicity. Abstract Trachemys scripta is a turtle species native to Central America. Since the 1950s, pond sliders have been imported worldwide as companion animals, but have often ended up in foreign ecosystems with great ecological consequences. Moreover, both autochthonous and invasive species of turtles can be carriers of pathogens, including Chlamydiaceae. In the present study, pulmonary tissues collected from four Trachemys scripta were tested with a 23S-targeting real-time PCR (rPCR) specific for the Chlamydiaceae family. The turtles were hosted in a rescue center for wild exotic animals located in northeastern Italy, and were found dead after the hibernation period. Two out of four individuals resulted positive in rPCR for the presence of Chlamydiaceae. Further characterization of this positivity was performed by phylogenetic analysis of the 16S rRNA and outer membrane protein A genes. The phylogenetic tree showed that these chlamydial strains are identical to a novel Chlamydia reported in 2017 in Polish freshwater turtles, and closely related to Chlamydia pneumoniae and to other chlamydial strains found in reptiles. This first finding evidences the presence of this Chlamydia strain in Italian turtles, but further studies will be necessary to confirm the presence and the strain pathogenicity and to evaluate its prevalence in the local turtles’ population.
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Affiliation(s)
- Laura Bellinati
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (A.N.); (L.C.)
- Correspondence:
| | - Stefano Pesaro
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali Sezione di Patologia Veterinaria, Università degli Studi di Udine, Via Sondrio, 33100 Udine, Italy;
| | - Federica Marcer
- Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, 35020 Legnaro, Italy;
| | - Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (A.N.); (L.C.)
| | - Alda Natale
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (A.N.); (L.C.)
| | - Letizia Ceglie
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (P.D.); (A.N.); (L.C.)
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Pace A, Vicari N, Rigamonti S, Magnino S, Borrelli L, Dipineto L, Fioretti A, Hochscheid S, Tavares L, Duarte A. Detection of Chlamydial DNA from Mediterranean Loggerhead Sea Turtles in Southern Italy. Animals (Basel) 2022; 12:ani12060715. [PMID: 35327112 PMCID: PMC8944518 DOI: 10.3390/ani12060715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Chlamydiae are obligate intracellular bacteria that include pathogens of human and veterinary importance. Several reptiles were reported to host chlamydial agents, but pathogenicity in these animals still needs clarification. Given that only one report of chlamydiosis was described in sea turtles, and that chlamydiae might also be detected in hosts without clinical signs, the current study examined asymptomatic Mediterranean loggerhead sea turtles for the presence of chlamydial DNA. Twenty loggerhead sea turtles, rehabilitated at the Marine Turtle Research Centre (Portici, Italy), were examined collecting ocular-conjunctival, oropharyngeal and nasal swabs. Samples were processed through quantitative and conventional PCR analyses to identify Chlamydiales and Chlamydiaceae, with particular attention to C. pecorum, C. pneumoniae, C. psittaci, and C. trachomatis. Although it was not possible to determine the species of chlamydiae involved, the detection of chlamydial DNA from the collected samples suggests that these microorganisms might act as opportunistic pathogens, and underlines the role of sea turtles as potential carriers. This study highlights the presence of chlamydial agents in sea turtles, and encourages further research to fully characterize these microorganisms, in order to improve the management of the health and conservation of these endangered species, and prevent potential zoonotic implications.
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Affiliation(s)
- Antonino Pace
- Marine Turtle Research Group, Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, 80055 Portici, Italy;
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, 80137 Naples, Italy; (L.B.); (L.D.); (A.F.)
- Correspondence: or
| | - Nadia Vicari
- National Reference Laboratory for Animal Chlamydioses, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Sede Territoriale di Pavia, 27100 Pavia, Italy; (N.V.); (S.R.); (S.M.)
| | - Sara Rigamonti
- National Reference Laboratory for Animal Chlamydioses, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Sede Territoriale di Pavia, 27100 Pavia, Italy; (N.V.); (S.R.); (S.M.)
| | - Simone Magnino
- National Reference Laboratory for Animal Chlamydioses, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Sede Territoriale di Pavia, 27100 Pavia, Italy; (N.V.); (S.R.); (S.M.)
| | - Luca Borrelli
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, 80137 Naples, Italy; (L.B.); (L.D.); (A.F.)
| | - Ludovico Dipineto
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, 80137 Naples, Italy; (L.B.); (L.D.); (A.F.)
| | - Alessandro Fioretti
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, 80137 Naples, Italy; (L.B.); (L.D.); (A.F.)
| | - Sandra Hochscheid
- Marine Turtle Research Group, Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, 80055 Portici, Italy;
| | - Luís Tavares
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisbon, Portugal; (L.T.); (A.D.)
| | - Ana Duarte
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisbon, Portugal; (L.T.); (A.D.)
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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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Liang L, Wen Y, Li Z, Liu P, Liu X, Tan S, Liu D, Zhou J, Tong D. Seroprevalence of Chlamydia abortus infection in yak (Bos grunniens) in Tibet, China. Ir Vet J 2021; 74:19. [PMID: 34193296 PMCID: PMC8246664 DOI: 10.1186/s13620-021-00199-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022] Open
Abstract
Chlamydia spp. are prevalent zoonotic pathogens that infect a wide variety of host species. Chlamydia abortus (C. abortus) infection in yaks has been reported in Gansu and Qinghai province, China. However, no data about C. abortus infection are available in yaks in Tibet, China. A total of 938 serum samples was collected from yaks in Tibet, China and specific antibodies against C. abortus were detected by the enzyme-linked immunosorbent assay (ELISA). The results showed that the overall seroprevalence of C. abortus in yaks was 104/938 (11.1 %, 95 % confidence interval [CI] 9.1–13.1). The prevalence in female and male yaks was 59/556 (10.6 %, 95 % CI 8.0-13.2) and 45/382 (11.8 %, 95 % CI 8.5–15.0), respectively with no significant difference (p > 0.05). The seroprevalence of antibodies to C. abortus in yaks ranged from 8.0 to 18.2 % among the six different areas, and the difference was also without statistical significance (p > 0.05). The prevalence among different age groups ranged from 7.0 to 15.9 %, with a higher prevalence among 1 to 2 years age category. The results demonstrate the presence of C. abortus infection in yaks in Tibet and may pose a risk for the general yak populations in addition to its potential impact on public health and the local Tibetan economy. To our knowledge, this is the first seroprevalence survey of C. abortus in yaks in Tibet, China.
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Affiliation(s)
- Lin Liang
- College of Veterinary Medicine, Northwest A&F University, 712100, Yangling, China
| | - Yuan Wen
- College of Veterinary Medicine, Northwest A&F University, 712100, Yangling, China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China
| | - Zhaocai Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China
| | - Ping Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China
| | - Xing Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China
| | - Shuming Tan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China
| | - Donghui Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China
| | - Jizhang Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China.
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, 712100, Yangling, China.
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13
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Köstlbacher S, Collingro A, Halter T, Schulz F, Jungbluth SP, Horn M. Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nat Commun 2021; 12:4021. [PMID: 34188040 PMCID: PMC8242063 DOI: 10.1038/s41467-021-24294-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the "Genomes from Earth's Microbiomes" initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.
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Affiliation(s)
- Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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14
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Chaiwattanarungruengpaisan S, Thongdee M, Anuntakarun S, Payungporn S, Arya N, Punchukrang A, Ramasoota P, Singhakaew S, Atithep T, Sariya L. A new species of Chlamydia isolated from Siamese crocodiles (Crocodylus siamensis). PLoS One 2021; 16:e0252081. [PMID: 34043689 PMCID: PMC8158970 DOI: 10.1371/journal.pone.0252081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/09/2021] [Indexed: 11/30/2022] Open
Abstract
Chlamydia is a known pathogen in both saltwater and freshwater crocodiles. However, the exact species/strain has not been clearly identified. In this study, we successfully cultivated Siamese crocodile Chlamydia in McCoy cells at a temperature of 30°C. Electron microscopy; phylogeny based on nine conserved taxonomically informative markers, on ompA, or on seven housekeeping genes; and whole-genome sequencing and analysis of the isolate confirmed the identity of the isolate as a new member of the genus Chlamydia, a new species that we name Chlamydia crocodili.
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Affiliation(s)
- Somjit Chaiwattanarungruengpaisan
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Metawee Thongdee
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Songtham Anuntakarun
- Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nlin Arya
- Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Apichart Punchukrang
- Faculty of Agricultural Technology, Songkhla Rajabhat University, Songkhla, Thailand
| | - Pongrama Ramasoota
- Center of Excellence for Antibody Research and Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sombat Singhakaew
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thassanant Atithep
- Frontier Research Center, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Ladawan Sariya
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
- * E-mail:
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15
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Draft Genome Sequences of Avian Chlamydia abortus Genotype G2 Strain 15-49d3, Isolated from Mallard, and Genotype 1V Strain 15-58d44, Isolated from Magpie in Poland. Microbiol Resour Announc 2021; 10:10/14/e01203-20. [PMID: 33833029 PMCID: PMC8032471 DOI: 10.1128/mra.01203-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Here, we report the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie in Poland. The total genome assembly lengths are 1,140,139 bp and 1,158,207 bp, respectively. Here, we report the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie in Poland. The total genome assembly lengths are 1,140,139 bp and 1,158,207 bp, respectively.
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16
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Vorimore F, Hölzer M, Liebler-Tenorio EM, Barf LM, Delannoy S, Vittecoq M, Wedlarski R, Lécu A, Scharf S, Blanchard Y, Fach P, Hsia RC, Bavoil PM, Rosselló-Móra R, Laroucau K, Sachse K. Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov. Syst Appl Microbiol 2021; 44:126200. [PMID: 34298369 DOI: 10.1016/j.syapm.2021.126200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022]
Abstract
The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other proven or potential pathogens in ruminants, birds, snakes, reptiles and turtles. During routine testing of 15 apparently healthy captive flamingos in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Sequence analysis of the 16S rRNA gene revealed high similarity to the uncultured Chlamydiales bacterium clone 122, which previously had been found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015, Chlamydiaceae-specific DNA was detected by PCR in 30.9% of wild birds. From these samples, three strains were successfully grown in cell culture. Ultrastructural analysis, comparison of 16S and 23S rRNA gene sequences, whole-genome analysis based on de novo hybrid-assembled sequences of the new strains as well as subsequent calculation of taxonomic parameters revealed that the relatedness of the flamingo isolates to established members of the family Chlamydiaceae was sufficiently distant to indicate that the three strains belong to two distinct species within a new genus. Based on these data, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov., as two new species of the genus.
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Affiliation(s)
- F Vorimore
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France.
| | - M Hölzer
- Robert Koch Institute, MF1 Bioinformatics, Berlin, Germany
| | - E M Liebler-Tenorio
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - L-M Barf
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
| | - S Delannoy
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - M Vittecoq
- Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles, France
| | - R Wedlarski
- Bioparc - Zoo de Doué la fontaine, 103 rue de Cholet, 49700 Doué la Fontaine, France
| | - A Lécu
- Parc Zoologique de Paris, avenue de Daumesnil, 75012 Paris, France
| | - S Scharf
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - Y Blanchard
- Unit of Viral Genetics and Biosafety, ANSES, Laboratory of Ploufragan, Ploufragan, France
| | - P Fach
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - R C Hsia
- University of Maryland, Electron Microscopy Core Imaging Facility, Baltimore, MD 21201, USA
| | - P M Bavoil
- University of Maryland, Department of Microbial Pathogenesis, Baltimore, MD 21201, USA
| | - R Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies, 07190 Esporles, Spain
| | - K Laroucau
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - K Sachse
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
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17
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Longbottom D, Livingstone M, Ribeca P, Beeckman DSA, van der Ende A, Pannekoek Y, Vanrompay D. Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species. BMC Genomics 2021; 22:159. [PMID: 33676404 PMCID: PMC7937271 DOI: 10.1186/s12864-021-07477-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chlamydia abortus and Chlamydia psittaci are important pathogens of livestock and avian species, respectively. While C. abortus is recognized as descended from C. psittaci species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of C. abortus. Such strains include C. psittaci strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both C. abortus and C. psittaci. RESULTS In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with C. abortus species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C. abortus in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with C. abortus strains. The analysis also suggested a closer evolutionary relationship between this strain and the major C. abortus clade, than to two other intermediary avian C. abortus strains or C. psittaci strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced C. abortus genomes as well as similar features to both C. abortus and C. psittaci species. The strain also possesses an extrachromosomal plasmid, as found in most C. psittaci species but absent from all sequenced classical C. abortus strains. CONCLUSION Overall, the results show that C. psittaci strain 84/2334 clusters very closely with C. abortus strains, and are consistent with the strain being a recent C. abortus ancestral species. This suggests that the strain should be reclassified as C. abortus. Furthermore, the identification of a C. abortus strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from C. abortus infection.
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Affiliation(s)
- David Longbottom
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK.
| | - Morag Livingstone
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK
| | - Paolo Ribeca
- Biomathematics and Statistics Scotland, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Delphine Sylvie Anne Beeckman
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium.,Current address: BASF Belgium Coordination Center CommV - Innovation Center Gent, Ghent, Belgium
| | - Arie van der Ende
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Daisy Vanrompay
- Department of Animal Science and Aquatic Ecology, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
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18
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Abstract
This paper provides an overview of the current knowledge of chlamydiae. These intracellular microorganisms belonging to the Chlamydiaceae family are widely distributed throughout the world. Constant development of culture-independent approaches for characterisation of microbial genomes enables new discoveries in the field of Chlamydia. The number of new taxa is continuously increasing as well as the range of hosts. New species and genotypes are constantly being discovered, particularly new avian and reptilian agents, which are discussed in this article. Interestingly, wild animals are the main hosts for new Chlamydia species including different species of bird, turtle and snake. The availability of next-generation sequencing opens up a new prospect for research and leads to deeper knowledge of these interesting microorganisms about which much is still to discover.
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19
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Chronic wasting associated with Chlamydia pneumoniae in three ex situ breeding facilities for tropical frogs. Antonie van Leeuwenhoek 2020; 113:2139-2154. [PMID: 33150542 PMCID: PMC7716926 DOI: 10.1007/s10482-020-01483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022]
Abstract
A number of different Chlamydia spp. have been detected in the class Amphibia with C. pneumoniae being the predominant species involved. Chlamydiae have been linked to mass mortality events, thereby representing significant pathogens that deserve attention with respect to worldwide amphibian decline. We here present six cases of chlamydiosis and asymptomatic chlamydial infections in different frog species from three ex situ amphibian conservation facilities. Clinical signs predominantly characterised by regurgitation, chronic wasting, lethargy and suspended breeding were associated with C. pneumoniae infection. Despite various treatment regimens, it was not possible to clear infections. However, intra vitam diagnostics succeeded from skin, faeces and urine for the first time.
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20
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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21
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Laroucau K, Ortega N, Vorimore F, Aaziz R, Mitura A, Szymanska-Czerwinska M, Cicerol M, Salinas J, Sachse K, Caro MR. Detection of a novel Chlamydia species in captive spur-thighed tortoises (Testudo graeca) in southeastern Spain and proposal of Candidatus Chlamydia testudinis. Syst Appl Microbiol 2020; 43:126071. [PMID: 32085936 DOI: 10.1016/j.syapm.2020.126071] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022]
Abstract
The spur-thighed tortoise (Testudo graeca) is an endangered Mediterranean tortoise that lives in North Africa, Southern Europe and Southwest Asia. In the wake of recent legislation making their keeping as domestic animals illegal, many of these animals have been returned to wildlife recovery centers in Spain. In the present study, a population of such tortoises showing signs of ocular disease and nasal discharge was examined for the presence of Chlamydia spp. Cloacal, conjunctival and/or choanal swabs were collected from 58 animals. Using a real-time PCR specific for the family Chlamydiaceae, 57/58 animals tested positive in at least one sample. While only a few samples proved positive for C. pecorum, sequencing of the 16S rRNA gene revealed a sequence identical to previously published sequences from specimens of German and Polish tortoises. Whole-genome sequences obtained from two conjunctival swab samples, as well as ANIb, TETRA values and a scheme based on 9 taxonomic marker genes revealed that the strain present in the Spanish tortoises represented a new yet non-classified species, with C. pecorum being its closest relative. We propose to designate the new species Candidatus Chlamydia testudinis.
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Affiliation(s)
- K Laroucau
- University Paris-Est, ANSES, Animal Health Laboratory, Bacterial Zoonoses Unit. Maisons-Alfort, France.
| | - N Ortega
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus Regional de Excelencia internacional, Campus Mare Nostrum, Universidad de Murcia, Spain
| | - F Vorimore
- University Paris-Est, ANSES, Animal Health Laboratory, Bacterial Zoonoses Unit. Maisons-Alfort, France
| | - R Aaziz
- University Paris-Est, ANSES, Animal Health Laboratory, Bacterial Zoonoses Unit. Maisons-Alfort, France
| | - A Mitura
- Department of Cattle and Sheep Diseases/Laboratory of Serological Diagnosis, National Veterinary Research Institute, Pulawy, Poland
| | - M Szymanska-Czerwinska
- Department of Cattle and Sheep Diseases/Laboratory of Serological Diagnosis, National Veterinary Research Institute, Pulawy, Poland
| | - M Cicerol
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus Regional de Excelencia internacional, Campus Mare Nostrum, Universidad de Murcia, Spain
| | - J Salinas
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus Regional de Excelencia internacional, Campus Mare Nostrum, Universidad de Murcia, Spain
| | - K Sachse
- Friedrich-Schiller-Universität Jena, Institut f. Bioinformatik, 07743 Jena, Germany
| | - M R Caro
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus Regional de Excelencia internacional, Campus Mare Nostrum, Universidad de Murcia, Spain
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22
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Abstract
Chlamydiae are obligate intracellular bacterial pathogens of humans. Infections in animals are also widespread with some species, such as Chlamydia psittaci, long recognised as a serious threat to human health. Critical to the public health response of any zoonotic disease outbreaks is reliable and up-to-date information on the epidemiology of the target pathogen. Aided by advances in the use of quantitative PCR, molecular typing and culture-independent genomic studies, significant recent work has highlighted an expanded diversity and host range of chlamydial pathogens in animals. New and unexpected cases of chlamydial zoonoses have now been recently documented in Australia and elsewhere, emphasising the importance of multi-disciplinary ‘One Health' collaboration and the use of standardised methods to detect and characterise chlamydial pathogens in humans and animals.
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23
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Mattmann P, Marti H, Borel N, Jelocnik M, Albini S, Vogler BR. Chlamydiaceae in wild, feral and domestic pigeons in Switzerland and insight into population dynamics by Chlamydia psittaci multilocus sequence typing. PLoS One 2019; 14:e0226088. [PMID: 31887111 PMCID: PMC6936790 DOI: 10.1371/journal.pone.0226088] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/18/2019] [Indexed: 11/18/2022] Open
Abstract
Feral pigeons, common wood pigeons and Eurasian collared doves are the most common representatives of the Columbidae family in Switzerland and are mostly present in highly populated, urban areas. Pigeons may carry various members of the obligate intracellular Chlamydiaceae family, particularly Chlamydia (C.) psittaci, a known zoonotic agent, and C. avium. The objective of the study was to identify the infection rates of common free-roaming pigeons for different Chlamydia species with the overall aim to assess the risk pigeons pose to public health. In this study, 431 pigeons (323 feral pigeons, 34 domestic pigeons, 39 Eurasian collared doves, 35 common wood pigeons) from several geographic locations in Switzerland were investigated for the presence of Chlamydiaceae. Samples consisted of pooled choanal-cloacal swabs (n = 174), liver samples (n = 52), and paired swab and liver samples from 205 pigeons (n = 410). All 636 samples were screened using a Chlamydiaceae family-specific 23S rRNA real-time PCR (qPCR). Subsequent species identification was performed by DNA-microarray assay, sequencing of a 16S rRNA gene fragment and a C. psittaci specific qPCR. In total, 73 of the 431 pigeons tested positive for Chlamydiaceae, of which 68 were positive for C. psittaci, four were C. avium-positive and one pigeon was co-infected with C. avium and C. psittaci. The highest infection rates were detected in feral (64/323) and domestic pigeons (5/34). Common wood pigeons (2/35) and Eurasian collared doves (2/39) revealed lower infection rates. Additionally, multilocus sequence typing of twelve selected C. psittaci-positive samples revealed closely related sequence types (ST) between and within different Swiss cities. Furthermore, liver and corresponding swab samples from the same bird were colonized by the same ST. Considering the high infection rates of C. psittaci in domestic and feral pigeons, close or frequent contact to these birds poses a human health risk.
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MESH Headings
- Animals
- Animals, Domestic
- Animals, Wild
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/classification
- Bacterial Outer Membrane Proteins/genetics
- Bird Diseases/diagnosis
- Bird Diseases/microbiology
- Chlamydiaceae/classification
- Chlamydiaceae/genetics
- Chlamydiaceae/isolation & purification
- Chlamydophila psittaci/genetics
- Chlamydophila psittaci/isolation & purification
- Columbidae
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Multilocus Sequence Typing
- Phylogeny
- Population Dynamics
- Psittacosis/diagnosis
- Psittacosis/microbiology
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/metabolism
- Switzerland
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Affiliation(s)
- Prisca Mattmann
- National Reference Centre for Poultry and Rabbit Diseases (NRGK), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Swiss Ornithological Institute, Sempach, Switzerland
| | - Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Martina Jelocnik
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Australia
| | - Sarah Albini
- National Reference Centre for Poultry and Rabbit Diseases (NRGK), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Barbara Renate Vogler
- National Reference Centre for Poultry and Rabbit Diseases (NRGK), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- * E-mail:
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24
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A cluster of Chlamydia serpentis cases in captive snakes. Vet Microbiol 2019; 240:108499. [PMID: 31902484 DOI: 10.1016/j.vetmic.2019.108499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 11/23/2022]
Abstract
Following the occurrence of sudden death cases in a zoo reptile collection, histological analyses conducted on tissues from two common adders suggested an infection due to Chlamydia. The survey was extended to 22 individual snakes from the same collection and a PCR analysis targeting a conserved gene in Chlamydiaceae revealed bacterial shedding in six of them. The infection resolved spontaneously in one snake whereas another one succumbed one month later. The antibiotic treatment administered (marbofloxacin) to the remaining four PCR positive animals stopped the mortalities and the shedding. Analysis of the 16S and 23S ribosomal gene sequences identified C. serpentis, a recently described novel chlamydial species in snakes. A PCR tool for a quick and specific identification of this new chlamydial species was developed in this study.
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25
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Sigalova OM, Chaplin AV, Bochkareva OO, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics 2019; 20:710. [PMID: 31510914 PMCID: PMC6740158 DOI: 10.1186/s12864-019-6059-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. RESULTS We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system. CONCLUSIONS This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.
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Affiliation(s)
- Olga M. Sigalova
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- current address: European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrei V. Chaplin
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga O. Bochkareva
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- current address: Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Pavel V. Shelyakin
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Vavilov Institute of General Genetics, RAS, Moscow, Russia
| | | | - Evgeny E. Akkuratov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- current address: Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Valentina Burskaia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail S. Gelfand
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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26
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Abstract
Between June and October 2013, 26 snakes of six viperid species kept in two adjoining rooms died ( n = 16) or were euthanized on medical (1) or welfare grounds (9). Two were from the main zoo collection, but the other 24 had been imported and quarantined for a minimum of 6 mo. Four of those that died and the single snake euthanized on medical grounds showed minor signs of respiratory disease prior to death, and five were weak, lethargic, and/or poor feeders. Frequent postmortem findings among all snakes were poor body condition (18) and respiratory disease (13). Seventeen cases were examined histologically, and pneumonia, sometimes with air sacculitis and/or tracheitis, was present in 15 individuals. Lung samples from 24 snakes were ferlavirus polymerase chain reaction (PCR) positive, and one of the two snakes for which only liver was available was also positive. The negative liver sample was from a snake that died of sepsis following anesthesia for surgical removal of a spindle cell sarcoma. Correlation with antemortem PCR testing of glottal and cloacal swabs in five cases was poor (sensitivity = 40%). Immunohistochemistry (IHC) for ferlaviruses on the tissues of 13 PCR-positive cases showed positive labeling in 7 only. Tissues samples from 22 ferlavirus PCR-positive snakes were examined for Chlamydia species by PCR, and 9 were positive, although DNA sequencing only confirmed two of three tested as Chlamydia pneumoniae. Immunohistochemistry for Chlamydia pneumoniae of seven cases (two Chlamydiales PCR positive, one of which was sequenced as C. pneumoniae, plus five negative) confirmed the Chlamydia PCR results. These two Chlamydiales PCR and IHC positive snakes were ferlavirus PCR positive, but IHC negative suggesting that, even though a ferlavirus was the predominant cause of the outbreak, in a few cases death may have been due to chlamydiosis with ferlavirus present, but not acting as the primary pathogen.
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27
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Draft Genome Sequence of Avian Chlamydia abortus Genotype G1 Strain 15-70d24, Isolated from Eurasian Teal in Poland. Microbiol Resour Announc 2019; 8:8/33/e00658-19. [PMID: 31416872 PMCID: PMC6696647 DOI: 10.1128/mra.00658-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of avian Chlamydia abortus genotype G1 strain 15-70d24, isolated from Eurasian teal in Poland. The total genome assembly length is 1,149,382 bp. Here, we report the draft genome sequence of avian Chlamydia abortus genotype G1 strain 15-70d24, isolated from Eurasian teal in Poland. The total genome assembly length is 1,149,382 bp.
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28
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Chlamydia buteonis, a new Chlamydia species isolated from a red-shouldered hawk. Syst Appl Microbiol 2019; 42:125997. [PMID: 31257045 DOI: 10.1016/j.syapm.2019.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/27/2019] [Accepted: 06/01/2019] [Indexed: 11/23/2022]
Abstract
Chlamydiaceae are obligate intracellular bacterial pathogens for humans and animals. A recent study highlighted that a Chlamydiaceae intermediary between C. psittaci and C. abortus can infect hawks. Here, an isolate was obtained upon passage of cloacal and conjunctival sac material collected from a female hatch-year red-shouldered hawk (Buteo lineatus) in cultured cells. The diseased bird, one of 12 birds housed in a rehabilitation center, developed conjunctivitis and later died. Swabs from both sites tested positive for Chlamydia using the QuickVue Chlamydia test. The isolate, named RSHA, tested negative in qPCR assays specific for C. psittaci and C. abortus, respectively. Analysis of the 16S rRNA, 23S rRNA and whole genome sequences as well as MLST, ANIb and TETRA values reveal that C. psittaci and C. abortus are the closest relatives of RSHA. However, the overall results strongly suggest a phylogenetic intermediate position between these two species. Therefore, we propose the introduction of a new species designated Chlamydia buteonis with RSHAT as the type strain.
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29
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Chlamydiaceae: Diseases in Primary Hosts and Zoonosis. Microorganisms 2019; 7:microorganisms7050146. [PMID: 31137741 PMCID: PMC6560403 DOI: 10.3390/microorganisms7050146] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 12/23/2022] Open
Abstract
Bacteria of the Chlamydiaceae family are a type of Gram-negative microorganism typified by their obligate intracellular lifestyle. The majority of the members in the Chlamydiaceae family are known pathogenic organisms that primarily infect the host mucosal surfaces in both humans and animals. For instance, Chlamydia trachomatis is a well-known etiological agent for ocular and genital sexually transmitted diseases, while C. pneumoniae has been implicated in community-acquired pneumonia in humans. Other chlamydial species such as C. abortus, C. caviae, C. felis, C. muridarum, C. pecorum, and C. psittaci are important pathogens that are associated with high morbidities in animals. Importantly, some of these animal pathogens have been recognized as zoonotic agents that pose a significant infectious threat to human health through cross-over transmission. The current review provides a succinct recapitulation of the characteristics as well as transmission for the previously established members of the Chlamydiaceae family and a number of other recently described chlamydial organisms.
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30
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Burnard D, Shao R. Mitochondrial genome analysis reveals intraspecific variation within Australian hard tick species. Ticks Tick Borne Dis 2019; 10:677-681. [DOI: 10.1016/j.ttbdis.2019.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 01/18/2019] [Accepted: 02/25/2019] [Indexed: 10/27/2022]
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31
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Bommana S, Polkinghorne A. Mini Review: Antimicrobial Control of Chlamydial Infections in Animals: Current Practices and Issues. Front Microbiol 2019; 10:113. [PMID: 30778341 PMCID: PMC6369208 DOI: 10.3389/fmicb.2019.00113] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022] Open
Abstract
Chlamydia are a genus of successful obligate intracellular pathogens spread across humans, wildlife, and domesticated animals. The most common species reported in livestock in this genus are Chlamydia abortus, Chlamydia psittaci, Chlamydia suis, and Chlamydia pecorum. Chlamydial infections trigger a series of inflammatory disease-related sequelae including arthritis, conjunctivitis, pneumonia, and abortion. Other bacteria in the phylum Chlamydiae have also been reported in livestock and wildlife but their impact on animal health is less clear. Control of chlamydial infections relies on the use of macrolides, fluoroquinolones, and tetracyclines. Tetracycline resistance (TETR) reported for porcine C. suis strains in association with the use of tetracycline feed is a potentially significant concern given experimental evidence highlighting that the genetic elements inferring TETR may be horizontally transferred to other chlamydial species. As documented in human Chlamydia trachomatis infections, relapse of infections, bacterial shedding post-antibiotic treatment, and disease progression despite chlamydial clearance in animals have also been reported. The identification of novel chlamydiae as well as new animal hosts for previously described chlamydial pathogens should place a renewed emphasis on basic in vivo studies to demonstrate the efficacy of existing and new antimicrobial treatment regimes. Building on recent reviews of antimicrobials limited to C. trachomatis and C. suis, this review will explore the use of antimicrobials, the evidence and factors that influence the treatment failure of chlamydial infections in animals and the future directions in the control of these important veterinary pathogens.
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Affiliation(s)
- Sankhya Bommana
- The Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Adam Polkinghorne
- The Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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32
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Phillips S, Quigley BL, Timms P. Seventy Years of Chlamydia Vaccine Research - Limitations of the Past and Directions for the Future. Front Microbiol 2019; 10:70. [PMID: 30766521 PMCID: PMC6365973 DOI: 10.3389/fmicb.2019.00070] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/15/2019] [Indexed: 11/30/2022] Open
Abstract
Chlamydia is a major bacterial pathogen that infects humans, as well as a wide range of animals, including marsupials, birds, cats, pigs, cattle, and sheep. Antibiotics are the only treatment currently available, however, with high rates of re-infection, there is mounting pressure to develop Chlamydia vaccines. In this review, we analyzed how Chlamydia vaccine trials have developed over the past 70 years and identified where future trials need to be focused. There has been a strong bias toward studies targeting C. muridarum and C. trachomatis within mice and a lack of studies matching chlamydial species to their end target host. Even though a large number of specific antigenic targets have been studied, the results from whole-cell vaccine targets show slightly more promising results overall. There has also been a strong bias toward systemic vaccine delivery systems, despite the finding that mucosal delivery systems have shown more promising outcomes. However, the only successful vaccines with matched chlamydial species/infecting host are based on systemic vaccine delivery methods. We highlight the extensive work done with mouse model trials and indicate that whole cell antigenic targets are capable of inducing an effective response, protecting from disease and reducing shedding rates. However, replication of these results using antigen preparations more conducive to commercial vaccine production has proven difficult. To date, the Major Outer Membrane Protein (MOMP) has emerged as the most suitable substitute for whole cell targets and its delivery as a combined systemic and mucosal vaccine is most effective. Finally, although mouse model trials are useful, differences between hosts and infecting chlamydial strains are preventing vaccine formulations from mouse models to be translated into larger animals or intended hosts.
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Affiliation(s)
- Samuel Phillips
- Genecology Research Centre, The University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Bonnie L Quigley
- Genecology Research Centre, The University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Peter Timms
- Genecology Research Centre, The University of the Sunshine Coast, Maroochydore, QLD, Australia
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33
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You J, Wu Y, Zhang X, Wang X, Gong J, Zhao Z, Zhang J, Zhang J, Sun Z, Li J, Guo W, Wang J, Wang Y, Li M, Zhang R, Yang Y, Ye J, Poudel A, Kaltenboeck B, Wang C. Efficient fecal-oral and possible vertical, but not respiratory, transmission of emerging Chlamydia gallinacea in broilers. Vet Microbiol 2019; 230:90-94. [PMID: 30827411 DOI: 10.1016/j.vetmic.2019.01.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 02/08/2023]
Abstract
Chlamydia gallinacea is an endemic Chlamydia agent in poultry with a worldwide distribution. The aim of this study was to investigate whether C. gallinacea can be transmitted via fecal-oral, respiratory and vertical routes. After co-housing with C. gallinacea-inoculated broilers (n = 10) for 15 days, over 90.0% of SPF broilers (n = 10) became C. gallinacea-positive in their oropharyngeal and cloacal swabs. Connection of isolators with ventilation tubing resulted in transmission of infectious bronchitis virus, but not of C. gallinacea, from infected broilers in one isolator to uninfected ones in the other isolator. Chlamydia-qPCR determined that 97.6% of shells of embryonated eggs (287/294) from a breeding farm were positive for C. gallinacea. C. gallinacea positivity in egg albumen increased significantly from 7.6% (10/128) before incubating to 44.4% (8/18) of 7-day incubation, and from 5.5% (7/128) to 38.9% (7/18) in egg yolk. After incubating for 19 days, C. gallinacea DNA was detected in heart (5/55, 9.1%), liver (3/55, 5.5%), spleen (7/55, 12.7%), lung (6/55, 10.1%), kidney (8/55; 14.5%) and intestine (4/55, 7.3%) of chicken embryos. Taken together, our data indicate that C. gallinacea can be efficiently transmitted by the fecal-oral route, but not via aerosol. Additionally, vertical transmission can occur via penetration of C. gallinacea from eggshell to albumen, yolk, and the growing embryo. Our findings provide essential information for the control of C. gallinacea in poultry farms.
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Affiliation(s)
- Jinfeng You
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Yantao Wu
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Xiaorong Zhang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Xiaobo Wang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Zhenhua Zhao
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Jianjun Zhang
- Sinopharm Yangzhou VAC Biological Engineering Co., Ltd., Yangzhou, China
| | - Jilei Zhang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Ziqiang Sun
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Jing Li
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Weina Guo
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Jiawei Wang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Yaoyao Wang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Min Li
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Rong Zhang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Yi Yang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Jianqiang Ye
- College of Veterinary Medicine, Yangzhou University Yangzhou, China
| | - Anil Poudel
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | | | - Chengming Wang
- College of Veterinary Medicine, Yangzhou University Yangzhou, China; College of Veterinary Medicine, Auburn University, Auburn, AL, USA.
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34
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First Report of Chlamydia abortus in Farmed Fur Animals. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4289648. [PMID: 30598995 PMCID: PMC6287152 DOI: 10.1155/2018/4289648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 11/29/2022]
Abstract
Chlamydia (C.) abortus, a globally distributed obligate intracellular bacterium, has attracted increasing interest according to its veterinary importance and zoonotic nature. C. abortus can infect a variety of animals and cause foetal loss in livestock resulting in economic loss. In this study, the samples collected from two farms of foxes (n=20), raccoon dogs (n=15) and minks (n=20), were investigated by Chlamydiaceae- and Chlamydia species-specific real-time PCR. The results showed that all the tested foxes (20/20) and raccoon dogs (15/15) harbored Chlamydia spp., while 5% of minks (1/20) were positive for Chlamydia spp. C. abortus was identified in all positive samples as the dominant Chlamydia species, with C. pecorum DNA coexistence in some of the rectal samples (7/20) taken from foxes. Phylogenetic analysis based on specific gene fragments of 16S rRNA, IGS-23S rRNA, and ompA revealed that all sequences obtained in this study were assigned to the Chlamydiaceae family with high similarity to C. abortus S26/3 and B577 previously identified in ruminants. This is the first report confirming that farmed foxes, raccoon dogs, and minks carry C. abortus. Further studies are needed to fully elucidate the epidemiology and pathogenicity of this pathogen in farmed fur animals as well as the potential risks to public health.
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Polkinghorne A, Borel N, Heijne M, Pannekoek Y. New evidence for domesticated animals as reservoirs of Chlamydia-associated community-acquired pneumonia. Clin Microbiol Infect 2018; 25:131-132. [PMID: 30394363 DOI: 10.1016/j.cmi.2018.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/11/2018] [Accepted: 10/23/2018] [Indexed: 11/27/2022]
Affiliation(s)
- A Polkinghorne
- Animal Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia.
| | - N Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - M Heijne
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Y Pannekoek
- Amsterdam UMC, University of Amsterdam, Amsterdam Centre for Infection and Immunity, Department of Medical Microbiology, Amsterdam, The Netherlands
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Taylor-Brown A, Pillonel T, Greub G, Vaughan L, Nowak B, Polkinghorne A. Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae. Genome Biol Evol 2018; 10:2587-2595. [PMID: 30202970 PMCID: PMC6171736 DOI: 10.1093/gbe/evy195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.
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Affiliation(s)
- Alyce Taylor-Brown
- USC Animal Research Centre, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Switzerland
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Barbara Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, Australia
| | - Adam Polkinghorne
- USC Animal Research Centre, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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Patiño LH, Camargo M, Muñoz M, Ríos-Chaparro DI, Patarroyo MA, Ramírez JD. Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis. Front Microbiol 2018; 9:1854. [PMID: 30186244 PMCID: PMC6113918 DOI: 10.3389/fmicb.2018.01854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.
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Affiliation(s)
- Luz H. Patiño
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan D. Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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Novel Chlamydia species isolated from snakes are temperature-sensitive and exhibit decreased susceptibility to azithromycin. Sci Rep 2018; 8:5660. [PMID: 29618824 PMCID: PMC5884828 DOI: 10.1038/s41598-018-23897-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/22/2018] [Indexed: 11/09/2022] Open
Abstract
Chlamydia species have recently been recognized as emerging pathogens in snakes. However, isolation of novel snake chlamydiae is critical and their growth characteristics are largely unknown. In this study, two novel chlamydial species are described: Chlamydia serpentis and Chlamydia poikilothermis, isolated after attempts on 23 cloacal and choanal swabs from 18 PCR-positive captive snakes originating from different Swiss snake collections. Isolation success, growth curve and infectivity rates over a 48-hour time period were dependent on temperature (37 °C for C. serpentis, 28 °C for C. poikilothermis). C. serpentis and C. poikilothermis were sensitive to tetracycline and moxifloxacin during evaluation by in vitro antibiotic susceptibility assay but intermediate to resistant (2–4 μg/ml) to azithromycin. Whole genome sequencing of the isolates provided proof of the novel species status, and gives insights into the evolution of these branches of genus Chlamydia.
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Rypuła K, Kumala A, Płoneczka-Janeczko K, Lis P, Karuga-Kuźniewska E, Dudek K, Całkosiński I, Kuźnik P, Chorbiński P. Occurrence of reproductive disorders in pig herds with and without Chlamydia suis infection - statistical analysis of breeding parameters. Anim Sci J 2018. [PMID: 29536596 DOI: 10.1111/asj.13000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chlamydiae are frequently encountered Gram-negative intracellular eubacteria that can cause clear manifestations or clinically asymptomatic disorders. C. suis and other chlamydia are primarily isolated in cases of reproductive disorders. This study was performed to estimate the impact of Chlamydia suis infection on reproduction in sows by analyzing reproduction rates and breeding parameters. The test was conducted on first generation (F1) pigs from Polish Landrace (PL) × Polish Large White (PLW). Sixty-four herds were investigated and 500 vaginal swabs were collected. Isolation of DNA was carried out directly from the swabs. All samples were analyzed for Chlamydia suis by real-time PCR with a locked nucleic acid (LNA)-containing probe. To analyze the impact of chlamydia infection on reproductive parameters, evaluation questionnaires were used. Reproductive problems were found in 77.3% of the farms tested. The receiver operating characteristic curve indicated that in the farms with 10 up to 120 sows, there were higher reproductive problems with chlamydia infection than in smaller and bigger pig farms. The most common problems were estrus repetition, which was reported by 57.81% of the surveyed farms, and the birth of dead piglets, which was reported by 31.25% of the investigated pig farms. Abortions, which were reported by 28.12% of the surveyed farms, were the least common reproductive disorders.
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Affiliation(s)
- Krzysztof Rypuła
- Division of Infectious Diseases of Animals and Veterinary Administration, Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Kumala
- Laboratory of Neurotoxicology and Environmental Diagnosis, Faculty of Health Science, Wroclaw Medical University, Wrocław, Poland
| | - Katarzyna Płoneczka-Janeczko
- Division of Infectious Diseases of Animals and Veterinary Administration, Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Paweł Lis
- Division of Infectious Diseases of Animals and Veterinary Administration, Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Ewa Karuga-Kuźniewska
- Division of Infectious Diseases of Animals and Veterinary Administration, Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Krzysztof Dudek
- Faculty of Mechanical Engineering, Technical University of Wrocław, Wrocław, Poland
| | - Ireneusz Całkosiński
- Laboratory of Neurotoxicology and Environmental Diagnosis, Faculty of Health Science, Wroclaw Medical University, Wrocław, Poland
| | - Patrycja Kuźnik
- Division of Infectious Diseases of Animals and Veterinary Administration, Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Paweł Chorbiński
- Division of Infectious Diseases of Animals and Veterinary Administration, Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
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Pillonel T, Bertelli C, Greub G. Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. Front Microbiol 2018. [PMID: 29515524 PMCID: PMC5826181 DOI: 10.3389/fmicb.2018.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Borel N, Polkinghorne A, Pospischil A. A Review on Chlamydial Diseases in Animals: Still a Challenge for Pathologists? Vet Pathol 2018; 55:374-390. [PMID: 29310550 DOI: 10.1177/0300985817751218] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chlamydiae have a worldwide distribution causing a wide range of diseases in human hosts, livestock, and companion animals as well as in wildlife and exotic species. Moreover, they can persist in their hosts as asymptomatic infections for extended periods of time. The introduction of molecular techniques has revolutionized the Chlamydia field by expanding the host range of known chlamydial species but also by discovering new species and even new families of bacteria in the broader order Chlamydiales. The wide range of hosts, diseases, and tissues affected by chlamydiae complicate the diagnosis such that standard diagnostic approaches for these bacteria are rare. Bacteria of the Chlamydiales order are small and their inclusions are difficult to detect by standard microscopy. With the exception of avian and ovine chlamydiosis, macroscopic and/or histologic changes might not be pathognomic or indicative for a chlamydial infection or even not present at all. Moreover, detection of chlamydial DNA in specimens in the absence of other methods or related pathological lesions questions the significance of such findings. The pathogenic potential of the majority of recently identified Chlamydia-related bacteria remains largely unknown and awaits investigation through experimental or natural infection models including histomorphological characterization of associated lesions. This review aims to summarize the historical background and the most important developments in the field of animal chlamydial research in the past 5 years with a special focus on pathology. It will summarize the current nomenclature, present critical thoughts about diagnostics, and give an update on chlamydial infections in domesticated animals such as livestock, companion animals and birds, as well as free-ranging and captive wild animals such as reptiles, fish, and marsupials.
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Affiliation(s)
- Nicole Borel
- 1 Department of Pathobiology, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Adam Polkinghorne
- 2 Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Andreas Pospischil
- 1 Department of Pathobiology, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
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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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Free-living and captive turtles and tortoises as carriers of new Chlamydia spp. PLoS One 2017; 12:e0185407. [PMID: 28950002 PMCID: PMC5614609 DOI: 10.1371/journal.pone.0185407] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/12/2017] [Indexed: 11/19/2022] Open
Abstract
A variety of Chlamydia species belonging to the Chlamydiaceae family have been reported in reptilian hosts but scarce data about their occurrence in turtles and tortoises are available. In this study, research was conducted to acquire information on invasive alien species (IAS) of turtles and indigenous turtles and tortoises, living both free and in captivity, as possible reservoirs of Chlamydiaceae. Analysis of specimens (pharyngeal and cloacal swabs and tissues) from 204 turtles and tortoises revealed an overall Chlamydiaceae prevalence of 18.3% and 28.6% among free-living and captive animals respectively, with variable levels of shedding. Further testing conducted with a species-specific real-time PCR and microarray test was unsuccessful. Subsequently sequencing was applied to genotype the Chlamydiaceae-positive samples. Almost the full lengths of the 16S rRNA and ompA genes as well as the 16S-23S intergenic spacer (IGS) and 23S rRNA domain I were obtained for 14, 20 and 8 specimens respectively. Phylogenetic analysis of 16S rRNA amplicons revealed two distinct branches. Group 1 (10 specimens), specific to freshwater turtles and reported here for the first time, was most closely related to Chlamydia (C.) pneumoniae strains and the newly described Candidatus C. sanzinia. Group 2 (four specimens), detected in Testudo spp. samples, showed highest homology to C. pecorum strains but formed a separate sub-branch. Finally, molecular analysis conducted on positive samples together with their geographical distribution in places distant from each other strongly suggest that Group 1 specimens correspond to a new species in the Chlamydiaceae family. In-depth studies of Chlamydia spp. from turtles and tortoises are needed to further characterise these atypical strains and address arising questions about their pathogenicity and zoonotic potential.
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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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Chlamydia gallinacea: a widespread emerging Chlamydia agent with zoonotic potential in backyard poultry. Epidemiol Infect 2017; 145:2701-2703. [PMID: 28768558 DOI: 10.1017/s0950268817001650] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chlamydia gallinacea, a new chlamydial agent, has been reported in four European countries as well as Argentina and China. Experimentally infected chickens with C. gallinacea in previous study showed no clinical signs but had significantly reduced gains in body weight (6·5-11·4%). Slaughterhouse workers exposed to infected chickens have developed atypical pneumonia, indicating C. gallinacea is likely a zoonotic agent. In this study, FRET-PCR confirmed that C. gallinacea was present in 12·4% (66/531) of oral-pharyngeal samples from Alabama backyard poultry. Phylogenetic comparisons based on ompA variable domain showed that 16 sequenced samples represented 14 biotypes. We report for the first time the presence of C. gallinacea in North America, and this warrants further research on the organism's pathogenicity, hosts, transmission, and zoonotic potential.
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Taylor-Brown A, Polkinghorne A. New and emerging chlamydial infections of creatures great and small. New Microbes New Infect 2017; 18:28-33. [PMID: 28560043 PMCID: PMC5436083 DOI: 10.1016/j.nmni.2017.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
Abstract
Until recently, our knowledge of the host range and diversity of members of the Chlamydiaceae, obligate intracellular bacterial pathogens of humans and animals, was thought to be nearly complete. Aided by advances in molecular diagnostics, a new picture is emerging, however, that the host barriers may be looser than previously thought for many chlamydial species. While cross-host transmission of chlamydial species is a concern for animal health, new reports highlight an emerging zoonotic risk for several species associated with intensification of farming and the widespread popularity of companion animals. The description of an expanded cohort of new species within this family from avian and reptilian hosts has also highlighted how much we still have to learn about the biology and pathogenicity of the Chlamydiaceae as a whole. Reports emerging about these relatives of the traditional chlamydial pathogens are matched by the continued identification of novel Chlamydia-related bacteria in the phylum Chlamydiae, providing evidence that many may be pathogenic to humans or animals and pose a zoonotic or vector-borne risk. The review examines the new hosts described for well-characterized chlamydial veterinary pathogens, emerging novel chlamydial species and the potential for these to cause disease in their respective hosts.
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Affiliation(s)
- A Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - A 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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Szymańska-Czerwińska M, Mitura A, Niemczuk K, Zaręba K, Jodełko A, Pluta A, Scharf S, Vitek B, Aaziz R, Vorimore F, Laroucau K, Schnee C. Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains. PLoS One 2017; 12:e0174599. [PMID: 28350846 PMCID: PMC5370153 DOI: 10.1371/journal.pone.0174599] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/10/2017] [Indexed: 11/29/2022] Open
Abstract
Wild birds are considered as a reservoir for avian chlamydiosis posing a potential infectious threat to domestic poultry and humans. Analysis of 894 cloacal or fecal swabs from free-living birds in Poland revealed an overall Chlamydiaceae prevalence of 14.8% (n = 132) with the highest prevalence noted in Anatidae (19.7%) and Corvidae (13.4%). Further testing conducted with species-specific real-time PCR showed that 65 samples (49.2%) were positive for C. psittaci whereas only one was positive for C. avium. To classify the non-identified chlamydial agents and to genotype the C. psittaci and C. avium-positive samples, specimens were subjected to ompA-PCR and sequencing (n = 83). The ompA-based NJ dendrogram revealed that only 23 out of 83 sequences were assigned to C. psittaci, in particular to four clades representing the previously described C. psittaci genotypes B, C, Mat116 and 1V. Whereas the 59 remaining sequences were assigned to two new clades named G1 and G2, each one including sequences recently obtained from chlamydiae detected in Swedish wetland birds. G1 (18 samples from Anatidae and Rallidae) grouped closely together with genotype 1V and in relative proximity to several C. abortus isolates, and G2 (41 samples from Anatidae and Corvidae) grouped closely to C. psittaci strains of the classical ABE cluster, Matt116 and M56. Finally, deep molecular analysis of four representative isolates of genotypes 1V, G1 and G2 based on 16S rRNA, IGS and partial 23S rRNA sequences as well as MLST clearly classify these isolates within the C. abortus species. Consequently, we propose an expansion of the C. abortus species to include not only the classical isolates of mammalian origin, but also avian isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.
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Affiliation(s)
| | - Agata Mitura
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Krzysztof Niemczuk
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Kinga Zaręba
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Agnieszka Jodełko
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Aneta Pluta
- Department of Biochemistry, National Veterinary Research Institute, Pulawy, Poland
| | - Sabine Scharf
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
| | - Bailey Vitek
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
| | - Rachid Aaziz
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - Fabien Vorimore
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - Karine Laroucau
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
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48
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Taylor-Brown A, Pillonel T, Bridle A, Qi W, Bachmann NL, Miller TL, Greub G, Nowak B, Seth-Smith HMB, Vaughan L, Polkinghorne A. Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria. Environ Microbiol 2017; 19:1899-1913. [PMID: 28205377 DOI: 10.1111/1462-2920.13694] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/12/2022]
Abstract
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridization. Giant grouper (Epinephelus lanceolatus) cultured in the same systems were epitheliocystis free. 16S rRNA gene sequencing revealed a novel member of the Candidatus Parilichlamydiaceae: Ca. Similichlamydia epinephelii. Using metagenomic approaches, we obtained an estimated 68% of the chlamydial genome, revealing that this novel chlamydial pathogen shares a number of key pathogenic hallmarks with the Chlamydiaceae, including an intact Type III Secretion system and several chlamydial virulence factors. This provides additional evidence that these pathogenic mechanisms were acquired early in the evolution of this unique bacterial phylum. The identification and genomic characterization of Ca. S. epinephelii provides new opportunities to study the biology of distantly-related chlamydial pathogens while shining a new light on the evolution of pathogenicity of the Chlamydiaceae.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Andrew Bridle
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia
| | - Weihong Qi
- Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland
| | - Nathan L Bachmann
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Terrence L Miller
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Cairns, Queensland, 4878, Australia
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Barbara Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia
| | - Helena M B Seth-Smith
- Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland.,Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
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