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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 However, the authors of this study conclude that the current taxonomic definition of C. abortus is outdated and should be amended to include two subgroups, mammalian and avian, the latter of which would include all isolates so far referred to as atypical C. psittaci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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Szabo KV, O’Neill CE, Clarke IN. Diversity in Chlamydial plasmids. PLoS One 2020; 15:e0233298. [PMID: 32469898 PMCID: PMC7259575 DOI: 10.1371/journal.pone.0233298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/01/2020] [Indexed: 11/30/2022] Open
Abstract
Background Evolutionary studies have been conducted that have investigated the chromosomal variance in the genus of Chlamydia. However, no all-encompassing genus-wide comparison has been performed on the plasmid. Therefore, there is a gap in the current knowledge on Chlamydia plasmid diversity. Aims This project is aimed to investigate and establish the nature and extent of diversity across the entire genus of Chlamydia, by comparing the sequences of all currently available plasmid carrying strains. Methods The PUBMED database was used to identify plasmid sequences from all available strains that met the set quality criteria for their inclusion in the study. Alignments were performed on the 51 strains that fulfilled the criteria using MEGA X software. Following that Maximum Likelihood estimation was used to construct 11 phylogenetic trees of the whole plasmid sequence, the individual 8 coding sequences, the iteron and a chromosomal gene ompA as a comparator. Results The genus-wide plasmid phylogeny produced three distinct lineages labelled as alpha, beta and gamma. Nineteen genotypes were found in the initial whole plasmid analysis. Their distribution was allocated as six C. pecorum, two C. pneumoniae, one C. gallinacea, one C. avium, one C. caviae, one C. felis, two C. psittaci, one C. trachomatis, one C. muridarum, and two C. suis. The chromosomal comparative gene ompA supported this distribution, with the same number of primary clades with the same species distribution. However, ompA sequence comparison resulted in fewer genotypes due to a reduced amount of available sequences (33 out of 51). All results were statistically significant. Conclusion The results of this study indicate that the common bacterial ancestor of all the species had a plasmid, which has diverged over time. Moreover, it suggests that there is a strong evolutionary selection towards these species retaining their plasmids due to its high level of conservation across the genus, with the notable exception of C. pneumoniae. Furthermore, the evolutionary analysis showed that the plasmid and the chromosome have co-evolved.
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Affiliation(s)
- Kolos V. Szabo
- Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom
- * E-mail:
| | - Colette E. O’Neill
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Ian N. Clarke
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
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Feodorova VA, Zaitsev SS, Khizhnyakova MA, Saltykov YV, Evstifeev VV, Khusainov FM, Yakovlev SI, Larionova OS, Motin VL. Data of de novo genome assembly of the Chlamydia psittaci strain isolated from the livestock in Volga Region, Russian Federation. Data Brief 2020; 29:105190. [PMID: 32071972 PMCID: PMC7015991 DOI: 10.1016/j.dib.2020.105190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 11/30/2022] Open
Abstract
Chlamydiae are obligate intracellular bacteria globally widespread across humans, wildlife, and domesticated animals. Chlamydia psittaci is a primarily zoonotic pathogen with multiple hosts, which can be transmitted to humans, resulting in psittacosis or ornithosis. Since this pathogen is a well-recognized threat to human and animal health, it is critical to unravel in detail the genetic make-up of this microorganism. Though many genomes of C. psittaci have been studied to date, little is known about the variants of chlamydial organisms causing infection in Russian livestock. This research is the first de novo genome assembly of the C. psittaci strain Rostinovo-70 of zoonotic origin that was isolated in Russian Federation. The results were obtained by using standard protocols of sequencing with the Illumina HiSeq 2500 and Oxford Nanopore MinION technology that generated 3.88 GB and 3.08 GB of raw data, respectively. The data obtained are available in NCBI DataBase (GenBank accession numbers are CP041038.1 & CP041039.1). The Multi-Locus Sequence Typing (MLST) showed that the strain Rostinovo-70 together with C. psittaci GR9 and C. psittaci WS/RT/E30 belong to the sequence type (ST)28 that could be further separated into two different clades. Despite C. psittaci Rostinovo-70 and C. psittaci GR9 formed a single clade, the latter strain did not contain a cryptic plasmid characteristis to Rostinovo-70. Moreover, the genomes of two strains differed significantly in the cluster of 30 genes that in Rostinovo-70 were closer to Chlamydia abortus rather than C. psittaci. The alignment of the genomes of C. psittaci and C. abortus in this area revealed the exact boarders of homologous recombination that occurred between two Chlamydia species. These findings provide evidence for the first time of genetic exchange between closely related Chlamydia species.
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Affiliation(s)
- Valentina A Feodorova
- Laboratory for Molecular Biology and NanoBiotechnology, Federal Research Center for Virology and Microbiology (FRCViM), Branch in Saratov, 410028, Saratov, Russia
| | - Sergey S Zaitsev
- Laboratory for Molecular Biology and NanoBiotechnology, Federal Research Center for Virology and Microbiology (FRCViM), Branch in Saratov, 410028, Saratov, Russia
| | - Mariya A Khizhnyakova
- Laboratory for Molecular Biology and NanoBiotechnology, Federal Research Center for Virology and Microbiology (FRCViM), Branch in Saratov, 410028, Saratov, Russia
| | - Yury V Saltykov
- Laboratory for Molecular Biology and NanoBiotechnology, Federal Research Center for Virology and Microbiology (FRCViM), Branch in Saratov, 410028, Saratov, Russia
| | - Vitaliy V Evstifeev
- Laboratory of Viral and Chlamydial Infections, Federal Center for Toxicological, Radiation and Biological Safety, 420074, Kazan, Republic of Tatarstan, Russia
| | - Fidail M Khusainov
- Laboratory of Viral and Chlamydial Infections, Federal Center for Toxicological, Radiation and Biological Safety, 420074, Kazan, Republic of Tatarstan, Russia
| | - Sergey I Yakovlev
- Laboratory of Viral and Chlamydial Infections, Federal Center for Toxicological, Radiation and Biological Safety, 420074, Kazan, Republic of Tatarstan, Russia
| | - Olga S Larionova
- Department for Microbiology, Biotechnology and Chemistry, Saratov State Agrarian University, 410003, Saratov, Russia
| | - Vladimir L Motin
- Department of Pathology, Department of Microbiology & Immunology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
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Van Lent S, Creasy HH, Myers GS, Vanrompay D. The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species. J Mol Microbiol Biotechnol 2016; 26:333-44. [DOI: 10.1159/000447092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022] Open
Abstract
Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of <i>pmp</i> coding sequences differs between <i>Chlamydia</i> species, but it is unknown whether the number of <i>pmp</i> coding sequences is constant within a <i>Chlamydia</i> species. The level of conservation of the Pmp proteins has previously only been determined for <i>Chlamydia trachomatis.</i> As different Pmp proteins might be indispensible for the pathogenesis of different <i>Chlamydia </i>species, this study investigated the conservation of Pmp proteins both within and across <i>C. trachomatis,</i><i>C. pneumoniae,</i><i>C. abortus,</i> and <i>C. psittaci.</i> The <i>pmp</i> coding sequences were annotated in 16 <i>C. trachomatis,</i> 6 <i>C. pneumoniae,</i> 2 <i>C. abortus,</i> and 16 <i>C. psittaci</i> genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed <i>Chlamydia </i>species. The length of coding sequences of <i>pmpA,</i><i>pmpB,</i> and <i>pmpH</i> was conserved among all analyzed genomes, while the length of <i>pmpE/F</i> and <i>pmpG,</i> and remarkably also of the subtype <i>pmpD,</i> differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in <i>C. trachomatis,</i><i>C. pneumoniae,</i><i>C. abortus,</i> and <i>C. psittaci</i>, respectively. PmpB was the most conserved Pmp across the 4 analyzed <i>Chlamydia</i> species.
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Wu H, Wang C, Jiang C, Xie Y, Liu L, Song Y, Ma X, Wu Y. Localization and characterization of two putative TMH family proteins in Chlamydia psittaci. Microbiol Res 2015; 183:19-25. [PMID: 26805615 DOI: 10.1016/j.micres.2015.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/23/2022]
Abstract
Chlamydia psittaci (C. psittaci), an obligate intracellular agent of psittacosis, causes an atypical pneumonia in humans. The transmembrane head proteins (TMH) of C. psittaci, putatively belong to the Inc family and presumably play similar roles. CPSIT_0844 and CPSIT_0846 were the putative TMH proteins of C. psittaci. To identify these two proteins, antisera were raised with fusion proteins which were prokaryotic expressed in Escherichia coli and purified. By immunofluorescence assay, CPSIT_0844 and CPSIT_0846 were localized in the inclusion membrane of C. psittaci-infected cells. By RT-PCR and western blot analysis to detect the temporal expression, CPSIT_0844 and CPSIT_0846 were detected as early as 12h post-infection (p.i.) and 6h p.i., separately; meanwhile, in secretions monitored with immunofluorescence assay, these proteins were observed in the inclusion membrane at 18h p.i. and remained in the inclusion membrane throughout the growth cycle. CPSIT_0844 and CPSIT_0846 could specifically be recognized by the antiserum of C. psittaci but failed to react with the antiserums of Chlamydia trachomatis and Chlamydia pneumoniae, which is consistent with the fact that they had no significant orthologs in C. trachomatis and C. pneumoniae. These results revealed that CPSIT_0844 and CPSIT_0846, the putative TMH family proteins, might be unique to C. psittaci and could be used to diagnose the infection caused by C. psittaci. Moreover, CPSIT_0844 and CPSIT_0846 could induce the expression of the inflammatory cytokines IL-1β, IL-6 and TNF-α in THP-1 cells, which might contribute to chlamydia-induced inflammatory pathologies.
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Affiliation(s)
- Haiying Wu
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China; Department of Laboratory Medicine, The Second Affiliated Hospital of University of South China, Hengyang 421001, China
| | - Chuan Wang
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang 421001, China
| | - Chuanhao Jiang
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China
| | - Yafeng Xie
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang 421001, China
| | - Liangzhuan Liu
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China
| | - Ying Song
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China
| | - Xiaohua Ma
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China
| | - Yimou Wu
- Institute of Pathogenic Biology, Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang 421001, China.
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6
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Opota O, Jaton K, Branley J, Vanrompay D, Erard V, Borel N, Longbottom D, Greub G. Improving the molecular diagnosis of Chlamydia psittaci and Chlamydia abortus infection with a species-specific duplex real-time PCR. J Med Microbiol 2015; 64:1174-1185. [PMID: 26297212 DOI: 10.1099/jmm.0.000139] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Chlamydia psittaci and Chlamydia abortus are closely related intracellular bacteria exhibiting different tissue tropism that may cause severe but distinct infection in humans. C. psittaci causes psittacosis, a respiratory zoonotic infection transmitted by birds. C. abortus is an abortigenic agent in small ruminants, which can also colonize the human placenta and lead to foetal death and miscarriage. Infections caused by C. psittaci and C. abortus are underestimated mainly due to diagnosis difficulties resulting from their strict intracellular growth. We developed a duplex real-time PCR to detect and distinguish these two bacteria in clinical samples. The first PCR (PCR1) targeted a sequence of the 16S-23S rRNA operon allowing the detection of both C. psittaci and C. abortus. The second PCR (PCR2) targeted the coding DNA sequence CPSIT_0607 unique to C. psittaci. The two PCRs showed 100 % detection for ≥ 10 DNA copies per reaction (1000 copies ml(- 1)). Using a set of 120 samples, including bacterial reference strains, clinical specimens and infected cell culture material, we monitored 100 % sensitivity and 100 % specificity for the detection of C. psittaci and C. abortus for PCR1. When PCR1 was positive, PCR2 could discriminate C. psittaci from C. abortus with a positive predictive value of 100 % and a negative predictive value of 88 %. In conclusion, this new duplex PCR represents a low-cost and time-saving method with high-throughput potential, expected to improve the routine diagnosis of psittacosis and pregnancy complication in large-scale screening programs and also during outbreaks.
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Affiliation(s)
- Onya Opota
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Katia Jaton
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - James Branley
- Department of Microbiology, Nepean Hospital, Penrith, Sydney, Australia
| | - Daisy Vanrompay
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Veronique Erard
- Clinic of Internal Medicine, Division of Infectious Diseases, HFR-Fribourg, Fribourg, Switzerland
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland
| | - David Longbottom
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, UK
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland.,Infectious Diseases Service, University Hospital of Lausanne, Lausanne, Switzerland
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Knittler MR, Sachse K. Chlamydia psittaci: update on an underestimated zoonotic agent. Pathog Dis 2014; 73:1-15. [PMID: 25853998 DOI: 10.1093/femspd/ftu007] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2014] [Indexed: 12/16/2022] Open
Abstract
Chlamydia (C.) psittaci is an economically relevant pathogen in poultry and pet birds, where it causes psittacosis/ornithosis, and also a human pathogen causing atypical pneumonia after zoonotic transmission. Despite its well-documented prevalence, the agent has received less attention by researchers than other Chlamydia spp. in the last decades. In the present paper, we review recently published data on C. psittaci infection and attempt to single out characteristic features distinguishing it from related chlamydial agents. It is remarkable that C. psittaci is particularly efficient in disseminating in the host organism causing systemic disease, which occasionally can take a fulminant course. At the cellular level, the pathogen's broad host cell spectrum (from epithelial cells to macrophages), its rapid entry and fast replication, proficient use of intracellular transport routes to mitochondria and the Golgi apparatus, the pronounced physical association of chlamydial inclusions with energy-providing cell compartments, as well as the subversive regulation of host cell survival during productive and persistent states facilitate the characteristic efficient growth and successful host-to-host spread of C. psittaci. At the molecular level, the pathogen was shown to upregulate essential chlamydial genes when facing the host immune response. We hypothesize that this capacity, in concert with expression of specific effectors of the type III secretion system and efficient suppression of selected host defense signals, contributes to successful establishment of the infection in the host. Concerning the immunology of host-pathogen interactions, C. psittaci has been shown to distinguish itself by coping more efficiently than other chlamydiae with pro-inflammatory mediators during early host response, which can, to some extent, explain the effective evasion and adaptation strategies of this bacterium. We conclude that thorough analysis of the large number of whole-genome sequences already available will be essential to identify genetic markers of the species-specific features and trigger more in-depth studies in cellular and animal models to address such vital topics as treatment and vaccination.
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Affiliation(s)
- Michael R Knittler
- Institute of Immunology, Friedrich-Loeffler-Institut, Isle of Riems, 07743 Jena, Germany
| | - Konrad Sachse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, 07743 Jena, Germany
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Knittler MR, Berndt A, Böcker S, Dutow P, Hänel F, Heuer D, Kägebein D, Klos A, Koch S, Liebler-Tenorio E, Ostermann C, Reinhold P, Saluz HP, Schöfl G, Sehnert P, Sachse K. Chlamydia psittaci: New insights into genomic diversity, clinical pathology, host–pathogen interaction and anti-bacterial immunity. Int J Med Microbiol 2014; 304:877-93. [DOI: 10.1016/j.ijmm.2014.06.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Whole-Genome Sequences of Low-Virulence Strain CB3 and Mild Strain CB7 of Chlamydia psittaci. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00456-14. [PMID: 24903864 PMCID: PMC4047443 DOI: 10.1128/genomea.00456-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Avian Chlamydia psittaci is an obligate intracellular zoonotic pathogen especially dispersed from birds, and it is known to cause pericarditis, pneumonia, lateral nasal adenitis, peritonitis, hepatitis, splenitis, and other diseases. Generalized infections result in fever, anorexia, lethargy, and diarrhea, depending on the chlamydial genotype and the affected bird species. Although many complete genomes of C. psittaci have been sequenced, we report here the genomes of two strains isolated from the free-living sparrows (strain CB3) and vinous-throated parrotbill (strain CB7) in China, which were first isolated from the spleens of healthy birds in a routine investigation.
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Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range. mBio 2013; 4:mBio.00604-12. [PMID: 23532978 PMCID: PMC3622922 DOI: 10.1128/mbio.00604-12] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chlamydia psittaci is an obligate intracellular bacterium. Interest in Chlamydia stems from its high degree of virulence as an intestinal and pulmonary pathogen across a broad range of animals, including humans. C. psittaci human pulmonary infections, referred to as psittacosis, can be life-threatening, which is why the organism was developed as a bioweapon in the 20th century and is listed as a CDC biothreat agent. One remarkable recent result from comparative genomics is the finding of frequent homologous recombination across the genome of the sexually transmitted and trachoma pathogen Chlamydia trachomatis. We sought to determine if similar evolutionary dynamics occurred in C. psittaci. We analyzed 20 C. psittaci genomes from diverse strains representing the nine known serotypes of the organism as well as infections in a range of birds and mammals, including humans. Genome annotation revealed a core genome in all strains of 911 genes. Our analyses showed that C. psittaci has a history of frequently switching hosts and undergoing recombination more often than C. trachomatis. Evolutionary history reconstructions showed genome-wide homologous recombination and evidence of whole-plasmid exchange. Tracking the origins of recombinant segments revealed that some strains have imported DNA from as-yet-unsampled or -unsequenced C. psittaci lineages or other Chlamydiaceae species. Three ancestral populations of C. psittaci were predicted, explaining the current population structure. Molecular clock analysis found that certain strains are part of a clonal epidemic expansion likely introduced into North America by South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Chlamydia psittaci is classified as a CDC biothreat agent based on its association with life-threatening lung disease, termed psittacosis, in humans. Because of the recent remarkable findings of frequent recombination across the genome of the human sexually transmitted and ocular trachoma pathogen Chlamydia trachomatis, we sought to determine if similar evolutionary dynamics occur in C. psittaci. Twenty C. psittaci genomes were analyzed from diverse strains that may play a pathogenic role in human disease. Evolution of the strains revealed genome-wide recombination occurring at a higher rate than for C. trachomatis. Certain strains were discovered to be part of a recent epidemic clonal expansion originating in South America. These strains may have been introduced into the United States from South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Our analyses indicate that C. psittaci strains have a history of frequently switching hosts and undergoing recombination.
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Seth-Smith HMB, Sait M, Sachse K, Gaede W, Longbottom D, Thomson NR. Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine. GENOME ANNOUNCEMENTS 2013; 1:e00078-12. [PMID: 23405306 PMCID: PMC3569293 DOI: 10.1128/genomea.00078-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 11/07/2012] [Indexed: 11/29/2022]
Abstract
Chlamydia psittaci is the etiological agent of psittacosis and is a zoonotic pathogen infecting birds and a variety of mammalian hosts. Here we report the genome sequence of the porcine strain 01DC12 which is representative of a novel clade of C. psittaci belonging to ompA genotype E.
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Affiliation(s)
- Helena M. B. Seth-Smith
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michelle Sait
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, United Kingdom
| | - Konrad Sachse
- Friedrich-Loeffler-Institute (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Jena, Germany
| | - Wolfgang Gaede
- State Institute for Consumer Protection of Saxony-Anhalt, Dept. for Veterinary Medicine, Stendal, Germany
| | - David Longbottom
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, United Kingdom
| | - Nicholas R. Thomson
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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12
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Voigt A, Schöfl G, Saluz HP. The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens. PLoS One 2012; 7:e35097. [PMID: 22506068 PMCID: PMC3323650 DOI: 10.1371/journal.pone.0035097] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/08/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis. RESULTS A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins. CONCLUSIONS This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.
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Affiliation(s)
- Anja Voigt
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Gerhard Schöfl
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Hans Peter Saluz
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
- Friedrich Schiller University, Jena, Germany
- * E-mail:
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Jiang J, Li J, Kwan HS, Au CH, Wan Law PT, Li L, Kam KM, Lun Ling JM, Leung FC. A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. BMC Res Notes 2012; 5:80. [PMID: 22289569 PMCID: PMC3296665 DOI: 10.1186/1756-0500-5-80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/31/2012] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes. FINDINGS Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%. CONCLUSIONS A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.
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Affiliation(s)
- Jingwei Jiang
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China.
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Jiang J, Li J, Leung FC. A cost-effective and universal strategy for complete prokaryotic genome sequencing proposed by computer simulation. Genome Biol 2011. [DOI: 10.1186/1465-6906-12-s1-p6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January – June 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2044675] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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