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Pereira IS, da Cunha M, Leal IP, Luís MP, Gonçalves P, Gonçalves C, Mota LJ. Identification of homologs of the Chlamydia trachomatis effector CteG reveals a family of Chlamydiaceae type III secreted proteins that can be delivered into host cells. Med Microbiol Immunol 2024; 213:15. [PMID: 39008129 PMCID: PMC11249467 DOI: 10.1007/s00430-024-00798-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/06/2024] [Indexed: 07/16/2024]
Abstract
Chlamydiae are a large group of obligate endosymbionts of eukaryotes that includes the Chlamydiaceae family, comprising several animal pathogens. Among Chlamydiaceae, Chlamydia trachomatis causes widespread ocular and urogenital infections in humans. Like many bacterial pathogens, all Chlamydiae manipulate host cells by injecting them with type III secretion effector proteins. We previously characterized the C. trachomatis effector CteG, which localizes at the host cell Golgi and plasma membrane during distinct phases of the chlamydial infectious cycle. Here, we show that CteG is a Chlamydiaceae-specific effector with over 60 homologs phylogenetically categorized into two distinct clades (CteG I and CteG II) and exhibiting several inparalogs and outparalogs. Notably, cteG I homologs are syntenic to C. trachomatis cteG, whereas cteG II homologs are syntenic among themselves but not with C. trachomatis cteG. This indicates a complex evolution of cteG homologs, which is unique among C. trachomatis effectors, marked by numerous events of gene duplication and loss. Despite relatively modest sequence conservation, nearly all tested CteG I and CteG II proteins were identified as type III secretion substrates using Yersinia as a heterologous bacterial host. Moreover, most of the type III secreted CteG I and CteG II homologs were delivered by C. trachomatis into host cells, where they localized at the Golgi region and cell periphery. Overall, this provided insights into the evolution of bacterial effectors and revealed a Chlamydiaceae family of type III secreted proteins that underwent substantial divergence during evolution while conserving the capacity to localize at specific host cell compartments.
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Affiliation(s)
- Inês Serrano Pereira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Maria da Cunha
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Inês Pacheco Leal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Maria Pequito Luís
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Paula Gonçalves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Carla Gonçalves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Luís Jaime Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.
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Palillo MB, Carrasco SE, Mishkin N, Palillo JA, Lynch DB, Lawton S, Aydin M, Mourino A, Lipman NS, Ricart Arbona RJ. Assessment of Antimicrobial Therapy in Eradicating Chlamydia muridarum in Research Mice: Immune Status and its Impact on Outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.600682. [PMID: 38979332 PMCID: PMC11230361 DOI: 10.1101/2024.06.28.600682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Chlamydia muridarum (Cm) is a moderately prevalent, gram-negative, intracellular bacterium that affects laboratory mice, causing subclinical to severe disease, depending on the host's immune status. The effectiveness of various antibiotic regimens aimed at eradicating Cm in both immunodeficient and immunocompetent laboratory mice was evaluated. NSG mice were cohoused with Cm-shedding BALB/cJ mice for 14 days to simulate natural exposure. Four groups of 8 infected NSG mice were treated for 7 days with either 0.08% sulfamethoxazole and 0.016% trimethoprim (TMS) in water, 0.0625% doxycycline in feed, 0.124%/0.025% TMS in feed, or 0.12% amoxicillin in feed. A control group was provided standard water and feed. The impact of treatment on gastrointestinal microbiota (GM) was performed through shotgun sequencing on the last day of treatment. TMS and Amoxicillin had negligible effects on GM, while doxycycline had the largest effect. All antibiotic treated NSG mice exhibited clinical disease, including dehydration, hunched posture, >20% weight loss, and dyspnea, leading to euthanasia 21-40 days post-treatment (32.6 ± 4.2 days; mean ± SD). Untreated controls were euthanized 14-33 days post-exposure (23.75 ± 5.9 days). All mice were fecal PCR positive for Cm at euthanasia. Histological evaluation revealed multifocal histiocytic and neutrophilic bronchointerstitial pneumonia and/or bronchiolitis featuring prominent intralesional chlamydial inclusion bodies in all mice. Subsequently, groups of 8 C57BL/6J, BALB/cJ, NOD.SCID, and NSG mice infected with Cm were treated with 0.124%/0.025% TMS in feed for 7 (BALB/cJ and C57BL/6J) or 21 days (NSG and NOD.SCID). All immunocompetent and NOD.SCID mice were negative for Cm by PCR 14 days post-treatment, remained clinically normal and had no evidence of Cm infection at necropsy, all NSG mice remained Cm positive and were euthanized. While these findings highlight the difficulties in eradicating Cm from highly immunodeficient mice, eradication of Cm from immunocompetent or moderately immunocompromised mice with antibiotics is feasible.
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Ghasemian E, Faal N, Pickering H, Sillah A, Breuer J, Bailey RL, Mabey D, Holland MJ. Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages. Microb Genom 2024; 10:001210. [PMID: 38445851 PMCID: PMC10999739 DOI: 10.1099/mgen.0.001210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Trachoma, a neglected tropical disease caused by Chlamydia trachomatis (Ct) serovars A-C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86 % of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection. A cohort study in 2002-2003 collected ocular swabs across nine Gambian villages during a 6 month follow-up study. To explore the genetic diversity of Ct within and between individuals, we conducted whole-genome sequencing (WGS) on a limited number (n=43) of Ct-positive samples with an omcB load ≥10 from four villages. WGS was performed using target enrichment with SureSelect and Illumina paired-end sequencing. Out of 43 WGS samples, 41 provided sufficient quality for further analysis. ompA analysis revealed that 11 samples had highest identity to ompA from strain A/HAR13 (NC_007429) and 30 had highest identity to ompA from strain B/Jali20 (NC_012686). While SvB genome sequences formed two distinct village-driven subclades, the heterogeneity of SvA sequences led to the formation of many individual branches within the Gambian SvA subclade. Comparing the Gambian SvA and SvB sequences with their reference strains, Ct A/HAR13 and Ct B/Jali20, indicated an single nucleotide polymorphism accumulation rate of 2.4×10-5 per site per year for the Gambian SvA and 1.3×10-5 per site per year for SvB variants (P<0.0001). Variant calling resulted in a total of 1371 single nucleotide variants (SNVs) with a frequency >25 % in SvA sequences, and 438 SNVs in SvB sequences. Of note, in SvA variants, highest evolutionary pressure was recorded on genes responsible for host cell modulation and intracellular survival mechanisms, whereas in SvB variants this pressure was mainly on genes essential for DNA replication/repair mechanisms and protein synthesis. A comparison of the sequences between observed separate infection events (4-20 weeks between infections) suggested that the majority of the variations accumulated in genes responsible for host-pathogen interaction such as CTA_0166 (phospholipase D-like protein), CTA_0498 (TarP) and CTA_0948 (deubiquitinase). This comparison of Ct SvA and SvB variants within a trachoma endemic population focused on their local evolutionary adaptation. We found a different variation accumulation pattern in the Gambian SvA chromosomal genes compared with SvB, hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies.
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Affiliation(s)
- Ehsan Ghasemian
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Nkoyo Faal
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Harry Pickering
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ansumana Sillah
- National Eye Health Programme, Ministry of Health, Kanifing, Gambia
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Robin L. Bailey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - David Mabey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Martin J. Holland
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
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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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Liu C, Mokashi NV, Darville T, Sun X, O’Connell CM, Hufnagel K, Waterboer T, Zheng X. A Machine Learning-Based Analytic Pipeline Applied to Clinical and Serum IgG Immunoproteome Data To Predict Chlamydia trachomatis Genital Tract Ascension and Incident Infection in Women. Microbiol Spectr 2023; 11:e0468922. [PMID: 37318345 PMCID: PMC10434056 DOI: 10.1128/spectrum.04689-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
We developed a reusable and open-source machine learning (ML) pipeline that can provide an analytical framework for rigorous biomarker discovery. We implemented the ML pipeline to determine the predictive potential of clinical and immunoproteome antibody data for outcomes associated with Chlamydia trachomatis (Ct) infection collected from 222 cis-gender females with high Ct exposure. We compared the predictive performance of 4 ML algorithms (naive Bayes, random forest, extreme gradient boosting with linear booster [xgbLinear], and k-nearest neighbors [KNN]), screened from 215 ML methods, in combination with two different feature selection strategies, Boruta and recursive feature elimination. Recursive feature elimination performed better than Boruta in this study. In prediction of Ct ascending infection, naive Bayes yielded a slightly higher median value of are under the receiver operating characteristic curve (AUROC) 0.57 (95% confidence interval [CI], 0.54 to 0.59) than other methods and provided biological interpretability. For prediction of incident infection among women uninfected at enrollment, KNN performed slightly better than other algorithms, with a median AUROC of 0.61 (95% CI, 0.49 to 0.70). In contrast, xgbLinear and random forest had higher predictive performances, with median AUROC of 0.63 (95% CI, 0.58 to 0.67) and 0.62 (95% CI, 0.58 to 0.64), respectively, for women infected at enrollment. Our findings suggest that clinical factors and serum anti-Ct protein IgGs are inadequate biomarkers for ascension or incident Ct infection. Nevertheless, our analysis highlights the utility of a pipeline that searches for biomarkers and evaluates prediction performance and interpretability. IMPORTANCE Biomarker discovery to aid early diagnosis and treatment using machine learning (ML) approaches is a rapidly developing area in host-microbe studies. However, lack of reproducibility and interpretability of ML-driven biomarker analysis hinders selection of robust biomarkers that can be applied in clinical practice. We thus developed a rigorous ML analytical framework and provide recommendations for enhancing reproducibility of biomarkers. We emphasize the importance of robustness in selection of ML methods, evaluation of performance, and interpretability of biomarkers. Our ML pipeline is reusable and open-source and can be used not only to identify host-pathogen interaction biomarkers but also in microbiome studies and ecological and environmental microbiology research.
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Affiliation(s)
- Chuwen Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Neha Vivek Mokashi
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xuejun Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine M. O’Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany
| | - Xiaojing Zheng
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Collingro A, Köstlbacher S, Siegl A, Toenshoff ER, Schulz F, Mitchell SO, Weinmaier T, Rattei T, Colquhoun DJ, Horn M. The Fish Pathogen "Candidatus Clavichlamydia salmonicola"-A Missing Link in the Evolution of Chlamydial Pathogens of Humans. Genome Biol Evol 2023; 15:evad147. [PMID: 37615694 PMCID: PMC10448858 DOI: 10.1093/gbe/evad147] [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] [Accepted: 07/22/2023] [Indexed: 08/25/2023] Open
Abstract
Chlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen "Candidatus Clavichlamydia salmonicola", representing a separate genus within the human and animal pathogenic Chlamydiaceae. The "Ca. Clavichlamydia salmonicola" genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of "Ca. Clavichlamydia salmonicola" allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.
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Affiliation(s)
- Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Alexander Siegl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Elena R Toenshoff
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich (ETH), Zürich, Switzerland
| | - Frederik Schulz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- DOE Joint Genome Institute, Berkeley, California, USA
| | | | - Thomas Weinmaier
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- 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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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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Sachse K, Hölzer M, Vorimore F, Barf LM, Sachse C, Laroucau K, Marz M, Lamkiewicz K. Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference. BMC Genomics 2023; 24:288. [PMID: 37248517 DOI: 10.1186/s12864-023-09370-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid. RESULTS Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2- 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps). CONCLUSIONS Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.
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Affiliation(s)
- Konrad Sachse
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany.
| | - Martin Hölzer
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353, Berlin, Germany
| | - Fabien Vorimore
- Laboratory for Animal Health, Identypath, ANSES Maisons-Alfort, Paris-Est University, 94706, Paris, France
| | - Lisa-Marie Barf
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre 3 / Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- Institute for Biological Information Processing 6 / Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Karine Laroucau
- Laboratory for Animal Health, Bacterial Zoonosis Unit, ANSES Maisons-Alfort, Paris-Est University, 94706, Paris, France
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- JRG Analytical MicroBioinformatics, Friedrich Schiller University Jena, 07743, Jena, Germany
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Luu LDW, Kasimov V, Phillips S, Myers GSA, Jelocnik M. Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny. Front Cell Infect Microbiol 2023; 13:1178736. [PMID: 37287464 PMCID: PMC10242142 DOI: 10.3389/fcimb.2023.1178736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis and C. pneumoniae. Since 1998, when the first Chlamydia genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in Chlamydia genomics and how whole genome sequencing has revolutionised our understanding of Chlamydia virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Vasilli Kasimov
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Samuel Phillips
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Luís MP, Pereira IS, Bugalhão JN, Simões CN, Mota C, Romão MJ, Mota LJ. The Chlamydia trachomatis IncM Protein Interferes with Host Cell Cytokinesis, Centrosome Positioning, and Golgi Distribution and Contributes to the Stability of the Pathogen-Containing Vacuole. Infect Immun 2023; 91:e0040522. [PMID: 36877064 PMCID: PMC10112248 DOI: 10.1128/iai.00405-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/13/2023] [Indexed: 03/07/2023] Open
Abstract
Chlamydia trachomatis is an obligate intracellular bacterial pathogen that causes ocular and urogenital infections in humans. The ability of C. trachomatis to grow intracellularly in a pathogen-containing vacuole (known as an inclusion) depends on chlamydial effector proteins transported into the host cell by a type III secretion system. Among these effectors, several inclusion membrane proteins (Incs) insert in the vacuolar membrane. Here, we show that human cell lines infected by a C. trachomatis strain deficient for Inc CT288/CTL0540 (renamed IncM) displayed less multinucleation than when infected by IncM-producing strains (wild type or complemented). This indicated that IncM is involved in the ability of Chlamydia to inhibit host cell cytokinesis. The capacity of IncM to induce multinucleation in infected cells was shown to be conserved among its chlamydial homologues and appeared to require its two larger regions predicted to be exposed to the host cell cytosol. C. trachomatis-infected cells also displayed IncM-dependent defects in centrosome positioning, Golgi distribution around the inclusion, and morphology and stability of the inclusion. The altered morphology of inclusions containing IncM-deficient C. trachomatis was further affected by depolymerization of host cell microtubules. This was not observed after depolymerization of microfilaments, and inclusions containing wild-type C. trachomatis did not alter their morphology upon depolymerization of microtubules. Overall, these findings suggest that IncM may exert its effector function by acting directly or indirectly on host cell microtubules.
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Affiliation(s)
- Maria Pequito Luís
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Department of Life Sciences, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Inês Serrano Pereira
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Department of Life Sciences, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Joana N. Bugalhão
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Department of Life Sciences, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Catarina N. Simões
- Department of Life Sciences, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Maria João Romão
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Luís Jaime Mota
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Department of Life Sciences, UCIBIO, Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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11
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Yenidünya Konuk E. Molecular Approaches to the Diagnosis of Chlamydia. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.109746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Chlamydia trachomatis is known as the most common bacterial infection agent to pass with sexual transition. This microorganism is an obligatory intracellular parasite. A variety of infections are caused by C. trachomatis, including trachoma, pneumonias in newborns, genital and urinary tract infections, and lymphogranuloma venereum (LGV), which is caused by LGV strains. The diagnosis of Chlamydia trachomatis can be made by cultures and isolations, antigens and antibodies (direct fluorescence, enzyme immunoassays), hybridization, or polymerase chain reaction (PCR). Each year, infection and diagnosis rates increase in the developed world. Since Chlamydia is mostly asymptomatic, screening, and treatment are a key to detecting cases. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and nucleic acid sequence-based amplification (NASBAa) molecular methods can be used for the detection, low concentration, quantification, and identification of organisms. While the traditional PCR method confirms its existence, it can quantify real-time PCR (RT-PCR). This method (RT-PCR) may have low sensitivity among variants of the same species. Also, PCR scans, which receive urine service, offer great advantages. PCR from initial void urine (FVU) samples is highly sensitive in detecting the organism. Urine Chlamydia screenings are more acceptable in large populations and asymptomatic detections.
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12
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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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13
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Fields KA, Bodero MD, Scanlon KR, Jewett TJ, Wolf K. A Minimal Replicon Enables Efficacious, Species-Specific Gene Deletion in Chlamydia and Extension of Gene Knockout Studies to the Animal Model of Infection Using Chlamydia muridarum. Infect Immun 2022; 90:e0045322. [PMID: 36350146 PMCID: PMC9753632 DOI: 10.1128/iai.00453-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
The genus Chlamydia consists of diverse, obligate intracellular bacteria that infect various animals, including humans. Although chlamydial species share many aspects of the typical intracellular lifestyle, such as the biphasic developmental cycle and the preference for invasion of epithelial cells, each chlamydial strain also employs sophisticated species-specific strategies that contribute to an extraordinary diversity in organ and/or tissue tropism and disease manifestation. In order to discover and understand the mechanisms underlying how these pathogens infect particular hosts and cause specific diseases, it is imperative to develop a mutagenesis approach that would be applicable to every chlamydial species. We present functional evidence that the region between Chlamydia trachomatis and Chlamydia muridarum pgp6 and pgp7, containing four 22-bp tandem repeats that are present in all chlamydial endogenous plasmids, represents the plasmid origin of replication. Furthermore, by introducing species-specific ori regions into an engineered 5.45-kb pUC19-based plasmid, we generated vectors that can be successfully transformed into and propagated under selective pressure by C. trachomatis serovars L2 and D, as well as C. muridarum. Conversely, these vectors were rapidly lost upon removal of the selective antibiotic. This conditionally replicating system was used to generate a tarP deletion mutant by fluorescence-reported allelic exchange mutagenesis in both C. trachomatis serovar D and C. muridarum. The strains were analyzed using in vitro invasion and fitness assays. The virulence of the C. muridarum strains was then assessed in a murine infection model. Our approach represents a novel and efficient strategy for targeted genetic manipulation in Chlamydia beyond C. trachomatis L2. This advance will support comparative studies of species-specific infection biology and enable studies in a well-established murine model of chlamydial pathogenesis.
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Affiliation(s)
- Kenneth A. Fields
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Maria D. Bodero
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Kaylyn R. Scanlon
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Travis J. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Katerina Wolf
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae. THE ISME JOURNAL 2022; 16:2725-2740. [PMID: 36042324 PMCID: PMC9666466 DOI: 10.1038/s41396-022-01305-9] [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: 12/21/2021] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022]
Abstract
Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.
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15
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Sturd N, Rucks EA. Chlamydia trachomatis. Trends Microbiol 2022; 31:535-536. [PMID: 36435731 DOI: 10.1016/j.tim.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022]
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16
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Rigamonti S, Floriano AM, Scaltriti E, Longbottom D, Livingstone M, Comandatore F, Pongolini S, Capucci L, Mandola ML, Bazzucchi M, Prati P, Vicari N. Comparative analysis of two genomes of Chlamydia pecorum isolates from an Alpine chamois and a water buffalo. BMC Genomics 2022; 23:645. [PMID: 36088280 PMCID: PMC9464383 DOI: 10.1186/s12864-022-08860-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
To date, whole genome sequencing has been performed mainly for isolates of Chlamydia trachomatis, C. pneumoniae, C. psittaci and C. abortus, but only a few isolates of C. pecorum have been entirely sequenced and this makes it difficult to understand its diversity and population structure. In this study the genome of two C. pecorum strains isolated from the lung of an Alpine chamois affected with pneumonia (isolate PV7855) and the brain of a water buffalo affected with meningoencephalomyelitis (isolate PV6959), were completely sequenced with MiSeq system (Illumina) and analyzed in their most polymorphic regions.
Results
The genome length and GC content of the two isolates were found to be consistent with other C. pecorum isolates and the gene content of polymorphic membrane proteins and plasticity zone was found to be very similar. Some differences were observed in the phospholipase genes for both isolates and in the number of genes in the plasticity zone, such as the presence of some hypothetical proteins in PV6959, not present in any other genomes analyzed in this study. Interestingly, PV6959 possesses an extra pmp and has an incomplete tryptophan biosynthesis operon. Plasmids were detected in both isolates.
Conclusions
Genome sequencing of the two C. pecorum strains did not reveal differences in length and GC content despite the origin from different animal species with different clinical disease. In the plasticity zone, the differences in the genes pattern might be related to the onset of specific symptoms or infection of specific hosts. The absence of a tryptophan biosynthesis pathway in PV6959 may suggest a strict relationship between C. pecorum and its host.
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Borges ÁH, Follmann F, Dietrich J. Chlamydia trachomatis vaccine development - a view on the current challenges and how to move forward. Expert Rev Vaccines 2022; 21:1555-1567. [PMID: 36004386 DOI: 10.1080/14760584.2022.2117694] [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: 11/04/2022]
Abstract
INTRODUCTION Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen in the world. A licensed vaccine is not yet available, but the first vaccines have entered clinical trials. AREAS COVERED : We describe the progress that has been made in our understanding of the type of immunity that a protective vaccine should induce, and the challenges that vaccine developers face. We also focus on the clinical development of a chlamydia vaccine. The first chlamydia vaccine candidate has now been tested in a clinical phase-I trial, and another phase-I trial is currently running. We discuss what it will take to continue this development and what future trial setups could look like. EXPERT OPINION The chlamydia field is coming of age and the first phase I clinical trial of a C. trachomatis vaccine has been successfully completed. We expect and hope that this will motivate various stakeholders to support further development of chlamydia vaccines in humans.
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Affiliation(s)
- Álvaro H Borges
- Statens Serum Institut, Department of Infectious Diseases Immunology, Kobenhavn, 2300 Denmark
| | | | - Jes Dietrich
- Statens Serum Institut, Department of Infectious Diseases Immunology, Kobenhavn, 2300 Denmark
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18
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Dimond ZE, Suchland RJ, Baid S, LaBrie SD, Soules KR, Stanley J, Carrell S, Kwong F, Wang Y, Rockey DD, Hybiske K, Hefty PS. Inter-species lateral gene transfer focused on the Chlamydia plasticity zone identifies loci associated with immediate cytotoxicity and inclusion stability. Mol Microbiol 2021; 116:1433-1448. [PMID: 34738268 PMCID: PMC9119408 DOI: 10.1111/mmi.14832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022]
Abstract
Chlamydia muridarum actively grows in murine mucosae and is a representative model of human chlamydial genital tract disease. In contrast, C. trachomatis infections in mice are limited and rarely cause disease. The factors that contribute to these differences in host adaptation and specificity remain elusive. Overall genomic similarity leads to challenges in the understanding of these significant differences in tropism. A region of major genetic divergence termed the plasticity zone (PZ) has been hypothesized to contribute to the host specificity. To evaluate this hypothesis, lateral gene transfer was used to generate multiple hetero-genomic strains that are predominately C. trachomatis but have replaced regions of the PZ with those from C. muridarum. In vitro analysis of these chimeras revealed C. trachomatis-like growth as well as poor mouse infection capabilities. Growth-independent cytotoxicity phenotypes have been ascribed to three large putative cytotoxins (LCT) encoded in the C. muridarum PZ. However, analysis of PZ chimeras supported that gene products other than the LCTs are responsible for cytopathic and cytotoxic phenotypes. Growth analysis of associated chimeras also led to the discovery of an inclusion protein, CTL0402 (CT147), and homolog TC0424, which was critical for the integrity of the inclusion and preventing apoptosis.
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Affiliation(s)
- Zoe E. Dimond
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Robert J. Suchland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Srishti Baid
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Scott D. LaBrie
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Katelyn R. Soules
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Jacob Stanley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Steven Carrell
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Forrest Kwong
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Yibing Wang
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - P. Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
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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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Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. BIOLOGY 2021; 10:biology10100997. [PMID: 34681096 PMCID: PMC8533590 DOI: 10.3390/biology10100997] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022]
Abstract
Chlamydia trachomatis, a Gram-negative bacterium that infects the rectum, urethra, congenital sites, and columnar epithelium of the cervix. It is a major cause of preventable blindness, ectopic pregnancy, and bacterial sexually transmitted infections worldwide. There is currently no licensed multi-epitope vaccination available for this pathogen. This study used core proteomics, immuno-informatics, and subtractive proteomics approaches to identify the best antigenic candidates for the development of a multi-epitope-based vaccine (MEBV). These approaches resulted in six vaccine candidates: Type III secretion system translocon subunit CopD2, SctW family type III secretion system gatekeeper subunit CopN, SycD/LcrH family type III secretion system chaperone Scc2, CT847 family type III secretion system effector, hypothetical protein CTDEC_0668, and CHLPN 76kDa-like protein. A variety of immuno-informatics tools were used to predict B and T cell epitopes from vaccine candidate proteins. An in silico vaccine was developed using carefully selected epitopes (11 CTL, 2 HTL & 10 LBL) and then docked with the MHC molecules (MHC I & MHC II) and human TLR4. The vaccine was coupled with Cholera toxin subunit B (CTB) adjuvant to boost the immune response. Molecular dynamics (MD) simulations, molecular docking, and MMGBSA analysis were carried out to analyze the molecular interactions and binding affinity of MEBV with TLR4 and MHC molecules. To achieve the highest level of vaccine protein expression, the MEBV was cloned and reverse-translated in Escherichia coli. The highest level of expression was achieved, and a CAI score of 0.97 was reported. Further experimental validation of the MEBV is required to prove its efficacy. The vaccine developed will be useful in preventing infections caused by C. trachomatis.
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21
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Tria FDK, Martin WF. Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes. Genome Biol Evol 2021; 13:6380140. [PMID: 34599337 PMCID: PMC8536544 DOI: 10.1093/gbe/evab224] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 12/20/2022] Open
Abstract
The contribution of gene duplications to the evolution of eukaryotic genomes is well studied. By contrast, studies of gene duplications in prokaryotes are scarce and generally limited to a handful of genes or careful analysis of a few prokaryotic lineages. Systematic broad-scale studies of prokaryotic genomes that sample available data are lacking, leaving gaps in our understanding of the contribution of gene duplications as a source of genetic novelty in the prokaryotic world. Here, we report conservative and robust estimates for the frequency of recent gene duplications within prokaryotic genomes relative to recent lateral gene transfer (LGT), as mechanisms to generate multiple copies of related sequences in the same genome. We obtain our estimates by focusing on evolutionarily recent events among 5,655 prokaryotic genomes, thereby avoiding vagaries of deep phylogenetic inference and confounding effects of ancient events and differential loss. We find that recent, genome-specific gene duplications are at least 50 times less frequent and probably 100 times less frequent than recent, genome-specific, gene acquisitions via LGT. The frequency of gene duplications varies across lineages and functional categories. The findings improve our understanding of genome evolution in prokaryotes and have far-reaching implications for evolutionary models that entail LGT to gene duplications ratio as a parameter.
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Affiliation(s)
- Fernando D K Tria
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Floridia-Yapur N, Rusman F, Diosque P, Tomasini N. Genome data vs MLST for exploring intraspecific evolutionary history in bacteria: Much is not always better. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104990. [PMID: 34224899 DOI: 10.1016/j.meegid.2021.104990] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genome-based phylogeny has been proposed to be more accurate than phylogeny based in a few genes as MLST-based phylogeny. However, much is not always better. Here we analyzed 368 complete genomes corresponding to 9 bacterial species in order to address intraspecific phylogeny. The studied species were: Burkholderia pseudomallei, Campylobacter jejuni, Chlamydia trachomatis, Helicobacter pylori, Klebsiella pneumoniae, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus and Streptococcus pyogenes. The intra-specific phylogenies were inferred using the complete genome sequences of different strains of these species and their MLST schemes. A supermatrix approach was used to infer maximum likelihood phylogenies in both cases. The phylogenetic incongruence between the supermatrix-based genome or MLST tree and individual trees (constructed from genome fragments or MLST genes, respectively) was analyzed. In supermatrix-based trees for genomes, most branches showed a high branch support; however, a high number of branches also showed high percentage of topologically incongruent individual trees. Interestingly, genome and MLST trees showed similar levels of incongruence in the phylogeny for each bacteria specie. Both genome and MLST approaches showed that C. trachomatis and S. aureus have a tree-like evolutionary history (low levels of internal incongruence). Instead, B. pseudomallei and S. pyogenes show high levels of incongruence (network-like evolutionary story) probably caused by HGT (horizontal gene transfer). Concluding, our analysis showed that: high branch supports obtained in genome phylogenies could be an artifact probably caused by data size; MLST is valid to address intraspecific phylogenetic structure; and, each species has its own evolutionary history, which could be affected by HGT to different extents.
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Affiliation(s)
- Noelia Floridia-Yapur
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina
| | - Fanny Rusman
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina
| | - Patricio Diosque
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina
| | - Nicolás Tomasini
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina.
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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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24
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Smolarczyk K, Mlynarczyk-Bonikowska B, Rudnicka E, Szukiewicz D, Meczekalski B, Smolarczyk R, Pieta W. The Impact of Selected Bacterial Sexually Transmitted Diseases on Pregnancy and Female Fertility. Int J Mol Sci 2021; 22:2170. [PMID: 33671616 PMCID: PMC7926516 DOI: 10.3390/ijms22042170] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Sexually transmitted infections (STIs) caused by Neisseria gonorrhoeae, Chlamydia trachomatis and Mycoplasma genitalium are a common cause of pelvic inflammatory disease (PID) which can lead to tubal factor infertility (TFI). TFI is one of the most common causes of infertility, accounting for 30% of female fertility problems. STIs can also have an impact on pregnancy, leading to adverse pregnancy outcomes. Escalating antibiotic resistance in Neisseria gonorrhoeae and Mycoplasma genitalium represents a significant problem and can be therapeutically challenging. We present a comprehensive review of the current treatment options, as well as the molecular approach to this subject. We have given special attention to molecular epidemiology, molecular diagnostics, current and new treatments, and drug resistance.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Chlamydia Infections/drug therapy
- Chlamydia Infections/etiology
- Chlamydia Infections/microbiology
- Drug Resistance, Bacterial/drug effects
- Fallopian Tubes/microbiology
- Fallopian Tubes/pathology
- Female
- Gonorrhea/drug therapy
- Gonorrhea/etiology
- Humans
- Infertility, Female/microbiology
- Molecular Diagnostic Techniques
- Molecular Epidemiology/methods
- Mycoplasma Infections/drug therapy
- Mycoplasma Infections/etiology
- Mycoplasma genitalium/pathogenicity
- Pregnancy
- Pregnancy Complications, Infectious/diagnosis
- Pregnancy Complications, Infectious/drug therapy
- Pregnancy Complications, Infectious/epidemiology
- Pregnancy Complications, Infectious/etiology
- Sexually Transmitted Diseases, Bacterial/complications
- Sexually Transmitted Diseases, Bacterial/diagnosis
- Sexually Transmitted Diseases, Bacterial/drug therapy
- Sexually Transmitted Diseases, Bacterial/epidemiology
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Affiliation(s)
- Katarzyna Smolarczyk
- Department of Dermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland; (K.S.); (B.M.-B.)
| | - Beata Mlynarczyk-Bonikowska
- Department of Dermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland; (K.S.); (B.M.-B.)
| | - Ewa Rudnicka
- Department of Gynaecological Endocrinology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Dariusz Szukiewicz
- Department of General and Experimental Pathology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Blazej Meczekalski
- Department of Gynaecological Endocrinology, Poznan University of Medical Sciences, 60-535 Poznan, Poland;
| | - Roman Smolarczyk
- Department of Gynaecological Endocrinology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Wojciech Pieta
- Department of Gynaecological Endocrinology, Medical University of Warsaw, 02-091 Warsaw, Poland;
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25
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Okude M, Matsuo J, Yamazaki T, Saito K, Furuta Y, Nakamura S, Thapa J, Okubo T, Higashi H, Yamaguchi H. Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis. Microbiol Immunol 2021; 65:115-124. [PMID: 33368645 DOI: 10.1111/1348-0421.12871] [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: 08/30/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/01/2022]
Abstract
We previously isolated a symbiotic environmental amoeba, harboring an environmental chlamydia, Neochlamydia S13. Interestingly, this bacterium failed to survive outside of host cells and was immediately digested inside other amoebae, indicating bacterial distribution via cytokinesis. This may provide a model for understanding organelle development and chlamydial pathogenesis and evolution; therefore, we assessed our hypothesis of Neochlamydia S13 distribution via cytokinesis by comparative analysis with other environmental Chlamydiae (Protochlamydia R18 and Parachlamydia Bn9 ). Dual staining with 4',6-diamidino-2-phenylindole and phalloidin revealed that the progeny of Neochlamydia S13 and Protochlamydia R18 existed in both daughter cells with a contractile ring on the verge of separation. However, in contrast to other environmental Chlamydiae, little Neochlamydia S13 16S ribosomal DNA was amplified from the culture supernatant. Interestingly, Neochlamydia S13 failed to infect aposymbiotic amoebae, indicating an intimate interaction with the host cells. Furthermore, its infectious rates in cultures expanded from a single amoeba were always maintained at 100%, indicating distribution via cytokinesis. We concluded that unlike other environmental Chlamydiae, Neochlamydia S13 has a unique ability to divide its progeny only via host amoebal cytokinesis. This may be a suitable model to elucidate the mechanism of cell organelle distribution and of chlamydial pathogenesis and evolution.
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Affiliation(s)
- Miho Okude
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.,School of Medical Technology, Health Sciences University of Hokkaido, Sapporo, Japan
| | - Tomohiro Yamazaki
- School of Medical Technology, Health Sciences University of Hokkaido, Sapporo, Japan
| | - Kentaro Saito
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Jeewan Thapa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Hideaki Higashi
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
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26
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The iron-dependent repressor YtgR is a tryptophan-dependent attenuator of the trpRBA operon in Chlamydia trachomatis. Nat Commun 2020; 11:6430. [PMID: 33353937 PMCID: PMC7755916 DOI: 10.1038/s41467-020-20181-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/12/2020] [Indexed: 11/08/2022] Open
Abstract
The trp operon of Chlamydia trachomatis is organized differently from other model bacteria. It contains trpR, an intergenic region (IGR), and the biosynthetic trpB and trpA open-reading frames. TrpR is a tryptophan-dependent repressor that regulates the major promoter (PtrpR), while the IGR harbors an alternative promoter (PtrpBA) and an operator sequence for the iron-dependent repressor YtgR to regulate trpBA expression. Here, we report that YtgR repression at PtrpBA is also dependent on tryptophan by regulating YtgR levels through a rare triple-tryptophan motif (WWW) in the YtgCR precursor. Inhibiting translation during tryptophan limitation at the WWW motif subsequently promotes Rho-independent transcription termination of ytgR, thereby de-repressing PtrpBA. Thus, YtgR represents an alternative strategy to attenuate trpBA expression, expanding the repertoire for trp operon attenuation beyond TrpL- and TRAP-mediated mechanisms described in other bacteria. Furthermore, repurposing the iron-dependent repressor YtgR underscores the fundamental importance of maintaining tryptophan-dependent attenuation of the trpRBA operon.
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27
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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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28
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Hölzer M, Barf LM, Lamkiewicz K, Vorimore F, Lataretu M, Favaroni A, Schnee C, Laroucau K, Marz M, Sachse K. Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species. Pathogens 2020; 9:E899. [PMID: 33126635 PMCID: PMC7694038 DOI: 10.3390/pathogens9110899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
To identify genome-based features characteristic of the avian and human pathogen Chlamydia(C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.
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Affiliation(s)
- Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Lisa-Marie Barf
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Fabien Vorimore
- Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France; (F.V.); (K.L.)
| | - Marie Lataretu
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Alison Favaroni
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany; (A.F.); (C.S.)
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany; (A.F.); (C.S.)
| | - Karine Laroucau
- Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France; (F.V.); (K.L.)
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
| | - Konrad Sachse
- RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany; (M.H.); (L.-M.B.); (K.L.); (M.L.); (M.M.)
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29
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Lipofectamine enhances Chlamydia infectivity in cell culture. Anal Biochem 2020; 610:113985. [PMID: 33065117 DOI: 10.1016/j.ab.2020.113985] [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: 06/08/2020] [Revised: 09/14/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022]
Abstract
Cultivation of Chlamydia species in cell lines requires centrifugation of the inoculum onto diethylaminoethyl-dextran-pretreated cell monolayers to improve the infection efficiency. Here we report that the addition of DNA transfection reagent Lipofectamine in the inoculum significantly enhances the infectivity of Chlamydia abortus in mouse fibroblast McCoy cells, with an infection efficiency equivalent to that of the centrifugation method. Similar enhancement effects of Lipofectamine on the infectivity of C. psittaci and C. trachomatis were also observed. This study provides an alternative and convenient method for the cultivation of Chlamydia species in vitro in the absence of centrifugation.
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30
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Peng L, Zhang H, Hu Z, Zhao Y, Liu S, Chen J. Nafamostat mesylate inhibits chlamydial intracellular growth in cell culture and reduces chlamydial infection in the mouse genital tract. Microb Pathog 2020; 147:104413. [PMID: 32712115 DOI: 10.1016/j.micpath.2020.104413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Urogenital Chlamydia trachomatis (C. trachomatis) infection is one of the most common bacterial sexually transmitted diseases worldwide. Untreated C. trachomatis infections that ascend to the upper genital tract lead to a series of severe complications. To search for novel antichlamydial drugs, we evaluated the effect of nafamostat mesylate (NM), a synthetic serine protease inhibitor, on chlamydial infection. NM inhibited chlamydial intracellular growth and reduced both the inclusion size and number in cell culture. NM may mainly target the intracellular reticulate bodies for inhibition. NM was also effective in enhancing chlamydial clearance from mouse genital tract when NM was applied to mice via intravaginal inoculation. The vaginal NM did not significantly alter inflammatory cytokine responses in the mouse genital tract. Thus, we have demonstrated a novel role of NM in inhibiting the obligate intracellular bacterium Chlamydia.
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Affiliation(s)
- Liang Peng
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongbo Zhang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zihao Hu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yujie Zhao
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shanshan Liu
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jianlin Chen
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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31
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Keb G, Fields KA. An Ancient Molecular Arms Race: Chlamydia vs. Membrane Attack Complex/Perforin (MACPF) Domain Proteins. Front Immunol 2020; 11:1490. [PMID: 32760406 PMCID: PMC7371996 DOI: 10.3389/fimmu.2020.01490] [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: 04/20/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Dynamic interactions that govern the balance between host and pathogen determine the outcome of infection and are shaped by evolutionary pressures. Eukaryotic hosts have evolved elaborate and formidable defense mechanisms that provide the basis for innate and adaptive immunity. Proteins containing a membrane attack complex/Perforin (MACPF) domain represent an important class of immune effectors. These pore-forming proteins induce cell killing by targeting microbial or host membranes. Intracellular bacteria can be shielded from MACPF-mediated killing, and Chlamydia spp. represent a successful paradigm of obligate intracellular parasitism. Ancestors of present-day Chlamydia likely originated at evolutionary times that correlated with or preceded many host defense pathways. We discuss the current knowledge regarding how chlamydiae interact with the MACPF proteins Complement C9, Perforin-1, and Perforin-2. Current evidence indicates a degree of resistance by Chlamydia to MACPF effector mechanisms. In fact, chlamydiae have acquired and adapted their own MACPF-domain protein to facilitate infection.
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Affiliation(s)
- Gabrielle Keb
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Kenneth A Fields
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
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32
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Rizza S, Mistrangelo M, Ribaldone DG, Morino M, Astegiano M, Saracco GM, Pellicano R. Proctitis: a glance beyond inflammatory bowel diseases. MINERVA GASTROENTERO 2020; 66:252-266. [PMID: 32218425 DOI: 10.23736/s1121-421x.20.02670-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proctitis is an inflammation involving the anus and the distal part of the rectum, frequently diagnosed in the context of inflammatory bowel diseases (IBD). Nevertheless, when the standard therapy for IBD is ineffective, it becomes necessary for the clinician to review alternative etiologies, beginning from the broad chapter of infectious causes up to rare causes such as radiation, ischemia, diversion and traumatisms. While it is possible to find infectious proctitides caused by pathogens generally inducing extensive colitis, the growing incidence of both sexually transmitted infections and isolated proctitis reported in the recent years require a lot of attention. The risk appears to be higher in individuals participating in anal intercourse, especially men having sex with men (MSM) or subjects who use sex toys and participate to sex parties, dark rooms and so on. The commonest implicated pathogens are Neysseria gonorrhoeae, Chlamydia trachomatis, Herpes Simplex virus and Treponema pallidum. Herpes and Chlamydia infections mainly occur in HIV-positive MSM patients. Since symptoms and signs are common independently from etiology, performing a differential diagnosis based on clinical manifestations is complicated. Therefore, the diagnosis is supported by the combination of clinical history and physical examination and, secondly, by endoscopic, serologic and microbiologic findings. Particular emphasis should be given to simultaneous infections by multiple organisms. The involvement of experts in infectious diseases and in sexual health is crucial for the diagnostic and therapeutic management. The available therapies, empirically initiated or specific, in many cases are able to guarantee a good prognosis and to prevent relapses.
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Affiliation(s)
- Stefano Rizza
- Unit of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Davide G Ribaldone
- Unit of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mario Morino
- Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Marco Astegiano
- Unit of Gastroenterology, Molinette Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Giorgio M Saracco
- Unit of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy.,Unit of Gastroenterology, Molinette Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Rinaldo Pellicano
- Unit of Gastroenterology, Molinette Hospital, Città della Salute e della Scienza, Turin, Italy -
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33
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Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG. Marine Sediments Illuminate Chlamydiae Diversity and Evolution. Curr Biol 2020; 30:1032-1048.e7. [PMID: 32142706 DOI: 10.1016/j.cub.2020.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/22/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay 91400, France
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Felix Homa
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Steffen L Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen 5020, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg 1790 AB, the Netherlands
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands.
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Banhart S, Schäfer EK, Gensch JM, Heuer D. Sphingolipid Metabolism and Transport in Chlamydia trachomatis and Chlamydia psittaci Infections. Front Cell Dev Biol 2019; 7:223. [PMID: 31637241 PMCID: PMC6787139 DOI: 10.3389/fcell.2019.00223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/20/2019] [Indexed: 12/05/2022] Open
Abstract
Chlamydia species infect a large range of vertebral hosts and have become of major economic and public health concern over the last decades. They are obligate intracellular bacteria that undergo a unique cycle of development characterized by the presence of two distinct bacterial forms. After infection of the host cell, Chlamydia are found inside a membrane-bound compartment, the inclusion. The surrounding membrane of the inclusion contributes to the host-Chlamydia interface and specific pathogen-derived Inc proteins shape this interface allowing interactions with distinct cellular proteins. In contrast to many other bacteria, Chlamydia species acquire sphingomyelin from the host cell. In recent years a clearer picture of how Chlamydia trachomatis acquires this lipid emerged showing that the bacteria interact with vesicular and non-vesicular transport pathways that involve the recruitment of specific RAB proteins and the lipid-transfer protein CERT. These interactions contribute to the development of a new sphingomyelin-producing compartment inside the host cell. Interestingly, recruitment of CERT is conserved among different Chlamydia species including Chlamydia psittaci. Here we discuss our current understanding on the molecular mechanisms used by C. trachomatis and C. psittaci to establish these interactions and to create a novel sphingomyelin-producing compartment inside the host cell important for the infection.
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Affiliation(s)
- Sebastian Banhart
- Unit 'Sexually Transmitted Bacterial Infections', Department for Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Elena K Schäfer
- Unit 'Sexually Transmitted Bacterial Infections', Department for Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jean-Marc Gensch
- Unit 'Sexually Transmitted Bacterial Infections', Department for Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Dagmar Heuer
- Unit 'Sexually Transmitted Bacterial Infections', Department for Infectious Diseases, Robert Koch Institute, Berlin, Germany
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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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Bakowski MA, McNamara CW. Advances in Antiwolbachial Drug Discovery for Treatment of Parasitic Filarial Worm Infections. Trop Med Infect Dis 2019; 4:tropicalmed4030108. [PMID: 31323841 PMCID: PMC6789823 DOI: 10.3390/tropicalmed4030108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 01/09/2023] Open
Abstract
The intracellular bacteria now known as Wolbachia were first described in filarial worms in the 1970s, but the idea of Wolbachia being used as a macrofilaricidal target did not gain wide attention until the early 2000s, with research in filariae suggesting the requirement of worms for the endosymbiont. This new-found interest prompted the eventual organization of the Anti-Wolbachia Consortium (A-WOL) at the Liverpool School of Tropical Medicine, who, among others have been active in the field of antiwolbachial drug discovery to treat filarial infections. Clinical proof of concept studies using doxycycline demonstrated the utility of the antiwolbachial therapy, but efficacious treatments were of long duration and not safe for all infected. With the advance of robotics, automation, and high-speed computing, the search for superior antiwolbachials shifted away from smaller studies with a select number of antibiotics to high-throughput screening approaches, centered largely around cell-based phenotypic screens due to the rather limited knowledge about, and tools available to manipulate, this bacterium. A concomitant effort was put towards developing validation approaches and in vivo models supporting drug discovery efforts. In this review, we summarize the strategies behind and outcomes of recent large phenotypic screens published within the last 5 years, hit compound validation approaches and promising candidates with profiles superior to doxycycline, including ones positioned to advance into clinical trials for treatment of filarial worm infections.
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An Asymptomatic Patient with Fatal Infertility Carried a Swedish Strain of Chlamydia trachomatis with Additional Deletion in The Plasmid orf1 that Belonged to A Different MLST Sequence Type. Microorganisms 2019; 7:microorganisms7070187. [PMID: 31261812 PMCID: PMC6681046 DOI: 10.3390/microorganisms7070187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Here, we present the first case of asymptomatic genital Chlamydial infection caused by the new emerging Chlamydia trachomatis (C.t.) ST13 strain genovar E, which has a double deletion of 377 bp and 17 bp in orf1 gene of the cryptic plasmid (ddCT). This case occurred in an infertile patient (case-patient) with a detectable level of Chlamydial antibodies and a spermatozoa deficiency known as azoospermia. Additionally, the ddCT strain showed the presence of a duplication of 44 bp in the plasmid orf3 and SNP in orf4, which were known as the typical characteristics of the Swedish variant of C.t. (nvCT) genovar E. Multilocus sequence typing (MLST) determined a significant difference between ddCT and nvCT in four alleles (oppA, hfiX, gitA and enoA). Both ddCT and nvCT were assigned to different genetic lineages and could be allocated to two different non-overlapping clonal complexes. Furthermore, ddCT demonstrated a considerable difference among 4–5 alleles in comparison with other C.t. strains of genovar E of ST4, ST8, ST12, and ST94, including the founder of a single relevant cluster, wtCT E/SW3 (Swedish genetic lineage). In contrast to other genovar E strains, ddCT had identical alleles with seven out of seven loci found in ST13 strains of genovars D and G, including the founder for this clonal group, D/UW-3/CX, and six out of seven loci found in its derivatives, such as ST6, ST10, and ST95 of genovars G and H. Nevertheless, MSTree V2 showed that ddCT and nvCT could have a common early ancestor, which is a parental C.t. G/9301 strain of ST9. A significant difference between ddCT and nvCT of genovar D (nvCT-D) that was recently found in Mexico was also determined as: (i) ddCT belonged to genovar E but not to genovar D; (ii) ddCT had a 44 bp duplication within the orf3 of the plasmid typical for nvCT; (iii) ddCT possessed an additional 17 bp deletion in the orf1. In conclusion, improved case management should include the clinical physician’s awareness of the need to enhance molecular screening of asymptomatic Chlamydia patients. Such molecular diagnostics might be essential to significantly reducing the global burden of Chlamydial infection on international public health.
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Abstract
The evolutionary separated Gram-negative Chlamydiales show a biphasic life cycle and replicate exclusively within eukaryotic host cells. Members of the genus Chlamydia are responsible for many acute and chronic diseases in humans, and Chlamydia-related bacteria are emerging pathogens. We revisit past efforts to detect cell wall material in Chlamydia and Chlamydia-related bacteria in the context of recent breakthroughs in elucidating the underlying cellular and molecular mechanisms of the chlamydial cell wall biosynthesis. In this review, we also discuss the role of cell wall biosynthesis in chlamydial FtsZ-independent cell division and immune modulation. In the past, penicillin susceptibility of an invisible wall was referred to as the "chlamydial anomaly." In light of new mechanistic insights, chlamydiae may now emerge as model systems to understand how a minimal and modified cell wall biosynthetic machine supports bacterial cell division and how cell wall-targeting beta-lactam antibiotics can also act bacteriostatically rather than bactericidal. On the heels of these discussions, we also delve into the effects of other cell wall antibiotics in individual chlamydial lineages.
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Chlamydia trachomatis Growth and Cytokine mRNA Response in a Prostate Cancer Cell Line. Adv Urol 2019; 2019:6287057. [PMID: 30800160 PMCID: PMC6360031 DOI: 10.1155/2019/6287057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/27/2018] [Accepted: 12/25/2018] [Indexed: 02/06/2023] Open
Abstract
In the present paper, we report that C. trachomatis can be efficiently propagated and affect mRNA expression for two major cytokines, relevant to tumor progression, in CWR-R1 cells, a malignant prostate cell line. CWR-R1 and McCoy cells, a classic cell line for chlamydial research, were grown and infected with C. trachomatis under similar conditions. Cell monolayers were harvested for RNA analysis and immunostaining with major outer membrane protein (MOMP) antibody at 24, 48, and 72 hours of the postinfection (hpi) period. It was shown that the infectious cycle of chlamydial pathogen in CWR-R1 cells resembles the progression of C. trachomatis infection in McCoy cells but with a few important differences. First of all, the initial stage of C. trachomatis propagation in CWR-R1 cells (24 hpi) was characterized by larger inclusion bodies and more intense, specific immunofluorescent staining of infected cells as compared with McCoy cells. Moreover, there was a corresponding increase in infective progeny formation in CWR-R1 cells along with mRNA for EUO, a crucial gene controlling the early phase of the chlamydial development cycle (24 hpi). These changes were more minimal and became statistically insignificant at a later time point in the infectious cycle (48 hpi). Altogether, these data suggest that the early phase of C. trachomatis infection in CWR-R1 cells is accompanied by more efficient propagation of the pathogen as compared with the growth of C. trachomatis in McCoy cells. Furthermore, propagation of C. trachomatis in CWR-R1 cells leads to enhanced transcription of interleukin-6 and fibroblast growth factor-2, genes encoding two important proinflammatory cytokines implicated in the molecular mechanisms of chemoresistance of prostate cancer and its ability to metastasize. The possible roles of reactive oxygen species and impaired mitochondrial oxidation in the prostate cancer cell line are discussed as factors promoting the early stages of C. trachomatis growth in CWR-R1 cells.
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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018; 19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.
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Floriano AM, Castelli M, Krenek S, Berendonk TU, Bazzocchi C, Petroni G, Sassera D. The Genome Sequence of "Candidatus Fokinia solitaria": Insights on Reductive Evolution in Rickettsiales. Genome Biol Evol 2018; 10:1120-1126. [PMID: 29659807 PMCID: PMC5905368 DOI: 10.1093/gbe/evy072] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
"Candidatus Fokinia solitaria" is an obligate intracellular endosymbiont of a unicellular eukaryote, a ciliate of the genus Paramecium. Here, we present the genome sequence of this bacterium and subsequent analysis. Phylogenomic analysis confirmed the previously reported positioning of the symbiont within the "Candidatus Midichloriaceae" family (order Rickettsiales), as well as its high sequence divergence from other members of the family, indicative of fast sequence evolution. Consistently with this high evolutionary rate, a comparative genomic analysis revealed that the genome of this symbiont is the smallest of the Rickettsiales to date. The reduced genome does not present flagellar genes, nor the pathway for the biosynthesis of lipopolysaccharides (present in all the other so far sequenced members of the family "Candidatus Midichloriaceae") or genes for the Krebs cycle (present, although not always complete, in Rickettsiales). These results indicate an evolutionary trend toward a stronger dependence on the host, in comparison with other members of the family. Two alternative scenarios are compatible with our results; "Candidatus Fokinia solitaria" could be either a recently evolved, vertically transmitted mutualist, or a parasite with a high host-specificity.
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Affiliation(s)
- Anna M Floriano
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Italy
| | - Michele Castelli
- Department of Biosciences, University of Milan, Italy.,Department of Veterinary Medicine, University of Milan, Italy
| | - Sascha Krenek
- Institute of Hydrobiology, Technische Universität Dresden, Germany
| | | | | | | | - Davide Sassera
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Italy
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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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Beder T, Saluz HP. Virulence-related comparative transcriptomics of infectious and non-infectious chlamydial particles. BMC Genomics 2018; 19:575. [PMID: 30068313 PMCID: PMC6090853 DOI: 10.1186/s12864-018-4961-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the phylum Chlamydiae are obligate intracellular pathogens of humans and animals and have a serious impact on host health. They comprise several zoonotic species with varying disease outcomes and prevalence. To investigate differences in virulence, we focused on Chlamydia psittaci, C. abortus and Waddlia chondrophila. Most threatening is C. psittaci, which frequently infects humans and causes psittacosis associated with severe pneumonia. The closest relative of C. psittaci is C. abortus, which shares the vast majority of genes but less frequently infects humans, and causes stillbirth and sepsis. W. chondrophila is more distantly related, and occasional human infections are associated with respiratory diseases or miscarriage. One possible explanation for differences in virulence originate from species-specific genes as well as differentially expressed homologous virulence factors. RESULTS RNA-sequencing (RNA-Seq) was applied to purified infectious elementary bodies (EBs) and non-infectious reticulate bodies (RBs) in order to elucidate the transcriptome of the infectious and replicative chlamydial states. The results showed that approximately half of all genes were differentially expressed. For a descriptive comparison, genes were categorised according to their function in the RAST database. This list was extended by the inclusion of inclusion membrane proteins, outer membrane proteins, polymorphic membrane proteins and type III secretion system effectors. In addition, the expression of fifty-six known and a variety of predicted virulence and immunogenic factors with homologs in C. psittaci, C. abortus and W. chondrophila was analysed. To confirm the RNA-Seq results, the expression of nine factors was validated using real-time quantitative polymerase chain reaction (RT-qPCR). Comparison of RNA-Seq and RT-qPCR results showed a high mean Pearson correlation coefficient of 0.95. CONCLUSIONS It was shown that both the replicative and infectious chlamydial state contained distinctive transcriptomes and the cellular processes emphasised in EBs and RBs differed substantially based on the chlamydial species. In addition, the very first interspecies transcriptome comparison is presented here, and the considerable differences in expression of homologous virulence factors might contribute to the differing infection rates and disease outcomes of the pathogens. The RNA-Seq results were confirmed by RT-qPCR and demonstrate the feasibility of interspecies transcriptome comparisons in chlamydia.
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Affiliation(s)
- Thomas Beder
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11A, 07745, Jena, Germany.,Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11A, 07745, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Hans Peter Saluz
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11A, 07745, Jena, Germany. .,Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany.
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45
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Almeida F, Luís MP, Pereira IS, Pais SV, Mota LJ. The Human Centrosomal Protein CCDC146 Binds Chlamydia trachomatis Inclusion Membrane Protein CT288 and Is Recruited to the Periphery of the Chlamydia-Containing Vacuole. Front Cell Infect Microbiol 2018; 8:254. [PMID: 30094225 PMCID: PMC6070772 DOI: 10.3389/fcimb.2018.00254] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/04/2018] [Indexed: 01/12/2023] Open
Abstract
Chlamydia trachomatis is an obligate intracellular human pathogen causing mainly ocular and genital infections of significant clinical and public health impact. C. trachomatis multiplies intracellularly in a membrane bound vacuole, known as inclusion. Both extracellularly and from within the inclusion, C. trachomatis uses a type III secretion system to deliver several effector proteins into the cytoplasm of host cells. A large proportion of these effectors, the inclusion membrane (Inc) proteins, are exposed to the host cell cytosol but possess a characteristic hydrophobic domain mediating their insertion in the inclusion membrane. By yeast two-hybrid, we found that C. trachomatis Inc CT288 interacts with the human centrosomal protein CCDC146 (coiled-coil domain-containing protein 146). The interaction was also detected by co-immunoprecipitation in mammalian cells either ectopically expressing CCDC146 and CT288 or ectopically expressing CCDC146 and infected by a C. trachomatis strain expressing epitope-tagged and inclusion membrane-localized CT288. In uninfected mammalian cells, ectopically expressed full-length CCDC146 (955 amino acid residues) localized at the centrosome; but in cells infected by wild-type C. trachomatis, its centrosomal localization was less evident and CCDC146 accumulated around the inclusion. Recruitment of CCDC146 to the inclusion periphery did not require intact host Golgi, microtubules or microfilaments, but was dependent on chlamydial protein synthesis. Full-length CCDC146 also accumulated at the periphery of the inclusion in cells infected by a C. trachomatis ct288 mutant; however, a C-terminal fragment of CCDC146 (residues 692–955), which interacts with CT288, showed differences in localization at the periphery of the inclusion in cells infected by wild-type or ct288 mutant C. trachomatis. This suggests a model in which chlamydial proteins other than CT288 recruit CCDC146 to the periphery of the inclusion, where the CT288-CCDC146 interaction might contribute to modulate the function of this host protein.
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Affiliation(s)
- Filipe Almeida
- Research Unit on Applied Molecular Biosciences (UCIBIO) - REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa da Caparica, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Maria P Luís
- Research Unit on Applied Molecular Biosciences (UCIBIO) - REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa da Caparica, Portugal
| | - Inês Serrano Pereira
- Research Unit on Applied Molecular Biosciences (UCIBIO) - REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa da Caparica, Portugal
| | - Sara V Pais
- Research Unit on Applied Molecular Biosciences (UCIBIO) - REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa da Caparica, Portugal
| | - Luís Jaime Mota
- Research Unit on Applied Molecular Biosciences (UCIBIO) - REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa da Caparica, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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46
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Watanabe T, Yamazaki S, Maita C, Matushita M, Matsuo J, Okubo T, Yamaguchi H. Lateral Gene Transfer Between Protozoa-Related Giant Viruses of Family Mimiviridae and Chlamydiae. Evol Bioinform Online 2018; 14:1176934318788337. [PMID: 30038484 PMCID: PMC6050620 DOI: 10.1177/1176934318788337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/21/2018] [Indexed: 11/23/2022] Open
Abstract
Obligate intracellular chlamydiae diverged into pathogenic and environmental
chlamydiae 0.7-1.4 billion years ago. While pathogenic chlamydiae have adapted
to a wide range of vertebrates, environmental chlamydiae inhabit unicellular
amoebae, the free-living Acanthamoeba. However, how and why
this divergence occurred remains unclear. Meanwhile, giant viruses consisting of
protozoa-related and protozoa-unrelated viruses have been discovered, with the
former group being suggested to have more influenced environmental chlamydiae
during their evolution while cohabiting host amoebae. Against this background,
we attempted to visualize genes of giant viruses in chlamydial genomes by
bioinformatic analysis mainly with comparative genome and phylogenic analysis,
seeking genes present in chlamydiae that are specifically shared with
protozoa-related giant viruses. As a result, in contrast to protozoa-unrelated
giant viruses, the genes of protozoa-related giant viruses were significantly
shared in both the chlamydia genomes depending on the giant virus type. In
particular, the prevalence of Mimiviridae genes among the
protozoa-related giant virus genes in chlamydial genomes was significantly high.
Meanwhile, the prevalence of protozoa-related giant virus genes in pathogenic
chlamydia genomes was consistently higher than those of environmental
chlamydiae; the actual number of sequences similar to giant virus was also
significantly predominant compared with those in the environmental chlamydial
genomes. Among them, the most prevalent of giant virus was in the case of
chlamydiae with Megavirus chiliensis; total of 1338 genes of
the chlamydiae were found to be shared with the virus (444 genes specific to
environmental chlamydiae, 892 genes shared between both chlamydiae, only two
genes in the pathogenic chlamydiae). Phylogenic analysis with most prevalent
sets (Megavirus chiliensis and Protochlamydia
EI2 or Chlamydia trachomatis L2 434Bu) showed the presence of
orthologs between these with several clustered. In addition, Pearson’s single
regression analysis revealed that almost the prevalence of the genes from the
giant viruses in chlamydial genomes was negatively and specifically correlated
with the number of chlamydial open reading frames (ORFs). Thus, these results
indicated the trace of lateral gene transfer between protozoa-related giant
viruses of family Mimiviridae and chlamydiae. This is the first
demonstration of a putative linkage between chlamydiae and the giant viruses,
providing us with a hint to understand chlamydial evolution.
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Affiliation(s)
- Takanori Watanabe
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Sumire Yamazaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Chinatsu Maita
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Mizue Matushita
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
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47
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Kim H, Kwak W, Yoon SH, Kang DK, Kim H. Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation. PLoS One 2018; 13:e0195139. [PMID: 29621277 PMCID: PMC5886423 DOI: 10.1371/journal.pone.0195139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/16/2018] [Indexed: 01/07/2023] Open
Abstract
Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree database constructed in our recent study. Tree reconciliation method was applied in order to calculate feasible HGT events. Following initial detection and an evaluation procedure, evidence of the HGT was identified in 548 gene families including 42 gene families transferred from outside of Chlamydiae phylum with high reliability. The donor species of inter-phylum HGT consists of 12 different bacterial and archaeal phyla, suggesting that Chlamydia might have even more various host range than in previous reports. In addition, each species of Chlamydia showed varying preference towards HGT, and genes engaged in HGT within Chlamydia and between other species showed different functional distribution. Also, examination of individual gene flows of niche-specific genes suggested that many of such genes are transferred mainly within Chlamydia genus. Our results uncovered novel features of HGT acting on Chlamydia genome evolution, and it would be also strong evidence that HGT is an ongoing process for intracellular pathogens. We expect that the results provide more insight into lineage- and niche-specific adaptations regarding their infectivity and pathogenicity.
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Affiliation(s)
- Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woori Kwak
- C&K genomics, Seoul National University Research Park, Seoul, Republic of Korea
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- C&K genomics, Seoul National University Research Park, Seoul, Republic of Korea
- * E-mail:
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48
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Abrahão J, Silva L, Silva LS, Khalil JYB, Rodrigues R, Arantes T, Assis F, Boratto P, Andrade M, Kroon EG, Ribeiro B, Bergier I, Seligmann H, Ghigo E, Colson P, Levasseur A, Kroemer G, Raoult D, La Scola B. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat Commun 2018; 9:749. [PMID: 29487281 PMCID: PMC5829246 DOI: 10.1038/s41467-018-03168-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/23/2018] [Indexed: 02/07/2023] Open
Abstract
Here we report the discovery of two Tupanvirus strains, the longest tailed Mimiviridae members isolated in amoebae. Their genomes are 1.44–1.51 Mb linear double-strand DNA coding for 1276–1425 predicted proteins. Tupanviruses share the same ancestors with mimivirus lineages and these giant viruses present the largest translational apparatus within the known virosphere, with up to 70 tRNA, 20 aaRS, 11 factors for all translation steps, and factors related to tRNA/mRNA maturation and ribosome protein modification. Moreover, two sequences with significant similarity to intronic regions of 18 S rRNA genes are encoded by the tupanviruses and highly expressed. In this translation-associated gene set, only the ribosome is lacking. At high multiplicity of infections, tupanvirus is also cytotoxic and causes a severe shutdown of ribosomal RNA and a progressive degradation of the nucleus in host and non-host cells. The analysis of tupanviruses constitutes a new step toward understanding the evolution of giant viruses. Giant viruses are the largest viruses of the known virosphere and their genetic analysis can provide insights into virus evolution. Here, the authors discover Tupanvirus, a unique giant virus that has an unusually long tail and contains the largest translational apparatus of the known virosphere.
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Affiliation(s)
- Jônatas Abrahão
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Lorena Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Ludmila Santos Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | | | - Rodrigo Rodrigues
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Thalita Arantes
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Felipe Assis
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Paulo Boratto
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Miguel Andrade
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, 70910-900, Brazil
| | - Erna Geessien Kroon
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Bergmann Ribeiro
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, 70910-900, Brazil
| | - Ivan Bergier
- Lab. Biomass Conversion, Embrapa Pantanal, R. 21 de Setembro 1880, 79320-900, Corumbá/MS, Brazil
| | - Herve Seligmann
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Ghigo
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Guido Kroemer
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, 94805, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, 75006, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, 75654, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, 75015, France.,Université Pierre et Marie Curie, Paris, 75005, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, 75015, France.,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, SE-171 76, Sweden
| | - Didier Raoult
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
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49
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Li X, Liang QF, Su GY, Wu LY, Lu XX, Wang NL. Current Research of Chlamydial Infection Diseases in China. Chin Med J (Engl) 2018; 131:486-489. [PMID: 29451157 PMCID: PMC5830837 DOI: 10.4103/0366-6999.225063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Xue Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Qing-Feng Liang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Guan-Yu Su
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Li-Yuan Wu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Xin-Xin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Ning-Li Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
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50
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Versteeg B, Bruisten SM, Pannekoek Y, Jolley KA, Maiden MCJ, van der Ende A, Harrison OB. Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease. BMC Genomics 2018; 19:130. [PMID: 29426279 PMCID: PMC5810182 DOI: 10.1186/s12864-018-4522-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/31/2018] [Indexed: 12/02/2022] Open
Abstract
Background Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. Results WGS data from 157 Ct isolates deposited in the Chlamydiales pubMLST database (http://pubMLST.org/chlamydiales/) were annotated with 902 genes including the core and accessory genome. Plasmid associated genes were annotated and a plasmid MLST scheme was defined allowing plasmid sequence types to be determined. Plasmid allelic variation was investigated. Phylogenetic relationships were examined using the Genome Comparator tool available in pubMLST. Phylogenetic analyses identified four distinct Ct core genome clusters and six plasmid clusters, with a strong association between the chromosomal genotype and plasmid. This in turn was linked to ompA genovars and disease phenotype. Horizontal genetic transfer of plasmids was observed for three urogenital-associated isolates, which possessed plasmids more commonly found in isolates resulting from ocular infections. The pgp3 gene was identified as the most polymorphic plasmid gene and pgp4 was the most conserved. Conclusion A strong association between chromosomal genome, plasmid type and disease was observed, consistent with previous studies. This suggests co-evolution of the Ct chromosome and their plasmids, but we confirmed that plasmid transfer can occur between isolates. These data provide a better understanding of the genetic diversity occurring across the Ct genome in association with the plasmid content. Electronic supplementary material The online version of this article (10.1186/s12864-018-4522-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bart Versteeg
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.
| | - Sylvia M Bruisten
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.,Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yvonne Pannekoek
- Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Keith A Jolley
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
| | - Martin C J Maiden
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
| | - Arie van der Ende
- Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Odile B Harrison
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
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