DOCSLIB.ORG

CRISPR System Acquisition and Evolution of an Obligate Intracellular

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
CRISPR System Acquisition and Evolution of an Obligate Intracellular bioRxiv preprint doi: https://doi.org/10.1101/028977; this version posted October 13, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 CRISPR system acquisition and evolution of an obligate intracellular 2 Chlamydia-related bacterium 3 4 Claire Bertelli1,2, Ousmane Cissé1, Brigida Rusconi1, Carole Kebbi-Beghdadi1, Antony Croxatto1, 5 Alexander Goesmann3, François Collyn1, Gilbert Greub°1 6 1 Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center 7 and University of Lausanne, Lausanne, Switzerland, 2 SIB Swiss Institute of Bioinformatics, Lausanne, 8 Switzerland 3 Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Gießen, Germany 9 10 °Corresponding author: 11 Gilbert Greub, MD PhD 12 Institute of Microbiology 13 University of Lausanne 14 1011 Lausanne 15 SWITZERLAND 16 Phone : +41-21-314 49 79 17 Fax : +41-21-341 40 60 18 e-mail : [email protected] 19 20 Running Title: The Protochlamydia CRISPR system 21 22 bioRxiv preprint doi: https://doi.org/10.1101/028977; this version posted October 13, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 23 ABSTRACT 24 Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered 25 within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from 26 the Protochlamydia genus, we sequenced de novo the full genome of Pr. naegleriophila combining 27 the advantages of two second-generation sequencing technologies. The assembled complete 28 genome comprises a 2,885,111 bp chromosome and a 145,285 bp megaplasmid. For the first time 29 within the Chlamydiales order, a CRISPR system, the immune system of bacteria, was discovered on 30 the chromosome. It is composed of a small CRISPR locus comprising eight repeats and the associated 31 cas and cse genes of the subtype I-E. A CRISPR locus was also found within Chlamydia sp. Diamant, 32 another Pr. naegleriophila strain whose genome was recently released, suggesting that the CRISPR 33 system was acquired by a common ancestor of these two members of Pr. naegleriophila, after the 34 divergence from Pr. amoebophila. The plasmid encodes an F-type conjugative system similar to that 35 found in the Pam100G genomic island of Pr. amoebophila suggesting an acquisition of this 36 conjugative system before the divergence of both Protochlamydia species and the integration of a 37 putative Pr. amoebophila plasmid into its main chromosome giving rise to the Pam100G genomic 38 island. Overall, this new Pr. naegleriophila genome sequence enables to investigate further the 39 dynamic processes shaping the genomes of Chlamydia-related bacteria. 40 bioRxiv preprint doi: https://doi.org/10.1101/028977; this version posted October 13, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 41 INTRODUCTION 42 A large diversity prevails in the order Chlamydiales, as suggested by the discovery of a large number 43 of Chlamydia and Chlamydia-related bacteria belonging to nine different families (Greub 2010; 44 Everett et al. 1999; Horn 2011) and the cross-examination of metagenomics data (Lagkouvardos et al. 45 2014). The family Parachlamydiaceae comprises five genera that are each represented by a small 46 number of isolated strains. The genus Protochlamydia was lately enriched by the isolation of a 47 Naegleria endosymbiont that presented 97.6% identity in the 16S rRNA with Pr. amoebophila UWE25 48 and was thus named Pr. naegleriophila strain KNic (Casson et al. 2008). Since other members of the 49 Parachlamydiaceae family were suspected to be associated with lung infections (Greub 2009), a 50 diagnostic PCR specific for Pr. naegleriophila was developed and applied to bronchoalveolar lavages. 51 Pr. naegleriophila DNA was detected in the bronchoalveolar lavage of an immunocompromised 52 patient with pneumonia by two PCRs targeting different genomic regions and the presence of the 53 bacterium in the sample was confirmed by direct immunofluorescence (Casson et al. 2008). These 54 results indicated a potential role of Pr. naegleriophila in lower respiratory tract infections. 55 A recent study including Chlamydia genomes and other members of the Planctomycetes- 56 Verrucomicrobia-Chlamydia superphylum suggested that the branch leading to Chlamydia was 57 shaped mainly by genome reduction and evidenced limited occurrence of gene birth, duplication and 58 transfer (Kamneva et al. 2012), as it is the case in other strict intracellular pathogens (Darby et al. 59 2007). On the contrary, the occurrence of large families of paralogs in the genome of Chlamydia- 60 related bacteria suggested an evolution by extensive gene duplication (Domman et al. 2014; Eugster 61 et al. 2007). The chromosome sequence of Pr. amoebophila UWE25 exhibited little evidence for the 62 occurrence of lateral gene transfer (Horn et al. 2004). However, a number of probable lateral gene 63 transfers were identified between Parachlamydia and other amoeba-infecting bacteria such as 64 Legionella (Gimenez et al. 2011), a process that may take place within the amoeba itself (Bertelli & 65 Greub 2012). The Pr. amoebophila genome presents a genomic island (Pam100G) that encodes a 66 type IV secretion system of the F-type that might be involved in conjugative DNA transfer (Greub et 67 al. 2004). A similar system was found on the plasmid of Simkania negevensis (Collingro et al. 2011) 68 and a partial operon was described in Parachlamydia acanthamoebae (Greub et al. 2009), suggesting 69 active DNA transfer capabilities in the ancestor of the Chlamydiales and some of its descendants. 70 Small interspaced repetitions were initially observed in E. coli (Ishino et al. 1987) and they were then 71 named CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats (Jansen et 72 al. 2002). Although found in 50% of bacteria and in 90% of archaea (Weinberger et al. 2012), a 73 CRISPR system had never been previously reported in a member of the order Chlamydiales bioRxiv preprint doi: https://doi.org/10.1101/028977; this version posted October 13, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 74 (Makarova et al. 2011). The CRISPR locus usually consists of a variable number (up to 587) of 23-47bp 75 repeats with some dyad symmetry, but not truly palindromic, interspaced by 21-72 bp spacers 76 (Horvath & Barrangou 2010). Associated with these repeats are 2 core cas genes and additional 77 subtype-specific genes putatively providing mechanistic specificity (Koonin & Makarova 2013). 78 Similarity between spacers and extrachromosomal elements first suggested a role in immunity 79 against phage infection and more generally against conjugation or transformation by acquisition of 80 external DNA (Bolotin et al. 2005). The CRISPR-Cas system was shown to mediate an antiviral 81 response thus inducing resistance to phage infection (Deveau et al. 2010), notably in E. coli (Brouns 82 et al. 2008). More recently, CRISPR-Cas systems were shown to regulate stress-related response, 83 changing gene expression and virulence traits in several pathogens among which is the intracellular 84 bacteria Francisella novicida (Sampson & Weiss 2014; Louwen et al. 2014). 85 In this contribution, we sequenced and analyzed the complete genome of Pr. naegleriophila strain 86 KNic and discovered two potentially antagonistic systems, a type IV secretion system likely implicated 87 in conjugative DNA transfer and a CRISPR system that generally controls foreign DNA acquisition. 88 Furthermore, the complete genome sequence of a new species within the genus Protochlamydia 89 offered the possibility to look into the genome dynamics throughout evolution by comparing Pr. 90 naegleriophila KNic gene content and genome architecture to its closest relatives of the family 91 Parachlamydiaceae. 92 93 RESULTS 94 Chromosome features and evolution 95 Pr. naegleriophila KNic possesses a 2’885’090 bp circular chromosome with a mean GC content of 96 42.7%. The genome size and the GC content are surprisingly high compared to the most closely- 97 related species, Pr. amoebophila (Table 1), but it is consistent with its closest relative Chlamydia sp. 98 Diamant, another Pr. naegleriophila strain (hereafter referred to as Pr. naegleriophila Diamant). The 99 chromosome of Pr. naegleriophila strain KNic is predicted to encode 2,415 proteins and exhibits four 100 ribosomal operons and 43 tRNAs, more than any other Chlamydiales (Table 1). Two types of spacers 101 are found between the 16S and the 23S rRNA: either a simple intergenic spacer or a spacer 102 containing two tRNAs for Ala and Ile. 103 The cumulative G versus C nucleotide bias (GC skew) presents a typical pyramidal shape (Figure S1) 104 that is expected in the absence of particular large genomic islands and confirms the assembly 105 accuracy. The GC skew of Pr. naegleriophila is smoother than that of Pr. amoebophila, and does not bioRxiv preprint doi: https://doi.org/10.1101/028977; this version posted October 13, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
Load more

Recommended publications
  • Expanding the Chlamydiae Tree
    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040 Expanding the Chlamydiae tree Insights into genome diversity and evolution JENNAH E. DHARAMSHI ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1203-3 UPPSALA urn:nbn:se:uu:diva-439996 2021 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedical Centre (BMC), Husargatan 3, Uppsala, Tuesday, 8 June 2021 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof. Dr. Alexander Probst (Faculty of Chemistry, University of Duisburg-Essen). Abstract Dharamshi, J. E. 2021. Expanding the Chlamydiae tree. Insights into genome diversity and evolution. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040. 87 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1203-3. Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles. Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions.
    [Show full text]
  • Product Description EN Bactoreal® Kit Chlamydiaceae
    Product Description BactoReal® Kit Chlamydiaceae For research only, not for diagnostic use BactoReal® Kit Chlamydiaceae Order no. Reactions Pathogen Internal positive control DVEB03113 100 FAM channel Cy5 channel DVEB03153 50 FAM channel Cy5 channel DVEB03111 100 FAM channel VIC/HEX channel DVEB03151 50 FAM channel VIC/HEX channel Kit contents: Detection assay for Chlamydia and Chlamydophila species Detection assay for internal positive control (control of amplification) DNA reaction mix (contains uracil-N glycosylase, UNG) Positive control for Chlamydiaceae Water Background: The Chlamydiaceae family currently includes two genera and one candidate genus: genus Chlamydia (including the species Chlamydia muridarum, Chlamydia suis, Chlamydia trachomatis), genus Chlamydophila (including the species Chlamydophila abortus, Chlamydophila caviae Chlamydophila felis, Chlamydia pecorum, Chlamydophila pneumoniae, Chlamydophila psittaci), and candidatus Clavochlamydia. All Chlamydiaceae are obligate intracellular Gram-negative bacteria that cause diseases in humans and animals worldwide. Description: BactoReal® Kit Chlamydiaceae is based on the amplification and detection of the 23S rRNA gene of C. muridarum, C. suis, C. trachomatis, C. abortus, C. caviae, C. felis, C. pecorum, C. pneumoniae and C. psittaci using real-time PCR. It allows the rapid and sensitive detection of the 23S rRNA gene of Chlamydiaceae from DNA samples purified from different sample material (e.g. with the QIAamp DNA Mini Kit). For subtyping please contact ingenetix. PCR-platforms: BactoReal® Kit Chlamydiaceae is developed and validated for the ABI PRISM® 7500 instrument (Life Technologies), LightCycler® 480 (Roche) and Mx3005P® QPCR System (Agilent), but is also suitable for other real-time PCR instruments. Sensitivity and specificity: BactoReal® Kit Chlamydiaceae detects at least 10 copies/reaction.
    [Show full text]
  • Lists of Names of Prokaryotic Candidatus Taxa
    NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code.
    [Show full text]
  • Author Manuscript Faculty of Biology and Medicine Publication
    Serveur Académique Lausannois SERVAL serval.unil.ch Author Manuscript Faculty of Biology and Medicine Publication This paper has been peer-reviewed but dos not include the final publisher proof-corrections or journal pagination. Published in final edited form as: Title: In Chlamydia veritas. Authors: Bavoil P, Kaltenboeck B, Greub G Journal: Pathogens and disease Year: 2013 Mar Volume: 67 Issue: 2 Pages: 89-90 DOI: 10.1111/2049-632X.12026 In the absence of a copyright statement, users should assume that standard copyright protection applies, unless the article contains an explicit statement to the contrary. In case of doubt, contact the journal publisher to verify the copyright status of an article. In Chlamydia veritas Patrik Bavoil1, Bernard Kaltenboeck2, Gilbert Greub* 3 1Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA; 2 Department of Pathobiology, Auburn University, Auburn, AL, USA; 3Institute of Microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland *Corresponding author: Gilbert Greub, MD PhD Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University of Lausanne Lausanne, Switzerland Phone: (00) 41 21 314 49 79 Fax: (00) 41 21 314 40 60 e-mail: [email protected] Word count: 874 Keywords: Chlamydia, taxonomy, genus, species 1 To the Editor: Microbial taxonomy is an essential tool used to classify strains into different clades, i.e. taxonomic units. While such a classification system is essential for both researchers and clinicians, it is often dismissed, or worse mutilated beyond recognition by the very people who should value it most. Indeed, despite the obvious importance of taxonomy, it is often considered by clinical and basic researchers as a useless arbitrary tool without much scientific basis, and to some it is just a painful reminder of years fruitlessly spent learning Latin in high school.
    [Show full text]
  • 'Parachlamydia Acanthamoebae In
    Richter, M; Matheis, F; Gönczi, E; Aeby, S; Spiess, B M; Greub, G (2010). Parachlamydia acanthamoebae in domestic cats with and without corneal disease. Veterinary Ophthalmology, 13(4):235-237. Postprint available at: http://www.zora.uzh.ch University of Zurich Posted at the Zurich Open Repository and Archive, University of Zurich. Zurich Open Repository and Archive http://www.zora.uzh.ch Originally published at: Veterinary Ophthalmology 2010, 13(4):235-237. Winterthurerstr. 190 CH-8057 Zurich http://www.zora.uzh.ch Year: 2010 Parachlamydia acanthamoebae in domestic cats with and without corneal disease Richter, M; Matheis, F; Gönczi, E; Aeby, S; Spiess, B M; Greub, G Richter, M; Matheis, F; Gönczi, E; Aeby, S; Spiess, B M; Greub, G (2010). Parachlamydia acanthamoebae in domestic cats with and without corneal disease. Veterinary Ophthalmology, 13(4):235-237. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: Veterinary Ophthalmology 2010, 13(4):235-237. Parachlamydia acanthamoebae in domestic cats with and without corneal disease Marianne Richter1, Franziska Matheis1, Enikö Gönczi2, Sébastien Aeby3, Bernhard Spiess1, Gilbert Greub3,* 1 Section of Ophthalmology, Equine Department, Vetsuisse Faculty, University of Zurich, Switzerland 2 Clinical Laboratory, Department of Farm Animals, Vetsuisse Faculty, University of Zurich, Switzerland 3 Centre of Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University
    [Show full text]
  • Changes in Microbial Communities and Associated Water and Gas Geochemistry Across a Sulfate Gradient in Coal Beds: Powder River Basin, USA
    Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA Authors: Hannah D. Schweitzer, Daniel Ritter, Jennifer McIntosh, Elliott Barnhart, Alfred B. Cunningham, David Vinson, William Orem, and Matthew W. Fields NOTICE: this is the author’s version of a work that was accepted for publication in Geochimica et Cosmochimica Acta. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Geochimica et Cosmochimica Acta, VOL# 245, (January 2019), DOI# 10.1016/j.gca.2018.11.009. Schweitzer, Hannah D., Daniel Ritter, Jennifer McIntosh, Elliott Barnhart, Alfred B. Cunningham, David Vinson, William Orem, and Matthew W. Fields, “Changes in microbial communities and associated water and gas geochemistry across redox gradients in coal beds: Powder River Basin, US,” Geochimica et Cosmochimica Acta, January 2019, 245: 495-513. doi: 10.1016/ j.gca.2018.11.009 Made available through Montana State University’s ScholarWorks scholarworks.montana.edu *Manuscript Title: Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA Authors: Hannah Schweitzer1,2,3, Daniel Ritter4, Jennifer McIntosh4, Elliott Barnhart5,3, Al B. Cunningham2,3, David Vinson6, William Orem7, and Matthew Fields1,2,3,* Affiliations: 1Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA 2Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA 3Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA 4Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, Arizona 85721, USA 5U.S.
    [Show full text]
  • Emended Description of the Order Chlamydiales, Proposal of Parachlamydiaceae Fam. Nov. and Simkaniaceae Fam. Nov., Each Containi
    International Journal of Systematic Bacteriology (1 999), 49,415-440 Printed in Great Britain Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms Karin D. E. Everett,'t Robin M. Bush* and Arthur A. Andersenl Author for correspondence: Karin D. E. Everett. Tel: + 1 706 542 5823. Fax: + 1 706 542 5771. e-mail : keverett@,calc.vet.uga.edu or kdeeverett @hotmail.com 1 Avian and Swine The current taxonomic classification of Chlamydia is based on limited Respiratory Diseases phenotypic, morphologic and genetic criteria. This classification does not take Research Unit, National Animal Disease Center, into account recent analysis of the ribosomal operon or recently identified Agricultural Research obligately intracellular organisms that have a chlamydia-like developmental Service, US Department of cycle of replication. Neither does it provide a systematic rationale for Agriculture, PO Box 70, Ames, IA 50010, USA identifying new strains. In this study, phylogenetic analyses of the 165 and 235 rRNA genes are presented with corroborating genetic and phenotypic * Department of Ecology & Evolutionary Biology, information to show that the order Chlamydiales contains at least four distinct University of California groups at the family level and that within the Chlamydiaceae are two distinct at Irvine, Irvine, lineages which branch into nine separate clusters. In this report a reclassification CA 92696, USA of the order Chlamydiales and its current taxa is proposed. This proposal retains currently known strains with > 90% 165 rRNA identity in the family Chlamydiaceae and separates other chlamydia-like organisms that have 80-90% 165 rRNA relatedness to the Chlamydiaceae into new families.
    [Show full text]
  • Characterization of a Neochlamydia-Like Bacterium Associated with Epitheliocystis in Cultured Arctic Charr Salvelinus Alpinus
    DISEASES OF AQUATIC ORGANISMS Vol. 76: 27–38, 2007 Published June 7 Dis Aquat Org Characterization of a Neochlamydia-like bacterium associated with epitheliocystis in cultured Arctic charr Salvelinus alpinus Andrew Draghi II1, Julie Bebak2, 6,*, Vsevolod L. Popov3, Alicia C. Noble2, Steven J. Geary1, 4, A. Brian West1, Philip Byrne5, Salvatore Frasca Jr.1, 4 1Department of Pathobiology and Veterinary Science and 4Center of Excellence for Vaccine Research, University of Connecticut, Storrs, Connecticut 06269-3089, USA 2The Conservation Fund’s Freshwater Institute, 1098 Turner Road, Shepherdstown, West Virginia 25443, USA 3Electron Microscopy Laboratory, Department of Pathology, The University of Texas Medical Branch, Galveston, Texas 77555-0609, USA 5Fisheries and Oceans Canada, Charlottetown, Prince Edward Island C1A 5T1, Canada 6Present address: US Department of Agriculture Agricultural Research Service, Aquatic Animal Health Research Laboratory, 990 Wire Road, Auburn, Alabama 36832, USA ABSTRACT: Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic charr Salvelinus alpinus. To characterize a bacterium associated with epitheliocystis in cultured charr, gills were sampled for histopathologic examination, conventional and immunoelectron microscopy, in situ hybridization, 16S ribosomal DNA (rDNA) amplification, sequence analysis and phylogenetic inference. Sampling was conducted at the Fresh- water Institute (Shepherdstown, West Virginia, USA) during outbreaks of epitheliocystis in April and May 2002. Granular, basophilic, cytoplasmic inclusions in charr gill were shown to stain with Macchi- avello, Lendrum’s phloxine-tartrazine and Gimenez histochemical techniques. Ultrastructurally, inclusions were membrane-bound and contained round to elongate reticulate bodies that were immunoreactive to an antibody against chlamydial lipopolysaccharide, suggesting the presence of similar epitopes.
    [Show full text]
  • Parachlamydia Acanthamoebae Detected During a Pneumonia Outbreak in Southeastern Finland, in 2017–2018
    microorganisms Article Parachlamydia acanthamoebae Detected during a Pneumonia Outbreak in Southeastern Finland, in 2017–2018 Kati Hokynar 1,* , Satu Kurkela 1 , Tea Nieminen 2 , Harri Saxen 2, Eero J. Vesterinen 3,4 , Laura Mannonen 1, Risto Pietikäinen 5 and Mirja Puolakkainen 1 1 Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland; Satu.Kurkela@helsinki.fi (S.K.); Laura.Mannonen@hus.fi (L.M.); Mirja.Puolakkainen@helsinki.fi (M.P.) 2 Children’s Hospital, University of Helsinki, FI-00029 Helsinki, Finland; tea.nieminen@hus.fi (T.N.); harri.saxen@helsinki.fi (H.S.) 3 Department of Ecology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; ejvest@utu.fi 4 Biodiversity Unit, University of Turku, FI-20014 Turku, Finland 5 Department of Internal Medicine, Kymenlaakso Central Hospital, FI-48210 Kotka, Finland; Risto.Pietikainen@kymsote.fi * Correspondence: kati.hokynar@helsinki.fi Received: 18 April 2019; Accepted: 14 May 2019; Published: 17 May 2019 Abstract: Community-acquired pneumonia (CAP) is a common disease responsible for significant morbidity and mortality. However, the definite etiology of CAP often remains unresolved, suggesting that unknown agents of pneumonia remain to be identified. The recently discovered members of the order Chlamydiales, Chlamydia-related bacteria (CRB), are considered as possible emerging agents of CAP. Parachlamydia acanthamoebae is the most studied candidate. It survives and replicates inside free-living amoeba, which it might potentially use as a vehicle to infect animals and humans. A Mycoplasma pneumoniae outbreak was observed in Kymenlaakso region in Southeastern Finland during August 2017–January 2018. We determined the occurrence of Chlamydiales bacteria and their natural host, free-living amoeba in respiratory specimens collected during this outbreak with molecular methods.
    [Show full text]
  • Current and Past Strategies for Bacterial Culture in Clinical Microbiology
    Current and Past Strategies for Bacterial Culture in Clinical Microbiology Jean-Christophe Lagier, Sophie Edouard, Isabelle Pagnier, Oleg Mediannikov, Michel Drancourt, Didier Raoult Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France SUMMARY ..................................................................................................................................................209 INTRODUCTION ............................................................................................................................................209 Downloaded from EARLY STRATEGIES AND GENERAL PRINCIPLES ...........................................................................................................209 Nonselective Culture Media ..............................................................................................................................210 Solid agar and coagulated serum......................................................................................................................210 Enriched media ........................................................................................................................................210 Selective Culture Media ..................................................................................................................................210 Organic and inorganic components and minerals ....................................................................................................210 Antibiotics and antiseptics.............................................................................................................................210
    [Show full text]
  • A Novel Chlamydia Parasite of Free-Living Amoebae
    CORE Metadata, citation and similar papers at core.ac.uk Provided by RERO DOC Digital Library “Candidatus Mesochlamydia elodeae” (Chlamydiae: Parachlamydiaceae), a novel chlamydia parasite of free-living amoebae Daniele Corsaro & Karl-Dieter Müller & Jost Wingender & Rolf Michel Abstract Vannella sp. isolated from waterweed Elodea sp. on the chlamydia parasite. High sequence similarity values of was found infected by a chlamydia-like organism. This organ- the 18S rDNA permitted to assign the amoeba to the species ism behaves like a parasite, causing the death through burst of Saccamoeba lacustris (Amoebozoa, Tubulinea). The bacterial its host. Once the vannellae degenerated, the parasite was endosymbiont naturally harbored by the host belonged to successfully kept in laboratory within a Saccamoeba sp. iso- Sphingomonas koreensis (Alpha-Proteobacteria). The chla- lated from the same waterweed sample, which revealed in fine mydial parasite showed a strict specificity for Saccamoeba through electron microscopy to harbor two bacterial endo- spp., being unable to infect a variety of other amoebae, in- symbionts: the chlamydial parasite we introduce and another cluding Acanthamoeba, and it was itself infected by a bacte- endosymbiont initially and naturally present in the host. riophage. Sequence similarity values of the 16S rDNA and Herein, we provide molecular-based identification of both phylogenetic analysis indicated that this strain is a new mem- the amoeba host and its two endosymbionts, with special focus ber of the family Parachlamydiaceae, for which we propose the name “Candidatus Mesochlamydia elodeae.” Introduction Chlamydiae constitute a large group of intracellular para- * D. Corsaro ( ) sites of eukaryotes, infecting amoebae and some inverte- Chlamydia Research Association (CHLAREAS), brates and vertebrates, including humans (Corsaro and 12 rue du Maconnais, 54500 Vandoeuvre-lès-Nancy, France Venditti 2004; Corsaro and Greub 2006).
    [Show full text]
  • Novel Chlamydia Species Isolated from Snakes Are Temperature
    www.nature.com/scientificreports There are amendments to this paper OPEN Novel Chlamydia species isolated from snakes are temperature- sensitive and exhibit decreased Received: 17 July 2017 Accepted: 22 March 2018 susceptibility to azithromycin Published: xx xx xxxx Eveline Staub1, Hanna Marti1, Roberta Biondi2, Aurora Levi2, Manuela Donati2, Cory Ann Leonard1, Serej D. Ley1,5, Trestan Pillonel 3, Gilbert Greub 3, Helena M. B. Seth-Smith1,4,6 & Nicole Borel1 Chlamydia species have recently been recognized as emerging pathogens in snakes. However, isolation of novel snake chlamydiae is critical and their growth characteristics are largely unknown. In this study, two novel chlamydial species are described: Chlamydia serpentis and Chlamydia poikilothermis, isolated after attempts on 23 cloacal and choanal swabs from 18 PCR-positive captive snakes originating from diferent Swiss snake collections. Isolation success, growth curve and infectivity rates over a 48-hour time period were dependent on temperature (37 °C for C. serpentis, 28 °C for C. poikilothermis). C. serpentis and C. poikilothermis were sensitive to tetracycline and moxifoxacin during evaluation by in vitro antibiotic susceptibility assay but intermediate to resistant (2–4 μg/ml) to azithromycin. Whole genome sequencing of the isolates provided proof of the novel species status, and gives insights into the evolution of these branches of genus Chlamydia. Bacteria within the order Chlamydiales are biologically unique, obligate intracellular pathogens afecting humans, wild and domesticated mammals and reptiles, comprising to date nine families (reviewed in)1. Diseases and complications caused can include late abortions, infertility, trachoma and pneumonia. Chlamydiosis has been detected in both free-ranging and captive reptiles, causing granulomatous lesions in inner organs2–5, prolifera- tive pneumonia6,7, necrotizing enteritis or myocarditis8, hepatitis and conjunctivitis9,10 or remaining asympto- matic7,11,12.
    [Show full text]