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Vorimore F, Hölzer M, Liebler-Tenorio EM, Barf LM, Delannoy S, Vittecoq M, Wedlarski R, Lécu A, Scharf S, Blanchard Y, Fach P, Hsia RC, Bavoil PM, Rosselló-Móra R, Laroucau K, Sachse K. Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov. Syst Appl Microbiol 2021; 44:126200. [PMID: 34298369 DOI: 10.1016/j.syapm.2021.126200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022]
Abstract
The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other proven or potential pathogens in ruminants, birds, snakes, reptiles and turtles. During routine testing of 15 apparently healthy captive flamingos in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Sequence analysis of the 16S rRNA gene revealed high similarity to the uncultured Chlamydiales bacterium clone 122, which previously had been found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015, Chlamydiaceae-specific DNA was detected by PCR in 30.9% of wild birds. From these samples, three strains were successfully grown in cell culture. Ultrastructural analysis, comparison of 16S and 23S rRNA gene sequences, whole-genome analysis based on de novo hybrid-assembled sequences of the new strains as well as subsequent calculation of taxonomic parameters revealed that the relatedness of the flamingo isolates to established members of the family Chlamydiaceae was sufficiently distant to indicate that the three strains belong to two distinct species within a new genus. Based on these data, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov., as two new species of the genus.
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Affiliation(s)
- F Vorimore
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France.
| | - M Hölzer
- Robert Koch Institute, MF1 Bioinformatics, Berlin, Germany
| | - E M Liebler-Tenorio
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - L-M Barf
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
| | - S Delannoy
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - M Vittecoq
- Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles, France
| | - R Wedlarski
- Bioparc - Zoo de Doué la fontaine, 103 rue de Cholet, 49700 Doué la Fontaine, France
| | - A Lécu
- Parc Zoologique de Paris, avenue de Daumesnil, 75012 Paris, France
| | - S Scharf
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - Y Blanchard
- Unit of Viral Genetics and Biosafety, ANSES, Laboratory of Ploufragan, Ploufragan, France
| | - P Fach
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - R C Hsia
- University of Maryland, Electron Microscopy Core Imaging Facility, Baltimore, MD 21201, USA
| | - P M Bavoil
- University of Maryland, Department of Microbial Pathogenesis, Baltimore, MD 21201, USA
| | - R Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies, 07190 Esporles, Spain
| | - K Laroucau
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - K Sachse
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
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2
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Colpaert M, Kadouche D, Ducatez M, Pillonel T, Kebbi-Beghdadi C, Cenci U, Huang B, Chabi M, Maes E, Coddeville B, Couderc L, Touzet H, Bray F, Tirtiaux C, Ball S, Greub G, Colleoni C. Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae. Commun Biol 2021; 4:296. [PMID: 33674787 PMCID: PMC7935935 DOI: 10.1038/s42003-021-01794-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
The order Chlamydiales includes obligate intracellular pathogens capable of infecting mammals, fishes and amoeba. Unlike other intracellular bacteria for which intracellular adaptation led to the loss of glycogen metabolism pathway, all chlamydial families maintained the nucleotide-sugar dependent glycogen metabolism pathway i.e. the GlgC-pathway with the notable exception of both Criblamydiaceae and Waddliaceae families. Through detailed genome analysis and biochemical investigations, we have shown that genome rearrangement events have resulted in a defective GlgC-pathway and more importantly we have evidenced a distinct trehalose-dependent GlgE-pathway in both Criblamydiaceae and Waddliaceae families. Altogether, this study strongly indicates that the glycogen metabolism is retained in all Chlamydiales without exception, highlighting the pivotal function of storage polysaccharides, which has been underestimated to date. We propose that glycogen degradation is a mandatory process for fueling essential metabolic pathways that ensure the survival and virulence of extracellular forms i.e. elementary bodies of Chlamydiales.
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Affiliation(s)
- Matthieu Colpaert
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Derifa Kadouche
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mathieu Ducatez
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Ugo Cenci
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Binquan Huang
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/School of Agriculture, Yunnan University, Kunming, China
| | - Malika Chabi
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Emmanuel Maes
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Bernadette Coddeville
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Loïc Couderc
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Hélène Touzet
- University of Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Fabrice Bray
- University of Lille, CNRS, USR 3290-MSAP-Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Catherine Tirtiaux
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Steven Ball
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Christophe Colleoni
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
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3
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Pillonel T, Bertelli C, Aeby S, de Barsy M, Jacquier N, Kebbi-Beghdadi C, Mueller L, Vouga M, Greub G. Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship. Genome Biol Evol 2019; 11:1334-1344. [PMID: 30949677 PMCID: PMC6490308 DOI: 10.1093/gbe/evz072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2019] [Indexed: 12/15/2022] Open
Abstract
The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8,534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of five female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named "Candidatus Rhabdochlamydia helvetica" whereas only few thousand reads mapped to the genome of "Candidatus Midichloria mitochondrii," a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of interphylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales), and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Sébastien Aeby
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Marie de Barsy
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Nicolas Jacquier
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Linda Mueller
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Manon Vouga
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
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4
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Bayramova F, Jacquier N, Greub G. Insight in the biology of Chlamydia-related bacteria. Microbes Infect 2017; 20:432-440. [PMID: 29269129 DOI: 10.1016/j.micinf.2017.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/14/2017] [Accepted: 11/21/2017] [Indexed: 01/21/2023]
Abstract
The Chlamydiales order is composed of obligate intracellular bacteria and includes the Chlamydiaceae family and several family-level lineages called Chlamydia-related bacteria. In this review we will highlight the conserved and distinct biological features between these two groups. We will show how a better characterization of Chlamydia-related bacteria may increase our understanding on the Chlamydiales order evolution, and may help identifying new therapeutic targets to treat chlamydial infections.
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Affiliation(s)
- Firuza Bayramova
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Nicolas Jacquier
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Gilbert Greub
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland.
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5
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Fehr AGJ, Ruetten M, Seth-Smith HMB, Nufer L, Voegtlin A, Lehner A, Greub G, Crosier PS, Neuhauss SCF, Vaughan L. A Zebrafish Model for Chlamydia Infection with the Obligate Intracellular Pathogen Waddlia chondrophila. Front Microbiol 2016; 7:1829. [PMID: 27917158 PMCID: PMC5114312 DOI: 10.3389/fmicb.2016.01829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/01/2016] [Indexed: 01/22/2023] Open
Abstract
Obligate intracellular chlamydial bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum are important pathogens of terrestrial and marine vertebrates, yet many features of their pathogenesis and host specificity are still unknown. This is particularly true for families such as the Waddliacea which, in addition to epithelia, cellular targets for nearly all Chlamydia, can infect and replicate in macrophages, an important arm of the innate immune system or in their free-living amoebal counterparts. An ideal pathogen model system should include both host and pathogen, which led us to develop the first larval zebrafish model for chlamydial infections with Waddlia chondrophila. By varying the means and sites of application, epithelial cells of the swim bladder, endothelial cells of the vasculature and phagocytosing cells of the innate immune system became preferred targets for infection in zebrafish larvae. Through the use of transgenic zebrafish, we could observe recruitment of neutrophils to the infection site and demonstrate for the first time that W. chondrophila is taken up and replicates in these phagocytic cells and not only in macrophages. Furthermore, we present evidence that myeloid differentiation factor 88 (MyD88) mediated signaling plays a role in the innate immune reaction to W. chondrophila, eventually by Toll-like receptor (TLRs) recognition. Infected larvae with depleted levels of MyD88 showed a higher infection load and a lower survival rate compared to control fish. This work presents a new and potentially powerful non-mammalian experimental model to study the pathology of chlamydial virulence in vivo and opens up new possibilities for investigation of other members of the PVC superphylum.
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Affiliation(s)
- Alexander G J Fehr
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
| | - Maja Ruetten
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
| | - Helena M B Seth-Smith
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of ZurichZurich, Switzerland; Functional Genomics Center Zurich, Molecular and Life Sciences, University of ZurichZurich, Switzerland
| | - Lisbeth Nufer
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
| | - Andrea Voegtlin
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zurich Zurich, Switzerland
| | - Angelika Lehner
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich Zurich, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
| | - Philip S Crosier
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland Auckland, New Zealand
| | | | - Lloyd Vaughan
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
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6
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Vouga M, Baud D, Greub G. Simkania negevensis, an insight into the biology and clinical importance of a novel member of the Chlamydiales order. Crit Rev Microbiol 2016; 43:62-80. [PMID: 27786615 DOI: 10.3109/1040841x.2016.1165650] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Simkania negevensis is a Chlamydia-related bacterium discovered in 1993 and represents the founding member of the Simkaniaceae family within the Chlamydiales order. As other Chlamydiales, it is an obligate intracellular bacterium characterized by a biphasic developmental cycle. Its similarities with the pathogenic Chlamydia trachomatis and Chlamydia pneumoniae make it an interesting bacterium. So far, little is known about its biology, but S. negevensis harbors various microbiological characteristics of interest, including a strong association of the Simkania-containing vacuole with the ER and the presence of an intron in the 23S rRNA encoding gene. Evidence of human exposition has been reported worldwide. However, there is a lack of robust clinical studies evaluating its implication in human diseases; current data suggest an association with pneumonia and bronchiolitis making S. negevensis a potential emerging pathogen. Owing to its fastidious growth requirements, the clinical relevance of S. negevensis is probably underestimated. In this review, we summarize the current knowledge on S. negevensis and explore future research challenges.
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Affiliation(s)
- Manon Vouga
- a Institute of Microbiology , Center for Research on Intracellular Bacteria, Faculty of Biology and Medicine, University and University Hospital of Lausanne , Lausanne , Switzerland.,b Department "Femme-Mère-Enfant" , Materno-Fetal and Obstetrics Research Unit, University Hospital , Lausanne , Switzerland
| | - David Baud
- a Institute of Microbiology , Center for Research on Intracellular Bacteria, Faculty of Biology and Medicine, University and University Hospital of Lausanne , Lausanne , Switzerland.,b Department "Femme-Mère-Enfant" , Materno-Fetal and Obstetrics Research Unit, University Hospital , Lausanne , Switzerland
| | - Gilbert Greub
- a Institute of Microbiology , Center for Research on Intracellular Bacteria, Faculty of Biology and Medicine, University and University Hospital of Lausanne , Lausanne , Switzerland.,c Infectious Diseases Unit , University hospital , Lausanne , Switzerland
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7
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Bou Khalil JY, Benamar S, Baudoin JP, Croce O, Blanc-Tailleur C, Pagnier I, Raoult D, La Scola B. Developmental Cycle and Genome Analysis of "Rubidus massiliensis," a New Vermamoeba vermiformis Pathogen. Front Cell Infect Microbiol 2016; 6:31. [PMID: 27014641 PMCID: PMC4791399 DOI: 10.3389/fcimb.2016.00031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/01/2016] [Indexed: 12/15/2022] Open
Abstract
The study of amoeba-associated Chlamydiae is a dynamic field in which new species are increasingly reported. In the present work, we characterized the developmental cycle and analyzed the genome of a new member of this group associated with Vermamoeba vermiformis, we propose to name “Rubidus massiliensis.” This bacterium is well-adapted to its amoeba host and do not reside inside of inclusion vacuoles after phagocytosis. It has a developmental cycle typical of this family of bacteria, with a transition from condensed elementary bodies to hypodense replicative reticulate bodies. Multiplication occurs through binary fission of the reticulate bodies. The genome of “R. massiliensis” consists of a 2.8 Mbp chromosome and two plasmids (pRm1, pRm2) consisting of 39,075 bp and 80,897 bp, respectively, a feature that is unique within this group. The Re-analysis of the Chlamydiales genomes including the one of “R. massiliensis” slightly modified the previous phylogeny of the tlc gene encoding the ADP/ATP translocase. Our analysis suggested that the tlc gene could have been transferred to plant and algal plastids before the transfer to Rickettsiales, and that this gene was probably duplicated several times.
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Affiliation(s)
- Jacques Y Bou Khalil
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille Université Marseille, France
| | - Samia Benamar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille Université Marseille, France
| | - Jean-Pierre Baudoin
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille Marseille, France
| | - Olivier Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille Université Marseille, France
| | - Caroline Blanc-Tailleur
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille Université Marseille, France
| | - Isabelle Pagnier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille Université Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille UniversitéMarseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de MarseilleMarseille, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, UM63 Centre National de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille UniversitéMarseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de MarseilleMarseille, France
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8
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Pilloux L, LeRoy D, Brunel C, Roger T, Greub G. Mouse Model of Respiratory Tract Infection Induced by Waddlia chondrophila. PLoS One 2016; 11:e0150909. [PMID: 26950066 PMCID: PMC4780729 DOI: 10.1371/journal.pone.0150909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/22/2016] [Indexed: 11/29/2022] Open
Abstract
Waddlia chondrophila, an obligate intracellular bacterium belonging to the Chlamydiales order, is considered as an emerging pathogen. Some clinical studies highlighted a possible role of W. chondrophila in bronchiolitis, pneumonia and miscarriage. This pathogenic potential is further supported by the ability of W. chondrophila to infect and replicate within human pneumocytes, macrophages and endometrial cells. Considering that W. chondrophila might be a causative agent of respiratory tract infection, we developed a mouse model of respiratory tract infection to get insight into the pathogenesis of W. chondrophila. Following intranasal inoculation of 2 x 108W. chondrophila, mice lost up to 40% of their body weight, and succumbed rapidly from infection with a death rate reaching 50% at day 4 post-inoculation. Bacterial loads, estimated by qPCR, increased from day 0 to day 3 post-infection and decreased thereafter in surviving mice. Bacterial growth was confirmed by detecting dividing bacteria using electron microscopy, and living bacteria were isolated from lungs 14 days post-infection. Immunohistochemistry and histopathology of infected lungs revealed the presence of bacteria associated with pneumonia characterized by an important multifocal inflammation. The high inflammatory score in the lungs was associated with the presence of pro-inflammatory cytokines in both serum and lungs at day 3 post-infection. This animal model supports the role of W. chondrophila as an agent of respiratory tract infection, and will help understanding the pathogenesis of this strict intracellular bacterium.
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Affiliation(s)
- Ludovic Pilloux
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Didier LeRoy
- Infectious Diseases Service, Department of Medicine, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Christophe Brunel
- Institute of Pathology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Thierry Roger
- Infectious Diseases Service, Department of Medicine, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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9
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Pizzetti I, Schulz F, Tyml T, Fuchs BM, Amann R, Horn M, Fazi S. Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake. Environ Microbiol 2015; 18:2405-17. [PMID: 26530333 DOI: 10.1111/1462-2920.13111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 12/01/2022]
Abstract
The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.
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Affiliation(s)
- Ilaria Pizzetti
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
| | - Frederik Schulz
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Tomáš Tyml
- University of South Bohemia, Faculty of Science, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Masaryk University, Department of Botany and Zoology, Faculty of Science, Kotlářská 2, 61137, Brno, Czech Republic
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Matthias Horn
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Stefano Fazi
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
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10
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Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Front Microbiol 2015; 6:101. [PMID: 25745418 PMCID: PMC4333871 DOI: 10.3389/fmicb.2015.00101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/26/2015] [Indexed: 12/25/2022] Open
Abstract
With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | - Sébastien Aeby
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
| | | | - James Clulow
- School of Biology, University of Lausanne Lausanne, Switzerland
| | | | - Samuel Rappo
- School of Biology, University of Lausanne Lausanne, Switzerland
| | | | | | | | - Paola Benaglio
- Department of Medical Genetics, University of Lausanne Lausanne, Switzerland
| | - Laurent Falquet
- Division of Biochemistry, Department of Biology, University of Fribourg Fribourg, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | | | - Walid H Gharib
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany
| | - Keith Harshman
- Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland
| | - Burkhard Linke
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany
| | - Ryo Miyazaki
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland
| | | | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
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11
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Taylor-Brown A, Vaughan L, Greub G, Timms P, Polkinghorne A. Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae. Pathog Dis 2014; 73:1-15. [PMID: 25854000 DOI: 10.1093/femspd/ftu009] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2014] [Indexed: 11/13/2022] Open
Abstract
Chlamydiae are obligate intracellular bacteria that share a unique but remarkably conserved biphasic developmental cycle that relies on a eukaryotic host cell for survival. Although the phylum was originally thought to only contain one family, the Chlamydiaceae, a total of nine families are now recognized. These so-called Chlamydia-like organisms (CLOs) are also referred to as 'environmental chlamydiae', as many were initially isolated from environmental sources. However, these organisms are also emerging pathogens, as many, such as Parachlamydia sp., Simkania sp. and Waddlia sp., have been associated with human disease, and others, such as Piscichlamydia sp. and Parilichlamydia sp., have been documented in association with diseases in animals. Their strict intracellular nature and the requirement for cell culture have been a confounding factor in characterizing the biology and pathogenicity of CLOs. Nevertheless, the genomes of seven CLO species have now been sequenced, providing new information on their potential ability to adapt to a wide range of hosts. As new isolation and diagnostic methods advance, we are able to further explore the richness of this phylum with further research likely to help define the true pathogenic potential of the CLOs while also providing insight into the origins of the 'traditional' chlamydiae.
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Affiliation(s)
- Alyce Taylor-Brown
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
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12
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Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00949-14. [PMID: 25342672 PMCID: PMC4208316 DOI: 10.1128/genomea.00949-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Criblamydia sequanensis is an amoeba-resisting bacterium recently isolated from the Seine River. This Chlamydia-related bacterium harbors a genome of approximately 3 Mbp and a megaplasmid of 89,525 bp. The plasmid encodes several efflux systems and an operon for arsenite resistance. This first genome sequence within the Criblamydiaceae family enlarges our view on the evolution and the ecology of this important bacterial clade largely understudied so far.
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13
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de Barsy M, Bottinelli L, Greub G. Antibiotic susceptibility of Estrella lausannensis, a potential emerging pathogen. Microbes Infect 2014; 16:746-54. [DOI: 10.1016/j.micinf.2014.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/05/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
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14
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Kebbi-Beghdadi C, Greub G. Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:309-24. [PMID: 24992529 DOI: 10.1111/1758-2229.12155] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/14/2014] [Accepted: 02/16/2014] [Indexed: 05/23/2023]
Abstract
Free-living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba-resisting microorganisms (ARMs), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as Legionella and Mycobacteria, and also several newly discovered Chlamydia-related bacteria, such as Parachlamydia acanthamoebae, Estrella lausannensis, Simkania negevensis or Waddlia chondrophila whose pathogenic role towards human or animal is strongly suspected. Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other ARMs and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast-growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that ARMs are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the Chlamydiales order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell-culture-based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.
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Affiliation(s)
- Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
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15
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Omsland A, Sixt BS, Horn M, Hackstadt T. Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities. FEMS Microbiol Rev 2014; 38:779-801. [PMID: 24484402 DOI: 10.1111/1574-6976.12059] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/08/2014] [Accepted: 01/13/2014] [Indexed: 01/07/2023] Open
Abstract
Chlamydiae are a group of obligate intracellular bacteria comprising important human and animal pathogens as well as symbionts of ubiquitous protists. They are characterized by a developmental cycle including two main morphologically and physiologically distinct stages, the replicating reticulate body and the infectious nondividing elementary body. In this review, we reconstruct the history of studies that have led to our current perception of chlamydial physiology, focusing on their energy and central carbon metabolism. We then compare the metabolic capabilities of pathogenic and environmental chlamydiae highlighting interspecies variability among the metabolically more flexible environmental strains. We discuss recent findings suggesting that chlamydiae may not live as energy parasites throughout the developmental cycle and that elementary bodies are not metabolically inert but exhibit metabolic activity under appropriate axenic conditions. The observed host-free metabolic activity of elementary bodies may reflect adequate recapitulation of the intracellular environment, but there is evidence that this activity is biologically relevant and required for extracellular survival and maintenance of infectivity. The recent discoveries call for a reconsideration of chlamydial metabolism and future in-depth analyses to better understand how species- and stage-specific differences in chlamydial physiology may affect virulence, tissue tropism, and host adaptation.
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Affiliation(s)
- Anders Omsland
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, NIAID, NIH, Hamilton, MT, USA
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