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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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Coers J, Newton HJ, Carlyon JA. Can't live outside you: a thematic issue on obligate intracellular bacterial pathogens. Pathog Dis 2021; 79:6458600. [PMID: 34891151 DOI: 10.1093/femspd/ftab054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 22710, USA.,Department of Immunology, Duke University Medical Center, Durham, NC 22710, USA
| | - Hayley J Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jason A Carlyon
- Department of Microbiology and Immunology, VCU School of Medicine, Virginia Commonwealth University (VCU) Medical Center, Richmond, VA 23298, USA
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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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Marti H, Bommana S, Read TD, Pesch T, Prähauser B, Dean D, Borel N. Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants. Front Microbiol 2021; 12:630293. [PMID: 34276577 PMCID: PMC8278220 DOI: 10.3389/fmicb.2021.630293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/03/2021] [Indexed: 01/01/2023] Open
Abstract
The Chlamydiaceae are a family of obligate intracellular, gram-negative bacteria known to readily exchange DNA by homologous recombination upon co-culture in vitro, allowing the transfer of antibiotic resistance residing on the chlamydial chromosome. Among all the obligate intracellular bacteria, only Chlamydia (C.) suis naturally integrated a tetracycline resistance gene into its chromosome. Therefore, in order to further investigate the readiness of Chlamydia to exchange DNA and especially antibiotic resistance, C. suis is an excellent model to advance existing co-culture protocols allowing the identification of factors crucial to promote homologous recombination in vitro. With this strategy, we co-cultured tetracycline-resistant with rifamycin group-resistant C. suis, which resulted in an allover recombination efficiency of 28%. We found that simultaneous selection is crucial to increase the number of recombinants, that sub-inhibitory concentrations of tetracycline inhibit rather than promote the selection of double-resistant recombinants, and identified a recombination-deficient C. suis field isolate, strain SWA-110 (1-28b). While tetracycline resistance was detected in field isolates, rifampicin/rifamycin resistance (RifR) had to be induced in vitro. Here, we describe the protocol with which RifR C. suis strains were generated and confirmed. Subsequent whole-genome sequencing then revealed that G530E and D461A mutations in rpoB, a gene encoding for the β-subunit of the bacterial RNA polymerase (RNAP), was likely responsible for rifampicin and rifamycin resistance, respectively. Finally, whole-genome sequencing of recombinants obtained by co-culture revealed that recombinants picked from the same plate may be sibling clones and confirmed C. suis genome plasticity by revealing variable, apparently non-specific areas of recombination.
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Affiliation(s)
- Hanna Marti
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Sankhya Bommana
- Division of Infectious Diseases, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Theresa Pesch
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Barbara Prähauser
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Deborah Dean
- Division of Infectious Diseases, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, United States.,Joint Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, United States.,Joint Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole Borel
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
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