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Seth-Smith H, Bommana S, Dean D, Read TD, Marti H. Chlamydia suis undergoes interclade recombination promoting Tet-island exchange. BMC Genomics 2024; 25:724. [PMID: 39060998 PMCID: PMC11282597 DOI: 10.1186/s12864-024-10606-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63). RESULTS We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream. CONCLUSIONS Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.
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Affiliation(s)
- Helena Seth-Smith
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Sankhya Bommana
- Division of Infectious Diseases and Global Health, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Deborah Dean
- Division of Infectious Diseases and Global Health, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Joint Graduate Program in Bioengineering, University of California Berkeley, University of California San Francisco, Berkeley and San Francisco, CA, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hanna Marti
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland.
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Marti H, Biggel M, Shima K, Onorini D, Rupp J, Charette SJ, Borel N. Chlamydia suis displays high transformation capacity with complete cloning vector integration into the chromosomal rrn-nqrF plasticity zone. Microbiol Spectr 2023; 11:e0237823. [PMID: 37882558 PMCID: PMC10715202 DOI: 10.1128/spectrum.02378-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The obligate intracellular Chlamydia genus contains many pathogens with a negative impact on global health and economy. Despite recent progress, there is still a lack of genetic tools limiting our understanding of these complex bacteria. This study provides new insights into genetic manipulation of Chlamydia with the opportunistic porcine pathogen Chlamydia suis, the only chlamydial species naturally harboring an antibiotic resistance gene, originally obtained by horizontal gene transfer. C. suis is transmissible to humans, posing a potential public health concern. We report that C. suis can take up vectors that lack the native plasmid, a requirement for most chlamydial transformation systems described to date. Additionally, we show that C. trachomatis, the most common cause for bacterial sexually transmitted infections and infectious blindness worldwide, can be transformed with C. suis vectors. Finally, the chromosomal region that harbors the resistance gene of C. suis is highly susceptible to complete vector integration.
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Affiliation(s)
- Hanna Marti
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Kensuke Shima
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Delia Onorini
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Steve J. Charette
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Canada
| | - Nicole Borel
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
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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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