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Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Herrera G, Ríos-Chaparro DI, Díaz-Arévalo D, Patarroyo MA, Lawley TD, Ramírez JD. Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. Virulence 2019; 10:657-676. [PMID: 31304854 PMCID: PMC6629180 DOI: 10.1080/21505594.2019.1637699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/23/2019] [Accepted: 06/25/2019] [Indexed: 01/23/2023] Open
Abstract
Some well-known Clostridiales species such as Clostridium difficile and C. perfringens are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertium and C. paraputrificum. Three fecal isolates were identified as Clostridium tertium (Gcol.A2 and Gcol.A43) and C. paraputrificum (Gcol.A11) during public health screening for C. difficile infections in Colombia. C. paraputrificum genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertium genomes than in the C. paraputrificum genomes. C. difficile tcdA and tcdB toxins encoding homologous sequences and other potential virulence factors were also identified. EndoA interferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertium genomes. toxA was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertium genomes compared with the C. paraputrificum genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Posgrado Interfacultades, Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
| | - Nitin Kumar
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Animal Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Trevor D. Lawley
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Camargo M, Díaz-Arévalo D, Roa-Molina NS, Tellez MA, Herrera G, Ríos-Chaparro DI, Birchenall C, Pinilla D, Pardo-Oviedo JM, Rodríguez-Leguizamón G, Josa DF, Lawley TD, Patarroyo MA, Ramírez JD. Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia. Sci Rep 2019; 9:11293. [PMID: 31383872 PMCID: PMC6683185 DOI: 10.1038/s41598-019-47688-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/22/2019] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia. In vitro tests were conducted to evaluate the cytopathic effect, the minimum inhibitory concentration of ten antimicrobial agents, the sporulation efficiency and the colony forming ability. Eleven different sequence types (STs) were found, the majority present individually in each sample, however in three samples two different STs were isolated. Interestingly, CO patients were infected with STs associated with hypervirulent strains (ST-1 in Clade-2). Three coexistence events (two STs simultaneously detected in the same sample) were observed always involving ST-8 from Clade-1. A total of 2,502 genes were present in 99% of the isolates with 95% of identity or more, it represents a core genome of 28.6% of the 8,735 total genes identified in the set of genomes. A high cytopathic effect was observed for the isolates positive for the two main toxins but negative for binary toxin (TcdA+/TcdB+/CDT- toxin production type), found only in Clade-1. Molecular markers conferring resistance to fluoroquinolones (cdeA and gyrA) and to sulfonamides (folP) were the most frequent in the analyzed genomes. In addition, 15 other markers were found mostly in Clade-2 isolates. These results highlight the regional differences that C. difficile isolates display, being in this case the CO isolates the ones having a greater number of accessory genes and virulence-associated factors.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Posgrado Interfacultades Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Genomics and Bioinformatics Department, North Dakota State University, Fargo, North Dakota, USA
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Milena Camargo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Animal Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
- Hygea group, Faculty of Health Sciences, Universidad de Boyacá, Tunja, Colombia
| | - Nelly S Roa-Molina
- Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Mayra A Tellez
- Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- PhD Programme in Biomedical and Biological Sciences, Faculty of Natural Sciences and Mathematics/School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Dora I Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Claudia Birchenall
- Hospital Universitario Mayor - Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Darío Pinilla
- Hospital Universitario Mayor - Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Juan M Pardo-Oviedo
- Hospital Universitario Mayor - Méderi, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia.
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