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Whole-Genome Sequence of Corynebacterium xerosis Strain GS1, Isolated from Yak in Gansu Province, China. Microbiol Resour Announc 2019; 8:8/37/e00556-19. [PMID: 31515333 PMCID: PMC6742784 DOI: 10.1128/mra.00556-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report here the isolation, sequencing of the complete closed genome, and annotation of Corynebacterium xerosis strain GS1. This strain was isolated from the liver lesion of a yak in Gansu Province, China. The genome consists of one chromosome with 2,738,835 bp and comprises 2,304 protein-coding genes. We report here the isolation, sequencing of the complete closed genome, and annotation of Corynebacterium xerosis strain GS1. This strain was isolated from the liver lesion of a yak in Gansu Province, China. The genome consists of one chromosome with 2,738,835 bp and comprises 2,304 protein-coding genes.
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Santos AS, Ramos RT, Silva A, Hirata R, Mattos-Guaraldi AL, Meyer R, Azevedo V, Felicori L, Pacheco LGC. Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species. Funct Integr Genomics 2018; 18:593-610. [PMID: 29752561 DOI: 10.1007/s10142-018-0610-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/28/2018] [Accepted: 04/16/2018] [Indexed: 12/24/2022]
Abstract
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy, using profile HMMs, we identified an enzyme with putative alpha-1,6-glycosidase activity only in some specific strains of C. diphtheriae and this may aid to understanding of the differential abilities to utilize glycogen and starch between the biovars.
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Affiliation(s)
- André S Santos
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Rommel T Ramos
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Raphael Hirata
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Ana L Mattos-Guaraldi
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Vasco Azevedo
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Liza Felicori
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil.
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Santos CS, Ramos JN, Vieira VV, Pinheiro CS, Meyer R, Alcantara-Neves NM, Ramos RT, Silva A, Hirata R, Felicori L, de Alegría Puig CR, Navas J, Azevedo V, Mattos-Guaraldi AL, Pacheco LGC. Efficient differentiation of Corynebacterium striatum, Corynebacterium amycolatum and Corynebacterium xerosis clinical isolates by multiplex PCR using novel species-specific primers. J Microbiol Methods 2017; 142:33-35. [PMID: 28888870 DOI: 10.1016/j.mimet.2017.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/28/2022]
Abstract
A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS.
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Affiliation(s)
- Carolina S Santos
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Juliana N Ramos
- National Institute for Quality Control in Health (INCQS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Veronica V Vieira
- Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Carina S Pinheiro
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | | | - Rommel T Ramos
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Raphael Hirata
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Liza Felicori
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos Ruiz de Alegría Puig
- Departamento de Biología Molecular, Universidad de Cantabria, Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Jesús Navas
- Departamento de Biología Molecular, Universidad de Cantabria, Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ana L Mattos-Guaraldi
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil.
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