Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans
<i>Nocardia</i> species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil <i>Nocardia</i...
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| Format: | Article |
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MDPI AG
2020-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/6/900 |
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| author | Gema Carrasco Sara Monzón María San Segundo Enrique García Noelia Garrido María J. Medina-Pascual Pilar Villalón Ana Ramírez Pilar Jiménez Isabel Cuesta Sylvia Valdezate |
| author_facet | Gema Carrasco Sara Monzón María San Segundo Enrique García Noelia Garrido María J. Medina-Pascual Pilar Villalón Ana Ramírez Pilar Jiménez Isabel Cuesta Sylvia Valdezate |
| author_sort | Gema Carrasco |
| collection | DOAJ |
| description | <i>Nocardia</i> species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil <i>Nocardia</i> strains from Lara State, Venezuela, were studied by 16S rRNA and <i>gyrB</i> (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven <i>Nocardia</i> species with one or two strains each, except for <i>Nocardia cyriacigeorgica</i> with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and <i>gyrB</i> analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 <i>N. cyriacigeorgica</i> strains found at five locations which grouped into a soil-only cluster. The soil strains of <i>N. cyriacigeorgica</i> showed fewer <i>gyr</i>B haplotypes than the examined human strains (13 vs. 17) but did show a larger number of <i>gyrB</i> SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (<i>p</i> ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public <i>N. cyriacigeorgica</i> genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name <i>Nocardia venezuelensis</i>). |
| first_indexed | 2024-03-10T19:10:26Z |
| format | Article |
| id | doaj.art-b43ac515b7e54f1e84b57825e85db1d9 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T19:10:26Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj.art-b43ac515b7e54f1e84b57825e85db1d92023-11-20T03:54:18ZengMDPI AGMicroorganisms2076-26072020-06-018690010.3390/microorganisms8060900Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from HumansGema Carrasco0Sara Monzón1María San Segundo2Enrique García3Noelia Garrido4María J. Medina-Pascual5Pilar Villalón6Ana Ramírez7Pilar Jiménez8Isabel Cuesta9Sylvia Valdezate10Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainBionformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainReference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainSoil Microbiology Laboratory, Microbiology and Parasitology Department, Pharmacy and Bioanalys Faculty, Los Andes University, Mérida 5101, VenezuelaReference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainReference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainReference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainSoil Microbiology Laboratory, Microbiology and Parasitology Department, Pharmacy and Bioanalys Faculty, Los Andes University, Mérida 5101, VenezuelaGenomics Laboratory, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainBionformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, SpainReference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain<i>Nocardia</i> species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil <i>Nocardia</i> strains from Lara State, Venezuela, were studied by 16S rRNA and <i>gyrB</i> (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven <i>Nocardia</i> species with one or two strains each, except for <i>Nocardia cyriacigeorgica</i> with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and <i>gyrB</i> analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 <i>N. cyriacigeorgica</i> strains found at five locations which grouped into a soil-only cluster. The soil strains of <i>N. cyriacigeorgica</i> showed fewer <i>gyr</i>B haplotypes than the examined human strains (13 vs. 17) but did show a larger number of <i>gyrB</i> SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (<i>p</i> ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public <i>N. cyriacigeorgica</i> genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name <i>Nocardia venezuelensis</i>).https://www.mdpi.com/2076-2607/8/6/900<i>Nocardia</i> spp.<i>Nocardia cyriacigeorgica</i>soilnocardiosis<i>gyrB</i>MLSA |
| spellingShingle | Gema Carrasco Sara Monzón María San Segundo Enrique García Noelia Garrido María J. Medina-Pascual Pilar Villalón Ana Ramírez Pilar Jiménez Isabel Cuesta Sylvia Valdezate Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans Microorganisms <i>Nocardia</i> spp. <i>Nocardia cyriacigeorgica</i> soil nocardiosis <i>gyrB</i> MLSA |
| title | Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans |
| title_full | Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans |
| title_fullStr | Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans |
| title_full_unstemmed | Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans |
| title_short | Molecular Characterization and Antimicrobial Susceptibilities of <i>Nocardia</i> Species Isolated from the Soil; A Comparison with Species Isolated from Humans |
| title_sort | molecular characterization and antimicrobial susceptibilities of i nocardia i species isolated from the soil a comparison with species isolated from humans |
| topic | <i>Nocardia</i> spp. <i>Nocardia cyriacigeorgica</i> soil nocardiosis <i>gyrB</i> MLSA |
| url | https://www.mdpi.com/2076-2607/8/6/900 |
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