Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation
The aim of this study was to reveal diagnostic biomarkers of considerable importance for common pathogenic <i>Nocardia</i>, utilizing pan-genomic and comparative genome analysis to accurately characterize clinical <i>Nocardia</i> infections. In this study, complete or assembl...
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| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
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| Series: | Pathogens |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-0817/14/1/35 |
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| Summary: | The aim of this study was to reveal diagnostic biomarkers of considerable importance for common pathogenic <i>Nocardia</i>, utilizing pan-genomic and comparative genome analysis to accurately characterize clinical <i>Nocardia</i> infections. In this study, complete or assembled genome sequences of common pathogenic <i>Nocardia</i> and closely related species were obtained from NCBI as discovery and validation sets, respectively. Genome annotation was performed using Prokka software, and pan-genomic analysis and extraction of <i>Nocardia</i> core genes were performed using BPGA software. Comparative genome analysis of these core genes with the validation-set gene sequences was then performed using BLAT, with a threshold of 30% amino acid coverage and identity, in order to distinguish specific core genes. Finally, candidate gene-specific primers were designed using Snapgene software and DNA samples were obtained from clinical <i>Nocardia</i> strains and closely related species for validation. The analysis identified eighteen core genes specific to <i>Nocardia</i> spp., four core genes specific to <i>N. farcinica</i>, and forty-six core genes specific to <i>N. cyriacigeorgica</i>. After rigorous clinical validation, one gene from <i>Nocardia</i> spp. and five genes from <i>N. cyriacigeorgica</i> were confirmed to have high specificity and therefore can be used as reliable biomarkers for accurate diagnosis of <i>Nocardia</i> infection. This pioneering research reveals diagnostic biomarkers of considerable significance, with the potential to substantially enhance the precise diagnosis of common pathogenic <i>Nocardia</i> infections, thereby laying the groundwork for innovative diagnostic methodologies in subsequent studies. |
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| ISSN: | 2076-0817 |