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...
Saved in:
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
|
| Series: | Pathogens |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-0817/14/1/35 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832587757793312768 |
|---|---|
| author | Chaohong Wang Xinmiao Jia Ming Wei Jun Yan Qing Sun Sibo Long Maike Zheng Yiheng Shi Guanglu Jiang Yan Zhao Hairong Huang Xinting Yang Li Gu Guirong Wang |
| author_facet | Chaohong Wang Xinmiao Jia Ming Wei Jun Yan Qing Sun Sibo Long Maike Zheng Yiheng Shi Guanglu Jiang Yan Zhao Hairong Huang Xinting Yang Li Gu Guirong Wang |
| author_sort | Chaohong Wang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-08fce1e022104ed0a2560c46ec8e3b70 |
| institution | Kabale University |
| issn | 2076-0817 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj-art-08fce1e022104ed0a2560c46ec8e3b702025-01-24T13:44:40ZengMDPI AGPathogens2076-08172025-01-011413510.3390/pathogens14010035Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary ValidationChaohong Wang0Xinmiao Jia1Ming Wei2Jun Yan3Qing Sun4Sibo Long5Maike Zheng6Yiheng Shi7Guanglu Jiang8Yan Zhao9Hairong Huang10Xinting Yang11Li Gu12Guirong Wang13Department of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaCenter for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, ChinaDepartment of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, ChinaDepartment of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaNational Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaDepartment of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaDepartment of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaDepartment of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaNational Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaDepartment of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaNational Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaTuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing 101100, ChinaDepartment of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, ChinaDepartment of Clinical Laboratory, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing 101100, ChinaThe 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.https://www.mdpi.com/2076-0817/14/1/35<i>Nocardia</i><i>N. cyriacigeorgica</i>diagnostic biomarkerpan-genome analysiscomparative genome analysis |
| spellingShingle | Chaohong Wang Xinmiao Jia Ming Wei Jun Yan Qing Sun Sibo Long Maike Zheng Yiheng Shi Guanglu Jiang Yan Zhao Hairong Huang Xinting Yang Li Gu Guirong Wang Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation Pathogens <i>Nocardia</i> <i>N. cyriacigeorgica</i> diagnostic biomarker pan-genome analysis comparative genome analysis |
| title | Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation |
| title_full | Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation |
| title_fullStr | Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation |
| title_full_unstemmed | Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation |
| title_short | Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation |
| title_sort | discovery of novel diagnostic biomarkers for common pathogenic i nocardia i through pan genome and comparative genome analysis with preliminary validation |
| topic | <i>Nocardia</i> <i>N. cyriacigeorgica</i> diagnostic biomarker pan-genome analysis comparative genome analysis |
| url | https://www.mdpi.com/2076-0817/14/1/35 |
| work_keys_str_mv | AT chaohongwang discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT xinmiaojia discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT mingwei discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT junyan discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT qingsun discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT sibolong discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT maikezheng discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT yihengshi discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT guanglujiang discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT yanzhao discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT haironghuang discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT xintingyang discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT ligu discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation AT guirongwang discoveryofnoveldiagnosticbiomarkersforcommonpathogenicinocardiaithroughpangenomeandcomparativegenomeanalysiswithpreliminaryvalidation |