Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections
BackgroundRecently, targeted next-generation sequencing (tNGS) have been extensively utilized for the identification of pathogens in pulmonary infections, there have been some studies systematically evaluating differences in the efficacy of tNGS and conventional microbiological tests (CMTs) in bronc...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-06-01
|
| Series: | Frontiers in Cellular and Infection Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1590881/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850225644832555008 |
|---|---|
| author | Qiugui Xu Qiumei Chen Wen Qiu Lili Liu Wan Zeng Jinling Chen Yangyang Li Zhen Guo Ling Rong Bigui Chen Jinxiu Yao Liye Yang |
| author_facet | Qiugui Xu Qiumei Chen Wen Qiu Lili Liu Wan Zeng Jinling Chen Yangyang Li Zhen Guo Ling Rong Bigui Chen Jinxiu Yao Liye Yang |
| author_sort | Qiugui Xu |
| collection | DOAJ |
| description | BackgroundRecently, targeted next-generation sequencing (tNGS) have been extensively utilized for the identification of pathogens in pulmonary infections, there have been some studies systematically evaluating differences in the efficacy of tNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid (BALF) specimens.MethodsA retrospective analysis was conducted on 203 patients with pulmonary infections treated in one tertiary hospital from July 2023 to February 2024. BALF specimens underwent parallel testing via tNGS and CMTs. Pathogen detection consistency, the drug resistance genes concordance with phenotypic drug sensitivity, and clinical impact of tNGS-guided therapy adjustments were analyzed. Furthermore, two patients with complex infections were selected for tNGS microbiological surveillance to evaluate the efficacy of monitoring severe pneumonia.ResultsThis study included 205 confirmed infectious BALF specimens (two patients were tested twice). tNGS identified 56 putative pathogens, compared to 20 by CMTs, with a significantly higher positive rate (99.5% vs. 35.6%, P<0.0001). The detection of pathogenic microorganisms using tNGS showed a high concordance rate with the results of CMTs. tNGS-guided therapy adjustments occurred in 17.2% (35/203) of patients. Resistance gene predictions aligned with the drug sensitivity results in 40% (6/15) of carbapenem-resistant organisms (CROs) and 80% (4/5) of methicillin-resistant Staphylococcus aureus (MRSA) cases. Additionally, for monitored two patients with severe pneumonia, the tNGS results were consistent with the culture and imaging test results during treatment.ConclusionsThe application of tNGS highlights its promise and significance in identifying potential pathogens, predicting drug resistance, and providing guidance for anti-infection therapies for severe pneumonia. It can be at least a complementary approach to CMTs reporting. |
| format | Article |
| id | doaj-art-fcd272f02afe495393b5bca86c8ebcd8 |
| institution | OA Journals |
| issn | 2235-2988 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-fcd272f02afe495393b5bca86c8ebcd82025-08-20T02:05:17ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-06-011510.3389/fcimb.2025.15908811590881Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infectionsQiugui Xu0Qiumei Chen1Wen Qiu2Lili Liu3Wan Zeng4Jinling Chen5Yangyang Li6Zhen Guo7Ling Rong8Bigui Chen9Jinxiu Yao10Liye Yang11Clinical Laboratory, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaClinical Laboratory, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaDepartment of Radiology, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaPrecision Medical Lab Center, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaClinical Laboratory, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaClinical Laboratory, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaClinical Laboratory, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaClinical Laboratory, Chest Hospital of Zhengzhou University, Zhengzhou, Henan, ChinaDepartment of Respiratory and Critical Care Medicine, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaDepartment of Respiratory and Critical Care Medicine, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaClinical Laboratory, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaPrecision Medical Lab Center, People’s Hospital of Yangjiang, Yangjiang, Guangdong, ChinaBackgroundRecently, targeted next-generation sequencing (tNGS) have been extensively utilized for the identification of pathogens in pulmonary infections, there have been some studies systematically evaluating differences in the efficacy of tNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid (BALF) specimens.MethodsA retrospective analysis was conducted on 203 patients with pulmonary infections treated in one tertiary hospital from July 2023 to February 2024. BALF specimens underwent parallel testing via tNGS and CMTs. Pathogen detection consistency, the drug resistance genes concordance with phenotypic drug sensitivity, and clinical impact of tNGS-guided therapy adjustments were analyzed. Furthermore, two patients with complex infections were selected for tNGS microbiological surveillance to evaluate the efficacy of monitoring severe pneumonia.ResultsThis study included 205 confirmed infectious BALF specimens (two patients were tested twice). tNGS identified 56 putative pathogens, compared to 20 by CMTs, with a significantly higher positive rate (99.5% vs. 35.6%, P<0.0001). The detection of pathogenic microorganisms using tNGS showed a high concordance rate with the results of CMTs. tNGS-guided therapy adjustments occurred in 17.2% (35/203) of patients. Resistance gene predictions aligned with the drug sensitivity results in 40% (6/15) of carbapenem-resistant organisms (CROs) and 80% (4/5) of methicillin-resistant Staphylococcus aureus (MRSA) cases. Additionally, for monitored two patients with severe pneumonia, the tNGS results were consistent with the culture and imaging test results during treatment.ConclusionsThe application of tNGS highlights its promise and significance in identifying potential pathogens, predicting drug resistance, and providing guidance for anti-infection therapies for severe pneumonia. It can be at least a complementary approach to CMTs reporting.https://www.frontiersin.org/articles/10.3389/fcimb.2025.1590881/fulltargeted next-generation sequencing (TNGS)conventional microbiological tests (CMTs)pulmonary infectionbronchoalveolar lavage fluid (BALF)pathogens |
| spellingShingle | Qiugui Xu Qiumei Chen Wen Qiu Lili Liu Wan Zeng Jinling Chen Yangyang Li Zhen Guo Ling Rong Bigui Chen Jinxiu Yao Liye Yang Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections Frontiers in Cellular and Infection Microbiology targeted next-generation sequencing (TNGS) conventional microbiological tests (CMTs) pulmonary infection bronchoalveolar lavage fluid (BALF) pathogens |
| title | Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections |
| title_full | Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections |
| title_fullStr | Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections |
| title_full_unstemmed | Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections |
| title_short | Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections |
| title_sort | application of targeted next generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections |
| topic | targeted next-generation sequencing (TNGS) conventional microbiological tests (CMTs) pulmonary infection bronchoalveolar lavage fluid (BALF) pathogens |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1590881/full |
| work_keys_str_mv | AT qiuguixu applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT qiumeichen applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT wenqiu applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT lililiu applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT wanzeng applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT jinlingchen applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT yangyangli applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT zhenguo applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT lingrong applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT biguichen applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT jinxiuyao applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections AT liyeyang applicationoftargetednextgenerationsequencingforpathogensdiagnosisanddrugresistancepredictioninbronchoalveolarlavagefluidofpulmonaryinfections |