Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections
Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid sa...
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MDPI AG
2025-06-01
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| author | Ha-eun Cho Min Jin Kim Jongmun Choi Yong-Hak Sohn Jae Joon Lee Kyung Sun Park Sun Young Cho Ki-Ho Park Young Jin Kim |
| author_facet | Ha-eun Cho Min Jin Kim Jongmun Choi Yong-Hak Sohn Jae Joon Lee Kyung Sun Park Sun Young Cho Ki-Ho Park Young Jin Kim |
| author_sort | Ha-eun Cho |
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| description | Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results—including bacterial/fungal cultures; PCR for <i>Mycobacterium tuberculosis</i> or cytomegalovirus; and the BioFire<sup>®</sup> FilmArray<sup>®</sup> Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)—underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002–0.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, <i>Candida</i> species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness. |
| format | Article |
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| institution | Kabale University |
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| language | English |
| publishDate | 2025-06-01 |
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| series | Microorganisms |
| spelling | doaj-art-a147e24dd4114e3c8bc9163cf99b7fd62025-08-20T03:29:35ZengMDPI AGMicroorganisms2076-26072025-06-01136133810.3390/microorganisms13061338Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract InfectionsHa-eun Cho0Min Jin Kim1Jongmun Choi2Yong-Hak Sohn3Jae Joon Lee4Kyung Sun Park5Sun Young Cho6Ki-Ho Park7Young Jin Kim8Department of Laboratory Medicine, Graduate School, Kyung Hee University, Kyung Hee University Hospital, Seoul 02447, Republic of KoreaDepartment of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of KoreaDepartment of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of KoreaDepartment of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of KoreaDepartment of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of KoreaDepartment of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of KoreaDepartment of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of KoreaDepartment of Infectious Diseases, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of KoreaDepartment of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of KoreaConventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results—including bacterial/fungal cultures; PCR for <i>Mycobacterium tuberculosis</i> or cytomegalovirus; and the BioFire<sup>®</sup> FilmArray<sup>®</sup> Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)—underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002–0.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, <i>Candida</i> species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness.https://www.mdpi.com/2076-2607/13/6/1338shotgun metagenomic sequencingbronchoalveolar fluid (BAL)lower respiratory infection |
| spellingShingle | Ha-eun Cho Min Jin Kim Jongmun Choi Yong-Hak Sohn Jae Joon Lee Kyung Sun Park Sun Young Cho Ki-Ho Park Young Jin Kim Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections Microorganisms shotgun metagenomic sequencing bronchoalveolar fluid (BAL) lower respiratory infection |
| title | Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections |
| title_full | Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections |
| title_fullStr | Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections |
| title_full_unstemmed | Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections |
| title_short | Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections |
| title_sort | shotgun metagenomic sequencing analysis as a diagnostic strategy for patients with lower respiratory tract infections |
| topic | shotgun metagenomic sequencing bronchoalveolar fluid (BAL) lower respiratory infection |
| url | https://www.mdpi.com/2076-2607/13/6/1338 |
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