Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome
Abstract Background Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation...
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | Annals of Clinical Microbiology and Antimicrobials |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12941-023-00608-9 |
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| author | Juan Zhong Yanfen Liu Na Luo Qiu Wei Qisi Su Jun Zou Xiaozhong Wu Xianzhen Huang Yuting Jiang Lijuan Liang Hongmian Li Jianyan Lin |
| author_facet | Juan Zhong Yanfen Liu Na Luo Qiu Wei Qisi Su Jun Zou Xiaozhong Wu Xianzhen Huang Yuting Jiang Lijuan Liang Hongmian Li Jianyan Lin |
| author_sort | Juan Zhong |
| collection | DOAJ |
| description | Abstract Background Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens. Results This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People’s Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS. Conclusions In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS. |
| first_indexed | 2024-03-12T23:25:02Z |
| format | Article |
| id | doaj.art-3cf394a86b2141fdbce2406f0f40776f |
| institution | Directory Open Access Journal |
| issn | 1476-0711 |
| language | English |
| last_indexed | 2024-03-12T23:25:02Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Annals of Clinical Microbiology and Antimicrobials |
| spelling | doaj.art-3cf394a86b2141fdbce2406f0f40776f2023-07-16T11:11:49ZengBMCAnnals of Clinical Microbiology and Antimicrobials1476-07112023-07-0122111210.1186/s12941-023-00608-9Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndromeJuan Zhong0Yanfen Liu1Na Luo2Qiu Wei3Qisi Su4Jun Zou5Xiaozhong Wu6Xianzhen Huang7Yuting Jiang8Lijuan Liang9Hongmian Li10Jianyan Lin11Department of Traditional Chinese Medicine, The First People’s Hospital of NanningThe Fourth People’s Hospital of NanningNanNing Center for Disease Control and PreventionDepartment of Traditional Chinese Medicine, The First People’s Hospital of NanningThe Fourth People’s Hospital of NanningThe Fourth People’s Hospital of NanningDepartment of Traditional Chinese Medicine, The First People’s Hospital of NanningThe Fourth People’s Hospital of NanningDepartment of Traditional Chinese Medicine, The First People’s Hospital of NanningNanning Yunju Biotechnology Co., LtdThe People’s Hospital of Guangxi Zhuang Autonomous RegionThe First People’s Hospital of NanningAbstract Background Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens. Results This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People’s Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS. Conclusions In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS.https://doi.org/10.1186/s12941-023-00608-9Acquired immunodeficiency syndromePulmonary infectionMetagenomic next-generation sequencingDiagnosis |
| spellingShingle | Juan Zhong Yanfen Liu Na Luo Qiu Wei Qisi Su Jun Zou Xiaozhong Wu Xianzhen Huang Yuting Jiang Lijuan Liang Hongmian Li Jianyan Lin Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome Annals of Clinical Microbiology and Antimicrobials Acquired immunodeficiency syndrome Pulmonary infection Metagenomic next-generation sequencing Diagnosis |
| title | Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome |
| title_full | Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome |
| title_fullStr | Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome |
| title_full_unstemmed | Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome |
| title_short | Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome |
| title_sort | metagenomic next generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome |
| topic | Acquired immunodeficiency syndrome Pulmonary infection Metagenomic next-generation sequencing Diagnosis |
| url | https://doi.org/10.1186/s12941-023-00608-9 |
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