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. 2024 Jul 8;28(1):225.
doi: 10.1186/s13054-024-05009-8.

Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review

Peng Zhang #  1 , Baoyi Liu #  2 , Shuang Zhang #  1 , Xuefei Chang  3 , Lihe Zhang  3 , Dejian Gu  4 , Xin Zheng  4 , Jiaqing Chen  2 , Saiyin Xiao  1 , Zhentao Wu  1 , Xuemin Cai  1 , Mingfa Long  1 , Wenjie Lu  2 , Mingzhu Zheng  2 , Rongrong Chen  4 , Rui Gao  4 , Yan Zheng  5 , Jinhua Wu  6 , Qiujuan Feng  6 , Gang He  7 , Yantang Chen  1 , Weihao Zheng  1 , Wanli Zuo  8   9 , Yanming Huang  10   11 , Xin Zhang  12   13
Affiliations

Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review

Peng Zhang et al. Crit Care. .

Abstract

Background: The precise identification of the underlying causes of infectious diseases, such as severe pneumonia, is essential, and the development of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, there is limited information on the systematic assessment of the clinical use of targeted next-generation sequencing (tNGS) in cases of severe pneumonia.

Methods: A retrospective analysis was conducted on 130 patients with severe pneumonia treated in the ICU from June 2022 to June 2023. The consistency of the results of tNGS, metagenomics next-generation sequencing (mNGS), and culture with the clinical diagnosis was evaluated. Additionally, the results for pathogens detected by tNGS were compared with those of culture, mNGS, and quantitative reverse transcription PCR (RT-qPCR). To evaluate the efficacy of monitoring severe pneumonia, five patients with complicated infections were selected for tNGS microbiological surveillance. The tNGS and culture drug sensitisation results were then compared.

Results: The tNGS results for the analysis of the 130 patients showed a concordance rate of over 70% with clinical diagnostic results. The detection of pathogenic microorganisms using tNGS was in agreement with the results of culture, mNGS, and RT-qPCR. Furthermore, the tNGS results for pathogens in the five patients monitored for complicated infections of severe pneumonia were consistent with the culture and imaging test results during treatment. The tNGS drug resistance results were in line with the drug sensitivity results in approximately 65% of the cases.

Conclusions: The application of tNGS highlights its promise and significance in assessing the effectiveness of clinical interventions and providing guidance for anti-infection therapies for severe pneumonia.

Keywords: Culture; Metagenomics next-generation sequencing; Severe pneumonia; Targeted next-generation sequencing.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Overview of the research scheme. A Flowchart of the experimental design. B Schematic diagram of tNGS sequencing assay steps
Fig. 2
Fig. 2
The infection status of 130 patients as well as the evaluation of the concordance between three methods (tNGS, culture, and mNGS) and the clinical diagnostic results. A Categorization of pathogenic infections in patients. B The subgroup profiles in which the concordance evaluation was conducted. C–G Evaluation of the concordance of tNGS, culture and mNGS methods with clinical diagnosis in different subgroups. Concordant and partial concordant (not affecting clinical judgement) were deemed to be consistent with the final diagnoses, and the remaining cases were considered incongruous with the final diagnoses. (H) Differences in clinical concordance between tNGS and the other two methods were compared using the χ2 test
Fig. 3
Fig. 3
Comparison of tNGS with culture for clinical microorganism detection. A Cluster analysis of pathogen detection in tNGS versus culture. B–H When tNGS detection was positive, it was divided into two groups with positive or negative culture detection and the RPM values of tNGS of the two groups were compared. The ROC curves were plotted using both positive tNGS and culture results as criteria
Fig. 4
Fig. 4
Comparison of tNGS with mNGS for clinical microorganism detection. A Cluster analysis of pathogen detection in tNGS versus mNGS. B–G When tNGS detection was positive, it was divided into two groups with positive or negative mNGS detection, and the RPM values of tNGS of the two groups were compared. In addition, when mNGS was positive, it was categorized into two groups with positive or negative tNGS results, and the RPM values of mNGS in the two groups were compared
Fig.5
Fig.5
Comparison of tNGS with RT-qPCR for COVID-19, influenza A virus and influenza B virus detections. A Cluster analysis of tNGS versus RT-qPCR for COVID-19, influenza A virus and influenza B virus detections. B and E In COVID-19 and influenza A virus, the RPM values of tNGS in the two groups were compared. The ROC curves were plotted using both positive tNGS and RT-qPCR results as criteria. C, D, and F In COVID-19 and influenza A virus, the CT values of the RT-qPCR of the two groups are compared
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