Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Apr;52(2):625-636.
doi: 10.1007/s15010-024-02185-1. Epub 2024 Feb 18.

Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice

Tangfeng Lv #  1 , Qi Zhao #  2 , Jia Liu #  3 , Song Wang  3 , Weiwei Wu  3 , Liyun Miao  4   5 , Ping Zhan  1 , Xiaoli Chen  6 , Manman Huang  3 , Mingxiang Ye  1 , Qiuxiang Ou  3 , Yeqing Zhang  7
Affiliations

Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice

Tangfeng Lv et al. Infection. 2024 Apr.

Abstract

Background: Infectious etiologies of lower respiratory tract infections (LRTIs) by the conventional microbiology tests (CMTs) can be challenging. Metagenomic next-generation sequencing (mNGS) has great potential in clinical use for its comprehensiveness in identifying pathogens, particularly those difficult-to-culture organisms.

Methods: We analyzed a total of 205 clinical samples from 201 patients with suspected LRTIs using mNGS in parallel with CMTs. mNGS results were used to guide treatment adjustments for patients who had negative CMT results. The efficacy of treatment was subsequently evaluated in these patients.

Results: mNGS-detected microorganisms in 91.7% (188/205) of the clinical samples, whereas CMTs demonstrated a lower detection rate, identifying microorganisms in only 37.6% (77/205) of samples. Compared to CMT results, mNGS exhibited a detection sensitivity of 93.5% and 95.4% in all 205 clinical samples and 180 bronchoalveolar lavage fluid (BALF) samples, respectively. A total of 114 patients (114/201; 56.7%) showed negative CMT results, among which 92 received treatment adjustments guided by their positive mNGS results. Notably, 67.4% (62/92) of patients demonstrated effective treatment, while 25% (23/92) experienced a stabilized condition. Subgroup analysis of cancer patients revealed that 41.9% (13/31) exhibited an effective response to treatment, and 35.5% (11/31) maintained a stable condition following medication adjustments guided by mNGS.

Conclusion: mNGS demonstrated great potential in identifying microorganisms of clinical significance in LRTIs. The rapid turnaround time and reduced susceptibility to the impact of antimicrobial administration make mNGS a valuable supplementary tool for diagnosis and treatment decision-making for suspected LRTIs in clinical practice.

Keywords: Conventional microbiology test; Diagnosis; Lower respiratory tract infection; Metagenomic next-generation sequencing.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Collaborators GL. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the Global Burden of Disease Study 2015. Lancet Infect Dis. 2017;17:1133–61. - DOI
    1. Feldman C, Shaddock E. Epidemiology of lower respiratory tract infections in adults. Expert Rev Respir Med. 2019;13:63–77. - PubMed - DOI
    1. Greene G, Hood K, Little P, Verheij T, Goossens H, Coenen S, Butler CC. Towards clinical definitions of lower respiratory tract infection (LRTI) for research and primary care practice in Europe: an international consensus study. Prim Care Respir J. 2011;20:299–306. - PubMed - PMC - DOI
    1. Korppi M, Heikkila P, Palmu S, Huhtala H, Csonka P. Antibiotic prescriptions for children with lower respiratory tract infections fell from 2014 to 2020, but misuse was still an issue. Acta Paediatr. 2022;111:1230–7. - PubMed - DOI
    1. Wei Gu SM, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol Mech Dis. 2019;14:319–38. - DOI

MeSH terms

LinkOut - more resources