Targeted Next-generation Sequencing for Antimicrobial Resistance Detection in Ventilator-associated Pneumonia

Overview

Journal Front Cell Infect Microbiol

Specialties Cell Biology
Infectious Diseases
Microbiology

Date 2025 Feb 17

PMID 39958934

Authors

Yuting Li

Yanfang Jiang

Hao Liu

Yao Fu

Junying Lu

Hongyan Li

Lulu Sheng

Dejian Gu

Dong Zhang

Affiliations

Soon will be listed here.

Abstract

Background: Ventilator-associated pneumonia (VAP) carries a high mortality rate in the intensive care units (ICUs) due to its widespread drug resistance. Traditional microbial cultures limited by speed and sensitivity, are often unable to help clinicians make effective diagnosis and treatment. Therefore, there is an urgent need for a rapid and accurate test that can identify both pathogens and their antimicrobial resistance (AMR) to improve the prognosis of patients with VAP.

Study Design: We analyzed samples from ICU patients with suspected VAP using both microbial tests and targeted next-generation sequencing (tNGS), comparing the results of tNGS pathogen and AMR detection against microbial culture and antimicrobial susceptibility testing (AST).

Results: Involving 199 patients with suspected VAP, tNGS showed a sensitivity rate of 98.98% for pathogen identification. While the sensitivity rate of microbial culture was just 66.84%. Additionally, tNGS performed almost half the turnaround time of microbial culture (1.66 days vs 3.00 days). For AMR, the overall consistency between AST and tNGS was 79.31%. The great performance particularly exhibited for carbapenem-penicillin-cephamycin resistance.

Conclusion: tNGS excels in identifying pathogens and AMR. Its rapid workflow makes it ideal for managing critically ill patients, enhancing treatment precision, and reducing antibiotic misuse.

References

Duszynska W, Idziak M, Smardz K, Burkot A, Grotowska M, Rojek S . Frequency, Etiology, Mortality, Cost, and Prevention of Respiratory Tract Infections-Prospective, One Center Study. J Clin Med. 2022; 11(13). PMC: 9267472. DOI: 10.3390/jcm11133764. View

Wu X, Liang R, Xiao Y, Liu H, Zhang Y, Jiang Y . Application of targeted next generation sequencing technology in the diagnosis of Mycobacterium Tuberculosis and first line drugs resistance directly from cell-free DNA of bronchoalveolar lavage fluid. J Infect. 2023; 86(4):399-401. DOI: 10.1016/j.jinf.2023.01.031. View

Wicky P, Dupuis C, Cerf C, Siami S, Cohen Y, Laurent V . Ventilator-Associated Pneumonia in COVID-19 Patients Admitted in Intensive Care Units: Relapse, Therapeutic Failure and Attributable Mortality-A Multicentric Observational Study from the OutcomeRea Network. J Clin Med. 2023; 12(4). PMC: 9961155. DOI: 10.3390/jcm12041298. View

Vacheron C, Lepape A, Savey A, Machut A, Timsit J, Comparot S . Attributable Mortality of Ventilator-associated Pneumonia Among Patients with COVID-19. Am J Respir Crit Care Med. 2022; 206(2):161-169. PMC: 9887408. DOI: 10.1164/rccm.202202-0357OC. View

Blauwkamp T, Thair S, Rosen M, Blair L, Lindner M, Vilfan I . Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019; 4(4):663-674. DOI: 10.1038/s41564-018-0349-6. View

Rezia A, Vijendra R . A clinical study on the pattern of antimicrobial drug use and drug resistance in patients with ventilator-associated pneumonia in a tertiary care hospital. Indian J Pharmacol. 2023; 55(2):89-96. PMC: 10335647. DOI: 10.4103/ijp.ijp_759_21. View

Cabrera-Tejada G, Chico-Sanchez P, Gras-Valenti P, Jaime-Sanchez F, Galiana-Ivars M, Balboa-Esteve S . Estimation of Additional Costs in Patients with Ventilator-Associated Pneumonia. Antibiotics (Basel). 2024; 13(1). PMC: 10812792. DOI: 10.3390/antibiotics13010002. View

Denis J, Lehingue S, Pauly V, Cassir N, Gainnier M, Leone M . Multidrug-resistant Pseudomonas aeruginosa and mortality in mechanically ventilated ICU patients. Am J Infect Control. 2019; 47(9):1059-1064. DOI: 10.1016/j.ajic.2019.02.030. View

Chiu C, Miller S . Clinical metagenomics. Nat Rev Genet. 2019; 20(6):341-355. PMC: 6858796. DOI: 10.1038/s41576-019-0113-7. View

10.

Stewart S, Robertson C, Pan J, Kennedy S, Haahr L, Manoukian S . Impact of healthcare-associated infection on length of stay. J Hosp Infect. 2021; 114:23-31. DOI: 10.1016/j.jhin.2021.02.026. View

11.

Li X, Liu Y, Li M, Bian J, Song D, Liu C . Epidemiological investigation of lower respiratory tract infections during influenza A (H1N1) pdm09 virus pandemic based on targeted next-generation sequencing. Front Cell Infect Microbiol. 2024; 13:1303456. PMC: 10755937. DOI: 10.3389/fcimb.2023.1303456. View

12.

Lin R, Xing Z, Liu X, Chai Q, Xin Z, Huang M . Performance of targeted next-generation sequencing in the detection of respiratory pathogens and antimicrobial resistance genes for children. J Med Microbiol. 2023; 72(11). DOI: 10.1099/jmm.0.001771. View

13.

Folkvardsen D, Thomsen V, Rigouts L, Rasmussen E, Bang D, Bernaerts G . Rifampin heteroresistance in Mycobacterium tuberculosis cultures as detected by phenotypic and genotypic drug susceptibility test methods. J Clin Microbiol. 2013; 51(12):4220-2. PMC: 3838044. DOI: 10.1128/JCM.01602-13. View

14.

Chen Q, Yi J, Liu Y, Yang C, Sun Y, Du J . Clinical diagnostic value of targeted next‑generation sequencing for infectious diseases (Review). Mol Med Rep. 2024; 30(3). DOI: 10.3892/mmr.2024.13277. View

15.

Folkvardsen D, Svensson E, Thomsen V, Rasmussen E, Bang D, Werngren J . Can molecular methods detect 1% isoniazid resistance in Mycobacterium tuberculosis?. J Clin Microbiol. 2013; 51(5):1596-9. PMC: 3647910. DOI: 10.1128/JCM.00472-13. View

16.

Peng J, Du B, Qin H, Wang Q, Shi Y . Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J Infect. 2021; 82(4):22-27. DOI: 10.1016/j.jinf.2021.01.029. View

17.

Zhang P, Liu B, Zhang S, Chang X, Zhang L, Gu D . Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review. Crit Care. 2024; 28(1):225. PMC: 11232260. DOI: 10.1186/s13054-024-05009-8. View

18.

Li S, Tong J, Liu Y, Shen W, Hu P . Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection. J Infect. 2022; 85(5):e127-e129. DOI: 10.1016/j.jinf.2022.08.022. View

19.

Gaston D, Miller H, Fissel J, Jacobs E, Gough E, Wu J . Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens. J Clin Microbiol. 2022; 60(7):e0052622. PMC: 9297812. DOI: 10.1128/jcm.00526-22. View

20.

Rinder H, Mieskes K, Loscher T . Heteroresistance in Mycobacterium tuberculosis. Int J Tuberc Lung Dis. 2001; 5(4):339-45. View