Diagnostic Significance of Metagenomic Next-Generation Sequencing for Community-Acquired Pneumonia in Southern China

Hanying Liu; Ying Zhang; Guiyang Chen; Shenghua Sun; Jiangang Wang; Fengyi Chen; Chun Liu; Quan Zhuang

doi:10.3389/fmed.2022.807174

Diagnostic Significance of Metagenomic Next-Generation Sequencing for Community-Acquired Pneumonia in Southern China

Front Med (Lausanne). 2022 Feb 15:9:807174. doi: 10.3389/fmed.2022.807174. eCollection 2022.

Authors

Hanying Liu¹, Ying Zhang², Guiyang Chen³, Shenghua Sun¹, Jiangang Wang⁴, Fengyi Chen⁵, Chun Liu¹, Quan Zhuang^{2

6}

Affiliations

¹ Department of Respiratory Diseases, The 3rd Xiangya Hospital, Central South University, Changsha, China.
² Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China.
³ Department of Cardiology, Hunan Aerospace Hospital, Changsha, China.
⁴ Department of Health Management, The 3rd Xiangya Hospital, Central South University, Changsha, China.
⁵ Vision Medicals Co. Ltd, Guangzhou, China.
⁶ Research Center of National Health Ministry on Transplantation Medicine, Changsha, China.

Abstract

Background: The morbidity and mortality of community-acquired pneumonia are relatively high, but many pneumonia pathogens cannot be identified accurately. As a new pathogen detection technology, metagenomic next-generation sequencing (mNGS) has been applied more and more clinically. We aimed to evaluate the diagnostic significance of mNGS for community-acquired pneumonia (CAP) in the south of China.

Methods: Our study selected CAP patients who visited the 3rd Xiangya Hospital from May 2019 to April 2021. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS and traditional microbiological culture. mNGS group: detected by both mNGS and BALF culture; control group: detected only by BALF or sputum culture. The diagnostic performance of pathogens and the antibiotic adjustments were compared within mNGS group.

Results: The incidence of acute respiratory distress syndrome (ARDS) was 28.3% in the mNGS group and 17.3% in the control group. Within the mNGS group, the positive rate of pathogens detected by mNGS was 64%, thus by BALF culture was only 28%. Pathogens detected by mNGS were consisted of bacteria (55%), fungi (18%), special pathogens (18%), and viruses (9%). The most detected pathogen by mNGS was Chlamydia psittaci. Among the pathogen-positive cases, 26% was not pathogen-covered by empirical antibiotics, so most of which were made an antibiotic adjustment.

Conclusions: mNGS can detect pathogens in a more timely and accurate manner and assist clinicians to adjust antibiotics in time. Therefore, we recommend mNGS as the complementary diagnosis of severe pneumonia or complicated infections.

Keywords: BALF; diagnostic significance; mNGS; pathogen; pneumonia.