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

Figure 1

Flowchart of case selection. From 6230 cases, a total of 370 community-acquired pneumonia cases were selected for further analysis. Patients in mNGS group did the mNGS and BALF culture at the same time. Patients in control group only did the BALF or sputum culture. mNGS, metagenomic next-generation sequencing.

Figure 2

The generalized workflow of mNGS for clinical pathogen diagnosis. The workflow has two components: (A) a wet lab protocol in which samples are collected, processed, extracted for nucleic acids, prepared into a sequencing library, and sequenced, and (B) a dry lab computational pipeline that includes microbial identification, statistical analysis, and interpretation. The sequencing library may be targeted, undergo DNA amplification, or both.

Figure 3

Comparison of positive rate of pathogens by BALF mNGS and culture. (A) The positive rate of mNGS and the types of pathogens detected. (B) The positive rate of BALF culture and the types of pathogens detected. BALF, bronchoalveolar lavage fluid; mNGS, metagenomic next-generation sequencing.

Figure 4

The overlap of positivity between BALF mNGS and BALF culture. Bacteria were the most detected, followed by fungi, special pathogens, and viruses. The positive rate of BALF culture in detecting Klebsiella pneumoniae and Acinetobacter baumannii was higher than that of mNGS. Chlamydia psittaci was the most detected by mNGS, followed by Haemophilus parainfluenzae and Candida albicans. All viruses, special pathogens, MTB and NTM were only detected by mNGS, and the BALF culture of these pathogens were negative. BALF, bronchoalveolar lavage fluid; mNGS, metagenomic next generation sequencing; MTB, Mycobacterium tuberculosis; NTM, nontuberculous mycobacteria.

Figure 5

Non-pathogenic pathogens detected by mNGS. A total of 64 different non-pathogenic pathogens were detected in the mNGS group. Human herpesvirus 5, Candida albicans, Human herpesvirus 4 are the most common non-pathogenic pathogens detected by mNGS. Acinetobacter baumannii, Candida albicans, Candida glabrata are the most common non-pathogenic pathogens detected by sputum culture. mNGS, metagenomic next-generation sequencing.

Figure 6

The coverage and adjustment of antibiotics in the mNGS group. (A) Among patients in the mNGS group, complete antibiotic coverage was 54 (43%); partial coverage was 41 (32%); and no coverage was 32 (25%). (B) Antibiotics were adjusted for 38 partially covered patients, and for 27 uncovered patients. mNGS, metagenomic next-generation sequencing.