Comprehensive virome analysis of the viral spectrum in paediatric patients diagnosed with Mycoplasma pneumoniae pneumonia

Qiong Guo; Lili Li; Chao Wang; Yiman Huang; Fenlian Ma; Shanshan Cong; Jingjing Tan; Lihong Yao; Aijun Chen; Lishu Zheng

doi:10.1186/s12985-022-01914-y

Comprehensive virome analysis of the viral spectrum in paediatric patients diagnosed with Mycoplasma pneumoniae pneumonia

Virol J. 2022 Nov 9;19(1):181. doi: 10.1186/s12985-022-01914-y.

Authors

Qiong Guo^{1

2}, Lili Li¹, Chao Wang¹, Yiman Huang¹, Fenlian Ma¹, Shanshan Cong¹, Jingjing Tan¹, Lihong Yao¹, Aijun Chen¹, Lishu Zheng³

Affiliations

¹ NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.
² Institute for HIV/AIDS and STD Prevention and Control, Beijing Center for Disease Prevention and Control, Beijing, China.
³ NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China. zhengls@ivdc.chinacdc.cn.

Abstract

Background: Among hospitalized children suffering from community-acquired pneumonia, Mycoplasma pneumoniae (MP) is one of the most common pathogens. MP often exists as a co-infection with bacteria or viruses, which can exacerbate the clinical symptoms. We investigated the pathogen spectrum in MP-positive and MP-negative samples from hospitalized children with respiratory tract infections in Beijing, China.

Method: This study included 1038 samples of nasopharyngeal aspirates obtained between April, 2017 and March, 2018 from hospitalized children under 6 years of age with respiratory tract infections. To explore the impact of MP infection on the composition of the pathogen spectrum, 185 nasopharyngeal aspirates (83 MP-positive/102 MP-negative) were randomly selected for next-generation sequencing and comprehensive metagenomics analysis. Real-time PCR was used to detect and verify common respiratory viruses.

Results: Of the 1038 samples, 454 (43.7%) were infected with MP. In children < 6 years of age, the MP infection rate gradually increased with age, with the highest rate of 74.2% in 5-6-year-olds. The results of metagenomics analysis revealed 11 human, animal and plant virus families, and bacteriophages, including common respiratory viruses, enteroviruses and anelloviruses. The virus family with the highest number of reads in both MP-positive and MP-negative samples was the Pneumoviridae, and the number of reads for human respiratory syncytial virus (HRSV) in MP-positive samples was higher than that in MP-negative samples. Among the 83 MP-positive samples, 47 (56.63%) were co-infected with viruses, the most common of which was influenza virus (IFV). The durations of hospitalization and fever were higher in patients with MP co-infection than MP single infection, but the difference was not statistically significant.

Conclusion: The viral family with the highest number of reads in both groups was Pneumoviridae, and the number of reads matched to HRSV in MP-positive samples was much higher than MP-negative samples. Co-infection of MP and IFV infection were the most cases.

Keywords: Metagenomics analysis; Mycoplasma pneumoniae; Next-generation sequencing; Pathogen spectrum; Respiratory virus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Child
Child, Preschool
Coinfection*
Humans
Infant
Mycoplasma pneumoniae / genetics
Pneumonia, Mycoplasma* / diagnosis
Pneumonia, Mycoplasma* / epidemiology
Respiratory Syncytial Virus, Human*
Respiratory Tract Infections*
Virome
Viruses* / genetics