Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing.

Yuping Song,Haoyi Weng,Agnes Sze Yin Leung,Man Fung Tang,Renee Wan Yi Chan,Gary Wing Kin Wong,Kin Pong Tao,Stephen Kwok Wing Tsui,Jamie Sui Lam Kwok,Ting Fan Leung,Maggie Haitian Wang,Jinpao Hou

doi:10.3389/fmicb.2021.792556

Abstract

Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that Moraxella catarrhalis and Dolosigranulum pigrum were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; Padj = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed D. pigrum was the only discriminative species across groups (LDA = 5.57, P = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively (P < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of D. pigrum. Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.

Highlights

MATERIALS AND METHODSPre-school age is a critical period for the occurrence of recurrent wheeze (RW) which is a strong risk factor for asthma
This study applied whole genome shotgun (WGS) to characterize the nasopharyngeal microbiome (NPM) in pre-school children hospitalized for RW who were positive for asthma predictive index (API), and explore the differences in NPM compositions and functional capabilities between RW cases and control groups and the possible effect of human rhinovirus (HRV) infection on such associations between NPM and pre-school wheezing
Three groups of Chinese pre-school children aged 2–5 years old were recruited: (a) children hospitalized for RW who were positive for stringent-asthma predictive index (S-API) (CastroRodríguez et al, 2000); (b) inpatient control (IC) children hospitalized for upper respiratory tract infection (URTI) with no respiratory distress, normal auscultation and chest radiograph, and no history of wheeze and asthma

Summary

MATERIALS AND METHODS

Pre-school age is a critical period for the occurrence of recurrent wheeze (RW) which is a strong risk factor for asthma. This study applied WGS to characterize the NPM in pre-school children hospitalized for RW who were positive for asthma predictive index (API), and explore the differences in NPM compositions and functional capabilities between RW cases and control groups and the possible effect of HRV infection on such associations between NPM and pre-school wheezing. Three groups of Chinese pre-school children aged 2–5 years old were recruited: (a) children hospitalized for RW who were positive for stringent-asthma predictive index (S-API) (CastroRodríguez et al, 2000); (b) inpatient control (IC) children hospitalized for upper respiratory tract infection (URTI) with no respiratory distress, normal auscultation and chest radiograph, and no history of wheeze and asthma These IC subjects were matched for gender and admission time (hospitalized within 1 week from the RW case recruitment) with RW patients; (c) CC children from nurseries and kindergartens who participated in our influenza surveillance study (Leung et al, 2017). P < 0.05 was set as the significance threshold

RESULTS

DISCUSSION

ETHICS STATEMENT

Findings

CONCLUSION