Metagenomic analysis reveals the abundance and diversity of ARGs in children's respiratory tract microbiomes

The correlation of respiratory microbiome and respiratory infections is frequently reported [ 1 Unger S.A. et al. The respiratory microbiome and respiratory infections. J Infection. 2017; 74: S84-S88 Abstract Full Text PDF PubMed Scopus (47) Google Scholar , 2 Eun B.W. et al. Mycoplasma pneumoniae in Korean children: the epidemiology of pneumonia over an 18-year period. J Infection. 2008; 56: 326-331 Abstract Full Text Full Text PDF PubMed Scopus (57) Google Scholar , 3 Toivonen L. et al. Respiratory syncytial virus infections in children 0-24 months of age in the community. J Infection. 2019; https://doi.org/10.1016/j.jinf.2019.09.002 Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar ], while different levels of the microbes in the respiratory microbiota is a leading cause of high morbidity and mortality. The respiratory metagenomic analysis illustrated that a significant difference between healthy children and children with pneumonia [ 4 Dai W. et al. An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia. Gigascience. 2019; 8 Crossref Scopus (9) Google Scholar ]. The emergence of plasmid-mediated antibiotic resistance (e.g., carbapenemases and mobile colistin resistance (mcr) genes) in respiratory microorganisms [ 5 David S. et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nature Microbiol. 2019; 4: 1919-1929 Crossref PubMed Scopus (275) Google Scholar , 6 Berglund B. et al. Colistin- and carbapenem-resistant Klebsiella pneumoniae carrying mcr-1 and blaOXA-48 isolated at a paediatric hospital in Vietnam. The J Antimicrobial Chemotherapy. 2017; PubMed Google Scholar ], has caused great attention in recent years. It is therefore critical to identify priority areas (respiratory microbiomes) on which to intensify public health intervention strategies [ 5 David S. et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nature Microbiol. 2019; 4: 1919-1929 Crossref PubMed Scopus (275) Google Scholar ]. Here we analyzed the children's respiratory tract metagenomes, including 171 healthy children and 76 children with pneumonia, to reveal the abundance and diversity of antibiotic resistance genes (ARGs) using the Comprehensive Antibiotic Resistance Database (CARD) [ 7 Jia B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017; 45: D566-D573 Crossref PubMed Scopus (1269) Google Scholar ] with 100% amino acid identity.