Genetic characterization of Mycoplasma pneumoniae in patients using clinical metagenomic next-generation sequencing data

Backgroud: This study aimed to utilize clinical metagenomic next-generation sequencing (mNGS) data to analyze the genomic characteristics of Mycoplasma pneumoniae (M. pneumoniae), thereby providing guidance for disease surveillance, prevention and control. Methods: Clinical samples were sequenced and subjected to mNGS on a MGISEQ-200 sequencer platform using 50bp single-end (SE50) mode. The metagenomic data of samples identified with M. pneumoniae infection (sequence coverage >90%) were de novo assembled for genome comparison, molecular typing and phylogenetic analysis. Results: Of the three genomes de novo assembled, two with high-quality sequences were analyzed. Genome comparison indicated that the inconsistent regions of the genome were mainly located on the repetitive DNA elements of M. pneumoniae. Genotyping revealed that the two characterized samples, one belonged to ST3 (P1 type 1), while the other was typed to ST7 (P1 type 2). In addition, the phylogenetic tree was constructed successfully with credible bootstrap values. Conclusion: The clinical mNGS using SE50 strategy could be used for M. pneumoniae detection in patients with low cost and short turnaround time. Meanwhile, the sequencing data could be used for genotyping and genetic characterization of M. pneumoniae as well if the sequence coverage and depth were high enough.