Abstract:

Objective To investigate the respiratory pathogen spectrum in patients with suspected pertussis using targeted next-generation sequencing（tNGS）. Methods Nasopharyngeal swabs and serum samples were collected from children patients with suspected pertussis in a district of Beijing from September to November 2023. Real-time polymerase chainreaction（PCR），bacterial culture of Bordetella pertussis，and tNGS were performed in nasopharyngeal swabs samples，and pertussis toxin IgG was performed in serum samples. The respiratory pathogen spectrum was analyzed based on tNGS results. Results A total of 40 nasopharyngeal swab and 40 serum samples from 40 patients of suspected pertussis were collected. The confirmed positive diagnosis rate of pertussis was 80.00%（32/40）. 22 patients could be diagnosed by pathogen-detecting methods（real-time PCR method or B. pertussis culture），while 21 patients could be diagnosed by serological testing methods. 17 patients were positive for B. pertussis targets by tNGS，and all being real-time PCR method positive patients. Pathogens number detected per sample ranged from 1 to 5 by tNGS，with B. pertussis targets ranking first or second in the number of multiple pathogen targets detected per sample. In 88.24%（15/17） of patients，two or more pathogens were detected，with haemophilusinfluenzae，staphylococcus aureus，streptococcus pneumoniae，and rhinovirus being the dominant types of pathogens. There was a positive correlation between the target concentration obtained from real-time PCR in 17 cases and the number of target reads obtained from tNGS. Conclusion NGS shows certain advantages in molecular quantitative identification during the early stages of pertussis patients and in recognizing multiple respiratory pathogens，and attention should be given to the study of mixed infections in pertussis patients.

Key words: Targeted next-generation sequencing, Pertussis, Cough, Culture method, Real-time polymerase chain reaction