The use of multiplex PCR for the detection of atypical pathogens in Egyptian children with CAP: a high rate of Bordetella pertussis in early infancy

Noussa R. El Basha, Hala H. Shaaban, Hassan A. El Atroush, May M. Sherif, Amani A. El Kholy

Atypical pathogen infections played an important role in community-acquired pneumonia (CAP) in children. Pathogen-specific clinical symptoms are often lacking, and it is difficult to detect atypical pathogens by culture methods. The use of multiplex polymerase chain reaction (PCR) methods enables testing for many pathogens simultaneously in a single analysis. To determine the role of atypical pathogens in children hospitalized with CAP. This cross-sectional study was conducted throughout a 2-year period from August 2015 to September 2017. It included 400 Egyptian children hospitalized with clinical diagnosis of CAP at a tertiary hospital in Cairo, Egypt. Sputum samples were collected from lower respiratory tract of all enrolled patients by mucus trap catheter for identification of Bordetella pertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophilia by using multiplex real-time PCR. Among the 400 CAP patients enrolled in this study, atypical pathogens were detected in 12/400 (3%) patients. Bordetella pertussis was detected in 2% of cases, and it was responsible for CAP in 8/104 (7.69%) infants in the age stratum ≤ 4 months; compared with pertussis-negative cases, pertussis-positive cases were younger and incompletely vaccinated (P values were 0.001 and 0.007, respectively). Mycoplasma pneumoniae was detected in 1% of cases, all were among the age stratum > 4 months ≤ 59 months in 4/272 (1.47%) children. In early infancy, Bordetella pertussis causes a significant proportion of hospitalized CAP cases; all were ≤ 4 months old and incompletely vaccinated. This finding could suggest the role of maternal immunization in developing countries.