Pre-Pandemic Distribution of Bacterial Species in Nasopharyngeal Swab Specimens from Pediatric and Adult Patients Detected via RT-PCR Using the Allplex Respiratory Panel

Background: Recently, panel-based molecular diagnostics for the simultaneous detection of respiratory viruses and bacteria in nasopharyngeal swab (NPS) specimens have been highlighted. We identified the distribution of bacterial species in NPS specimens collected from pediatric and adult patients by employing RT-PCR (Allplex respiratory panel 4, RP4, Seegene) to estimate its applicability in a panel-based assay for detecting respiratory viruses. Methods: We used 271 and 173 NPS specimens from pediatric and adult patients, respectively. The results of the Allplex RP4 panel using NPS (NPS-RP4) from adult patients were compared with those of the Seeplex PneumoBacter ACE Detection assay (Seegene), which used sputum for testing (sputum-Seeplex). Results: A total of 147 specimens (54.2%) were positive for the NPS-RP4 panel in pediatric patients. There were 94, 77, 10, 3, 3, and 2 specimens that were positive for Haemophilus influenzae (HI), Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP), Chlamydia pneumoniae (CP), Bordetella pertussis (BP), and B. parapertussis (BPP), respectively. Among 173 adult patients, 39 specimens (22.5%) were positive in the NPS-RP4. Thirty specimens were positive for HI, and 13 were positive for SP. One specimen tested positive for both MP and Legionella pneumophila (LP). CP, BP, and BPP results were all negative. However, 126 specimens (72.8%) had positive results with sputum-Seeplex (99 SP, 59 HI, three LP, and two MP), and the overall percentage of agreement between the two assays was 39.3% in the adult patients. Conclusions: Bacterial species in NPS from more than half of pediatric patients were detected. Performing the Allplex RP4 assay with NPS revealed additional respiratory bacteria that are not detected in current clinical practices, which do not include bacterial testing, demanding the use of sputum specimens. However, the use of NPS showed low agreement with standard assays using sputum in adult patients. Thus, more research is needed to develop a reliable RT-PCR method using NPS specimens in adult patients.