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

doi:10.3390/life13091840

. 2023 Aug 30;13(9):1840.

doi: 10.3390/life13091840.

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

Dong-Hyun Lee¹, Young-Jin Choi², Jieun Kim³, Eunhee Han⁴, Mi-Hyun Bae⁵

Affiliations

¹ Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju 52727, Republic of Korea.
² Department of Pediatrics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea.
³ Division of Infectious Disease, Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea.
⁴ Department of Laboratory Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea.
⁵ Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea.

PMID: 37763244
PMCID: PMC10532938
DOI: 10.3390/life13091840

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

Dong-Hyun Lee et al. Life (Basel). 2023.

. 2023 Aug 30;13(9):1840.

doi: 10.3390/life13091840.

Authors

Dong-Hyun Lee¹, Young-Jin Choi², Jieun Kim³, Eunhee Han⁴, Mi-Hyun Bae⁵

Affiliations

¹ Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju 52727, Republic of Korea.
² Department of Pediatrics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea.
³ Division of Infectious Disease, Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea.
⁴ Department of Laboratory Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea.
⁵ Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea.

PMID: 37763244
PMCID: PMC10532938
DOI: 10.3390/life13091840

Abstract

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.

Keywords: Allplex respiratory panel; RT-PCR; bacteria; nasopharyngeal swab; panel-based assay; respiratory infection.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Prevalence of bacterial species in the different age groups of pediatric patients. Overall prevalence was the highest in the 2–4-year age group (70.3%). The most prevalent species in the <2-year age group was *S. pneumoniae* (25.5%) and *H. influenzae* in the 2–4-year (47.3%) and 5–17-year age groups (37.2%). The prevalence of *M. pneumoniae* was the highest in the 5–17-year age group (6.4%).

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References

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1. Mandelia Y., Procop G.W., Richter S.S., Worley S., Liu W., Esper F. Dynamics and predisposition of respiratory viral co-infections in children and adults. Clin. Microbiol. Infect. 2021;27:631.e1–631.e6. doi: 10.1016/j.cmi.2020.05.042. - DOI - PubMed
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1. Berg A.S., Inchley C.S., Fjaerli H.O., Leegaard T.M., Lindbaek M., Nakstad B. Clinical features and inflammatory markers in pediatric pneumonia: A prospective study. Eur. J. Pediatr. 2017;176:629–638. doi: 10.1007/s00431-017-2887-y. - DOI - PubMed

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[1] Liu L., Oza S., Hogan D., Chu Y., Perin J., Zhu J., Lawn J.E., Cousens S., Mathers C., Black R.E. Global, regional, and national causes of under-5 mortality in 2000-15: An updated systematic analysis with implications for the Sustainable Development Goals. Lancet. 2016;388:3027–3035. doi: 10.1016/S0140-6736(16)31593-8. - DOI - PMC - PubMed

[2] Liu L., Oza S., Hogan D., Chu Y., Perin J., Zhu J., Lawn J.E., Cousens S., Mathers C., Black R.E. Global, regional, and national causes of under-5 mortality in 2000-15: An updated systematic analysis with implications for the Sustainable Development Goals. Lancet. 2016;388:3027–3035. doi: 10.1016/S0140-6736(16)31593-8. - DOI - PMC - PubMed

[3] Choe Y.J., Choe S.A., Cho S.I. Trends in Infectious Disease Mortality, South Korea, 1983–2015. Emerg. Infect. Dis. 2018;24:320–327. doi: 10.3201/eid2402.170862. - DOI - PMC - PubMed

[4] Choe Y.J., Choe S.A., Cho S.I. Trends in Infectious Disease Mortality, South Korea, 1983–2015. Emerg. Infect. Dis. 2018;24:320–327. doi: 10.3201/eid2402.170862. - DOI - PMC - PubMed

[5] Mandelia Y., Procop G.W., Richter S.S., Worley S., Liu W., Esper F. Dynamics and predisposition of respiratory viral co-infections in children and adults. Clin. Microbiol. Infect. 2021;27:631.e1–631.e6. doi: 10.1016/j.cmi.2020.05.042. - DOI - PubMed

[6] Mandelia Y., Procop G.W., Richter S.S., Worley S., Liu W., Esper F. Dynamics and predisposition of respiratory viral co-infections in children and adults. Clin. Microbiol. Infect. 2021;27:631.e1–631.e6. doi: 10.1016/j.cmi.2020.05.042. - DOI - PubMed

[7] Brealey J.C., Sly P.D., Young P.R., Chappell K.J. Viral bacterial co-infection of the respiratory tract during early childhood. FEMS Microbiol. Lett. 2015;362:fnv062. doi: 10.1093/femsle/fnv062. - DOI - PubMed

[8] Brealey J.C., Sly P.D., Young P.R., Chappell K.J. Viral bacterial co-infection of the respiratory tract during early childhood. FEMS Microbiol. Lett. 2015;362:fnv062. doi: 10.1093/femsle/fnv062. - DOI - PubMed

[9] Berg A.S., Inchley C.S., Fjaerli H.O., Leegaard T.M., Lindbaek M., Nakstad B. Clinical features and inflammatory markers in pediatric pneumonia: A prospective study. Eur. J. Pediatr. 2017;176:629–638. doi: 10.1007/s00431-017-2887-y. - DOI - PubMed

[10] Berg A.S., Inchley C.S., Fjaerli H.O., Leegaard T.M., Lindbaek M., Nakstad B. Clinical features and inflammatory markers in pediatric pneumonia: A prospective study. Eur. J. Pediatr. 2017;176:629–638. doi: 10.1007/s00431-017-2887-y. - DOI - PubMed

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

Affiliations

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

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Affiliations

Abstract

Conflict of interest statement

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