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. 2022 Nov 17;22(1):860.
doi: 10.1186/s12879-022-07851-z.

Bacterial colonization of the upper airways of children positive and negative for SARS-CoV-2 during the COVID-19 pandemic

Vincentia Rizke Ciptaningtyas  1   2   3 , Rebriarina Hapsari  4   5 , Endang Sri Lestari  4   5 , Helmia Farida  4   5 , Quirijn de Mast  6 , Marinus Isaäk de Jonge  7
Affiliations

Bacterial colonization of the upper airways of children positive and negative for SARS-CoV-2 during the COVID-19 pandemic

Vincentia Rizke Ciptaningtyas et al. BMC Infect Dis. .

Abstract

Background: Our understanding of the influence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bacterial colonization in the children's upper nasopharyngeal tract during the coronavirus infectious disease (COVID-19) pandemic is limited. This study aimed to determine whether there were any differences in bacterial colonization between asymptomatic children with or without a positive SARS-CoV-2 quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) results in the community setting.

Methods: A cross-sectional community-based exploratory study was conducted from March to May 2021 in Semarang, Central Java Province, Indonesia. Using stored nasopharyngeal swabs collected from children under 18 years as a contact tracing program, we performed a real-time quantitative (qPCR) for the most important bacterial colonizing pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Klebsiella pneumoniae.

Results: Swabs from a total of 440 children were included in this study, of which 228 (51.8%) were RT-qPCR-confirmed SARS-CoV-2 positive. In the 440 children, colonization rates were highest for H. influenzae (61.4%), followed by S. pneumoniae (17.5%), S. aureus (12.0%), and K. pneumoniae (1.8%). The co-occurrence of both S. pneumoniae and H. influenzae in the upper respiratory tract was significantly associated with a SARS-CoV-2 negative RT-qPCR. In contrast, colonization with only S. aureus was more common in SARS-CoV-2-positive children.

Conclusion: Overall, this exploratory study concludes that there is a significant difference in the bacterial nasopharyngeal colonization pattern between SARS-CoV-2 positive and negative in asymptomatic children in the community in Indonesia.

Keywords: Bacterial colonization; COVID-19 pandemic; Children; Indonesia.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Cq value distribution among isolated bacteria. Violin plot representation of Cq value of S. aureus, S. pneumoniae, K. pneumoniae, and H. influenzae from positive samples (Cq values < 40)
See this image and copyright information in PMC

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