Childhood lower respiratory tract infections linked to residential airborne bacterial and fungal microbiota
Fakunle, Adekunle G; Jafta, Nkosana; Bossers, Alex; Wouters, Inge M; Kersen, Warner van; Naidoo, Rajen N; Smit, Lidwien A M
(2023) Environmental Research, volume 231, issue Pt 1
(Article)
Abstract
Residential microbial composition likely contributes to the development of lower respiratory tract infections (LRTI) among children, but the association is poorly understood. We aimed to study the relationship between the indoor airborne dust bacterial and fungal microbiota and childhood LRTI in Ibadan, Nigeria. Ninety-eight children under the age of five
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years hospitalized with LRTI were recruited and matched by age (±3 months), sex, and geographical location to 99 community-based controls without LRTI. Participants’ homes were visited and sampled over a 14-day period for airborne house dust using electrostatic dustfall collectors (EDC). In airborne dust samples, the composition of bacterial and fungal communities was characterized by a meta-barcoding approach using amplicons targeting simultaneously the bacterial 16S rRNA gene and the internal-transcribed-spacer (ITS) region-1 of fungi in association with the SILVA and UNITE database respectively. A 100-unit change in house dust bacterial, but not fungal, richness (OR 1.06; 95%CI 1.03–1.10) and a 1-unit change in Shannon diversity (OR 1.92; 95%CI 1.28–3.01) were both independently associated with childhood LRTI after adjusting for other indoor environmental risk factors. Beta-diversity analysis showed that bacterial (PERMANOVA p < 0.001, R2 = 0.036) and fungal (PERMANOVA p < 0.001, R2 = 0.028) community composition differed significantly between homes of cases and controls. Pair-wise differential abundance analysis using both DESEq2 and MaAsLin2 consistently identified the bacterial phyla Deinococcota (Benjamini-Hochberg (BH) adjusted p-value <0.001) and Bacteriodota (BH-adjusted p-value = 0.004) to be negatively associated with LRTI. Within the fungal microbiota, phylum Ascomycota abundance (BH adjusted p-value <0.001) was observed to be directly associated with LRTI, while Basidiomycota abundance (BH adjusted p-value <0.001) was negatively associated with LRTI. Our study suggests that early-life exposure to certain airborne bacterial and fungal communities is associated with LRTI among children under the age of five years.
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Keywords: Indoor microbiota, Lower respiratory tract infections, Under-five children, High-throughput sequencing, Sub-saharan africa
ISSN: 0013-9351
Publisher: Academic Press Inc.
Note: Funding Information: The study was supported by the European Respiratory Society – ERS Short-term Research Fellowship April 2020 (STRF April 2020)- STRTF202004-00799. Also, we acknowledge the support received from the College of Health (CHS) PhD Scholarship of the University of KwaZulu-Natal, South Africa and the Institute of Risk Assessment, Utrecht University The Netherlands.We acknowledge the support received from the College of Health (CHS) PhD Scholarship of the University of KwaZulu-Natal, South Africa and the Institute of Risk Assessment, Utrecht University, The Netherlands. We also appreciate the contributions of the IRAS laboratory technicians (Gijs van Riel, Hadassa van Hoorn, Peter Scherpenisse, Jack Spithoven and Monique Tersteeg - Zijderveld) who assisted with DNA extractions and Jack Spithoven for providing assistance with the transportation of the EDCs. Funding Information: The study was supported by the European Respiratory Society – ERS Short-term Research Fellowship April 2020 (STRF April 2020)- STRTF202004-00799 . Also, we acknowledge the support received from the College of Health (CHS) PhD Scholarship of the University of KwaZulu-Natal, South Africa and the Institute of Risk Assessment , Utrecht University The Netherlands . Funding Information: We acknowledge the support received from the College of Health (CHS) PhD Scholarship of the University of KwaZulu-Natal, South Africa and the Institute of Risk Assessment, Utrecht University, The Netherlands . We also appreciate the contributions of the IRAS laboratory technicians (Gijs van Riel, Hadassa van Hoorn, Peter Scherpenisse, Jack Spithoven and Monique Tersteeg - Zijderveld) who assisted with DNA extractions and Jack Spithoven for providing assistance with the transportation of the EDCs. Publisher Copyright: © 2023 Elsevier Inc.
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