Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants

Achal Dhariwal, Polona Rajar, Gabriela Salvadori, Heidi Aarø Åmdal, Dag Berild, Ola Didrik Saugstad, Drude Fugelseth, Gorm Greisen, Ulf Dahle, Kirsti Haaland and Fernanda Cristina Petersen ()
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Achal Dhariwal: University of Oslo
Polona Rajar: University of Oslo
Gabriela Salvadori: University of Oslo
Heidi Aarø Åmdal: University of Oslo
Dag Berild: Oslo University Hospital
Ola Didrik Saugstad: University of Oslo
Drude Fugelseth: Oslo University Hospital
Gorm Greisen: Copenhagen University Hospital Rigshospitalet
Ulf Dahle: Norwegian Institute of Public Health
Kirsti Haaland: Oslo University Hospital
Fernanda Cristina Petersen: University of Oslo

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8–10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.

Date: 2024
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DOI: 10.1038/s41467-024-50433-7

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