Nasal resistome development in infants with cystic fibrosis in the first year of life

Aurélie Allemann, Julia G. Kraemer, Insa Korten, Kathryn Ramsey, Carmen Casaulta, Daniel Wüthrich, Alban Ramette, Andrea Endimiani, Philipp Latzin, Markus Hilty, Jürg Barben, Carmen Casaulta, Andreas Jung, Elisabeth Kieninger, Insa Korten, Philipp Latzin, Alexander Moeller, Anne Mornand, Gaudenz Hafen, Dominik Müller-SuterNicolas Regamey, Isabelle Rochat, Florian Singer, Renate Spinas, Daniel Trachsel, Sophie Yammine, Maura Zanolari

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5 Citations (Scopus)


Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non- susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.

Original languageEnglish
Article number212
JournalFrontiers in Microbiology
Issue numberFEB
Publication statusPublished - 26 Feb 2019
Externally publishedYes


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