Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life.

Allemann, Aurélie; Krämer, Julia G.; Korten, Insa; Ramsey, Kathryn; Casaulta, Carmen; Wüthrich, Daniel; Ramette, Alban Nicolas; Endimiani, Andrea; Latzin, Philipp; Hilty, Markus (2019). Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Frontiers in Microbiology, 10(212), p. 212. Frontiers 10.3389/fmicb.2019.00212

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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.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Research
04 Faculty of Medicine > Department of Gynaecology, Paediatrics and Endocrinology (DFKE) > Clinic of Paediatric Medicine

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Allemann, Aurélie, Krämer, Julia Gabriele, Korten, Insa Christina Severine, Ramsey, Kathryn Angela, Casaulta, Carmen, Wüthrich, Daniel, Ramette, Alban Nicolas, Endimiani, Andrea, Latzin, Philipp, Hilty, Markus


600 Technology > 610 Medicine & health






[4] Swiss National Science Foundation




Anette van Dorland

Date Deposited:

12 Jun 2019 16:14

Last Modified:

05 Dec 2022 15:28

Publisher DOI:


PubMed ID:


Additional Information:

Insa Korten, Kathryn Ramsey, Carmen Casaulta, Philipp Latzin: Forschungsgruppe Pneumologie (Pädiatrie), Universitätsklinik für Kinderheilkunde und Pädiatrische Pneumologie

Uncontrolled Keywords:

antibiotics beta-lactamases functional metagenomics nasal swabs resistance




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