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Front Microbiol. 2019 Feb 26;10:212. doi: 10.3389/fmicb.2019.00212. eCollection 2019.

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

Author information

1
Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
2
Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
3
Institute for Work and Health (IST), University of Lausanne and University of Geneva, Epalinges, Switzerland.
4
Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland.
5
Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland.
6
Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.

Abstract

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.

KEYWORDS:

antibiotics; beta-lactamases; functional metagenomics; nasal swabs; resistance

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