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Front. Microbiol. | doi: 10.3389/fmicb.2019.00212

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

aurelie Allemann1, Julia Kraemer1, Insa Korten2, Kathryn Ramsey2, Carmen Casaulta2,  Alban Ramette1,  Andrea Endimiani1,  Philipp Latzin2 and  Markus Hilty1*
  • 1University of Bern, Switzerland
  • 2Universitätsspital Bern, Switzerland

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 analyse 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 analysed 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 characterisation of the resistome can help in clinical decision-making in patients with CF.

Keywords: functional metagenomics, Nasal swabs, Beta-lactam antibiotic, antibiotic resistance, cystic fibrosis

Received: 18 Jul 2018; Accepted: 24 Jan 2019.

Edited by:

Paolo Visca, Università degli Studi Roma Tre, Italy

Reviewed by:

Lorenza Putignani, Bambino Gesù Children Hospital (IRCCS), Italy
Annamaria Bevivino, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Italy  

Copyright: © 2019 Allemann, Kraemer, Korten, Ramsey, Casaulta, Ramette, Endimiani, Latzin and Hilty. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Markus Hilty, University of Bern, Bern, Switzerland,