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-Suter & 7 others Nicolas Regamey, Isabelle Rochat, Florian Singer, Renate Spinas, Daniel Trachsel, Sophie Yammine, Maura Zanolari

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number00212
JournalFrontiers in Microbiology
Volume10
Issue numberFEB
DOIs
Publication statusPublished - 26 Feb 2019
Externally publishedYes

Fingerprint

Child Development
Nose
Cystic Fibrosis
Anti-Bacterial Agents
Microbiota
Nanopores
Phenotype
Metagenomics
Amoxicillin-Potassium Clavulanate Combination
Lactams
Cefuroxime
Sulfamethoxazole Drug Combination Trimethoprim
Chloramphenicol
Ampicillin
Microbial Drug Resistance
Tetracycline
Coinfection
Respiratory System
Clone Cells
Bacteria

Cite this

Allemann, A., Kraemer, J. G., Korten, I., Ramsey, K., Casaulta, C., Wüthrich, D., ... Zanolari, M. (2019). Nasal resistome development in infants with cystic fibrosis in the first year of life. Frontiers in Microbiology, 10(FEB), [00212]. https://doi.org/10.3389/fmicb.2019.00212
Allemann, Aurélie ; Kraemer, Julia G. ; Korten, Insa ; Ramsey, Kathryn ; Casaulta, Carmen ; Wüthrich, Daniel ; Ramette, Alban ; Endimiani, Andrea ; Latzin, Philipp ; Hilty, Markus ; Barben, Jürg ; Casaulta, Carmen ; Jung, Andreas ; Kieninger, Elisabeth ; Korten, Insa ; Latzin, Philipp ; Moeller, Alexander ; Mornand, Anne ; Hafen, Gaudenz ; Müller-Suter, Dominik ; Regamey, Nicolas ; Rochat, Isabelle ; Singer, Florian ; Spinas, Renate ; Trachsel, Daniel ; Yammine, Sophie ; Zanolari, Maura. / Nasal resistome development in infants with cystic fibrosis in the first year of life. In: Frontiers in Microbiology. 2019 ; Vol. 10, No. FEB.
@article{d472d7a4875e41b791b72e11485ada29,
title = "Nasal resistome development in infants with cystic fibrosis in the first year of life",
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 na{\"i}ve 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",
author = "Aur{\'e}lie Allemann and Kraemer, {Julia G.} and Insa Korten and Kathryn Ramsey and Carmen Casaulta and Daniel W{\"u}thrich and Alban Ramette and Andrea Endimiani and Philipp Latzin and Markus Hilty and J{\"u}rg Barben and Carmen Casaulta and Andreas Jung and Elisabeth Kieninger and Insa Korten and Philipp Latzin and Alexander Moeller and Anne Mornand and Gaudenz Hafen and Dominik M{\"u}ller-Suter and Nicolas Regamey and Isabelle Rochat and Florian Singer and Renate Spinas and Daniel Trachsel and Sophie Yammine and Maura Zanolari",
year = "2019",
month = "2",
day = "26",
doi = "10.3389/fmicb.2019.00212",
language = "English",
volume = "10",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media SA",
number = "FEB",

}

Allemann, A, Kraemer, JG, Korten, I, Ramsey, K, Casaulta, C, Wüthrich, D, Ramette, A, Endimiani, A, Latzin, P, Hilty, M, Barben, J, Casaulta, C, Jung, A, Kieninger, E, Korten, I, Latzin, P, Moeller, A, Mornand, A, Hafen, G, Müller-Suter, D, Regamey, N, Rochat, I, Singer, F, Spinas, R, Trachsel, D, Yammine, S & Zanolari, M 2019, 'Nasal resistome development in infants with cystic fibrosis in the first year of life' Frontiers in Microbiology, vol. 10, no. FEB, 00212. https://doi.org/10.3389/fmicb.2019.00212

Nasal resistome development in infants with cystic fibrosis in the first year of life. / Allemann, Aurélie; Kraemer, Julia G.; Korten, Insa; Ramsey, Kathryn; Casaulta, Carmen; Wüthrich, Daniel; Ramette, Alban; Endimiani, Andrea; Latzin, Philipp; Hilty, Markus; Barben, Jürg; Casaulta, Carmen; Jung, Andreas; Kieninger, Elisabeth; Korten, Insa; Latzin, Philipp; Moeller, Alexander; Mornand, Anne; Hafen, Gaudenz; Müller-Suter, Dominik; Regamey, Nicolas; Rochat, Isabelle; Singer, Florian; Spinas, Renate; Trachsel, Daniel; Yammine, Sophie; Zanolari, Maura.

In: Frontiers in Microbiology, Vol. 10, No. FEB, 00212, 26.02.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Nasal resistome development in infants with cystic fibrosis in the first year of life

AU - Allemann, Aurélie

AU - Kraemer, Julia G.

AU - Korten, Insa

AU - Ramsey, Kathryn

AU - Casaulta, Carmen

AU - Wüthrich, Daniel

AU - Ramette, Alban

AU - Endimiani, Andrea

AU - Latzin, Philipp

AU - Hilty, Markus

AU - Barben, Jürg

AU - Casaulta, Carmen

AU - Jung, Andreas

AU - Kieninger, Elisabeth

AU - Korten, Insa

AU - Latzin, Philipp

AU - Moeller, Alexander

AU - Mornand, Anne

AU - Hafen, Gaudenz

AU - Müller-Suter, Dominik

AU - Regamey, Nicolas

AU - Rochat, Isabelle

AU - Singer, Florian

AU - Spinas, Renate

AU - Trachsel, Daniel

AU - Yammine, Sophie

AU - Zanolari, Maura

PY - 2019/2/26

Y1 - 2019/2/26

N2 - 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.

AB - 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.

KW - Antibiotics

KW - Beta-lactamases

KW - Functional metagenomics

KW - Nasal swabs

KW - Resistance

UR - http://www.scopus.com/inward/record.url?scp=85066131996&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2019.00212

DO - 10.3389/fmicb.2019.00212

M3 - Article

VL - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - FEB

M1 - 00212

ER -