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 language | English |
|---|---|
| Article number | 00212 |
| Journal | Frontiers in Microbiology |
| Volume | 10 |
| Issue number | FEB |
| DOIs | |
| Publication status | Published - 26 Feb 2019 |
| Externally published | Yes |
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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 journal › Article
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 -