A. ALLEMANN¹, M. MIKA¹, I. KORTEN², P. LATZIN², C. CASAULTA², M. HILTY<sup>1

1</sup>Institute for Infectious Diseases, University of Bern, Bern, Switzerland, ²Division of Respiratory Medicine, Department of Pediatrics, Inselspital and University of Bern, Bern, Switzerland

Patients with cystic fibrosis (CF) have a rich microbial colonization of the respiratory tract, contract early frequent respiratory infections and receive multiple antibiotic treatments. The influence of antibiotic therapies on microbiota and its resistance genes reservoir (the resistome) is poorly understood. While resistance mechanisms of single pathogens are routinely investigated, other bacteria may secret metabolites (i.e. β-lactamase) and provide a cross-protection to potential pathogens. Therefore, we aim to describe the microbiota profile and resistome of the upper respiratory tract in infants with CF within the first year of life using culture-independent methods.

Samples were selected from a collection of nasal swabs taken bi-weekly from patients with CF during their first year of life. DNA was extracted and microbiota characterization was performed using 16S pyrosequencing. For the functional detection of antibiotic resistance genes, large fragments of genomic DNA (2-9kb) were cloned and expressed into E. coli. Resistant clones were recovered by culturing against different antibiotics. The genes conferring resistance were identified by sequencing.

Up to now, we have investigated the dynamics of the resistome in one infant with CF over the first year of life. Profiling of the microbiota composition showed substantial increase in the bacterial diversity after antibiotic administration (Shannon Diversity Index). A gene with 91% similarity with a class A β-lactamase was identified in a sample collected subsequent to amoxicillin-clavulanic acid administration. The genes blaZ, folA and lytA, which are frequently observed in Staphylococcus aureus, were identified as genes conferring resistance towards ampicillin and cotrimoxazole (TMP-SMX), respectively.

Within this pilot study, using culture-independent methods, we observed an increase in the bacterial diversity and changes in the resistome of the nasal microbiota from a child with CF after antibiotics administrations. Information about the resistome may have the potential to optimize antibiotic treatment regimes in patients with CF.