Multilocus amplicon sequencing of Pseudomonas aeruginosa cystic fibrosis airways isolates collected prior to and after early antipseudomonal chemotherapy.
BACKGROUND
Early antimicrobial chemotherapy can prevent or at least delay chronic cystic fibrosis (CF) airways infections with Pseudomonas aeruginosa.


METHODS
During a 10-year study period P. aeruginosa was detected for the first time in 54 CF patients regularly seen at the CF centre Hannover. Amplicon sequencing of 34 loci of the P. aeruginosa core genome was performed in baseline and post-treatment isolates of the 15 CF patients who had remained P. aeruginosa - positive after the first round of antipseudomonal chemotherapy.


RESULTS
Deep sequencing uncovered coexisting alternative nucleotides at in total 33 of 55,284 examined genome positions including six non-synonymous polymorphisms in the lasR gene, a key regulator of quorum sensing. After early treatment 42 of 50 novel nucleotide substitutions had emerged in exopolysaccharide biosynthesis, efflux pump and porin genes.


CONCLUSIONS
Early treatment selects pathoadaptive mutations in P. aeruginosa that are typical for chronic infections of CF lungs.
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
Sebastian
S
Fischer
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
Leonie
L
Greipel
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
Jens
J
Klockgether
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
Marie
M
Dorda
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
Lutz
L
Wiehlmann
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
Nina
N
Cramer
Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany. Electronic address: tuemmler.burkhard@mh-hannover.de.
Burkhard
B
Tümmler
D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics; D015373:Bacterial Typing Techniques / Q000379:methods; D002648:Child; D002908:Chronic Disease; D003550:Cystic Fibrosis / Q000150:complications / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology; D016903:Drug Monitoring / Q000379:methods; D005260:Female; D005858:Germany / Q000453:epidemiology; D006801:Humans; D007223:Infant; D008297:Male; D058885:Multilocus Sequence Typing / Q000379:methods; D011552:Pseudomonas Infections / Q000175:diagnosis / Q000209:etiology / Q000503:physiopathology; D011550:Pseudomonas aeruginosa / Q000187:drug effects / Q000302:isolation & purification / Q000502:physiology; D061665:Time-to-Treatment; D055815:Young Adult
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins
Amplicon sequencing; Cystic fibrosis; Early antipseudomonal treatment; Pseudomonas aeruginosa; Single nucleotide polymorphism