Data from: Antimicrobial resistance genes and antibiotic use in chronic lung disease: A bronchoscopy study of the lower airways microbiome

Background: Antimicrobial resistance genes (ARGs) in the
respiratory microbiome are poorly characterized. We compared the presence
of ARGs in healthy controls with chronic lung disease patients in a
cross-sectional study, adjusted for time since antibiotic use.
Methods: Bronchoalveolar lavage was collected from 100 controls,
93 COPD, 13 asthma, 34 sarcoidosis, 12 idiopathic pulmonary fibrosis (IPF)
patients, and 11 patients with unclassifiable interstitial lung disease
(uILD). Participants had not used antibiotics for 14 days prior to
sampling. Shotgun metagenomic sequencing was performed with Illumina
NovaSeq. ARGs were identified using the National Database of
Antibiotic-Resistant Organisms. Sample reads were normalized to counts per
million. Results: In total, 38% of controls had at least one ARG,
compared with 51%, 39%, 65%, and 83% of COPD, asthma, sarcoidosis, and IPF
patients, respectively (p=0.01). ARGs against tetracycline (33%) were the
most common ARG class, followed by beta-lactam and macrolide resistance
(both 26%). In a logistic regression analysis adjusted for sex, age, body
composition, smoking, and antibiotics use, the OR (95% CI) for having ARGs
in the lower airways was 1.30 (0.70-2.41) in COPD, 1.00 (0.29-3.52) in
asthma, 3.52 (1.40-8.83) in sarcoidosis, and 6.40 (1.25-32.73) in IPF, and
3.27 (0.76-14.16) in uILD compared with controls. Overall mean (SD) ARG
counts per million were 403.8 (537.7) in the 35 subjects who had used
antibiotics ≤ 3 months before bronchoscopy, compared with 197.6 (355.9) in
the 228 subjects without (p=0.02).
Conclusion: The presence of ARGs in the lower
airways microbiome was significantly higher in patients with sarcoidosis
and IPF than in controls. The counts per million for ARGs was
significantly associated with recent antibiotic use.