Impact of antibiotics on the respiratory microbiome in CRDs

AntibioticSample analysedType of treatmentImpact of antibiotics on diversity of the microbiomeImpact on relative abundance of bacterial taxaDiseaseReference
Association of different antibiotic class in treatment of CF exacerbation episodesSputumDiverse antibiotic treatments for a course of 8–9 years↓ α-diversity (inverse Simpson index)CF[30]
SputumDiverse antibiotics used for the treatment of acute PEx↑ Species richness through PEx and treatment periods, but return to the baseline state during recovery periodPrevotella melaninogenica and Streptococcus sanguinis
Veillonella parvula during treatment period, but return to baseline state in post-recovery samples
SputumDiverse antibiotics used for the treatment of acute PExEither very little change through exacerbation cycle or return to baseline state on the post-recovery sampleNo taxa modification associated with clinical stage, including treatmentCF[32]
Oral macrolidesOropharyngeal swab12 months of twice daily oral doses of 400 mg of erythromycinNo impact on α-diversity measuresDifference between treated and placebo groups:
Actinomyces and Streptococcus
Haemophilus after 48 weeks of treatment
Oropharyngeal swab6 months of 250 mg daily azithromycin for 5 days and then 250 mg 3 times per weekImpact on β-diversity measuresFusobacteria
Firmicutes during treatment compared with untreated group, but return to pre-treatment state after a 1-month washout period
Severe asthma[34]
Sputum12 months of low-dose azithromycin↓ Faith's phylogenetic diversity↓ Gammaproteobacteria (including H. influenzae) after 48 weeks of azithromycin treatment compared with placebo groupSevere asthma[35]
Bronchoalveolar  lavage of the right upper lung lobe6 weeks of low-dose azithromycin↓ Shannon's diversity indexPrevotella, Staphylococcus and Haemophilus
Anaerococcus between pre- and post-treatment state
Moderate and severe asthma[36]
SputumLow-dose erythromycinIncrease of genus richness between baseline and 48 weeks in treated group but no difference with placebo groupNo change in composition of airway microbiome in P. aeruginosa-dominated subgroup
H. influenzae and ↑ P. aeruginosa in non-P. aeruginosa-dominated subgroup
SputumTreatment of exacerbations exclusively by antibiotics (without addition of corticosteroids) (two treatments azithromycin, one by ofloxacin, one by trimethoprim-sulfamethoxazole)↓ of multiple taxa, mainly ProteobacteriaCOPD[38]
β-lactamsNasal swabsVarious courses of treatments of several weeks, mostly (71%) β-lactams↑ Shannon's diversity indexMoraxellaceae
↑ other bacterial families (this increase was verified after more than one antibiotic treatment)
Bronchoalveolar lavage,  sputum or deep throat swabsCourses of treatment including β-lactams (25 of 31 involving a single β-lactam molecule) for acute PEx↓ α-diversity between exacerbation and treatment
↓ α-diversity at therapeutic doses between baseline and treatment
↑ α-diversity at sub-therapeutic doses at the same time points
Haemophilus, Clostridiales and Lachnospiraceae
Fusobacterium and Pseudomonas in the group treated at therapeutic doses between baseline and treatment samples
No difference was observed in the sub-therapeutic group at the same time points
No difference in the bacterial composition was observed in the two groups between post-recovery and baseline samples, or between exacerbation and treatment samples
SputumTreatment of exacerbation episodes, 19 of 23 treatments including β-lactamsMinimal impact on global community structure↓ RA of some low abundance taxa with antibiotic treatment: Gemella, two Pasteurella OTUs, two Streptococcus OTUs, Oribacterium and NeisseriaCF[41]
SputumTreatment of exacerbation episodes by associations including at least one i.v. β-lactam↑ Shannon's diversity index in the first 72 h of treatment
Return to the baseline state after 8–10 days of treatment
P. aeruginosa
↑ anaerobes (Prevotella and Veillonella), in the first 72 h of treatment but return to the baseline state after 8–10 days of treatment
SputumCycle of 28 days of AZLI treatment followed by a 28-day period without treatmentNo significant change in Shannon's diversity index or Bray-Curtis β-diversity index in one AZLI cycle
↓ Shannon's diversity index
↓ Bray–Curtis β-diversity with ↑ AZLI cycles
AminoglycosidesSputumA 1-month treatment with TIP↓ average species richness (Shannon and Simpson diversity indices) after 1 week of therapy
Return to baseline state after the end of TIP therapy
Most changes noticed between baseline state and first week of treatment occurring among low abundance taxa, mostly facultative and obligate anaerobes (Neisseria, Megasphaera, Granulicatella, Haemophilus, Streptococcus, Gemella, Rothia, Veillonella, Oribacterium)CF[44]
SputumTIP or TIS during at least 1 yearNo difference in Shannon's diversity indexParvimonasCF[45]

CRD: chronic respiratory disease; CF: cystic fibrosis; PEx: pulmonary exacerbation; BE: bronchiectasis; COPD: chronic obstructive pulmonary disease; RA: relative abundance; OTU: operational taxonomic unit; i.v.: intravenous; AZLI: aztreonam lysine for inhalation; TIP: tobramycin inhaled powder; TIS: tobramycin inhaled solution.