Antibiotic resistance: the lung microbiota pays a heavy price

Broad-spectrum antibiotics used for treating lung infections are regarded as one of the principal contributors to the overall burden of antibiotic resistance.

About this article

Created 25 August 2021

Updated 12 October 2021

Historically, the lungs of healthy individuals were considered sterile; the description of the LRT microbiota (Lower Respiratory Tract, from larynx to alveoli of the lungs)¹ is a recent achievement.^2,3 Along with viral and fungal communities, six bacterial phyla dominate a healthy lung microbiota: Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Acidobacteria, and Actinobacteria.^1,2,4

“In Western populations, the treatment of lung infections is a primary driver of antibiotic resistance.⁴”

A loss of diversity in the lung microbiota

Microbial dysbiosis is observed in a range of respiratory disorders, including lung infection, asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF).^5,6 But only few studies have explored the direct effects of antibiotics on lung microbiota. Recent investigation has shown that azithromycin treatment decreased bacterial diversity in patients with persistent uncontrolled asthma;¹ however clinical benefits are still controversial.^1,7,8 In COPD patients, azithromycin treatment lowered alpha diversity;¹ in those suffering from CF, antibiotics appear to be the primary drivers of decreased airway microbiota diversity.⁵

The gut-lung axis

Respiratory diseases, chronic lung disorders and microbial infections are often accompanied by intestinal symptoms.¹²Indeed, the intestinal ecosystem undergoes change during the course of several lung diseases.¹² While the underling mechanism remains unclear, reciprocal influence between the gut and the lungs could, in part, explain why antibiotic-induced dysbiosis of the gut microbiota in early-life may be a risk factor for subsequent allergic rhinitis and asthma.^1,12

The plague of broad-spectrum antibiotics

While the misuse of antibiotics is known to lead to the emergence and selection of resistant bacteria, antibiotic prophylaxis, without a microbial diagnosis, is still widely used to treat lung infections.⁴ Of the 12 antibiotic-resistant ‘priority pathogens’ listed by the WHO, 4 affect lungs: Pseudomonas aeruginosa, Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus aureus.^4,9 There is agreement among the scientific community as a key route to minimize antimicrobial resistance that the disease management of lung infections needs to be improved.^4,10,11

Promoting research, raising awareness

The Global Alliance Against Respiratory Diseases (GARD), launched by the WHO in 2006 to help combat chronic respiratory diseases, asserts: “Physicians worldwide now face situations in which infected patients cannot be treated adequately because the responsible bacterium is totally resistant to available antibiotics.¹¹”
At the European level, the ERS (European Respiratory Society) is involved in promoting scientific research, providing access to resources and raising awareness among the public and political decision makers. “Science, education and advocacy are at the core of everything we do.” Its latest monograph, ‘The lung microbiome’,¹³ reviews the different components of the respiratory microbiome, examines how diseases (asthma, COPD, cancer…) emerge and discusses new developments and therapies.