A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease.

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PubMed ID: 30787368

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Wootton DG, Cox MJ, Gloor GB, Litt D, Hoschler K, German E, Court J, Eneje O, Keogan L, Macfarlane L, Wilks S, Diggle PJ, Woodhead M, Moffatt MF, Cookson WOC, Gordon SB

Sci Rep. Feb 2019. doi: 10.1038/s41598-018-38090-5

COMMENT: Community-acquired pneumonia (CAP) is one of the most common infectious diseases and is an important cause of mortality and morbidity worldwide. The bacterial aetiology of CAP is unclear because of the practical difficulties in obtaining timely specimens and the selectivity of sputum culture. By 16S rRNA gene sequencing, the authors have studied the adult sputum microbiota in patiens with acute CAP.


We determined the microbiota in sputum samples obtained from a large series of adults with carefully phenotyped CAP. Our aim was to inform trials of stratifed, empiric antibiotic therapy by determining how clinical characteristics predict sputum microbiota in this population.


Comparing all sputum samples, an airway commensal bacterium of the genus Veillonella spp. (Veillonella_1328) was on average the most relatively abundant.

The second most relatively abundant OTU was a Streptococcus sp. (Streptococcus_4318). We compared the relative abundance of this and all other OTUs of the genus Streptococci spp. with the concentration of S. pneumoniae in sputum expressed as genome copies per millilitre (mL) and measured by qPCR of the lytA gene. (...) the relative abundance of the OTU Streptococcus_4318 was strongly associated with the concentration of S. pneumoniae in each sputum sample.

Similarly,  we found a strong association between the most relatively abundant Haemophilus spp. OTU (Haemophilus_617) and the concentration of H. influenzae in sputum as measured by qPCR of the Hi-hpd gene. 

Chronic lung disease had the only significant association (P = 0.03) on the bacterial composition of sputum. (...) Haemophilus_617 was responsible for driving much of the variation in sputum composition among this cohort.

Patients with chronic lung disease were more likely to have a high relative abundance of Haemophilus_617  than those without chronic lung disease (OR = 5, CI 1.2–29.6, P = 0.015). 


(...) in hospitalised adults with non-severe CAP, the presence of chronic lung disease predicts the frequent dominance of a Haemophilus sp. These results alone should not be used to change practice but should inform a randomised trial comparing a standard empirical antibiotic regime with another expanded to cover Nontypable Haemophilus influenzae in patients who develop CAP on a background of chronic lung disease. 



Raquel Ruiz-Arroyo