1. Pulmonary microbes identified by 16S sequencing of tracheal aspirate samples in two neonatal units in the UK
- Author
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Grace Logan, Sailesh Kotecha, David Gallacher, Richard Wach, Julian R. Marchesi, Nigel Klein, and Dagmar Alber
- Subjects
Operational taxonomic unit ,Microbial DNA ,Bronchopulmonary dysplasia ,business.industry ,Medicine ,Ribosomal RNA ,business ,16S ribosomal RNA ,medicine.disease ,DNA sequencing ,Paired-end tag ,Deep sequencing ,Microbiology - Abstract
Introduction: Respiratory infections in preterm infants contribute to the development of chronic lung disease of prematurity, also known as bronchopulmonary dysplasia. Next generation sequencing of microbial genes could replace traditional culture-based methods. Aims: We used next generation sequencing to identify microbial communities in tracheal aspirates (TA) obtained from ventilated preterm infants. Methods: TA samples were obtained daily in the first week of life then twice weekly until day 28 or until extubation, from 47 ventilated preterm infants at two UK neonatal units. Total bacterial load was estimated by qPCR of the 16S bacterial rRNA gene from DNA extracted from TA cell pellet. Next generation paired end sequencing of the V3-V4 region identified the microbes present. IL6 and IL8 concentration were measured in TA samples. Results: Sequencing results were positive in 47 of 276 samples (17%). Positive TAs were associated with higher microbial load and higher IL6 and IL8 concentrations, suggesting an infective process. Serial TA samples showed episodic peaks of microbial load. 93.6% of positive TAs contained a dominant operational taxonomic unit (>50% of reads) suggesting 28 infective episodes in 20 infants. The most commonly identified dominant genera was Staphylococci. Sequencing depth using this methodology was unable to identify organisms to a species level. Conclusion: Microbial DNA was not detectable in TA samples of preterm infants in the absence of infection most likely due to absence of microbes or below detection levels. 16S rRNA sequencing identified dominant genera suggesting respiratory infections, as evidenced by an increase in IL-6 and IL-8.
- Published
- 2018