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Intestinal microbiome development in stable preterm infants: a longitudinal study

Presented at the Neonatal Society 2018 Summer Meeting.

Hutchinson R1,4, Wade WG2, Millar M3, Wong K1, Wilks M3, Stacey F4, Costeloe K1, Fleming P1,4

1 Blizard Institute, Queen Mary University of London
2 Centre for Host-Microbiome Interactions, King’s College London
3 Department of infection, Barts NHS Trust
4 Neonatal Intensive Care Unit, Homerton University Hospital NHS Foundation Trust

Background: It has been suggested that dysbiosis of the preterm gut is implicated in the pathogenesis of necrotising enterocolitis (NEC) and late-onset sepsis (LOS) (1,2). Existing studies of the preterm gut microbiome are frequently limited by low sampling frequency, a short assessment period, and/or failure to account for the presence of possible microbiome modulators. We hypothesise that longitudinal study of the microbiome of individual subjects, controlling for these factors, may elicit important unrecognised patterns of microbiome development.

Methods: This research was nested in a study investigating microbial colonisation in preterm infants born <32/40 GA – funded by Barts Charity, and received ethical approval from London (Chelsea) REC. A subset of ‘stable’ infants was identified (i.e. no episodes of LOS/NEC; only one antibiotic course restricted to the immediate postnatal period; and >75% of samples obtained when not on antibiotics). We aimed to obtain stools on a daily basis from birth up to 12 weeks of age, corrected GA of 37 weeks, or discharge. Bacterial DNA was extracted from these samples, and community profiling was performed on the V4 region of the 16S rRNA gene using Illumina MiSeq.

Results: 14 subjects (median GA 31w, median BW 1279g, 13 born by caesarean section) were identified as meeting the inclusion criteria. A median of 18 samples/subject were obtained, over a median of 38 days (samples were skewed to a later age, as stool frequency increased). After an initial period of instability, where no consistency in colonisation was noted within the cohort, samples were rapidly dominated by Enterobacteriaceae, with all subjects producing early samples with >80% abundance. Thereafter, Enterobacteriaceae proportions generally diminished to ~50%, as other facultative and obligate anaerobes increased in abundance. An exception to this was the only subject in the cohort born prematurely secondary to chorioamnionitis and delivered vaginally, who maintained high proportions (>90%) ofEnterobacteriaceae. A variety of facultative/obligate anaerobic families were seen to dominate in individual subjects (e.g. BacteroidaceaeVeillonellaceaeBifidobacteriaceaeEnterococcaceae), and community composition remained largely consistent over time within subjects.

Conclusion: This study corroborates previous data demonstrating early dominance of Enterobacteriaceae in the preterm gut. However, it also demonstrates a subsequent colonisation pattern with a variety of anaerobic taxa, which has not been previously explicitly described.

Corresponding author: richard.hutchinson@doctors.org.uk

1. Neu J, Walker WA. Necrotizing Enterocolitis. New England Journal of Medicine 2011; 364: 255-264
2. Lin PW, Stoll BJ. Necrotising enterocolitis. The Lancet; 368: 1271-1283

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