Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

Background: Necrotizing enterocolitis (NEC) is a devastating intestinal disease that afflicts 10% of extremely preterm infants. The contribution of early intestinal colonization to NEC onset is not understood, and predictive biomarkers to guide prevention are lacking. We analyzed banked stool and urine samples collected prior to disease onset from infants 99% versus 99% versus 38% in the other NEC cases and 84% in controls, P = 0.01). NEC preceded by Firmicutes dysbiosis occurred earlier (onset, days 7 to 21) than NEC preceded by Proteobacteria dysbiosis (onset, days 19 to 39). All NEC cases lacked Propionibacterium and were preceded by either Firmicutes (≥98% relative abundance, days 4 to 9) or Proteobacteria (≥90% relative abundance, days 10 to 16) dysbiosis, while only 25% of controls had this phenotype (predictive value 88%, P = 0.001). Analysis of days 4 to 9 urine samples found no metabolites associated with all NEC cases, but alanine was positively associated with NEC cases that were preceded by Firmicutes dysbiosis (P < 0.001) and histidine was inversely associated with NEC cases preceded by Proteobacteria dysbiosis (P = 0.013). A high urinary alanine:histidine ratio was associated with microbial characteristics (P < 0.001) and provided good prediction of overall NEC (predictive value 78%, P = 0.007). Conclusions: Early dysbiosis is strongly involved in the pathobiology of NEC. These striking findings require validation in larger studies but indicate that early microbial and metabolomic signatures may provide highly predictive biomarkers of NEC

Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants

<div><p>Objective</p><p>Late onset sepsis (LOS) contributes to mortality and morbidity in preterm infants. We tested the hypotheses that microbes causing LOS originate from the gut, and that distortions in the gut microbial community increases subsequent risk of LOS.</p><p>Study Design</p><p>We examined the gut microbial community in prospectively collected stool samples from preterm infants with LOS and an equal number of age-matched controls at two sites (Cincinnati, OH and Birmingham, AL), by sequencing the bacterial 16S rDNA. We confirmed our findings in a subset of infants by whole genome shotgun sequencing, and analyzed the data using R and LEfSe.</p><p>Results</p><p>Infants with LOS in Cincinnati, as compared to controls, had less abundant <i>Actinobacteria</i> in the first samples after birth (median 18 days before sepsis onset), and less abundant <i>Pseudomonadales</i> in the last samples collected prior to LOS (median 8 days before sepsis onset). Infants with LOS in Birmingham, as compared to controls, had no differences identified in the first sample microbial communities, but <i>Lactobacillales</i> was less abundant in the last samples prior to LOS (median 4 days before sepsis onset). Sequencing identified detectable levels of the sepsis-causative organism in stool samples prior to disease onset for 82% of LOS cases.</p><p>Conclusions</p><p>Translocation of gut microbes may account for the majority of LOS cases. Distortions in the fecal microbiota occur prior to LOS, but the form of distortion depends on timing and site. The microbial composition of fecal samples does not predict LOS onset in a generalizable fashion.</p></div

First sample classification tree results.

<p>(A) Birmingham results, showing infants colonized with <i>Streptococcaceae</i> and infants with higher levels of <i>Clostridia</i> are at greater risk of sepsis. (B) Cincinnati results, showing that infants colonized with greater relative abundance of <i>Actinobacteria</i> and infants with lower relative abundance of <i>Bacilli</i> are protected from sepsis.</p

Barplots of taxa identified as differential abundant in cases and controls at genus level and higher in Cincinnati.

<p>Y-axis was transformed by taking the base ten logarithm of the number of reads plus one. Samples were rarefied to 2000 reads per sample prior to creating the plots. Median number of reads of <i>Pseudomonadales</i> in controls was 0, range was 0 to 1251. Median number of reads of <i>Pseudomonadales</i> in cases was 0, range was 0 to 9. No control samples had reads of <i>Prevotella</i>. Median number of reads of <i>Prevotella</i> in cases was 0, range was 0 to 384. Family <i>Prevotellaceae</i> was also significantly different between cases and controls, it is not shown here because it had a correlation of 1 with genus <i>Prevotella</i>. All other differences identified by LEfSe were at the OTU level. All differences identified by LEfSe in the Birmingham last sample analysis were at the OTU level.</p