Background Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared. Results Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC ( P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP ( P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria ( P = 0.045) and Bacteroidetes ( P = 0.024) were significantly higher in NEC and SIP infants, respectively. Conclusions Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls. Electronic supplementary material The online version of this article (10.1186/s12866-019-1426-6) contains supplementary material, which is available to authorized users.

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Background: In an era of improved management and treatment options, this study aims to describe the long-term outcomes and factors predictive of outcomes of neonatalonset intestinal failure (IF) due to surgical short bowel syndrome (SBS). Methods: Retrospective, single-center cohort study of infants born between January 2011 and December 2018 with inclusion criteria: <44 weeks postmenstrual age at SBS diagnosis, <28 days on admission, parenteral nutrition dependence >60 days, and documented intestinal resection. Primary outcomes included survival and achievement of enteral autonomy (EA). Data analysis utilized Fisher.s exact test, Kruskal-Wallis test, survival analysis methods, Cox proportional hazards regression, linear regression and logistic regression.Results: Ninety-five patients (males 56%) were studied with median follow-up of 38 months (IQR 19, 59). Survival at last follow-up was 96%, and EA was achieved in 85%.Forty-eight patients had documented residual bowel length (RBL) with median length of 49 cm (IQR 36, 80). Survival in patients with RBL of <30cm (n = 8), 30-59cm (n = 19), and >60cm (n = 21) was 100%, 95%, and 95% respectively. Shorter RBL was associated with longer time to achieve EA (p = 0.007), but not with survival (p = 0.81). Delay in achieving EA was associated with absence of ileocecal valve (p = 0.002) and bloodstream infections (p < 0.001). Peak conjugated bilirubin correlated with increased mortality (p = 0.002). Conclusion:Overall high rate of survival and achievement of EA was found in neonatal onset IF due to SBS. EA but not survival was correlated with RBL. Ileocecal valve, bloodstream infections, and conjugated bilirubin levels were the other predictive factors of outcomes.