Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure

ObjectiveNecrotizing enterocolitis (NEC) is the most common surgical emergency in preterm infants, and pathogenesis associates with changes in the fecal microbiome. As fecal samples incompletely represent microbial communities in intestinal mucosa, we sought to determine the NEC tissue-specific microbiome and assess its contribution to pathogenesis.DesignWe amplified and sequenced the V1-V3 hypervariable region of the bacterial 16S rRNA gene extracted from intestinal tissue and corresponding fecal samples from 12 surgical patients with NEC and 14 surgical patients without NEC. Low quality and non-bacterial sequences were removed, and taxonomic assignment was made with the Ribosomal Database Project. Operational taxonomic units were clustered at 97%. We tested for differences between NEC and non-NEC samples in microbiome alpha- and beta-diversity and differential abundance of specific taxa between NEC and non-NEC samples. Additional analyses were performed to assess the contribution of other demographic and environmental confounding factors on the infant tissue and fecal microbiome.ResultsThe fecal and tissue microbial communities were different. NEC was associated with a distinct microbiome, which was characterized by low diversity, higher abundances of Staphylococcus and Clostridium_sensu_stricto, and lower abundances of Actinomyces and Corynebacterium. Infant age and vancomycin exposure correlated with shifts in the tissue microbiome.ConclusionThe observed low diversity in NEC tissues suggests that NEC is associated with a bacterial bloom and a distinct mucosal bacterial community. The exact bacterial species that constitute the bloom varied by infant and were strongly influenced by age and exposure to vancomycin.

研究目的：坏死性小肠结肠炎（Necrotizing enterocolitis, NEC）是早产儿最常见的外科急重症，其发病机制与粪便微生物组的改变密切相关。鉴于粪便样本无法完全反映肠黏膜的微生物群落构成，本研究旨在明确坏死性小肠结肠炎的组织特异性微生物组，并评估其在发病机制中的作用。研究设计：本研究对12例坏死性小肠结肠炎手术患者及14例非坏死性小肠结肠炎手术患者的肠组织与对应粪便样本中提取的细菌16S rRNA基因（16S ribosomal RNA gene）V1-V3高变区进行扩增并测序。去除低质量序列及非细菌序列后，采用核糖体数据库项目（Ribosomal Database Project, RDP）进行分类学注释；以97%的相似性阈值开展操作分类单元（Operational taxonomic units, OTU）聚类。本研究分析了坏死性小肠结肠炎组与非坏死性小肠结肠炎组样本在微生物组α多样性（alpha diversity）与β多样性（beta diversity）上的差异，以及两组间特定分类群的丰度差异。此外，本研究还通过额外分析评估了其他人口统计学及环境混杂因素对婴儿肠组织与粪便微生物组的影响。研究结果：粪便与肠组织的微生物群落构成存在显著差异。坏死性小肠结肠炎与独特的微生物组特征相关：该微生物组表现为多样性降低，葡萄球菌属（Staphylococcus）与狭义梭菌属（Clostridium sensu stricto）的丰度升高，而放线菌属（Actinomyces）与棒状杆菌属（Corynebacterium）的丰度降低。婴儿年龄及万古霉素暴露史与肠组织微生物组的变化显著相关。研究结论：本研究观察到坏死性小肠结肠炎组织中微生物多样性降低，提示坏死性小肠结肠炎与细菌过度增殖及独特的黏膜细菌群落密切相关。构成该过度增殖菌群的具体细菌种类因婴儿个体而异，且受年龄及万古霉素暴露史的显著影响。