Raveh-Sadka Tali, Firek Brian, Sharon Itai, Baker Robyn, Brown Christopher T, Thomas Brian C, Morowitz Michael J, Banfield Jillian F
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
ISME J. 2016 Dec;10(12):2817-2830. doi: 10.1038/ismej.2016.83. Epub 2016 Jun 3.
The potentially critical stage of initial gut colonization in premature infants occurs in the hospital environment, where infants are exposed to a variety of hospital-associated bacteria. Because few studies of microbial communities are strain-resolved, we know little about the extent to which specific strains persist in the hospital environment and disperse among infants. To study this, we compared 304 near-complete genomes reconstructed from fecal samples of 21 infants hospitalized in the same intensive care unit in two cohorts, over 3 years apart. The genomes represent 159 distinct bacterial strains, only 14 of which occurred in multiple infants. Enterococcus faecalis and Staphylococcus epidermidis, common infant gut colonists, exhibit diversity comparable to that of reference strains, inline with introduction of strains from infant-specific sources rather than a hospital strain pool. Unlike other infants, a pair of sibling infants shared multiple strains, even after extensive antibiotic administration, suggesting overlapping strain-sources and/or genetic selection drive microbiota similarities. Interestingly, however, five strains were detected in infants hospitalized three years apart. Three of these were also detected in multiple infants in the same year. This finding of a few widely dispersed and persistent bacterial colonizers despite overall low potential for strain dispersal among infants has implications for understanding and directing healthy colonization.
早产儿肠道初始定植的潜在关键阶段发生在医院环境中，在此环境下，婴儿会接触到各种与医院相关的细菌。由于对微生物群落的研究很少能解析到菌株水平，我们对特定菌株在医院环境中的持续存在程度以及在婴儿之间的传播情况知之甚少。为了研究这一问题，我们比较了从两个队列中在同一重症监护病房住院的21名婴儿的粪便样本中重建的304个近乎完整的基因组，这两个队列相隔3年。这些基因组代表了159种不同的细菌菌株，其中只有14种出现在多个婴儿体内。粪肠球菌和表皮葡萄球菌是常见的婴儿肠道定植菌，它们表现出与参考菌株相当的多样性，这与来自婴儿特定来源而非医院菌株库的菌株引入情况一致。与其他婴儿不同，一对同胞婴儿即使在大量使用抗生素后仍共享多种菌株，这表明重叠的菌株来源和/或基因选择推动了微生物群的相似性。然而，有趣的是，在相隔三年住院的婴儿中检测到了五种菌株。其中三种在同一年的多个婴儿中也被检测到。尽管婴儿之间菌株传播的总体可能性较低，但仍发现了一些广泛传播且持续存在的细菌定植菌，这一发现对于理解和引导健康定植具有重要意义。
