Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Microbiome. 2018 Jun 20;6(1):112. doi: 10.1186/s40168-018-0493-5.
The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants.
Over 2832 swabs, wipes, and air samples were collected from 16 private-style NICU rooms housing very low birth weight (< 1500 g), premature (< 31 weeks' gestation) infants. For each infant, room samples were collected daily, Monday through Friday, for 1 month. The first samples from the first infant and the last samples from the last infant were collected 383 days apart. Twenty-two NICU locations spanning room surfaces, hands, electronics, sink basins, and air were collected. Results point to an incredibly simple room community where 5-10 taxa, mostly skin-associated, account for over 50% of the amplicon reads. Biomass estimates reveal four to five orders of magnitude difference between the least to the most dense microbial communities, air, and sink basins, respectively. Biomass trends from bioaerosol samples and petri dish dust collectors suggest occupancy to be a main driver of suspended biological particles within the NICU. Using a machine learning algorithm to classify the origin of room samples, we show that each room has a unique microbial fingerprint. Several important taxa driving this model were dominant gut colonizers of infants housed within each room.
Despite regular cleaning of hospital surfaces, bacterial biomass was detectable at varying densities. A room-specific microbiome signature was detected, suggesting microbes seeding NICU surfaces are sourced from reservoirs within the room and that these reservoirs contain actively dividing cells. Collectively, the data suggests that hospitalized infants, in combination with their caregivers, shape the microbiome of NICU rooms.
新生儿重症监护病房（NICU）中包含一群免疫系统尚未发育完全和微生物组尚未形成的患者。这些患者通常在同一个病房中待上数月，并且先前的研究已经表明，这些婴儿的肠道微生物组通常与 NICU 中的微生物相似。然而，人们对长时间内 NICU 病房相关细菌的身份、持久性和绝对丰度知之甚少。在这里，我们将液滴数字 PCR（ddPCR）、16S rRNA 基因调查和最近发表的婴儿肠道样本宏基因组学数据相结合，推断出 NICU 微生物组受其病房居住者影响的程度。
我们从 16 间私人风格的 NICU 病房收集了超过 2832 个拭子、擦拭物和空气样本，这些病房中均居住有极低出生体重（<1500 克）和早产（<31 周妊娠）的婴儿。每个婴儿的样本均于周一至周五每天收集一次，持续一个月。第一个婴儿的第一批样本和最后一个婴儿的最后一批样本之间相隔 383 天。我们收集了 22 个 NICU 位置的样本，包括房间表面、手、电子产品、水槽盆地和空气。结果表明，病房的微生物群落非常简单，只有 5-10 种细菌，主要是皮肤相关的细菌，占扩增子读数的 50%以上。生物量估计显示，空气和水槽盆地分别是微生物密度相差四到五个数量级的最稀疏和最密集的微生物群落。来自生物气溶胶样本和培养皿灰尘收集器的生物量趋势表明，入住 NICU 的患者是造成其中悬浮生物颗粒的主要驱动因素。使用机器学习算法对房间样本的来源进行分类，我们表明每个房间都有独特的微生物指纹。该模型中的几个重要分类群是每个房间内入住婴儿的肠道定植优势菌。
尽管经常对医院表面进行清洁，但仍可检测到不同密度的细菌生物量。检测到一个特定于房间的微生物组特征，表明播种 NICU 表面的微生物来源于房间内的储源，并且这些储源含有活跃分裂的细胞。总的来说，这些数据表明住院婴儿及其护理人员共同塑造了 NICU 病房的微生物组。
