Objective Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control. Design We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care. Results SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specifically Bifidobacterium, at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment. Conclusion Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy. Data are available in a public, open access repository. Data are available upon reasonable request. Sequencing data from the PICnIC-ARCTIC Study are available at (ERP156474). Sequencing data from baseline critically ill children are available at (ERP156475).

中文翻译：

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在一项试点集群随机试验（ARCTIC 研究）中，消化道感染控制的短期选择性净化不会增加抗菌药物耐药性负担

目的 消化道选择性净化（SDD）是一种经过充分研究但备受争议的加强感染控制的医疗干预措施。在这里，我们的目的是描述与传统感染控制相比，接受 SDD 强化感染控制治疗的危重儿童的微生物组和抗菌素耐药性 (AMR) 基因谱的变化。设计 我们在 SDD 试点多中心集群随机试验中，对从危重机械通气患者收集的系列口咽和粪便样本进行了鸟枪法宏基因组微生物组和耐药组分析。比较微生物组和 AMR 谱的纵向和组间变化。在同意的患者中，获得了 89 名危重儿童的粪便微生物组基线样本。此外，还对 17 名接受 SDD 强化感染控制治疗的儿童和 19 名接受标准护理的儿童收集了危重病期间和之后的样本。结果 SDD 对危重儿童的 α 和 β 多样性的影响比标准护理更大。治疗停止时，机械通气结束时，SDD 患者的微生物组以放线菌群为主，特别是双歧杆菌。与接受标准护理的儿童相比，在接受 SDD 治疗的儿童中，肠道微生物群发生了明显的改变，这些儿童返回了晚期纵向样本。与标准护理相比，临床相关的 AMR 基因负荷不受 SDD 增强感染控制的影响。与标准治疗相比，SDD 不会影响口腔微生物组的组成。结论 与标准抗菌治疗相比，SDD 的短期干预导致危重儿童机械通气结束时微生物组发生变化，但不会导致 AMR 基因库发生变化。数据可在公共、开放访问存储库中获取。数据可根据合理要求提供。 PICnIC-ARCTIC 研究的测序数据可在以下网址获取：（ERP156474）。基线危重儿童的测序数据可在以下网址获得：（ERP156475）。