Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.
Genome Med. 2021 Apr 7;13(1):54. doi: 10.1186/s13073-021-00869-z.
Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs.
We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016-April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study.
Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents.
Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation.
养老院居民肠道定植多重耐药菌（MDRO）的比例增加。我们评估了该人群中 MDRO 的定植和传播情况，确定了 MDRO 定植的临床危险因素，并研究了肠道微生物群在提供 MDRO 定植抵抗力方面的作用。
我们在荷兰的一家养老院进行了一项前瞻性队列研究。在四个时间点（2016 年 10 月至 2017 年 4 月）收集人口统计学、流行病学和临床数据，间隔 2 个月。为了获得纵向数据，从居民中收集粪便样本，至少在两个时间点进行分析。最终，有 27 名居民被纳入研究，共分析了 93 份粪便样本，其中 27 份（29.0%）为 MDRO 阳性。在整个 6 个月的研究中，有 12 名居民（44.4%）在至少一个时间点被 MDRO 定植。
单变量广义估计方程逻辑回归表明，在过去 2 个月内使用抗生素和在过去 1 年内住院与 MDRO 定植有关。通过全基因组测序对 MDRO 分离株进行特征分析表明，大肠杆菌 ST131 是最常见的 MDRO，并且鉴定了特定病房的大肠杆菌 ST131 簇。通过 16S rRNA 基因扩增子测序进行的微生物组分析显示，MDRO 阳性和阴性样本之间以及定植过和未定植过 MDRO 的居民之间，α或β多样性均无差异。在整个 6 个月的研究中，有 3 种细菌分类群（Dorea、Atopobiaceae 和 Lachnospiraceae ND3007 组）在从未定植过 MDRO 的居民中更为丰富。在几个居民中观察到双歧杆菌的异常高丰度。对具有宏基因组学的样本子集的进一步研究表明，各种双歧杆菌属物种高度丰富，其中长双歧杆菌株在居民中随时间保持一致，但在居民之间存在差异。
我们的研究为肠道微生物群在养老院中老年人对 MDRO 定植的抵抗力方面提供了新的证据。Dorea、Atopobiaceae 和 Lachnospiraceae ND3007 组可能与 MDRO 定植的保护有关。此外，我们报告了多个居民中几种双歧杆菌属物种的异常高丰度，并排除了这是由于益生菌补充的可能性。
