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Background  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.    Methods  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.    Results  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.    Conclusions  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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13073-021-00869-z.

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home