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

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.

Developing Gut Microbiota Exerts Colonisation Resistance to Clostridium (syn. Clostridioides) difficile in Piglets

Clostridium (syn. Clostridioides) difficile is considered a pioneer colonizer and may cause gut infection in neonatal piglets. The aim of this study was to explore the microbiota-C. difficile associations in pigs. We used the DNA from the faeces of four sows collected during the periparturient period and from two to three of their piglets (collected weekly until nine weeks of age) for the determination of bacterial community composition (sequencing) and C. difficile concentration (qPCR). Furthermore, C. difficile-negative faeces were enriched in a growth medium, followed by qPCR to verify the presence of this bacterium. Clostridium-sensu-stricto-1 and Lactobacillus spp. predominated the gut microbiota of the sows and their offspring. C. difficile was detected at least once in the faeces of all sows during the entire sampling period, albeit at low concentrations. Suckling piglets harboured C. difficile in high concentrations (up to log10 9.29 copy number/g faeces), which gradually decreased as the piglets aged. Enrichment revealed the presence of C. difficile in previously C. difficile-negative sow and offspring faeces. In suckling piglets, the C. difficile level was negatively correlated with carbohydrate-fermenting bacteria, and it was positively associated with potential pathogens. Shannon and richness diversity indices were negatively associated with the C. difficile counts in suckling piglets. This study showed that gut microbiota seems to set conditions for colonisation resistance against C. difficile in the offspring. However, this conclusion requires further research to include host-specific factors.

The regenerating family member 3 β instigates IL-17A-mediated neutrophil recruitment downstream of NOD1/2 signalling for controlling colonisation resistance independently of microbiota community structure

ObjectiveLoss of the Crohn’s disease predisposing NOD2 gene results in an intestinal microenvironment conducive for colonisation by attaching-and-effacing enteropathogens. However, it remains elusive whether it relies on the intracellular recruitment of the serine-threonine kinase RIPK2 by NOD2, a step that is required for its activation of the transcription factor NF-κB.DesignColonisation resistance was evaluated in wild type and mutant mice, as well as in ex-germ-free (ex-GF) mice which were colonised either with faeces from Ripk2-deficient mice or with bacteria with similar preferences for carbohydrates to those acquired by the pathogen. The severity of the mucosal pathology was quantified at several time points postinfection by using a previously established scoring. The community resilience in response to infection was evaluated by 16S ribosomal RNA gene sequence analysis. The control of pathogen virulence was evaluated by monitoring the secretion of Citrobacter-specific antibody response in the faeces.ResultsPrimary infection was similarly outcompeted in ex-GF Ripk2-deficient and control mice, demonstrating that the susceptibility to infection resulting from RIPK2 deficiency cannot be solely attributed to specific microbiota community structures. In contrast, delayed clearance of Citrobacter rodentium and exacerbated histopathology were preceded by a weakened propensity of intestinal macrophages to afford innate lymphoid cell activation. This tissue protection unexpectedly required the regenerating family member 3β by instigating interleukin (IL) 17A-mediated neutrophil recruitment to the intestine and subsequent phosphorylation of signal transducer and activator of transcription 3.ConclusionsThese results unveil a previously unrecognised mechanism that efficiently protects from colonisation by diarrhoeagenic bacteria early in infection.

Evaluation of colonisation resistance in stool of human donors using ex vivo, in vitro and in vivo assays

The indigenous microbiota is the population of microorganisms normally present on the surface and mucosa of an individual, where it performs essential health functions, including the colonisation resistance (CR) against pathogens. To identify the bacteria responsible and the mechanisms involved in the CR, the germ-free (GF) animal model has been used, because in vitro studies cannot always be extrapolated to what occurs in vivo. In this study, ex vivo antagonism assays against seven enteropathogenic bacteria using stools from 15 healthy human donors confirmed that the CR showed individual variation. Using in vitro antagonism assays, 14 strains isolated from dominant faecal microbiota of donors with elevated CR were selected for mono-association in GF mice to test the in vivo antagonism against Salmonella enterica ser. Typhimurium. Mice mono-associated with Enterococcus hirae strain 8.2, Bacteroides thetaiotaomicron strain 16.2 and Lactobacillus ruminis strain 18.1 had significant reductions in faecal counts of the pathogen during the challenge. After five days of infection, the group associated with E. hirae 8.2 showed a reduction in the translocation of S. Typhimurium to the spleen, while the group associated with L. ruminis 18.1 presented an increased translocation to the liver. The histological data confirmed these results and revealed that the mice associated with E. hirae 8.2 showed fewer lesions on ileum and liver, compared to the damage caused by S. Typhimurium alone, while in mice associated with L. ruminis 18.1 there was significantly worse lesions. Concluding, from the dominant faecal microbiota from healthy human with high CR, through ex vivo, in vitro and in vivo assays, a bacterium was characterised for its high CR potential, being a candidate for probiotic use.

Colonial Debt, Resistance to U.S. Military Presence, Trustworthiness of Pro-U.S. Military Information Sources, and Support for the Military Buildup on Guam

In this exploratory study, a representative community survey of 319 registered voters was conducted in the island of Guam to analyse the relationships between colonial debt (an internalised acceptance of colonisation), resistance to U.S. military presence, support for an impending U.S. military buildup in the island, and the perceived trustworthiness of information sources supportive of the buildup — that is, U.S. officials and the Pacific Daily News, a local newspaper. Results suggest that colonial debt was associated with less resistance to U.S. military presence, more support for the military buildup, and higher trustworthiness of two information sources supportive of the buildup. Resistance to U.S. military presence was linked with less support for the buildup and less trustworthiness of the two information sources. Implications and limitations are discussed.