Transmission of antimicrobial resistance within and between care settings in Liverpool including NHS wards, intermediate care and long term residential care Infections and Infestations
Conditions
Interventions
Following consent and enrolment participants will be asked to provide up to five stool samples or rectal swabs over a 2-week period of site-specific sampling. Each site will be revisited approximately
Sponsors
Liverpool School of Tropical Medicine
Eligibility
Sex/Gender
All
Inclusion criteria
Inclusion criteria: All current adult (aged =18 years) residents of the study sampling location during the sampling period
Exclusion criteria
Exclusion criteria: Residents being managed with palliative intent in whom active treatment has been withdrawn
Design outcomes
Primary
| Measure | Time frame |
|---|---|
| The presence of ESBL-E/CPE will be defined by selective culture of stool or rectal swab. Samples will be collected from all residents of the sampling area (hospital ward or care home) at 5 time-points over the two week sampling period at that location. Sample areas will be visited 4 times over the course of the study at 12 week intervals. If participants are still present the sampling schedule will be repeated. Hazard ratio of ESBL-E/CPE acquisition: The ESBL-E/CPE presence/absence data will be used to fit multistate Markov models. In these models participants can be either colonised or uncolonised with a transition rate between each state. The transition rate is governed by a linear combination of covariates, which can be included in such a way that the effect of the covariate can be interpreted as a hazard ratio. Hence by including care home (versus hospitalisation) as a covariate in the models this will generate a hazard ratio of ESBL acquisition for care home residency versus hospitalisation. | — |
Secondary
| Measure | Time frame |
|---|---|
| 1. Parameter values for effect of covariates from multistate models including hazard of ESBL-E/CPE acquisition measured by including other covariates in the Markov multistate models, this will generate estimates of the effect of the included covariates, analogously to the hazard ratio of ESBL acquisition described above. The values of these parameters (i.e. estimated quantities from the model) will allow an understanding of the effect of the included covariates. 2. Description of putative transmission events (bacteria and mobile genetic elements and routes within and between hospitals and care facilities. We will sequence the genomes of cultures bacteria using short read whole genome sequencing and map them to a reference genome. We can then compare genomes using the number of single nucleotide polymorphisms (SNPs) between them. Very closely related bacteria (i.e., < 10 SNPs) are putative transmission events. We will describe these transmission events in terms of which compartments (patient, environment, staff) are most linked to allow an understanding of likely transmission routes ). To describe mobile genetic elements we will use long read sequencing with a similar analysis. 3. Longitudinal description of within-host ESBL-E/CPE diversity. We will describe within-participant diversity by limited diversity metagenomics following selective culture of samples for ESBL-E/CPE. This technique allows sequencing of all ESBL-E/CPE organisms in a sample with subsequent computation reconstruction of the different bacteria present. We will present a descriptive analysis of the diversity of ESBL-E/CPE strains within participants and the effect on the diversity of exposure to antimicrobials, hospitalisation, and residence in care homes. | — |
Countries
England, United Kingdom
Contacts
Public ContactMaria Moore
Outcome results
None listed