Urinary Microbiome Sequencing Approaches
Research type
Research Study
Full title
Quantitative mapping of the microbiome and resistome in urinary tract infection among women: a pump-priming interdisciplinary study.
IRAS ID
287821
Contact name
Amal Gadalla
Contact email
Sponsor organisation
Cardiff University
Clinicaltrials.gov Identifier
AC1150IF02 , ISSF Project Reference Number
Duration of Study in the UK
1 years, 4 months, 30 days
Research summary
Title: bacterial DNA reading approaches to identify bacterial communities and their antibiotics resistance genes in urinary tract infections (UTI).
UTI is one of the most common infections in the community, particularly among women. Poor response (resistance) to the most commonly used antibiotics has reached 34%. Routine microbiology does not reveal a causative agent for all patients with UTI symptoms. Identification of the whole bacterial population (microbiome) in urine that is not usually detectable by routine microbiology testing (bacterial culture), but detectable by DNA reading technologies (sequencing) might help the diagnosis of UTI. In the near future research, we are interested in investigating the individuals’ bacterial microbiome variation over time, specifically the prolonged carriage of antibiotic resistant bacteria. The current proposed study is a pilot study to determine the most appropriate DNA sequencing methods to use in larger studies. Here we will identify the best bacterial DNA sequencing methods to describe the bacterial microbiome and its antibiotic resistance profile (resistome) present in human urine. We will target bacteria not only floating in the urine but also bacteria within the human cells that are normally shed in urine. We will apply advanced DNA sequencing to compare two approaches; 1) direct testing using extracted bacterial DNA from urine and 2) indirect by using DNA extracted from bacteria grown after the routine microbiology culture of urine. Using advanced computational technology, we will then identify the bacterial microbiome and genes associated with antibiotic resistance in these samples. To achieve these objectives, we will be utilizing surplus urine samples and its bacterial isolates stored at the Microbiology Laboratory at Public Health Wales (PHW). Urine samples will be from non-identifiable patients with UTI symptoms who had either positive or negative urine culture.REC name
East Midlands - Leicester Central Research Ethics Committee
REC reference
21/EM/0056
Date of REC Opinion
22 Feb 2021
REC opinion
Favourable Opinion