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Title: Evaluation of new diagnostic technologies for rapid detection of urinary pathogens and their antibiotic resistances
Author: Schmidt, K.
Awarding Body: University of East Anglia
Current Institution: University of East Anglia
Date of Award: 2017
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Background: Most urinary tract infections (UTIs) are trivial; but complicated UTIs are a growing reason for hospitalisation in the UK, and are among the commonest sources of sepsis. Increasing resistance among uropathogens complicates treatment and drives wider empirical use of previously-reserved antibiotics. Rapid precise detection of pathogens and resistances, without culture, might better guide early therapy in deteriorating UTI patients. Methods: Two approaches were evaluated: i) MALDI-TOF mass spectrometry for direct identification of pathogens from urine together with multiplex, tandem PCR (MT-PCR) for resistance gene profiling. MALDI-TOF was also explored for rapid detection of β-lactamase activity in bacteria harvested from urine; ii) MinION sequencing for bacterial and resistance gene identification, again directly from urine. As background, an epidemiological surveillance of uropathogens from the Norfolk and Norwich University Hospital in July and November 2014 was performed. Results: Direct MALDI-TOF on urines could achieve rapid bacterial identification within 1.5 h and also allowed direct detection of extended-spectrum β-lactamase (ESBL) activity. MT-PCR showed satisfactory results in detecting the commonest resistance genes in Enterobacteriaceae directly from urines and cultivated isolates within 3 h. Weaker association was found between streptomycin resistance and aadA1/A2/A3 genes. Fluoroquinolone-susceptible and -resistant Escherichia coli were distinguished by the melting temperatures of their gyrA product. MinION sequencing correctly identified uropathogens and their resistances in all urine samples within < 5 h, without culture. Acquired resistance genes agreed with resistance phenotypes and closely matched Illumina sequencing, albeit with poor discrimination within some β-lactamase families (e.g. blaTEM). Epidemiological surveillance showed E. coli predominant in all age groups and location types, with high resistance rates to amoxicillin and trimethoprim. Conclusion: Either a MALDI-TOF plus PCR or a sequencing approach could significantly shorten the time required for microbiological investigation of urosepsis, allowing clinicians to adjust therapy before the second dose of a typical (i.e. q8h) antibiotic.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available