Evaluation of new diagnostic technologies for rapid detection of urinary pathogens and their antibiotic resistances

Schmidt, K. (2017) Evaluation of new diagnostic technologies for rapid detection of urinary pathogens and their antibiotic resistances. Doctoral thesis, University of East Anglia.

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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)

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Depositing User: Stacey Armes
Date Deposited: 22 Mar 2018 15:01
Last Modified: 31 Dec 2020 01:38
URI: https://ueaeprints.uea.ac.uk/id/eprint/66564

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