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Fast identification of Escherichia coli in urinary tract infections using a virulence gene based PCR approach in a novel thermal cycler.

Abstract：

:Uropathogenic Escherichia coli (UPEC) is the most common causal agent of urinary tract infections (UTIs) in humans. Currently, clinical detection methods take hours (dipsticks) to days (culturing methods), limiting rapid intervention. As an alternative, the use of molecular methods could improve speed and accuracy, but their applicability is complicated by high genomic variability within UPEC strains. Here, we describe a novel PCR-based method for the identification of E. coli in urine. Based on in silico screening of UPEC genomes, we selected three UPEC-specific genes predicted to be involved in pathogenesis (c3509, c3686 (yrbH) and chuA), and one E. coli-specific marker gene (uidA). We validated the method on 128 clinical (UTI) strains. Despite differential occurrences of these genes in uropathogenic E. coli, the method, when using multi-gene combinations, specifically detected the target organism across all samples. The lower detection limit, assessed with model UPEC strains, was approximately 104 CFU/ml. Additionally, the use of this method in a novel ultrafast PCR thermal cycler (Nextgen PCR) allowed a detection time from urine sampling to identification of only 52 min. This is the first study that uses such defined sets of marker genes for the detection of E. coli in UTIs. In addition, we are the first to demonstrate the potential of the Nextgen thermal cycler. Our E. coli identification method has the potential to be a rapid, reliable and inexpensive alternative for traditional methods.

journal_name

J Microbiol Methods

journal_title

Journal of microbiological methods

authors

Brons JK,Vink SN,de Vos MGJ,Reuter S,Dobrindt U,van Elsas JD

doi

10.1016/j.mimet.2019.105799

subject

Has Abstract

pub_date

2020-02-01 00:00:00

pages

105799

eissn

0167-7012

issn

1872-8359

pii

S0167-7012(19)30963-7

journal_volume

169

pub_type

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