Development of a web tool for Escherichia coli subtyping based on fimH alleles:Running title: Development of E. coli fimH sub-typing web-tool

ABSTRACT The aim of this study was to construct a valid publicly available method for in silico fimH subtyping of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multilocus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available at https://bitbucket.org/genomicepidemiology/fimtyper , the database is freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db , and a service implementing the software is available at https://cge.cbs.dtu.dk/services/FimTyper . FimTyper was validated on three data sets: one containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study (data set 1), one containing whole-genome sequence (WGS) data of 243 third-generation-cephalosporin-resistant E. coli isolates (data set 2), and one containing a randomly chosen subset of 40 E. coli isolates from data set 2 that were subjected to conventional fimH subtyping (data set 3). The combination of the three data sets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 42 fimH subtypes from the Sanger sequences from data set 1 and successfully analyzed all 243 draft genomes from data set 2. FimTyper subtyping of the Sanger sequences and WGS data from data set 3 were in complete agreement. Additionally, fimH subtyping was evaluated on a phylogenetic network of 122 sequence type 131 (ST131) E. coli isolates. There was perfect concordance between the typology and fimH -based subclones within ST131, with accurate identification of the pandemic multidrug-resistant clonal subgroup ST131- H 30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH subtyping, highly suitable for surveillance and outbreak detection. </jats:p

Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E. coli clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect E. coli and the urine strain's clonotype. Based on a database of clonotype-specific antibiograms, the acceptability of various antibiotics for empiric therapy was inferred using a 20%, 10%, and 30% allowed resistance threshold. The test's performance characteristics and possible effects on prescribing were assessed. The rapid test identified E. coli clonotypes directly in patients' urine within 25-35 minutes, with high specificity and sensitivity compared to culture. Antibiotic selection based on a clonotype-specific antibiogram could reduce the relative likelihood of antibiotic/pathogen mismatch by ≥ 60%. Compared to observed prescribing patterns, clonal diagnostics-guided antibiotic selection could safely double the use of trimethoprim/sulfamethoxazole and minimize fluoroquinolone use. In summary, a rapid clonotyping test showed promise for improving empiric antibiotic prescribing for E. coli UTI, including reversing preferential use of fluoroquinolones over trimethoprim/sulfamethoxazole. The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care

Distribution of cases when 7-SNP test allowed the use of FQ ^a, T/S ^a, and/or CZ ^a.

<p>Distribution of cases when 7-SNP test allowed the use of FQ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174132#t003fn001" target="_blank">^a</a>, T/S <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174132#t003fn001" target="_blank">^a</a>, and/or CZ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174132#t003fn001" target="_blank">^a</a>.</p

Performance characteristics of the 7-SNP test for detecting <i>Escherichia coli</i> in urine samples.

<p>Performance characteristics of the 7-SNP test for detecting <i>Escherichia coli</i> in urine samples.</p

Prescription of antibiotics.

<p>Prescription of antibiotics.</p

Comparison of antibiotic resistance prevalence among study vs. local reference <i>Escherichia coli</i> isolates for the 10 most frequent study clonotypes.

<p>^a For each CT (clonotype) the most prevalent (≥ 90% of isolates) sequence type (ST), as determined by multilocus sequence typing, is shown, with its subclone determined by CH typing (H) in parentheses, where applicable. For CTs represented by multiple STs (each accounting for ≤ 90% of the constituent isolates) up to four major STs and the corresponding H subclones are listed. ^b CT571 comprises ST14 (H27), ST404 (H27) and ST1193 (H64), which all belong to clonal complex of ST14. ^c For the study set and local reference set (‘Ref’), antibiotic resistance prevalence for all <i>E</i>. <i>coli</i> and for major clonotypes is given as percent of resistant isolates in relation to the total number of isolates, overall or within the clonotype; green color indicates resistance below conventional threshold (≤ 20%), red color–above it (> 20%); the resistance within study and reference sets was compared individually for each antibiotic using a two-sided Fisher’s exact test; * P < .05.</p

Clonotypes identified in study urine samples by the 7-SNP test.

<p>Solid lines separate the 12 most frequent clonotypes (≥ 12 samples each) from the minor clonotypes.</p

Prescription rate and antibiotic-pathogen mismatch in different scenarios of antibiotic choice.

<p>Prescription rate and antibiotic-pathogen mismatch in different scenarios of antibiotic choice.</p