Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection
Veronika Tchesnokova
Hovhannes Avagyan
Elena Rechkina
Diana Chan
Mariya Muradova
Helen Ghirmai Haile
Matthew Radey
Scott Weissman
Kim Riddell
Delia Scholes
James R. Johnson
Evgeni V. Sokurenko
10.1371/journal.pone.0174132
https://plos.figshare.com/articles/dataset/Bacterial_clonal_diagnostics_as_a_tool_for_evidence-based_empiric_antibiotic_selection/4794706
<div><p>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 <i>Escherichia coli</i>, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for <i>E</i>. <i>coli</i> clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect <i>E</i>. <i>coli</i> 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 <i>E</i>. <i>coli</i> 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 <i>E</i>. <i>coli</i> 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.</p></div>
2017-03-28 18:21:43
urine strain
coli clonal-level antibiograms
cohort study
care patients
resistance threshold
Antibiotic selection
empiric therapy
clonotyping test
clonal pathogen
antimicrobial stewardship
empiric antibiotic
evidence-based empiric antibiotic selection
coli UTI
Urinary tract infections
evidence-based medicine
urine samples
performance characteristics
clonotype-specific antibiogram
antibiotic use
broad-spectrum agents
clonal diagnostics approach
Bacterial clonal diagnostics
clonal diagnostics-guided antibiotic selection
Escherichia coli
coli clonotypes
fluoroquinolone use
antibiotic selection
empiric antibiotic selection
clonotype-specific antibiograms
clonal distribution
novel PCR-based clonotyping assay
antibiotic resistance