Abstract
Background/Aims E.coli infections of the urinary tract (UTI) are among the most common infections worldwide. U.S. costs of UTI care are >$1B annually. Recently, there has been rapid worldwide emergence of resistant E.coli, which increases the percentage of serious events and the difficulty of care. One contributing factor may be that usual care typically involves presumptive antibiotic treatment, with antimicrobial sensitivity results available only after 1–2 days. Inappropriate treatment during that interval is suboptimal for the patient and facilitates E.coli resistance. We conducted a 1-year pilot of a potential new diagnostic technology to test for E.coli infection at the clonal level by: 1) optimizing PCR methods to directly and rapidly test urine samples for two E.coli sub-strains (clones) in a community lab setting (Group Health [GH]); 2) using this method to identify two highly-resistant sub-strains in GH samples; and 3) comparing usual care prescribing patterns to potential prescribing based on sub-strain results, focusing on the “drug-bug mismatch”.
Methods A research strategy developed at the University of Washington to diagnose E.coli sub-strains was adapted to a commercial PCR platform for two selected sub-strains: ST131 and ST69. We tested 653 urine samples for presence of ST131 and ST69 and reviewed EMRs to collect the clinical diagnoses and antibiotics prescribed at the visit.
Results In the GH lab, the PCR-based diagnostic test required about 1.5 hrs. Prevalence (UW-confirmed) was 10% (65/653) for ST131 and 5% (33/653) for ST69. Of 200 EMR reviews to date, these two clones represent 65% (17/26) of fluoroquinolone and 17% (5/29) of trimethoprim/sulfa resistant isolates. Five percent (9/200) of patients were empirically prescribed therapy for which the isolate was resistant. Adjustment of the original prescribed antibiotic based on the E.coli clonal identity would reduce the drug-bug mismatch by 55%.
Conclusions These methods delivered accurate, economical results, at the clonal level, faster than usual lab methods. The two E.coli sub-strains are found in a sizable percentage of the isolates that are resistant to the main E.coli therapies. Clonal-based diagnostic strategies can offer opportunities to improve antibiotic prescribing and to impact the continued spread of antimicrobial resistance.
