Objective To develop and evaluated a rapid multiplex-qPCR to identify fecal carriers of multi-drug resistant extra-intestinal pathogenic E. coli clonal groups. Methods Men presenting for transrectal prostate biopsy (TPB) at the San Diego Veterans Affairs Medical Center underwent rectal culture immediately prior to TPB. Rectal swabs were streaked ciprofloxacin-supplemented (4 mg/L) MacConkey agar plates, identified, and susceptibility tested. The same swab was sent to the University of Washington for qPCR test (EST200) targeting two major MDR-ExPEC clonal groups – ST131 and ST69 that combined were expected to represent majority of fluoroquinolone as well as trimethoprim-sulfamethoxazole resistant E. coli. We calculate test characteristics including the area under the receiver operative curve (AUC). Results We enrolled 104 men from 11/5/2013 to 6/10/2014. Fluoroquinolone - resistant E. coli were cultured from 19.2% (20/104) of rectal swabs and 26% (27/104) of all swabs were positive for EST200 by PCR. The test characteristics comparing the EST200 to the culture-based detection of fluoroquinolone-resistance were 75%, 86%, 94%, and 56%, respectively. The AUC was 0.84 for the EST200 to detect fluoroquinolone resistance prior to TPB. Conclusions Compared to the reference standard rectal culture, EST200 was able to detect majority of fluoroquinolone resistant E. coli on rectal swabs prior to prostate biopsy.
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