Clinical validation of loop-mediated isothermal amplification for the detection of Escherichia coli sequence type complex 131

Abstract

ABSTRACT The dissemination of Escherichia coli multidrug-resistant (MDR) STc131 is related to its persistence in the human gastrointestinal tract as efficient gut colonizers. Infection and prevention measures are the cornerstones for preventing STc131 spread. Oral decolonization therapies that target ST131 are being developed. There are no rapid methods available to identify STc131 in human specimens. A loop-mediated isothermal amplification (LAMP) assay (named LAMP-ST131) was developed for the detection of STc131 on well-characterized E. coli isolates and then compared to culture and PCR for urines and stool swabs. With E. coli isolates ( n = 720), LAMP-ST131 had a sensitivity (sens) of 100% [95% confidence interval (C.I.) = 98.1–100%)] and a specificity (spec) of 98.9% (95% C.I. = 97.5–99.5%). On urines ( n = 550), LAMP-ST131 had a sens of 97.6% (95% C.I. = 89.68–94.33%) and a spec of 92.3% (95% C.I. = 87.68–99.88%), while on stool swabs ( n = 278), LAMP-ST131 had a sens of 100% (95% C.I. = 88.7–100%) and a spec of 83.9% (95% C.I. = 78.8–87.9%). LAMP-ST131 detected 10 (urines) and 100 (stool swabs) gene copies/μL. LAMP-ST131 accurately identified STc131 within E. coli isolates and human specimens. The implementation of LAMP-ST131 will aid genomic surveys, enable the rapid implementation of effective infection prevention measures, and identify patients suitable for ST131 decolonization therapies. Such approaches will curb the spread of STc131 and decrease incidence rates of global MDR E. coli infections. IMPORTANCE We developed an accurate non-culture-based loop-mediated isothermal amplification (LAMP) methodology for the detection of (sequence type) STc131 among Escherichia coli isolates and human specimens. The use of LAMP-ST131 for global genomic surveillance studies and to identify patients that are suitable for ST131 decolonization therapies will be important for decreasing multidrug-resistant E. coli infections across the globe.