Clinical study on the application of nanopore targeted sequencing technology for rapid and accurate detection of pathogens in patients with complicated urinary tract infections / 中华泌尿外科杂志

ABSTRACT

Objective:To evaluate the clinical value of nanopore targeted sequencing (NTS) in pathogens detection in urinary tract by comparing the results of different tests performed on the same urine sample.Methods:The results of NTS and urine culture test collected from 326 patients in the Department of Urology of People's Hospital of Wuhan University from July 2020 to June 2021 were retrospectively analyzed. There were 224 males and 102 females. The average age was (56.88 ± 14.58)years old. χ 2 test and Student’s test and Wilcoxon's sign rank test were used to analyze the differences of the pathogen detection rate, pathogen types results and detection time consuming between NTS and urine culture. The clinical value of the NTS in rapid detection of urinary pathogens was evaluated. Results:Among 326 hospitalized patients, the urinary tract microbes’ detecting rate of NTS was significantly higher than that of urine culture[67.80%(221/326)vs. 23.93%(78/326), χ2=130.25, P<0.01]. The uropathogens detecting rate of NTS was significantly higher than that of urine culture[54.29%(177/326)vs. 23.31%(76/326), χ2=38.95, P<0.01]. The number of urinary tract microbes detected by NTS was significantly higher than that of urine culture ( Z=11.49, P<0.01), the number of uropathogens was significantly higher than that of urine culture ( Z=9.67, P<0.01). The detection time of NTS and urine culture positive samples was (24.29±2.65) h and (49.28±11.30) h, the difference was statistically significant ( t =39.48, P<0.01). The results obtained by using NTS and urine culture were consistent in 135 (41.41%) samples. In 150 (46.01%) samples, NTS could detect the urinary tract microbes while urine culture cannot find, of which 112 cases (34.36%) were uropathogenic. In 27 cases (8.28%), more pathogens were detected by NTS except those from urine culture. In 6 cases (1.84%) re-detecting NTS after antibiotic therapy, the number of reads of primary uropathogen decreased gradually with the growth of colonizing bacteria or opportunistic pathogens appeared in the end. Re-examinations of urine culture could verify the results of NTS detection on admission in 5 cases (1.53%). NTS in 2 cases (0.61%) could cover the uropathogens of subsequent several urine cultures. Conclusions:NTS has the advantages of rapid, sensitive and comprehensive detection of urinary tract infection pathogens. When urine culture is not yet reported or even negative, NTS already has a certain clinical reference value and can be used as an effective supplement to urine culture, which is conducive to the comprehensive judgment of the patient's condition.