Research Information System
INFECTIOUS DISEASES AND CLINICAL MICROBIOLOGY, vol.1, no.3, pp.128-133, 2019 (ESCI)
Objective: Timely diagnosis is crucial for successful treatment of infections. Contemporary diagnostics of clinically significant infections relies on a variety of laboratory-based tests. However, the routine microbiological methods, per se are not always confirmatory for the accurate diagnosis in some cases with a significant time delay. Rapid detection of causative agents using nanopore-based metagenomic sequencing is reported in a case of suspected tuberculosis not confirmed using conventional microbiology diagnostics, and in a case of suspected brucellosis with delayed confirmation by conventional microbiology. Materials and Methods: This report includes two cases. Patient-1 was clinically diagnosed with peritoneal tuberculosis while Patient-2 had relapsing brucellosis. Cultures and PCR were negative for the peritoneal fluid of Patient-1. Serological determinants for brucellosis were under the thresholds for Patient-2. The blood culture was positive for Brucella spp; however, the results were available only after seven days. Peritoneal fluid and blood sample were obtained from Patient-1 and Patient-2, respectively. Total DNA was extracted using commercial kits. Shotgun metagenomic sequencing was performed using Oxford Nanopore Technologies. Read-event data were base-called by the software Metrichor using workflow v2.39.3. Results: For Patient-1, the first Mycobacterium tuberculosis reads were confidently detected in 20 minutes, for Patient-2 the first Brucella melitensis read was detected at 30-minutes-time-point. Overall, the pathogens were detected within 6 hours. We demonstrated a real-time nanopore sequencing technology for the rapid detection of infectious agents in two crucial cases where traditional microbiological methods failed to reveal the pathogens. Conclusion: In this report, we present that real-time sequencing can not only detect conventionally unrevealed pathogens, but it can achieve this in a tight time-frame. Therefore, it could be said that the nanopore sequencing has the promise to enhance our ability to diagnose infectious diseases.