Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit

Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections

“…Comparison of NS to SC found that on average NS could identify up to 77% of cultured bacterial species and 76% of cultured fungal species, and predicted up to 81% of observed AMR phenotypes. These results are comparable to previous studies comparing NS and SC results ( 17 , 28 , 38 , 52 ), suggesting that NS could be used to guide early antimicrobial therapy following surgery. Given the speed with which NS can identify microbial species and predict AMR phenotypes, future investigations should determine whether NS can be used in replacement of bile cultures for detection and characterization of bile microbes.…”

“…Increased depth of AMR typing has the potential to improve antimicrobial therapy by enabling a more targeted approach. In a recent 10-week clinical trial, same-day NS results were used to make changes to antibiotic treatment of bacterial respiratory infection in a UK intensive care unit ( 17 ). In the majority of cases, NS results resulted in one of more antibiotics being stopped completely or a more narrow-spectrum treatment being administered ( 17 ).…”

“…Bile cultures are often polymicrobial, a mixture of anaerobic and aerobic species, carry multiple antimicrobial resistance (AMR) phenotypes, and contain fungal species ( 11 , 14 – 16 ). This contributes to delays in timely results, and the temporal separation between the initial broad-spectrum treatment and the acquisition of all the diagnostic information often results in uncertainty and the administration of multiple empirical antimicrobials ( 17 ). Moreover, an estimated 30% of SSIs are associated with negative culture results ( 18 ), and bile cultures have been found to be poor predictors of AMR patterns in postoperative infections ( 16 ).…”

“…However, in practice, these technologies require at least 16 h for the sequencing run alone, and analysis of the sequencing data can only be performed once the sequence run has concluded ( 24 , 28 ). When considering sample preparation and analysis, this leads to an overall sample-to-result turnaround time greater than 24 h. Recently, there has been growing interest in metagenomic Nanopore sequencing (NS) for rapid microbial identification and AMR genotyping ( 17 , 28 – 45 ). NS involves use of protein nanoparticles set in electrically-resistant polymer membranes contained within devices referred to as flow cells ( 46 , 47 ).…”

“…Changes to the electrical current are used to determine nucleotide base sequence (base calling) ( 46 , 47 ), enabling real-time sequence analysis and detection of microbial DNA/RNA to be performed. This has reduced overall sample-to-answer time to as little as 6 h ( 17 , 28 , 38 ), and clinical application of the technology has been demonstrated in several proof-of-concept studies that highlight its ability to detect and characterize microbes from a wide array of sample types ( 28 , 38 – 45 ), to monitor AMR in the hospital setting ( 29 – 32 ) and carry out real-time surveillance of viral outbreaks ( 33 – 37 ).…”