Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing
Abstract Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2–4 days. Early and accurate antibiotic prescriptio...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-55635-z |
| _version_ | 1827310264367710208 |
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| author | Jawad Ali Wenche Johansen Rafi Ahmad |
| author_facet | Jawad Ali Wenche Johansen Rafi Ahmad |
| author_sort | Jawad Ali |
| collection | DOAJ |
| description | Abstract Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2–4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102–104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103–107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods. |
| first_indexed | 2024-04-24T19:56:56Z |
| format | Article |
| id | doaj.art-49ddf18d31b64a098e59d16443a799cf |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-24T19:56:56Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-49ddf18d31b64a098e59d16443a799cf2024-03-24T12:16:51ZengNature PortfolioScientific Reports2045-23222024-03-0114111610.1038/s41598-024-55635-zShort turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencingJawad Ali0Wenche Johansen1Rafi Ahmad2Department of Biotechnology, Inland Norway University of Applied SciencesDepartment of Biotechnology, Inland Norway University of Applied SciencesDepartment of Biotechnology, Inland Norway University of Applied SciencesAbstract Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2–4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102–104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103–107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.https://doi.org/10.1038/s41598-024-55635-z |
| spellingShingle | Jawad Ali Wenche Johansen Rafi Ahmad Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing Scientific Reports |
| title | Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing |
| title_full | Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing |
| title_fullStr | Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing |
| title_full_unstemmed | Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing |
| title_short | Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing |
| title_sort | short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing |
| url | https://doi.org/10.1038/s41598-024-55635-z |
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