28 June 2024 | Ela Sauerborn, Nancy Carolina Corredor, Tim Reska, Albert Perlas, Samir Vargas da Fonseca Atum, Nick Goldman, Nina Wantia, Clarissa Prazeres da Costa, Ebenezer Foster-Nyarko, Lara Urban
The article discusses the application of real-time genomics, specifically nanopore sequencing, to enhance the accuracy of antibiotic resistance profiling in clinical settings. The authors present a case study involving a multi-drug resistant *Klebsiella pneumoniae* infection to demonstrate how real-time genomics can detect low-abundance plasmid-mediated resistance, which is often missed by conventional methods. They compare the performance of real-time genomics with clinically established diagnostics, such as MALDI-TOF MS and VITEK2, and show that real-time genomics can accurately identify novel antibiotic resistance genes, such as the blaKPC-14 gene, which confer resistance to Ceftazidime-Avibactam (CAZ-AVI). This capability has significant implications for clinical decision-making and patient outcomes, as it allows for the early administration of appropriate antibiotics and reduces the risk of resistance transmission. The study highlights the potential of real-time genomics to improve clinical management and patient outcomes, particularly in complex infections where traditional methods may fall short. The authors also discuss the limitations of their study, including the need for larger sample sizes and more frequent sampling, and emphasize the importance of further research to fully integrate real-time genomics into clinical practice.The article discusses the application of real-time genomics, specifically nanopore sequencing, to enhance the accuracy of antibiotic resistance profiling in clinical settings. The authors present a case study involving a multi-drug resistant *Klebsiella pneumoniae* infection to demonstrate how real-time genomics can detect low-abundance plasmid-mediated resistance, which is often missed by conventional methods. They compare the performance of real-time genomics with clinically established diagnostics, such as MALDI-TOF MS and VITEK2, and show that real-time genomics can accurately identify novel antibiotic resistance genes, such as the blaKPC-14 gene, which confer resistance to Ceftazidime-Avibactam (CAZ-AVI). This capability has significant implications for clinical decision-making and patient outcomes, as it allows for the early administration of appropriate antibiotics and reduces the risk of resistance transmission. The study highlights the potential of real-time genomics to improve clinical management and patient outcomes, particularly in complex infections where traditional methods may fall short. The authors also discuss the limitations of their study, including the need for larger sample sizes and more frequent sampling, and emphasize the importance of further research to fully integrate real-time genomics into clinical practice.