Ela Sauerborn from the Helmholtz Al Institute in Munich, Germany, presented at the Nanopore Community Meeting on the “Detection of hidden antibiotic resistance through real-time genomics.” They spoke about a specific case they published on complex pneumonia. Real-time genomics in the clinical microbiology lab is of interest. Sauerborn talked about the increase in carbapenem-resistant Enterobacteriales. They shared the typical microbiology and antibiotic resistance testing timeline in a hospital in Munich, for example. The team is comparing sequencing to culture-based approaches. The results provided information consistent with culture-based techniques and additional plasmid information. Sauerborn shared a case study from the hospital of a patient with a complex antibiotic-resistant infection. The team sequenced isolates before and after the treatment using R9.4.1 flowcells and Rapid Barcoding kits. The post-isolate had a relatively new carbapenem resistance gene. Deeper sequencing revealed the KPC-14 copy with eight hours of additional sequencing when exploring the pre-treatment isolate. The sequences have been assembled into complete genomes with the MLST profile of the KPC-14. It, therefore, seems that there was a single strain. Sauerborn emphasized the speed and accuracy of this diagnostics approach.
