Cells from all 1218 isolates were pooled and nucleic acids were extracted using the Qiagen DNeasy kit according to the manufacturers protocol and DNA quality and concentration was assessed using a Nanodrop spectrophotometer and Qubit fluorometer (Thermo Scientific). Full length (V1 - V9) 16S amplicons were generated using the Oxford Nanopore 16S barcoding kit 24 v14 (Oxford Nanopore) according to the manufacturers instructions. Sequencing libraries were loaded onto R10.4.1 flow cells.