Mannheimia haemolytica whole genome sequencing
Prior to library preparation, the extracted DNA was amplified using the REPLI-g Midi Kit (Qiagen, Germany) following the manufacturers instructions. Amplified DNA was debranched to prevent pore clogging during sequencing, as suggested by Oxford Nanopore Technologies (SQK-LSK112, Oxford Nanopore Technologies, Oxford, United Kingdom). Library preparation was performed using the Native Barcoding Kit 24 V14 (SQK-NBD114.24, Oxford Nanopore Technologies, Oxford, United Kingdom) following manufacturers instructions. M. haemolytica isolates with identical animal IDs were assigned to the same flow cell (n=24 isolates per flow cell) to avoid batch effect when comparing swab types. Animal ID was randomized to flow cell, and unique barcodes were assigned to each M. haemolytica isolate within a given sequencing pool. DNA was sequenced on a PromethION P2 Solo or PromethION P2 Integrated sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom) using the R10.4.1 flow cell and the Super Accurate Model (MinKNOW v23.07.15/Guppy v7.1.4 and  MinKNOW v24.11.8/Dorado v7.6.7, respectively). Flow cells were run for 72 hours. Isolates that failed to assemble at least one contig with over 1 Mb after sequencing were re-prepped and sequenced following the same procedures.