DNA was extracted from IS and NP/OP swab samples using the DNeasy PowerSoil Pro kit (QIAGEN) on QIAcube robots.  Libraries were prepared from up to 10 ng of extracted DNA using the Illumina DNA Prep kit and IDT for Illumina unique dual indexes. Negative extraction controls (reagents only) and negative library controls (microbial DNA-free water) were processed alongside the NP/OP and IS samples to assess background contamination from reagents and the environment. Sequencing libraries were combined into two separate pools, which were sequenced on the Illumina MiniSeq to evaluate quality and barcode distribution. Each pool was then sequenced on two lanes of an S4 300-cycle kit using an Illumina NovaSeq 6000 instrument (Center for Applied Genomics, Childrens Hospital of Philadelphia).