Marker frequency analysis samples were prepared from bacterial cultures collected in stationary growth phases. Stationary-phase samples were obtained by extending incubation of overnight cultures for an additional 8 h. Cells were collected by centrifugation and pellets were immediately stored at -20C. Genomic DNA was extracted from cell pellets using the GeneMATRIX Bacterial & Yeast Genomic DNA Purification Kit (EurX). Sequencing libraries were prepared using the TruSeq DNA PCR-Free Library Preparation protocol (Illumina) and sequenced on Illumina HiSeq 2500 (paired-end 100 bp) or NextSeq 500 (paired-end 150 bp) platforms.