Citrobacter rodentium STAMP barcode and whole genome sequencing

Sequencing data monitoring the diversity of a population of the diarrhea causing bacterium Citrobacter rodentium during colonization of its natural host, mice. To enable monitoring during infection we introduced short, random, ~20 nucleotide DNA tags (barcodes) at a neutral location in the C. rodentium genome. We monitored barcode diversity using high-throughput DNA sequencing and the STAMP (Sequence Tag-based Analysis of Microbial Populations) computational framework. We also performed whole genome sequencing on individual isolates to monitor genetic changes that occurred during infection. For more information see our preprint on bioRxiv: https://doi.org/10.1101/2022.10.11.511778