This dataset is part of a dry-lab interlaboratory study conducted across Germany, regarding bacterial outbreak detection based on NGS data, with a focus on bioinformatic analysis of four species to identify potential variability caused by different data analysis approaches and human interpretation. Participants were asked to follow their usual in-house protocols while adhering to the general guidelines. A quality assessment (with sample exclusion) was followed by 7-gene Multilocus-Sequence Typing (MLST), core genome Multilocus Sequencing Typing (cgMLST), and SNP calling. The participants were then asked to identify clusters. The study was not intended to resemble a standard proficiency test with a passing/failing grade, but rather to investigate and quantify obvious variability in the results and, where possible, the reasons for it. For this purpose, the datasets included borderline cases in terms of quality.