Klebsiella aerogenes complex cgMLST scheme

This is a chewBBACA-generated cgMLST scheme used for typing Klebsiella aerogenes complex (KAC) species to clonal cluster (CC) level.

Usage Instructions

1. Install chewBBACA.
2. Install cgmlst-dists.
3. Pull all files in this repository.
4. Run AlleleCall in chewBBACA with the downloaded files. Example command: chewBBACA.py AlleleCall -i /path/to/InputAssemblies -g /path/to/KAC_wgMLST -o /path/to/OutputFolderName --cpu 20 --genes-list KAC_cgMLST_2067
5. Concatenate the output file named results_alleles.tsv with the pre-called dataset named pre-called_cgMLST_dataset.tsv.
6. Run cgmlst-dists on the combined dataset to obtain the pairwise cgMLST distances.
7. You may gather the distance matrix, using csvtk or R, to find out the closest genome and the number of different loci in the pre-called dataset for each of your query genomes.
8. Check pre-defined CC for each pre-called genome and evaluate the distance using the pre-defined cutoff for CC determination.

Citation

Please cite the following work when using this database:

Feng, Y., Yang, Y., Hu, Y., Xiao, Y., Xie, Y., Wei, L., Wen, H., Zhang, L., McNally, A., and Zong, Z. (2024). Population genomics uncovers global distribution, antimicrobial resistance, and virulence genes of the opportunistic pathogen Klebsiella aerogenes. Cell Reports, 43. https://doi.org/10.1016/j.celrep.2024.114602