Genomic dissection of an enteroaggregative Escherichia coli strain isolated from bacteremia reveals insights into its hybrid pathogenic potential

01_EC092_r1_FastQC_rawdata.pdf, 02_EC092_r2_FastQC_rawdata.pdf: output file from EC092 genome raw data generated by FastQC analysis; 03_EC092_MultiQC_rawdata.pdf: output file from EC092 genome raw data analysis by MultiQC; 04_EC092_readlengthHistogram.txt: output file from EC092 genome raw data analysis by Readlenght; 05_EC092_R1_PE_fastpCleaned_fastQC.pdf, 06_EC092_R1_SingleEnd_fastpCleaned_fastQC.pdf, 07_EC092_R2_PE_fastpCleaned_fastQC.pdf and 08_EC092_R2_SingleEnd_fastpCleaned_fastQC.pdf: output file from EC092 genome processed data analysis by FastQC; 09_MultiQC_EC092_processed_data.pdf: output file from EC092 genome processed data analysis by MultiQC; 10_EC092_PE_readlengthHistogram.txt, 11_EC092_SE_r1_readlengthHistogram.txt and 12_EC092_SE_r2_readlengthHistogram.txt: output file from EC092 genome processed data analysis by Readlenght; 13_EC092_prokka_output.txt: output file generated by EC092 assembled genome by Prokka analysis; 14_EC092_quast_output.ods: output file generated by EC092 assembled genome by Quast analysis; 15_EC092_Abricate_ecoli_vf_output.txt: output files generated in EC092 genome analysis by Abricate; 16_EC092_NCBI Blast_Pic 042, 17_EC092_NCBI Blast_Pet 042.pdf, 18_EC092_ NCBI Blast_Sat CFT073.pdf and 19_EC092_NCBI Blast_SepA Shigella Flexneri.pdf: protein sequence alignments between EC092 SPATEs predicted amino acid sequence and reference strains; 20_EC092_ClermonTyping Report.pdf: output generated from EC092 genome analysis by Clermont typing online tool; 21_EC092_MLST_CGE.pdf, 22_EC092_Resfinder_CGE.pdf, 23_EC092_Serotypefinder_CGE.pdf: output generated from EC092 genome analysis by Center for genomic epidemiology online tools; 24_EC092_adhesion_invasion_DB_FINAL.txt, 25_EC092_autotransporters_DB_FINAL.txt, 26_EC092_target_genes_DB_FINAL.txt, 27_EC092_Fimbriae_DB_FINAL.txt, 28_EC092_TVISS_DB_FINAL.txt, 29_EC092_iron_uptake_DB_FINAL.txt and 30_EC092_toxins_DB_FINAL.txt: raw data generated for heatmaps constructions; 31_EC092_tree_ecoli_pathotypes.tre and 32_EC092_tree_ecoli_EAEC.tre: raw data generated by KSNP4 analysis during phylogenetic trees constructions; 33_EC092_aap_split_452.txt, 34_K44V1_aap_split_218.txt, 35_K45V1_aap_split_234.txt, 36_EC092_aggR_split_446.txt, 37_K44V1_aggR_split_244.txt, 38_K45V1_aggR_split_3.txt, 39_EC092_aaiA-P_split_421.txt, 40_K44V1_aaiA-P_split_189.txt, 41_K45V1_aaiA-P_split_193.txt, 42_EC092_aaiQ-W_split_433.txt, 43_K44V1_aaiQ-W_split_203.txt, 44_K45V1_aaiQ-W_split_209.txt, 45_EC092_aaiX_split_110.txt, 46_K44V1_aaiX_split_207.txt, 47_K45V1_aaiX_split_212.txt, 48_EC092_aat_split_355.txt, 49_K44V1_aat_split_186.txt, 50_K45V1_aat_split_218.txt, 51_EC092_pet_split_453.txt, 52_K44V1_pet_split_228.txt, 53_K45V1_pet_split_239.txt, 54_EC092_pic_split_433.txt, 55_K44V1_pic_split_203.txt, 56_K45V1_pic_split_209.txt, 57_EC092_sat_split_110.txt, 58_K44V1_sat_split_7.txt, 59_K45V1_sat_split_10.txt, 60_EC092_sepA_split_435.txt, 61_K44V1_sepA_split_206.txt, 62_K45V1_sepA_split_211.txt: raw data deposited in NCBI used for genetic neighborhood analysis in Easyfig; 63_EC092_SPATEs_production_blott.pdf: immunoblottings raw images from SPATEs production by EC092; 64_EC092_serum_resisntance_CFU.xlsx: colony forming units counting for bacterial survival after EC092 serum resistance assay; 65_EC092_serumresistance_data_and_graph.pdf: logCFU from serum resistance assay plotted by Graphpad Prism.