Bacterial Genomic Sequences (FASTA) from Bloodstream Infections in Acute Leukemia Patients with Sepsis

Custom FASTA databases substantially enhance taxonomic accuracy in metagenomic analyses by mitigating redundancy and misannotations inherent in standard references (Simon et al., 2019; Van Uffelen et al., 2024). By incorporating context-specific genomes—such as host-relevant or environment-specific taxa—they improve alignment precision and reduce false positives. These curated databases also facilitate consistent benchmarking and enable more reliable tool evaluation (Ames et al., 2013), making them indispensable for robust metagenomic interpretation in both clinical and environmental settings. To meet the specific diagnostic and research needs of our centre, we constructed a custom database targeting pathogens commonly implicated in sepsis, encompassing both Gram-positive and Gram-negative bacteria, as well as prevalent fungal species. Despite their typical classification as contaminants or commensals, organisms like Burkholderia spp., Micrococcus spp., non-aureus Staphylococcus spp., and Bacillus spp. were deliberately included due to the immunocompromised status of many patients at our institution. The BioFire® BCID2 panel was used as a reference for defining a comprehensive and clinically relevant organism list (Table 1).The final database was derived by selecting only those FASTA sequences corresponding to species listed in Table 1, sourced from two main references:The Pathogenic Microbial Bowtie2 index by Nikolay Oskolkov [1], andThe 16S rRNA database curated by the Emu pipeline [2].References[1] Oskolkov, Nikolay (2022). Bowtie2 index for pathogenic microbial species of NCBI NT from May 2020. NBIS / SciLifeLab. https://doi.org/10.17044/scilifelab.21185887.v1[2] Curry, K.D., Wang, Q., Nute, M.G. et al. (2022). Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nat Methods, 19, 845–853. https://doi.org/10.1038/s41592-022-01520-4 — Database link TaxaTaxa SubtypeAcinetobacter calcoaceticus-baumannii complex (ACB complex)Acinetobacter baumanniiAcinetobacter calcoaceticus Acinetobacter pittiiAcinetobacter nosocomialisEnterococcus Enterococcus faeciumEnterococcus faecalis Enterococcus aviumEnterococcus casseliflavusEnterococcus durans Enterococcus gallinarumEnterococcus hirae Enterococcus disparEnterococcus saccharolyticusSphingomonas paucimobilisSphingomonas paucimobilisElizabethkingia Elizabethkingia Elizabethkingia meningosepticaElizabethkingia meningosepticaListeria monocytogenes (1/2a , 1/2b, 4b)Listeria monocytogenes (1/2a , 1/2b, 4b)Neisseria meningitidisNeisseria meningitidisPseudomonas aeruginosaPseudomonas aeruginosaCandidaCandida albicansCandida glabrataCandida krusei (Issatchenkia orientalis)Candida tropicalis Candida parapsilosisCandida kudriavzevii (Pichia kudriavzevii )Haemophilus influenzae Haemophilus influenzae  Hib (Type 2)Haemophilus influenzae  Hib (Type 1)Staphylococcus aureusStaphylococcus aureusStaphylococcus epidermidisStaphylococcus hominisStaphylococcus haemolyticusStaphylococcus lugdunensisStaphylococcus saprophyticusStreptococcusStreptococcus agalactiaeStreptococcus pneumoniaeStreptococcus pyogenesStreptococcus gallolyticusStreptococcus gordoniiStreptococcus intermediusStreptococcus mutansStreptococcus pseudintermediusEnterobacteriaceae / Enterobacteriaceae (cloacal)Enterobacter dissolvensEnterobacter asburiaeEnterobacter hormaecheiEscherichia coliEscherichia coliKlebsiella Klebsiella oxytocaKlebsiella pneumoniaeProteus spp.Proteus mirabilisProteus hauseriProteus penneriProteus vulgarisSerratia marcescensSerratia marcescensShigellaShigella boydiiShigella dysenteriaeShigella flexneriShigella sonneiPseudomonas Pseudomonas aeruginosaPseudomonas putidaSalmonella TyphiSalmonella TyphiMorganella morganiiMorganella morganiiProvidencia spp.Providencia spp.Yersinia enterocoliticaYersinia enterocoliticaListeria monocytogenesListeria monocytogenesMicrococcus spp.Micrococcus spp.Trichosporon sppTrichosporon  sppCandida aurisCandida aurisEnterobacter aerogenesEnterobacter aerogenesMicrococcus luteusMicrococcus luteusBacillus spp.Bacillus spp.Geotrichum sp.Geotrichum sp.Stenotrophomonas maltophiliaStenotrophomonas maltophilia.Burkholderia Burkholderia cepaciaBurkholderia  multivoransBurkholderia cenocepacia