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], and The 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 Taxa Taxa Subtype Acinetobacter calcoaceticus-baumannii complex (ACB complex) Acinetobacter baumannii Acinetobacter calcoaceticus Acinetobacter pittii Acinetobacter nosocomialis Enterococcus Enterococcus faecium Enterococcus faecalis Enterococcus avium Enterococcus casseliflavus Enterococcus durans Enterococcus gallinarum Enterococcus hirae Enterococcus dispar Enterococcus saccharolyticus Sphingomonas paucimobilis Sphingomonas paucimobilis Elizabethkingia Elizabethkingia Elizabethkingia meningoseptica Elizabethkingia meningoseptica Listeria monocytogenes (1/2a , 1/2b, 4b) Listeria monocytogenes (1/2a , 1/2b, 4b) Neisseria meningitidis Neisseria meningitidis Pseudomonas aeruginosa Pseudomonas aeruginosa Candida Candida albicans Candida glabrata Candida krusei (Issatchenkia orientalis) Candida tropicalis Candida parapsilosis Candida kudriavzevii (Pichia kudriavzevii ) Haemophilus influenzae Haemophilus influenzae Hib (Type 2) Haemophilus influenzae Hib (Type 1) Staphylococcus aureus Staphylococcus aureus Staphylococcus epidermidisStaphylococcus hominisStaphylococcus haemolyticus Staphylococcus lugdunensisStaphylococcus saprophyticus Streptococcus Streptococcus agalactiae Streptococcus pneumoniae Streptococcus pyogenes Streptococcus gallolyticus Streptococcus gordonii Streptococcus intermedius Streptococcus mutans Streptococcus pseudintermedius Enterobacteriaceae / Enterobacteriaceae (cloacal) Enterobacter dissolvens Enterobacter asburiae Enterobacter hormaechei Escherichia coli Escherichia coli Klebsiella Klebsiella oxytoca Klebsiella pneumoniae Proteus spp. Proteus mirabilis Proteus hauseri Proteus penneri Proteus vulgaris Serratia marcescens Serratia marcescens Shigella Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonnei Pseudomonas Pseudomonas aeruginosa Pseudomonas putida Salmonella Typhi Salmonella Typhi Morganella morganii Morganella morganii Providencia spp. Providencia spp. Yersinia enterocolitica Yersinia enterocolitica Listeria monocytogenes Listeria monocytogenes Micrococcus spp. Micrococcus spp. Trichosporon spp Trichosporon spp Candida auris Candida auris Enterobacter aerogenes Enterobacter aerogenes Micrococcus luteus Micrococcus luteus Bacillus spp. Bacillus spp. Geotrichum sp. Geotrichum sp. Stenotrophomonas maltophilia Stenotrophomonas maltophilia. Burkholderia Burkholderia cepacia Burkholderia multivorans Burkholderia cenocepacia