DOI: 10.5281/zenodo.16721528
title: Bacterial Genomic Sequences (FASTA) from Bloodstream Infections in Acute Leukemia Patients with Sepsis

description: 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