DOI: 10.5281/zenodo.13235446
title: BacSPaD: A robust bacterial strains' pathogenicity resource based on integrated and curated genomic metadata

description: The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis.In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5,502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface, accessible at https://bacspad.altrabio.com.
description: Metadata fields



Description







pathogenicity_label



Labeling according to pathogenicity - either non-pathogenic to humans (NHP) or pathogenic to humans (HP).





genome_id



Genome ID from Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database.





genome_name



Genome name.





strain



Strain name according to National Center for Biotechnology Information (NCBI) taxonomy.





species



Species name according to NCBI taxonomy.





genus



Genus name according to NCBI taxonomy.





family



Family name according to NCBI taxonomy.





order



Order name according to NCBI taxonomy.





class



Class name according to NCBI taxonomy.





phylum



Phylum name according to NCBI taxonomy.





biosample_accession



Biosample accession number ID from NCBI.





taxon_id



Taxon ID from NCBI taxonomy.





serovar



Taxonomy below subspecies; a variant which is usually based on its antigenic properties. Same as serotype (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





biovar



Variant distinguished by its unique biochemical or physiological traits (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





pathovar



Taxonomy below subspecies; a variety usually based on its pathogenic properties. Sometimes used as equivalent to subspecies. (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/)





mlst



Genotypic identifier based on housekeeping gene sequences.





other_typing



Strain typing or characterization methods beyond the standard approaches such as MLST (Multilocus Sequence Typing). Each "genotype" followed by a number (e.g., genotype:1 or genotype:1903) denotes a unique genetic profile or pattern that has been identified in the microbial species under investigation.





culture_collection



Reference to a deposited microbial strain in a repository, identified by a unique accession number.





type_strain



Indication if it is a type strain (‘yes’ or ‘’). A type strain is a nomenclatural standard for a particular bacterial species, serving as a reference point for its definition and identification.





completion_date



Date of project completion.





publication



Associated scientific publication identifier.





bioproject_accession



Unique identifier to corresponding project in NCBI.





assembly_accession



Unique identifier to corresponding genome assembly in NCBI. Refers to a specific version of a genome assembly submitted to a database like NCBI's GenBank. 





genbank_accessions



Unique identifier(s) of GenBank assembly/assemblies in NCBI. 





refseq_accessions



Unique identifiers assigned to sequences within the Reference Sequence (RefSeq) database. RefSeq sequences are curated by NCBI staff and collaborators.





sequencing_centers



Sequencing center (e.g. University ‘x’, Hospital ‘y’).





sequencing_platform



Sequencing platform (e.g. Illumina, PacBio).





sequencing_depth



Average number of times each nucleotide in a genome is sequenced. 





assembly_method



Methodology used to assemble the genomic sequences. 





chromosomes



Number of associated chromosomes.





plasmids



Number of associated plasmids.





contigs



Number of associated contigs.





genome_length



Genome length measured in base pairs (bp). 





gc_content



Measure of the proportion of guanine (G) and cytosine (C) nucleotides in the DNA sequence, expressed as a percentage of the total nucleotide composition.





patric_cds



Number of protein-coding sequences (CDS) annotated or sourced from PATRIC (previous version of BV-BRC).





refseq_cds



Number of protein-coding sequences (CDS) annotated or sourced from RefSeq database.





isolation_source



Corresponding origin of isolation. This attribute provides information about the ecological niche or source of the bacterial strain.





isolation_comments



Additional notes or comments regarding the isolation of a specific bacterial strain.





collection_date



Date on which a specific bacterial strain was collected or isolated from its source.





isolation_country



Country associated with the biological sample isolation. 





geographic_location



Geographical descriptors associated with the biological sample isolation.





other_environmental



Supplementary attribute to describe specific environmental conditions or contexts associated with the biological sample.





host_gender



Host gender.





host_age



Host age.





host_health



Host health status or condition. 





body_sample_site



Specific anatomical site or location from which the biological sample was collected.





other_clinical



Additional clinical information or metadata associated with the biological sample.





antimicrobial_resistance



This field shows genomes that have been specifically tested against certain antibiotics and the resulting phenotype from that test. Note that a genome can have multiple antibiotic phenotypes, such as being resistant to one drug and susceptible to another. Values in this field include ‘Resistant’,’Susceptible’ or ‘Intermediate’ (https://www.bv-brc.org/docs/quick_references/organisms_taxon/antimicrobial_resistance.html).





antimicrobial_resistance_evidence



Indicates the information source behind the AMR designation. Allowable values include "Computational Prediction”, "Computational Method" , and "AMR Panel” (https://www.bv-brc.org/docs/quick_references/organisms_taxon/antimicrobial_resistance.html)





gram_stain_bvbrc



Gram staining information (“positive” or “negative”) sourced from BV-BRC.





cell_shape



Cell shape information (e.g. Bacilli, Cocci).





motility



Motility information (“yes”: motile, “no”: non-motile).





temperature_range



Indication on phenotype associated with range of temperature at which the organism is known to thrive, survive, or exhibit optimal growth (e.g. ‘Mesophilic’).





optimal_temperature



Optimal temperature at which the organism is known to exhibit optimal growth.





oxygen_requirement



Specific oxygen conditions a microorganism requires to survive; Values include ‘Aerobic’, ‘Anaerobic’, ‘Facultative’, or ‘Microaerophilic’.





habitat



Natural or artificial habitat in which the bacteria resides or was found.





disease



Host disease.





comments



Supplementary information in form of comments providing further contextual details.





additional_metadata



Supplementary metadata providing further contextual details.





env_broad_scale



Broad-scale environmental context (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





env_local_scale



Local-scale environmental context (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





env_medium



Environmental medium/material. keywords describing the material displaced by the entity during sampling (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





isol_growth_condt



Description or url indication of isolation and growth condition specifications (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





project_name



A concise name that describes the overall project (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





pathogenicity_details



Additional bacterial strain information on pathogenicity (e.g;. ‘commensal’, or ‘diphtheria-like symptoms’).





host_disease



Name of relevant disease, e.g. Salmonella gastroenteritis (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





host_health_state



Information regarding health state of the individual sampled at the time of sampling (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





host_disease_outcome



Final outcome of disease, e.g., death, chronic disease, recovery.





host_description



Additional host information not included in other defined vocabulary fields (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





host_disease_stage



Stage of disease at the time of sampling (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





pathotype



Bacterial specific pathotype (e.g. Eschericia coli - STEC, UPEC) - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/.





subsource_note



Subsource note.  Further details about the origin, isolation method, or other relevant information regarding the sample used.





note



Additional note. This can include details about the source of the sequence, experimental conditions, characteristics of the organism, or any other relevant information.





description



Further details on isolation source or organism.





biotic_relationship



Observed biotic relationship (['', 'free living', 'parasite', 'commensal', ‘symbiont’]) - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/





biome



Major environment type(s) where sample was collected (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).





host_status



Information on host health status.





risk_group



Risk group classification - based on their potential hazard to human health and the environment (species-level, ranges from 1 to 3; 3 representing the highest hazard).





Note on infection mode



Further details on infection mode.





checkm_compl_final



Genome completeness (%) according to CheckM tool v1.1.6. 





checkm_contam_final



Genome contamination (%) according to CheckM tool v1.1.6. 





disease_category



Disease category (e.g. “Respiratory diseases”). 





disease_subcategory



Subcategory of the main disease category (e.g. “Pneumonia”). When the specific infectious disease name is not available, an associated keyword is given instead (e.g. “Pertussis”).





isolation_source_category



Isolation source category (e.g. “Respiratory tract”). 





disease_comb



Combination of the disease category and disease subcategory (e.g. Respiratory Diseases - Pneumonia).