Genomic Typing, Antimicrobial Resistance Gene, Virulence Factor and Plasmid Replicon Dataset for the Important Pathogenic Bacteria Acinetobacter baumannii

The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates usually called 'the clones of high risk' often drive the spread of resistance within particular species. 

Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and developing of spread prevention measures. However, the availability and uniformity of the data derived from the genomic sequences often represents a bottleneck for such investigations. 

In this dataset, we present the results of a comprehensive genomic epidemiology analysis of 47,738 genomes (available in Genbank on March 10, 2026, which have passed reliability tests) of a dangerous bacterial pathogen Acinetobacter baumannii. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), intrinsic blaOXA-51-like gene variants, capsular (KL) and oligosaccharide (OCL) types, and cgMLST profiles are presented, as well as the assignment of particular isolates to twelve known international clones of high risk. The presence of antimicrobial resistance genes, virulence factors and plasmid replicons within the genomes is also reported. 

These data will be useful for researchers in the field of A. baumannii genomic epidemiology, resistance analysis and prevention measure development.

·         Summary table (table_summary): Contains typing information for all isolates, such as MLST sequence type (ST), international clones of high risk (IC) assignments, and capsule synthesis loci (KL) and lipooligosaccharide outer core loci (OCL)-based types.

·         AMR gene table (table_amr): Lists the AMR genes found in the genomes of all isolates, specifically those known to confer resistance to various classes of antimicrobial drugs.

·         Virulence gene table (table_vfdb): Provides information on the presence of genes encoding virulence factors as identified in the VFDB (Virulence Factor Database).

·         Plasmid replicon table (table_plasmid): Details the plasmid replicons detected in the genomes of the isolates.

·         cgMLST profile table (table_cgmlst): Includes the cgMLST profiles for the isolates, offering higher resolution and more detailed comparison than traditional MLST.

The instructions for the implementation of typical database use-case scenarios in Linux environment are provided in 'how_to_use.txt'.

The methods used for building the database and thorough description of file formats are provided in 'readme.pdf'.