A comprehensive repository of Acinetobacter baumannii to understand the molecular landscape of antimicrobial resistance
| S.No. | Field Name | Full Description of fields |
| 1 | Resistance profile | Resistance profile of complete and draft genome sequences of AB against commonly used antibiotics |
| 2 | Antibiogram | Antibiogram (MIC values) of complete and draft genome sequences of AB against commonly used antibiotics |
| 3 | Gene ID | Gene ids of the reference genome of AB i.e. Acinetobacter baumannii ATCC 17978 |
| 4 | Locus tag | Locus tag of reference genome of AB i.e. Acinetobacter baumannii ATCC 17978 |
| 5 | Protein ID | Protein ID of reference genome of AB i.e. Acinetobacter baumannii ATCC 17978 |
| 6 | Gene product | The product name of the gene |
| 7 | Protein function | The function performed by the protein |
| 8 | Protein length | The length of the protein |
| 9 | Localization | Localization of protein |
| 10 | Strain name | Name of the strain |
| 11 | Essentiality of the gene product | Whether the essentiality of the gene product is for survival of AB or for the virulence |
| 12 | Reported inhibitor | Reported inhibitor of the potential genes i.e (Essential genes or drug targets) |
| 13 | Criterion of essentiality | The criterion used to check the essentiality of the genes |
| 14 | Assay/technique performed | The detailed description of the assay/technique performed for the essentiality of the gene product |
| 15 | Condition of essentiality | The condition of the gene essentiality i.e. in vivo or in vitro |
| 16 | Evidance of drug targets | Genetic/Biochemical/computation evidance of drug targets |
| 17 | Validation of drug targets | Drug targets validated in vivo or in vitro |
| 18 | Non-human homologs | The non-human homolgs of the drug targets and essential genes |
| 19 | Non-human octamer homolgs | Non-human octamer homologs of drug targets and essential genes |
| 20 | Pan genome | Core genes of the drug targets and essential genes |
| 21 | Variant/Invariant genes | The potential drug targets has also been categorised as the invarint and variant genes |
| 22 | Pathway | The name of the pathway |
| 23 | EC number | Enzyme commission number |
| 24 | Reaction | The reaction of the pathway |
| 25 | Product | The product of the reaction |
| 26 | Reactant | The reactant of the reaction |
| 27 | Substrate | the substrate of the reaction |
| 28 | PDB ID | PDB Ids of Acinetobacter baumannii |
| 29 | Chain ID | Chain Ids of Acinetobacter baumannii |
| 30 | Structure title | Structure title of PDB structure |
| 31 | Ligand ID | Ligand ID of PDB structure |
| 32 | Ligand name | Ligand name of PDB structure |
| 33 | Functional unit of proteins | Homomer, heteromer |
| 34 | Chain length | Chain length of protein structure |
| 35 | Co-crystallized structure | Co-crystallized structure of Proteins |
| 36 | Natural substrate | Natural substrate of proteins |
| 37 | Mutant available | Mutant defined in PDB structure |
| 38 | Experimental methods | Experimental methods used to generate PDB structure |
| 39 | Macromoleculae name | Macromoleculae name of PDB |
| 40 | Sigma factors | The locus tag and protein name of sigma factors |
| 41 | Two component system | The locus tag and protein name of two component system |
| 42 | Transcription factors | The locus tag and protein name of transcription factors |
| 43 | Experimental evidance | Experimental evidance of sigma factors, two-component systm and transcription factors |
| 44 | Gene ontology (Molecular function) | Gene ontology (Molecular function) of sigma factors, transcription factors and TCS |
| 45 | Gene ontology (Cellular component) | Gene ontology (Cellular component) of sigma factors, transcription factors and TCS |
| 46 | Gene ontology (Biological process) | Gene ontology (Biological process) of sigma factors, transcription factors and TCS |
| 47 | Gene name | Gene name of drug resistant determinants |
| 48 | Strain name | Strain name of the corresponding Dr determinanats |
| 49 | Locus tag of DR determinants | Locus tag of DR determinants of different strains |
| 50 | Protein ID of DR determinants | Protein ID of DR determinants of different strains |
| 51 | Product of DR determinants | Product of DR determinants |
| 52 | Locus tag of DR determinats | Locus tag of reference strain of the corresponding DR determinats |
| 53 | Antibiotic name | Name of the antibiotic against which gene is showing resistance |
| 54 | Antibiotic class | Class of the antibiotic against which gene is showing resistance |
| 55 | Broad mechanism of resistance | Specific mechanism of resistance |
| 56 | Specific mechanism of resistance | Specific mechanism of resistance |
| 57 | Enzyme class | Class of enzymes of DR determinants |
| 58 | Similar mechanism of resistance in other species | Similar mechanism of resistance in other species |
| 59 | Mutation observed | Mutation observed in DR determinats |
| 60 | Role of mutation | Role of mutation in conferring resistance |
| 61 | Insertion elements | Insertion elements accompained with DR determinants |
| 62 | Associated with | DR determinants associated with chromosome or plasmids |
Ans. Acinetobacter baumannii (AB) is identified as the most critical drug resistant (DR) pathogen by WHO. It is, therefore, imperative that drug resistant determinants and trends of antibiotic resistance are understood across various clinical isolates of AB. It is crucial that the genomic determinants of various clinically resistant phenotypes are consolidated along with detailed annotation so as to understand the entire molecular landscape of drug resistance in AB. Towards this, we have developed a comprehensive repository of drug resistant determinants of AB i.e. ‘Ab-AMR’. It is expected that the genotype-phenotype correlation data on drug resistant determinants of clinical isolates with extensive annotation of AB reference genome makes ‘Ab-AMR’ a unique resource. We believe that this platform will offer a one-stop-shop resource for comprehensive annotation of AB genomes.
Ans. Ab-AMR consists drug resistance profile of 788 clinical isolates. The antibiogram (MIC values according to EUCAST and CLSI standard) of 788 isolates and 364 drug resistant determinants with reported resistance mechanisms along with detailed annotation have also been compiled. A. baumannii ATCC 17978 (Accession-CP000521.1), the reference strain, was annotated on January 1, 2014 and subsequently re-annotated on March 21, 2017 (NZ_CP018664.1). Therefore, the genome comparison of both, 2014 and 2017 versions was performed for maintaining the correct annotations as most of the literature refers to the earlier version of the reference genome. In CRAB, the reference coordinates of the revised reference genome (NZ_CP018664.1) are used to represent manually curated data on 614 essential genes, 81 reported drug targets, 1334 genes with known pathway with 1211 reactions, 221 PDB structures, 118 transcription factors, 4 sigma factors, 14 two component systems with their detailed annotation.
Ans. Yes, you can use Ab-AMR database’s complex query builder for the prioritization of potential drug targets. So far, 614 essential genes and 81 drug targets have been reported for CRAB. Out of which 58 genes were both drug targets and essential genes. This data along with detailed information have been embedded in Ab-AMR. The user can prioritize the potential genes by selecting core, no-human homologs, no-human octamer and invariant genes.
Ans.The reference genome of AB 17978 has 3838 genes in total. Out of which, 637 genes have been reported either as a drug targets or as an essential genes required for the survival and virulence of the bacteria. The pathway annotation has been done for all 3838 genes using Biocyc, KEGG (KASS) and PATRIC and detailed information such as pathway name along with Reaction, reactant, substrate and product has been compiled in Ab-AMR. To discriminate, essential and non-essential pathways, you can retrieve data of 637 genes by mentioning in the simple search text box, either specific pathway name or just simple type pathway and select essential pathways from the field list.
Ans.Yes, you can search for the genes conferring resistance to particular antibiotics by mentioning a particular antibiotic name in the simple search page under "DR determinants of particular antibiotics".
Ans. Extensive literature study was performed to get the genes of TF, Sigma and TCS. The annotated genes have been mapped on AB reference genome. The user has to mention either the name of the gene or the name of protein to fetch the information of TF, sigma and transcription factor.
Ans.Yes, You can discriminate the genes associated with either plasmid or chromosome by mentioning associated term (Plasmid or chromosome) in the text field of the search page.
Ans. Yes, You can discriminate the genes associated with different resistance mechanisms by mentioning associated term in the text field of the search page.
Ans. Yes, you can get the DR determinates data associated with IS elements by simply typing either IS elements name or by simply mentioning IS elements
Ans. If you find any errors in the resource, please contact any one of the team members present in the Contact us page.
Ans. The HOME page of Ab-AMR gives you the detailed information of 788 genomes of AB.