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Updated manual curation for misannotated genes
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- RSA2 was mapped to ARO:3004445. This mapping was changed in the ARO to ARO:3005440. db_harmonisation should pick this up, but temporarily the issue is resolved through manual curation.
- grdA_1_QJX10702 (in resfinder curation) & EstD (in resfinder & megares curation) were mapped directly to drug classes. They are now mapped to correct parent AROs. grdA_1_QJX10702 -> ARO:3007380 and EstD -> ARO:3000557
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@Vedanth-Ramji
Vedanth-Ramji committed Jun 24, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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### Manual curation
- argannot_curation: (Tet)tetH:EF460464:6286-7839:1554 was incorrectly annotated as ARO:3004797 which is a beta-lactamase due to a loose RGI hit. This was manually curated to ARO:3000175.
- deeparg, megares, resfinderfg & sarg curation: ARO:3004445 -> ARO:3005440, this was due to a change in the ARO and the ARO number for the RSA2 gene changing. **db_harmonisation must change to take this into account**
> Incorrectly curated genes. Previously, they were directly mapped to drug classes. Correct parent ARO term has now been given.
> - resfinder_curation: grdA_1_QJX10702 -> 3007380 & EstDL136_1_JN242251 -> 3000557
> - megares_curation: MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD -> 3000557
## 0.4.0 - 10 June

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23 changes: 12 additions & 11 deletions argnorm/data/manual_curation/deeparg_curation.tsv
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Original ID ARO Gene Name in CARD Description
CP000034.1.gene2198.p01|FEATURES|ompF|multidrug|ompF 3000265 porin OmpF
AAB08925|FEATURES|tetU|tetracycline|tetU 3004650 tet(U)
CP000647.1.gene2517.p01|FEATURES|ompF|multidrug|ompF 3000265 porin OmpF
gi:504720116:ref:WP_014907218.1:|FEATURES|ompF|multidrug|ompF 3000265 porin OmpF
AM180355.1.gene2260.p01|FEATURES|ermC|MLS|ermC 3000250 ErmC
gi:501976562:ref:WP_012681429.1:|FEATURES|cystathionine_beta-lyase_patB|unclassified|cystathionine_beta-lyase_patB 3000025 patB
CP000034.1.gene2198.p01|FEATURES|ompF|multidrug|ompF 3000265 porin OmpF
AAB08925|FEATURES|tetU|tetracycline|tetU 3004650 tet(U)
CP000647.1.gene2517.p01|FEATURES|ompF|multidrug|ompF 3000265 porin OmpF
gi:504720116:ref:WP_014907218.1:|FEATURES|ompF|multidrug|ompF 3000265 porin OmpF
AM180355.1.gene2260.p01|FEATURES|ermC|MLS|ermC 3000250 ErmC
gi:501976562:ref:WP_012681429.1:|FEATURES|cystathionine_beta-lyase_patB|unclassified|cystathionine_beta-lyase_patB 3000025 patB
gi:447201629:ref:WP_001278885.1:|FEATURES|cob(I)alamin_adenolsyltransferase|unclassified|cob(I)alamin_adenolsyltransferase 0010004 RND type drug efflux https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696896/
gi:489831097:ref:WP_003734834.1:|FEATURES|cystathionine_beta-lyase_patB|unclassified|cystathionine_beta-lyase_patB 3000025 patB
gi:685904080:ref:WP_031644138.1:|FEATURES|cystathionine_beta-lyase_patB|unclassified|cystathionine_beta-lyase_patB 3000025 patB
NP_253005.1|FEATURES|MvaT|multidrug|MvaT 3004069 MvaT
NP_417544.5|FEATURES|patA|fluoroquinolone|patA 3000024 patA
NP_416340.1|FEATURES|mgrB|multidrug|mgrB 3003820 mgrB
gi:489831097:ref:WP_003734834.1:|FEATURES|cystathionine_beta-lyase_patB|unclassified|cystathionine_beta-lyase_patB 3000025 patB
gi:685904080:ref:WP_031644138.1:|FEATURES|cystathionine_beta-lyase_patB|unclassified|cystathionine_beta-lyase_patB 3000025 patB
NP_253005.1|FEATURES|MvaT|multidrug|MvaT 3004069 MvaT
NP_417544.5|FEATURES|patA|fluoroquinolone|patA 3000024 patA
NP_416340.1|FEATURES|mgrB|multidrug|mgrB 3003820 mgrB
AUW34359.1|FEATURES|RSA-2|beta-lactam|RSA-2 3005440 RSA2 beta-lactamase ARO number of RSA2 had been changed.
139 changes: 70 additions & 69 deletions argnorm/data/manual_curation/megares_curation.tsv
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Original ID ARO Description
MEG_8443|Drugs|Pleuromutilin|Pleuromutilin-resistant_23S_rRNA_mutation|P23S|RequiresSNPConfirmation 3005083
MEG_8443|Drugs|Pleuromutilin|Pleuromutilin-resistant_23S_rRNA_mutation|P23S|RequiresSNPConfirmation 3005083
MEG_4060|Metals|Multi-metal_resistance|Multi-metal_resistance_protein|MREA Metal resistance. No mapping
MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD 3000387
MEG_1732|Drugs|Lipopeptides|Daptomycin-resistant_mutant|CLS|RequiresSNPConfirmation 3003092
MEG_2933|Drugs|Mycobacterium_tuberculosis-specific_Drug|Para-aminosalicylic_acid_resistant_mutant|FOLC|RequiresSNPConfirmation 3004157
MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD 3000557
MEG_1732|Drugs|Lipopeptides|Daptomycin-resistant_mutant|CLS|RequiresSNPConfirmation 3003092
MEG_2933|Drugs|Mycobacterium_tuberculosis-specific_Drug|Para-aminosalicylic_acid_resistant_mutant|FOLC|RequiresSNPConfirmation 3004157
MEG_8700|Multi-compound|Biocide_and_metal_resistance|Biocide_and_metal_ABC_efflux_pumps|SITABCD Metal + Biocide resistance. No mapping
MEG_8447|Drugs|Fluoroquinolones|Fluoroquinolone-resistant_DNA_topoisomerases|PARC|RequiresSNPConfirmation 3000274
MEG_6241|Drugs|betalactams|Class_A_betalactamases|SHV 3001059
MEG_7974|Drugs|betalactams|Class_C_betalactamase_regulator|AMPCR|RequiresSNPConfirmation 3000076
MEG_3987|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004546
MEG_6055|Drugs|Mycobacterium_tuberculosis-specific_Drug|Para-aminosalicylic_acid_resistant_mutant|RIBD|RequiresSNPConfirmation 3004184
MEG_6144|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|RPSL|RequiresSNPConfirmation 3003395
MEG_8447|Drugs|Fluoroquinolones|Fluoroquinolone-resistant_DNA_topoisomerases|PARC|RequiresSNPConfirmation 3000274
MEG_6241|Drugs|betalactams|Class_A_betalactamases|SHV 3001059
MEG_7974|Drugs|betalactams|Class_C_betalactamase_regulator|AMPCR|RequiresSNPConfirmation 3000076
MEG_3987|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004546
MEG_6055|Drugs|Mycobacterium_tuberculosis-specific_Drug|Para-aminosalicylic_acid_resistant_mutant|RIBD|RequiresSNPConfirmation 3004184
MEG_6144|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|RPSL|RequiresSNPConfirmation 3003395
MEG_3745|Multi-compound|Drug_and_biocide_and_metal_resistance|Drug_and_biocide_and_metal_RND_efflux_pumps|MDTA Metal + Biocide resistance. No mapping
MEG_8140|Drugs|Aminoglycosides|Gentamicin-resistant_ATP-binding_protein|GRDA 3003949
MEG_5285|Drugs|betalactams|Class_A_betalactamases|OXY 3002390
MEG_8140|Drugs|Aminoglycosides|Gentamicin-resistant_ATP-binding_protein|GRDA 3003949
MEG_5285|Drugs|betalactams|Class_A_betalactamases|OXY 3002390
MEG_8643|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_MFS_efflux_pumps|QACAB Biocide resistance. No mapping
MEG_8644|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_MFS_efflux_pumps|QACAB Biocide resistance. No mapping
MEG_3071|Drugs|Fusidic_acid|Fusidic_acid-resistant_mutation|FUSE|RequiresSNPConfirmation 3003737
MEG_3986|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004174
MEG_3071|Drugs|Fusidic_acid|Fusidic_acid-resistant_mutation|FUSE|RequiresSNPConfirmation 3003737
MEG_3986|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004174
MEG_2062|Metals|Copper_resistance|Copper_resistance_protein|COPL Metal resistance. No mapping
MEG_8646|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_SMR_efflux_pumps|QACD Biocide resistance. No mapping
MEG_6137|Drugs|Lipopeptides|Daptomycin-resistant_beta-subunit_of_RNA_polymerase_RpoB|RPOBL|RequiresSNPConfirmation 3003287
MEG_6136|Drugs|Lipopeptides|Daptomycin-resistant_beta-subunit_of_RNA_polymerase_RpoB|RPOBL|RequiresSNPConfirmation 3003285
MEG_6137|Drugs|Lipopeptides|Daptomycin-resistant_beta-subunit_of_RNA_polymerase_RpoB|RPOBL|RequiresSNPConfirmation 3003287
MEG_6136|Drugs|Lipopeptides|Daptomycin-resistant_beta-subunit_of_RNA_polymerase_RpoB|RPOBL|RequiresSNPConfirmation 3003285
MEG_1180|Drugs|Multi-drug_resistance|Multi-drug_RND_efflux_regulator|ASMA Muti-drug resistance. No mapping
MEG_1179|Drugs|Multi-drug_resistance|Multi-drug_RND_efflux_regulator|ASMA Muti-drug resistance. No mapping
MEG_8642|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_MFS_efflux_pumps|QACAB Biocide resistance. No mapping
MEG_497|Drugs|betalactams|Class_C_betalactamases|ACT 3000072
MEG_497|Drugs|betalactams|Class_C_betalactamases|ACT 3000072
MEG_8087|Biocides|Aldehyde_resistance|Aldehyde_degradation|FORMA Biocide resistance. No mapping
MEG_2114|Drugs|Phenicol|Chloramphenicol_phosphotransferase|CPT 3000249
MEG_2114|Drugs|Phenicol|Chloramphenicol_phosphotransferase|CPT 3000249
MEG_8651|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_SMR_efflux_pumps|QACL Biocide resistance. No mapping
MEG_5337|Drugs|Fluoroquinolones|Fluoroquinolone-resistant_DNA_topoisomerases|PARC|RequiresSNPConfirmation 3000274
MEG_7344|Drugs|Glycopeptides|VanA-type_resistance_protein|VANA 3000010
MEG_5780|Drugs|Lipopeptides|Daptomycin-resistant_mutant|PGSA|RequiresSNPConfirmation 3003323
MEG_5337|Drugs|Fluoroquinolones|Fluoroquinolone-resistant_DNA_topoisomerases|PARC|RequiresSNPConfirmation 3000274
MEG_7344|Drugs|Glycopeptides|VanA-type_resistance_protein|VANA 3000010
MEG_5780|Drugs|Lipopeptides|Daptomycin-resistant_mutant|PGSA|RequiresSNPConfirmation 3003323
MEG_8647|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_SMR_efflux_pumps|QACF Biocide resistance. No mapping
MEG_4033|Drugs|MLS|Macrolide_phosphotransferases|MPHB 3000318
MEG_4033|Drugs|MLS|Macrolide_phosphotransferases|MPHB 3000318
MEG_8645|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_SMR_efflux_pumps|QACC Biocide resistance. No mapping
MEG_3980|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004165
MEG_1|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|A16S|RequiresSNPConfirmation 3003485
MEG_6963|Drugs|Tetracyclines|Tetracycline-resistant_16S_ribosomal_subunit_protein|TET16S|RequiresSNPConfirmation 3003510
MEG_3588|Drugs|Lipopeptides|Daptomycin-resistant_mutant|LIAFSR|RequiresSNPConfirmation 3003077
MEG_5781|Drugs|Phenicol|Phenicol-resistant_23S_rRNA_mutation|PH23S|RequiresSNPConfirmation 3004180
MEG_3980|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004165
MEG_1|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|A16S|RequiresSNPConfirmation 3003485
MEG_6963|Drugs|Tetracyclines|Tetracycline-resistant_16S_ribosomal_subunit_protein|TET16S|RequiresSNPConfirmation 3003510
MEG_3588|Drugs|Lipopeptides|Daptomycin-resistant_mutant|LIAFSR|RequiresSNPConfirmation 3003077
MEG_5781|Drugs|Phenicol|Phenicol-resistant_23S_rRNA_mutation|PH23S|RequiresSNPConfirmation 3004180
MEG_3857|Metals|Mercury_resistance|Mercury_resistance_protein|MERC Metal resistance. No mapping
MEG_3982|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004163
MEG_2430|Drugs|betalactams|Class_A_betalactamases|CTX 3000016
MEG_3982|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004163
MEG_2430|Drugs|betalactams|Class_A_betalactamases|CTX 3000016
MEG_8648|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_SMR_efflux_pumps|QACG Biocide resistance. No mapping
MEG_8650|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_SMR_efflux_pumps|QACH Biocide resistance. No mapping
MEG_3445|Drugs|Mycobacterium_tuberculosis-specific_Drug|Isoniazid-resistant_mutant|KASA|RequiresSNPConfirmation 3003463
MEG_7259|Drugs|Aminoglycosides|Aminoglycoside-resistant_arabinosyltransferase|TLYA|RequiresSNPConfirmation 3003465
MEG_1983|Drugs|betalactams|Class_C_betalactamases|CMY 3002095
MEG_7075|Drugs|Tetracyclines|Tetracycline_resistance_MFS_efflux_pumps|TETE 3000173
MEG_3983|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004177
MEG_6147|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|RRSH|RequiresSNPConfirmation 3003372
MEG_8254|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004836
MEG_6493|Drugs|betalactams|Class_A_betalactamases|SHV 3001139
MEG_3993|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004168
MEG_1319|Drugs|betalactams|Class_A_betalactamases|BLASME 3002379
MEG_5208|Drugs|betalactams|Class_D_betalactamases|OXA 3001410
MEG_2414|Drugs|betalactams|Class_A_betalactamases|CTX 3001904
MEG_2421|Drugs|betalactams|Class_A_betalactamases|CTX 3001927
MEG_3976|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004134
MEG_6875|Drugs|betalactams|Class_A_betalactamases|TEM 3000884
MEG_3989|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004179
MEG_6964|Drugs|Tetracyclines|Tetracycline-resistant_16S_ribosomal_subunit_protein|TET16S|RequiresSNPConfirmation 3003499
MEG_2|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|A16S|RequiresSNPConfirmation 3003512
MEG_3975|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004169
MEG_2423|Drugs|betalactams|Class_A_betalactamases|CTX 3001932
MEG_3445|Drugs|Mycobacterium_tuberculosis-specific_Drug|Isoniazid-resistant_mutant|KASA|RequiresSNPConfirmation 3003463
MEG_7259|Drugs|Aminoglycosides|Aminoglycoside-resistant_arabinosyltransferase|TLYA|RequiresSNPConfirmation 3003465
MEG_1983|Drugs|betalactams|Class_C_betalactamases|CMY 3002095
MEG_7075|Drugs|Tetracyclines|Tetracycline_resistance_MFS_efflux_pumps|TETE 3000173
MEG_3983|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004177
MEG_6147|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|RRSH|RequiresSNPConfirmation 3003372
MEG_8254|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004836
MEG_6493|Drugs|betalactams|Class_A_betalactamases|SHV 3001139
MEG_3993|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004168
MEG_1319|Drugs|betalactams|Class_A_betalactamases|BLASME 3002379
MEG_5208|Drugs|betalactams|Class_D_betalactamases|OXA 3001410
MEG_2414|Drugs|betalactams|Class_A_betalactamases|CTX 3001904
MEG_2421|Drugs|betalactams|Class_A_betalactamases|CTX 3001927
MEG_3976|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004134
MEG_6875|Drugs|betalactams|Class_A_betalactamases|TEM 3000884
MEG_3989|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004179
MEG_6964|Drugs|Tetracyclines|Tetracycline-resistant_16S_ribosomal_subunit_protein|TET16S|RequiresSNPConfirmation 3003499
MEG_2|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|A16S|RequiresSNPConfirmation 3003512
MEG_3975|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004169
MEG_2423|Drugs|betalactams|Class_A_betalactamases|CTX 3001932
MEG_8263|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_RND_efflux_pumps|MTRC|RequiresSNPConfirmation Biocide resistance. No mapping
MEG_985|Drugs|Aminoglycosides|Aminoglycoside_O-nucleotidyltransferases|ANT4-PRIME 3000229
MEG_3979|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004176
MEG_3990|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004171
MEG_2425|Drugs|betalactams|Class_A_betalactamases|CTX 3002002
MEG_3129|Drugs|betalactams|Class_A_betalactamases|GES 3002337
MEG_3131|Drugs|betalactams|Class_A_betalactamases|GES 3002350
MEG_6146|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|RRSC|RequiresSNPConfirmation 3003333
MEG_3393|Drugs|betalactams|Class_B_betalactamases|IMP 3002223
MEG_3991|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004133
MEG_8679|Drugs|Oxazolidinone|Oxazolidinone-resistant_23S_rRNA_mutation|RRL|RequiresSNPConfirmation 3004937
MEG_2427|Drugs|betalactams|Class_A_betalactamases|CTX 3001982
MEG_1490|Drugs|Cationic_antimicrobial_peptides|Cationic_peptide-resistant_16S_ribosomal_subunit_protein|CAP16S|RequiresSNPConfirmation 3003223
MEG_2393|Drugs|betalactams|Class_A_betalactamases|CTX 3001960
MEG_333|Drugs|Aminoglycosides|Aminoglycoside_N-acetyltransferases|AAC6-PRIME 3002578
MEG_3396|Drugs|betalactams|Class_B_betalactamases|IMP 3002205
MEG_1544|Drugs|betalactams|Class_A_betalactamases|CARB 3002243
MEG_2429|Drugs|betalactams|Class_A_betalactamases|CTX 3001943
MEG_5148|Drugs|betalactams|Class_D_betalactamases|OXA 3001555
MEG_7604|Drugs|Glycopeptides|VanD-type_accessory_protein|VANYD 3002957
MEG_8253|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004836
MEG_985|Drugs|Aminoglycosides|Aminoglycoside_O-nucleotidyltransferases|ANT4-PRIME 3000229
MEG_3979|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004176
MEG_3990|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004171
MEG_2425|Drugs|betalactams|Class_A_betalactamases|CTX 3002002
MEG_3129|Drugs|betalactams|Class_A_betalactamases|GES 3002337
MEG_3131|Drugs|betalactams|Class_A_betalactamases|GES 3002350
MEG_6146|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|RRSC|RequiresSNPConfirmation 3003333
MEG_3393|Drugs|betalactams|Class_B_betalactamases|IMP 3002223
MEG_3991|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004133
MEG_8679|Drugs|Oxazolidinone|Oxazolidinone-resistant_23S_rRNA_mutation|RRL|RequiresSNPConfirmation 3004937
MEG_2427|Drugs|betalactams|Class_A_betalactamases|CTX 3001982
MEG_1490|Drugs|Cationic_antimicrobial_peptides|Cationic_peptide-resistant_16S_ribosomal_subunit_protein|CAP16S|RequiresSNPConfirmation 3003223
MEG_2393|Drugs|betalactams|Class_A_betalactamases|CTX 3001960
MEG_333|Drugs|Aminoglycosides|Aminoglycoside_N-acetyltransferases|AAC6-PRIME 3002578
MEG_3396|Drugs|betalactams|Class_B_betalactamases|IMP 3002205
MEG_1544|Drugs|betalactams|Class_A_betalactamases|CARB 3002243
MEG_2429|Drugs|betalactams|Class_A_betalactamases|CTX 3001943
MEG_5148|Drugs|betalactams|Class_D_betalactamases|OXA 3001555
MEG_7604|Drugs|Glycopeptides|VanD-type_accessory_protein|VANYD 3002957
MEG_8253|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004836
MEG_6148|Drugs|betalactams|Class_A_betalactamases|RSA 3005440 ARO number of RSA2 had been changed.
12 changes: 6 additions & 6 deletions argnorm/data/manual_curation/resfinder_curation.tsv
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Expand Up @@ -9,7 +9,7 @@ VanC2XY_1_EU151754 glycopeptide resistance gene cluster VanC 3000246 https://www
VanHAX_PT_1_DQ018710 glycopeptide resistance gene cluster VanA 3000236 https://www.ncbi.nlm.nih.gov/nuccore/DQ018710.1 5109-7715 Part of VanA cluster (ARO:3000236)
VanHAX_PA_1_DQ018711 glycopeptide resistance gene cluster VanA 3000236 https://www.ncbi.nlm.nih.gov/nuccore/DQ018711.1?report=fasta 3168-5750 Part of VanA cluster (ARO:3000236)
VanHAX_PT_2_AY926880 glycopeptide resistance gene cluster VanA 3000236 https://www.ncbi.nlm.nih.gov/nuccore/AY926880.2?report=fasta 2771-5377 Part of VanA cluster (ARO:3000236)
dldHA2X_1_AL939117 D-Ala-D-Ala ligase 3003970 https://www.ncbi.nlm.nih.gov/nuccore/AL939117.1 53343-56013
dldHA2X_1_AL939117 D-Ala-D-Ala ligase 3003970 https://www.ncbi.nlm.nih.gov/nuccore/AL939117.1 53343-56013
VanHBX_1_AF192329 glycopeptide resistance gene cluster VanB 3000238 https://www.ncbi.nlm.nih.gov/nuccore/AF192329 27871-30477 Part of VanB cluster (ARO:3000238)
VanHBX_2_U35369 glycopeptide resistance gene cluster VanB 3000238 https://www.ncbi.nlm.nih.gov/nuccore/U35369.1?report=fasta 4007-6613 "Part of VanB cluster (ARO:3000238). Contains ARO:3002943, ARO:3002950"
VanC4XY_1_EU151752 glycopeptide resistance gene cluster VanC 3000246 https://www.ncbi.nlm.nih.gov/nuccore/EU151752.1?report=fasta 29-1650 Part of VanC cluster (ARO:3000246)
Expand Down Expand Up @@ -43,8 +43,8 @@ blaBKC-1_1_KP689347 BKC-1 3004757 Reverse complement in resfinder db.
mph(A)_1_D16251 mphA 3000316 Reverse complement in resfinder db.
qepA1_1_AB263754 QepA2 3004103 Reverse complement in resfinder db.
tet(43)_1_GQ244501 tet(43) 3000573 Reverse complement in resfinder db.
blaSPG-1_1_KP109680 SPG-1 3003720
blaBIM-1_1_CP016446 BlaB 3004201
grdA_1_QJX10702 3007382 Parent ARO mapping
aac(3)-I_1_AJ877225 AAC(3)-I 3007384
EstDL136_1_JN242251 3000387 Parent ARO mapping
blaSPG-1_1_KP109680 SPG-1 3003720
blaBIM-1_1_CP016446 BlaB 3004201
grdA_1_QJX10702 3007380 Parent ARO mapping
aac(3)-I_1_AJ877225 AAC(3)-I 3007384
EstDL136_1_JN242251 3000557 Parent ARO mapping
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