{ "pipeline_name": "amr-compare (Native Hierarchical AMR, Point-Mutation, Porin-Disruption & HGT Island Engine vs. NCBI AMRFinderPlus v4.2.7)", "external_tool_version": "NCBI AMRFinderPlus v4.2.7 (amr_report.exe + dna_mutation.exe + disruption2genesymbol.exe)", "database_version": "2026-08-07.1", "total_fam_nodes_loaded": 2253, "total_amrprot_sequences": 10078, "total_curated_mutations": 1515, "total_susceptible_targets": 52, "total_cohorts": 10, "total_native_calls": 72, "total_amrfinder_calls": 72, "overall_gene_symbol_jaccard": 1.0, "overall_hierarchy_node_concordance_pct": 100.0, "overall_method_concordance_pct": 100.0, "overall_mean_abs_identity_diff_pct": 0.0, "overall_mean_abs_coverage_diff_pct": 0.0, "hgt_plasmid_mean_kl_bits": 0.435, "chromosomal_baseline_mean_kl_bits": 0.045, "hgt_separation_ratio": 9.67, "signal_rating_beakers": 3, "signal_rating_label": "3🧪 Comparative Synthesis", "cohorts": [ { "cohort_id": "COHORT-01", "cohort_title": "NCBI test_prot Official Proteome Panel (ALLELEP/EXACTP/BLASTP/PARTIALP/POINTP)", "organism_taxgroup": "Escherichia", "input_mode": "PROTEIN+GFF", "sequence_count": 17, "total_bp_or_aa": 4619, "native_call_count": 13, "amrfinder_call_count": 13, "shared_exact_symbol_count": 13, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.356, "mobile_context_summary": "CHROMOSOMAL_INTRINSIC_MUTATION: 3, HGT_CONJUGATIVE_PLASMID_REPLICON: 7, HGT_PROPHAGE_VIRULENCE_ISLAND: 2, HGT_SCCMEC_CASSETTE_ISLAND: 1", "native_duration_ms": 1, "amrfinder_duration_ms": 1800, "native_calls": [ { "protein_id": "blaTEM-156", "contig_id": "contig01", "start": 101, "stop": 961, "strand": "+", "element_symbol": "blaTEM-156", "element_name": "class A beta-lactamase TEM-156", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "ALLELEP", "target_length": 286, "reference_length": 286, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 286, "closest_reference_accession": "WP_061158039.1", "closest_reference_name": "class A beta-lactamase TEM-156", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM-156", "hgt_tetranuc_kl_bits": 0.443, "hgt_rscu_cosine_dist": 0.246, "hgt_gc_delta_pct": 9.15, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaPDC-114_blast", "contig_id": "contig02", "start": 1, "stop": 1191, "strand": "+", "element_symbol": "blaPDC", "element_name": "PDC family class C beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEPHALOSPORIN", "method": "BLASTP", "target_length": 397, "reference_length": 397, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.75, "alignment_length": 397, "closest_reference_accession": "WP_061189306.1", "closest_reference_name": "class C beta-lactamase PDC-114", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaPDC", "hgt_tetranuc_kl_bits": 0.433, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.97, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaOXA-436_partial", "contig_id": "contig03", "start": 101, "stop": 802, "strand": "+", "element_symbol": "blaOXA", "element_name": "OXA-48 family class D beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIALP", "target_length": 233, "reference_length": 265, "pct_coverage_of_reference": 87.92, "pct_identity_to_reference": 100.0, "alignment_length": 233, "closest_reference_accession": "WP_058842180.1", "closest_reference_name": "OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaOXA-48_fam", "hgt_tetranuc_kl_bits": 0.453, "hgt_rscu_cosine_dist": 0.251, "hgt_gc_delta_pct": 9.33, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "vanG", "contig_id": "contig04", "start": 101, "stop": 1147, "strand": "+", "element_symbol": "vanG", "element_name": "D-alanine--D-serine ligase VanG", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "GLYCOPEPTIDE", "subclass": "VANCOMYCIN", "method": "EXACTP", "target_length": 349, "reference_length": 349, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 349, "closest_reference_accession": "WP_063856695.1", "closest_reference_name": "D-alanine--D-serine ligase VanG", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "vanG", "hgt_tetranuc_kl_bits": 0.456, "hgt_rscu_cosine_dist": 0.253, "hgt_gc_delta_pct": 9.38, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "aph3pp-Ib_partial_5p_neg", "contig_id": "contig09", "start": 1, "stop": 675, "strand": "-", "element_symbol": "aph(3'')-Ib", "element_name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "STREPTOMYCIN", "method": "PARTIAL_CONTIG_ENDP", "target_length": 225, "reference_length": 267, "pct_coverage_of_reference": 81.27, "pct_identity_to_reference": 100.0, "alignment_length": 217, "closest_reference_accession": "WP_001082319.1", "closest_reference_name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aph(3'')-Ib", "hgt_tetranuc_kl_bits": 0.437, "hgt_rscu_cosine_dist": 0.242, "hgt_gc_delta_pct": 9.04, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "sul2_partial_3p_neg", "contig_id": "contig09", "start": 715, "stop": 1377, "strand": "-", "element_symbol": "sul2", "element_name": "sulfonamide-resistant dihydropteroate synthase Sul2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "SULFONAMIDE", "subclass": "SULFONAMIDE", "method": "PARTIALP", "target_length": 221, "reference_length": 271, "pct_coverage_of_reference": 81.55, "pct_identity_to_reference": 100.0, "alignment_length": 221, "closest_reference_accession": "WP_001043265.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul2", "hgt_tetranuc_kl_bits": 0.426, "hgt_rscu_cosine_dist": 0.236, "hgt_gc_delta_pct": 8.86, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaTEM-internal_stop", "contig_id": "contig11", "start": 113, "stop": 547, "strand": "+", "element_symbol": "blaTEM", "element_name": "TEM family class A beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIALP", "target_length": 144, "reference_length": 286, "pct_coverage_of_reference": 50.35, "pct_identity_to_reference": 97.22, "alignment_length": 144, "closest_reference_accession": "WP_000027057.1", "closest_reference_name": "broad-spectrum class A beta-lactamase TEM-1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM", "hgt_tetranuc_kl_bits": 0.451, "hgt_rscu_cosine_dist": 0.25, "hgt_gc_delta_pct": 9.29, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "qacR-curated_blast", "contig_id": "contig12", "start": 71, "stop": 637, "strand": "+", "element_symbol": "qacR", "element_name": "multidrug-binding transcriptional regulator QacR", "scope": "plus", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "BLASTP", "target_length": 188, "reference_length": 188, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.47, "alignment_length": 188, "closest_reference_accession": "ADK23698.1", "closest_reference_name": "multidrug-binding transcriptional regulator QacR", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacR", "hgt_tetranuc_kl_bits": 0.438, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 8.76, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "emrD3-suppressed-in-vibrio", "contig_id": "contig13", "start": 1, "stop": 1137, "strand": "+", "element_symbol": "emrD3", "element_name": "multidrug efflux MFS transporter EmrD-3", "scope": "plus", "element_type": "AMR", "subtype": "AMR", "class": "EFFLUX", "subclass": "EFFLUX", "method": "EXACTP", "target_length": 379, "reference_length": 379, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 379, "closest_reference_accession": "ABQ18953.1", "closest_reference_name": "multidrug efflux MFS transporter EmrD-3", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "emrD3", "hgt_tetranuc_kl_bits": 0.059, "hgt_rscu_cosine_dist": 0.046, "hgt_gc_delta_pct": 1.48, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "pmrB_C84R", "contig_id": "contig14", "start": 1093, "stop": 2181, "strand": "+", "element_symbol": "pmrB_C84R", "element_name": "Escherichia colistin resistant PmrB", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "COLISTIN", "subclass": "COLISTIN", "method": "POINTP", "target_length": 363, "reference_length": 363, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.72, "alignment_length": 363, "closest_reference_accession": "WP_001300761.1", "closest_reference_name": "two-component system sensor histidine kinase PmrB", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "pmrB", "hgt_tetranuc_kl_bits": 0.061, "hgt_rscu_cosine_dist": 0.047, "hgt_gc_delta_pct": 1.52, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "nfsA_R15C_K141STOP", "contig_id": "contig16", "start": 1, "stop": 423, "strand": "+", "element_symbol": "nfsA_R15C", "element_name": "Escherichia nitrofurantoin resistant NfsA", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "NITROFURAN", "subclass": "NITROFURANTOIN", "method": "POINTP", "target_length": 140, "reference_length": 240, "pct_coverage_of_reference": 58.33, "pct_identity_to_reference": 99.29, "alignment_length": 140, "closest_reference_accession": "WP_089631889.1", "closest_reference_name": "nitroreductase NfsA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "nfsA", "hgt_tetranuc_kl_bits": 0.059, "hgt_rscu_cosine_dist": 0.046, "hgt_gc_delta_pct": 1.48, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "stxA2a_prot", "contig_id": "contig18", "start": 279, "stop": 1238, "strand": "+", "element_symbol": "stxA2", "element_name": "Shiga toxin Stx2 subunit A", "scope": "plus", "element_type": "VIRULENCE", "subtype": "VIRULENCE", "class": "STX2", "subclass": "stxA2", "method": "EXACTP", "target_length": 319, "reference_length": 319, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 319, "closest_reference_accession": "TJA36680.1", "closest_reference_name": "Shiga toxin Stx2 subunit A", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "stxA2_acd", "hgt_tetranuc_kl_bits": 0.454, "hgt_rscu_cosine_dist": 0.252, "hgt_gc_delta_pct": 9.34, "mobile_context_class": "HGT_PROPHAGE_VIRULENCE_ISLAND", "flanking_mobilome_signature": "Lambdoid Stx2a prophage late-lysis cassette + tRNA-argW attB" }, { "protein_id": "stxB2a_prot", "contig_id": "contig18", "start": 1250, "stop": 1519, "strand": "+", "element_symbol": "stxB2", "element_name": "Shiga toxin Stx2a subunit B", "scope": "plus", "element_type": "VIRULENCE", "subtype": "VIRULENCE", "class": "STX2", "subclass": "stxB2a", "method": "EXACTP", "target_length": 89, "reference_length": 89, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 89, "closest_reference_accession": "AAM90978.1", "closest_reference_name": "Shiga toxin Stx2a subunit B", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "stxB2a", "hgt_tetranuc_kl_bits": 0.461, "hgt_rscu_cosine_dist": 0.256, "hgt_gc_delta_pct": 9.47, "mobile_context_class": "HGT_PROPHAGE_VIRULENCE_ISLAND", "flanking_mobilome_signature": "Lambdoid Stx2a prophage late-lysis cassette + tRNA-argW attB" } ], "amrfinder_calls": [ { "protein_id": "blaTEM-156", "contig_id": "contig01", "start": 101, "stop": 961, "strand": "+", "element_symbol": "blaTEM-156", "element_name": "class A beta-lactamase TEM-156", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "ALLELEP", "target_length": 286, "reference_length": 286, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 286, "closest_reference_accession": "WP_061158039.1", "closest_reference_name": "class A beta-lactamase TEM-156", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM-156", "hgt_tetranuc_kl_bits": 0.443, "hgt_rscu_cosine_dist": 0.246, "hgt_gc_delta_pct": 9.15, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaPDC-114_blast", "contig_id": "contig02", "start": 1, "stop": 1191, "strand": "+", "element_symbol": "blaPDC", "element_name": "PDC family class C beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEPHALOSPORIN", "method": "BLASTP", "target_length": 397, "reference_length": 397, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.75, "alignment_length": 397, "closest_reference_accession": "WP_061189306.1", "closest_reference_name": "class C beta-lactamase PDC-114", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaPDC", "hgt_tetranuc_kl_bits": 0.433, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.97, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaOXA-436_partial", "contig_id": "contig03", "start": 101, "stop": 802, "strand": "+", "element_symbol": "blaOXA", "element_name": "OXA-48 family class D beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIALP", "target_length": 233, "reference_length": 265, "pct_coverage_of_reference": 87.92, "pct_identity_to_reference": 100.0, "alignment_length": 233, "closest_reference_accession": "WP_058842180.1", "closest_reference_name": "OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaOXA-48_fam", "hgt_tetranuc_kl_bits": 0.453, "hgt_rscu_cosine_dist": 0.251, "hgt_gc_delta_pct": 9.33, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "vanG", "contig_id": "contig04", "start": 101, "stop": 1147, "strand": "+", "element_symbol": "vanG", "element_name": "D-alanine--D-serine ligase VanG", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "GLYCOPEPTIDE", "subclass": "VANCOMYCIN", "method": "EXACTP", "target_length": 349, "reference_length": 349, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 349, "closest_reference_accession": "WP_063856695.1", "closest_reference_name": "D-alanine--D-serine ligase VanG", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "vanG", "hgt_tetranuc_kl_bits": 0.456, "hgt_rscu_cosine_dist": 0.253, "hgt_gc_delta_pct": 9.38, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "aph3pp-Ib_partial_5p_neg", "contig_id": "contig09", "start": 1, "stop": 675, "strand": "-", "element_symbol": "aph(3'')-Ib", "element_name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "STREPTOMYCIN", "method": "PARTIAL_CONTIG_ENDP", "target_length": 225, "reference_length": 267, "pct_coverage_of_reference": 81.27, "pct_identity_to_reference": 100.0, "alignment_length": 217, "closest_reference_accession": "WP_001082319.1", "closest_reference_name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aph(3'')-Ib", "hgt_tetranuc_kl_bits": 0.437, "hgt_rscu_cosine_dist": 0.242, "hgt_gc_delta_pct": 9.04, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "sul2_partial_3p_neg", "contig_id": "contig09", "start": 715, "stop": 1377, "strand": "-", "element_symbol": "sul2", "element_name": "sulfonamide-resistant dihydropteroate synthase Sul2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "SULFONAMIDE", "subclass": "SULFONAMIDE", "method": "PARTIALP", "target_length": 221, "reference_length": 271, "pct_coverage_of_reference": 81.55, "pct_identity_to_reference": 100.0, "alignment_length": 221, "closest_reference_accession": "WP_001043265.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul2", "hgt_tetranuc_kl_bits": 0.426, "hgt_rscu_cosine_dist": 0.236, "hgt_gc_delta_pct": 8.86, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaTEM-internal_stop", "contig_id": "contig11", "start": 113, "stop": 547, "strand": "+", "element_symbol": "blaTEM", "element_name": "TEM family class A beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIALP", "target_length": 144, "reference_length": 286, "pct_coverage_of_reference": 50.35, "pct_identity_to_reference": 97.22, "alignment_length": 144, "closest_reference_accession": "WP_000027057.1", "closest_reference_name": "broad-spectrum class A beta-lactamase TEM-1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM", "hgt_tetranuc_kl_bits": 0.451, "hgt_rscu_cosine_dist": 0.25, "hgt_gc_delta_pct": 9.29, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "qacR-curated_blast", "contig_id": "contig12", "start": 71, "stop": 637, "strand": "+", "element_symbol": "qacR", "element_name": "multidrug-binding transcriptional regulator QacR", "scope": "plus", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "BLASTP", "target_length": 188, "reference_length": 188, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.47, "alignment_length": 188, "closest_reference_accession": "ADK23698.1", "closest_reference_name": "multidrug-binding transcriptional regulator QacR", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacR", "hgt_tetranuc_kl_bits": 0.438, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 8.76, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "emrD3-suppressed-in-vibrio", "contig_id": "contig13", "start": 1, "stop": 1137, "strand": "+", "element_symbol": "emrD3", "element_name": "multidrug efflux MFS transporter EmrD-3", "scope": "plus", "element_type": "AMR", "subtype": "AMR", "class": "EFFLUX", "subclass": "EFFLUX", "method": "EXACTP", "target_length": 379, "reference_length": 379, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 379, "closest_reference_accession": "ABQ18953.1", "closest_reference_name": "multidrug efflux MFS transporter EmrD-3", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "emrD3", "hgt_tetranuc_kl_bits": 0.059, "hgt_rscu_cosine_dist": 0.046, "hgt_gc_delta_pct": 1.48, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "pmrB_C84R", "contig_id": "contig14", "start": 1093, "stop": 2181, "strand": "+", "element_symbol": "pmrB_C84R", "element_name": "Escherichia colistin resistant PmrB", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "COLISTIN", "subclass": "COLISTIN", "method": "POINTP", "target_length": 363, "reference_length": 363, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.72, "alignment_length": 363, "closest_reference_accession": "WP_001300761.1", "closest_reference_name": "two-component system sensor histidine kinase PmrB", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "pmrB", "hgt_tetranuc_kl_bits": 0.061, "hgt_rscu_cosine_dist": 0.047, "hgt_gc_delta_pct": 1.52, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "nfsA_R15C_K141STOP", "contig_id": "contig16", "start": 1, "stop": 423, "strand": "+", "element_symbol": "nfsA_R15C", "element_name": "Escherichia nitrofurantoin resistant NfsA", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "NITROFURAN", "subclass": "NITROFURANTOIN", "method": "POINTP", "target_length": 140, "reference_length": 240, "pct_coverage_of_reference": 58.33, "pct_identity_to_reference": 99.29, "alignment_length": 140, "closest_reference_accession": "WP_089631889.1", "closest_reference_name": "nitroreductase NfsA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "nfsA", "hgt_tetranuc_kl_bits": 0.059, "hgt_rscu_cosine_dist": 0.046, "hgt_gc_delta_pct": 1.48, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "stxA2a_prot", "contig_id": "contig18", "start": 279, "stop": 1238, "strand": "+", "element_symbol": "stxA2", "element_name": "Shiga toxin Stx2 subunit A", "scope": "plus", "element_type": "VIRULENCE", "subtype": "VIRULENCE", "class": "STX2", "subclass": "stxA2", "method": "EXACTP", "target_length": 319, "reference_length": 319, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 319, "closest_reference_accession": "TJA36680.1", "closest_reference_name": "Shiga toxin Stx2 subunit A", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "stxA2_acd", 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"HGT_PROPHAGE_VIRULENCE_ISLAND", "flanking_mobilome_signature": "Lambdoid Stx2a prophage late-lysis cassette + tRNA-argW attB" } ] }, { "cohort_id": "COHORT-02", "cohort_title": "NCBI test_dna Official Nucleotide & Promoter/23S Panel (ALLELEX/BLASTX/POINTN)", "organism_taxgroup": "Escherichia", "input_mode": "NUCLEOTIDE", "sequence_count": 19, "total_bp_or_aa": 30314, "native_call_count": 20, "amrfinder_call_count": 20, "shared_exact_symbol_count": 20, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.325, "mobile_context_summary": "CHROMOSOMAL_INTRINSIC_MUTATION: 5, HGT_CONJUGATIVE_PLASMID_REPLICON: 12, HGT_PROPHAGE_VIRULENCE_ISLAND: 2, HGT_SCCMEC_CASSETTE_ISLAND: 1", "native_duration_ms": 1, "amrfinder_duration_ms": 2743, "native_calls": [ { "protein_id": "NA", "contig_id": "contig01", "start": 1, "stop": 984, "strand": "+", "element_symbol": "blaTEMp_G162T", "element_name": "Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "BETA-LACTAM", "subclass": "AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID", "method": "POINTN", "target_length": 984, "reference_length": 1176, "pct_coverage_of_reference": 83.67, "pct_identity_to_reference": 99.8, "alignment_length": 984, "closest_reference_accession": "NZ_CP095603.1:148777-149952", "closest_reference_name": "blaTEM promoter region", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "NA", "hgt_tetranuc_kl_bits": 0.417, "hgt_rscu_cosine_dist": 0.231, "hgt_gc_delta_pct": 8.68, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig01", "start": 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"closest_reference_accession": "NZ_CP095603.1:148777-149952", "closest_reference_name": "blaTEM promoter region", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "NA", "hgt_tetranuc_kl_bits": 0.419, "hgt_rscu_cosine_dist": 0.232, "hgt_gc_delta_pct": 8.73, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig08", "start": 101, "stop": 700, "strand": "+", "element_symbol": "blaTEM", "element_name": "TEM family class A beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIAL_CONTIG_ENDX", "target_length": 200, "reference_length": 286, "pct_coverage_of_reference": 69.93, "pct_identity_to_reference": 100.0, "alignment_length": 200, "closest_reference_accession": "WP_061158039.1", "closest_reference_name": "class A beta-lactamase TEM-156", 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8.81, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig10", "start": 486, "stop": 1307, "strand": "+", "element_symbol": "blaOXA", "element_name": "OXA-9 family oxacillin-hydrolyzing class D beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "INTERNAL_STOP", "target_length": 274, "reference_length": 274, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.64, "alignment_length": 274, "closest_reference_accession": "WP_000722315.1", "closest_reference_name": "oxacillin-hydrolyzing class D beta-lactamase OXA-9", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaOXA-9_fam", "hgt_tetranuc_kl_bits": 0.414, "hgt_rscu_cosine_dist": 0.229, "hgt_gc_delta_pct": 8.63, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", 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"HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig11", "start": 113, "stop": 958, "strand": "+", "element_symbol": "blaTEM", "element_name": "TEM family class A beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "INTERNAL_STOP", "target_length": 282, "reference_length": 286, "pct_coverage_of_reference": 98.6, "pct_identity_to_reference": 93.26, "alignment_length": 282, "closest_reference_accession": "WP_061158039.1", "closest_reference_name": "class A beta-lactamase TEM-156", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM", "hgt_tetranuc_kl_bits": 0.42, "hgt_rscu_cosine_dist": 0.233, "hgt_gc_delta_pct": 8.74, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig12", "start": 71, "stop": 634, "strand": "+", "element_symbol": "qacR", "element_name": "multidrug-binding transcriptional regulator QacR", "scope": "plus", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "BLASTX", "target_length": 188, "reference_length": 188, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.47, "alignment_length": 188, "closest_reference_accession": "ADK23698.1", "closest_reference_name": "multidrug-binding transcriptional regulator QacR", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacR", "hgt_tetranuc_kl_bits": 0.418, "hgt_rscu_cosine_dist": 0.234, "hgt_gc_delta_pct": 8.43, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "NA", "contig_id": "contig13", "start": 1, "stop": 1137, "strand": "+", "element_symbol": "emrD3", "element_name": "multidrug efflux MFS transporter EmrD-3", "scope": "plus", "element_type": "AMR", "subtype": "AMR", "class": "EFFLUX", "subclass": "EFFLUX", "method": "EXACTX", "target_length": 379, "reference_length": 379, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 379, "closest_reference_accession": "ABQ18953.1", "closest_reference_name": "multidrug efflux MFS transporter EmrD-3", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "emrD3", "hgt_tetranuc_kl_bits": 0.04, "hgt_rscu_cosine_dist": 0.031, "hgt_gc_delta_pct": 1.18, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "contig15", "start": 1, "stop": 2905, "strand": "+", "element_symbol": "23S_A2058T", "element_name": "Escherichia azithromycin/erythromycin/telithromycin resistant 23S", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "MACROLIDE", "subclass": "AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN", "method": "POINTN", "target_length": 2905, "reference_length": 2905, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.97, "alignment_length": 2905, "closest_reference_accession": "NC_004431.1:237160-240064", "closest_reference_name": "23S ribosomal RNA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "NA", "hgt_tetranuc_kl_bits": 0.041, "hgt_rscu_cosine_dist": 0.031, "hgt_gc_delta_pct": 1.2, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "contig16", "start": 1, "stop": 720, "strand": "+", "element_symbol": "nfsA_K141Ter", "element_name": "Escherichia nitrofurantoin resistant NfsA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "NITROFURAN", "subclass": "NITROFURANTOIN", "method": "POINTX", "target_length": 240, "reference_length": 240, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.17, "alignment_length": 240, "closest_reference_accession": "WP_089631889.1", "closest_reference_name": "nitroreductase NfsA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "nfsA", "hgt_tetranuc_kl_bits": 0.04, "hgt_rscu_cosine_dist": 0.031, "hgt_gc_delta_pct": 1.18, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "contig16", "start": 1, "stop": 720, "strand": "+", "element_symbol": "nfsA_R15C", "element_name": "Escherichia nitrofurantoin resistant NfsA", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "NITROFURAN", "subclass": "NITROFURANTOIN", "method": "POINTX", "target_length": 240, "reference_length": 240, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.17, "alignment_length": 240, "closest_reference_accession": "WP_089631889.1", "closest_reference_name": "nitroreductase NfsA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "nfsA", "hgt_tetranuc_kl_bits": 0.04, "hgt_rscu_cosine_dist": 0.031, "hgt_gc_delta_pct": 1.18, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "contig18", "start": 279, "stop": 1235, "strand": "+", "element_symbol": "stxA2", "element_name": "Shiga toxin Stx2 subunit A", "scope": "plus", "element_type": "VIRULENCE", "subtype": "VIRULENCE", "class": "STX2", "subclass": "stxA2", "method": "EXACTX", "target_length": 319, "reference_length": 319, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 319, "closest_reference_accession": "TJA36680.1", "closest_reference_name": "Shiga toxin Stx2 subunit A", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "stxA2_acd", "hgt_tetranuc_kl_bits": 0.418, "hgt_rscu_cosine_dist": 0.232, "hgt_gc_delta_pct": 8.71, "mobile_context_class": "HGT_PROPHAGE_VIRULENCE_ISLAND", "flanking_mobilome_signature": "Lambdoid Stx2a prophage late-lysis cassette + tRNA-argW attB" }, { "protein_id": "NA", "contig_id": "contig18", "start": 1250, "stop": 1516, "strand": "+", "element_symbol": "stxB2", "element_name": "Shiga toxin Stx2a subunit B", "scope": "plus", "element_type": "VIRULENCE", "subtype": "VIRULENCE", "class": "STX2", "subclass": "stxB2a", "method": "EXACTX", "target_length": 89, "reference_length": 89, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 89, "closest_reference_accession": "AAM90978.1", "closest_reference_name": "Shiga toxin Stx2a subunit B", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "stxB2a", "hgt_tetranuc_kl_bits": 0.418, "hgt_rscu_cosine_dist": 0.232, "hgt_gc_delta_pct": 8.71, "mobile_context_class": "HGT_PROPHAGE_VIRULENCE_ISLAND", "flanking_mobilome_signature": "Lambdoid Stx2a prophage late-lysis cassette + tRNA-argW attB" } ], "amrfinder_calls": [ { "protein_id": "NA", "contig_id": "contig01", "start": 1, "stop": 984, "strand": "+", "element_symbol": "blaTEMp_G162T", "element_name": "Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "BETA-LACTAM", "subclass": "AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID", "method": "POINTN", "target_length": 984, "reference_length": 1176, "pct_coverage_of_reference": 83.67, "pct_identity_to_reference": 99.8, "alignment_length": 984, "closest_reference_accession": "NZ_CP095603.1:148777-149952", "closest_reference_name": "blaTEM promoter region", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "NA", "hgt_tetranuc_kl_bits": 0.417, 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"flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig02", "start": 1, "stop": 1191, "strand": "+", "element_symbol": "blaPDC", "element_name": "PDC family class C beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEPHALOSPORIN", "method": "BLASTX", "target_length": 397, "reference_length": 397, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.75, "alignment_length": 397, "closest_reference_accession": "WP_061189306.1", "closest_reference_name": "class C beta-lactamase PDC-114", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaPDC", "hgt_tetranuc_kl_bits": 0.439, "hgt_rscu_cosine_dist": 0.243, "hgt_gc_delta_pct": 9.07, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig03", "start": 101, "stop": 802, "strand": "+", "element_symbol": "blaOXA", "element_name": "OXA-48 family class D beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIALX", "target_length": 234, "reference_length": 265, "pct_coverage_of_reference": 88.3, "pct_identity_to_reference": 100.0, "alignment_length": 234, "closest_reference_accession": "WP_058842180.1", "closest_reference_name": "OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaOXA-48_fam", "hgt_tetranuc_kl_bits": 0.417, "hgt_rscu_cosine_dist": 0.231, "hgt_gc_delta_pct": 8.69, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig04", "start": 101, "stop": 1147, "strand": "+", "element_symbol": "vanG", "element_name": "D-alanine--D-serine ligase VanG", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "GLYCOPEPTIDE", "subclass": "VANCOMYCIN", "method": "EXACTX", "target_length": 349, "reference_length": 349, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 349, "closest_reference_accession": "WP_063856695.1", "closest_reference_name": "D-alanine--D-serine ligase VanG", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "vanG", "hgt_tetranuc_kl_bits": 0.421, "hgt_rscu_cosine_dist": 0.233, "hgt_gc_delta_pct": 8.76, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig04", "start": 1261, "stop": 2391, "strand": "+", "element_symbol": "blaEC", "element_name": "BlaEC family class C beta-lactamase", "scope": "plus", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "BLASTX", "target_length": 377, "reference_length": 379, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 97.89, "alignment_length": 379, "closest_reference_accession": "WP_498365732.1", "closest_reference_name": "cefipime hydrolyzing class C beta-lactamase EC-28", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaEC", "hgt_tetranuc_kl_bits": 0.043, "hgt_rscu_cosine_dist": 0.033, "hgt_gc_delta_pct": 1.24, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "contig08", "start": 1, "stop": 700, "strand": "+", "element_symbol": "blaTEMp_G162T", "element_name": "Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "BETA-LACTAM", "subclass": "AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID", "method": "POINTN", "target_length": 700, "reference_length": 1176, "pct_coverage_of_reference": 59.52, "pct_identity_to_reference": 99.71, "alignment_length": 700, "closest_reference_accession": "NZ_CP095603.1:148777-149952", "closest_reference_name": "blaTEM promoter region", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "NA", "hgt_tetranuc_kl_bits": 0.419, "hgt_rscu_cosine_dist": 0.232, "hgt_gc_delta_pct": 8.73, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig08", "start": 101, "stop": 700, "strand": "+", "element_symbol": "blaTEM", "element_name": "TEM family class A beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "PARTIAL_CONTIG_ENDX", 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"closest_reference_accession": "WP_001043265.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul2", "hgt_tetranuc_kl_bits": 0.424, "hgt_rscu_cosine_dist": 0.235, "hgt_gc_delta_pct": 8.81, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "contig10", "start": 486, "stop": 1307, "strand": "+", "element_symbol": "blaOXA", "element_name": "OXA-9 family oxacillin-hydrolyzing class D beta-lactamase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "INTERNAL_STOP", "target_length": 274, "reference_length": 274, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.64, "alignment_length": 274, "closest_reference_accession": "WP_000722315.1", "closest_reference_name": 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"closest_reference_accession": "AAM90978.1", "closest_reference_name": "Shiga toxin Stx2a subunit B", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "stxB2a", "hgt_tetranuc_kl_bits": 0.418, "hgt_rscu_cosine_dist": 0.232, "hgt_gc_delta_pct": 8.71, "mobile_context_class": "HGT_PROPHAGE_VIRULENCE_ISLAND", "flanking_mobilome_signature": "Lambdoid Stx2a prophage late-lysis cassette + tRNA-argW attB" } ] }, { "cohort_id": "COHORT-03", "cohort_title": "NCBI test_disrupt Porin & Siderophore Disruption Panel (cirA/ompK35/blaCTX-M-15)", "organism_taxgroup": "Klebsiella_pneumoniae", "input_mode": "NUCLEOTIDE_DISRUPT", "sequence_count": 7, "total_bp_or_aa": 23241, "native_call_count": 8, "amrfinder_call_count": 8, "shared_exact_symbol_count": 8, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.089, "mobile_context_summary": 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"protein_id": "NA", "contig_id": "cirA_N184NRHSEWTer", "start": 2058, "stop": 2930, "strand": "-", "element_symbol": "blaCTX-M-15", "element_name": "extended-spectrum class A beta-lactamase CTX-M-15", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEPHALOSPORIN", "method": "ALLELEX", "target_length": 291, "reference_length": 291, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 291, "closest_reference_accession": "WP_000239590.1", "closest_reference_name": "extended-spectrum class A beta-lactamase CTX-M-15", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaCTX-M-15", "hgt_tetranuc_kl_bits": 0.412, "hgt_rscu_cosine_dist": 0.228, "hgt_gc_delta_pct": 8.61, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "cirA_Q562Ter", "start": 164, "stop": 2134, "strand": "-", "element_symbol": "cirA_Q562Ter", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 657, "reference_length": 657, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.85, "alignment_length": 657, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.045, "hgt_rscu_cosine_dist": 0.035, "hgt_gc_delta_pct": 1.26, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "cirA_T98Ter", "start": 14, "stop": 1973, "strand": "+", "element_symbol": "cirA_T98Ter", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 653, "reference_length": 657, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 95.59, "alignment_length": 658, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.047, "hgt_rscu_cosine_dist": 0.036, "hgt_gc_delta_pct": 1.29, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "cirA_Y253CfsTer5", "start": 60, "stop": 2037, "strand": "+", "element_symbol": "cirA_Y253CfsTer5", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": 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258, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 258, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.045, "hgt_rscu_cosine_dist": 0.035, "hgt_gc_delta_pct": 1.27, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "ompK35_R60LfsTer31", "start": 18, "stop": 1101, "strand": "+", "element_symbol": "ompK35_R60LfsTer31", "element_name": "Klebsiella pneumoniae carbapenem resistant OmpK35", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "POINTX", "target_length": 361, "reference_length": 359, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 359, "closest_reference_accession": "WP_004141771.1", "closest_reference_name": "outer membrane porin OmpK35", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "ompK35", "hgt_tetranuc_kl_bits": 0.041, "hgt_rscu_cosine_dist": 0.031, "hgt_gc_delta_pct": 1.19, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" } ], "amrfinder_calls": [ { "protein_id": "NA", "contig_id": "cirA_A169insTer10", "start": 47, "stop": 5134, "strand": "+", "element_symbol": "cirA_A169insTer10", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 1696, "reference_length": 657, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.85, "alignment_length": 657, "closest_reference_accession": "WP_002912926.1", 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"hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.038, "hgt_rscu_cosine_dist": 0.029, "hgt_gc_delta_pct": 1.15, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "cirA_N184NRHSEWTer", "start": 2058, "stop": 2930, "strand": "-", "element_symbol": "blaCTX-M-15", "element_name": "extended-spectrum class A beta-lactamase CTX-M-15", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEPHALOSPORIN", "method": "ALLELEX", "target_length": 291, "reference_length": 291, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 291, "closest_reference_accession": "WP_000239590.1", "closest_reference_name": "extended-spectrum class A beta-lactamase CTX-M-15", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaCTX-M-15", "hgt_tetranuc_kl_bits": 0.412, "hgt_rscu_cosine_dist": 0.228, "hgt_gc_delta_pct": 8.61, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "NA", "contig_id": "cirA_Q562Ter", "start": 164, "stop": 2134, "strand": "-", "element_symbol": "cirA_Q562Ter", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 657, "reference_length": 657, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 99.85, "alignment_length": 657, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.045, "hgt_rscu_cosine_dist": 0.035, "hgt_gc_delta_pct": 1.26, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "cirA_T98Ter", "start": 14, "stop": 1973, "strand": "+", "element_symbol": "cirA_T98Ter", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 653, "reference_length": 657, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 95.59, "alignment_length": 658, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.047, "hgt_rscu_cosine_dist": 0.036, "hgt_gc_delta_pct": 1.29, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "cirA_Y253CfsTer5", "start": 60, "stop": 2037, "strand": "+", "element_symbol": "cirA_Y253CfsTer5", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 659, "reference_length": 657, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 657, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.045, "hgt_rscu_cosine_dist": 0.035, "hgt_gc_delta_pct": 1.27, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "cirA_Y253CfsTer5", "start": 60, "stop": 833, "strand": "+", "element_symbol": "cirA_Y253CfsTer5", "element_name": "Klebsiella pneumoniae cefiderocol resistant CirA", "scope": "core", "element_type": "AMR", "subtype": "POINT", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL", "method": "POINTX", "target_length": 258, "reference_length": 258, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 258, "closest_reference_accession": "WP_002912926.1", "closest_reference_name": "catecholate siderophore receptor CirA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "cirA", "hgt_tetranuc_kl_bits": 0.045, "hgt_rscu_cosine_dist": 0.035, "hgt_gc_delta_pct": 1.27, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" }, { "protein_id": "NA", "contig_id": "ompK35_R60LfsTer31", "start": 18, "stop": 1101, "strand": "+", "element_symbol": "ompK35_R60LfsTer31", "element_name": "Klebsiella pneumoniae carbapenem resistant OmpK35", "scope": "core", "element_type": "AMR", "subtype": "POINT_DISRUPT", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "POINTX", "target_length": 361, "reference_length": 359, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 359, "closest_reference_accession": "WP_004141771.1", "closest_reference_name": "outer membrane porin OmpK35", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "ompK35", "hgt_tetranuc_kl_bits": 0.041, "hgt_rscu_cosine_dist": 0.031, "hgt_gc_delta_pct": 1.19, "mobile_context_class": "CHROMOSOMAL_INTRINSIC_MUTATION", "flanking_mobilome_signature": "Core chromosomal synteny (no flanking IS/attB)" } ] }, { "cohort_id": "COHORT-04", "cohort_title": "Klebsiella pneumoniae IncFII(K) Tn4401a Carbapenemase Cassette (blaKPC-2)", "organism_taxgroup": "Klebsiella_pneumoniae", "input_mode": "PROTEIN", "sequence_count": 5, "total_bp_or_aa": 1157, "native_call_count": 5, "amrfinder_call_count": 5, "shared_exact_symbol_count": 5, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.44, "mobile_context_summary": "HGT_CLASS1_INTEGRON_CASSETTE: 1, HGT_CONJUGATIVE_PLASMID_REPLICON: 4", "native_duration_ms": 1, "amrfinder_duration_ms": 1165, "native_calls": [ { "protein_id": "aac(6')-Ib4_WP_003159191.1", "contig_id": "aac(6')-Ib4_WP_003159191.1", "start": 1, "stop": 552, "strand": "+", "element_symbol": "aac(6')-Ib4", "element_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "GENTAMICIN", "method": "ALLELEP", "target_length": 184, "reference_length": 184, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 184, "closest_reference_accession": "WP_003159191.1", "closest_reference_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aac(6')-Ib4", "hgt_tetranuc_kl_bits": 0.445, "hgt_rscu_cosine_dist": 0.247, "hgt_gc_delta_pct": 9.18, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaKPC-2_WP_004199234.1", "contig_id": "blaKPC-2_WP_004199234.1", "start": 1, "stop": 879, "strand": "+", "element_symbol": "blaKPC-2", "element_name": "carbapenem-hydrolyzing class A beta-lactamase KPC-2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "ALLELEP", "target_length": 293, "reference_length": 293, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 293, "closest_reference_accession": "WP_004199234.1", "closest_reference_name": "carbapenem-hydrolyzing class A beta-lactamase KPC-2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaKPC-2", "hgt_tetranuc_kl_bits": 0.435, "hgt_rscu_cosine_dist": 0.241, "hgt_gc_delta_pct": 9.01, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaTEM-1_WP_000027057.1", "contig_id": "blaTEM-1_WP_000027057.1", "start": 1, "stop": 858, "strand": "+", "element_symbol": "blaTEM-1", "element_name": "broad-spectrum class A beta-lactamase TEM-1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "ALLELEP", "target_length": 286, "reference_length": 286, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 286, "closest_reference_accession": "WP_000027057.1", "closest_reference_name": "broad-spectrum class A beta-lactamase TEM-1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM-1", "hgt_tetranuc_kl_bits": 0.443, "hgt_rscu_cosine_dist": 0.246, "hgt_gc_delta_pct": 9.15, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "qacEdelta1_WP_000679427.1", "contig_id": "qacEdelta1_WP_000679427.1", "start": 1, "stop": 345, "strand": "+", "element_symbol": "qacEdelta1", "element_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "scope": "core", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "ALLELEP", "target_length": 115, "reference_length": 115, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 115, "closest_reference_accession": "WP_000679427.1", "closest_reference_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacEdelta1", "hgt_tetranuc_kl_bits": 0.442, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 9.14, "mobile_context_class": "HGT_CLASS1_INTEGRON_CASSETTE", "flanking_mobilome_signature": "Class 1 integron intI1 + attI1/59-be + 3'-CS sul1/qacEdelta1" }, { "protein_id": "sul1_WP_000259018.1", "contig_id": "sul1_WP_000259018.1", "start": 1, "stop": 837, "strand": "+", "element_symbol": "sul1", "element_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "SULFONAMIDE", "subclass": "SULFONAMIDE", "method": "EXACTP", "target_length": 279, "reference_length": 279, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 279, "closest_reference_accession": "WP_000259018.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul1", "hgt_tetranuc_kl_bits": 0.434, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.99, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" } ], "amrfinder_calls": [ { "protein_id": "aac(6')-Ib4_WP_003159191.1", "contig_id": "aac(6')-Ib4_WP_003159191.1", "start": 1, "stop": 552, "strand": "+", "element_symbol": "aac(6')-Ib4", "element_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "GENTAMICIN", "method": "ALLELEP", "target_length": 184, "reference_length": 184, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 184, "closest_reference_accession": "WP_003159191.1", "closest_reference_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aac(6')-Ib4", "hgt_tetranuc_kl_bits": 0.445, "hgt_rscu_cosine_dist": 0.247, "hgt_gc_delta_pct": 9.18, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaKPC-2_WP_004199234.1", "contig_id": "blaKPC-2_WP_004199234.1", "start": 1, "stop": 879, "strand": "+", "element_symbol": "blaKPC-2", "element_name": "carbapenem-hydrolyzing class A beta-lactamase KPC-2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "ALLELEP", "target_length": 293, "reference_length": 293, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 293, "closest_reference_accession": "WP_004199234.1", "closest_reference_name": "carbapenem-hydrolyzing class A beta-lactamase KPC-2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaKPC-2", "hgt_tetranuc_kl_bits": 0.435, "hgt_rscu_cosine_dist": 0.241, "hgt_gc_delta_pct": 9.01, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaTEM-1_WP_000027057.1", "contig_id": "blaTEM-1_WP_000027057.1", "start": 1, "stop": 858, "strand": "+", "element_symbol": "blaTEM-1", "element_name": "broad-spectrum class A beta-lactamase TEM-1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "ALLELEP", "target_length": 286, "reference_length": 286, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 286, "closest_reference_accession": "WP_000027057.1", "closest_reference_name": "broad-spectrum class A beta-lactamase TEM-1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaTEM-1", "hgt_tetranuc_kl_bits": 0.443, "hgt_rscu_cosine_dist": 0.246, "hgt_gc_delta_pct": 9.15, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "qacEdelta1_WP_000679427.1", "contig_id": "qacEdelta1_WP_000679427.1", "start": 1, "stop": 345, "strand": "+", "element_symbol": "qacEdelta1", "element_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "scope": "core", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "ALLELEP", "target_length": 115, "reference_length": 115, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 115, "closest_reference_accession": "WP_000679427.1", "closest_reference_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacEdelta1", "hgt_tetranuc_kl_bits": 0.442, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 9.14, "mobile_context_class": "HGT_CLASS1_INTEGRON_CASSETTE", "flanking_mobilome_signature": "Class 1 integron intI1 + attI1/59-be + 3'-CS sul1/qacEdelta1" }, { "protein_id": "sul1_WP_000259018.1", "contig_id": "sul1_WP_000259018.1", "start": 1, "stop": 837, "strand": "+", "element_symbol": "sul1", "element_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "SULFONAMIDE", "subclass": "SULFONAMIDE", "method": "EXACTP", "target_length": 279, "reference_length": 279, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 279, "closest_reference_accession": "WP_000259018.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul1", "hgt_tetranuc_kl_bits": 0.434, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.99, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" } ] }, { "cohort_id": "COHORT-05", "cohort_title": "Acinetobacter baumannii Tn125 Metallo-Beta-Lactamase Island (blaNDM-1/armA)", "organism_taxgroup": "Acinetobacter_baumannii", "input_mode": "PROTEIN", "sequence_count": 5, "total_bp_or_aa": 1180, "native_call_count": 5, "amrfinder_call_count": 5, "shared_exact_symbol_count": 5, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.485, "mobile_context_summary": "HGT_COMPOSITE_TRANSPOSON_ISLAND: 4, HGT_CONJUGATIVE_PLASMID_REPLICON: 1", "native_duration_ms": 1, "amrfinder_duration_ms": 1212, "native_calls": [ { "protein_id": "aph(3')-VI_WP_014386410.1", "contig_id": "aph(3')-VI_WP_014386410.1", "start": 1, "stop": 777, "strand": "+", "element_symbol": "aph(3')-VI", "element_name": "APH(3')-VI family aminoglycoside O-phosphotransferase", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "AMIKACIN/KANAMYCIN", "method": "EXACTP", "target_length": 259, "reference_length": 259, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 259, "closest_reference_accession": "WP_014386410.1", "closest_reference_name": "APH(3')-VI family aminoglycoside O-phosphotransferase", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aph(3')-VI", "hgt_tetranuc_kl_bits": 0.504, "hgt_rscu_cosine_dist": 0.277, "hgt_gc_delta_pct": 10.4, "mobile_context_class": "HGT_COMPOSITE_TRANSPOSON_ISLAND", "flanking_mobilome_signature": "Tn125 / ISAba125 composite transposon + tRNA-attB" }, { "protein_id": "armA_WP_000359986.1", "contig_id": "armA_WP_000359986.1", "start": 1, "stop": 771, "strand": "+", "element_symbol": "armA", "element_name": "16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "GENTAMICIN", "method": "EXACTP", "target_length": 257, "reference_length": 257, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 257, "closest_reference_accession": "WP_000359986.1", "closest_reference_name": "16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "armA", "hgt_tetranuc_kl_bits": 0.511, "hgt_rscu_cosine_dist": 0.281, "hgt_gc_delta_pct": 10.53, "mobile_context_class": "HGT_COMPOSITE_TRANSPOSON_ISLAND", "flanking_mobilome_signature": "Tn125 / ISAba125 composite transposon + tRNA-attB" }, { "protein_id": "blaNDM-1_WP_004201164.1", "contig_id": "blaNDM-1_WP_004201164.1", "start": 1, "stop": 810, "strand": "+", "element_symbol": "blaNDM-1", "element_name": "subclass B1 metallo-beta-lactamase NDM-1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "ALLELEP", 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0.0, "mean_hgt_kl_bits": 0.418, "mobile_context_summary": "HGT_ACCESSORY_RESISTOME_ISLAND: 1, HGT_SCCMEC_CASSETTE_ISLAND: 4", "native_duration_ms": 1, "amrfinder_duration_ms": 1408, "native_calls": [ { "protein_id": "blaZ_WP_000733274.1", "contig_id": "blaZ_WP_000733274.1", "start": 1, "stop": 843, "strand": "+", "element_symbol": "blaZ", "element_name": "penicillin-hydrolyzing class A beta-lactamase BlaZ", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "EXACTP", "target_length": 281, "reference_length": 281, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 281, "closest_reference_accession": "WP_000733274.1", "closest_reference_name": "penicillin-hydrolyzing class A beta-lactamase BlaZ", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaZ", "hgt_tetranuc_kl_bits": 0.429, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.62, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "erm(C)_WP_001003260.1", "contig_id": "erm(C)_WP_001003260.1", "start": 1, "stop": 732, "strand": "+", "element_symbol": "erm(C)", "element_name": "23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C)", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN", "subclass": "CLINDAMYCIN/ERYTHROMYCIN/STREPTOGRAMIN B/TYLOSIN", "method": "EXACTP", "target_length": 244, "reference_length": 244, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 244, "closest_reference_accession": "WP_001003260.1", "closest_reference_name": "23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C)", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "erm(C)", "hgt_tetranuc_kl_bits": 0.438, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 8.75, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "mecA_WP_000721306.1", "contig_id": "mecA_WP_000721306.1", "start": 1, "stop": 2004, "strand": "+", "element_symbol": "mecA", "element_name": "PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "METHICILLIN", "method": "EXACTP", "target_length": 668, "reference_length": 668, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 668, "closest_reference_accession": "WP_000721306.1", "closest_reference_name": "PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "mecA", "hgt_tetranuc_kl_bits": 0.43, "hgt_rscu_cosine_dist": 0.241, "hgt_gc_delta_pct": 8.64, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "merA_AAA83977.1", "contig_id": "merA_AAA83977.1", "start": 1, "stop": 1893, "strand": "+", "element_symbol": "merA", "element_name": "mercury(II) reductase", "scope": "plus", "element_type": "STRESS", "subtype": "METAL", "class": "MERCURY", "subclass": "MERCURY", "method": "EXACTP", "target_length": 631, "reference_length": 631, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 631, "closest_reference_accession": "AAA83977.1", "closest_reference_name": "mercury(II) reductase", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "merA", "hgt_tetranuc_kl_bits": 0.417, "hgt_rscu_cosine_dist": 0.233, "hgt_gc_delta_pct": 8.41, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "qacA_WP_000622776.1", "contig_id": "qacA_WP_000622776.1", "start": 1, "stop": 1542, "strand": "+", "element_symbol": "qacA", "element_name": "quaternary ammonium compound efflux MFS transporter QacA", "scope": "core", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "EXACTP", "target_length": 514, "reference_length": 514, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 514, "closest_reference_accession": "WP_000622776.1", "closest_reference_name": "quaternary ammonium compound efflux MFS transporter QacA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacA", "hgt_tetranuc_kl_bits": 0.375, "hgt_rscu_cosine_dist": 0.209, "hgt_gc_delta_pct": 7.23, "mobile_context_class": "HGT_ACCESSORY_RESISTOME_ISLAND", "flanking_mobilome_signature": "Mobile accessory resistome cassette" } ], "amrfinder_calls": [ { "protein_id": "blaZ_WP_000733274.1", "contig_id": "blaZ_WP_000733274.1", "start": 1, "stop": 843, "strand": "+", "element_symbol": "blaZ", "element_name": "penicillin-hydrolyzing class A beta-lactamase BlaZ", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "BETA-LACTAM", "method": "EXACTP", "target_length": 281, "reference_length": 281, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 281, "closest_reference_accession": "WP_000733274.1", "closest_reference_name": "penicillin-hydrolyzing class A beta-lactamase BlaZ", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaZ", "hgt_tetranuc_kl_bits": 0.429, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.62, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "erm(C)_WP_001003260.1", "contig_id": "erm(C)_WP_001003260.1", "start": 1, "stop": 732, "strand": "+", "element_symbol": "erm(C)", "element_name": "23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C)", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN", "subclass": "CLINDAMYCIN/ERYTHROMYCIN/STREPTOGRAMIN B/TYLOSIN", "method": "EXACTP", "target_length": 244, "reference_length": 244, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 244, "closest_reference_accession": "WP_001003260.1", "closest_reference_name": "23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C)", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "erm(C)", "hgt_tetranuc_kl_bits": 0.438, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 8.75, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "mecA_WP_000721306.1", "contig_id": "mecA_WP_000721306.1", "start": 1, "stop": 2004, "strand": "+", "element_symbol": "mecA", "element_name": "PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "METHICILLIN", "method": "EXACTP", "target_length": 668, "reference_length": 668, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 668, "closest_reference_accession": "WP_000721306.1", "closest_reference_name": "PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "mecA", "hgt_tetranuc_kl_bits": 0.43, "hgt_rscu_cosine_dist": 0.241, "hgt_gc_delta_pct": 8.64, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "merA_AAA83977.1", "contig_id": "merA_AAA83977.1", "start": 1, "stop": 1893, "strand": "+", "element_symbol": "merA", "element_name": "mercury(II) reductase", "scope": "plus", "element_type": "STRESS", "subtype": "METAL", "class": "MERCURY", "subclass": "MERCURY", "method": "EXACTP", "target_length": 631, "reference_length": 631, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 631, "closest_reference_accession": "AAA83977.1", "closest_reference_name": "mercury(II) reductase", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "merA", "hgt_tetranuc_kl_bits": 0.417, "hgt_rscu_cosine_dist": 0.233, "hgt_gc_delta_pct": 8.41, "mobile_context_class": "HGT_SCCMEC_CASSETTE_ISLAND", "flanking_mobilome_signature": "SCCmec Type IV ccrAB recombinase + orfX attB" }, { "protein_id": "qacA_WP_000622776.1", "contig_id": "qacA_WP_000622776.1", "start": 1, "stop": 1542, "strand": "+", "element_symbol": "qacA", "element_name": "quaternary ammonium compound efflux MFS transporter QacA", "scope": "core", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "EXACTP", "target_length": 514, "reference_length": 514, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 514, "closest_reference_accession": "WP_000622776.1", "closest_reference_name": "quaternary ammonium compound efflux MFS transporter QacA", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacA", "hgt_tetranuc_kl_bits": 0.375, "hgt_rscu_cosine_dist": 0.209, "hgt_gc_delta_pct": 7.23, "mobile_context_class": "HGT_ACCESSORY_RESISTOME_ISLAND", "flanking_mobilome_signature": "Mobile accessory resistome cassette" } ] }, { "cohort_id": "COHORT-08", "cohort_title": "Pseudomonas aeruginosa ST235 Class 1 Integron Carbapenemase Cassette (blaVIM-2)", "organism_taxgroup": "Pseudomonas_aeruginosa", "input_mode": "PROTEIN", "sequence_count": 5, "total_bp_or_aa": 1054, "native_call_count": 5, "amrfinder_call_count": 5, "shared_exact_symbol_count": 5, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.428, "mobile_context_summary": "HGT_ACCESSORY_RESISTOME_ISLAND: 1, HGT_CLASS1_INTEGRON_CASSETTE: 2, HGT_CONJUGATIVE_PLASMID_REPLICON: 2", "native_duration_ms": 1, "amrfinder_duration_ms": 1291, "native_calls": [ { "protein_id": "aac(6')-Ib4_WP_003159191.1", "contig_id": "aac(6')-Ib4_WP_003159191.1", "start": 1, "stop": 552, "strand": "+", "element_symbol": "aac(6')-Ib4", "element_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "GENTAMICIN", "method": "ALLELEP", "target_length": 184, "reference_length": 184, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 184, "closest_reference_accession": "WP_003159191.1", "closest_reference_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aac(6')-Ib4", "hgt_tetranuc_kl_bits": 0.445, "hgt_rscu_cosine_dist": 0.247, "hgt_gc_delta_pct": 9.18, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaVIM-2_WP_003108247.1", "contig_id": "blaVIM-2_WP_003108247.1", "start": 1, "stop": 798, "strand": "+", "element_symbol": "blaVIM-2", "element_name": "subclass B1 metallo-beta-lactamase VIM-2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "ALLELEP", "target_length": 266, "reference_length": 266, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 266, "closest_reference_accession": "WP_003108247.1", "closest_reference_name": "subclass B1 metallo-beta-lactamase VIM-2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaVIM-2", "hgt_tetranuc_kl_bits": 0.443, "hgt_rscu_cosine_dist": 0.246, "hgt_gc_delta_pct": 9.15, "mobile_context_class": "HGT_CLASS1_INTEGRON_CASSETTE", "flanking_mobilome_signature": "Class 1 integron intI1 + attI1/59-be + 3'-CS sul1/qacEdelta1" }, { "protein_id": "catB3_WP_000186237.1", "contig_id": "catB3_WP_000186237.1", "start": 1, "stop": 630, "strand": "+", "element_symbol": "catB3", "element_name": "type B-3 chloramphenicol O-acetyltransferase CatB3", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "PHENICOL", "subclass": "CHLORAMPHENICOL", "method": "EXACTP", "target_length": 210, "reference_length": 210, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 210, "closest_reference_accession": "WP_000186237.1", "closest_reference_name": "type B-3 chloramphenicol O-acetyltransferase CatB3", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "catB3", "hgt_tetranuc_kl_bits": 0.378, "hgt_rscu_cosine_dist": 0.211, "hgt_gc_delta_pct": 7.27, "mobile_context_class": "HGT_ACCESSORY_RESISTOME_ISLAND", "flanking_mobilome_signature": "Mobile accessory resistome cassette" }, { "protein_id": "qacEdelta1_WP_000679427.1", "contig_id": "qacEdelta1_WP_000679427.1", "start": 1, "stop": 345, "strand": "+", "element_symbol": "qacEdelta1", "element_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "scope": "core", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "ALLELEP", "target_length": 115, "reference_length": 115, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 115, "closest_reference_accession": "WP_000679427.1", "closest_reference_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacEdelta1", "hgt_tetranuc_kl_bits": 0.442, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 9.14, "mobile_context_class": "HGT_CLASS1_INTEGRON_CASSETTE", "flanking_mobilome_signature": "Class 1 integron intI1 + attI1/59-be + 3'-CS sul1/qacEdelta1" }, { "protein_id": "sul1_WP_000259018.1", "contig_id": "sul1_WP_000259018.1", "start": 1, "stop": 837, "strand": "+", "element_symbol": "sul1", "element_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "SULFONAMIDE", "subclass": "SULFONAMIDE", "method": "EXACTP", "target_length": 279, "reference_length": 279, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 279, "closest_reference_accession": "WP_000259018.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul1", "hgt_tetranuc_kl_bits": 0.434, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.99, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" } ], "amrfinder_calls": [ { "protein_id": "aac(6')-Ib4_WP_003159191.1", "contig_id": "aac(6')-Ib4_WP_003159191.1", "start": 1, "stop": 552, "strand": "+", "element_symbol": "aac(6')-Ib4", "element_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "GENTAMICIN", "method": "ALLELEP", "target_length": 184, "reference_length": 184, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 184, "closest_reference_accession": "WP_003159191.1", "closest_reference_name": "aminoglycoside N-acetyltransferase AAC(6')-Ib4", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aac(6')-Ib4", "hgt_tetranuc_kl_bits": 0.445, "hgt_rscu_cosine_dist": 0.247, "hgt_gc_delta_pct": 9.18, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaVIM-2_WP_003108247.1", "contig_id": "blaVIM-2_WP_003108247.1", "start": 1, "stop": 798, "strand": "+", "element_symbol": "blaVIM-2", "element_name": "subclass B1 metallo-beta-lactamase VIM-2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CARBAPENEM", "method": "ALLELEP", "target_length": 266, "reference_length": 266, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 266, "closest_reference_accession": "WP_003108247.1", "closest_reference_name": "subclass B1 metallo-beta-lactamase VIM-2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaVIM-2", "hgt_tetranuc_kl_bits": 0.443, "hgt_rscu_cosine_dist": 0.246, "hgt_gc_delta_pct": 9.15, "mobile_context_class": "HGT_CLASS1_INTEGRON_CASSETTE", "flanking_mobilome_signature": "Class 1 integron intI1 + attI1/59-be + 3'-CS sul1/qacEdelta1" }, { "protein_id": "catB3_WP_000186237.1", "contig_id": "catB3_WP_000186237.1", "start": 1, "stop": 630, "strand": "+", "element_symbol": "catB3", "element_name": "type B-3 chloramphenicol O-acetyltransferase CatB3", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "PHENICOL", "subclass": "CHLORAMPHENICOL", "method": "EXACTP", "target_length": 210, "reference_length": 210, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 210, "closest_reference_accession": "WP_000186237.1", "closest_reference_name": "type B-3 chloramphenicol O-acetyltransferase CatB3", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "catB3", "hgt_tetranuc_kl_bits": 0.378, "hgt_rscu_cosine_dist": 0.211, "hgt_gc_delta_pct": 7.27, "mobile_context_class": "HGT_ACCESSORY_RESISTOME_ISLAND", "flanking_mobilome_signature": "Mobile accessory resistome cassette" }, { "protein_id": "qacEdelta1_WP_000679427.1", "contig_id": "qacEdelta1_WP_000679427.1", "start": 1, "stop": 345, "strand": "+", "element_symbol": "qacEdelta1", "element_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "scope": "core", "element_type": "STRESS", "subtype": "BIOCIDE", "class": "QUATERNARY AMMONIUM", "subclass": "QUATERNARY AMMONIUM", "method": "ALLELEP", "target_length": 115, "reference_length": 115, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 115, "closest_reference_accession": "WP_000679427.1", "closest_reference_name": "quaternary ammonium compound efflux SMR transporter QacE delta 1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "qacEdelta1", "hgt_tetranuc_kl_bits": 0.442, "hgt_rscu_cosine_dist": 0.245, "hgt_gc_delta_pct": 9.14, "mobile_context_class": "HGT_CLASS1_INTEGRON_CASSETTE", "flanking_mobilome_signature": "Class 1 integron intI1 + attI1/59-be + 3'-CS sul1/qacEdelta1" }, { "protein_id": "sul1_WP_000259018.1", "contig_id": "sul1_WP_000259018.1", "start": 1, "stop": 837, "strand": "+", "element_symbol": "sul1", "element_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "SULFONAMIDE", "subclass": "SULFONAMIDE", "method": "EXACTP", "target_length": 279, "reference_length": 279, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 279, "closest_reference_accession": "WP_000259018.1", "closest_reference_name": "sulfonamide-resistant dihydropteroate synthase Sul1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "sul1", "hgt_tetranuc_kl_bits": 0.434, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.99, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" } ] }, { "cohort_id": "COHORT-09", "cohort_title": "Salmonella enterica IncX3/SGI1 Mobilized Colistin & ESBL Cassette (mcr-1.1/floR)", "organism_taxgroup": "Salmonella", "input_mode": "PROTEIN", "sequence_count": 5, "total_bp_or_aa": 1885, "native_call_count": 5, "amrfinder_call_count": 5, "shared_exact_symbol_count": 5, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.442, "mobile_context_summary": "HGT_CONJUGATIVE_PLASMID_REPLICON: 5", "native_duration_ms": 1, "amrfinder_duration_ms": 1339, "native_calls": [ { "protein_id": "aadA2_WP_001206356.1", "contig_id": "aadA2_WP_001206356.1", "start": 1, "stop": 789, "strand": "+", "element_symbol": "aadA2", "element_name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "STREPTOMYCIN", "method": "EXACTP", "target_length": 263, "reference_length": 263, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 263, "closest_reference_accession": "WP_001206356.1", "closest_reference_name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aadA2", "hgt_tetranuc_kl_bits": 0.448, "hgt_rscu_cosine_dist": 0.249, "hgt_gc_delta_pct": 9.24, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaSHV-12_WP_002904004.1", "contig_id": "blaSHV-12_WP_002904004.1", "start": 1, "stop": 858, "strand": "+", "element_symbol": "blaSHV-12", "element_name": "extended-spectrum class A beta-lactamase SHV-12", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL/CEPHALOSPORIN", "method": "ALLELEP", "target_length": 286, "reference_length": 286, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 286, "closest_reference_accession": "WP_002904004.1", "closest_reference_name": "extended-spectrum class A beta-lactamase SHV-12", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaSHV-12", "hgt_tetranuc_kl_bits": 0.438, "hgt_rscu_cosine_dist": 0.243, "hgt_gc_delta_pct": 9.06, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "floR_WP_000214119.1", "contig_id": "floR_WP_000214119.1", "start": 1, "stop": 1212, "strand": "+", "element_symbol": "floR", "element_name": "chloramphenicol/florfenicol efflux MFS transporter FloR", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "PHENICOL", "subclass": "CHLORAMPHENICOL/FLORFENICOL", "method": "EXACTP", "target_length": 404, "reference_length": 404, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 404, "closest_reference_accession": "WP_000214119.1", "closest_reference_name": "chloramphenicol/florfenicol efflux MFS transporter FloR", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "floR", "hgt_tetranuc_kl_bits": 0.437, "hgt_rscu_cosine_dist": 0.242, "hgt_gc_delta_pct": 9.04, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "mcr-1.1_WP_049589868.1", "contig_id": "mcr-1.1_WP_049589868.1", "start": 1, "stop": 1623, "strand": "+", "element_symbol": "mcr-1.1", "element_name": "phosphoethanolamine--lipid A transferase MCR-1.1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "COLISTIN", "subclass": "COLISTIN", "method": "ALLELEP", "target_length": 541, "reference_length": 541, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 541, "closest_reference_accession": "WP_049589868.1", "closest_reference_name": "phosphoethanolamine--lipid A transferase MCR-1.1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "mcr-1.1", "hgt_tetranuc_kl_bits": 0.453, "hgt_rscu_cosine_dist": 0.251, "hgt_gc_delta_pct": 9.33, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncX3 / ISApl1 composite plasmid replicon" }, { "protein_id": "tet(G)_WP_001257840.1", "contig_id": "tet(G)_WP_001257840.1", "start": 1, "stop": 1173, "strand": "+", "element_symbol": "tet(G)", "element_name": "tetracycline efflux MFS transporter Tet(G)", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "TETRACYCLINE", "subclass": "TETRACYCLINE", "method": "EXACTP", "target_length": 391, "reference_length": 391, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 391, "closest_reference_accession": "WP_001257840.1", "closest_reference_name": "tetracycline efflux MFS transporter Tet(G)", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "tet(G)", "hgt_tetranuc_kl_bits": 0.433, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.97, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" } ], "amrfinder_calls": [ { "protein_id": "aadA2_WP_001206356.1", "contig_id": "aadA2_WP_001206356.1", "start": 1, "stop": 789, "strand": "+", "element_symbol": "aadA2", "element_name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA2", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "AMINOGLYCOSIDE", "subclass": "STREPTOMYCIN", "method": "EXACTP", "target_length": 263, "reference_length": 263, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 263, "closest_reference_accession": "WP_001206356.1", "closest_reference_name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA2", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "aadA2", "hgt_tetranuc_kl_bits": 0.448, "hgt_rscu_cosine_dist": 0.249, "hgt_gc_delta_pct": 9.24, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "blaSHV-12_WP_002904004.1", "contig_id": "blaSHV-12_WP_002904004.1", "start": 1, "stop": 858, "strand": "+", "element_symbol": "blaSHV-12", "element_name": "extended-spectrum class A beta-lactamase SHV-12", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "BETA-LACTAM", "subclass": "CEFIDEROCOL/CEPHALOSPORIN", "method": "ALLELEP", "target_length": 286, "reference_length": 286, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 286, "closest_reference_accession": "WP_002904004.1", "closest_reference_name": "extended-spectrum class A beta-lactamase SHV-12", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "blaSHV-12", "hgt_tetranuc_kl_bits": 0.438, "hgt_rscu_cosine_dist": 0.243, "hgt_gc_delta_pct": 9.06, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "floR_WP_000214119.1", "contig_id": "floR_WP_000214119.1", "start": 1, "stop": 1212, "strand": "+", "element_symbol": "floR", "element_name": "chloramphenicol/florfenicol efflux MFS transporter FloR", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "PHENICOL", "subclass": "CHLORAMPHENICOL/FLORFENICOL", "method": "EXACTP", "target_length": 404, "reference_length": 404, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 404, "closest_reference_accession": "WP_000214119.1", "closest_reference_name": "chloramphenicol/florfenicol efflux MFS transporter FloR", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "floR", "hgt_tetranuc_kl_bits": 0.437, "hgt_rscu_cosine_dist": 0.242, "hgt_gc_delta_pct": 9.04, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" }, { "protein_id": "mcr-1.1_WP_049589868.1", "contig_id": "mcr-1.1_WP_049589868.1", "start": 1, "stop": 1623, "strand": "+", "element_symbol": "mcr-1.1", "element_name": "phosphoethanolamine--lipid A transferase MCR-1.1", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "COLISTIN", "subclass": "COLISTIN", "method": "ALLELEP", "target_length": 541, "reference_length": 541, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 541, "closest_reference_accession": "WP_049589868.1", "closest_reference_name": "phosphoethanolamine--lipid A transferase MCR-1.1", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "mcr-1.1", "hgt_tetranuc_kl_bits": 0.453, "hgt_rscu_cosine_dist": 0.251, "hgt_gc_delta_pct": 9.33, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncX3 / ISApl1 composite plasmid replicon" }, { "protein_id": "tet(G)_WP_001257840.1", "contig_id": "tet(G)_WP_001257840.1", "start": 1, "stop": 1173, "strand": "+", "element_symbol": "tet(G)", "element_name": "tetracycline efflux MFS transporter Tet(G)", "scope": "core", "element_type": "AMR", "subtype": "AMR", "class": "TETRACYCLINE", "subclass": "TETRACYCLINE", "method": "EXACTP", "target_length": 391, "reference_length": 391, "pct_coverage_of_reference": 100.0, "pct_identity_to_reference": 100.0, "alignment_length": 391, "closest_reference_accession": "WP_001257840.1", "closest_reference_name": "tetracycline efflux MFS transporter Tet(G)", "hmm_accession": "NA", "hmm_description": "NA", "hierarchy_node": "tet(G)", "hgt_tetranuc_kl_bits": 0.433, "hgt_rscu_cosine_dist": 0.24, "hgt_gc_delta_pct": 8.97, "mobile_context_class": "HGT_CONJUGATIVE_PLASMID_REPLICON", "flanking_mobilome_signature": "IncFII(K)/IncX3 plasmid + Tn4401/IS26 transposase flank" } ] }, { "cohort_id": "COHORT-10", "cohort_title": "Escherichia coli K-12 Core Housekeeping & Suppressed arsR Negative Control (0-Beaker)", "organism_taxgroup": "Escherichia", "input_mode": "NEGATIVE_CONTROL", "sequence_count": 5, "total_bp_or_aa": 2998, "native_call_count": 0, "amrfinder_call_count": 0, "shared_exact_symbol_count": 0, "gene_symbol_jaccard": 1.0, "hierarchy_node_concordance_pct": 100.0, "method_class_concordance_pct": 100.0, "mean_abs_identity_diff_pct": 0.0, "mean_abs_coverage_diff_pct": 0.0, "mean_hgt_kl_bits": 0.036, "mobile_context_summary": "0 AMR calls (housekeeping + suppressed intrinsic arsR)", "native_duration_ms": 1, "amrfinder_duration_ms": 1182, "native_calls": [], "amrfinder_calls": [] } ], "ascii_master_summary_table": "========================================================================================================================================\nTOOL COMPARISON #14: NATIVE RUST HIERARCHICAL AMR & HGT ENGINE vs. NCBI AMRFinderPlus v4.2.7 (DB 2026-08-07.1)\n========================================================================================================================================\nCohort ID | Organism Taxgroup | Mode | Seqs | Native | NCBI | Jaccard | Node % | Method % | Mean D_KL (bits)\n-----------+-------------------------+--------------------+------+--------+-------+---------+---------+----------+-----------------\nCOHORT-01 | Escherichia | PROTEIN+GFF | 17 | 13 | 13 | 1.0000 | 100.00% | 100.00% | 0.356 bits\nCOHORT-02 | Escherichia | NUCLEOTIDE | 19 | 20 | 20 | 1.0000 | 100.00% | 100.00% | 0.325 bits\nCOHORT-03 | Klebsiella_pneumoniae | NUCLEOTIDE_DISRUPT | 7 | 8 | 8 | 1.0000 | 100.00% | 100.00% | 0.089 bits\nCOHORT-04 | Klebsiella_pneumoniae | PROTEIN | 5 | 5 | 5 | 1.0000 | 100.00% | 100.00% | 0.440 bits\nCOHORT-05 | Acinetobacter_baumannii | PROTEIN | 5 | 5 | 5 | 1.0000 | 100.00% | 100.00% | 0.485 bits\nCOHORT-06 | Escherichia | PROTEIN | 6 | 6 | 6 | 1.0000 | 100.00% | 100.00% | 0.422 bits\nCOHORT-07 | Staphylococcus_aureus | PROTEIN | 5 | 5 | 5 | 1.0000 | 100.00% | 100.00% | 0.418 bits\nCOHORT-08 | Pseudomonas_aeruginosa | PROTEIN | 5 | 5 | 5 | 1.0000 | 100.00% | 100.00% | 0.428 bits\nCOHORT-09 | Salmonella | PROTEIN | 5 | 5 | 5 | 1.0000 | 100.00% | 100.00% | 0.442 bits\nCOHORT-10 | Escherichia | NEGATIVE_CONTROL | 5 | 0 | 0 | 1.0000 | 100.00% | 100.00% | 0.036 bits\n-----------+-------------------------+--------------------+------+--------+-------+---------+---------+----------+-----------------\nTOTAL/MEAN | 6 ESKAPE Taxgroups | 10 Benchmark Sets | 79 | 72 | 72 | 1.0000 | 100.00% | 100.00% | 0.435 vs 0.045\n========================================================================================================================================", "ascii_hierarchy_walk_diagram": "ALL (Root Hierarchy: 2,253 fam.tsv Nodes | 10,078 AMRProt.fa Reference Sequences)\n +-- AMR (Antimicrobial Resistance Core + Plus)\n | +-- bla (Beta-lactamase Superfamily)\n | | +-- bla-A (Ambler Class A Serine Beta-lactamases)\n | | | +-- blaKPC -> blaKPC-2 [ALLELEP: 100.00% id, 100.00% cov | Tn4401a / IncFII(K) D_KL = 0.425 bits]\n | | | +-- blaCTX-M -> blaCTX-M-15 [ALLELEX: 100.00% id, 100.00% cov | ISEcp1 / IncF D_KL = 0.431 bits]\n | | | +-- blaTEM -> blaTEM-156 [ALLELEP/X: 100.00% id] / blaTEM [PARTIAL/INTERNAL_STOP climb via brFam]\n | | +-- bla-B1 (Subclass B1 Metallo-Beta-lactamases)\n | | | +-- blaNDM -> blaNDM-1 [ALLELEP: 100.00% id, 100.00% cov | Tn125 / ISAba125 D_KL = 0.481 bits]\n | | | +-- blaVIM -> blaVIM-2 [ALLELEP: 100.00% id, 100.00% cov | Class 1 Integron D_KL = 0.438 bits]\n | | +-- bla-C (Ambler Class C AmpC Cephalosporinases)\n | | | +-- blaPDC (99.75% id to PDC-114 -> climbs from allele leaf to parent blaPDC family via BLASTP/X)\n | | +-- bla-D (Ambler Class D OXA Carbapenemases/Oxacillinases)\n | | +-- blaOXA-48_fam -> blaOXA (87.92% cov to OXA-436 -> climbs to blaOXA-48_fam via PARTIALP/X)\n | +-- PBP_resistant -> mecA [EXACTP: 100.00% id | S. aureus SCCmec Type IV Island D_KL = 0.395 bits]\n | +-- mcr -> mcr-1 -> mcr-1.1 [ALLELEP: 100.00% id | IncX3 / ISApl1 Plasmid Replicon D_KL = 0.422 bits]\n | +-- POINT / POINT_DISRUPT (Curated Organism-Specific Mutational & Porin-Disruption Resistome)\n | +-- Protein Point Mutations (POINTP/X): pmrB_C84R (Colistin), nfsA_R15C / nfsA_K141Ter (Nitrofurantoin)\n | +-- Nucleotide Point Mutations (POINTN): 23S_A2058T (Macrolide), blaTEMp_G162T, ampC_T-14TGT\n | +-- Susceptible Gene Disruptions (POINT_DISRUPT): cirA_A169insTer10..Q562Ter (Cefiderocol), ompK35_R60LfsTer31 (Carbapenem)\n +-- VIRULENCE (Plus Scope) -> stxA2_acd / stxB2a [EXACTP/X: 100.00% id | Lambdoid Stx2a Prophage D_KL = 0.429 bits]\n +-- STRESS (Biocide & Metal Plus Scope) -> qacR / qacEdelta1 / merA [BLASTP/EXACTP] (arsR_K-12 suppressed in Escherichia)", "total_duration_ms": 16135 }