Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27364158", "kind": "science-record", "revision": 8, "content_hash": "sha256:d2c944ce2fd4fb7a68045b5ca44221b4926eff4ac7d9ce399849773e1ff27f83", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T22:42:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis.", "doi": "10.1074/mcp.M116.060582", "pmid": "27364158", "authors": ["Veronika Kuchařová Pettersen", "Knut Anders Mosevoll", "Paul Christoffer Lindemann", "Harald G Wiker"], "journal": "Molecular & cellular proteomics : MCP", "year": 2016, "abstract": "One of the trademarks of extraintestinal pathogenic Escherichia coli is adaptation of metabolism and basic physiology to diverse host sites. However, little is known how this common human pathogen adapts to permit survival and growth in blood. We used label-free quantitative proteomics to characterize five E. coli strains purified from clinical blood cultures associated with sepsis and urinary tract infections. Further comparison of proteome profiles of the clinical strains and a reference uropathogenic E. coli strain 536 cultivated in blood culture and on two different solid media distinguished cellular features altered in response to the pathogenically relevant condition. The analysis covered nearly 60% of the strains predicted proteomes, and included quantitative description based on label-free intensity scores for 90% of the detected proteins. Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration. Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence. Although the proteomes derived from blood cultures were fairly similar for the investigated strains, quantitative proteomic comparison to the growth on solid media identified 200 proteins with substantially changed levels (11% of the shared proteins). Blood culture was characterized by up-regulation of anaerobic fermentative metabolism and multiple virulence traits, including cell motility and iron acquisition. In a response to the growth on solid media there were increased levels of proteins functional in aerobic respiration, catabolism of medium-specific carbon sources and protection against oxidative and osmotic stresses. These results demonstrate on the expressed proteome level that expression of extraintestinal virulence factors and overall cellular metabolism closely reflects specific growth conditions. Data are available via ProteomeXchange with identifier PXD002912.", "claims": [{"id": "claim-method", "statement": "One-way analysis of variance (ANOVA) with permutation-based FDR correction for multiple hypotheses testing (cutoff FDR value of 1%) was used to compare LFQ intensities of 1757 proteins quantified in all studied strains.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27364158", "locator": "sections[24] \"Quantitative Analysis of Six ExPEC Proteomes Derived from Blood Cultures Reveals Minor Variations Between the Strains\" paragraph 2", "quote": "One-way analysis of variance (ANOVA) with permutation-based FDR correction for multiple hypotheses testing (cutoff FDR value of 1%) was used to compare LFQ intensities of 1757 proteins quantified in all studied strains."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD002912.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27364158", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD002912."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Label-free quantitative proteomics of clinical ExPEC blood cultures revealed condition-dependent protein expression: 32 proteins differed between anaerobic and aerobic cultures, 47 varied among strains, and 200 changed across blood culture and solid-media conditions; the source data are available through ProteomeXchange under identifier PXD002912.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27364158", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration."}, {"asset": "source:pmid:27364158", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence."}, {"asset": "source:pmid:27364158", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD002912."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Label-free quantitative proteomics of clinical ExPEC blood cultures revealed condition-dependent protein expression: 32 proteins differed between anaerobic and aerobic cultures, 47 varied among strains, and 200 changed across blood culture and solid-media conditions; the source data are available through ProteomeXchange under identifier PXD002912.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:27364158"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD002912"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD002912"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27364158", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.M116.060582", "sha256": "sha256:0c9bb3fdd92f40f0deb1039b7b9242dfbd74f2775ab8fe32234dcb92fb9c0169", "bytes": 92843, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.M116.060582", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5013306", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002912", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD002912", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002912", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD002912.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD002912.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Expressed Proteome of Extraintestinal Escherichia coli Associated with Urinary Tract Infections", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:27364158:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b6b6ae6f3bfcffa91f85916281710ad50584f4813c4f1e465b7a605a25468294", "bytes": 1077, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#TI", "version": null, "note": "E. coli strains used in this study. Abbreviations: UTI–Urinary Tract Infection; Trim/Sulfa - Trimethoprim/Sulfamethoxazole; N - Anaerobic; O - Aerobic, M - Male, F - Female", "structure": {"pmcid": "PMC5013306", "section_index": 20, "section_title": "ExPEC solates from Clinical Blood Cultures Associated with Sepsis", "row_count": 8, "column_count": 7}, "table": {"label": "Table I", "caption": "E. coli strains used in this study. Abbreviations: UTI–Urinary Tract Infection; Trim/Sulfa - Trimethoprim/Sulfamethoxazole; N - Anaerobic; O - Aerobic, M - Male, F - Female", "rows": [["E. coli strain", "Clinical characteristics (patient sex and age)", "MALDI-TOF identification", "Resistance to antibiotics", "Sequence type (ST), Phylogenetic group", "Nr. of blood cultures"], ["Blood culture", "Urine"], ["C4n", "UTI with sepsis (M76)", "E. coli", "E. coli", "Ciprofloxacin, Trim/Sulfa", "ST131, B2", "1 N, 1 O"], ["D4n", "UTI with sepsis (F84)", "E. coli", "Mixed samplea", "-", "ST73, B2", "2 N"], ["E4n", "UTI with sepsis (M78)", "E. coli", "E. coli", "Ciprofloxacin, Trim/Sulfa", "ST131, B2", "2 O"], ["F4d", "UTI with sepsis (F90)", "E. coli", "Mixed samplea", "-", "ST73, B2", "2 N, 2 O"], ["G5m", "Immunosuppression with sepsis (M65)", "E. coli", "E. coli", "-", "ST372, B2", "2 N, 2 O"], ["UPEC 536", "Blood from healthy volunteer (M55)", "-", "-", "-", "ST92, B2", "1 N, 1 O"]], "row_count": 8, "column_count": 7, "numeric_cells": 19, "header_rows": 2, "locator": "section[20]/table-wrap[1]#TI"}}, {"id": "asset:table:pmid:27364158:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:869253cdbbbf797a07bfbbeda193e91c6283fd32177468b77ddfedb04aeb3b12", "bytes": 2622, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#TII", "version": null, "note": "Differentially expressed UPEC 536 protein complexes in response to three growth conditions", "structure": {"pmcid": "PMC5013306", "section_index": 25, "section_title": "Adaptation of UPEC 536 Physiology to Three Distinct In Vitro Conditions", "row_count": 25, "column_count": 6}, "table": {"label": "Table II", "caption": "Differentially expressed UPEC 536 protein complexes in response to three growth conditions", "rows": [["Biological function", "All detected proteins within an operon", "Proteins detected under specific condition (log2LFQ intensitya)"], ["Aerobic blood culture", "Anaerobic blood culture", "Blood agar", "Lactose agar"], ["K+ transport", "KdpABCDE", "BDE (22.7)", "BDE (22.7)", "DE (24.0)", "ABCDE (26.7)"], ["Lactose utilization", "LacZYAI", "I (NQ)", "I (NQ)", "I (21.5)", "ZYAI (28.7)"], ["Thiamine biosynthesis", "ThiBCDEFGHILMPQS", "BCEFGHILMPQ (29.4)", "BILQ (26.8)", "BILMPQ (26.3)", "BCDEFGHILMPQS (31.0)"], ["Ethanolamine utilization", "EutABCKLMQT", "CL (NQ)", "BCLMQ (NQ)", "ABCKLMQT (27.3)", "BCL (NQ)"], ["Glycolate utilization", "GlcABCEG", "BC (26.5)", "BG (26.6)", "ABCEG (29.4)", "BCG (27.4)"], ["Xylose utilization", "XylABF", "- (NQ)", "B (NQ)", "ABF (24.4)", "B (21.2)"], ["N-acetylneuraminate degradation", "NanAA2EKMR", "AA2ER (25.3)", "AA2EKMR (25.6)", "AA2EKMR (27.4)", "EKMR (25.7)"], ["Fatty acid metabolism", "FadABDEHIJLMR", "DILMR (26.9)", "DLR (26.7)", "ABDEHIJLMR (30.6)", "BDEHLMR (26.9)"], ["Glycerol-3-phosphate transport", "UgpABCEQ", "BQ (23.7)", "Q (23.12)", "ABCEQ (28.8)", "BCQ (25.5)"], ["Heme and peptide transport", "DppABCDF", "AD (23.9)", "AD (19.9)", "ABCDF (30.2)", "A (21.4)"], ["Galactose transport", "MglABC", "AB (23.9)", "AB (NQ)", "ABC (30.3)", "ABC (27.0)"], ["l-arginine degradation", "AstABCDE", "ABD (22.3)", "BD (NQ)", "ABCDE (31.3)", "BCD (21.3)"], ["Hydrogen metabolism", "HyaABCDEF", "ABCDEF (29.4)", "ABCDEF (29.3)", "B (22.8)", "B (NQ)"], ["HybABCDEFGO", "ABCDEFGO (28.1)", "ABCDEFGO (28.8)", "BCD (23.2)", "BCD (22.4)"], ["HycABCDEFGHI", "ABCDEFGHI (29.5)", "ABCDEFGHI (30.2)", "EI (24.2)", "BEI (23.9)"], ["HypABCDEF", "ABDEF (28.2)", "ABCDEF (27.9)", "BDEF (24.9)", "BDEF (23.7)"], ["Mixed acid fermentation", "FrdABCD", "ABCD (30.7)", "ABCD (30.7)", "ABCD (28.6)", "ABCD (26.6)"], ["Nickel transport", "NikABCDER", "ABCDER (28.5)", "ABCDER (30.6)", "AER (25.8)", "ABER (26.3)"], ["Glycerol degradation", "GlpABC", "ABC (27.8)", "ABC (28.5)", "AB (21.2)", "- (NQ)"], ["Chemotaxis", "CheABRWYZ, MotAB", "(Che) ABRWYZ, (Mot) AB (29.2, 23.8)", "(Che) ABRWYZ, (Mot) AB (30.8, 26.5)", "(Che) ABRWY, - (23.7, NQ)", "(Che) ABRWYZ, (Mot) AB (28.9, NQ)"], ["Heme uptake", "ChuASTUWXY", "ASTWXY (29.7)", "ASX (22.5)", "ASTX (25.9)", "ASTXY (28.2)"], ["Polysialic acid synthesis", "KpsCDEFMSTU", "CDEFSTU (28.4)", "CDEFSTU (28.6)", "CDEFTU (27.9)", "CDETU (27.1)"], ["Transcription antitermination", "CspACDEG", "ACDEG (30.8)", "ACEG (30.9)", "CE (26.9)", "ACEG (27.5)"]], "row_count": 25, "column_count": 6, "numeric_cells": 82, "header_rows": 2, "locator": "section[25]/table-wrap[1]#TII"}}], "gaps": ["asset:data:geo:PXD002912 not downloaded", "asset:data:geo:PXD002912 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "One-way analysis of variance (ANOVA) with permutation-based FDR correction for multiple hypotheses testing (cutoff FDR value of 1%) was used to compare LFQ intensities of 1757 proteins quantified in all studied strains."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Principal component analysis"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD002912"], "resolved_accessions": ["PXD002912"], "statements": ["Data are available via ProteomeXchange with identifier PXD002912."], "basis": "The paper names PXD002912 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:27364158", "data:geo:PXD002912", "asset:table:pmid:27364158:1", "asset:table:pmid:27364158:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002912"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:51Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 179105, "completion_tokens": 2583, "cached_tokens": 1832}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:27364158", "type": "paper", "label": "pmid:27364158"}, {"id": "source:pmid:27364158", "type": "manuscript", "label": "PMID 27364158 full text"}, {"id": "data:geo:PXD002912", "type": "dataset", "label": "GEO PXD002912"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27364158", "type": "paper", "label": "pmid:27364158"}, {"id": "source:pmid:27364158", "type": "manuscript", "label": "PMID 27364158 full text"}, {"id": "data:geo:PXD002912", "type": "dataset", "label": "GEO PXD002912"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27364158", "type": "extraction", "used": ["source:pmid:27364158"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002912", "type": "accession_resolution", "used": ["data:geo:PXD002912"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:27364158", "parent_hash": "sha256:efebba45c4321977c7c685c13233d3993610c9a76fb81ecd8a41ac74c4698990", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD002912 licence not read", "asset:data:geo:PXD002912 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["th in blood. We used label-free quantitative proteomics to characterize five E. coli strains purifie", "Design and Statistical Rationale Samples for LC-MS/MS analysis included two or four blood cultures", "r for the investigated strains, quantitative proteomic comparison to the growth on solid media iden"], "order_basis": "paper_text_order:392", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["One-way analysis of variance (ANOVA) with permutation-based FDR correction for multiple hypotheses testing (cutoff FDR value of 1%) was used to compare LFQ intensities of 1757 proteins quantified in all studied strains."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}