Genomic and phenotypic characterization of Pseudomonas aeruginosa isolates from two Mexican cystic fibrosis attention centers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39440985", "kind": "science-record", "revision": 3, "content_hash": "sha256:6b4f2cf52dc392e2443ad912250cd7f8eb95da8841d838d9d4ff91441b464a85", "created_at": "2026-11-01T20:29:42Z", "updated_at": "2026-11-01T22:13:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genomic and phenotypic characterization of Pseudomonas aeruginosa isolates from two Mexican cystic fibrosis attention centers.", "doi": "10.1128/spectrum.01100-24", "pmid": "39440985", "authors": ["Luis Ángel Núñez-García", "José Manuel Feliciano-Guzmán", "Christian Daniel Mireles-Davalos", "José Raúl López-Sántiz", "Jesús Elías Ovando-Fonseca", "Eduardo Becerril-Vargas", "María Elena Jiménez-Martínez", "Nadia Rodríguez-Medina", "Ulises Garza-Ramos", "Carlos Córdova-Fletes", "Elvira Garza-González"], "journal": "Microbiology spectrum", "year": 2024, "abstract": "Thirty-nine clinical isolates of Pseudomonas aeruginosa collected from 11 cystic fibrosis (CF) patients at two CF attention centers over 10 years were subjected to whole genome sequencing (WGS). Phenotypic tests (i.e., elastase, motility, biofilm, growth rate, and antibiotic susceptibility) were performed to correlate results. A single strain of P. aeruginosa was found to persist over time in longitudinal isolates. No transmission between patients or centers was observed. A tendency to lack genes related to pyoverdine, flagellum, pili, and O-antigen was observed, whereas those related to biofilm, phenazine, and pyochelin were conserved among isolates. In a patient with a 10-year follow-up, a single strain of P. aeruginosa persisted and showed a gradual decrease in elastase activity and growth rate, demonstrating an adaptive phenotype.IMPORTANCEThis study investigates the genomic and phenotypic characteristics of Pseudomonas aeruginosa isolates from Mexican cystic fibrosis (CF) patients, an underrepresented group in CF research. To our knowledge, it is the first to use whole genome sequencing (WGS) to study longitudinally collected P. aeruginosa isolates from this population, evaluating both genomic features and clonal relationships. Remarkably, the study includes samples from one patient over 10 years, offering an extended observation time compared to existing literature. Unlike similar studies, which often lack phenotypic testing, this research incorporates various virulence-related phenotypic assays, enhancing our understanding of gene-to-phenotype correlations. Two potential mechanisms for the loss of elastolytic activity were identified. Furthermore, we conduct an in-depth mobilome analysis, an area that remains largely unexplored in CF contexts. Whole genome sequencing data are publicly available through the NCBI SRA database, facilitating further re-analysis for studies on P. aeruginosa in CF, as well as epidemiological and population structure research.", "claims": [{"id": "claim-method", "statement": "Data were determined to follow a normal distribution by the Shapiro-Wilk test and were further compared against the first isolate using Dunnett’s test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39440985", "locator": "sections[9] \"Specific growth rate (µ)\" paragraph 2", "quote": "Data were determined to follow a normal distribution by the Shapiro-Wilk test and were further compared against the first isolate using Dunnett’s test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) short read archive under project number PRJNA1010856.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39440985", "locator": "sections[27] \"DATA AVAILABILITY\" paragraph 2", "quote": "The raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) short read archive under project number PRJNA1010856."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In a patient with a 10-year follow-up, a single strain of P. aeruginosa persisted and showed a gradual decrease in elastase activity and growth rate, demonstrating an adaptive phenotype.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39440985", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In a patient with a 10-year follow-up, a single strain of P. aeruginosa persisted and showed a gradual decrease in elastase activity and growth rate, demonstrating an adaptive phenotype."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "In a patient with a 10-year follow-up, a single strain of P. aeruginosa persisted and showed a gradual decrease in elastase activity and growth rate, demonstrating an adaptive phenotype.", "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:39440985"], "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": "blocked", "blocked_on": "data:accession_unresolved", "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:PRJNA1010856"], "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:PRJNA1010856"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39440985", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1128/spectrum.01100-24", "sha256": "sha256:7f778d8e5455e6b8f620107fa1908baf8fb7dea222d4274d10c5b91f994c90bf", "bytes": 43273, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1128/spectrum.01100-24", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11619361", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA1010856", "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=PRJNA1010856", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA1010856", "version": null, "note": "The raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) short read archive under project number PRJNA1010856.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) short read archive under project number PRJNA1010856.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PRJNA1010856 not downloaded", "asset:data:geo:PRJNA1010856 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "BLAST"}}, {"id": "method-2", "family": "sequence_alignment", "specific": "msa", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "multiple sequence alignment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Dunnett’s test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data were determined to follow a normal distribution by the Shapiro-Wilk test and were further compared against the first isolate using Dunnett’s test."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "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": "R4", "reachable": false, "accessions": ["PRJNA1010856"], "resolved_accessions": [], "statements": ["The raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) short read archive under project number PRJNA1010856."], "basis": "The paper names PRJNA1010856, but the accession does not resolve in the repository (not_in_ncbi_bioproject), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:39440985", "data:geo:PRJNA1010856"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJNA1010856"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:36:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11589, "completion_tokens": 1318, "cached_tokens": 256}}, "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:39440985", "type": "paper", "label": "pmid:39440985"}, {"id": "source:pmid:39440985", "type": "manuscript", "label": "PMID 39440985 full text"}, {"id": "data:geo:PRJNA1010856", "type": "dataset", "label": "GEO PRJNA1010856"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39440985", "type": "paper", "label": "pmid:39440985"}, {"id": "source:pmid:39440985", "type": "manuscript", "label": "PMID 39440985 full text"}, {"id": "data:geo:PRJNA1010856", "type": "dataset", "label": "GEO PRJNA1010856"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39440985", "type": "extraction", "used": ["source:pmid:39440985"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJNA1010856", "type": "accession_resolution", "used": ["data:geo:PRJNA1010856"], "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:39440985", "parent_hash": "sha256:4c1b9ac2fa02a2c040a46290299a9f723c6d3aade48e81fe5081295d1847e8c5", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PRJNA1010856 licence not read", "asset:data:geo:PRJNA1010856 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["BLAST"], "order_basis": "analysis_only", "id": "assay:1"}]}