{ "schemaVersion": "BASE-biological-assertion/1.1.0", "caseStudy": { "slug": "antibiotic-resistance", "title": "How Antibiotic Resistance Spreads" }, "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "groups": [ { "id": "variation-selection", "title": "Variation & Selection", "description": "Mutation supplies variants; antimicrobial exposure changes their relative success.", "assertionIds": [ "resistance-variation-can-precede-selection", "resistance-antibiotics-select-population", "resistance-has-multiple-mechanisms" ] }, { "id": "gene-transfer", "title": "Horizontal Gene Transfer", "description": "Resistance determinants can also move between cells, with context-dependent outcomes.", "assertionIds": [ "resistance-genes-can-move-horizontally" ] }, { "id": "environmental-evidence", "title": "Environmental Resistance Evidence", "description": "What the cave isolates show—and what they do not establish.", "assertionIds": [ "resistance-is-found-in-cave-isolates", "cave-isolates-show-enzyme-resistance", "resistance-history-varies-by-drug-and-host" ] } ], "assertions": [ { "id": "resistance-variation-can-precede-selection", "version": 1, "subjectId": "concept-genetic-variation", "predicate": "CAN_PRECEDE", "objectId": "process-antimicrobial-resistance", "statement": "Heritable resistance variants can be present before antimicrobial exposure; selection can then change their frequency in a bacterial population.", "qualifier": "The classic Luria–Delbrück experiment tested resistance to bacteriophage in E. coli, not an antibiotic. It supports the general distinction between mutation and selection, while drug-specific mechanisms require separate evidence.", "evidenceKind": "primary_study", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "luria-delbruck-1943", "relation": "supports", "sourceRecordId": "Genetics 28:491–511; DOI:10.1093/genetics/28.6.491", "sourceVersion": "Published 1943" } ] }, { "id": "resistance-antibiotics-select-population", "version": 1, "subjectId": "concept-antibiotic", "predicate": "SELECTS_FOR", "objectId": "process-antimicrobial-resistance", "statement": "An antibiotic can reduce susceptible bacteria more than resistant bacteria, increasing the resistant fraction among survivors and descendants.", "qualifier": "The outcome depends on the drug, concentration, exposure schedule, organism, and fitness costs. 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This finding does not prove that a specific cave gene entered a clinical pathogen or identify the full evolutionary history of resistance.", "evidenceKind": "primary_study", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "cave-antibiotic-resistance", "relation": "supports", "sourceRecordId": "PMID:22509370; DOI:10.1371/journal.pone.0034953", "sourceVersion": "Published 2012; sampled cave region described as isolated for over 4 million years" } ] }, { "id": "cave-isolates-show-enzyme-resistance", "version": 1, "subjectId": "taxon-bacteria", "predicate": "CAN_INACTIVATE_ANTIBIOTICS_BY", "objectValue": "Glycosylation and kinase-mediated phosphorylation in particular cave isolates", "statement": "The cave study characterized enzyme-mediated resistance to some macrolides, including glycosylation and phosphorylation mechanisms in particular isolates.", "qualifier": "These mechanisms were demonstrated for selected isolates and compounds; they should not be generalized to all environmental resistance or all antibiotics.", "evidenceKind": "primary_study", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "cave-antibiotic-resistance", "relation": "supports", "sourceRecordId": "PMID:22509370; DOI:10.1371/journal.pone.0034953", "sourceVersion": "Published 2012" } ] }, { "id": "resistance-history-varies-by-drug-and-host", "version": 1, "subjectId": "process-antimicrobial-resistance", "predicate": "HAS_CONTEXT_DEPENDENT_HISTORY", "objectValue": "Selection, gene acquisition, and resistance mechanisms differ across bacteria and antimicrobials", "statement": "Resistance is not one trait with one origin: the genetic mechanism, ecological reservoir, and selection history differ across organism–drug combinations.", "qualifier": "The cave case demonstrates pre-clinical environmental resistance in a sampled community, but it does not quantify how much environmental resistance contributes to any particular clinical resistance problem.", "evidenceKind": "mechanistic_review", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "cave-antibiotic-resistance", "relation": "supports", "sourceRecordId": "PMID:22509370", "sourceVersion": "Published 2012" }, { "referenceId": "openstax-drug-resistance", "relation": "qualifies", "sourceRecordId": "OpenStax Microbiology 14.5: Drug Resistance", "sourceVersion": "Edition/version not recorded in this snapshot" } ] } ], "limitation": "Resistance is specific to an organism–drug pair and assay. The Lechuguilla Cave study tested a subset of culturable isolates; it does not demonstrate direct transfer into clinical pathogens or identify the origin of a particular clinical resistance trait.", "release": { "snapshotSchemaVersion": "BASE-case-snapshot/1.0.0", "exportedAt": "2026-10-11T01:16:28.342Z", "caseContentRevision": 1, "diagramRevision": 1, "diagramId": "antibiotic-resistance-case-map", "sourceCommitSha": "e97dc5327f9d807ecaf44b77e87ddf6f3f6d2bc2", "snapshotSha256": "b51f0ae273b260d05778baa694fef83bf8ba2de78f6fda17375b1ed11e795f87" }, "snapshot": { "releaseInputs": { "caseContentRevision": 1, "diagramRevision": 1, "diagramId": "antibiotic-resistance-case-map", "sourceCommitSha": "e97dc5327f9d807ecaf44b77e87ddf6f3f6d2bc2" }, "caseStudy": { "slug": "antibiotic-resistance", "title": "How Antibiotic Resistance Spreads", "area": "Microbiology · Genetics · Evolution", "question": "Can bacteria become resistant because they need to, or does a population change through variation and selection?", "overview": "Bacterial populations can contain heritable differences before exposure. An antibiotic removes susceptible cells more effectively, while resistant cells may survive and reproduce. Resistance genes can also move between bacteria.", "mechanism": [ "Resistance can arise through mutation or acquisition of genetic material; the resulting phenotype is inherited only if the relevant genetic change persists and is expressed.", "The classic Luria–Delbrück fluctuation experiment used bacteriophage resistance, not antibiotics. Its variation among replicate cultures supported the idea that resistant variants can arise before selection is applied.", "An antibiotic then changes which bacteria survive and reproduce. It selects among variants; it does not ensure that every exposed cell becomes resistant or that one specific mutation will appear.", "Different drug–organism combinations use different mechanisms, such as drug inactivation, target changes, reduced permeability, or efflux. Susceptibility is measured for a particular isolate and drug.", "Resistance determinants can also move between bacteria by conjugation, transformation, or transduction. Transfer does not guarantee expression, persistence, or a clinically important phenotype.", "Bhullar and colleagues tested culturable bacteria from a Lechuguilla Cave sample; some tested strains resisted multiple antibiotics, and selected isolates used enzyme-mediated mechanisms. The result is a sample-specific observation, not a map of all cave microbes or clinical resistance origins." ], "evidence": "This case separates classic mutation-versus-selection evidence from antibiotic-specific mechanisms and horizontal gene transfer. The cave study shows that resistance phenotypes exist in one sampled environmental community; it does not prove direct gene transfer into pathogens or quantify environmental contributions to a clinical resistance problem.", "entityIds": [ "taxon-bacteria", "taxon-escherichia-coli", "concept-antibiotic", "process-antimicrobial-resistance", "process-horizontal-gene-transfer", "process-transformation", "process-transduction", "process-conjugation", "concept-genetic-variation" ], "references": [ "hhmi-antibiotic-resistance", "openstax-prokaryotes", "openstax-drug-resistance", "luria-delbruck-1943", "cave-antibiotic-resistance" ], "assertionIds": [ "resistance-variation-can-precede-selection", "resistance-antibiotics-select-population", "resistance-has-multiple-mechanisms", "resistance-genes-can-move-horizontally", "resistance-is-found-in-cave-isolates", "cave-isolates-show-enzyme-resistance", "resistance-history-varies-by-drug-and-host" ], "check": [ { "question": "What does antibiotic exposure do to a population with resistant and susceptible cells?", "answer": "It selects among them: susceptible cells are more likely to be inhibited or killed, while resistant cells have a higher chance to survive and reproduce." }, { "question": "What is one way resistance can spread between bacteria?", "answer": "Horizontal gene transfer can move resistance genes between cells, for example by conjugation." }, { "question": "What did the Lechuguilla Cave study establish?", "answer": "Some tested culturable isolates from the sampled cave community resisted multiple antibiotics, and selected strains had enzyme-mediated mechanisms. It did not show that cave genes entered clinical pathogens." }, { "question": "What is the limitation of using the Luria–Delbrück experiment as antibiotic evidence?", "answer": "The classic experiment tested resistance to bacteriophage, not an antibiotic. It demonstrates a general mutation-and-selection principle; drug-specific claims need drug-specific evidence." } ] }, "diagram": { "revision": 1, "id": "antibiotic-resistance-case-map", "title": "Antibiotics change which bacteria leave descendants", "subtitle": "Resistance spreads through variation, selection, and sometimes gene transfer.", "note": "Antibiotic exposure does not direct bacteria to invent a useful mutation. Resistance can come from mutation or acquired genes; drug exposure favors cells with effective resistance mechanisms. The particular mechanism and history differ across species and drugs.", "sources": [ { "label": "HHMI BioInteractive · Origins of Antibiotic Resistance", "href": "https://www.biointeractive.org/classroom-resources/origins-antibiotic-resistance" }, { "label": "OpenStax Microbiology · Drug resistance", "href": "https://openstax.org/books/microbiology/pages/14-5-drug-resistance" } ], "lanes": [ { "label": "Natural selection in a bacterial population", "note": "A treatment changes survival and reproduction, not the direction of mutation.", "links": [ "can be present before", "can select for" ], "assertionIds": [ "resistance-variation-can-precede-selection", "resistance-antibiotics-select-population" ], "nodes": [ { "label": "Heritable resistance variation", "detail": "Resistance variants may be present before drug exposure, or determinants may be acquired.", "href": "/concept/genetic-variation" }, { "label": "Antibiotic exposure", "detail": "A particular drug and concentration inhibit susceptible bacteria more strongly.", "href": "/concept/antibiotic" }, { "label": "A larger resistant fraction among survivors and descendants", "detail": "Resistant cells may survive and reproduce; the population outcome depends on the organism, drug, and mechanism.", "href": "/process/antimicrobial-resistance" } ] }, { "label": "A second route: horizontal gene transfer", "note": "Resistance determinants can move between bacteria by several mechanisms.", "links": [ "can spread by" ], "assertionIds": [ "resistance-genes-can-move-horizontally" ], "nodes": [ { "label": "Antimicrobial resistance", "detail": "The relevant determinant may be carried on a mobile genetic element; transfer does not guarantee expression or persistence.", "href": "/process/antimicrobial-resistance" }, { "label": "Horizontal gene transfer", "detail": "Routes include conjugation, transformation, or transduction.", "href": "/process/horizontal-gene-transfer" } ] } ] }, "connectedRecords": [ { "id": "taxon-bacteria", "type": "taxon", "slug": "bacteria", "name": "Bacteria", "canonicalName": "Bacteria", "summary": "One of the three domains of cellular life, comprising prokaryotic organisms with extensive metabolic and ecological diversity." }, { "id": "taxon-escherichia-coli", "type": "taxon", "slug": "escherichia-coli", "name": "Escherichia coli", "canonicalName": "Escherichia coli", "summary": "A diverse bacterial species that includes harmless strains as well as strains associated with disease." }, { "id": "concept-antibiotic", "type": "concept", "slug": "antibiotic", "name": "Antibiotic", "canonicalName": "Antibiotic", "summary": "A medicine that kills or inhibits susceptible bacteria; antibiotics do not treat viral infections." }, { "id": "process-antimicrobial-resistance", "type": "process", "slug": "antimicrobial-resistance", "name": "Antimicrobial Resistance", "canonicalName": "Antimicrobial resistance", "summary": "A heritable or acquired microbial property that reduces susceptibility to an antimicrobial agent." }, { "id": "process-horizontal-gene-transfer", "type": "process", "slug": "horizontal-gene-transfer", "name": "Horizontal Gene transfer", "canonicalName": "Horizontal gene transfer", "summary": "Movement of genetic material between organisms outside parent-to-offspring inheritance." }, { "id": "process-transformation", "type": "process", "slug": "transformation", "name": "Bacterial Transformation", "canonicalName": "Bacterial transformation", "summary": "Uptake and incorporation of extracellular DNA by a competent bacterial cell." }, { "id": "process-transduction", "type": "process", "slug": "transduction", "name": "Bacterial Transduction", "canonicalName": "Bacterial transduction", "summary": "Transfer of bacterial DNA between cells by a bacteriophage." }, { "id": "process-conjugation", "type": "process", "slug": "conjugation", "name": "Bacterial Conjugation", "canonicalName": "Bacterial conjugation", "summary": "Contact-associated transfer of DNA between bacterial cells, often involving a conjugative plasmid." }, { "id": "concept-genetic-variation", "type": "concept", "slug": "genetic-variation", "name": "Genetic Variation", "canonicalName": "Genetic variation", "summary": "Differences in genetic material among individuals or populations, generated and reshaped by multiple processes." } ], "references": [ { "id": "hhmi-antibiotic-resistance", "title": "Origins of Antibiotic Resistance", "publisher": "HHMI BioInteractive", "url": "https://www.biointeractive.org/classroom-resources/origins-antibiotic-resistance", "kind": "guide" }, { "id": "openstax-prokaryotes", "title": "Structure of Prokaryotes: Bacteria and Archaea", "publisher": "OpenStax Biology 2e", "url": "https://openstax.org/books/biology-2e/pages/22-2-structure-of-prokaryotes-bacteria-and-archaea", "kind": "textbook" }, { "id": "openstax-drug-resistance", "title": "Drug Resistance", "publisher": "OpenStax Microbiology", "url": "https://openstax.org/books/microbiology/pages/14-5-drug-resistance", "kind": "textbook" }, { "id": "luria-delbruck-1943", "title": "Mutations of Bacteria from Virus Sensitivity to Virus Resistance", "publisher": "Luria & Delbrück · Genetics 28:491–511", "url": "https://doi.org/10.1093/genetics/28.6.491", "kind": "article" }, { "id": "cave-antibiotic-resistance", "title": "Antibiotic resistance is prevalent in an isolated cave microbiome", "publisher": "Bhullar et al. · PMID 22509370", "url": "https://pubmed.ncbi.nlm.nih.gov/22509370/", "kind": "article" } ], "mechanismEvidence": { "schemaVersion": "BASE-biological-assertion/1.1.0", "context": { "scope": "Bacterial populations; 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selection can then change their frequency in a bacterial population.", "qualifier": "The classic Luria–Delbrück experiment tested resistance to bacteriophage in E. coli, not an antibiotic. It supports the general distinction between mutation and selection, while drug-specific mechanisms require separate evidence.", "evidenceKind": "primary_study", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "luria-delbruck-1943", "relation": "supports", "sourceRecordId": "Genetics 28:491–511; DOI:10.1093/genetics/28.6.491", "sourceVersion": "Published 1943" } ] }, { "id": "resistance-antibiotics-select-population", "version": 1, "subjectId": "concept-antibiotic", "predicate": "SELECTS_FOR", "objectId": "process-antimicrobial-resistance", "statement": "An antibiotic can reduce susceptible bacteria more than resistant bacteria, increasing the resistant fraction among survivors and descendants.", "qualifier": "The outcome depends on the drug, concentration, exposure schedule, organism, and fitness costs. Selection changes population frequencies; it does not make every exposed bacterium resistant.", "evidenceKind": "educational_resource", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "openstax-drug-resistance", "relation": "supports", "sourceRecordId": "OpenStax Microbiology 14.5: Drug Resistance", "sourceVersion": "Edition/version not recorded in this snapshot" }, { "referenceId": "hhmi-antibiotic-resistance", "relation": "context", "sourceRecordId": "HHMI BioInteractive: Origins of Antibiotic Resistance", "sourceVersion": "Educator resource; version not recorded" } ] }, { "id": "resistance-has-multiple-mechanisms", "version": 1, "subjectId": "process-antimicrobial-resistance", "predicate": "CAN_INVOLVE", "objectValue": "Drug inactivation, target modification, reduced uptake, or active efflux", "statement": "Bacterial resistance can arise through distinct mechanisms, including drug-inactivating enzymes, altered targets, reduced permeability, and efflux.", "qualifier": "A mechanism must be tied to a specific organism–drug pair and tested phenotype; this list is not a diagnosis of an isolate.", "evidenceKind": "educational_resource", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "openstax-drug-resistance", "relation": "supports", "sourceRecordId": "OpenStax Microbiology 14.5: Drug Resistance", "sourceVersion": "Edition/version not recorded in this snapshot" } ] }, { "id": "resistance-genes-can-move-horizontally", "version": 1, "subjectId": "process-antimicrobial-resistance", "predicate": "CAN_SPREAD_BY", "objectId": "process-horizontal-gene-transfer", "statement": "Resistance determinants can move between bacteria through horizontal gene transfer, including conjugation, transformation, or transduction.", "qualifier": "Transfer does not guarantee that a gene is expressed, maintained, or effective in a new host; compatibility and selection shape its fate.", "evidenceKind": "educational_resource", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "openstax-prokaryotes", "relation": "supports", "sourceRecordId": "OpenStax Biology 2e: Structure of Prokaryotes", "sourceVersion": "Edition/version not recorded in this snapshot" }, { "referenceId": "hhmi-antibiotic-resistance", "relation": "context", "sourceRecordId": "HHMI BioInteractive: Origins of Antibiotic Resistance", "sourceVersion": "Educator resource; version not recorded" } ] }, { "id": "resistance-is-found-in-cave-isolates", "version": 1, "subjectId": "taxon-bacteria", "predicate": "STUDIED_FOR_ANTIBIOTIC_SUSCEPTIBILITY_IN", "objectValue": "A sample of culturable Lechuguilla Cave isolates; some tested strains resisted as many as 14 antibiotics", "statement": "A study of culturable bacteria from Lechuguilla Cave found antibiotic resistance in the sampled community; some tested strains resisted multiple drugs, including 14 compounds in the panel.", "qualifier": "The number describes selected culturable isolates and the tested panel, not every cave microorganism. This finding does not prove that a specific cave gene entered a clinical pathogen or identify the full evolutionary history of resistance.", "evidenceKind": "primary_study", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "cave-antibiotic-resistance", "relation": "supports", "sourceRecordId": "PMID:22509370; DOI:10.1371/journal.pone.0034953", "sourceVersion": "Published 2012; sampled cave region described as isolated for over 4 million years" } ] }, { "id": "cave-isolates-show-enzyme-resistance", "version": 1, "subjectId": "taxon-bacteria", "predicate": "CAN_INACTIVATE_ANTIBIOTICS_BY", "objectValue": "Glycosylation and kinase-mediated phosphorylation in particular cave isolates", "statement": "The cave study characterized enzyme-mediated resistance to some macrolides, including glycosylation and phosphorylation mechanisms in particular isolates.", "qualifier": "These mechanisms were demonstrated for selected isolates and compounds; they should not be generalized to all environmental resistance or all antibiotics.", "evidenceKind": "primary_study", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "cave-antibiotic-resistance", "relation": "supports", "sourceRecordId": "PMID:22509370; DOI:10.1371/journal.pone.0034953", "sourceVersion": "Published 2012" } ] }, { "id": "resistance-history-varies-by-drug-and-host", "version": 1, "subjectId": "process-antimicrobial-resistance", "predicate": "HAS_CONTEXT_DEPENDENT_HISTORY", "objectValue": "Selection, gene acquisition, and resistance mechanisms differ across bacteria and antimicrobials", "statement": "Resistance is not one trait with one origin: the genetic mechanism, ecological reservoir, and selection history differ across organism–drug combinations.", "qualifier": "The cave case demonstrates pre-clinical environmental resistance in a sampled community, but it does not quantify how much environmental resistance contributes to any particular clinical resistance problem.", "evidenceKind": "mechanistic_review", "context": { "scope": "Bacterial populations; resistance mechanisms and selection are drug- and isolate-specific", "organism": "Bacteria; the cited resistance experiment uses Escherichia coli and bacteriophage, while the cave study sampled a mixed culturable community", "taxonId": "2", "population": "Laboratory cultures and selected culturable isolates; not a complete survey of all environmental microbes", "location": "Lechuguilla Cave, New Mexico, for the cave-resistance study", "exposureContext": "Selection occurs under a particular antimicrobial and concentration; environmental isolates were tested against a defined antibiotic panel." }, "references": [ { "referenceId": "cave-antibiotic-resistance", "relation": "supports", "sourceRecordId": "PMID:22509370", "sourceVersion": "Published 2012" }, { "referenceId": "openstax-drug-resistance", "relation": "qualifies", "sourceRecordId": "OpenStax Microbiology 14.5: Drug Resistance", "sourceVersion": "Edition/version not recorded in this snapshot" } ] } ], "limitation": "Resistance is specific to an organism–drug pair and assay. The Lechuguilla Cave study tested a subset of culturable isolates; it does not demonstrate direct transfer into clinical pathogens or identify the origin of a particular clinical resistance trait." } } }