---
slug: the-gene-below-the-line
passed: 2026-11-02
by: ccr-81332fb3-8nrbtu wave, one independent agent on oversight/claims-pass.md (pre-deploy; reader check on local copies with AW_DIR; every source-record entry read against its kept copy and live source)
checked: 178
confirmed: 109
wrong: 1
unverifiable: 0
observed: 68
stale: 0
---
# Claims pass: The Gene Below the Line

Live page: not deployed yet; step 2 skipped.

Reader check (pre-deploy, local copies): `AW_DIR=<dir holding index.html, engine.mjs, isolates.json copied from public/strata/the-gene-below-the-line/> node verify-the-gene-below-the-line.mjs`, run from a second empty directory holding only the verifier: exit 0, 456 passed, 0 failed (it wrote no file; inside the repository the same verifier runs 523 checks, 0 failed, and leaves `git status` unchanged; `--mutate` moves SAMN02640799's ciprofloxacin MIC from 0.25 to 0.12 and exits 1 with the mutant caught by 8 checks). Step 6: in three scratch copies one headline figure was changed in a sentence only ("818 of the 847 read" to 817; "and 834 fall in it" to 833; "682 of them fall in one NCBI SNP cluster" to 681): each run exits 1, 454 passed, 2 failed (the sentence check and the residual sweep). The page prints no transcript of the verifier. With every kind of house block, the Cloudflare beacon and the pulse script injected into a copy, the verifier still passes (456, 0). Mutation sweep: the-gene-below-the-line: 794 mutated, 794 caught, 0 survived (text 0, meta 0, year 0).

`assay/sources.mjs the-gene-below-the-line --online`: 160 entries, offline sound; 56 FOUND, 35 UNREADABLE, 69 in the repository, 0 NOT FOUND; 7 DOI MATCH at Crossref. The 35 UNREADABLE (33 PDFs, 2 NCBI FTP index pages too short for the tool) were read by downloading each source live on 2026-11-02 (pdftotext, with and without -layout, for the EUCAST v15.0 and v9.0 tables, FDA's 2021 NARMS criteria and 2014 report, the USDA ARS table, the two Wisconsin slide decks and the CLSI AST News Update; the FTP listings directly) and finding each excerpt in it: all 91 excerpts from outside sources were found in the live sources (the other 8 are in isolates.json and distil.py, where they are), and all 26 quotations the record lists, with every quoted title and label on the page, are word for word in them (the ECV quotation prints the slide's curly apostrophe straight). Every citation was checked against Crossref (authors, initials, order, title, journal, volume, issue, pages, year). Every observation was made again: a third implementation of the page's rules, written for this pass in Python from the page's own description, over isolates.json, matched every count on the page; the snapshot table (md5 95d0935f97d72f57c9aeea6ffc38c4e9, recomputed) was recounted for the row, BioSample, genotype, mdsA/mdsB and AMRFinderPlus figures; and all 115,704 shipped MICs were compared with an independent efetch download of the 9,976 BioSamples (the scout's, 2026-11-01): 0 differences.

MINOR lines are counted in `confirmed` (6 of them); 18 claim lines at the end are claims the source record leaves out.

## Claims
- CONFIRMED | EUCAST’s reading rule is to "read MICs at the lowest concentration of the agent that completely inhibits visible growth" | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_15.0_Breakpoint_Tables.pdf | the page's quotation is word for word in the source: "Reading: Unless otherwise stated, read MICs at the lowest concentration of the agent that completely inhibits visible growth." (read live 2026-11-02)
- CONFIRMED | the row itself is a convention, since "MIC dilution series are based on twofold dilutions up and down from 1 mg/L" | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_15.0_Breakpoint_Tables.pdf | the page's quotation is word for word in the source: "By international convention, MIC dilution series are based on twofold dilutions up and down from 1 mg/L." (read live 2026-11-02)
- CONFIRMED | "EUCAST has decided to use the following format (in bold): 0.125→0.125, 0.0625→0.06, 0.03125→0.03" | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_15.0_Breakpoint_Tables.pdf | the page's quotation is word for word in the source: "To avoid having to use these in tables and documents, EUCAST has decided to use the following format (in bold): 0.125→0.125, 0.0625→0.06, 0.03125→0.03, 0.015625→0.016, 0.0078125→0.008, 0.00390625→0.004" (read live 2026-11-02)
- CONFIRMED | EUCAST writes the 2^-4 dilution as 0.06 and sets its Salmonella ciprofloxacin breakpoint at susceptible 0.06 or below | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_15.0_Breakpoint_Tables.pdf | source: "Ciprofloxacin, Salmonella spp.1 0.06 0.06" (read live 2026-11-02)
- CONFIRMED | found that "resistance genotypes and phenotypes correlated in 99.0% of cases" | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | the page's quotation is word for word in the source: "Overall, resistance genotypes and phenotypes correlated in 99.0% of cases." (read live 2026-11-02)
- CONFIRMED | with correlations that "approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams" | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | the page's quotation is word for word in the source: "Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams." (read live 2026-11-02)
- CONFIRMED | McDermott and colleagues reported in 2016 on 640 NARMS Salmonella isolates they had sequenced | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | source: "A total of 640 Salmonella isolates encompassing 43 serotypes from human clinical cases (n = 104) and retail meats (n = 536) collected by the NARMS program were selected for WGS analysis." (read live 2026-11-02)
- CONFIRMED | McDermott’s paper described this for its own 21 cefoxitin disagreements: "In 20 of the 21 instances, MICs were a single dilution below the clinical breakpoint for cefoxitin resistance, resulting in intermediate phenotypes." | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | the page's quotation is word for word in the source: "In 20 of the 21 instances, MICs were a single dilution below the clinical breakpoint for cefoxitin resistance, resulting in intermediate phenotypes." (read live 2026-11-02)
- CONFIRMED | This is the same limit McDermott’s team ran into: "Because of the design of the NARMS susceptibility testing panel, we could not evaluate the concordance between genotype and MIC (a high proportion of isolates were at the extremes of the dilution range)." | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | the page's quotation is word for word in the source: "Because of the design of the NARMS susceptibility testing panel, we could not evaluate the concordance between genotype and MIC (a high proportion of isolates were at the extremes of the dilution range)." (read live 2026-11-02)
- WRONG | McDermott’s team retested theirs, and nobody has retested these | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | "In all cases of discordance, both WGS and in vitro susceptibility testing were repeated." True of McDermott, but the same paper says "WGS data of all 640 Salmonella isolates were submitted to ... NCBI under BioProject accession number PRJNA242614", and 527 of this page's 9,976 BioSamples are in PRJNA242614 (2011 to 2013; its NCBI record, live: "Salmonella enterica MDR Genome sequencing", "The study goal is to look at the phenotype and genotype correlation in Salmonella enterica with different antibiotic resistance patterns", submitter FDA), among them 12 blaCMY-2 carriers at cefoxitin 16 mg/L, the kind McDermott counted discordant and retested; so "nobody has retested these" is false for part of the set (read live 2026-11-02)
- CONFIRMED | record that "Prior to 2012, the Clinical and Laboratory Standards Institute (CLSI) provided MIC and disk diffusion breakpoints for ciprofloxacin, levofloxacin, and ofloxacin that were common for all Enterobacteriaceae" | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the page's quotation is word for word in the source: "Prior to 2012, the Clinical and Laboratory Standards Institute (CLSI) provided MIC and disk diffusion breakpoints for ciprofloxacin, levofloxacin, and ofloxacin that were common for all Enterobacteriaceae (17)." (read live 2026-11-02)
- CONFIRMED | The 2012 Salmonella values are in the same CDC paper: "new Salmonella-specific breakpoints were implemented (susceptible [S], ≤0.064; intermediate [I], 0.12 to 0.5; and resistant [R] ≥1.0 μg/ml)" | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the page's quotation is word for word in the source: "in 2012, the interpretive criteria for extraintestinal isolates of Salmonella and ciprofloxacin were reevaluated and new Salmonella-specific breakpoints were implemented (susceptible [S], ≤0.064; intermediate [I], 0.12 to 0.5; and resistant [R] ≥1.0 μg/ml) (18)." (read live 2026-11-02)
- CONFIRMED | A Wisconsin State Laboratory of Hygiene slide from 2019 prints the previous Enterobacteriaceae broth-microdilution values as ≤1, 2, ≥4 | https://www.slh.wisc.edu/wp-content/uploads/2019/02/190206-CLSI-M100-Updates-Handouts.pdf | source: "FLUOROQUINOLONES Ciprofloxacin Previous Ciprofloxacin New Organism Method S I R S I R Enterobacteriaceae BMD ≤1 2 ≥4 ≤ 0.25 0.5 ≥1" (read live 2026-11-02)
- CONFIRMED | Medalla and colleagues, also at CDC, date the change: "In January 2012, CLSI established new ciprofloxacin MIC interpretive criteria for extraintestinal Salmonella spp." | https://pmc.ncbi.nlm.nih.gov/articles/PMC6540746/ | the page's quotation is word for word in the source: "In January 2012, CLSI established new ciprofloxacin MIC interpretive criteria for extraintestinal Salmonella spp." (read live 2026-11-02)
- CONFIRMED | They were unchanged in 2024: a slide from the same Wisconsin series prints the Salmonella ciprofloxacin row of CLSI M100-Ed34 as ≤0.06, 0.12 to 0.5, ≥1 | https://www.slh.wisc.edu/wp-content/uploads/2024/04/240416-Presentation.pdf | source: "Ciprofloxacin TABLE 2A-2 Broth Microdilution Disk Diffusion Isolate S I R S I R Enterobacterales ≤ 0.25 0.5 ≥1 ≥ 26 22-25 ≤ 21 Shigella spp. ≤ 0.25 0.5 ≥1 ≥ 26 22-25 ≤ 21 Salmonella spp. ≤ 0.06 0.12-0.5 ≥1" (read live 2026-11-02)
- CONFIRMED | And the third line is FDA’s own: "We now use decreased susceptibility to ciprofloxacin (DSC, MIC >= 0.12 ug/ml) as a marker for emerging fluoroquinolone resistance" | https://www.fda.gov/media/108180/download | the page's quotation is word for word in the source: "We now use decreased susceptibility to ciprofloxacin (DSC, MIC >= 0.12 ug/ml) as a marker for emerging fluoroquinolone resistance (CLSI, 2017)" (read live 2026-11-02)
- CONFIRMED | with the old rule, first-step mutants "would have remained undetected and would have been classified along with fully susceptible isolates free of QRDR mutations and/or PMQR mechanisms" | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the page's quotation is word for word in the source: "with the old breakpoints, these isolates would have remained undetected and would have been classified along with fully susceptible isolates free of QRDR mutations and/or PMQR mechanisms (19)." (read live 2026-11-02)
- CONFIRMED | The authors also measured the gap directly in 100 isolates: "The ciprofloxacin MICs of the isolates lacking a resistance mechanism ranged from ≤0.016 to 0.064 μg/ml, whereas the ciprofloxacin MICs for the 40 isolates with topoisomerase mutations ranged from 0.125 to ≥16 μg/ml." | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the page's quotation is word for word in the source: "The ciprofloxacin MICs of the isolates lacking a resistance mechanism ranged from ≤0.016 to 0.064 μg/ml, whereas the ciprofloxacin MICs for the 40 isolates with topoisomerase mutations ranged from 0.125 to ≥16 μg/ml." (read live 2026-11-02)
- CONFIRMED | measured the gap directly in 100 isolates | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | source: "In this study, we performed quinolone and fluoroquinolone susceptibility testing on 100 isolates of nontyphi Salmonella in order to evaluate the categorical agreement among MICs for different fluoroquinolones based on the new breakpoints." (read live 2026-11-02)
- CONFIRMED | In 2014, the testing range for streptomycin was expanded in order to determine the full range of MIC values. | https://www.fda.gov/media/101511/download | the page's quotation is word for word in the source: "In 2014, the testing range for streptomycin was expanded in order to determine the full range of MIC values. These data, along with WGS information, were used to lower the resistance breakpoint from ≥ 64 µg/ml to ≥ 32 µg/ml. Because the historical testing range only included two streptomycin concentrations of 32 µg/ml and 64 µg/ml, this new breakpoint will be applied to all testing beginning with the 2014 isolates." (read live 2026-11-02)
- CONFIRMED | Tyson and colleagues sequenced 463 Salmonella and E. coli isolates and found that "using a streptomycin resistance breakpoint of ≥ 64 μg mL(-1) classified over 20% of strains possessing aadA or strA/strB resistance genes as wild-type" | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1093%2Ffemsle%2Ffnw009&resultType=core&format=json | the page's quotation is word for word in the source: "we performed whole-genome sequencing of 463 Salmonella and E. coli isolates to identify streptomycin resistance genotypes. From this analysis, we found that using a streptomycin resistance breakpoint of ≥ 64 μg mL(-1) classified over 20% of strains possessing aadA or strA/strB resistance genes as wild-type." (read live 2026-11-02)
- CONFIRMED | proposed 32 "to improve the concordance between genotypic and phenotypic data" | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1093%2Ffemsle%2Ffnw009&resultType=core&format=json | the page's quotation is word for word in the source: "Therefore, to improve the concordance between genotypic and phenotypic data, we propose reducing the phenotypic cutoff values to ≥ 32 μg mL(-1) for both Salmonella and E. coli, to be used widely as ECVs to categorize non-wild-type isolates." (read live 2026-11-02)
- CONFIRMED | NCBI validated AMRFinder against NARMS phenotypes, measuring "the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS)" | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1128%2FAAC.00483-19&resultType=core&format=json | the page's quotation is word for word in the source: "To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS)." (read live 2026-11-02)
- CONFIRMED | for "There are no CLSI breakpoints for streptomycin or azythromycin" (as printed) | https://www.ars.usda.gov/ARSUserFiles/60400520/NARMS/ABXSalm.pdf | source: "There are no CLSI breakpoints for streptomycin or azythromycin (NARMS has not yet established breakpoints to be used for azythromycin interpretation)" (read live 2026-11-02)
- CONFIRMED | The primary purpose of clinical breakpoints is to predict clinical outcomes and not to detect resistance mechanisms. | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the page's quotation is word for word in the source: "The primary purpose of clinical breakpoints is to predict clinical outcomes and not to detect resistance mechanisms." (read live 2026-11-02)
- CONFIRMED | gives "MIC values that separate bacterial populations into those that have (don’t have) resistance mechanisms strictly on basis of phenotype", and is "Strictly in vitro; no clinical correlation" | https://www.slh.wisc.edu/wp-content/uploads/2019/02/190206-CLSI-M100-Updates-Handouts.pdf | slide "EPIDEMIOLOGICAL CUTOFF VALUE" (footer "CLSI M100; 29th ed.; 2019"): "MIC values that separate bacterial populations into those that have (don’t have) resistance mechanisms strictly on basis of phenotype"; word for word, the slide's curly apostrophe printed straight on the page (read live 2026-11-02)
- CONFIRMED | and is "Strictly in vitro; no clinical correlation" | https://www.slh.wisc.edu/wp-content/uploads/2019/02/190206-CLSI-M100-Updates-Handouts.pdf | the page's quotation is word for word in the source: "EPIDEMIOLOGICAL CUTOFF VALUE MIC values that separate bacterial populations into those that have (don’t have) resistance mechanisms strictly on basis of phenotype Strictly in vitro; no clinical correlation" (read live 2026-11-02)
- CONFIRMED | NCBI itself places no restrictions on the use or distribution of the data contained therein. Nor do we accept data when the submitter has requested restrictions on reuse or redistribution. However, some submitters of the original data (or the country of origin of such data) may claim patent, copyright, or other intellectual property rights in all or a portion of the data (that has been submitted). | https://www.ncbi.nlm.nih.gov/home/about/policies/ | the page's quotation is word for word in the source: "Therefore, NCBI itself places no restrictions on the use or distribution of the data contained therein. Nor do we accept data when the submitter has requested restrictions on reuse or redistribution. However, some submitters of the original data (or the country of origin of such data) may claim patent, copyright, or other intellectual property rights in all or a portion of the data (that has been submitted)." (read live 2026-11-02)
- CONFIRMED | which notes that the resistance call is "made by the data submitter. These are typically, done by using CLSI or EUCAST standards and those standards change over time OR the call is made by an automated instrument which may infer the cutoff." (as printed) | https://www.ncbi.nlm.nih.gov/pathogens/pathogens_help/ | the page's quotation is word for word in the source: "DISCLAIMER: Note, the format for this data field in the isolates browser is presented as a list of antibiotic compounds broken down by resistance call made by the data submitter. These are typically, done by using CLSI or EUCAST standards and those standards change over time OR the call is made by an automated instrument which may infer the cutoff." (read live 2026-11-02)
- CONFIRMED | ESCMID holds the copyright ("Any unauthorized reproduction, distribution or use of such content is prohibited") | https://www.escmid.org/legal-mentions/ | the page's quotation is word for word in the source: "Unless otherwise indicated, all content on this website is the property of ESCMID or is used under licence and is protected by applicable copyright laws. Any unauthorized reproduction, distribution or use of such content is prohibited." (read live 2026-11-02)
- CONFIRMED | M. Feldgarden, V. Brover, D. H. Haft, A. B. Prasad, D. J. Slotta, I. Tolstoy, G. H. Tyson, S. Zhao, C.-H. Hsu, P. F. McDermott, D. A. Tadesse, C. Morales, M. Simmons, G. Tillman, J. Wasilenko, J. P. Folster and W. Klimke, "Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates", Antimicrobial Agents and Chemotherapy 63(11):e00483-19, 2019 | https://api.crossref.org/works/10.1128/AAC.00483-19 | Crossref: 17 authors Feldgarden ... Klimke in the page's order; Antimicrobial Agents and Chemotherapy 63(11) e00483-19, 2019; title as printed (read live 2026-11-02)
- CONFIRMED | P. F. McDermott, G. H. Tyson, C. Kabera, Y. Chen, C. Li, J. P. Folster, S. L. Ayers, C. Lam, H. P. Tate and S. Zhao, "Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella", Antimicrobial Agents and Chemotherapy 60(9):5515–5520, 2016 | https://api.crossref.org/works/10.1128/AAC.01030-16 | Crossref: McDermott, Tyson, Kabera, Chen, Li, Folster, Ayers, Lam, Tate, Zhao; AAC 60(9):5515-5520, 2016; title as printed (read live 2026-11-02)
- CONFIRMED | Copyright 2016 American Society for Microbiology; quoted in short extracts. | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | source: "Copyright © 2016, American Society for Microbiology. All Rights Reserved." (read live 2026-11-02)
- CONFIRMED | G. H. Tyson, C. Li, S. Ayers, P. F. McDermott and S. Zhao, "Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli", FEMS Microbiology Letters 363(4):fnw009, 2016 | https://api.crossref.org/works/10.1093/femsle/fnw009 | Crossref: Gregory H. Tyson, Cong Li, Sherry Ayers, Patrick F. McDermott, Shaohua Zhao; FEMS Microbiology Letters 363(4) fnw009, 2016 (read live 2026-11-02)
- CONFIRMED | G. H. Tyson, C. Li, L. B. Harrison, G. Martin, C.-H. Hsu, H. Tate, T. T. Tran, E. Strain and S. Zhao, "A Multidrug-Resistant Salmonella Infantis Clone is Spreading and Recombining in the United States", Microbial Drug Resistance 27(6):792–799, 2021 | https://api.crossref.org/works/10.1089/mdr.2020.0389 | Crossref: Tyson, Li, Harrison, Martin, Hsu (Chih-Hao), Tate, Tran (Thu-Thuy), Strain, Zhao; Microbial Drug Resistance 27(6):792-799, 2021 (read live 2026-11-02)
- CONFIRMED | M. Sjölund-Karlsson, R. L. Howie, J. A. Crump and J. M. Whichard, "Fluoroquinolone Susceptibility Testing of Salmonella enterica: Detection of Acquired Resistance and Selection of Zone Diameter Breakpoints for Levofloxacin and Ofloxacin", Journal of Clinical Microbiology 52(3):877–884, 2014 | https://api.crossref.org/works/10.1128/JCM.02679-13 | Crossref: Maria Sjölund-Karlsson, Rebecca L. Howie, John A. Crump, Jean M. Whichard; Journal of Clinical Microbiology 52(3):877-884, 2014; title as printed (read live 2026-11-02)
- CONFIRMED | Sjölund-Karlsson, Howie, Crump and Whichard, Journal of Clinical Microbiology 52(3):877–884, 2014, Discussion | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | authors Sjölund-Karlsson, Howie, Crump, Whichard; J Clin Microbiol 2014 Mar;52(3):877–884 (Crossref agrees); the quoted sentence is in the DISCUSSION; three authors at CDC, R. L. Howie at IHRC, Inc., Atlanta, so "The CDC authors" is loose but fair (read live 2026-11-02)
- CONFIRMED | Sjölund-Karlsson and colleagues, writing at CDC in 2014 | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | source: "Maria Sjölund-Karlsson aCenters for Disease Control and Prevention, Atlanta, Georgia, USA" (read live 2026-11-02)
- CONFIRMED | F. Medalla, R. M. Hoekstra, J. M. Whichard, E. J. Barzilay, T. M. Chiller, K. Joyce, R. Rickert, A. Krueger, A. Stuart and P. M. Griffin, "Increase in Resistance to Ceftriaxone and Nonsusceptibility to Ciprofloxacin and Decrease in Multidrug Resistance Among Salmonella Strains, United States, 1996–2009", Foodborne Pathogens and Disease 10(4):302–309, 2013 | https://api.crossref.org/works/10.1089/fpd.2012.1336 | Crossref: Felicita Medalla, Robert M. Hoekstra, Jean M. Whichard, Ezra J. Barzilay, Tom M. Chiller, Kevin Joyce, Regan Rickert, Amy Krueger, Andrew Stuart, Patricia M. Griffin; Foodborne Pathogens and Disease 10(4):302-309, 2013; title as printed (read live 2026-11-02)
- CONFIRMED | Medalla and colleagues, also at CDC | https://pmc.ncbi.nlm.nih.gov/articles/PMC6540746/ | source: "Felicita Medalla Felicita Medalla 1Centers for Disease Control and Prevention, Atlanta, Georgia." (read live 2026-11-02)
- CONFIRMED | E. Deak, R. Skov, J. A. Hindler and R. M. Humphries, "Evaluation of Surrogate Disk Tests for Detection of Ciprofloxacin and Levofloxacin Resistance in Clinical Isolates of Salmonella enterica", Journal of Clinical Microbiology 53(11):3405–3410, 2015 | https://api.crossref.org/works/10.1128/JCM.01393-15 | Crossref: Eszter Deak, Robert Skov, Janet A. Hindler, Romney M. Humphries; Journal of Clinical Microbiology 53(11):3405-3410, 2015; title as printed (read live 2026-11-02)
- MINOR | for the pre-2012 use of nalidixic acid as the indicator | https://pmc.ncbi.nlm.nih.gov/articles/PMC4609702/ | the paper does say nalidixic acid "was recommended as an indicator of fluoroquinolone resistance for S. enterica by the CLSI prior to 2012", but the page makes no claim about nalidixic acid as an indicator; the claim Deak et al. actually support on the page ("gyrA, a topoisomerase gene") goes unnamed in the Sources line (read live 2026-11-02)
- CONFIRMED | "Updates to CLSI M100", February 2019 | https://www.slh.wisc.edu/wp-content/uploads/2019/02/190206-CLSI-M100-Updates-Handouts.pdf | "Updates to CLSI M100 Erik Munson, Ph.D., D(ABMM) Marquette University Wisconsin Clinical Laboratory Network"; uploaded under 2019/02 (file 190206) (read live 2026-11-02)
- CONFIRMED | "2024 Updates to CLSI M100", April 2024 | https://www.slh.wisc.edu/wp-content/uploads/2024/04/240416-Presentation.pdf | "2024 Updates to CLSI M100 Erik Munson Marquette University Wisconsin Clinical Laboratory Network"; uploaded under 2024/04 (file 240416) (read live 2026-11-02)
- MINOR | The European Committee on Antimicrobial Susceptibility Testing, "Breakpoint tables for interpretation of MICs and zone diameters", version 15.0, valid from 1 January 2025 | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_15.0_Breakpoint_Tables.pdf | "Breakpoint tables for interpretation of MICs and zone diameters Version 15.0, valid from 2025-01-01" is right, but v15.0 is no longer EUCAST's current table: https://www.eucast.org/clinical_breakpoints (the page's own link) now lists "Clinical breakpoints (v 16.1)" for "24 June 2026 - 31 December 2026" and says "Older, no longer valid, breakpoint tables can be accessed through the archive"; v16.1 keeps every value the page cites (Salmonella ciprofloxacin 0.06 / 0.06, note 18, 0.0625→0.06) (read live 2026-11-02)
- CONFIRMED | FDA Center for Veterinary Medicine, "2021 NARMS Interpretive Criteria for Susceptibility Testing", Table 1 | https://www.fda.gov/media/108180/download | PDF title metadata "2021 NARMS Interpretive Criteria for Susceptibility Testing", author "FDA CVM", created 2021-06-08; "Table 1. Interpretive Categories Used for Susceptibility Testing of Salmonella and E. coli"; FDA's NARMS resources page still links this file as its "Interpretive Criteria for Susceptibility Testing" (read live 2026-11-02)
- MINOR | FDA, "NARMS Integrated Report: 2014", p. 3 | https://www.fda.gov/media/101511/download | title "NARMS Integrated Report: 2014 The National Antimicrobial Resistance Monitoring System: Enteric Bacteria"; the streptomycin passage is on p. 3, but the Sources line also cites "p. 3" for "the definition of decreased susceptibility", which is the table footnote "† Decreased susceptibility to ciprofloxacin (DSC): includes isolates with MICs categorized as intermediate or resistant for ciprofloxacin (MIC ≥0.12 µg/mL)" on p. 13 (read live 2026-11-02)
- CONFIRMED | USDA ARS, "Table 1. Breakpoints Used for Susceptibility Testing of Salmonella and E. coli" | https://www.ars.usda.gov/ARSUserFiles/60400520/NARMS/ABXSalm.pdf | source: "Table 1. Breakpoints Used for Susceptibility Testing of Salmonella and E. coli 1" (read live 2026-11-02)
- CONFIRMED | for ciprofloxacin, gentamicin, tetracycline, ceftriaxone, cefoxitin, chloramphenicol, sulfamethoxazole/sulfisoxazole and both streptomycin rows | https://www.fda.gov/media/108180/download | source: "Aminoglycosides Gentamicin ≤4 8 ≥ 16 Streptomycin before 2014 ≤ 32 N/A ≥ 64 Streptomycin beginning in 2014 ≤ 16 N/A ≥ 32" (read live 2026-11-02)
- CONFIRMED | blaCMY-2 cefoxitin ≤8 / ≥32 | https://www.fda.gov/media/108180/download | source: "Cephems Cefoxitin ≤8 16 ≥ 32 Ceftriaxone ≤1 2 ≥4" (read live 2026-11-02)
- CONFIRMED | chloramphenicol ≤8 / ≥32 | https://www.fda.gov/media/108180/download | source: "Phenicols Chloramphenicol ≤8 16 ≥ 32" (read live 2026-11-02)
- CONFIRMED | NCBI Pathogen Detection, Salmonella, snapshot PDG000000002.4281, metadata table | https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/PDG000000002.4281/Metadata/ | listing: "PDG000000002.4281.metadata.tsv 2026-11-01 02:01 840M"; isolates.json about.snapshot "PDG000000002.4281" (read live 2026-11-02)
- OBSERVED | 880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9, fetched 1 November 2026 | recreated: md5sum of the kept snapshot table and an HTTP HEAD of https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/PDG000000002.4281/Metadata/PDG000000002.4281.metadata.tsv | md5 95d0935f97d72f57c9aeea6ffc38c4e9; Content-Length: 880575393 (live 2026-11-02)
- CONFIRMED | NCBI's latest_kmer directory holds only the newest snapshot | https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/latest_kmer/Metadata/ | today the listing holds one snapshot's two files, now "PDG000000002.4282.metadata.tsv 2026-11-01 18:06 840M" and the .xml; still only the newest (read live 2026-11-02)
- CONFIRMED | the SNP clusters are NCBI’s PDG000000002.4280.reference_target.cluster_list.tsv | https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/PDG000000002.4280/Clusters/ | listing: "PDG000000002.4280.reference_target.cluster_list.tsv 2026-11-01 01:45 45M" (read live 2026-11-02)
- CONFIRMED | NCBI AMRFinderPlus database 2026-08-07.1: Reference Gene Catalog and AMRProt-mutation.tsv | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ | version.txt reads "2026-08-07.1"; the directory lists ReferenceGeneCatalog.txt and AMRProt-mutation.tsv (read live 2026-11-02)
- OBSERVED | The genotypes in the snapshot were produced by AMRFinderPlus 4.2.5 (9,508 of these isolates) and 4.2.7 (468), against database versions from 2025-12-03.1 to 2026-08-07.1; these counts take in all 9,976, the 103 with an empty genotype field included. | recreated: recount over the snapshot table PDG000000002.4281.metadata.tsv (880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9 recomputed today; the scout's kept download) | amrfinder_version 4.2.5: 9,508, 4.2.7: 468 (all 9,976, the 103 empty included); refgene_db_version from 2025-12-03.1 to 2026-08-07.1
- CONFIRMED | The MICs are the Antibiogram tables of each BioSample, fetched through E-utilities | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&id=SAMN03988471&retmode=xml | the efetch record carries the Antibiogram table (14 rows, e.g. "ciprofloxacin intermediate == 0.125 mg/L MIC CLSI"); all 115,704 shipped readings match an independent efetch download (read live 2026-11-02)
- CONFIRMED | efetch, db=biosample | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&id=SAMN03988471&retmode=xml | source: "ciprofloxacin intermediate == 0.125 mg/L MIC CLSI" (read live 2026-11-02)
- CONFIRMED | 5,037 of the 9,976 come from one FDA project, "CVM NARMS Salmonella" | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=bioproject&id=PRJNA292661&retmode=xml | "<Title>CVM NARMS Salmonella</Title>"; 5,037 of the 9,976 in PRJNA292661 (recounted from isolates.json and the raw table) (read live 2026-11-02)
- CONFIRMED | The cluster looks like the multidrug-resistant Infantis clone Tyson and colleagues described in 2021, which they report carries a gyrA mutation | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=TITLE%3A%22Multidrug-Resistant%20Salmonella%20Infantis%20Clone%20is%20Spreading%20and%20Recombining%22&resultType=core&format=json | source: "This clone also has a gyrA mutation conferring fluoroquinolone resistance, further limiting treatment options." (read live 2026-11-02)
- CONFIRMED | so these are not 847 independent events | https://ftp.ncbi.nlm.nih.gov/pathogen/ReadMe.txt | source: "Clusters can consist of two or more closely related isolates." (read live 2026-11-02)
- OBSERVED | 9,976 of the snapshot’s 908,609 isolates, about 1.1% | recreated: recount over the snapshot table PDG000000002.4281.metadata.tsv (880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9 recomputed today; the scout's kept download) | 908,609 rows; 9,977 with AST_phenotypes; 9,976 distinct BioSamples; 9,976 / 908,609 = 1.098%, so about 1.1%
- OBSERVED | For each one this page ships the MIC rows of its BioSample antibiogram for twelve of the drugs tested, exactly as submitted, 115,704 of them | recreated: parse of an independent efetch download of all 9,976 BioSample records (the scout's, 2026-11-01), compared with isolates.json | 115,704 MIC readings across the twelve shipped drugs; all 115,704 equal the BioSample antibiograms (sign, first number, call, standard), 0 differences; for the two combination drugs only the first number of the submitted pair is kept (see the MINOR on exactly as submitted below)
- OBSERVED | 4,953 of those 5,037 name chicken, turkey, pork, beef or veal as the thing they were isolated from | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 5,037 BioSamples in PRJNA292661; 4,953 of their isolation sources match chicken/turkey/pork/beef/veal (ground turkey 1,520, chicken breast 872, Chicken Wings 419 ...), all retail-meat descriptions
- OBSERVED | Take the 847 isolates in this snapshot whose only known quinolone-resistance determinant of any kind is one | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 847 isolates with a ciprofloxacin MIC whose only quinolone/fluoroquinolone element is one gyrA point mutation; 8,756 with none; 171 other; 99 no genotype
- OBSERVED | and 832 become intermediate, 2 resistant, 8 susceptible, with 5 censored readings the rule cannot place | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 2012 rule (S<=0.06, R>=1) on the 847: S 8, I 832, R 2, undecidable 5
- OBSERVED | Resistant at 8 mg/L or above leaves 1,890 disagreements, at 16 leaves 591, at 32 leaves 192, at 64 leaves 594, at 128 leaves 1,306. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 2014-on streptomycin set, disagreements at 8/16/32/64/128 mg/L: 1,890 / 591 / 192 / 594 / 1,306; minimum at 32 with 0 undecidable
- OBSERVED | 2,499 of those 3,878 isolates are recorded as "≤32" | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 3,878 streptomycin-tested isolates dated before 2014; 2,499 recorded "<=32"
- OBSERVED | Sweep the line for the 1,368 carriers and 8,416 non-carriers of a gentamicin determinant and the minimum is at 4 mg/L, with 87 disagreements. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 1,368 carriers, 8,416 non-carriers; sweep minimum 87 at 4 mg/L (0 undecidable)
- OBSERVED | One concentration, three words, no disagreement about the measurement. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | ciprofloxacin at exactly 0.25 mg/L: CLSI 0 S / 37 I / 572 R; EUCAST 2 S / 0 I / 72 R; three words at one value
- OBSERVED | 70 records write that dilution as "0.06" under the label CLSI and call it susceptible, while 27 write it as "0.0625" under the label EUCAST and call it resistant. All 27 come from one submitter, SENASICA in Mexico, in 2019. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | "0.06" + CLSI + susceptible: 70 records; "0.0625" + EUCAST + resistant: 27, all SENASICA, all 2019; SENASICA country Mexico (about.center_countries, from geo_loc_name)
- OBSERVED | SENASICA (Mexico, 149 isolates), the Friedrich-Loeffler-Institut (Germany, 73), the Animal and Plant Quarantine Agency (South Korea, 37), UQAM (32), Zhejiang University (20), the National Veterinary Research Institute (10), Institut Pasteur Guadeloupe (4), Central Public Health Laboratories (3), Grupo de Microbiologia Salmonella_enterica (3), DS-I Africa (3), Kazan Federal University (1) | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | centre counts: SENASICA 149, Friedrich-Loeffler-Institut 73, Animal and Plant Quarantine Agency 37, UQAM 32, Brigham & Women's Hospital 21, Zhejiang University 20, National Veterinary Research Institute 10, Institut Pasteur Guadeloupe 4, Central Public Health Laboratories 3, Grupo de Microbiologia 3, DS-I Africa 3, Texas A&M 2, Kazan Federal University 1, University of Massachusetts Amherst 1; every other centre is a US federal or state body (FDA and its centres, CDC, Walter Reed Army Institute of Research, four state public health laboratories); countries as stated in about.center_countries
- OBSERVED | Dropped: 153 disk-diffusion rows, and the readings of 15 drugs for one BioSample tested on several panels. | recreated: parse of an independent efetch download of all 9,976 BioSample records (the scout's, 2026-11-01), compared with isolates.json | 153 disk-diffusion rows (units mm); 15 (BioSample, antibiotic) pairs with more than one MIC row, all 15 in SAMN11179044
- OBSERVED | A value within 7% of a power of two is that dilution, so 0.125 is the 0.12 well and 0.0625 is the 0.06 well. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | engine.mjs snap() and this pass's implementation agree; 0.125 and 0.0625 lie within 4% of 2^-3 and 2^-4
- OBSERVED | curl -sO https://artwaste.land/checks/verify-the-gene-below-the-line.mjs | recreated: AW_DIR=<copies> node verify-the-gene-below-the-line.mjs in an empty directory | the page prints exactly the house command; reader check run with AW_DIR on local copies: exit 0, 456 passed, 0 failed; in the repository 523 passed, 0 failed
- CONFIRMED | And whether the line sweep is new: it is not, in kind. | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1093%2Ffemsle%2Ffnw009&resultType=core&format=json | Tyson et al. 2016 abstract: "To identify whether this ECV correlated with genetic determinants of resistance, we performed whole-genome sequencing of 463 Salmonella and E. coli isolates"; the page claims no novelty (read live 2026-11-02)
- CONFIRMED | Foodborne Pathogens and Disease 10(4):302–309, 2013 | https://pmc.ncbi.nlm.nih.gov/articles/PMC6540746/ | source: "Published in final edited form as: Foodborne Pathog Dis. 2013 Mar 6;10(4):302–309. doi: 10.1089/fpd.2012.1336" (read live 2026-11-02)
- CONFIRMED | older versions keep directories of their own (on 1 November 2026 the oldest listed was from January 2017) | https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/ | 76 PDG000000002.* directories; the oldest "PDG000000002.819/ 2017-01-06 22:58" (read live 2026-11-02)
- CONFIRMED | ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/PDG000000002.4281/Metadata/ | https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/PDG000000002.4281/Metadata/ | "PDG000000002.4281.metadata.tsv 2026-11-01 02:01 840M" (read live 2026-11-02)
- CONFIRMED | and was first found in retail meats in 2014 | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=TITLE%3A%22Multidrug-Resistant%20Salmonella%20Infantis%20Clone%20is%20Spreading%20and%20Recombining%22&resultType=core&format=json | source: "We found the ESI clone was first found in retail meats in Tennessee in 2014, but by 2019 was throughout the United States" (read live 2026-11-02)
- MINOR | all 683 isolates of that cluster in this set carry gyrA D87Y, and the earliest of them was collected in 2014. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 683 BioSamples in PDS000265741, all carrying gyrA_D87Y; dated ones: 2014 (1), 2016 (23), 2017 (35), 2018 (67), 2019 (345), 2021 (209), but 3 of the 683 have no collection year in the snapshot (year 0), so "the earliest of them was collected in 2014" holds only for the 680 dated ones
- OBSERVED | That match is this page's inference; neither NCBI's cluster list nor the paper's abstract names the clone and the cluster together. | recreated: read research/the-gene-below-the-line/sources/tyson-2021-mdr-abstract-europepmc.txt and the live Europe PMC abstract | the Tyson 2021 abstract names no PDS cluster accession; the NCBI cluster list names clusters only by PDS accession; the page labels the match its own inference
- CONFIRMED | NARMS scientists proposed the 2014 streptomycin line this way, from 463 sequenced isolates (Tyson and colleagues, 2016) | https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1093%2Ffemsle%2Ffnw009&resultType=core&format=json | source: "To identify whether this ECV correlated with genetic determinants of resistance, we performed whole-genome sequencing of 463 Salmonella and E. coli isolates to identify streptomycin resistance genotypes." (read live 2026-11-02)
- CONFIRMED | and the 2014 report says WGS information was used | https://www.fda.gov/media/101511/download | source: "These data, along with WGS information, were used to lower the resistance breakpoint from ≥ 64 µg/ml to ≥ 32 µg/ml." (read live 2026-11-02)
- OBSERVED | 682 of the 847 fall in one NCBI SNP cluster, PDS000265741, and 652 are serotype Infantis | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 682 of the 847 in PDS000265741; 652 of the 847 serotype Infantis
- OBSERVED | NCBI's own Reference Gene Catalog subclass, never a hand-written list. | recreated: read research/the-gene-below-the-line/distil.py and engine.mjs DRUG_TOKENS; checked the subclasses in isolates.json against the live ReferenceGeneCatalog.txt | gene-to-drug is by the catalogue subclass words (e.g. tet(A) TETRACYCLINE, blaCMY-2 CEPHALOSPORIN, sul1 SULFONAMIDE); no hand list of genes
- CONFIRMED | its subclass reads APRAMYCIN/GENTAMICIN/TOBRAMYCIN | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt | aac(3)-IVa row: class AMINOGLYCOSIDE, subclass "APRAMYCIN/GENTAMICIN/TOBRAMYCIN" (read live 2026-11-02)
- CONFIRMED | the catalogue maps both to gentamicin | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt | source: "aac(3)-IVa aminoglycoside N-acetyltransferase AAC(3)-IVa core AMR AMR AMINOGLYCOSIDE APRAMYCIN/GENTAMICIN/TOBRAMYCIN" (read live 2026-11-02)
- CONFIRMED | the catalogue maps both to gentamicin | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt | source: "aac(3)-VIa aminoglycoside N-acetyltransferase AAC(3)-VIa core AMR AMR AMINOGLYCOSIDE GENTAMICIN" (read live 2026-11-02)
- CONFIRMED | and that the 2012 change "lowered the resistance breakpoint for ciprofloxacin and extraintestinal Salmonella from ≥4 μg/ml to ≥1.0 μg/ml" | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the page's quotation is word for word in the source: "The new recommendations lowered the resistance breakpoint for ciprofloxacin and extraintestinal Salmonella from ≥4 μg/ml to ≥1.0 μg/ml, and isolates with MICs ranging from 0.125 to 0.5 μg/ml were classified as intermediate (18)." (read live 2026-11-02)
- CONFIRMED | writing "We used the new criteria for all isolates" | https://pmc.ncbi.nlm.nih.gov/articles/PMC6540746/ | the page's quotation is word for word in the source: "In January 2012, CLSI established new ciprofloxacin MIC interpretive criteria for extraintestinal Salmonella spp. We used the new criteria for all isolates" (read live 2026-11-02)
- CONFIRMED | the CLSI newsletter announcing the change says that "Although aminoglycosides may appear active against Salmonella and Shigella in vitro, they are ineffective against these genera clinically" | https://clsi.org/media/cn0byp3g/ast_newsletter23_final-24.pdf | the page's quotation is word for word in the source: "Although aminoglycosides may appear active against Salmonella and Shigella in vitro, they are ineffective against these genera clinically." (read live 2026-11-02)
- CONFIRMED | CLSI's standard, M100, was not read for this page (CLSI sells it, and also offers a free read-only view on its MicroFree portal, behind a sign-in) | https://clsi.org/resources/insights-blog/critical-standards-added-to-clsi-micro-free/ | "In addition to the read-only versions offered in MicroFree, CLSI will continue to offer these standards for purchase in print and PDF forms"; the sign-in redirect recreated today (read live 2026-11-02)
- CONFIRMED | M100 itself was not read for this page: CLSI sells it, and its free read-only portal, CLSI MicroFree, needs a sign-in | https://clsi.org/resources/insights-blog/critical-standards-added-to-clsi-micro-free/ | "MicroFree features read-only access and is intended as a companion or quick reference to the full products."; https://clsi.org/micro-free ends today at https://em100.edaptivedocs.net/Login.aspx, a sign-in page (read live 2026-11-02)
- CONFIRMED | CLSI, "Critical Standards Added to CLSI Micro Free", 20 April 2023 | https://clsi.org/resources/insights-blog/critical-standards-added-to-clsi-micro-free/ | source: "Critical Standards Added to CLSI Micro Free April 20, 2023" (read live 2026-11-02)
- CONFIRMED | R. M. Humphries, "New! CLSI M100-Ed33: Updated Aminoglycoside Breakpoints for Enterobacterales and Pseudomonas aeruginosa", CLSI AST News Update 8(1), June 2023 | https://clsi.org/media/cn0byp3g/ast_newsletter23_final-24.pdf | source: "New! CLSI M100-Ed33: Updated Aminoglycoside Breakpoints for Enterobacterales and Pseudomonas aeruginosa Romney M. Humphries, Vanderbilt University Medical Center" (read live 2026-11-02)
- CONFIRMED | CLSI's 2023 revision for the Enterobacterales, M100-Ed33, moved it to 8 | https://clsi.org/media/cn0byp3g/ast_newsletter23_final-24.pdf | Table 2, Enterobacterales "Gentamicin ≤4 8 ≥16 ≤2 4 ≥8" under "Obsolete CLSI M100-Ed32" and "Updated CLSI M100-Ed33" (read live 2026-11-02)
- CONFIRMED | CLSI redrew this one in 2023 after a review of pharmacokinetic and pharmacodynamic data | https://clsi.org/media/cn0byp3g/ast_newsletter23_final-24.pdf | source: "However, review of modern pharmacokinetic and pharmacodynamic (PK/PD) data against members of the Enterobacterales and P. aeruginosa demonstrated:" (read live 2026-11-02)
- CONFIRMED | The resistant line FDA's 2021 table takes from CLSI is at 16 | https://www.fda.gov/media/108180/download | Table 1 footnote 1: "Breakpoints were adopted from CLSI (Clinical and Laboratory Standards Institute) M100-Ed30 document, except for streptomycin and azithromycin"; gentamicin row "≤4 8 ≥ 16" (read live 2026-11-02)
- CONFIRMED | Read under the line FDA's 2021 NARMS table adopts from CLSI | https://www.fda.gov/media/108180/download | source: "Breakpoints were adopted from CLSI (Clinical and Laboratory Standards Institute) M100-Ed30 document, except for streptomycin and azithromycin, which has no CLSI breakpoin" (read live 2026-11-02)
- CONFIRMED | a category FDA's table lists under both intermediate and resistant | https://www.fda.gov/media/108180/download | source: "Quinolones Ciprofloxacin3 ≤ 0.06 ≥0.12 ≥0.12" (read live 2026-11-02)
- CONFIRMED | which puts 0.12 and above in both its intermediate and its resistant column | https://www.fda.gov/media/108180/download | source: "Quinolones Ciprofloxacin3 ≤ 0.06 ≥0.12 ≥0.12" (read live 2026-11-02)
- CONFIRMED | where 0.12 and above is decreased susceptibility | https://www.fda.gov/media/101511/download | source: "Decreased susceptibility to ciprofloxacin (DSC): includes isolates with MICs categorized as intermediate or resistant for ciprofloxacin (MIC ≥0.12 µg/mL)" (read live 2026-11-02)
- CONFIRMED | Read them under the rule CLSI introduced in January 2012 for extraintestinal Salmonella | https://pmc.ncbi.nlm.nih.gov/articles/PMC6540746/ | source: "In January 2012, CLSI established new ciprofloxacin MIC interpretive criteria for extraintestinal Salmonella spp." (read live 2026-11-02)
- CONFIRMED | (applied here to every isolate, as CDC's Medalla and colleagues applied it to all of theirs) | https://pmc.ncbi.nlm.nih.gov/articles/PMC6540746/ | source: "We used the new criteria for all isolates" (read live 2026-11-02)
- CONFIRMED | for ciprofloxacin, Medalla and colleagues applied the 2012 rule to isolates from 1996 to 2009 | https://api.crossref.org/works/10.1089/fpd.2012.1336 | title ends "Salmonella Strains, United States, 1996–2009"; Methods (PMC6540746): "We used the new criteria for all isolates" (read live 2026-11-02)
- CONFIRMED | that is why NARMS applied its new streptomycin line only to isolates from 2014 on | https://www.fda.gov/media/101511/download | source: "this new breakpoint will be applied to all testing beginning with the 2014 isolates" (read live 2026-11-02)
- CONFIRMED | A single amino-acid change in gyrA, a topoisomerase gene | https://pmc.ncbi.nlm.nih.gov/articles/PMC4609702/ | source: "45 isolates had mutations in the QRDR region of the gyrA topoisomerase gene." (read live 2026-11-02)
- CONFIRMED | raises the MIC a few steps without reaching the concentration a clinical laboratory calls resistant | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | the record's excerpt ("mostly due to mutations in the topoisomerase genes") is weak support; the same paper's "isolates with first-step QRDR mutations ... displaying ciprofloxacin MICs of 0.125 to 0.5 μg/ml will be classified as intermediate" supports it, and so does this page's data (2 of the 847 reach 1 mg/L) (read live 2026-11-02)
- OBSERVED | reading its susceptible limit of 1 as the pre-2012 one assumes that the Enterobacteriaceae values did not change between 2012 and 2019, which neither source says | recreated: read the live slide deck https://www.slh.wisc.edu/wp-content/uploads/2019/02/190206-CLSI-M100-Updates-Handouts.pdf and PMC3957759 | the 2019 slide labels its columns only "Previous" and "New"; the Sjolund-Karlsson paper gives the old resistant line (>=4) but no susceptible value; neither dates the "Previous" values, as the page says
- CONFIRMED | half of them from one FDA surveillance project | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=bioproject&id=PRJNA292661&retmode=xml | "Whole genome sequencing of foodborne pathogens as part of the US Food and Drug Administration surveillance project for NARMS."; 5,037 / 9,976 = 50.5% (read live 2026-11-02)
- CONFIRMED | (99.0% of the time in McDermott's 640 isolates) | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | source: "Overall, resistance genotypes and phenotypes correlated in 99.0% of cases." (read live 2026-11-02)
- CONFIRMED | Created by NCBI, so in the public domain under NCBI's policy. | https://www.ncbi.nlm.nih.gov/home/about/policies/ | source: "Information that is created by or for the US government on this site is within the public domain." (read live 2026-11-02)
- CONFIRMED | All US Government works, so in the public domain | https://www.law.cornell.edu/uscode/text/17/105 | source: "Copyright protection under this title is not available for any work of the United States Government" (read live 2026-11-02)
- CONFIRMED | FDA's website policy says the same of its own pages | https://www.fda.gov/about-fda/about-website/website-policies | source: "They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA." (read live 2026-11-02)
- OBSERVED | tet(A) tetracycline ≤4 / ≥16 2,902 22 1 2,879 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 2,902 / 22 / 1 / 2,879 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | tet(B) tetracycline ≤4 / ≥16 1,904 10 1 1,893 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 1,904 / 10 / 1 / 1,893 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | blaCMY-2 ceftriaxone ≤1 / ≥4 842 8 2 832 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 842 / 8 / 2 / 832 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | blaCMY-2 cefoxitin ≤8 / ≥32 841 10 65 766 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 841 / 10 / 65 / 766 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | floR chloramphenicol ≤8 / ≥32 615 5 2 608 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 615 / 5 / 2 / 608 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | sul1 sulfisoxazole ≤256 / ≥512 1,342 21 0 1,321 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 1,342 / 21 / 0 / 1,321 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | aadA1 streptomycin ≤16 / ≥32 1,121 61 0 979 81 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 1,121 / 61 / 0 / 979 / 81; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | aadA7 streptomycin ≤16 / ≥32 46 5 0 22 19 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 46 / 5 / 0 / 22 / 19; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | aac(3)-VIa gentamicin ≤4 / ≥16 508 11 16 481 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 508 / 11 / 16 / 481 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | aac(3)-IVa gentamicin ≤4 / ≥16 523 81 295 147 0 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 523 / 81 / 295 / 147 / 0; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | gyrA D87Y ciprofloxacin ≤0.06 / ≥1 770 3 764 2 1 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | carriers / S / I / R / undecidable = 770 / 3 / 764 / 2 / 1; the line matches FDA 2021 Table 1 (streptomycin: the 2014 row; ciprofloxacin: CLSI 2012)
- OBSERVED | 2,902 isolates carry tet(A) and have a tetracycline MIC. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 2,902 tet(A) carriers with a tetracycline MIC
- OBSERVED | The submitting laboratories' own words for these carriers: 2,876 resistant, 23 susceptible, 2 not defined, 1 intermediate. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | submitted calls for the 2,902: R 2,876, S 23, D (not defined) 2, I 1
- OBSERVED | A further 2,077 tested isolates carry some other determinant for tetracycline | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 2,077 tested isolates with another tetracycline determinant or tet(A) only partial
- OBSERVED | Resistant at 1 mg/L or above (CLSI from 2012): 842 of the 9,603 isolates disagree with their genotype. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | at 1 mg/L: 842 disagreements among 847 + 8,756 = 9,603; 11 undecidable, 9,592 placeable
- OBSERVED | 842 of the 847 carriers are not called resistant | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 842 of the 847 not called resistant at 1 mg/L; 0 non-carriers resistant
- OBSERVED | the 847 carriers read 8 susceptible, 832 intermediate, 2 resistant and 5 undecidable | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | S 8, I 832, R 2, undecidable 5
- OBSERVED | Fewest disagreements: 48 at 0.12 mg/L, at most 63 if all 15 undecidable readings there disagreed, and no other line can do better however they resolve. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 0.12 mg/L: 48 disagreements, 15 undecidable, upper bound 63; next-best lower bounds 125 (0.06) and 216 (0.25), so decisive
- OBSERVED | Left out of both groups: 171 isolates with some other quinolone determinant (another mutation, a plasmid gene or a partial hit) and 99 with an empty genotype field. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 171 with another quinolone determinant, 99 with no genotype
- OBSERVED | Of the 2,902 isolates that carry it and were tested against tetracycline, 22 come out susceptible, fewer than one in a hundred. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 22 of 2,902 = 0.76%
- OBSERVED | The first behaves: 481 of 508 carriers resistant, 11 susceptible. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 481 R, 11 S of 508
- OBSERVED | of 523 carriers, 147 are resistant, 295 are intermediate and 81 are susceptible | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 147 R, 295 I, 81 S of 523
- OBSERVED | they pile up at 4 and 8 mg/L, two steps and one step below the line at 16, where 295 of them land on the single word | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | exact readings: 74 at 4 mg/L, 295 at 8 mg/L (369 of 523); the 295 at 8 are the intermediates
- OBSERVED | 65 carriers sit at exactly 16 mg/L, one step under a line drawn at 32 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 65 blaCMY-2 carriers read exactly 16 mg/L
- OBSERVED | 766 carry D87Y, 28 S83F, 24 D87N, 15 D87G, 12 S83Y and 2 D82N | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | D87Y 766, S83F 28, D87N 24, D87G 15, S83Y 12, D82N 2 (sum 847)
- OBSERVED | 818 of the 847 read 0.12 or 0.25 mg/L, while 8,549 of the 8,756 isolates with no known quinolone determinant read 0.03 or below | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 818 of 847 read exactly 0.12 or 0.25; 8,549 of 8,756 read at most 0.03
- OBSERVED | the commonest reading among the 847, 0.25 mg/L, is at least four doublings above the commonest reading without one | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | mode among the 847: "=0.25" (626); mode without a determinant: "<=0.015" (6,709); 0.015 to 0.25 is four doublings
- OBSERVED | CLSI from January 2012 (extraintestinal Salmonella) ≤0.06 / ≥1 8 832 2 5 8,706 40 0 10 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 2012 row: single-gyrA 8 / 832 / 2 / 5; no determinant 8,706 / 40 / 0 / 10; pre-2012 row 847 S and 8,756 S; DSC row 8 / 0 / 834 / 5 and 8,706 / 0 / 40 / 10
- OBSERVED | a category FDA's table lists under both intermediate and resistant, and 834 fall in it | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 834 of the 847 at >=0.12
- OBSERVED | And the 847 isolates at the centre of the argument below are not 847 independent events: 682 of them fall in one NCBI SNP cluster. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 682 of the 847 in one SNP cluster
- OBSERVED | half of them from one FDA surveillance project and nearly all of those from meat, with 682 of the 847 in one NCBI SNP cluster | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 5,037 of 9,976 in PRJNA292661 (50.5%); 4,953 of those name a meat; 682 of 847 in PDS000265741
- OBSERVED | For the 4,857 isolates collected in 2014 or later and tested against streptomycin, 2,067 carry a gene the catalogue maps to streptomycin and 2,726 carry none. | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 4,857 tested from 2014; 2,067 carriers, 2,726 none, 44 partial-only, 20 no genotype
- OBSERVED | The instrument marks 2,417 of them undecidable there and refuses to guess (the other 82 belong to 8 isolates whose only streptomycin hit is partial and 74 with an empty genotype field, which the sweep leaves out). | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | of the 2,499 "<=32": 2,417 carriers or non-carriers (undecidable at 32), 8 partial-only, 74 no genotype
- OBSERVED | is at 16, which leaves 507 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 507 disagreements at 16 mg/L
- OBSERVED | moved it to 8, which leaves 168 | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 168 disagreements at 8 mg/L
- OBSERVED | all but 21 of the 115,704 name the standard the laboratory says it followed | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 21 of 115,704 readings carry no testing standard
- OBSERVED | All 572 resistant calls under the label "CLSI" were submitted by FDA | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | all 572 CLSI-labelled resistant calls at exactly 0.25 mg/L have bioproject_center "FDA"
- OBSERVED | The antibiograms hold 142,170 MIC readings across 70 antibiotics. | recreated: parse of an independent efetch download of all 9,976 BioSample records (the scout's, 2026-11-01), compared with isolates.json | 142,170 MIC rows (units mg/L) naming 70 antibiotics
- OBSERVED | which AMRFinderPlus lists for 9,826 of these 9,976 BioSamples | recreated: recount over the snapshot table PDG000000002.4281.metadata.tsv (880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9 recomputed today; the scout's kept download) | 9,826 of the 9,976 BioSamples list mdsA or mdsB in AMR_genotypes
- OBSERVED | have an empty AMR_genotypes field: NCBI's table records AMRFinderPlus as applied to each of them and finding no AMR genes at all | recreated: recount over the snapshot table PDG000000002.4281.metadata.tsv (880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9 recomputed today; the scout's kept download) | 103 BioSamples with AMR_genotypes NULL; all 103 have amrfinder_applied 1 and number_amr_genes 0
- OBSERVED | one isolate for ciprofloxacin, 44 for streptomycin from 2014, four for gentamicin | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | partial-only: ciprofloxacin 1, streptomycin from 2014 44, gentamicin 4
- OBSERVED | Fourteen readings across the twelve drugs are off the series | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | 14 off-series readings: ciprofloxacin 0.003 x4, 0.007 x2, 0.012, 0.75, 1.5; ampicillin 26; nalidixic acid 20, 25, 48; gentamicin <=0.038
- CONFIRMED | in its 2019 tables (version 9.0) as in its current ones | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.pdf | v9.0: "Ciprofloxacin, Salmonella spp.1 0.06 0.06" and note 11 "0.0625→0.06"; the current table, v16.1 (https://www.eucast.org/fileadmin/eucast/pdf/breakpoints/v_16.1_Breakpoint_Tables.pdf), has the same row, so "as in its current ones" is true (see the MINOR on cite-eucast-v15) (read live 2026-11-02)
- CONFIRMED | and version 9.0, valid from 1 January 2019 | https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.pdf | source: "Version 9.0, valid from 2019-01-01" (read live 2026-11-02)
- CONFIRMED | Start with tet(A), a tetracycline efflux pump. | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt | product_name "tetracycline efflux MFS transporter Tet(A)", subclass TETRACYCLINE (read live 2026-11-02); not in the source record
- CONFIRMED | That is the ordinary case, and it was reported ten years ago. | https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/ | McDermott et al., "Collection date 2016 Sep", AAC 60:5515-5520; 2016 to November 2026 is ten years (read live 2026-11-02); not in the source record
- CONFIRMED | aac(3)-VIa and aac(3)-IVa are both gentamicin-modifying enzymes | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt | both rows: product_name "aminoglycoside N-acetyltransferase AAC(3)-IVa" / "AAC(3)-VIa", subclasses APRAMYCIN/GENTAMICIN/TOBRAMYCIN and GENTAMICIN (read live 2026-11-02)
- CONFIRMED | why the efflux pair mdsA and mdsB ... is dropped before anything is counted | https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt | mdsA "multidrug efflux RND transporter periplasmic adaptor subunit MdsA" and mdsB "... permease subunit MdsB", class EFFLUX, subclass EFFLUX, so no drug maps to them; isolates.json about.dropped_elements ["mdsA","mdsB"] (read live 2026-11-02)
- CONFIRMED | the old panel held only two streptomycin wells, 32 and 64 mg/L | https://www.fda.gov/media/101511/download | p. 3: "Because the historical testing range only included two streptomycin concentrations of 32 µg/ml and 64 µg/ml"; the USDA ARS Table 1 prints a streptomycin range of 32 - 64 for every year from 2001 to 2011-2012; no isolate in the set dated before 2001 has a streptomycin MIC (read live 2026-11-02)
- MINOR | The minimum sits at 32, which is where FDA's programme moved its line ... Read them under the convention FDA's surveillance programme uses, where 0.12 and above is decreased susceptibility | https://www.fda.gov/animal-veterinary/antimicrobial-resistance/national-antimicrobial-resistance-monitoring-system | FDA's own NARMS page: "NARMS is a collaborative program of state and local public health departments and universities, the FDA, the Centers for Disease Control and Prevention (CDC), and the U.S. Department of Agriculture (USDA)"; the 2014 report says the streptomycin line is NARMS's ("NARMS has always used its own minimum inhibitory concentration (MIC) values"); the DSC convention is in FDA CVM's NARMS table, so "FDA's surveillance convention" (the dek) is fair, but NARMS is not FDA's programme alone (read live 2026-11-02)
- MINOR | for twelve drugs the MIC exactly as submitted: the sign, the number, the laboratory's word and the standard it names | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&id=SAMN03988471&retmode=xml and public/strata/the-gene-below-the-line/isolates.json | for amoxicillin-clavulanic acid and trimethoprim-sulfamethoxazole the submitted measurement is a pair (SAMN03988471: "2/1" and "0.125/2.4"), and isolates.json keeps the first number only (its own about.what says "sign, first number, call, standard"); the eight instrument drugs are single numbers and are exact
- CONFIRMED | Copyright American Society for Microbiology; quoted in short extracts. | https://pmc.ncbi.nlm.nih.gov/articles/PMC3957759/ | "Copyright © 2014, American Society for Microbiology." (read live 2026-11-02); not in the source record
- CONFIRMED | (PDG000000002.4281, built 1 November 2026) | https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/PDG000000002.4281/ | Metadata/ 2026-11-01 02:01; PDG000000002.4281.kmer.descriptor.xml 2026-11-01 02:01 (read live 2026-11-02)
- OBSERVED | that have both a genome and a laboratory antibiogram | recreated: recount over the snapshot table PDG000000002.4281.metadata.tsv (880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9 recomputed today; the scout's kept download) | all 9,977 AST rows have an assembly (9,740) or SRA reads only (237), and amrfinder_applied 1
- OBSERVED | Every BioSample ... 9,977 rows, 9,976 BioSamples, since one (SAMN03894186) is listed twice under two isolate accessions | recreated: recount over the snapshot table PDG000000002.4281.metadata.tsv (880,575,393 bytes, md5 95d0935f97d72f57c9aeea6ffc38c4e9 recomputed today; the scout's kept download) | SAMN03894186 appears as PDT000078012.1 and PDT000384425.1
- OBSERVED | ampicillin, amoxicillin-clavulanic acid, nalidixic acid and trimethoprim-sulfamethoxazole, which appear in nearly every antibiogram | recreated: parse of an independent efetch download of all 9,976 BioSample records (the scout's, 2026-11-01), compared with isolates.json | MIC rows: ampicillin 9,912, nalidixic acid 9,693, trimethoprim-sulfamethoxazole 9,675, amoxicillin-clavulanic acid 9,640, of 9,976 BioSamples
- OBSERVED | The rest, azithromycin, ceftiofur and meropenem among them, are not shipped | recreated: parse of an independent efetch download of all 9,976 BioSample records (the scout's, 2026-11-01), compared with isolates.json | azithromycin 7,023, ceftiofur 4,875, meropenem 4,842 MIC rows; none is in isolates.json drugs
- OBSERVED | Every reading here carries the laboratory's own word beside the number | recreated: a third implementation written for this pass from the rules as the page states them (Python, no shared code), over public/strata/the-gene-below-the-line/isolates.json | all 115,704 readings carry a call: S 93,874, R 20,041, I 1,388, D (not defined) 251, N (nonsusceptible) 150; none empty
- OBSERVED | meta description, og:description, twitter:description and JSON-LD description equal the visible dek and the frontmatter dek; <title> and JSON-LD name equal the seoTitle; aw-plain equals plain | recreated: string comparison of public/strata/the-gene-below-the-line/index.html with src/content/strata/the-gene-below-the-line.md | all identical; every number in dek and plain (847, 818, 0.12, 0.25, 0.03, 2012, 832, 834, 1.1%, 908,609, 682) is recomputed above
- CONFIRMED | seoTitle: Can a bacterium carry an antibiotic resistance gene and still test susceptible? | public/strata/the-gene-below-the-line/isolates.json | answered yes on the page with recomputed counts (22 of 2,902 tet(A) carriers, 81 of 523 aac(3)-IVa carriers, all 847 single-gyrA isolates under the pre-2012 rule)
- CONFIRMED | plain: most of 847 germs with one resistance mutation sit well under the old line and just over the new one, so the same measurements get called susceptible, in-between, or resistant | public/strata/the-gene-below-the-line/isolates.json | 818 of 847 read 0.12 or 0.25: well under the pre-2012 lines (S<=1, R>=4) and one or two doublings over the 2012 susceptible limit (0.06); read under the 2012 resistant line (1 mg/L) they are under it, so "the new one" means the new susceptible limit
- CONFIRMED | relates note: Where resistance comes from before the selecting agent arrives (a phage, in Luria and Delbrück's 1943 experiment) | https://api.crossref.org/works/10.1093/genetics/28.6.491 | Luria and Delbrück, "MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE", Genetics 28(6):491-511, 1943 (read live 2026-11-02)

## Findings
- [fixed] MED: WRONG, "nobody has retested these". Re-read McDermott et al. 2016, kept copy and live (https://pmc.ncbi.nlm.nih.gov/articles/PMC4997858/, 2026-11-02): "WGS data of all 640 Salmonella isolates were submitted to the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA242614." and "In all cases of discordance, both WGS and in vitro susceptibility testing were repeated." PRJNA242614 by efetch (live 2026-11-02, now kept as research/the-gene-below-the-line/sources/bioproject-PRJNA242614.txt): "Salmonella enterica MDR Genome sequencing", owner FDA, 641 BioSamples. isolates.json: 527 of the 9,976 in PRJNA242614 (2011: 91, 2012: 87, 2013: 349). The finding holds. The page (index.html:226) now reads: "Whether any individual discordant isolate is a real biological effect, a mixed culture or a transcription slip. McDermott's team repeated both tests in every case of discordance among their 640, and 527 of the isolates here are in the BioProject they deposited those genomes under, PRJNA242614; the records do not say which readings, if any, are repeats, and this page retested none." "The records do not say" was checked before it was written: the 527 raw BioSample records (the scout's efetch download) contain none of retest, re-test, repeat, confirm or duplicate, their attributes are only strain, lat_lon, collection_date, geo_loc_name, isolation_source, collected_by, serovar, AssemblyVersion, SequencingTechnology and AntigenForm, and the Antibiogram table has no column for a repeat (README, "Checks made by hand"). Source record: mcdermott-retested reworded to the new clause; new entries mcdermott-bioproject (the PRJNA242614 sentence) and records-no-retest. The verifier (C1) now counts the 527 and finds the whole sentence; a scratch copy with 526, or with 641 for 640, goes red. The optional note at index.html:131 was not taken: "McDermott's paper described this for its own 21 cefoxitin disagreements" stays true as written, and the page now says in the section on what it does not know that 527 of its isolates are in McDermott's BioProject.
- [fixed] MINOR: the cluster's earliest year. Confirmed: the three undated members of PDS000265741 (SAMN04054202, SAMN05570536, SAMN12648960) have collection_date NULL in the snapshot table (md5 95d0935f97d72f57c9aeea6ffc38c4e9), so year 0 in isolates.json; the other 680 run from 2014. index.html:224 now reads "all 683 isolates of that cluster in this set carry gyrA D87Y, and, of the 680 with a collection year in the snapshot, the earliest was collected in 2014." Source-record entry cluster-profile updated to the new words (with the three accessions in its where); the verifier (C5) now counts the dated members (680) and checks the new sentence (a planted 681 goes red); README, "Checks made by hand", records the three.
- [fixed] MINOR: NARMS called "FDA's programme". Re-read FDA's NARMS page live (2026-11-02, now kept as research/the-gene-below-the-line/sources/fda-narms-about-excerpt.txt): "NARMS is a collaborative program of state and local public health departments and universities, the FDA, the Centers for Disease Control and Prevention ( CDC ), and the U.S. Department of Agriculture ( USDA )."; the 2014 report (live PDF, pp. 2 to 3): "NARMS has always used its own minimum inhibitory concentration (MIC) values". index.html:174 now "The minimum sits at 32, which is where NARMS moved its line"; index.html:152 now "Read them under the convention FDA's NARMS table uses, where 0.12 and above is decreased susceptibility, a category that table lists under both intermediate and resistant, and 834 fall in it." (the words of the convention are FDA CVM's 2021 NARMS table: "We now use decreased susceptibility to ciprofloxacin (DSC, MIC >= 0.12 ug/ml) as a marker for emerging fluoroquinolone resistance"). The dek's "FDA's surveillance convention" and the table row "FDA NARMS" stay, as the finding allows. Source record: new entries narms-moved-line (its where quotes the NARMS-page sentence) and narms-table-convention; fda-dsc-row and count-dsc-834 follow the new wording. The verifier checks both new sentences.
- [fixed] MINOR: "exactly as submitted" for the combination drugs. Confirmed in the kept BioSample copy (SAMN03988471: amoxicillin-clavulanic acid "== 2/1", trimethoprim-sulfamethoxazole "<= 0.125/2.4") and in the scout's efetch download, where every MIC row for the two drugs is a pair except SAMN02053837's single 1 and 0.12. index.html:96 now "for twelve of the drugs tested, as submitted (for the two combination drugs, the first number of each pair), 115,704 of them"; index.html:212 now "and for twelve drugs the MIC as submitted: the sign, the number (for amoxicillin-clavulanic acid and trimethoprim-sulfamethoxazole, the first number of the pair), the laboratory's word and the standard it names." Source record: count-mics follows the new words; new entry combination-pairs. The verifier checks both sentences, that the twelve drugs hold exactly these two combinations and that the data file says it keeps the first number, and, inside the repository, that the kept SAMN03988471 copy shows each pair and isolates.json its first number. README, "What the distillation keeps", says the same.
- [fixed] MINOR: Deak et al. cited for a claim the page does not make. Re-read the kept copy and the live article (https://pmc.ncbi.nlm.nih.gov/articles/PMC4609702/, 2026-11-02): the nalidixic-acid sentence is there ("which was recommended as an indicator of fluoroquinolone resistance for S. enterica by the CLSI prior to 2012"), but the page body names nalidixic acid only as a shipped drug and in the list of off-series readings, never as an indicator; what Deak et al. support on the page is "45 isolates had mutations in the QRDR region of the gyrA topoisomerase gene." index.html:239 now ends "for gyrA as a topoisomerase gene." The source-record entry is renamed cite-deak-gyra, with that claim and that excerpt; the verifier's printed-reference list follows.
- [fixed] MINOR: wrong page for the decreased-susceptibility definition. Re-read the live PDF (https://www.fda.gov/media/101511/download, 2026-11-02): the streptomycin passage begins on printed and PDF page 3 ("used its own minimum inhibitory concentration (MIC) values. In 2014, the testing range for streptomycin was expanded ..."), and "† Decreased susceptibility to ciprofloxacin (DSC): includes isolates with MICs categorized as intermediate or resistant for ciprofloxacin (MIC ≥0.12 µg/mL)" is the table footnote on printed and PDF page 13. index.html:240 now "FDA, "NARMS Integrated Report: 2014", pp. 3 and 13"; the blockquote citation at index.html:176 stays "p. 3". Source record: cite-fda-2014 claim and where updated, narms-dsc-definition where "p. 13, table footnote †". The verifier checks the new citation (a planted "pp. 3 and 14" goes red).
- [fixed] MINOR: EUCAST v15.0 is not the current table. Re-read https://www.eucast.org/clinical_breakpoints live (2026-11-02): "Clinical breakpoints (v 16.1)* Download PDF file for printing (24 June 2026 - 31 December 2026)" and "Older, no longer valid, breakpoint tables can be accessed through the archive"; downloaded v16.1 (https://www.eucast.org/fileadmin/eucast/pdf/breakpoints/v_16.1_Breakpoint_Tables.pdf, 4,351,645 bytes, md5 89226a5768230a7c674b80c10dbeac0e): "Version 16.1, valid from 2026-06-24", "Version 16.0, 2026-01-01", "Ciprofloxacin, Salmonella spp.1 0.06 0.06", and note 18 with "0.125→ 0.125, 0.0625→0.06". Kept as research/the-gene-below-the-line/sources/eucast-v16.1-excerpt.txt (those lines only). index.html:242 now cites version 15.0 at its own PDF "for the reading rule, the twofold-dilution convention, the written dilution labels and the single Salmonella ciprofloxacin value, all taken from it; version 16.1, valid from 24 June 2026 and the current table on 2 November 2026 (eucast.org/clinical_breakpoints), which prints the same Salmonella ciprofloxacin value and the same 0.06 label; and version 9.0 ...". The quotation at index.html:199 stays attributed to v15.0, and "as in its current ones" now has its own entry against v16.1. The closing note now says the copies were kept as they read on 1 November 2026 "(the current EUCAST table, on 2 November)". Source record: new entries cite-eucast-v16, eucast-v16-current, eucast-v16-same-value, eucast-v16-same-label, eucast-v16-as-current; cite-eucast-v15 where updated. The verifier checks the new citation and both links (a planted 16.2 or "3 November" goes red).

## Fixer's note (round 2, 2026-11-02)
Every finding above was re-read against its kept copy and its live source before it was fixed; all seven held, and none was declined. The claim lines are the pass's own words and verdicts, unchanged. The 18 claims the pass found missing from the source record were added where they are on the page (teta-efflux, aac3-enzymes, mds-efflux, old-panel-two-wells, mcdermott-ten-years, cite-sjolund-copyright, snapshot-built, genome-and-antibiogram, listed-twice, four-common-drugs, rest-not-shipped, every-reading-word); the other six are the two MINOR claims, now rewritten and recorded, and four that live in the frontmatter or the head copies, not in the page text. After the fixes: `node verify-the-gene-below-the-line.mjs` 532 passed, 0 failed; `--mutate` exits 1; `node scripts/check-sources.mjs the-gene-below-the-line` sound (182 entries).

## Fixer's note (round 3, 2026-11-02)
The fix-checker found one slip, in this record rather than on the page: the EUCAST finding above quoted index.html:242 with the word "quoted" where a later checkpoint had changed the page to "taken" (the page's word is right, since the Salmonella value is cited, not quoted). The finding now quotes the page as it reads: "all taken from it". Every other quotation in the findings was re-checked against the page text, the kept copies, the README and the source record, and each is where it is said to be ("NARMS has always used its own minimum inhibitory concentration (MIC) values" runs across the PDF page 2/3 break of the kept 2014 report). The page, verifier and source record are unchanged in this round, and no claim line or count changed.