Reply to Cohen and Denning
Bibliographic record
Abstract
To the Editor—We agree with Cohen and Denning [1] that the large-scale use of antifungals in agriculture on crops is a potential threat to human populations, because resistant fungi that develop can be transmitted to humans [2]. We also agree that the issue of antimicrobial resistance should not be confined solely to the large-scale use of antibiotics. Overuse of antifungals (especially azole use) is an important issue. We also need to be concerned about possible large-scale use of antivirals in agriculture—for example, reports of amantidine and other anti-influenza antiviral use in poultry in China because of H5N1 outbreaks in fowl flocks [3, 4]—and then with the resultant risk of influenza strains developing resistance to antivirals if acquired by swine and/or humans. However, if we look at the likely numbers of persons adversely affected by the use of antimicrobials in agriculture, resistant bacteria currently involve many more persons than resistant fungi. Despite decades of concern and some interventions, we still have much poorer control of antibiotics in food animals than is needed; for example, there is still large-scale use of antibiotics as growth promoters around the world. These are reasons why efforts to control the use of antimicrobials to date have predominantly focused on antibiotics. Another issue complicating which terms we use is that historically the word antibiotic has referred to antibacterial agents. However, there seems to be some controversy about what that term means. Some believe that antibiotic refers only to natural products or derivatives (eg, penicillins, cephalosporins, and tetracyclines) and that synthetic antibiotics (eg, fluoroquinolones and sulphonamides) are not antibiotics but rather antimicrobials. We remain uncertain as to where this definition/distinction came from, but it seems to be well accepted and is probably why nearly all national and international surveillance programs seem to preferentially use the term antimicrobial when discussing antibacterial agent activity. This is also the term the World Health Organization has used. When just speaking about agents that have activity against bacteria, we might need to use the term antibacterial rather than antibiotic if we want the meaning to be narrow but also include non-natural products. However, antibacterial is not as well known a term, and its use may just add to the confusion. Our preference would be to use the term antibiotic when referring to agents that are antibacterial and are used systemically in humans and animals. However, we believe antimicrobial is what the vast majority of groups have adopted currently, and hence we have used that term instead. We agree with Cohen and Denning that the antimicrobials used in the nonhuman sector are a much broader category than antibacterials alone. Other groups of antimicrobials (eg, antifungals, antiparasitics, and antivirals) also need to be considered to see how we can better control overuse and/or inappropriate use. Potential conflicts of interest. J. M. C. has received grants from Alberta Innovates-Health Solutions, personal fees and nonfinancial support from Pfizer, nonfinancial support from bioMérieux, and other support from the National Collaborating Centre for Infectious Diseases (Canada). A. A. has received personal fees from the Davoltera company (within the frame of the French law for innovation and research) and Cepheid and has received grants from the Agence Nationale pour le Recherche and from the European Union FP7 program. S. A. M. has been granted contracts from Health Canada and the Ontario Ministry of Agriculture, Food and Rural Affairs. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.004 | 0.033 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.003 | 0.004 |
| Scholarly communication | 0.003 | 0.006 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.040 | 0.045 |
| Insufficient payload (model declined to judge) | 0.006 | 0.006 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".