Validation / Papers / Kovacs 2026

Genome-wide association study of Mycoplasma anserisalpingitidis strains for antibiotic susceptibility

Microbiology susceptibility testing · research paper · AMR (R), through the amr adapter

How to read this page. In this validation, a script plays the scientist. It gives the answers that we wrote before the run, from the methods of the paper. A known value comes from the paper, from a tutorial or from a check that we ran. This page has no combined run of the paper yet.

No run is scored for this paper yet.

The paper

Kovács ÁB et al. Genome-wide association study of Mycoplasma anserisalpingitidis strains for antibiotic susceptibility. Scientific Reports (2026). doi:10.1038/s41598-026-39804-w

Related sources:

Data: Supplementary Table 1 of the paper (41598_2026_39804_MOESM3_ESM.xlsx), CC BY 4.0. doi:10.1038/s41598-026-39804-w

What it measured

The study measured the MIC of nine drugs for 110 strains of Mycoplasma anserisalpingitidis by broth microdilution. It gives the MIC50 and the MIC90 of each drug. The MIC50 is the value at the 0.5 n-th place of the ordered list. The MIC90 is the value at the 0.9 n-th place. The species has no clinical breakpoints.

Data

Supplementary Table 1 of the paper, sheet 1. fetch.sh downloads the workbook from the Springer static content server and writes mycoplasma_mics.csv: the strain, the species and the MIC of nine drugs, with ASCII limit signs. Size: 23 KB Excel workbook with 110 strains.

License: CC BY 4.0

Data source

The instruction

A script sends this message as the scientist.

ScientistGive the MIC50 and the MIC90 of each drug.

Basis: Methods and Results of the paper. The paper states the rank rule for the MIC50 and the MIC90.

The decisions

The model asks questions during a run. A script gives these answers to the questions of the model. We wrote the answers before the run.

**Table 1 |** Answers that a script gives to the questions of the model.
Decision	Value	Source
Breakpoint standard and version	`none (this species has no clinical breakpoints; do not interpret S, I or R)`	Results. The paper gives MIC50 and MIC90 only and says that no breakpoints exist.
Host	`human`	Not used. The benchmark asks for no S, I or R.
Isolates from urine	`auto`	Not used.
MIC values with a limit sign	`standard`	Not used for MIC50 and MIC90. These tools rank a value with a ">" sign above the same number.
Use the EUCAST pharmacokinetic and pharmacodynamic breakpoints	`true`	Not used.
What the percent susceptible counts	`S only`	Not used.
Geometric mean of MIC values with a limit sign	`next dilution`	Not used. The paper gives no geometric mean.
Other questions of the agent	`Use the values in the decision record.`	Not in the paper. The benchmark answers each free question with this text, so that the record of decisions stays the only source of the settings.

Known values

The tolerance is the largest difference from the known value that we accept. We set it before the run. Exact: the number must be the same.

**Table 2 |** Known values for Kovacs 2026.
Value	Known value	Tolerance	Source
`tylvalosin_mic50`MIC50 of tylvalosin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tylvalosin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	0.5	± 0.001	Printed in the paper
`tylvalosin_mic90`MIC90 of tylvalosin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tylvalosin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	2	± 0.001	Printed in the paper
`oxytetracycline_mic50`MIC50 of oxytetracycline in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Oxytetracycline. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	16	± 0.001	Printed in the paper
`oxytetracycline_mic90`MIC90 of oxytetracycline in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Oxytetracycline. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	64	± 0.001	Printed in the paper
`doxycycline_mic50`MIC50 of doxycycline in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Doxycycline. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	5	± 0.001	Printed in the paper
`doxycycline_mic90`MIC90 of doxycycline in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Doxycycline. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	10	± 0.001	Printed in the paper
`tiamulin_mic50`MIC50 of tiamulin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tiamulin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	0.625	± 0.001	Printed in the paper
`tiamulin_mic90`MIC90 of tiamulin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tiamulin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	2.5	± 0.001	Printed in the paper
`tylosin_mic50`MIC50 of tylosin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tylosin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	16	± 0.001	Printed in the paper
`tylosin_mic90`MIC90 of tylosin in ug/ml (the paper prints 64 or more) Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tylosin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	64	± 0.001	Printed in the paper
`lincomycin_mic50`MIC50 of lincomycin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Lincomycin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	2	± 0.001	Printed in the paper
`spectinomycin_mic50`MIC50 of spectinomycin in ug/ml Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Spectinomycin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	8	± 0.001	Printed in the paper
`tilmicosin_mic50`MIC50 of tilmicosin in ug/ml (the paper prints 64 or more) Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tilmicosin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	64	± 0.001	Printed in the paper
`tilmicosin_mic90`MIC90 of tilmicosin in ug/ml (the paper prints 64 or more) Source of the known value Printed in the paperWhere: Results of the paper, MIC50 and MIC90 of Tilmicosin. The paper prints it, in some cases as 64 or more.Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, Results	64	± 0.001	Printed in the paper
`enrofloxacin_mic50_printed` (reference)MIC50 of enrofloxacin as printed in the paper (more than 10; does not reproduce, computed 5) Source of the known value Printed in the paperWhere: Results of the paper, MIC50 of enrofloxacin: more than 10 ug/ml. The table gives 5 ug/ml for the median strain; only 38 of 110 strains have 10 or more.Check: check.py gives 5 (check.out).Note in the list of known values: paper, Results; reference only, computed 5	10	± 0.001	Printed in the paper

Latest scored run

No run is scored for this paper yet.

Notes

Triage notes by the maintainers

The text below is from the triage notes. We show it as the maintainers wrote it.

Classes: a = tool or adapter fault, b = harness fault, c = benchmark spec fault, d = model fault.

claude-haiku-5-5 run 1 (blind): 20261009-033411-7b04, computed 14/14, reported 14/14 (the reference item is not in the counts), 129 s, 0 paths outside the allow list.

Run	Item	Expected	Got	Class	Cause	Fix
1	enrofloxacin_mic50_printed (reference)	10	5	none	The paper prints "more than 10". The table gives 5. Expected.	none
1	none (failed call)			b	`inspect_data` cannot read `src/tools/inspect_data.py` in a worktree under `.claude/worktrees`.	none. The fault is in the harness sandbox for worktrees.

Other findings:

The model called mic_summary once and wrote the MIC50 and MIC90 of nine drugs. Two run_script calls checked the ranks.
The reference item shows "match" because the logged value 10 (the MIC90 of doxycycline) is near the printed value. The report line for reference items is only a note.