Validation / Papers / Kresken 2021

Comparative in vitro activity of piperacillin-tazobactam and temocillin against third-generation cephalosporin-resistant, carbapenem-susceptible Escherichia coli and Klebsiella pneumoniae

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

Kresken M, Pfeifer Y, Werner G. Comparative in vitro activity of piperacillin-tazobactam and temocillin against third-generation cephalosporin-resistant, carbapenem-susceptible Escherichia coli and Klebsiella pneumoniae. GMS Infectious Diseases 9:Doc08 (2021). doi:10.3205/id000077

Related sources:

Data: Kresken M, Pfeifer Y, Werner G. Temocillin susceptibility in Enterobacterales with an ESBL/AmpC phenotype. Zenodo record 6575080 (mirror of Dryad), CC0. doi:10.5061/dryad.931zcrjkc

What it measured

The study tested 109 isolates of E. coli and K. pneumoniae from the PEG surveillance of 2016 and 2017 by broth microdilution (ISO 20776-1). It split the isolates by resistance to third-generation cephalosporins. For each group and for piperacillin/tazobactam and temocillin, it gives the MIC50, the MIC90 and the percent of isolates that are susceptible by the EUCAST breakpoints of January 2021 (version 11.0).

Data

Zenodo record 6575080, file Data_MICs_PEG_2016_17_temocillin_data_set_11062021.xlsx (mirror of Dryad 10.5061/dryad.931zcrjkc). fetch.sh writes temocillin_mics.csv: the isolate, the species, the group by third-generation cephalosporin resistance (cefotaxime MIC above 2 or ceftazidime MIC above 4 mg/L) and the MIC of five drugs, named with the drug name. Size: 19 KB Excel workbook with 109 isolates.

License: CC0 for the data. The paper is CC BY 4.0.

Data source

The instruction

A script sends this message as the scientist.

ScientistGive the number of isolates, the MIC50, the MIC90 and the percent susceptible for each species, cephalosporin group and drug.

Basis: Abstract, Methods (EUCAST v 11.0, broth microdilution) and Results of the paper. The temocillin breakpoint of EUCAST v 11.0 separates S (MIC 0.001 or less) from R (MIC above 16). The paper counts S and I together as susceptible.

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	`EUCAST 2021`	Methods. EUCAST breakpoint table version 11.0, January 2021. The R package AMR names this table EUCAST 2021.
Host	`human`	The isolates come from patients.
Isolates from urine	`auto`	Not in the paper. The paper does not separate urine isolates, so the benchmark uses the AMR default.
MIC values with a limit sign	`standard`	Not used. The data file stores each value as a number without a limit sign.
Use the EUCAST pharmacokinetic and pharmacodynamic breakpoints	`true`	Not in the paper. The AMR default. The species breakpoints decide the result for both drugs.
What the percent susceptible counts	`S and I`	Results. The paper counts the isolates with a temocillin MIC of 16 mg/L or less as susceptible, which is S and I together.
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 Kresken 2021.
Value	Known value	Tolerance	Source
`ecoli_r_tzp_pct`Percent susceptible, Escherichia coli, 3GC-resistant, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-resistant, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	79.3	± 0.06	Printed in the paper
`ecoli_r_tzp_mic50`MIC50 in mg/L, Escherichia coli, 3GC-resistant, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-resistant, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	2	± 0.001	Printed in the paper
`ecoli_r_tzp_mic90`MIC90 in mg/L, Escherichia coli, 3GC-resistant, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-resistant, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	32	± 0.001	Printed in the paper
`ecoli_r_tmo_pct`Percent susceptible, Escherichia coli, 3GC-resistant, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-resistant, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	94.8	± 0.06	Printed in the paper
`ecoli_r_tmo_mic50`MIC50 in mg/L, Escherichia coli, 3GC-resistant, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-resistant, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	8	± 0.001	Printed in the paper
`ecoli_r_tmo_mic90`MIC90 in mg/L, Escherichia coli, 3GC-resistant, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-resistant, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	16	± 0.001	Printed in the paper
`ecoli_s_tzp_pct`Percent susceptible, Escherichia coli, 3GC-susceptible, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-susceptible, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	93.3	± 0.06	Printed in the paper
`ecoli_s_tzp_mic50`MIC50 in mg/L, Escherichia coli, 3GC-susceptible, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-susceptible, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	1	± 0.001	Printed in the paper
`ecoli_s_tzp_mic90`MIC90 in mg/L, Escherichia coli, 3GC-susceptible, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-susceptible, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	4	± 0.001	Printed in the paper
`ecoli_s_tmo_pct`Percent susceptible, Escherichia coli, 3GC-susceptible, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-susceptible, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	100.0	± 0.06	Printed in the paper
`ecoli_s_tmo_mic50`MIC50 in mg/L, Escherichia coli, 3GC-susceptible, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-susceptible, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	4	± 0.001	Printed in the paper
`ecoli_s_tmo_mic90`MIC90 in mg/L, Escherichia coli, 3GC-susceptible, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Escherichia coli, 3GC-susceptible, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	16	± 0.001	Printed in the paper
`kp_r_tzp_pct`Percent susceptible, Klebsiella pneumoniae, 3GC-resistant, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-resistant, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	57.1	± 0.06	Printed in the paper
`kp_r_tzp_mic50`MIC50 in mg/L, Klebsiella pneumoniae, 3GC-resistant, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-resistant, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	8	± 0.001	Printed in the paper
`kp_r_tzp_mic90`MIC90 in mg/L, Klebsiella pneumoniae, 3GC-resistant, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-resistant, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	128	± 0.001	Printed in the paper
`kp_r_tmo_pct`Percent susceptible, Klebsiella pneumoniae, 3GC-resistant, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-resistant, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	90.5	± 0.06	Printed in the paper
`kp_r_tmo_mic50`MIC50 in mg/L, Klebsiella pneumoniae, 3GC-resistant, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-resistant, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	8	± 0.001	Printed in the paper
`kp_r_tmo_mic90`MIC90 in mg/L, Klebsiella pneumoniae, 3GC-resistant, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-resistant, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	16	± 0.001	Printed in the paper
`kp_s_tzp_pct`Percent susceptible, Klebsiella pneumoniae, 3GC-susceptible, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-susceptible, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	93.3	± 0.06	Printed in the paper
`kp_s_tzp_mic50`MIC50 in mg/L, Klebsiella pneumoniae, 3GC-susceptible, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-susceptible, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	1	± 0.001	Printed in the paper
`kp_s_tzp_mic90`MIC90 in mg/L, Klebsiella pneumoniae, 3GC-susceptible, piperacillin/tazobactam Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-susceptible, piperacillin/tazobactam).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	8	± 0.001	Printed in the paper
`kp_s_tmo_pct`Percent susceptible, Klebsiella pneumoniae, 3GC-susceptible, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-susceptible, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	100.0	± 0.06	Printed in the paper
`kp_s_tmo_mic50`MIC50 in mg/L, Klebsiella pneumoniae, 3GC-susceptible, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-susceptible, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	2	± 0.001	Printed in the paper
`kp_s_tmo_mic90`MIC90 in mg/L, Klebsiella pneumoniae, 3GC-susceptible, temocillin Source of the known value Printed in the paperWhere: Abstract and Results text of the paper (Klebsiella pneumoniae, 3GC-susceptible, temocillin).Check: check.py gives the same value from the data (check.out).Note in the list of known values: paper, abstract and Results text	8	± 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, before the fix): 20261009-032643-b18d, computed 16/24, reported 17/24, 103 s, 14 tool calls (9 failed).
claude-haiku-5-5 run 2 (blind, after the fix): 20261009-032859-0ef4, computed 24/24, reported 24/24, 155 s, 0 paths outside the allow list.

Run	Item	Expected	Got	Class	Cause	Fix
1	all percent items	79.3 and others	79, 109, 58	b	The R package AMR was in a library folder (R-library-micro) that blind mode does not allow. Every AMR call failed with "there is no package called AMR". The model then used a Python fallback that has no breakpoints.	AMR is in the library folder /Volumes/T7/guided-analysis/tools/R-library, which blind mode allows. The install text of the adapter names this folder.
1, 2	none (failed call)			b	`inspect_data` cannot read `src/tools/inspect_data.py` in a worktree under `.claude/worktrees`. The model reads the file with `read_file` instead.	none. The fault is in the harness sandbox for worktrees.

Other findings:

The computed score takes the logged number nearest to the expected value. The items for MIC50 and MIC90 have small whole numbers (1, 2, 4, 8, 16) that many logged values match. The 8 percent items are the strict test: each needs the right standard (EUCAST 2021) and the right counting rule (S and I).
With "S only" the percent susceptible of temocillin is 0 for every group. The decision susceptible_definition decides this result. The benchmark answers S and I, as the paper does.