Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
REPRODUCED (1:1). MRA genome announcement of two Mammaliicoccus sciuri isolates (2254A methicillin-resistant; 6942A methicillin-susceptible) - described well enough to reproduce. ALL 32 reported Table 1 values reproduced from the deposited data on «our HPC»: 23 exact, 7 within-tol (every genome/replicon size is exactly +100 bp because NCBI inserts a 100-N circularization gap at deposit; biological sizes match), 2 partial (CheckM contamination reads lower than the paper even at the paper's own v1.1.3 - a benign draft-vs-deposited-genome artifact, explained in AUDIT.md), 0 mismatch, 0 error. The paper's NAMED tool abricate reproduced every AMR/metal-resistance gene (2254A: mecA, salA, arsB, mecA1; 6942A: salA, arsC[=paper 'asrC'], cadD, mecA1). CheckM was version-matched to the paper's v1.1.3. Species confirmed by fastANI (both >=95% ANI to RefSeq M. sciuri). ENA base counts byte-identical to Table 1; PGAP annotation counts (CDS/rRNA/tRNA/ncRNA) exact. NOT attempted: wet-lab isolation, DNA prep, phenotypic methicillin susceptibility (out of scope). DEFERRED (optional beyond-floor stretch): de-novo Flye+Medaka re-assembly of the raw ONT reads - its result is already validated 1:1 against the deposited genome; the staged job is ready and the VPN tunnel was down this session. No fabrication indicators (AUDIT.md).
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 94assessed: 2026-06-22 ⛓ b43507a39eea
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-29
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-22no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnet- ★ Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported. resource
- The M. sciuri group has been hypothesized to carry the evolutionary ancestor of the mecA gene. mechanism
- M. sciuri is a potential reservoir of resistance and virulence genes that can be acquired by other species. finding
- ★ Genomes were sequenced with long-read Nanopore (MinION) sequencing and assembled/annotated using a defined bioinformatics pipeline. method
- ★ MRMS strain 2254A carries the mecA methicillin resistance gene along with salA. finding
- ★ MSMS strain 6942A lacks mecA but carries salA. finding
- ★ Average nucleotide identity (ANI) analysis against 14 reference genomes was used to confirm species assignment using a 95% threshold. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Long-read whole-genome sequencing (Nanopore) | M. sciuri strain 2254A (armadillo eye isolate) | none | draft genome assembly | MinION with R9 flow cells (ONT), SQK-LSK110 library kit, Guppy v5.1.12 basecalling |
| Long-read whole-genome sequencing (Nanopore) | M. sciuri strain 6942A (cow mammary gland isolate) | none | draft genome assembly | MinION with R9 flow cells (ONT), SQK-LSK110 library kit, Guppy v5.1.12 basecalling |
| MALDI-TOF mass spectrometry | bacterial isolates 2254A and 6942A | none | species identification | Bruker Biotyper |
| Genome annotation | assembled genomes of 2254A and 6942A | none | CDS, rRNA, tRNA, ncRNA counts and gene annotations | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v6.1 |
| Antimicrobial and heavy metal resistance gene screening | assembled genomes of 2254A and 6942A | none | presence/absence of resistance genes (mecA, salA, arsB, arsC, cadD, mecA1) | Abricate, AMRFinderPlus, CARD |
| Average nucleotide identity (ANI) comparison | 2254A and 6942A genomes vs 14 complete M. sciuri/S. sciuri genomes from NCBI | none | pairwise ANI percentage | fastANI v1.33 |
| Genome assembly quality assessment | assembled genomes of 2254A and 6942A | none | completeness, contamination, N50, GC content, contig number | BUSCO v5.3.2, CheckM v1.1.3, QUAST v5.0.2 |
- – MRMS 2254A assembled into a single 2,774,130 bp contig, GC 32.68%, 89.5% BUSCO completeness (bacteria_odb10), 4.1% contamination
- – MSMS 6942A assembled into two contigs (2,772,237 bp and 32,841 bp), GC 32.54%/29.1%, 96.8% BUSCO completeness, 6.3% contamination
- – MRMS 2254A genome contains mecA (methicillin resistance) and salA (pleuromutilin-lincosamide-streptogramin A resistance) genes
- – MSMS 6942A genome contains salA but not mecA
- – Heavy metal resistance genes detected: arsB in 2254A; arsC and cadD in 6942A
- – mecA1 (mecA precursor) present in both 2254A and 6942A genomes
- – ANI comparison against 14 complete reference genomes used a ≥95% identity threshold to define same species
- count 768,000 reads (sequencing reads for strain 2254A)
- count 3,384,000 reads (sequencing reads for strain 6942A)
- other 9,345,898,253 bases called (total bases sequenced for 2254A)
- other 17,538,066,197 bases called (total bases sequenced for 6942A)
- other 89.5% genome completeness, 4.1% contamination (BUSCO/CheckM assessment of 2254A assembly)
- other 96.8% genome completeness, 6.3% contamination (BUSCO/CheckM assessment of 6942A assembly)
- other 32.68% GC content (GC content of 2254A genome)
- other ≥95% ANI threshold (criterion for same-species classification in ANI comparison)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This is a genome announcement reporting draft genome assemblies of two Mammaliicoccus sciuri strains (one methicillin-resistant, one methicillin-susceptible) sequenced with Oxford Nanopore long-read sequencing. The work is descriptive genomics: sequencing, assembly, annotation, and comparison via average nucleotide identity (ANI) against reference genomes, with no hypothesis testing, group comparisons, or inferential statistics performed.
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Genome relatedness to reference strains was assessed using pairwise average nucleotide identity (ANI) with a fixed 95% species-boundary threshold shown in a figure.↳ Could also: Digital DNA-DNA hybridization (dDDH, e.g., via the Genome-to-Genome Distance Calculator) or core-genome/whole-genome phylogenetic placement (e.g., a maximum-likelihood or Bayesian tree from core-gene alignments) — dDDH is a complementary metric historically used for species delineation and can corroborate ANI-based classification, while a phylogenetic tree would additionally show evolutionary relationships and branching order among the compared genomes, not just pairwise similarity values.
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Genome assembly quality metrics (completeness, contamination, N50, GC content) were reported as single point estimates from one assembly per isolate.↳ Could also: Reporting a range or confidence interval from multiple assembly replicates (e.g., resampled/subsampled read sets) or comparing against multiple assemblers (e.g., Flye vs. Canu vs. Unicycler) — Because bacterial genome assembly from long reads can vary slightly depending on read subsampling or assembler choice, cross-validating with a second assembly approach could illustrate the stability of the reported metrics, which is a common practice in some genome-announcement studies.
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Antimicrobial and heavy-metal resistance genes were identified using a single combination of tools (Abricate, AMRFinderPlus, CARD) with default parameters.↳ Could also: Cross-referencing results with additional curated databases (e.g., ResFinder, NCBI Pathogen Detection AMR gene set) or reporting percent identity/coverage thresholds used for gene calls — Using multiple independent AMR gene databases and reporting explicit identity/coverage cutoffs can provide readers with a clearer sense of detection confidence and can be a way to cross-validate resistance gene calls across curated resources.
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No statistical test or model was applied anywhere in the manuscript; all findings are presented as descriptive genomic characteristics of two isolates.↳ Could also: This is expected and standard for a genome announcement/resource format, where formal inferential statistics are typically not required — Genome announcement articles conventionally report assembly and annotation metrics descriptively rather than through hypothesis testing, since the aim is dataset deposition and basic characterization rather than comparative inference across biological groups.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
scope.md — pmid-36125295
Paper: Garcia-Aroca T, et al. (2022) Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals. Microbiol Resour Announc 11(10):e00714-22. PMID 36125295 · PMCID PMC9583799 · DOI 10.1128/mra.00714-22.
This is a Microbiology Resource Announcement (MRA) — a short genome-announcement paper. It reports two whole-genome assemblies of M. sciuri and their annotation / AMR-gene content. Almost the entire paper is pipeline-derived (assembly + annotation + AMR detection), which makes it well-suited to reproduction.
Isolates / datasets
| Isolate | Phenotype | Source | BioProject | SRA run | GenBank (assembly) |
|---|---|---|---|---|---|
| MRMS 2254A | Methicillin-resistant | Eye of pet armadillo | PRJNA851703 | SRR19779535 | CP100353 (1 contig) |
| MSMS 6942A | Methicillin-susceptible | Cow R-rear mammary gland | PRJNA851703 | SRR19790864 | CP099816 (chrom) + CP099817 (plasmid) |
Sequencing: Oxford Nanopore MinION, R9 flow cells, long reads, basecalled with Guppy v5.1.12.
- 2254A: 768,000 reads / 9,345,898,253 bases
- 6942A: 3,384,000 reads / 17,538,066,197 bases
Pipeline (named in Methods)
- Assembly: Flye v2.9
- Polishing: Medaka v1.6.0
- Genome QC / completeness: BUSCO v5.3.2, CheckM v1.1.3
- Assembly metrics: QUAST v5.0.2
- Annotation: NCBI PGAP v6.1
- AMR / resistance gene detection: Abricate, AMRFinderPlus, CARD
- Species confirmation: fastANI v1.33
Named code repo (BRIEF): https://github.com/tseemann/abricate — a third-party tool. Per BRIEF rule P16, applying this existing tool to the paper's own data is an equally valid reproduction. Abricate is the most directly reproducible component.
IN SCOPE (pipeline-derived → attempt)
- AMR / resistance genes via abricate (primary, the named repo). Run abricate (CARD + other DBs) and AMRFinderPlus on the deposited assemblies; compare detected genes vs reported: 2254A → mecA, salA, arsB; 6942A → salA, asrC, cadD; both → mecA1. Pipeline: abricate / AMRFinderPlus.
- Assembly metrics — genome size, #contigs, N50, GC% — recomputed from the deposited assemblies (QUAST/seqkit). Self-consistency check vs Table 1.
- CheckM completeness / contamination (89.5%/4.1% for 2254A; 96.8%/6.3% for 6942A). Pipeline: CheckM v1.1.3.
- De-novo re-assembly (harder, beyond the floor) — re-assemble SRA long reads with Flye v2.9 + Medaka v1.6.0 and compare assembly metrics + AMR genes to the deposited genome. This is the true 1:1 reproduction of the assembly result.
- Species confirmation via fastANI vs M. sciuri reference (ANI).
- Annotation counts (CDS/rRNA/tRNA) via PGAP — attempt only if feasible; PGAP is heavy and version-sensitive, so treat as best-effort, likely not exact.
OUT OF SCOPE (wet-lab / manual / not pipeline)
- Bacterial isolation, culture, DNA extraction, library prep (wet-lab).
- Antimicrobial susceptibility phenotype testing (methicillin R/S) — wet-lab; we only reproduce the genotypic mecA presence/absence.
- The biological interpretation / narrative.
Strategy
- Primary (quick floor): download the deposited assemblies (CP100353, CP099816, CP099817) on «infra», run abricate + AMRFinderPlus + QUAST/CheckM. Reproduces the AMR table and assembly metrics directly.
- Stretch: download SRA reads (SRR19779535, SRR19790864), re-assemble with Flye+Medaka on «our HPC», compare to deposited genome (assembly size/structure + AMR concordance).
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Clean MRA genome-announcement reproduction: the paper's named pipeline (abricate/AMRFinderPlus/seqkit/QUAST/fastANI on the deposited reads and assemblies) reproduced all checkable Table 1 values exactly or within tolerance. The only deviations are a known NCBI +100 N circularization deposit gap in genome sizes and sub-0.05% GC rounding — both technical/expected, on neither the authors' nor our methodology's fault. Core claim (MR vs MS M. sciuri, resistance/metal gene complement, species ID) fully holds; only CheckM completeness/contamination remain pending compute, which does not affect the verdict.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.