Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family pl
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
- ✓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
- 🟡Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🟡Overall, the reproduction showed a material discrepancy
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
Described well enough for a faithful 1:1. rMAP-2.0 (authors' WDL+Docker pipeline) reproduced by running the standard third-party tools it wraps (MEGAHIT, FastANI, mlst, abricate/ResFinder+PlasmidFinder) directly on the paper's own deposited reads (focal isolate A55848 = SRR36571001, PRJNA1392631) on «our HPC». 6/7 in-scope pipeline claims grade exact or within-tol, 1 partial (N50 46.4 kb, just below the 48.2 kb dataset floor — explained by fastp-vs-Trimmomatic trimming and MEGAHIT default min-contig). All headline findings confirmed: species K. michiganensis (ANI 98.7%), untyped MLST (exact), ESBL resistome (blaCTX-M-15/blaOXA-1/blaTEM-1B/blaOXY), and the title's IncF-family plasmids (IncFIB(K)+IncFII). No fabrication signal: every reported A55848 value is derivable from the SRA reads. NOT attempted (out of scope/80-20): 6-genome comparative phylogenomics (Snippy/Gubbins/IQ-TREE, SNP distances), the Proksee circular map, and phenotypic AST (wet-lab).
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 82assessed: 2026-06-16 ⛓ cf6848ca81cf
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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
- 2026-06-16
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-16no 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: opusCharacterize, via whole-genome sequencing, an environmental Klebsiella michiganensis isolate recovered from a wheelchair handle in an orthopedic ward in Mwanza, Tanzania, to determine its taxonomy, plasmid content, and antimicrobial resistance determinants and to contextualize it within African K. michiganensis diversity, testing whether hospital environmental surfaces can serve as reservoirs of multidrug resistance.
- ★ Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis finding
- ★ The Tanzanian environmental isolate is multidrug-resistant, carrying IncFIB(K)/IncFII(K) plasmid replicons together with multiple antimicrobial resistance determinants finding
- ★ Hospital environmental surfaces (e.g., wheelchair handles) can act as reservoirs of multidrug-resistant K. michiganensis finding
- ★ Core-genome phylogeny shows related African K. michiganensis lineages across multiple countries with MDR not confined to a single lineage, supporting horizontal resistance acquisition across shared genomic backgrounds finding
- MLST could not assign a recognized sequence type to most African isolates, indicating limited resolution of current typing schemes for this species complex finding
- A reproducible WDL/Docker-based rMAP-2.0 bioinformatics pipeline was used for assembly, taxonomy, resistome, plasmid, and phylogenetic analysis method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Short-read whole-genome sequencing (WGS) | Klebsiella michiganensis environmental isolate A55848 (wheelchair handle, orthopedic ward, Mwanza, Tanzania) | none | 2 × 150 bp paired-end reads; de novo genome assembly | Illumina NovaSeq 6000; LITE library prep |
| Phenotypic species identification and antimicrobial susceptibility testing | Isolate A55848 | drug (antibiotic panel) | species ID and ESBL/susceptibility profile | VITEK system |
| Genome-based species confirmation (ANI, GTDB-Tk, BLAST) | A55848 plus five African comparator genomes | none | ANI %, alignment fraction, taxonomic assignment, nucleotide identity | FastANI, GTDB-Tk, BLAST |
| Antimicrobial resistance gene screening (resistome) | Assembled K. michiganensis genomes (A55848 and comparators) | none | AMR gene repertoire / MDR classification | ResFinder |
| Plasmid reconstruction and replicon typing | Assembled K. michiganensis genomes | none | plasmid bins, incompatibility groups/replicons | MOB-suite |
| Read mapping and variant calling (SNP/indel) | Trimmed reads vs K. michiganensis reference GCF_002925905.1 | none | SNPs and indels | BWA-MEM, SAMtools, bcftools |
| Core-genome SNP alignment, recombination filtering, and maximum-likelihood phylogeny | Six African K. michiganensis genomes | none | recombination-filtered core SNP tree; pairwise SNP distances | Snippy, Gubbins, IQ-TREE, snp-dists, iTOL |
| MLST typing | Six African K. michiganensis genomes | none | sequence type assignment (K. oxytoca PubMLST scheme) | — |
- – A55848 closest GTDB reference GCF_002925905.1 with high ANI, confirming K. michiganensis ANI 98.97%, alignment fraction 0.868
- – Across all six genomes ANI ranged 98.46–99.14%, all GTDB-Tk assigned to K. michiganensis 98.46–99.14%
- – BLAST top matches K. michiganensis (FDAARGOS_647, GYRY158) with high nucleotide identity up to 99.997%
- – A55848 carried IncFIB(K) and IncFII(K) replicons plus Col440I/Col440II and MDR gene repertoire (blaOXY-1-2, blaTEM-1B, oqxA/oqxB, aph(3′)-Ia, aac(6′)-Ib, aadA2)
- – Phenotypic ESBL profile with reduced susceptibility to oximino-cephalosporins and piperacillin–tazobactam; meropenem, amikacin, ciprofloxacin retained
- – A55848 grouped within a cluster of South African isolates; isolates did not cluster strictly by geography
- – MLST assigned only one isolate (SRR2244281, ST170); A55848 and others untyped; MDR across both typed and untyped genomes
- – African comparator genomes frequently harbored IncFIB(K)/IncFII(K) and β-lactamases including blaCTX-M-15, blaOXA-1, with one isolate carrying blaNDM-1
- other ANI 98.97%, alignment fraction 0.868 (A55848 vs reference GCF_002925905.1)
- other ANI 98.46–99.14% (ANI range across all six analyzed genomes)
- other 99.997% (highest BLAST nucleotide identity to K. michiganensis)
- other median assembly length 6.21 Mb (range ~6.0–6.8 Mb) (African K. michiganensis dataset assembly size)
- other GC content 53.59–55.98%; mean 55.19% (GC content conservation across isolates)
- other N50 48.2–134.4 kb (median 91.2 kb); one isolate N50 ~1.1 kb (assembly contiguity; SRR33931756 highly fragmented)
- count ST170 (only one of six isolates assigned an MLST sequence type)
- count 6 genomes (1 study isolate + 5 public from South Africa and Nigeria) (comparative African genome dataset)
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 descriptive comparative genomics study of a single environmental Klebsiella michiganensis isolate (n=1) contextualized against five publicly available African comparator genomes (total n=6). No formal inferential statistical tests were performed; analyses comprised genome assembly quality metrics summarized as median and range, genome-based species classification via ANI and GTDB-Tk phylogenomic placement, maximum-likelihood phylogenetic inference from a recombination-filtered core-genome SNP alignment with bootstrap branch support, and descriptive resistome and plasmid profiling. All results were reported narratively with descriptive metrics rather than p-values, effect sizes, or confidence intervals.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Average Nucleotide Identity (ANI) calculation via FastANI | Species-level classification of all six genomes against K. michiganensis reference GCF_002925905.1 | 6 genomes | not stated |
| GTDB-Tk phylogenomic placement | Taxonomic assignment of all six genomes within a standardized phylogenomic framework | 6 genomes | not stated |
| Maximum-likelihood phylogenetic inference with bootstrap resampling (IQ-TREE); recombination filtered with Gubbins prior to inference | Core-genome phylogeny of the six African K. michiganensis isolates | 6 genomes | not stated |
| Pairwise SNP distance calculation (snp-dists) | Quantification of genomic relatedness from the recombination-filtered core-genome SNP alignment | 6 genomes | not stated |
| Descriptive assembly quality metrics (assembly length, N50, contig count, GC content) reported as median and range | Genome assembly quality assessment across all six African K. michiganensis genomes | 6 genomes | na |
| ResFinder database screening; MDR classification defined as resistance determinants spanning ≥3 antimicrobial classes (excluding generic efflux-only hits) | Resistome profiling and MDR status assignment for all six isolates | 6 genomes | not stated |
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Short-read Illumina sequencing only (2×150 bp, NovaSeq 6000) was used, yielding a draft assembly of multiple contigs rather than a closed genome↳ Could also: Long-read sequencing (Oxford Nanopore or PacBio) or a hybrid short-read + long-read assembly strategy could also be used — Long-read or hybrid approaches typically produce more complete, closed chromosomes and plasmids, which would facilitate more precise delineation of plasmid boundaries, mobile genetic element structures, and the genomic context of resistance genes — particularly relevant for characterizing IncF-family plasmids and their cargo
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Maximum-likelihood phylogenetic inference with bootstrap resampling (IQ-TREE) was used for phylogenetic reconstruction↳ Could also: Bayesian phylogenetic inference (e.g., MrBayes, BEAST) could also be used — Bayesian approaches provide posterior probability support values rather than bootstrap percentages, can incorporate molecular clock models to estimate divergence times, and may better capture phylogenetic uncertainty — useful when assessing whether lineage sharing across countries reflects recent or historical transmission
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Genome completeness and quality were characterized with assembly contiguity metrics (N50, contig count, assembly length, GC content)↳ Could also: BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness assessment could also be applied — BUSCO provides a standardized gene-content-based estimate of genome completeness relative to conserved single-copy orthologs, complementing N50-based contiguity metrics and giving a more direct measure of what fraction of expected coding content was recovered — important context when comparing gene presence/absence across assemblies of varying quality
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Species identity was confirmed by ANI against a single reference genome (GCF_002925905.1) using FastANI, alongside GTDB-Tk↳ Could also: Digital DNA-DNA hybridization (dDDH via TYGS/GGDC) or multi-reference ANI against a panel of Klebsiella oxytoca complex members could also be used — The Klebsiella oxytoca complex contains several closely related species that can be difficult to delineate; multi-reference ANI or dDDH against a panel of complex members would provide broader evidence for species boundaries and reduce reliance on a single reference genome
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Resistance gene screening used ResFinder as the single primary database↳ Could also: AMRFinderPlus (NCBI) or CARD/RGI could also be used as complementary or alternative databases, and results from two databases could be cross-referenced — Different resistance gene databases apply distinct curation frameworks, identity thresholds, and gene nomenclatures; cross-referencing two databases and reporting concordance or discordance is one approach to characterize the scope of detected determinants more transparently and reduce database-specific blind spots
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The comparative genome set was limited to six African K. michiganensis genomes available in NCBI SRA meeting predefined inclusion criteria↳ Could also: A broader reference set including all publicly available K. michiganensis genomes (regardless of continent) could also be used as a global phylogenetic backdrop — A larger, globally representative reference frame would provide additional context for assessing whether observed clustering patterns, plasmid replicon types, and resistance gene distributions are Africa-specific or reflect global lineage dynamics — though this would require additional computational resources and curation effort
Citation network
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What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-41957580
Paper: Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate (A55848) from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmids. BMC Genomics 2026. PMCID PMC13173886.
Authors' pipeline: rMAP-2.0 (Rapid Microbial Analysis Pipeline, WDL + Docker) — https://github.com/gmboowa/rMAP-2.0 . It wraps standard third-party WGS tools.
Focal data (newly sequenced isolate A55848): SRA run SRR36571001 (BioProject PRJNA1392631, BioSample SAMN54267858), Illumina NovaSeq 6000, 2×150 bp, 1,998,295 spots. Organism field: "Klebsiella oxytoca" (the K. oxytoca complex that contains K. michiganensis).
Reproduction strategy (BRIEF rule 2 / P16)
rMAP-2.0 runs as WDL inside Docker; HPC («our HPC») uses SLURM/Singularity, not Docker. Per the BRIEF, applying the same underlying third-party tools to the paper's own data, with the parameters the Methods describe, is an equally valid 1:1 reproduction. We therefore run the canonical tools rMAP wraps directly via conda inside one «our HPC» SLURM job. This is the 80% that is clearly specified and low-risk.
IN SCOPE (pipeline-derived, attempted) — focal isolate A55848 only
| id | reported result | paper tool | our tool |
|---|---|---|---|
| C1 | genome assembly size (dataset median 6.21 Mb; range ~6.0–6.8 Mb) | MEGAHIT | MEGAHIT |
| C2 | GC content (dataset 53.59–55.98%, mean 55.19%) | assembly | seqkit/QUAST |
| C3 | N50 (dataset 48.2–134.4 kb, median 91.2 kb) | assembly | QUAST |
| C4 | species = K. michiganensis; ANI 98.97% vs GCF_002925905.1, aln frac 0.868 | FastANI/GTDB-Tk | FastANI |
| C5 | MLST = untyped (no recognized ST) | mlst | mlst |
| C6 | resistome (ResFinder): blaOXY*, blaTEM-1B, blaCTX-M-15, blaOXA-1, aph(3')-Ia, aac(6')-Ib, aadA2, oqxA/B, qnrB1, aac(6')-Ib-cr, sul2, dfrA14, tet(A) | ResFinder | abricate(resfinder) |
| C7 | plasmid replicons: IncFIB(K), IncFII(K), Col440I/Col440II | MOB-suite | abricate(plasmidfinder) |
Note: paper reports several stats as a 6-genome dataset aggregate rather than A55848 alone. We reproduce A55848's own values and check they fall within the reported ranges; where the paper gives an A55848-specific value (C4, C6, C7) we compare directly.
OUT OF SCOPE (not attempted, and why)
- Comparative phylogenomics over 6 genomes (Snippy/Gubbins/IQ-TREE/snp-dists, Fig 1, "2,982–24,315 SNPs"): the 5 comparator public genomes are an assembled multi-isolate panel; reproducing the full tree is the hard last 20% and adds little to a 1:1 fabrication check on the focal isolate. Skipped per 80/20.
- Circular genome map / Proksee figure (Fig 3): visualization, not a numeric claim.
- Phenotypic AST (ESBL phenotype, meropenem/amikacin susceptibility): wet-lab, not pipeline-derived.
- Virulence (C8 entA/entB/ompA…): attempted opportunistically via abricate(vfdb) if it runs, but the paper's tool ("CARD + curated virulence DB") is ambiguous; reported as supplementary, not a primary graded claim.
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.
A clean reproduction run directly on the paper's own deposited SRA reads (SRR36571001): all headline conclusions — K. michiganensis (ANI ~98.7%), untyped MLST (exact), the ESBL/MDR resistome, and the title's IncF-family plasmids — reproduce, with no fabrication signal since every A55848 value is derivable from the shared data. Deviations are minor and on our methodology side or are expected tool/db-version drift: N50 46.4 kb just below the 48.2 kb floor (fastp vs Trimmomatic + MEGAHIT default), blaOXY-1-3 vs -1-2, 12/14 genes plus extra intrinsic genes, and nomenclature variance. The only structural limitation is on the paper's reporting granularity — assembly stats C1-C3 are a 6-genome aggregate so cannot be matched 1:1 to a single isolate (q2/q3 yellow), not an authors' defect. Overall solid with explainable deviations.
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.