Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.
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
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- 🟡Reported values were not (fully) derivable from the shared data
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 to reproduce: YES. The repo (CJREID/ST372 @ 4840b5d) ships every downstream intermediate, so the secondary analysis is fully auditable. By an INDEPENDENT Python recompute (not the authors' R script), 7 of 9 in-scope claims reproduce EXACTLY: genome counts 300/72/13/13 (C1), 3,493 core genes (C2), 13 clusters (C4), cluster sizes 202/86/44/22 (C5), 43/15/15 closely-related cross-source SNP pairs (C6), 76 Scoary panGWAS genes split 40/16/11/9 (C7), and fimH9 in 304 genomes/74.7% (C8) -- all 1:1 with the paper. Two are partial: the 22,504 core SNPs and 3.16 Mbp alignment length (C3) are uncheckable because the core-alignment FASTA is not shipped; and running the authors' own monolithic R script end-to-end (C9) is blocked by abricateR version drift, though all the numbers it would produce were reproduced by other means. No mismatches and no fabrication concerns. NOT attempted (out of scope): wet-lab sequencing of the 122 new isolates, full read->assembly of all 407 genomes, IslandViewer web predictions, and the hand-curated M1/M2/M3 genotype/island schematics. One reviewer note: the paper's '76 genes at BH<1E-20' requires the additional non-hypothetical + Odds_ratio>1 (over-represented) filter that the script applies but the text understates.
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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
- 2026-06-30
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-30no 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: sonnetIt is unknown whether Escherichia coli ST372 strains from dogs and humans represent shared or distinct populations, and what genomic traits might explain the prominence of ST372 in dogs or its presence in humans.
- ★ Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types. finding
- ★ Cluster M, comprising almost half of the collection, contains two divergent human-restricted clades carrying different O:H types than the rest of the cluster. finding
- ★ There is evidence of transmission of ST372 between dogs and humans within different phylogenetic clusters, including cluster M. finding
- ★ Multiple independent acquisitions of the pdu propanediol utilization operon occurred in clusters dominated by canine-source isolates, possibly linked to diet. finding
- ★ Loss of the pdu operon and acquisition of K antigen virulence genes characterize human-restricted ST372 lineages. finding
- ★ O:H type generally corresponds tightly with phylogenetic cluster but not with host source, while fimH allele shows no correspondence with cluster. finding
- A global collection of 407 E. coli ST372 whole-genome sequences was assembled and analysed to define population structure, O:H types and accessory genome associations. resource
- Pan-genome-wide association study (Scoary) with a Benjamini-Hochberg adjusted P-value cutoff of 1E-20 was used to identify genes associated with fastbaps clusters. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Whole-genome sequencing (Illumina, Hackflex library prep) | E. coli ST372 isolates from dogs, humans, wildlife and environment (n=122 newly sequenced) | none | genome sequence/assembly | Illumina NovaSeq S4 (Novogene); MiSeq V2 Nano QC |
| Core genome maximum-likelihood phylogenetics | 407 ST372 genomes plus ST127 outgroup strain SRR5336297 | none | phylogenetic tree topology and clustering | IQ-TREE 2.0.3, GTR+F+R model, 1000 bootstrap replicates |
| Population structure clustering (fastbaps) | core gene alignment of 407 ST372 genomes | none | assignment of isolates to 13 clusters (A-M) | Fastbaps with 'baps' prior |
| Pairwise core SNP distance analysis | core SNP alignment (22,504 bp) from 407 ST372 genomes | none | pairwise SNP distances between isolates | snp-sites 2.5.1, snp-dists 0.6.3 |
| Pan-genome-wide association study (panGWAS) | ST372 pan-genome vs fastbaps cluster membership | none | genes significantly associated with clusters (adjusted P-value) | Scoary 1.6.16 |
| In silico gene screening | draft genome assemblies of 407 ST372 isolates | none | presence/absence of AMR, virulence, plasmid replicon, serotype and IS genes | ABRicate 1.0.1 against CARD, VFDB, PlasmidFinder, SerotypeFinder, ISFinder, custom ColV/virulence DB |
| Genomic island prediction | selected ST372 genomes carrying GWAS-identified genotypes vs ST127 reference ECONIH2 | none | predicted genomic island boundaries and content | IslandViewer 4 |
| In silico MLST, serotyping and fimH typing | draft genome assemblies of 407 ST372 isolates | none | ST confirmation, O:H type, fimH allele, pMLST plasmid type | MLST 2.19.0, SerotypeFinder, pMLST (CGE tools), PointFinder |
- – Cluster M was the largest phylogenetic cluster, comprising 202/407 (49.6%) of sequences 49.6%
- – Cluster M contained most canine sequences (120/202) and most human sequences in the collection (56/72 human total, 77.8%) 56/72 (77.8%)
- – Canine-source sequences dominated the overall study collection 300/407 (73.7%)
- – 29 human sequences and 1 environmental sequence formed a divergent human-dominated clade within cluster M carrying O18:H31, distinct from the O83:H31-dominant remainder of the cluster 29 sequences
- – Clusters G, L and J were canine-dominated but also contained human sequences, each associated with a distinct O:H type (O4:H31, O15:H31, O117:H28 respectively) shared between canine and human isolates
- – fimH9 was the major fimH allele identified across all sources and clusters 304/407 (74.7%)
- ▲ Multiple acquisitions of the pdu propanediol utilization operon occurred in canine-dominated clusters
- – Human-restricted lineages showed loss of the pdu operon and acquisition of K antigen virulence genes
- count 407 ST372 whole-genome sequences (285 public, 122 newly generated) (total study collection size)
- count 300 canine-source sequences (73.7%) (source distribution of collection)
- count 72 human-source sequences (17.7%) (source distribution of collection)
- count 202/407 (49.6%) (size of cluster M)
- count 56/72 human sequences (77.8%) in cluster M (human sequence enrichment in cluster M)
- pvalue Benjamini-Hochberg adjusted P-value cutoff of 1E-20 (significance threshold for Scoary gene-cluster associations)
- count 304/407 (74.7%) carried fimH9 allele (dominant fimH allele frequency)
- other 3,160,664 bp core gene alignment (3493 genes); 22,504 bp core SNP alignment (basis for phylogenetic and SNP distance analyses)
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 genomic epidemiology study of 407 E. coli ST372 whole-genome sequences that relies primarily on bioinformatic and phylogenetic methods rather than classical inferential statistics: population structure was defined via a maximum-likelihood core-genome phylogeny (IQTree, bootstrap support) and Bayesian clustering (fastbaps), and a pan-genome-wide association study (Scoary) with a Benjamini-Hochberg-adjusted p-value cutoff was used to link genes to cluster membership. Most other results (host/source, O:H type, fimH allele distributions, SNP distances) are reported descriptively as counts and percentages or pairwise distance summaries rather than through explicit hypothesis tests.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Scoary pan-genome-wide association (gene-trait association test) | association between fastbaps cluster membership and pan-genome gene presence/absence | — | not stated |
| Maximum-likelihood phylogenetic inference with non-parametric bootstrap support (IQTree, GTR+F+R model, 1000 replicates) | core-genome phylogeny of ST372 (Fig. 2) | 3,160,664 bp core gene alignment of 3493 genes from all ST372 sequences plus an ST127 outgroup | not stated |
| Fastbaps Bayesian clustering (BAPS prior) | definition of population structure clusters A-M | core gene alignment and maximum-likelihood tree from all ST372 sequences (n=407) | not stated |
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Gene-cluster associations were identified using Scoary with a Benjamini-Hochberg-adjusted p-value cutoff of 1E-20.↳ Could also: Bacterial GWAS tools that explicitly model or correct for population structure/clonal relatedness, such as pyseer with a linear mixed model or phylogeny-aware fixed-effects correction — this can help distinguish gene-trait associations arising from a direct functional link versus those arising simply through shared ancestry (lineage effects), a common consideration in bacterial GWAS.
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Population structure was defined using fastbaps clustering applied to the core-genome alignment and tree.↳ Could also: Complementary clustering approaches such as hierBAPS, PopPUNK, or recombination-aware clustering (e.g., ClonalFrameML) — cross-checking cluster assignments with an independent method, or one that explicitly accounts for recombination, can provide additional support for the boundaries drawn between lineages.
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Phylogenetic relationships were inferred from a single maximum-likelihood tree (IQ-TREE, GTR+F+R model) with 1000 bootstrap replicates for node support.↳ Could also: A recombination-aware tree-building step (e.g., Gubbins or ClonalFrameML) applied to the core alignment prior to or alongside the ML tree, or a Bayesian phylogenetic approach (e.g., BEAST) — recombination is common in bacterial core genomes and accounting for it can refine branch-length estimates and topology, complementing bootstrap-based confidence in the ML tree.
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The Benjamini-Hochberg-adjusted p-value cutoff for Scoary associations was set at a very low value (1E-20), described partly as a way to manage the number of candidate genes.↳ Could also: Reporting effect sizes (e.g., odds ratios) and confidence intervals for top gene-cluster associations alongside the adjusted p-value threshold — pairing a significance threshold with an effect-size estimate lets readers gauge both the statistical evidence and the practical strength of each association.
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Distributions of source/host, O:H type, and fimH allele across phylogenetic clusters were summarized descriptively as counts and percentages (Fig. 1).↳ Could also: Formal categorical association tests such as chi-squared or Fisher's exact tests (with a multiplicity correction across the multiple category comparisons) — a formal test statistic and p-value would complement the descriptive percentages, offering a quantitative measure of how strongly source, O:H type, or fimH allele associate with cluster.
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Relatedness between canine and non-canine sequences was assessed via pairwise core-genome SNP distances (matrix from snp-dists).↳ Could also: Summarizing within- versus between-cluster SNP-distance distributions (e.g., median and IQR) or applying a defined SNP-distance threshold with a transmission-cluster inference method — this could offer a more formal, quantitative summary of relatedness signal to complement the pairwise distance matrix.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-36752777
Paper: Elankumuran et al. 2023, Microb Genom 9(2):000930. "Identification of genes
influencing the evolution of Escherichia coli ST372 in dogs and humans."
Code: https://github.com/CJREID/ST372 (authors' own; branch main).
Data: SRA BioProjects PRJNA678027 (MVC genomes) + PRJNA827950 (collaborator); 407 ST372 genomes total (285 public + 122 newly sequenced).
What the repo ships (key for scope)
The repo ships all downstream intermediate files under data/, so the entire
secondary analysis is reproducible without re-running the upstream read→assembly steps:
data/roary/gene_presence_absence.Rtab(15.7 MB) — Roary pangenome matrix (0/1)data/roary/ST372.roary.meta.csv— pangenome + metadata joindata/iqtree/core_gene_alignment.OGremoved.contree— ML phylogeny (consensus tree)data/fastbaps/ST372.fastbaps.csv— fastbaps cluster assignmentsdata/snps/CGA.snp-dists.csv— pairwise core-genome SNP distance matrixdata/scoary/cluster/— 13 Scoary panGWAS result files (one per cluster)data/meta/ST372_Metadata_*.csv,MVC_specimens.csv— sample metadatadata/summaries/— mlst.txt, ST372_serotype.tsv, ST372.fimH.csv, genotype.txt, assembly_stats.txt, bracken_report.txt, pMLST.txt, pointfinder.txt, ST372.pUTI89.tabscripts/ST372_analysis.R(53 KB) — produces all figures + supplementary tables.
IN SCOPE (pipeline-derived; we attempt)
| # | Reported result | Pipeline / source file | Strategy |
|---|---|---|---|
| C1 | 407 genomes total (300 canine, 72 human, 13 wild, 13 env) | metadata + Rtab columns | count |
| C2 | Core genome = 3,493 genes; 3,160,664 bp alignment | Roary gene_presence_absence.Rtab |
recompute core-gene count at Roary thresholds |
| C3 | 22,504 core SNP sites | snp-sites on core alignment (alignment NOT shipped) | partial — cross-check via snp-dists |
| C4 | 13 fastbaps clusters (A–M) | ST372.fastbaps.csv |
count unique clusters |
| C5 | Cluster sizes: M=202 (49.6%), G=86 (21.1%), L=44 (10.8%), J=22 (5.41%) | fastbaps + metadata | count per cluster |
| C6 | 43 closely-related canine–human pairs ≤30 SNPs | CGA.snp-dists.csv + source metadata |
recompute pairwise |
| C7 | 76 Scoary-significant genes (BH-adjusted P<1E-20); per-cluster 40/16/11/9 (M/G/L/J) | data/scoary/cluster/* |
recompute threshold count |
| C8 | Serotype O83:H31 dominant in M (167/202); fimH9 most prevalent (304, 74.7%) | serotype.tsv, fimH.csv | recompute |
| C9 | Authors' ST372_analysis.R runs and regenerates figures/tables |
R 4.1.x + packages | execute end-to-end |
OUT OF SCOPE (not attempted; reasons)
- Wet-lab: DNA extraction, Illumina sequencing of the 122 new isolates (lab work).
- Full upstream read→assembly (fastp→Kraken2→Shovill) for 407 genomes: raw assemblies/ the core alignment FASTA are not shipped; re-deriving the 3.16 Mbp alignment + 22,504 SNPs would require assembling all 407 (massive, and depends on exact public-genome set). We treat C3 as partial (cross-checked, not re-derived). A subset assembly of the newly-sequenced PRJNA678027 reads is feasible as a dataset-profiling spot check.
- IslandViewer 4 predictions (web service, not scriptable deterministically).
- Manual genotype/island schematic curation (M1/M2/M3 hand-defined genotypes).
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.
This is a strong, near-1:1 reproduction: 7 of 9 in-scope claims reproduce exactly by an independent Python recompute from the authors' deposited intermediate files (CJREID/ST372 @ 4840b5d), with no mismatches and no fabrication signal. The two partials are both benign — C3's 22,504 SNPs and 3.16 Mbp alignment length are uncheckable only because the core-alignment FASTA was not shipped (data-availability, not authors' defect), and C9's failure to run the monolithic R script end-to-end stems from abricateR version drift. The one reporting nit is that the '76 genes at BH<1E-20' headline (C7) actually needs the full non-hypothetical + Odds_ratio>1 filter to land exactly, an understated-method issue worth noting but not a discrepancy. Overall quality is green with q5 marked yellow purely because two values are not derivable from the shared data.
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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