Gut Pathogens Retracts 2019 Study on E. coli Toxins After Image Overlap Concerns

The journal Gut Pathogens has formally retracted a 2019 study that examined the prevalence and pathological effects of two important virulence factors produced by Escherichia coli: the genotoxin colibactin and cytotoxic necrotizing factor 1, commonly abbreviated CNF1. The retraction, published on 18 September 2026 as volume 18, article number 75 of the journal, was issued by the Editor-in-Chief after post-publication scrutiny revealed serious problems with the figures that underpinned the paper’s experimental claims. According to the retraction notice, multiple pairs of images in the article appeared to partially overlap with one another, despite allegedly representing different experimental conditions, and the authors were unable to provide a satisfactory explanation or the underlying data needed to resolve the concerns.

The retracted paper, originally published on 19 May 2019 in Gut Pathogens under the title ‘Prevalence and pathologic effects of colibactin and cytotoxic necrotizing factor-1 (Cnf 1) in Escherichia coli: experimental and bioinformatics analyses,’ was authored by a team of Egyptian researchers working across two institutions. Radwa N. Morgan and Hala A. Farrag were affiliated with the Drug Radiation Research Department at the National Centre for Radiation Research and Technology, part of the Egyptian Atomic Energy Authority in Cairo, while Sarra E. Saleh and Mohammad M. Aboulwafa were based in the Microbiology and Immunology Department of the Faculty of Pharmacy at Ain Shams University, also in Cairo. Aboulwafa served as the corresponding author of the work.

The specific concerns documented in the retraction notice are detailed and methodical. Figure 1C and Figure 1F were found to partially overlap with each other, as were Figure 2C and Figure 2D. In addition, Figure 3D and Figure 3F showed partial overlap, and the two panels of Figure 6, panels a and b, also appeared to overlap. In each case, the overlapping images were supposed to depict different experimental conditions, meaning that identical or near-identical image regions had been used to represent results that should have been distinct. This pattern of duplication is one of the most common triggers for retractions in the scientific literature, because it undermines the reader’s ability to trust that the reported data were independently generated.

When such concerns are raised, the standard editorial process gives authors an opportunity to respond. In this instance, the retraction notice states plainly that the authors were unable to provide a satisfactory explanation or supporting data to address the concerns. Faced with unresolved questions about the integrity of the figures, the Editor-in-Chief concluded that the journal could no longer have confidence in the reliability of the research presented in the article, the formal threshold for a retraction under the guidelines that govern most scholarly publishers. Notably, the retraction is contested: Mohammad M. Aboulwafa has stated on behalf of all the authors that they disagree with the retraction. The retraction notice records this disagreement, which is standard practice, but a contested retraction still stands, and the article remains formally withdrawn from the scientific record.

The subject matter of the retracted study makes the retraction particularly relevant to researchers working on gut microbiology and bacterial pathogenesis. Colibactin is a genotoxin produced by certain strains of E. coli and related Enterobacteriaceae that live in the human gut. It is a polyketide-peptide hybrid molecule synthesized by enzymes encoded on the pks genomic island, and it works by cross-linking DNA in host cells. This DNA damage can trigger cell cycle arrest and cell death, and it has been implicated in the formation of characteristic mutational signatures found in colorectal cancer genomes. Because of this link to cancer biology, colibactin has been one of the most intensively studied bacterial toxins of the past decade, with laboratories around the world working to understand how it is produced, how it reaches host cells, and how its activity shapes the tumor microenvironment in the intestine.

Cytotoxic necrotizing factor 1, the second toxin examined in the retracted paper, is a different kind of weapon in the E. coli arsenal. Rather than damaging DNA, CNF1 is a bacterial protein toxin that permanently activates Rho GTPases, the molecular switches that control the actin cytoskeleton of host cells. By locking these switches in their active state, CNF1 causes dramatic cytoskeletal rearrangements, cell enlargement, and multinucleation, effects that contribute to tissue damage and inflammation. CNF1-producing strains are associated with urinary tract infections, meningitis, and other extraintestinal diseases, and the toxin has also been studied for its effects on epithelial barrier integrity and immune cell behavior. Studies of how prevalent these two virulence factors are in clinical and environmental E. coli populations, and what pathological effects they produce, sit squarely within the aims and scope of Gut Pathogens, which covers the microbiology, immunology, and pathogenesis of the gastrointestinal tract.

The retracted study combined laboratory experiments with bioinformatics analyses, an approach that has become increasingly common in microbiology as researchers pair phenotypic characterization of bacterial isolates with genomic and computational screening for virulence genes. Work of this kind typically involves collecting E. coli strains, testing them for the presence of toxin-encoding genes, measuring the pathological effects of toxin-producing isolates on cultured cells or model systems, and using computational tools to compare the genetic determinants of virulence across strains. Because such studies inform how scientists assess the disease potential of E. coli populations, retractions in this area matter to the wider field: findings that cannot be trusted may distort the perceived prevalence of dangerous toxin types or misdirect follow-up research.

The case also illustrates the ongoing evolution of post-publication peer review and image integrity screening. Journals and publishers increasingly use automated tools and expert forensic analysis to detect duplicated or manipulated images in published figures, and readers are encouraged to report concerns long after a paper’s publication date. The seven-year gap between the original publication in May 2019 and the retraction in September 2026 reflects the time such investigations can take, involving correspondence between the journal, the authors, and their institutions, and the careful documentation of specific figure-level concerns. The retraction notice itself is open access, ensuring that anyone who encounters the original paper through databases or citation trails will be directed to the notice explaining why the article was withdrawn.

For the research community, the practical consequences of a retraction are significant. The retracted article should no longer be cited as reliable evidence, and databases such as PubMed and the journal’s own website will flag it as retracted. The original article remains accessible online, as is standard practice, but it is watermarked and linked to the retraction notice so that readers understand its status. The authors’ disagreement with the retraction does not alter this status; the editorial decision rests on the journal’s judgment that the reliability of the findings cannot be assured. The retraction notice also notes that the article was published open access under a Creative Commons license, and Springer Nature’s standard publisher’s note regarding jurisdictional claims applies to the notice itself.

The broader lesson for microbiology and for science publishing is that the credibility of research on bacterial virulence factors depends on the integrity of the underlying experimental data. Colibactin and CNF1 remain genuine and important subjects of investigation, with well-documented roles in DNA damage, colorectal carcinogenesis, and cytoskeletal toxicity, and legitimate research on these toxins continues across many laboratories. Questions about the prevalence of toxin-producing E. coli strains and their pathological effects remain scientifically important, and they will be answered, as always, by studies whose figures, data, and analyses can withstand scrutiny. The retraction of this particular paper removes one unreliable data point from the literature while leaving the underlying scientific questions open for future, verifiable work.

Subject of Research: Retraction of a study on colibactin and cytotoxic necrotizing factor 1 production by Escherichia coli

Article Title: Retraction Note: Prevalence and pathologic effects of colibactin and cytotoxic necrotizing factor‑1 (Cnf 1) in Escherichia coli: experimental and bioinformatics analyses

Article References: Morgan, R. N., Saleh, S. E., Farrag, H. A., & Aboulwafa, M. M. (2026). Retraction Note: Prevalence and pathologic effects of colibactin and cytotoxic necrotizing factor‑1 (Cnf 1) in Escherichia coli: experimental and bioinformatics analyses. Gut Pathogens, 18(1), Article 75. https://doi.org/10.1186/s13099-026-00882-w

Image Credits: AI Generated

DOI: 10.1186/s13099-026-00882-w

Keywords: Escherichia coli, colibactin, CNF1, bacterial toxins, retraction, Gut Pathogens, research integrity, image duplication, gut microbiology, virulence factors, post-publication review, Springer Nature