Reference Errors in Microbiology Literature: ‘Pyroptosis’ and Others

Abstract

References in the published microbiology literature provide the foundation for current scientific knowledge within the field. However, reference errors can occur, as discussed here including an illustrative example on the origin of the term ‘pyroptosis.’

Main Text

Scientific publications enable microbiologists to communicate new findings and ideas, thus shaping the state of current knowledge within the field. References are a critical component of scientific publications, as an accurate understanding of prior literature provides the necessary foundation for new research. Proper citations allow authors to contextualize their findings, acknowledge the work of others, and build on previous results. They also facilitate the readers’ ability to verify sources of information and identify related studies. In addition, citations constitute the basis for metrics to evaluate the impact of journals, papers, and individual authors. There can be consequences of citation-based metrics on perceived academic performance, and even decisions related to hiring and promotion.

Different types of errors related to references may occur, including simple typographical mistakes in authors’ names, article titles, page numbers, or other details. Reference management software and technical editing procedures employed by many journals are designed to minimize these types of errors and ensure correct and complete bibliographic information. However, these protective measures are not sufficient to ensure that the cited reference(s) appropriately support a given statement. Citation of partially or completely inappropriate references undermines the accuracy and reliability of scientific literature. Once published, inaccurate or inappropriate citations may be taken as fact and repeated in further publications.

An example of this phenomenon is the incorrect citing of the Trends in Microbiology paper published in 2001 by D’Souza and Heitman entitled, “Dismantling the Cryptococcus Coat” [1] as the source for the term ‘pyroptosis’. The word ‘pyroptosis’ was instead proposed by Cookson and Brennan in a paper entitled “Pro-inflammatory Programmed Cell Death”, which was published in the same issue of Trends in Microbiology [2]. In this article, Cookson and Brennan postulated “the evolution of a pro-inflammatory program to remove potentially dangerous cells, like the process that takes the life of Salmonella-infected macrophages.” The word ‘pyroptosis’ was proposed as a counterpoint to ‘apoptosis’, and incorporated the Greek root ‘pyro’ to denote the inflammatory outcome of pyroptosis. Over the subsequent years, pyroptosis has become a widely-studied form of regulated cell death in the field of microbiology, as it is initiated in response to many microbial infections, including Salmonella [3].

As indicated by the title, the D’Souza and Heitman paper discusses the biosynthesis of the cryptococcal capsule, and makes no mention of ‘pyroptosis’, yet has been repeatedly cited as the source of this term (representative examples in Table 1). Presumably this error originated from a mistaken page number, as the correct reference is directly adjacent to the miscited paper in the original journal issue. Other authors may have propagated the error by simply copying the incorrect citation without considering its appropriateness or verifying the original source.

Table 1:

Example Publications Incorrectly Citing D’Souza and Heitman as the Source for the Term ‘Pyroptosis’

Excerpt from text	Publication
“In 2001, D’Souza et al. pointed out the term of pyroptosis, which comes from the Greek roots pyro (fire/fever) and ptosis (to-sis, falling), to describe pro-inflammatory programmed cell death.7”	Yu, P. et al. (2021) Pyroptosis: mechanisms and diseases. Signal Transduct Target Ther 6 (1), 128. Number [8] in Reference List.
“However, the phenomenon was first thought to be apoptosis until 2001 when D’Souza et al. coined the term pyroptosis …[215,216].”	Babamale, A.O. and Chen, S.T. (2021) Nod-like Receptors: Critical Intracellular Sensors for Host Protection and Cell Death in Microbial and Parasitic Infections. Int J Mol Sci 22 (21). Number [9] in Reference List.
“Among the numerous different cell death pathways, cell pyroptosis, a pathway initially identified in 2001 by D’Souza et al. [6]…”	Li, G.S. et al. (2022) Prognostic signature of esophageal adenocarcinoma based on pyroptosis-related genes. BMC Med Genomics 15 (1), 50. Number [10] in Reference List.
“Pyroptosis was identified by D’Souza et al. in 2001 and described as proinflammatory programmed cell death, which is different from apoptosis.197”	Tong, L. et al. (2022) Current understanding of osteoarthritis pathogenesis and relevant new approaches. Bone Res 10 (1), 60. Number [11] in Reference List.
“The term “pyroptosis” was first proposed in D’Souza’s article (1).”	Mo, W. et al. (2022) Bibliometric analysis of global research trends on pyroptosis in lung disease. Front Immunol 13, 978552. Number [12] in Reference List.
“It was not until 2001 that D’Souza et al. coined the term pyroptosis to describe inflammatory programmed cell death (16).”	Li, X. et al. (2022) Potential therapeutic role of pyroptosis mediated by the NLRP3 inflammasome in type 2 diabetes and its complications. Front Endocrinol (Lausanne) 13, 986565. Number [13] in Reference List.
“It was initially pointed out by Friedlander and was named by D’Souza to distinguish it from apoptosis [57,58].”	Tanaka, N. and Sakamoto, T. (2023) Mint3 as a Potential Target for Cooling Down HIF-1alpha-Mediated Inflammation and Cancer Aggressiveness. Biomedicines 11 (2). Number [14] in Reference List.
“The term “pyroptosis” was firstly proposed by D’Souza in 2001 to describe a highly inflammatory form of RCD [169].”	Sheng, S.Y. et al. (2023) Regulated cell death pathways in cardiomyopathy. Acta Pharmacol Sin 44 (8), 1521–1535. Number [15] in Reference List.

A PubMed search (performed on September 10, 2024) for publications that reference the D’Souza and Heitman paper in regards to pyroptosis, suggested the mis-citation first appeared in 2021, 20 years after publication of the original articles. The error was subsequently perpetuated and has been repeated in a total of 42 separate publications, as of the search date. In the year 2023, there were 21 citations of the D’Souza and Heitman paper related to pyroptosis, and 110 papers that cited the Cookson and Brennan paper. Thus, of the total 131 citations last year, 16% reference a completely irrelevant paper, demonstrating the growing frequency of this erroneous citation in the recent literature.

This case serves as a useful example because the miscited paper is entirely unrelated to ‘pyroptosis’, making it objectively identifiable as an inaccurate reference. In addition to this type of easily recognizable error, more subtle mistakes can occur when relevant references are misquoted or when evidence is overinterpreted. A few published studies have sought to identify and catalog these types of citation errors within various scientific disciplines. Related to microbiology, Hol et al [4] examined the quality of citations of a pioneering paper on probiotic supplementation and found that 175 of the 603 total quotations (29.0%) were inaccurate. Common errors were overstatement and generalization of the findings from the original article, including statements regarding probiotic effects on fecal microbiota composition, which were not examined in the initial study. In addition to undermining the accuracy of the scientific literature, using citations that lack appropriate evidence for a given statement can influence medical decision-making and potentially harm patients. The Coronavirus Disease 2019 (COVID-19) pandemic demonstrated the significant impact on medical care that can result from overinterpretation of published studies on potential antivirals [5].

Microbiologists should be aware that scientific publications may contain reference errors, such as those highlighted here, and take steps to limit propagation of these errors. Students may tend to accept published statements without question, but trainees in microbiology should be cautioned that publications can contain inaccurate or misleading citations. When reading articles, scientists should maintain a critical mindset, emphasizing the value of reviewing primary evidence to independently verify cited sources and understand the history and current state of a field. These steps can help scientists recognize and prevent propagation of reference errors.

When drafting a manuscript, authors must thoughtfully choose each reference to ensure that statements are well-supported by rigorous data and scientific ideas are correctly attributed. Relying solely on the accuracy of previously published citations is not sufficient. A practical rule of thumb is to refrain from citing a paper that an author has not actually read and confirmed to provide appropriate support for the given statement. If authors take personal responsibility for reference accuracy, this would minimize the number of reference errors and improve the rigor of the scientific literature. In addition, peer reviewers and editors must carefully scrutinize manuscripts, including references, before acceptance and publication. Peer reviewers should have deep expertise in the field and be able to recognize inaccurate statements or misattribution, and raise these issues for correction during the manuscript review process. In the future, artificial intelligence-based tools may be routinely used to identify and verify appropriate citations, but this will require ongoing improvements, as current accuracy may still be limited [6, 7]. Together, these steps can prevent citation errors from making their way into published scientific articles. As illustrated here, once an error has been published, it may be quickly perpetuated and become embedded in the scientific literature.