Bacteria, fungi, parasites, prions and viruses cause a variety of diseases that have important medical, agricultural, and economic consequences. Moreover, the study of microbes continues to provide novel insights into such fundamental processes as the molecular basis of cellular and organismal function. PLOS Pathogens reflects the full breadth of research in these areas by publishing outstanding original articles that significantly advance the understanding of pathogens and how they interact with their host organisms. PLOS Pathogens provides immediate free access to all content, ensuring that authors reach the widest possible audience as soon as a manuscript is published. Topics include (but are not limited to) adaptive and innate immune defenses as well as pathogen countermeasures, emerging pathogens, evolution, genomics and gene regulation, model host organisms, pathogen-cell biology, pathogenesis, prions, proteomics and signal transduction, rational vaccine design, structural biology, and virulence factors. For further information, please see the journal scope.
PLOS applies the Creative Commons Attribution (CC BY) license to all works we publish. Under the CC BY license, authors retain ownership of the copyright for their article, but authors allow anyone to download, reuse, reprint, modify, distribute, and/or copy articles in PLOS journals, so long as the original authors and source are cited. No permission is required from the authors or the publishers.
To provide open access, PLOS journals use a business model in which our expenses—including those of peer review, journal production, and online hosting and archiving—are recovered in part by charging a publication fee to the authors or research sponsors for each article they publish. The fees vary by journal.
PLOS is committed to the widest possible global participation in open access publishing. To determine the appropriate fee, we use a country-based pricing model, which is based on the country that provides 50% or more of the primary funding for the research that is being submitted. Research articles funded by Upper Middle and High Income Countries incur our standard publication fees. Corresponding authors who are affiliated with one of our Institutional Members are eligible for a discount on this fee. Such authors will be informed of the discount applicable after submission of their manuscript.
Fees for Low and Lower Middle Income Countries are calculated according to the PLOS Global Participation Initiative pricing program for manuscripts submitted after 9am Pacific Time on September 4, 2012 (this program is not retroactive).
Our fee waiver policy, whereby PLOS offers to waive or further reduce the payment required of authors who cannot pay the full amount charged for publication, remains in effect. Editors and reviewers have no access to whether authors are able to pay; decisions to publish are only based on editorial criteria.
To be considered for publication in PLOS Pathogens, any given manuscript must satisfy the following criteria:
Our aim is to provide all authors with an efficient, courteous, and constructive editorial process. To achieve its required level of quality, PLOS Pathogens is highly selective in the manuscripts that it publishes; rejections rates are high. To ensure the fairest and most objective decision-making, the editorial process is run as a partnership between the PLOS Pathogens Editor-in-Chief, a Deputy Editor, a team of Section Editors (SEs), and a group of academic experts who act as Associate Editors (AEs). These individuals are leaders in their fields and represent the full breadth of pathogen-related research.
Submitted manuscripts are first reviewed by a group of relevant SEs, who may decide to reject the paper or send it on to an AE for further review. The AE is most often a member of the PLOS Pathogens Editorial Board, but occasionally a guest of the Board is invited to serve in this capacity. The AE evaluates the paper and decides whether it describes a sufficient body of work to support a major advance in a particular field. If so, the paper is sent out for external peer review, at which stage the technical and scientific merits of the work are carefully considered. Once the reviews have been received and considered by the editors, a decision letter to the corresponding author is drafted and sent.
The decision will be within one of the following categories:
PLOS Pathogens encourages input from the community regarding editorial and publishing policies. However, appeals against manuscript decisions must be a) limited to the specific manuscript in question, b) made only by the corresponding author, and c) sent by e-mail to plospathogens [at] plos.org. Telephone calls or other informal appeals are discouraged and will not be considered. Appeals will only be considered when a reviewer or editor is thought to have made a significant factual error or when his/her objectivity is compromised by a documented competing interest, and when a reversal based on either of these grounds would change the original decision. The journal staff will ask for confirmation of the reason(s) in the first instance. If the authors proceed, the original editor(s) will usually be asked to consider the appeal. Additional editorial board members may also be consulted. Each appeal is treated on its merits and the journal cannot make any guarantees about the turnaround time or outcome. Appeals of decisions made before review will only be considered in exceptional circumstances. Appeals of decisions noted as final will not be considered.
When authors are unsure whether their work satisfies the basic requirements for publication in PLOS Pathogens, we are happy to consider presubmission inquiries. If you would like to submit an informal presubmission inquiry to see if a manuscript is appropriate in principle, please login or register for a new account within our online submission system, choosing 'Submit Presubmission Inquiry' from the list of Author Tasks. Required for all Presubmission Inquiries are contact information, a cover letter, and an abstract.
Responses to these inquiries are normally provided within one week. Responses may take longer if consultation between members of the editorial board is required. If you are invited to submit your manuscript, we will do our best to provide an expeditious initial assessment of the complete manuscript for suitability and then, if warranted, external peer review.
To be of most use to authors and editors, presubmission enquiries should consist of the following:
A) A COVER LETTER of approximately 600 words that provides brief answers to the following questions:
B) A REFERENCED ABSTRACT of approximately 300 words. For the purpose of the presubmission enquiry submission form, the referenced abstract should include up to 10 key references that put your work into context. Please do not submit your entire manuscript. The abstract should be structured as follows:
This section should describe clearly the rationale for the study being done and the previous work relevant to the study. It should end with a statement of the specific question or hypothesis being addressed.
Mention the techniques used without going into extensive methodological detail, and outline the most important results. Include sample sizes for key experiments as appropriate. Please also outline any limitations of the study that may have a bearing on the results.
Provide the take-home message of your article as clearly as possible. You may also include a brief, more general interpretation of the results and / or specific recommendations for future research. Please note, however, that the editors will pay most attention to the direct conclusions of the work being presented, rather than some possible future avenues being opened.
PLOS Pathogens publishes original research that clearly demonstrates novelty, importance to a particular field, biological significance, and conclusions that are justified by the study.
Our aim is to make the editorial process rigorous and consistent, and to offer the best possible support to our authors throughout this process. Authors are encouraged to decide how best to present their ideas, results, and conclusions. The writing style should be concise and accessible. Editors may make suggestions for how to achieve this, as well as suggestions for cuts or additions that could be made to the article to strengthen the argument.
Although we encourage submissions from around the globe, we require that manuscripts be submitted in English. As a step towards overcoming language barriers, we encourage authors fluent in other languages to provide copies of their full articles or abstracts in other languages. Translations should be submitted as supporting information and listed, together with other supporting information files, at the end of the article text.
Most Research Articles published in PLOS Pathogens are organized into the following sections: Title, Authors, Affiliations, Abstract, Author Summary, Introduction, Results, Discussion, Materials and Methods, Acknowledgments, References, Figure Legends, and Tables. Uniformity in format facilitates the experience of readers and users of the journal. To provide flexibility, however, authors are also able to include the Materials and Methods section before the Results section or before the Discussion section. Please also note that the Results and Discussion can be combined into one Results/Discussion section. All manuscripts must contain line numbers. Although we have no firm length restrictions for the entire manuscript, we urge authors to present and discuss their findings concisely.
The title should be specific to the project, yet concise. It should be comprehensible to readers outside your field. Avoid specialist abbreviations, if possible. Titles should be presented in title case, meaning that all words except for prepositions, articles, and conjunctions should be capitalized. Please ensure the title in the manuscript is the same as that entered into our submission form. Please also provide, in the submission form only, a brief Short Title (or "running head") of no more than 50 characters.
Detection of Specific Sequences among DNA Fragments Separated by Gel Electrophoresis
Provide the first names or initials (if used), middle names or initials (if used), surnames, and affiliations—department, university or organization, city, state/province (if applicable), and country—for all authors. One of the authors should be designated as the corresponding author. It is the corresponding author's responsibility to ensure that the author list, and the summary of the author contributions to the study, is accurate and complete. If the article has been submitted on behalf of a consortium, all consortium members and affiliations should be listed after the Acknowledgments.
The abstract of the paper should be succinct; it must not exceed 300 words. Authors should mention the techniques used without going into methodological detail and should summarize the most important results. While the abstract is conceptually divided into three sections (Background, Methodology/Principal Findings, and Conclusions/Significance), please do not apply these distinct headings to the abstract within the article file. Please do not include any citations and avoid specialist abbreviations.
We ask that all authors of research articles include a 150–200 word non-technical summary of the work as part of the manuscript to immediately follow the abstract. This text is subject to editorial change, should be written in the first-person voice, and should be distinct from the scientific abstract. Aim to highlight where your work fits within a broader context; present the significance or possible implications of your work simply and objectively; and avoid the use of acronyms and complex terminology wherever possible. The goal is to make your findings accessible to a wide audience that includes both scientists and non-scientists. Authors may benefit from consulting with a science writer or press officer to ensure they effectively communicate their findings to a general audience. Examples are available at:
The introduction should put the focus of the manuscript into a broader context. As you compose the introduction, think of readers who are not experts in this field. Include a brief review of the key literature. If there are relevant controversies or disagreements in the field, they should be mentioned so that a non-expert reader can delve into these issues further. The introduction should conclude with a brief statement of the overall aim of the experiments and a comment about whether that aim was achieved.
The results section should provide details of all of the experiments that are required to support the conclusions of the paper. There is no specific word limit for this section, but details of experiments that are peripheral to the main thrust of the article and that detract from the focus of the article should not be included. The section may be divided into subsections, each with a concise subheading. Large datasets, including raw data, should be submitted as supporting files; these are published online alongside the accepted article. The results section should be written in the past tense.
The discussion should spell out the major conclusions of the work along with some explanation or speculation on the significance of these conclusions. How do the conclusions affect the existing assumptions and models in the field? How can future research build on these observations? What are the key experiments that must be done? The discussion should be concise and tightly argued. The results and discussion may be combined into one section, if desired.
This section should provide enough detail for reproduction of the findings. Protocols for new methods should be included, but well-established protocols may simply be referenced. While we do encourage authors to submit all appendices, detailed protocols, or details of the algorithms for newer or less well-established methods, please do so as Supporting Information files. These are not included in the typeset manuscript, but are downloadable and fully searchable from the HTML version of the article.
People who contributed to the work but do not fit the criteria for authors should be listed in the Acknowledgments, along with their contributions. You must also ensure that anyone named in the Acknowledgments agrees to being so named.
Details of the funding sources that have supported the work should be confined to the funding statement provided in the online submission system. Do not include them in the Acknowledgments.
Only published or accepted manuscripts should be included in the reference list. Papers that have been submitted but not yet accepted should not be cited. Limited citation of unpublished work should be included in the body of the text only as “unpublished data.” All “personal communications” citations should be supported by a letter from the relevant authors.
Because all references will be linked electronically as much as possible to the papers they cite, proper formatting of the references is crucial. For convenience, a number of reference software companies supply PLOS style files (e.g., Reference Manager, EndNote).
1. Hou WR, Hou YL, Wu GF, Song Y, Su XL, et al. (2011) cDNA, genomic sequence cloning and overexpression of ribosomal protein gene L9 (rpL9) of the giant panda (Ailuropoda melanoleuca). Genet Mol Res 10: 1576-1588.
Note: Use of a DOI number for the full-text article is acceptable as an alternative to or in addition to traditional volume and page numbers.
Accepted, unpublished papers
Same as above, but “In press” appears instead of the page numbers.
Electronic Journal Articles
1. Huynen MMTE, Martens P, Hilderlink HBM (2005) The health impacts of globalisation: a conceptual framework. Global Health 1: 14. Available: http://www.globalizationandhealth.com/content/1/1/14. Accessed 25 January 2012.
1. Bates B (1992) Bargaining for life: A social history of tuberculosis. Philadelphia: University of Pennsylvania Press. 435 p.
1. Hansen B (1991) New York City epidemics and history for the public. In: Harden VA, Risse GB, editors. AIDS and the historian. Bethesda: National Institutes of Health. pp. 21-28.
The aim of the figure legend should be to describe the key messages of the figure, but the figure should also be discussed in the text. An enlarged version of the figure and its full legend will often be viewed in a separate window online, and it should be possible for a reader to understand the figure without switching back and forth between this window and the relevant parts of the text. Each legend should have a concise title of no more than 15 words that can stand alone, without the use of figure part labels. The overall legend itself should be succinct, while still explaining all figure parts, symbols and abbreviations. Avoid lengthy descriptions of methods.
Tables should be included at the end of the manuscript file and cited sequentially in the text. All tables should have a concise title. Footnotes can be used to explain abbreviations. Citations should be indicated using the same style as outlined above. Tables should not occupy more than one printed page; larger tables can be published as online supporting information. Tables must be cell-based; do not use picture elements, text boxes, tabs, or returns in tables. Please ensure that all tables conform to our Guidelines for Figure and Table Preparation when preparing them.
The use of standardized nomenclature in all fields of science and medicine is an essential step toward the integration and linking of scientific information reported in published literature. We will enforce the use of correct and established nomenclature wherever possible:
All appropriate datasets, images, and information should be deposited in public resources. Please provide the relevant accession numbers (and version numbers, if appropriate). Accession numbers should be provided in parentheses after the entity on first use. Suggested databases include, but are not limited to:
In addition, as much as possible, please provide accession numbers or identifiers for all entities such as genes, proteins, mutants, diseases, etc., for which there is an entry in a public database, for example:
Providing accession numbers allows linking to and from established databases and integrates your article with a broader collection of scientific information.
Please keep abbreviations to a minimum and define them upon first use in the text. Non-standard abbreviations should not be used unless they appear at least three times in the text.
It is important that you include a cover letter with your manuscript. Please explain why this manuscript is suitable for publication in PLOS Pathogens; why will your paper inspire the other members of your field, and how will it drive research forward? You are free to recommend a suitable Associate Editor to handle your submission; however, the editors reserve the right to contact an alternative—either from the board or a guest editor—if it is considered more appropriate. Please note that the cover letter will be available to the editors and to external peer reviewers as necessary, so be careful not to reveal anything of a confidential nature.
It is the responsibility of the corresponding author to ensure that all authors are aware of and approve the submission of the manuscript, its content, authorship, and order of authorship. Confirmation of this action is required at submission of all manuscripts.
The involvement of any professional medical writer in publication must be declared. We encourage authors to consult the European Medical Writers' Association Guidelines on the role of medical writers. For all PLOS journals, the corresponding author must submit the manuscript, related files, and all required data and information. From the point of submission through to publication, all communication related to that manuscript will be directed to and received from the corresponding author only.
PLOS Pathogens bases its criteria for authorship on those outlined in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals, which are summarized below. The contributions of all authors must be described. Contributions that fall short of authorship should be mentioned in the acknowledgments.
"Authorship credit should be based on
Authors should meet conditions 1, 2, and 3.
- substantial contribution to conception and design, or acquisition of data, or analysis and interpretation of data;
- drafting the article or revising it critically for important intellectual content; and
- final approval of the version to be published
When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript (3). These individuals should fully meet the criteria for authorship defined above and editors will ask these individuals to complete journal-specific author and competing interests disclosure forms. When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name.
Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship. All persons designated as authors should qualify for authorship, and all those who qualify should be listed. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content."
PLOS journals follow the COPE guidelines covering changes in authorship. Please note that if any changes to the list of authors of a manuscript are necessary after the initial submission of a manuscript to a PLOS journal but before its publication, the corresponding author may be asked to provide written confirmation that all authors consent to the change(s). The journal also reserves the right to request written confirmation from all authors (including those added, removed, or moved in the author order). Such written consent may be required before the revised submission is sent to the editors.
This section should describe sources of funding that have supported the work. Please include relevant grant numbers and the URL of any funder's Web site. Please also include this sentence: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct, you must describe the role of any sponsors or funders, and amend the aforementioned sentence as needed.
The submitting author is asked at submission to declare, on behalf of all authors, whether there are any financial, personal, or professional interests that could be construed to have influenced the paper. The information entered here will appear in the published version, so please do not include the same in the manuscript file.
Reviewers are also asked to declare any interests that might interfere with their objective assessment of a manuscript. Any relevant competing interests of authors must be available to editors and reviewers during the review process and will be stated in published articles. Read more about PLOS's Competing Interests Policy.
Our submission system supports a limited range of formats for text and graphics. The following file formats/types and manuscript information are required before submission. If you are concerned about the suitability of your files, please contact us at plospathogens [at] plos.org.
Articles can be submitted for review in DOC, DOCX, RTF, or PDF. Any articles that have been prepared in LaTeX will be accepted for review, but only in PDF format. After acceptance, only text files (RTF or DOC) of the revised manuscript and tables can be accepted for use in the production process.
If your manuscript is or will be in DOCX and contains equations, you must follow the instructions below to make sure that your equations are editable when the file enters production.
If you have not yet composed your article, you can ensure that the equations in your DOCX file remain editable in DOC by enabling “Compatibility Mode” before you begin. To do this, open a new document and save as Word 97-2003 (*.doc). Several features of Word 2007/10 will now be inactive, including the built-in equation editing tool. You can insert equations in one of the two ways listed below.
If you have already composed your article as DOCX and used its built-in equation editing tool, your equations will become images when the file is saved down to DOC. To resolve this problem, re-key your equations in one of the two following ways.
If, when saving your final document, you see a message saying “Equations will be converted to images,” your equations are no longer editable and PLOS will not be able to accept your file.
Articles prepared in LaTeX may be submitted in PDF format for use during the review process. After acceptance, however, .tex files and formatting information will be required as a zipped file. Please consult our LaTeX Guidelines for a list of what will be required.
Tables must conform to our Guidelines for Figure and Table Preparation and placed at the end of the article DOC or RTF file. Accepted LaTeX submissions only should have table files—which must also conform to these guidelines—uploaded individually into the online submission system.
For the article to be accepted for publication, the author will need to supply high-resolution versions of the figures in TIF or EPS format only. When preparing your figures, please ensure that the files conform to our Guidelines for Figure and Table Preparation. Please do not upload panels for a single figure separately (for example, Figure 1A, Figure 1B-1D, Figure 1E); each figure file should be a single montage of all panels. Queries can be sent to figures [at] plos.org.
If you are uploading your files in EPS format, please use the "create outlines" option under the type menu in Illustrator so that all text and fonts appear as intended in print. If you need additional help with figure preparation, please contact figures [at] plos.org.
PLOS does not accept vector EPS figures generated using LaTeX. We only accept LaTeX generated figures in TIFF format. Export your LaTeX files as PDFs, and then open them in GIMP or Photoshop and save as TIFF. In general, Figures must be generated in a standalone graphics application such as Adobe Illustrator, InkScape, PyMol, MatLab, SAS, etc. Please see our Figure Guidelines for more information.
PLOS applies the Creative Commons Attribution (CC BY) license to all figures we publish, which allows them to be freely used, distributed, and built upon as long as proper attribution is given. Please do not submit any figures that have been previously copyrighted unless you have express written permission from the copyright holder to publish under the CC BY license.
We encourage authors to submit essential supporting files and multimedia files along with their manuscripts. All supporting material will be subject to peer review, and should be smaller than 10 MB in size because of the difficulties that some users will experience in loading or downloading files of a greater size.
Supporting files should fall into one of the following categories: Dataset, Figure, Table, Text, Protocol, Audio, or Video. All supporting information should be referred to in the manuscript with a leading capital S (e.g., Figure S4 for the fourth supporting information figure). The numbered title and caption for each supporting information file should be included in the main article file, after the titles and captions for the main figures.
Supporting files will not be included in the typeset PDF, but will be referenced in the text and hosted online.
Supporting files may be submitted in a variety of formats, but should be publication-ready, as these files are not copyedited. Carefully consider whether your supporting information needs to be searchable and/or editable, and choose the most suitable format accordingly. See the Supporting Information Guidelines for more details about our requirements for supporting information and multimedia files.
We have provided a Submission Checklist to help you prepare your materials for submission and to make the online submission process as straightforward as possible. Please take the time to look through the list before submitting your article.
Please login or register at our online submission system to begin the submission process. Files can be uploaded individually or together in a single ZIP file, and are automatically combined into a single PDF file, which must be approved by the author at the end of the submission process. This merged PDF is for internal and external peer review only. Original source files will be used to prepare accepted articles for publication.
The front section of PLOS Pathogens is a forum for the publication of articles of broad interest to the community of researchers studying pathogens and pathogen-host interactions. Articles in the magazine section will mostly be commissioned, but we welcome your ideas for articles. If you would like to write a Review or Opinion please first submit a presubmission inquiry. There are no publication charges associated with these articles.
Reviews: These are peer-reviewed articles on rapidly advancing or topical areas in pathogen research and of broad interest to the entire pathogens community. Generally such pieces will canvass briefly any existing literature on a particular topic and speculate on future directions of this course of study. These articles should be no more than 3000 words with 5 figures and a maximum of 100 references.
Opinions: The Opinions section is intended to provide a place for the expression of views on topical, emerging or controversial issues ranging from experimental science to those involving science and public-health policy, education and training. It is also a forum in which colleagues can respond, with room for speculation, to previously stated opinions or observations. A successful Opinion piece will make a compelling case for a particular point of view, but will do so, mindful of existing controversies or alternative views, and will make an effort to integrate these into the discussion. While primary data are typically not included in these submissions, if the author chooses to include data, it should be subjected to rigorous review as would any research article. These articles should be no more than 1000 words with 3 figures and a maximum of 100 references.
Editorials: Written by the journal's editors, these occasional pieces can cover announcements, highlights of journal content, position statements, and journal updates.
Pearls: The goal of a "Pearl" is to describe within a short space a small number of significant and interesting facts about a topic in the world of pathogens. While articles are meant to be current, the audience is meant to be broad. Thus, an article should be readable by scientists working on a completely different pathogen, and they should avoid details relevant only to insiders in a field. Rather they should summarize succinctly the key exciting and important facts on a topic at a level that would allow it to be used in a graduate course. Pearls should be no more than 1500 words with 1-2 figures/tables and a maximum of 20 references.
Pearls may take one of the two following formats:
Before formal acceptance of the article for publication, the manuscript and all related files will be checked by PLOS staff to ensure that they comply with all essential formatting and manuscript preparation requirements. Please note that manuscripts are not subject to detailed copyediting. Therefore, please carefully review your manuscript, paying special attention to spelling, punctuation, and grammar, as well as scientific content. Authors who believe their manuscripts would benefit from in-depth professional copyediting are encouraged to use language-editing and copyediting services, such as the ones offered below (in alphabetical order):
PLOS neither endorses nor takes responsibility for contracting with any of these individuals/companies, but we do recognize the value of the services they provide.
When an article has been accepted for publication, the manuscript files are transferred into our production system and will be published in PDF and HTML formats, with an XML download option. Articles are published online on a weekly schedule and archived in PubMed Central/PubMed within 5 to 10 days of publication.