There are no charges to authors for submissions or publications in Pathogens and Immunity. The journal is funded by a charitable endowment. As part of the submission process, authors are required to check off to ensure compliance with the following items. Submissions that do not adhere to these guidelines may be returned to the authors.

  • Review Pathogens and Immunity's editorial policies and ethical guidelines.
  • The submission has not been previously published, nor is it before another journal for consideration (or an explanation has been provided in Comments to the Editor).
  • The submission file is in OpenOffice, Microsoft Word, RTF or pdf document file format and will maintain styles such as superscript, subscript, and italics.
  • All information and graphics are contained in a single file.
  • Where available, URLs for the references have been provided.
  • All authors have agreed to the submission of this manuscript.
  • All relevant conflicts of interests are stated in the manuscript. If none, also state in manuscript.
  • Funding sources related to the manuscript must be stated in the manuscript.
  • You may, if you wish, provide unedited complete reviews from another named journal together with your response to these critiques that may assist in the review.
  • There is not a word count limit for submissions, but we prefer that accepted manuscript contain fewer than 6,000 words.

STOP! These are all of the guidelines you need for your initial submission.

Accepted Manuscript Guidelines
Manuscript Formatting
How-to Submit with Video
How to Submit Revisions with Video
How to Receive/Review/Resubmit Copyedits



If the paper is accepted for publication, the authors will be asked to resubmit the work in the Pathogens and Immunity format.

Manuscripts for publication must be written in English and submitted electronically. Hardcopy manuscripts and those not following the below requirements are not acceptable.

  • Manuscripts should be in MS Word format. While not required, we encourage the use of the Pathogens and Immunity journal formatting template, which can be downloaded here in Word format.
  • Please limit manuscripts to ≤ 6,000 words and ≤ 6 figures/tables.
  • The use of commercial citation management software is required. For in-text citations, tables and figures, bibliographies and other citation requirements, see REFERENCES section.
  • Use italics for bacterial and viral taxa at the level of family and below.
    The author(s) must either maintain the copyright or have permission from the copyright holder to reproduce any image that is submitted.
  • Any information that might identify a patient or hospital should be removed from all images. If a photograph of an identifiable patient is used, the patient should complete and sign a release form.

Tables and Figures – Detailed Requirements

Tables and figures must meet the file types, sizes, and resolutions identified by NLM guidelines. Figures should be clearly constructed with readily comprehensible panels and legends. We strongly recommend as few panels per figure as are necessary for clarity of presentation. Figures containing more than 8 panels are discouraged.


Place tables within the manuscript file and be sure each table is cited in the text. Do not use any other program, tabs or spaces to align columns.

  • If a table cannot be created in Word, please submit it as an image.
  • Number tables consecutively in the order of their first citation in the text and supply a title for each.
  • Titles should be short but self-explanatory so readers can understand the table content without having to refer to the text.
  • When referencing table parts in a caption, use lowercase superscripts a, b, c, etc. Examples:
    • aReference to column one, row one
    • bReference to column two, row three


  • Final figures should be included in the manuscript, and supplementary files uploaded as individual high-resolution files. The file types, sizes and resolutions must meet the NLM guidelines, and names must correspond to the reference in the text.
  • For citing tables and figures, see REFERENCES section.



The following sections, if applicable, should be included in a single manuscript file:

Title Page: Manuscripts should include a first page with Title and Standfirst (an introductory sentence that summarizes the main point of the article (Optional: Could be used in the TOC).

Author List: Manuscripts should include all authors listed by full name. Email addresses for each will be required by our submission platform. The email addresses can be provided as part of the manuscript or separately in the body of an email. Follow ICMJE Recommendations for authorship requirements. Include superscript references for each author’s affiliations (Example: Joe A. Smith1, Jane B. Smith2).

Identify the corresponding author and provide an e-mail address and telephone number, which will be published with the article.

Affiliations: A list of organizations or institutions should be listed preceded by the superscript reference number in the author list. The list of institutions should be in order by reference numbers. Separate institutions with a semicolon. Locations, including geographic designations that are part of the name, do not need to be translated into English. Please refer to the Getty Thesaurus of Geographic Names for the common English preferred designation for the city, state or province, and country.

Example: 1Department of Medicine, Emory University, Atlanta, Georgia; 2Division of Infectious Diseases, University of Tennessee School of Medicine, Memphis, Tennessee

Abstract: An abstract of 150 to 250 words should be included using the headings listed below
Please provide an abstract of 150 to 250 words. It should consist of four paragraphs that briefly describe the problem being addressed in the study, how the study was performed, the salient results, and what the authors conclude from the results. These should be labeled:

  • Background
  • Methods
  • Results
  • Conclusions
  • Keywords (a list of 5-10 of the most important terms related to your research subject from the library of Medical Subject Headings [MeSH]).

Do not include undefined abbreviations or unspecified references, or use citations in the abstract. Manuscripts about clinical trials should include the clinical trial registration number at the end of the abstract.

Graphical Abstract (optional): This is an image or visual element that summarizes the article.


Methods: If human subjects were involved, the Methods section should include a statement that informed consent was obtained from human study participants or their parents or guardians, and that human experimentation guidelines of the United States Department of Health and Human Services and/or those of the authors' institution were followed in the conduct of clinical research, under a protocol reviewed and approved by an appropriate institutional review committee.

In the case of animal subjects research, a statement that experimentation was performed in compliance with the U.S. Department of Health and Human Services Guide for the Care and Use of Laboratory Animals (or otherwise similar guidelines), and that the study was approved by an appropriate institutional review committee.




Funding Sources: Any funding related to the study or manuscript must be clearly stated.

Conflicts of Interests: Relevant conflicts must be clearly stated. If none, this must be clearly stated.

References: Pathogens and Immunity requires the use of a commercial citation manager such as Endnote (strongly preferred), Zotero or Mendeley. We can accept manuscripts using other citation managers as long as the software used integrates with Microsoft Word. Manuscripts that do not use a citation manager will not be considered.

References should be styled according to “NLM (Grant Format) for PAI Journal” output style.
The EndNote output style can be downloaded HERE. When using EndNote, please make sure to select "Link in-text citations to references in the bibliography" and "Underline Linked in-text citations" in the EndNote Format Bibliography menu. Ensure a similar feature is used in citation software other than EndNote.

References should be numbered consecutively in the order in which they are first mentioned in the text. In-text citations to the references should be made in brackets (Examples: [1], [20], [21]). This style is included in the NIH (Grant Format) for PAI Journal EndNote output style.

In-text references to Figures and Tables should be written as Figure 1 and Table 1 in the text. To identify the part of any element, it should be written as Figure 1A. Use Digital Object Identifiers (DOI) when applicable.

While the NLM (Grant Format) for PAI Journal output style should ensure proper formatting, it is also important to visually ensure the bibliography is formatted correctly.

Explanation of Format:
Lastname FM, (list all authors, no “et al”). Title of Article with Major Words Only in Capital Letters. Title of Pub. Year;Volume(Number):Page(s)-Page(s). Epub yyyy/mm/dd. doi: doi. PubMed PMID: pmid#; PMCID: pmcid#.

Fomina DS, Lysenko MA, Beloglazova IP, Mutovina ZY, Poteshkina NG, Samsonova IV, Kruglova TS, Chernov AA, Karaulov AV. Temporal Clinical and Laboratory Response to Interleukin-6 Receptor Blockade With Tocilizumab in 89 Hospitalized Patients With COVID-19 Pneumonia. Pathog Immun. 2020;5(1):327-41. Epub 2020/10/23. doi: 10.20411/pai.v5i1.392. PubMed PMID: 33089038; PMCID: PMC7556411.



Download Instructional PDF

  • Log in to
  • You will be on your Queue page
    • Click on “NEW SUBMISSION”
  • In Journal Section, select the appropriate section for your manuscript from the drop-down menu (Example, “Articles”)
  • In Submission Checklist, place a checkmark in the boxes next to the statements.
  • Add any comments for the Editor.
  • Click “Save and continue”
  • In Upload Submission File, select "Article Text" in the "Article Component" and upload your file.
  • Click “Continue." Click "Continue" again, and finally, click "Complete."
  • The system will provide you a list of the submission file/s to be uploaded, click "Save and Continue."
  • Under Enter Metadata, paste the title of your manuscript and your abstract in the boxes provided.
  • Click “Save and Continue”
  • Click “Finish Submission”
  • You will receive an email that your submission has been received. The editors also will receive an email that you have uploaded a submission. You will know within one week whether the manuscript has been sent on to reviewers for further consideration.
  • Through our online journal management system, you can track your submission's progress through the editorial process by logging back in to the journal web site and checking the status of your submission on your "Queue" page.





When submitting revisions, make sure to provide a point-by-point response to the reviewers' comments either as part of the revised manuscript or upload as a separate file.






Download a step-by-step PDF with four steps to mark-up a pdf.

Download a step-by-step PDF on how to download copyedits to your manuscript and then return it to the editors.