Instructions for Authors — Journal of Clinical Microbiology

Source: http://jcm.asm.org/journal/jcm/submit

Request Username

Can't sign in? Forgot your username?

Enter your email address below and we will send you your username

JCM publishes the most current research related to the laboratory diagnosis of human and animal infections and the role of the laboratory in the management of infectious diseases, antimicrobial susceptibility testing, and the epidemiology of infections.

ASM offers authors the opportunity to perform a pre-submission check of their manuscript to ensure compliance with JCM’s requirements with Paperpal Preflight. Paperpal Preflight is a free service that automatically identifies common issues that could delay peer review or require extra revisions so they can be corrected before submitting. Authors also have the option to pay a fee to receive an edited version of the manuscript with suggestions for improving language and conforming to the journal requirements.

• Research Articles
• Minireviews
• Point-Counterpoint
• The Brief Case
• Photo Quiz
• Commentaries
• Letters to the Editor

ASM Journals are now Format Neutral.

ASM primary research journals will consider for publication manuscripts that have been posted in a recognized not-for-profit preprint archive. Please review our preprint policy for more information.

• Rapid decisions (34 median calendar days to first decision)
• Expedited review for manuscripts previously reviewed by certain highly selective non-ASM journals
• Expert peer review with constructive recommendations to improve your manuscript
• Published by a scientific society that invests back in the community
• Compliant with Funder Mandates
• No publication fees for Minireviews
• 95% of articles cited within two years of publication

All six primary research journals remain open access—unlocking more opportunities for authors and expanding access for readers, fueling collaboration and innovation across the microbial sciences.

This checklist offers the links and information you need to prepare your initial submission to an ASM journal. (This information does not apply to revisions.)

Review journal-specific formatting for information about article type guidelines and word counts.

For your initial submission to any ASM journal, the ASM ChronosHub submission portal is the starting point. Depending on the journal, you may complete your submission in the ChronosHub submission portal or be redirected to the eJournalPress (eJP) peer review system to complete your submission there.

• 1: Find Your Journal- Choose an ASM journalthat’s a good fit for your manuscript. To learn more, review its About the Journal menu:- Editorial Board / Board of Editors / Masthead
• Scope

• FAQs

• Menu on an ASM Journal page

• 2: Review Your Journal’s Formatting Requirements- Initial submissions are - format-neutral(see Step 3).- Visit the - ASM Journals Formatting Information for Specific Journals pageto find the following information for each journal:- Article Types
• Word count guidance
• Content requirements for article types published by the journal
• Reference style guidance

• Links to templates (LaTeX templates and MRA Word document templates)

• Submission and Review Processpage- Information about submitting initial and revised manuscripts

• FAQs related to the review process

• 3: Prepare Your Submission- We offer - format-neutralinitial submissions. At this stage, since you may already have your paper formatted, you don’t have to worry about following our formatting rules for word counts, reference style, sections, importance paragraph, etc. If you'd like to review or follow these rules, see Step 2.- The following files are required at initial submission: - A cover letter that explains your paper's scientific importance and its interest to your journal’s readers

• A manuscript text file that includes the full article and any tables
• You may include figures and supplemental material in the manuscript text file or upload them as separate files. - Requirements - Minimum (format-neutral) Initial Submission - Final Revision - Cover letter - ✔ - ✔ - Authors (indicate corresponding author(s) and affiliations) - ✔ - ✔ - Title - ✔ - ✔ - Abstract word count (see step 2) - ✔ - ✔ - Data availability paragraph - ✔ - ✔ - Word (.docx / .rtf); LaTex (.tex) - PDFs permitted - ✔ - Formatting, abbreviations, title page, sections, word counts, etc. per - your journal’srequirements listed on the Formatting page (see Step 2)- ✔ - Separate files for supplemental materials and figures - ✔ - Figure file size (review our - file size tipsif you need help)- 15 MB - 20 MB - Continuous line numbers (will be automatically added to your Word file) - ✔ - Per our format-neutral process, you are not required to use a specific format or section for - data availabilityin your document, but we expect to see the following information represented:- Data description
• Name(s) of the repository/repositories

• Digital object identifiers (DOIs) or accession numbers (add URLs)

• 4: Review ASM's Editorial Policies- We - provide guidanceon data sharing, open access, reproducibility, and data citation.- During the submission process, you will be asked to agree to, or briefly explain how your manuscript fits in with, several ASM policies: - Image Integrity

• Conflict of Interest
• Duplicate Publications
• Biosafety/biosecurity
• Licensing and Open Access
• For the Data Citation and Data Availability sections, please review the following:
• Also note that during the submission process, you will be asked to verify that you have your institution's IRB/IACUC approval, if applicable.
• 5: Review ASM's Publication Fees- During the submission process, you will be asked to agree to pay any applicable - publication feesshould your paper be accepted. (ASM does not charge a submission fee.) We recommend you review- ASM’s green and gold open access (OA) optionsand an overview of- how ASM meets funder requirementsbefore submitting to make sure you are in compliance with any funder mandates related to OA publication.- ASM membersreceive discounts on page charges, article processing charges (APCs), and/or supplemental fees.
• 6: Gather Information- During the submission process, you will be asked to provide specific information about your paper. Some of it may require research, or consulting co-authors, so you may wish to prepare it in advance. - ### About the Authors, Editors, and Reviewers- Required
• All author names
• All author emails
• All author affiliations (if author(s) not already added to our submission system)
• If your manuscript includes a study group/consortium, you will need to include an email address for a group representative who isn't already listed in the author byline.
• ORCID iDof the- corresponding authoronly
• Names of any preferred editors (identify using journal's editorial board page – see Step 2)

• Name, email, and institution of at least 3 preferred peer reviewers

• Optional

• ORCID iDsof the- contributing authors
• Author contributions or CRediT roles
• Contact information for authors’ institution(s) (e.g., address)
• Authors' social media handles
• Name, email, and institution of any non-preferred peer reviewers

• About Your Research and Manuscript- Required (if applicable)

• Funding information, including grant reference numbers
• Keywords – may also be used to help find reviewers and research areas associated with the manuscript
• Preferred journal section and research area(s)
• Information about any companion manuscripts
• Preprint server and DOI (note that you may be asked if all authors agree to cross-post to bioRxiv)
• Optional
• A social media blurb about your paper (250 characters max) that we may use to promote it, if published

• Public Information Office or media contact information for your institution (if you would like them to be notified for press release purposes)

• Required

• 7: Go to the Journal's Electronic Submission System- Links to the submission portal for every ASM journal can be found - here.- Create an account or log in. Follow the steps to upload your file(s), enter information, review, and complete your submission. - Contact - your journal’s stafffor help with your account.- Submission portal
• 8: What to Expect Next- All authors will receive a confirmation email letting you know that your submission was successful. - Per Step 2, check your journal's Submission and Review Process page for details on when to expect to hear back on your paper's status. - Contact your journal's staffwith any questions.- We wish you the best of luck on your submission!

To submit one of the JCM article types, please read the formatting details on this page, then follow the submission guidelines. You can also review our Initial Submission Checklist to help prepare your submission.

For initial submissions, to make things easier for authors, ASM Journals welcomes papers in any format (what we call "format-neutral submissions").

Find additional guidance on the following topics within ASM's Author Center:

• Templates (LaTeX, Overleaf)
• Abbreviations
• Nomenclature
• Figures and Tables
• Errata, Author Corrections, Retractions
• References
• Supplemental Material
• Reporting Guidelines
• Language Editing Services

Other helpful resources: Initial Submission Checklist, Publication Fees.

Learn about our new Microbiology Resource Announcements® (MRA) Companion Articles pathway for ASM authors.

• Subjects Covered: laboratory diagnosis, infectious disease management, antimicrobial stewardship, and epidemiological insights.
• Each manuscript should present the results of an independent, cohesive study; numbered series titles are not permitted.
• Research Articles are peer reviewed prior to publication.
• Word Count Guidance: 3,000 words (excluding Abstract, Materials and Methods, References, tables, and figure legends). Manuscripts will not be rejected based solely on word count.

Title Page Details

• Components Include: title, byline, authors names and affiliations, and corresponding author information.
• Title: use unique, clear, and concise titles. Avoid main title/subtitle format, complete sentences, and unnecessary articles.
• Author Information: include names and affiliations at the time the work was done. For some manuscript types, contributor roles (CRediT roles) can be added during the submission process.
• Affiliation Indications: use superscript numbers after authors' last names for affiliations. Separate multiple affiliation numbers with commas. Each affiliation should have its own line.
• Corresponding Author(s): include the e-mail address(es) of the corresponding author(s). This will be published and used to send proofs and publication notifications.
• Co-First Authors: include a footnote explaining the order of names.
• Study Groups in Byline: a study group can be listed as a coauthor if its members meet authorship and accountability requirements. If not, mention the group in the Acknowledgments section.
• Please review ASM Journals criteria for authorshipbefore submitting.

Abstract

• Word Limit: maximum of 250 words.
• Content: abstracts should summarize the paper's basic content without extensive details and include a summary statement. Readers should be able to understand the abstract without referring to the text. Avoid abbreviations, references, and diagrams. The abstract must be able to stand alone from the article. References cited in the abstract should be clear and not require readers to review the References section. The citation should omit the article title. If it’s essential to include references in your abstract, please follow these formatting guidelines:
• (P. S. Satheshkumar, A. S. Weisberg, and B. Moss, J Virol 87:10700 –10709, 2013, https://doi.org/10.1128/JVI.01258-13)
• (J. H. Coggin, Jr., p. 93–114, inD. O. Fleming and D. L. Hunt, ed., Biological Safety. Principles and Practices, 4th ed., 2006)
• “... in a recent report by D. A. Hopwood (mBio 4:e00612-13, 2013, https://doi.org/10.1128/mBio.00612-13) …”

Importance Statement

• Word Limit: maximum of 150 words.
• Content: the importance should be a separate section with its own heading “Importance.” This section should provide a nontechnical explanation of the significance of the study to the field. Avoid abbreviations and references, and indicate the specific organism under study. When it is essential to include a reference, use the format shown in the “Abstract” section.

Introduction

• Provide enough information for readers to understand and evaluate the study's results without needing to refer to previous publications.
• State the hypothesis or rationale of the study.
• Choose references that provide relevant background instead of exhaustive topic reviews.

Materials and Methods

• Provide sufficient technical information to allow experiments to be repeated and support reproducibility.
• Provide sources for all media (that is, name and location of manufacturer) or components of a new formulation.
• When centrifugation conditions are critical, give enough information for the procedure to be repeated: make of centrifuge, model of rotor, temperature, time at maximum speed, and centrifugal force (× g rather than revolutions per minute).
• For standard materials and methods, a reference or recommended product is sufficient.
• If several alternative methods are commonly used, identify the method briefly and cite the reference. For example, stating "cells were broken by ultrasonic treatment as previously described (9)" allows the reader to assess the method without referring to previous publications.
• Describe new methods completely and include sources of unusual chemicals, reagents, equipment, or microbial strains.
• If you used many microbial strains or mutants, include tables identifying the sources (that is, sources from whom the strains were obtained) and properties of strains, mutants, bacteriophages, and plasmids used in large numbers.

Data and Method Description in Results

• Describe methods used in only one experiment in the Results section or briefly in a table footnote or figure legend.
• We expect authors to identify the sources of strains.

Results

• Include the rationale or design of the experiments and the results.
• Extensive interpretation should occur in the Discussion section.
• Present results as text, table(s), or figure(s). Avoid using graphs for data that can be more clearly communicated and interpreted in text or tables. Examples include:
• Double-reciprocal plots used to determine apparent Km values are typically stated in the text. Only in unusual cases should these values appear in graphs.

• Graphs illustrating other methods commonly used to derive kinetic or physical constants (for example, reduced-viscosity plots and plots used to determine sedimentation velocity) don’t typically need to be shown. These are also only shown in unusual circumstances.

• Either standard deviation values or standard errors of the means must accompany all tabular data. The number of replicate determinations (or animals) for these calculations must be included.

• Accompany significance statements with probability values. The statistical procedure used should be mentioned in the Materials and Methods section.
• Limit figures (particularly photomicrographs and electron micrographs) to those necessary to show findings. Cite all figures and tables in the text.

Discussion

Provide an interpretation of results in relation to previous work and the experimental system at hand. Avoid repetition of the Results or Introduction sections. In short papers, Results and Discussion sections may be combined.

Data Availability Statement

• Add a section at the end of the text detailing new accession numbers for nucleotide and amino acid sequences, microarray data, protein structures, gene expression data, and MycoBank data.
• Provide references and URLs for these accession numbers.
• We encourage authors whose manuscripts contain quantitative real-time PCR applications to read the article concerning minimum information for publication of quantitative real-time PCR experiments (the MIQE guidelines) by Bustin et al. (Clin Chem 55:611–612, 2009)for guidance on what information to include in their submission.

• We also encourage authors to review the ASM Journals Open Data Policybefore submitting.

• Minireviews may be either solicited or submitted by authors responding to a recognized need. Suggestions can be emailed to the Minireview Editor.

• Minireviews are peer reviewedprior to publication.
• Minireviews are not intended to be comprehensive reviews of the literature. They are focused discussions and relevant updates on topics of interest to clinical microbiologists.
• Authors shouldn’t include unpublished data, but discussions of the author's own work may be included.
• Learn more from the editors.

Elements of a Minireview

• Items outlined in the “Title Page Details”section
• Items outlined in the “Abstract”section
• Main text may have up to 6,000 words (doesn't include tables, figures, or references)

• May have a maximum of three tables or figures

• Submissions are by invitation.

• Commentaries are subject to review.
• These reflect topics relevant to JCM readers and are meant to encourage discussion.

Elements of a Commentary

• Items outlined in the “Title Page Details”section
• Items outlined in the “Abstract”section
• Main text may have up to a total of 6,000 words (doesn't include tables, figures, or references)
• May contain a maximum of 2 tables or figures

• May have up to 30 references

• Submissions are by invitation.

• Editors review these papers before publication, but they don’t follow the default single-anonymized (previously called single-blind) peer review process.
• The editor will review the submissions and may return them with comments and/or suggested revisions.
• Decisions are made by the JCM editor or the editor in chief.
• Two experts present contrasting views on current infectious disease lab diagnosis issues.

Elements of a Point-Counterpoint Article

• 200-word Introduction written by a JCM editor explaining the importance of the issue. The issue will then be presented as a question.
• Two experts each write a 1,000-word commentary supporting their view. One expert advocates for a position while the other expert takes the opposing position.
• One table or one figure may be included.
• These are evidence-based papers and may have up to 10 references.
• Unpublished or in-press data which reflect current practice may be used but should not be the sole basis for a position.

These should be relevant to clinical microbiology and designed to be educational. The audience includes people training and practicing in clinical microbiology and infectious disease.

Cases should be typical of routine clinical microbiology practice and not represent rare or obscure events.

Cases that depend primarily on the identification of an organism in an image are better suited for the Photo Quiz.

Elements of The Brief Case

Case Presentation

• 300-500-word case summary
• 800-1,100-word discussion that addresses questions/issues from the case, focusing on organism identification, applied technology, or clinical tests
• May contain a maximum of 2 tables or figures
• Three multiple-choice, self-assessment questions based on the case and discussion

Closing Section

• Self-assessment answers are provided and questions are repeated with the correct answers and brief explanations.
• There can be up to four sentences for each multiple-choice question.

• Includes “Take-Home Points” that have 3-5 key points from the case, without references.

• Presents relevant, interesting, new observations in clinical microbiology, where images provide the essential information.

• This article includes a two-part case presentation with at least one figure and an answer to the quiz.

Photo Quiz Case Presentation

• The presentation is limited to 200-300 words.
• The figure should be a high-resolution TIFF or EPS file, approximately 6.5 inches wide by 4.625 inches high. Include a short legend and cite the figure in the case presentation.
• Follow a recently published Photo Quiz for correct formatting.

Answer to Photo Quiz

• The answer is limited to 200-300 words.
• Include four to six references.
• A figure in the answer portion is optional. If you have submitted a short video, refer to it in a figure legend and include a still photo.

JCM publishes Comment Letters and New-Data Letters. Comment Letters discuss and refer to articles published in ASM journals.

Preparing your Letter:

• Comment Letters and New-Data Letters should include no more than 500 words.
• Follow the format of a recently published Letter.
• Use the JCM submission systemto submit your work and specify the type of Letter you are submitting.
• Note that some indexing services may not include Letters to the Editor.

Review Process

• Comment Letters are assigned to the editor who handled the article in question. They may undergo peer review. While we encourage authors to submit a reply, we don’t require a reply from the author.
• New-Data Letters undergo the standard peer review process.

The Acknowledgments section in a manuscript recognizes the types of support and assistance authors have received. This section includes statements about financial support, personal assistance, and potential conflicts of interest. It also outlines the responsibility of authors to comply with funding agency requirements and provides guidance on disclosing funding sources during submission.

• State sources of direct financial support (for example, grants, fellowships, and scholarships, and others) and the role of funding agencies.
• Include a funding statement in Acknowledgments indicating what role, if any, the funding agency played in your study.
• Example Funding Statement: “The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.”
• Funding agencies may have specific wording requirements, and authors should make sure the language is in compliance when submitting a revised manuscript.
• In cases where research is not funded by any specific project grant, you don’t need to list them. You can include the following statement in your manuscript: “This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.”
• Indirect Support: disclose indirect financial support (for example, commercial affiliations, consultancies, stock or equity interests, and patent-licensing arrangements) and relevant relationships.

Include statements disclaiming endorsement or approval of the views reflected in the paper or of a product mentioned as separate paragraph in Acknowledgments.

Authors will be asked to include funding information when submitting a revised manuscript. You will need to provide the following information:

• List any sources of funding.
• Provide relevant grant numbers where possible, and the authors associated with the specific funding sources.
• If your revised manuscript is accepted, the funding source information you provided in the submission form will be published, so please review that information carefully to make sure it’s accurate and complete.
• If you provide no information in the Funding Sources fields, it is assumed that you received no funding.
• Review our funding information pageto learn how we collect and use this information.

Authors may include a statement that specifies contributor roles in a separate paragraph in the Acknowledgments section. ASM encourages transparency in authorship by publishing author contribution statements using the CRediT taxonomy recommended by NISO.

Authors have the option of assigning contributor roles for some manuscript types during the submission process.

• Appendixes can contain additional material to help readers.
• Appendixes should not have distinct titles, authors, or references.
• If appendix authors are not listed in the main article or in the Acknowledgments section, rewrite the appendix so that it can be considered for publication as an independent article.
• Label equations, tables, and figures in appendixes with the letter "A" to distinguish them from the main text (e.g., Fig. A1).

Key Takeaways

• Ensure high-quality images: submit figures with the right resolution and size.
• Individual files should not exceed 15 MB at initial submission and 20 MB at revision.
• Review our image manipulation guidelinesbefore submitting your work.
• Follow guidelines for colors: RGB is preferred. Consider those with visual impairments.
• Provide effective descriptions: legends should be clear and informative, explaining the figures without needing to refer to the main text.
• Seek permissions: obtain and provide necessary permissions for reproducing or modifying images.
• Add cover images: consider submitting a standout image from your work to be published in an issue as part of the journal's Table of Contents.

Refer to the Figures and Table section on the Writing Your Paper webpage for additional guidance.

• Supplemental material definition: material that provides extra non-essential content, which fosters greater understanding of research findings.
• Data Policy: large or complex data sets should be deposited in a public repository rather than submitted as supplemental material.
• Submission requirements: all content can be in a single file. For final revisions, supplemental material must be uploaded separately, with a file size limit of 15 MB (100 MB for videos).
• Reference formatting: references related only to the supplemental material should be included within the supplemental files, not in the References section of the main manuscript. Supplemental items should be numbered with an “S” and submitted in specified standard formats.
• Accepted supplemental material: publication fees apply to supplemental material; modifications post-publication require a formal correction; copyright remains with the author but requires a license permitting ASM to post the content.

• Refer to the Supplemental Material section on the Writing Your Paper webpagefor additional guidance.

• References are numbered in the order in which they are cited in the article (citation-sequence reference system). In the text, references are cited parenthetically by number in sequential order. Data that are not published or not peer reviewed are simply cited parenthetically in the text.

• Refer to the Reference section on the Writing Your Paperwebpage that offers examples to help you format your references in line with ASM reference style, covering a variety of reference types from journal articles to online sources.

For initial submissions, we welcome papers in any format. We encourage you to create and upload one manuscript file that includes the full text, tables, and figures. You have control over the formatting when you first submit: the reference style, the arrangement of sections of the paper, and other formatting issues are at your discretion at the initial submission. We also require you to provide a cover letter.

While the manuscript format is up to you, we do limit the file type. Your manuscript may be a DOCX, PDF, RTF, or LaTeX file. For the smoothest submission process, we recommend DOCX for your manuscript file.

• While we offer LaTex Templates for most ASM journals, you aren't required to use them.
• We also offer Word templates for. You aren't required to use the templates, but we strongly encourage you to, as it speeds up the process.Microbiology Resource Announcements
• When you submit an AAM ContributiontomBioyou will need to provide publication-ready files, meetmBio-specific requirements, and followASM formatting guidelines.
• When you submit a revision or a resubmission you will need to provide publication-ready files, meet journal-specific article type requirements, and followASM formatting guidelines.

• ASM does not charge a submission fee for any ASM journal.

• Review the Initial Submission Checklistfor more details on this process.

• Review the submission and review process information for your ASM journal of choice.
• Review our publication feesfor details related to publishing costs.

UPDATED February 2025

Authors may publish their research as open access in either an ASM open access journal or the six Subscribe to Open (S2O) journals under certain conditions (see below).

• ASM Animal Microbiology™
• ASM Case Reports- ®
• ASM Food Microbiology™
• Journal of Microbiology & Biology Education- ®
• mBio- ®
• Microbiology Resource Announcements- ®
• Microbiology Spectrum- ®
• mSphere- ®
• mSystems- ®

*In 2025, ASM adopted a Subscribe to Open subscription model for its six primary research, subscription-based journals. This aligns with ASM's mission of disseminating high-impact research and accelerating scientific advancement globally. *

Articles in ASM S2O journals are published open access if the journal's Sustainability Target is met for the year or if the corresponding author is affiliated with an institution that is a current subscriber to the journal.

Learn how ASM S2O journals  comply with funder mandates.

Authors who did not previously select open access may contact the ASM journal staff to arrange it.

• Antimicrobial Agents and Chemotherapy- ®
• Applied and Environmental Microbiology- ®
• Infection and Immunity- ®
• Journal of Bacteriology- ®
• Journal of Clinical Microbiology- ®
• Journal of Virology- ®

Open access is not available for articles published in Clinical Microbiology Reviews® or

• ASM journals compliance with funder mandates
• Open access fees (APCs) licensing, and other open access resources
• Article-based workflow and average time to publication

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.

For your initial submission to any ASM journal, the ASM ChronosHub submission portal is the starting point. Depending on the journal, you may complete your submission in the ChronosHub submission portal or be redirected to the eJournalPress (eJP) peer review system to complete your submission there.

The ChronosHub portal is ASM’s platform for initial manuscript submissions only. Authors must use the ASM eJP peer review system to submit revisions and resubmissions.

Links to each submission site appear below.

Know Before You Submit

• ASM does not charge a submission fee.
• ASM requires corresponding authors to provide an ORCID iD during the submission process. You can register for an ORCID iDif you do not have one.
• Login credentials for the ASM ChronosHub submission portal, the eJP peer review system, andASM membershipare established and maintained separately.
• Authors can find technical assistance and system tips in the ChronosHub FAQsand on the “Help for Authors” page of each ASM eJP peer review system journal site.