American Society for Microbiology Ethical Guidelines for Authors (2013)

Organization: 

American Society for Microbiology

Source: 

American Society for Microbiology

Date Approved: 

Agust 2013

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American Society for Microbiology Ethical Guidelines for Authors

INSTRUCTIONS TO AUTHORS
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EDITORIAL POLICY

Use of Microbiological Information and General Requirements

Use of Microbiological Information

The Council Policy Committee (CPC) of the American Society for Microbiology affirms the long-standing position of the Society that microbiologists will work for the proper and beneficent application of science and will call to the attention of the public or the appropriate authorities misuses of microbiology or of information derived from microbiology. ASM members are obligated to discourage any use of microbiology contrary to the welfare of humankind, including the use of microbes as biological weapons. Bioterrorism violates the fundamental principles expressed in the Code of Ethics of the Society and is abhorrent to ASM and its members.

ASM recognizes that there are valid concerns regarding the publication of information in scientific journals that could be put to inappropriate use as described in the CPC resolution mentioned above. Members of the ASM Journals Board will evaluate the rare manuscript that might raise such issues during the review process. However, as indicated elsewhere in these Instructions, research articles must contain sufficient detail, and material/information must be made available, to permit the work to be repeated by others. Supply of materials should be in accordance with laws and regulations governing the shipment, transfer, possession, and use of biological materials and must be for legitimate, bona fide research needs. We ask that authors pay particular attention to the NSAR Select Agent/Toxin list on the CDC website and the U.S. Government Policy for Oversight of Life Sciences Dual Use Research of Concern (March 2012; http://www.phe.gov/s3/dualuse/Documents/us-policy-durc-032812.pdf).

Ethical Guidelines

As a member of the Committee on Publication Ethics (COPE), ASM adheres to COPE's Best Practice Guidelines and expects authors to observe the high standards of publication ethics set out by COPE. ASM requirements for submitted manuscripts are consistent with the Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals, as last updated by the International Committee of Medical Journal Editors in August 2013 (http://www.icmje.org/).

Authors are expected to adhere to the highest ethical standards. The following sections of these Instructions include detailed information about ASM’s ethical standards. Failure to comply with the policies described in these Instructions may result in a letter of reprimand, a suspension of publishing privileges in ASM journals, and/or notification of the authors’ institutions. Authors employed by companies whose policies do not permit them to comply with ASM policies may be sanctioned as individuals and/or ASM may refuse to consider manuscripts having authors from such companies. The ASM Journals Board wishes to clarify the following in particular.

Plagiarism. Misappropriating another person’s intellectual property constitutes plagiarism. This includes copying sentences or paragraphs verbatim (or almost verbatim) from someone else’s work, even if the original work is cited in the references. The NIH ORI publication “Avoiding Plagiarism, Self-Plagiarism, and Other Questionable Writing Practices: a Guide to Ethical Writing” can help authors identify questionable writing practices.

Plagiarism is not limited to the text; it can involve any part of the manuscript, including figures and tables, in which material is copied from another publication without permission and attribution. An author may not reuse his or her own previously published work without attribution; this is considered text recycling (also known as self-plagiarism).

ASM has incorporated plagiarism detection software into its online submission and peer review system in order to help editors verify the originality of submitted manuscripts. Selected manuscripts are scanned and compared with databases. If plagiarism is detected, COPE guidelines on plagiarism will be followed.

Image manipulation. Submitted figures must reflect original data. Please refer to the “Image manipulation” section in Illustrations and Tables for an overview of permissible manipulations, unacceptable adjustments, and required information to be disclosed in the figure legends of images.

ASM applies forensic imaging tools to screen selected manuscripts for inappropriate manipulation of figures. If unacknowledged and/or inappropriate image manipulations are detected, the matter will be referred to the journal's ethics panel for consideration.

Fabrication, manipulation, and falsification of data. As a member of the Committee on Publication Ethics (COPE), ASM encourages authors to consult COPE’s “Code of Conduct and Best Practice Guidelines for Journal Editors” (http://publicationethics.org/files/Code_of_conduct_for_journal_editors_0.pdf). Fabrication, manipulation, and falsification of data constitute misconduct. As defined by the U.S. Department of Health and Human Services, fabrication is “making up data or results and recording or reporting them,” and falsification is “manipulating research materials, equipment, or processes, or changing or omitting data or results such that the research is not accurately represented in the research record” (42 Code of Federal Regulations, §93.103). All sources and methods used to obtain and analyze data, including any electronic preprocessing, should be fully disclosed; detailed explanations should be provided for any exclusions.

Preprint policy. ASM Journals will consider for publication manuscripts that have been posted in a recognized not-for-profit preprint archive provided that upon acceptance of the manuscript for publication, the author is still able to grant ASM copyright or agree to the terms of an Open Access license and pay the associated fee. It is the responsibility of authors to inform the journal at the time of submission if and where their article has been previously posted, and if the manuscript is accepted for publication in an ASM journal, authors are required to update the preprint with a citation to the final published article that includes the DOI along with a link.

Primary publication. Manuscripts submitted to the journal must represent reports of original research, and the original data must be available for review by the editor if necessary.

By submitting a manuscript to the journal, the authors guarantee that they have the authority to publish the work and that the manuscript, or one with substantially the same content, was not published previously, is not being considered or published elsewhere, and was not rejected on scientific grounds by another ASM journal. It is incumbent upon the author to acknowledge any prior publication, including his/her own articles, of the data contained in a manuscript submitted to an ASM journal. A copy of the relevant work should be submitted with the paper as supplemental material not for publication. Whether the material constitutes the substance of a paper and therefore renders the manuscript unacceptable for publication is an editorial decision.

In the event that the authors' previously published figures and/or data are included in a submitted manuscript, it is incumbent upon the corresponding author to (i) identify the duplicated material and acknowledge the source on the submission form, (ii) obtain permission from the original publisher (i.e., copyright owner), (iii) acknowledge the duplication in the figure legend, and (iv) cite the original article.

A paper is not acceptable for submission to an ASM journal if it, or its substance, has been made publicly available in the following:

  • A serial, periodical, or book
  • A conference report or symposium proceedings
  • A technical bulletin or company white paper
  • A public website (see ”Preprint policy“)
  • Any other retrievable source

The following do not preclude submission to, or publication by, an ASM journal.

  • Posting of a method/protocol on a public website
  • Posting of a limited amount of original data on a personal/university/corporate website or websites of small collaborative groups working on a problem
  • Deposit of unpublished sequence data in a public database
  • Preliminary disclosures of research findings as meeting posters, webcast as meeting presentations, or published in abstract form as adjuncts to a meeting, e.g., part of a program
  • Posting of theses and dissertations on a personal/university-hosted website

Availability of materials. By publishing in the journal, the authors agree that, subject to requirements or limitations imposed by laws or governmental regulations of the United States, any materials and data that are reasonably requested by others will be made available. Such materials may include, but are not limited to, DNAs, viruses, microbial strains, mutant animal strains, cell lines, and antibodies that are described in the article. These must be available from a national collection or be made available in a timely fashion, at reasonable cost, and in limited quantities to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.

Similarly, the authors agree to make available computer programs, originating in the authors' laboratory, that are the only means of confirming the conclusions reported in the article but that are not available commercially. The program(s) and suitable documentation regarding its (their) use may be provided by any of the following means: (i) as a program transmitted via the Internet, (ii) as an Internet server-based tool, or (iii) as a compiled or assembled form on a suitable medium. It is expected that the material will be provided in a timely fashion and at reasonable cost to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.

Permissions

The corresponding author is responsible for obtaining permission from both the original author and the original publisher (i.e., the copyright owner) to reproduce or modify figures and tables and to reproduce text (in whole or in part) from previous publications.

Permission(s) must be obtained no later than the modification stage. The original signed permission(s) must be identified as to the relevant item in the ASM manuscript (e.g., “permissions for Fig. 1 in AAC00123-15”) and submitted to the ASM production editor on request. In addition, a statement indicating that the material is being reprinted with permission must be included in the relevant figure legend or table footnote of the manuscript. Reprinted text must be enclosed in quotation marks, and the permission statement must be included as running text or indicated parenthetically.

It is expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted.

For supplemental material intended for posting by ASM (see “Supplemental Material”), if the authors of the AAC manuscript are not also the owners of the supplemental material, the corresponding author must send to ASM signed permission from the copyright owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating in the supplemental material any copyright notices required by the owner.

Authorship

(i) Authorship criteria. ASM journals follow the criteria for authorship as outlined in the International Committee of Medical Journal Editors (ICMJE) Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals (www.icmje.org). Briefly, an author is one who makes a substantial contribution to the design, execution, and/or analysis and interpretation of experiments in addition to drafting, revising, and/or approving the initial submission and any subsequent versions of the article. All authors of a manuscript must have agreed to its submission and are responsible for appropriate portions of its content. Submission of a paper before all coauthors have read and approved it is considered an ethical violation.

(ii) Author contribution statements. As explained in the ICMJE recommendations, all persons designated as authors should qualify for authorship, and all those who qualify should be listed. ASM encourages transparency in authorship by publishing author contribution statements. Authors are strongly encouraged to include such statements in the Acknowledgments section.

(iii) Corresponding author. The corresponding author takes primary responsibility for communicating with the journal and coauthors throughout the submission, peer review, and publication processes. The corresponding author is responsible for ensuring that all coauthors have read and approved submissions, including appropriate citations, acknowledgments, and byline order. Additionally, the corresponding author and the study's primary investigator(s), if different, are required to have examined the raw data represented in the manuscript, affirm that such representations accurately reflect the original data, and ensure that the original data are preserved and retrievable.

(iv) Consortium authorship. A study group, surveillance team, working group, consortium, or the like (e.g., the Active Bacterial Core Surveillance Team) may be listed as a coauthor in the byline if its contributing members satisfy the requirements for authorship and accountability as described in these Instructions. The names (and institutional affiliations, if desired) of the contributing members only may be given as a separate paragraph in the Acknowledgments section. If the contributing members of the group associated with the work do not fulfill the criteria of substantial contribution to and responsibility for the paper, the group may not be listed in the author byline. Instead, it and the names of its contributing members may be listed in the Acknowledgments section.

(v) Professional writers. “Ghost authorship” is not permitted by ASM. Professional writers should be mentioned in the Acknowledgments section rather than be included in the byline. To avoid perceived conflicts of interest, writer affiliations and specific contributions (for example, writing assistance, technical editing, language editing, or proofreading) must be disclosed.

(vi) Nonauthor contributions. Contributions from individuals who do not meet the ICMJE criteria for authorship should be acknowledged in the Acknowledgments section. Those that provided assistance, e.g., supplied strains or reagents or critiqued the paper, should not be listed as authors. Acquisition of funding, data collection, or general supervision of the research group does not qualify a person or persons for authorship. As mentioned above, professional writers do not meet authorship criteria and should be mentioned in the Acknowledgments section. Specific contributions for each nonauthor contributor should be included.

(vii) Byline order and changes. All authors must agree to the order in which their names are listed in the byline. Statements regarding equal contributions by two or more authors (e.g., “C.J. and Y.S. contributed equally to ...”) are permitted as footnotes to bylines and must be agreed to by all of the authors. A change in authorship (order of listing, addition or deletion of a name, or corresponding author designation) after submission of the manuscript will be implemented only after receipt of signed statements of agreement from all parties involved.

(viii) Authorship disputes. Disputes about authorship may delay or prevent review and/or publication of the manuscript. Should the individuals involved be unable to reach an accord, review and/or publication of the manuscript can proceed only after the matter is investigated and resolved by the authors' institution(s) and an official report provided to ASM. ASM does not itself investigate or attempt to resolve authorship disputes but will follow institutional recommendations, as appropriate.

ORCID. ASM Journals is a member of Open Researcher and Contributor ID (ORCID) and publishes author ORCID numbers in articles. ORCID is an open, nonprofit, community-driven effort to create and maintain a registry of unique researcher identifiers; it is a transparent method of linking research activities and output to these identifiers. In the eJournal Press (eJP) submission system, authors are encouraged to use or create an ORCID number, which can be linked to manuscripts and publications for which a researcher serves as an author. This can be helpful in distinguishing authors with common names. Additional information about ORCID is available on ORCID's website.

Conflict of Interest

All authors are expected to disclose, in the manuscript submittal letter, any commercial affiliations as well as consultancies, stock or equity interests, and patent-licensing arrangements that could be considered to pose a conflict of interest regarding the submitted manuscript. (Inclusion of a company name in the author address lines of the manuscript does not constitute disclosure.) Details of the disclosure to the editor will remain confidential. However, it is the responsibility of authors to provide, in the Acknowledgments section, a general statement disclosing conflicting interests relevant to the study. Examples of potentially conflicting interests include relationships, financial or otherwise, that might detract from an author's objectivity in presentation of study results and interests whose value would be enhanced by the results presented. All funding sources for the project, institutional and corporate, should be credited in the Funding Information section, as described below. In addition, if a manuscript concerns a commercial product, the manufacturer's name must be indicated in the Materials and Methods section or elsewhere in the text, as appropriate, in an obvious manner.

Copyright

For authors who do not opt to publish their papers as open access, ASM requires the corresponding author to sign a copyright transfer agreement on behalf of all the authors.

In the copyright transfer agreement signed by an author, ASM grants to that author (and coauthors) the right to republish discrete portions of his/her (their) article in any other publication (print, CD-ROM, and other electronic forms) of which he/she is (they are) the author(s) or editor(s), on the condition that appropriate credit is given to the original ASM publication. This republication right also extends to posting on a host computer to which there is access via the Internet. Except as indicated below, significant portions of the article may not be reprinted/posted without ASM's prior written permission, however, as this would constitute duplicate publication.

Authors may post their own published articles on their personal or university-hosted (but not corporate, government, or similar) websites without ASM's prior written permission provided that appropriate credit is given (i.e., the copyright lines shown at the bottom of the first page of the PDF version).

Works authored solely by U.S. government employees are not subject to copyright protection, so there is no copyright to be transferred. However, the other provisions of the copyright transfer agreement, such as author representations of originality and authority to enter into the agreement, apply to U.S. government employee-authors as well as to other authors.

When funds from the Wellcome Trust or Research Councils UK are used to pay an article open access fee, the article will be published under the Creative Commons Attribution license (CC-BY) in accordance with the funding organization's open access policies. Authors will be required to notify ASM and complete the Author Warranty and Provisional License to Publish at the time of submission.

Copyright for supplemental material (see “Supplemental Material”) remains with the author, but a license permitting the posting by ASM is included in the article copyright transfer agreement. If the author of the article is not also the copyright owner of the supplemental material, the corresponding author must send to ASM signed permission from the owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating into the supplemental material any copyright notices required by the owner.

Funding Agency Repositories

The National Institutes of Health (NIH) requests that its grantee and intramural authors provide copies of their accepted manuscripts to PubMed Central (PMC) for posting in the PMC Public Access Repository. However, AAC authors are automatically in compliance with this policy and need take no action themselves. For the past several years, ASM has deposited in PubMed Central all publications from all ASM journals. Further, ASM policy is that all primary research articles are made available to everyone, free, 6 months after publication through PubMed Central, HighWire, and international PubMed Central-like repositories. By having initiated these policies, ASM is in full compliance with NIH Policy.

ASM also allows AAC authors whose work was supported by funding agencies that have public access requirements like those of the NIH (e.g., the Wellcome Trust) to post their accepted manuscripts in publicly accessible electronic repositories maintained by those funding agencies. If a funding agency does not itself maintain such a site, then ASM allows the author to fulfill that requirement by depositing the manuscript (not the typeset article) in an appropriate institutional or subject-based open repository established by a government or noncommercial entity.

Since ASM makes the final, typeset articles from its primary-research journals available free of charge on the ASM Journals and PMC websites 6 months after final publication, ASM requests that when submitting the accepted manuscript to PMC or a similar public access site, the author specify that the posting release date for the manuscript be no earlier than 6 months after publication of the typeset article by ASM and that a link to the published manuscript on the journal website be provided.

Use of Human Subjects or Animals in Research

Authors of manuscripts describing research involving human subjects or animal experimentation must obtain review and approval (or review and waiver) from their Institutional Review Board (IRB) or Institutional Animal Care and Use Committee (IACUC), as appropriate, prior to manuscript submission. Authors of manuscripts that describe multisite research must obtain approval from each institution’s IRB or IACUC, as appropriate. Documentation of IRB or IACUC status must be made available upon request. In the event that institutional review boards or committees do not exist, the authors must ensure that their research is carried out in accordance with the Declaration of Helsinki, as revised in 2013 (http://www.wma.net/en/30publications/10policies/b3/). A statement of IRB or IACUC approval or waiver (and reason for waiver) or a statement of adherence to the Declaration of Helsinki must be included in the Materials and Methods section.

Patient Identification

Informed consent is not needed if the patient cannot be identified from any material in a manuscript. In the absence of informed consent, identifying details, such as patient initials, specific dates, specific geographic exposures, or other identifying features (including body features in figures), should be omitted, but this must not alter the scientific meaning. Important information that is relevant to the scientific meaning should be stated so that the patient cannot be identified, e.g., by stating a season instead of a date or a region instead of a city. If a patient can be identified from the material in a manuscript, all efforts should be made to obtain informed consent to publish from patients or parents/legal guardians of minors. Informed consent requires that the patient have the opportunity to see the manuscript prior to submission. The written consent must state either that the patient has seen the complete manuscript or that the patient declines to do so. Patient consent should be archived with the authors and be available upon request. A statement attesting the receipt and archiving of written patient consent should be included in the published article.

Nucleotide and Amino Acid Sequences

Newly determined nucleotide and/or amino acid sequence data must be deposited and GenBank/ENA/DDBJ accession numbers must be included in the manuscript no later than the modification stage of the review process. It is expected that the sequence data will be released to the public no later than the publication (online posting) date of the accepted manuscript. The accession numbers should be included in a separate paragraph at the end of the Materials and Methods section for full-length papers or at the end of the text for Short-Form papers. If conclusions in a manuscript are based on the analysis of sequences and a GenBank/ENA/DDBJ accession number is not provided at the time of the review, authors should provide the annotated sequence data as supplemental material not for publication.

It is expected that, when previously published sequence accession numbers are cited in a manuscript, the original citations (e.g., journal articles) will be included in the References section when possible or reasonable.

Authors are also expected to do elementary searches and comparisons of nucleotide and amino acid sequences against the sequences in standard databases (e.g., GenBank) immediately before manuscripts are submitted and again at the proof stage.

Analyses should specify the database, and the date of each analysis should be indicated as, e.g., January 2015. If relevant, the version of the software used should be specified.

See “Presentation of Nucleic Acid Sequences” for nucleic acid sequence formatting instructions.

The URLs of the databases mentioned above are as follows: DNA Data Bank of Japan (DDBJ), http://www.ddbj.nig.ac.jp/; European Nucleotide Archive (ENA), http://www.ebi.ac.uk/ena/; and GenBank, National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/nucleotide.

Proper Use of Locus Tags as Systematic Identifiers for Genes

To comply with recommendations from the International Nucleotide Sequence Database (INSD) Collaborators and to avoid conflicts in gene identification, researchers should implement the following two fundamental guidelines as standards for utilization of locus tags in genome analysis, annotation, submission, reporting, and publication. (i) Locus tag prefixes are systematic gene identifiers for all of the replicons of a genome and as such should be associated with a single genome project submission. (ii) New genome projects must be registered with the INSD, and new locus tag prefixes must be assigned in cooperation with the INSD to ensure that they conform to the agreed-upon criteria.

Structural Determinations

Coordinates for new structures of macromolecules determined by X-ray crystallography or cryo-electron microscopy must be deposited in the Protein Data Bank and assigned identification codes must be included in the manuscript no later than the modification stage of the review process. It is expected that the coordinates will be released to the public no later than the publication (online posting) date of the accepted manuscript. Authors are encouraged to send coordinates with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section for full-length papers or at the end of the text for Short-Form papers.

The URLs for coordinate deposition are http://rcsb-deposit.rutgers.edu/ and http://pdbdep.protein.osaka-u.ac.jp/en/.

Microarray, Next-Generation Sequencing, or Other High-Throughput Functional Genomics Data

The entire set of supporting microarray, next-generation sequencing, or other high-throughput functional genomics data must be deposited in the appropriate public database (e.g., GEO, ArrayExpress, or CIBEX) and the assigned accession number(s) must be included in the manuscript no later than the modification stage of the review process. It is expected that the data will be released to the public no later than the publication (online posting) date of the accepted manuscript. Authors are encouraged to send the relevant data with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section for full-length papers or at the end of the text for Short-Form papers.

The URLs of the databases mentioned above are as follows: Gene Expression Omnibus (GEO), http://www.ncbi.nlm.nih.gov/geo/; ArrayExpress, http://www.ebi.ac.uk/arrayexpress/; and Center for Information Biology Gene Expression Database (CIBEX), http://cibex.nig.ac.jp/data/index.html.

Culture Deposition

AAC expects authors to deposit strains used in therapeutic activity assessments and studies of mechanisms of action, resistance, and cross-resistance in publicly accessible culture collections and to refer to the collections and strain numbers in the text. Since the authenticity of subcultures of culture collection specimens that are distributed by individuals cannot be ensured, authors should indicate laboratory strain designations and donor sources as well as original culture collection identification numbers.

MycoBank

New scientific names of fungi along with key nomenclatural and descriptive material must be deposited in MycoBank (http://www.mycobank.org/) and the assigned accession number(s) must be included in the manuscript no later than the modification stage of the review process. It is expected that the data will be released to the public no later than the publication (online posting) date of the accepted manuscript. Authors are encouraged to send the relevant data with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section for full-length papers and at the end of the text for Short-Form papers.

Supplemental Material

Supplemental material will be peer reviewed along with the manuscript and must be uploaded to the eJournalPress (eJP) peer review system at initial manuscript submission. The decision to publish the material online with the accepted article is made by the editor. It is possible that a manuscript will be accepted but that the supplemental material will not be.

The number of supplemental material files is limited to 10. Supplemental files should be submitted in the following standard formats.

  • Text, figures, tables, and legends should be included in a single PDF file. All figures and tables should be numbered independently and cited at the relevant point in the manuscript text, e.g., "Fig. S1", "Fig. S2","Table S3", etc. Do not duplicate data by presenting them in both the text of the manuscript and a supplemental figure. Each legend should appear below its corresponding figure or table. The maximum file size is 8 MB. Please review this sample file for guidance.
  • Data set (Excel [.xls]) files should include a brief description of how the data are used in the paper. The maximum file size is 20 MB. Please review this sample file for guidance.
  • Movies (Audio Video Interleave [.avi], QuickTime [.mov], or MPEG files) should be submitted at the desired reproduction size and length, and should be accompanied by a legend. The maximum file size is 20 MB.

Unlike the manuscript, supplemental material will not be edited by the ASM Journals staff and proofs will not be made available. References related to supplemental material only should not be listed in the References section of an article; instead, include them with the supplemental material. Supplemental material will always remain associated with its article and is not subject to any modifications after publication.

Material that has been published previously (print or online) is not acceptable for posting as supplemental material. Instead, the appropriate reference(s) to the original publication should be made in the manuscript.

Copyright for the supplemental material remains with the author, but a license permitting the posting by ASM is included in the copyright transfer agreement completed by the corresponding author. If you are not the copyright owner, you must provide to ASM signed permission from the owner that allows posting of the material, as a supplement to your article, by ASM. You are responsible for including in the supplemental material any copyright notices required by the owner.

See also Publication Fees.”

Warranties and Exclusions

Articles published in this journal represent the opinions of the authors and do not necessarily represent the opinions of ASM. ASM does not warrant the fitness or suitability, for any purpose, of any methodology, kit, product, or device described or identified in an article. The use of trade names is for identification purposes only and does not constitute endorsement by ASM.

Submission, Review, and Publication Processes

Submission Process

All submissions to AAC must be made electronically via the eJournalPress (eJP) online submission and peer review system at the following URL: http://aac.msubmit.net/cgi-bin/main.plex. (E-mailed submissions will not be accepted.) First-time users must create an Author account, which may be used for submitting to all ASM journals. Instructions for creating an Author account are available at the above URL via the “help for authors” link, and step-by-step instructions for submitting a manuscript via eJP are also available through the same link on the log-in screen or on the account holder's home page. Information on file types acceptable for electronic submission can be found under the Files heading in the help for authors screen.

Review Process

All manuscripts are considered to be confidential and are reviewed by the editors, members of the editorial board, or qualified ad hoc reviewers. To expedite the review process, authors must recommend at least three reviewers who have expertise in the field, who are not members of their institution(s), who have not recently been associated with their laboratory(ies), and who could not otherwise be considered to pose a conflict of interest regarding the submitted manuscript. Impersonation of another individual during the review process is considered serious misconduct. At least one recommended reviewer must be a member of the journal's editorial board. Please provide, where indicated on the submission form, contact information for suggested reviewers who are not editorial board members.

To facilitate the review, copies of in-press and submitted manuscripts that are important for judgment of the present manuscript should be included as supplemental material not for publication.

When a manuscript is submitted to the journal, it is given a control number (e.g., AAC00123-15) and assigned to one of the editors. (Always refer to this control number in communications with the editor and the Journals Department.) It is the responsibility of the corresponding author to inform the coauthors of the manuscript's status throughout the submission, review, and publication processes. The reviewers operate under strict guidelines set forth in "Guidelines for Reviewers" and are expected to complete their reviews expeditiously.

The corresponding author is notified, generally within 4 to 6 weeks after submission, of the editor's decision to accept, reject, or require modification. When modification is requested, the corresponding author must either submit the modified version within 2 months or withdraw the manuscript. A point-by-point response to the reviews must be uploaded as a separate file (identified as such), and a compare copy of the manuscript (without figures) should be included as a Marked Up Manuscript.

Manuscripts that have been rejected with the option to resubmit, or withdrawn after being returned for modification, may be resubmitted to the same ASM journal if the major criticisms have been addressed. A manuscript rejected on scientific grounds or on the basis of its general suitability for publication by one ASM journal, with the exception of mBio, is considered rejected by all other ASM journals. A rejection from mBio does not disqualify a manuscript from being newly submitted to another ASM journal (the rejection by mBio need not be mentioned in the cover letter). A manuscript rejected solely on the basis of scope may be resubmitted to a more appropriate ASM journal.

The cover letter of every resubmitted manuscript must state that the manuscript is a resubmission, and the former manuscript control number must be provided. A point-by-point response to the review(s) must be uploaded as a separate file (identified as such), and a copy of the revised manuscript tracking the changes must be included as a Marked Up Manuscript. Manuscripts resubmitted to the same journal are normally handled by the original editor. Manuscripts rejected with the option to resubmit may be resubmitted only once unless permission has been obtained from the original editor or from the editor in chief.

Notification of Acceptance

When an editor has decided that a manuscript is acceptable for publication on the basis of scientific merit, the author and the Journals Department are notified. A PDF version of the accepted manuscript is posted online as soon as possible (see "AAC Accepts").

The text files undergo an automated preediting, cleanup, and tagging process specific to the particular article type, and the illustrations are examined. If all files have been prepared according to the criteria set forth in these Instructions and those in the eJP online manuscript submission system, the acceptance procedure will be completed successfully. If there are problems that would cause extensive corrections to be made at the copyediting stage or if the files are not acceptable for production, ASM Journals staff will contact the corresponding author. Once all the material intended for publication has been determined to be adequate, the manuscript is scheduled for the next available issue. The editorial staff of the ASM Journals Department completes the editing of the manuscript to bring it into conformity with prescribed standards.

AAC Accepts (articles that are published online ahead of print)

For its primary-research journals, ASM posts online PDF versions of manuscripts that have been peer reviewed and accepted but not yet copyedited. This feature is called “[journal acronym] Accepts” (e.g., AAC Accepts) and is accessible from the Journals website. The manuscripts are published online as soon as possible after acceptance, on a weekly basis, before the copyedited, typeset articles are published. They are posted “as is” (i.e., as submitted by the authors at the modification stage) and do not reflect ASM editorial changes. No corrections/changes to the PDF manuscripts are accepted. Accordingly, there likely will be differences between the AAC Accepts manuscripts and the final, typeset articles. The manuscripts remain listed on the AAC Accepts page until the final, typeset articles are posted. At that point, the manuscripts are removed from the AAC Accepts page. The manuscripts are under subscription access control until 6 months after the typeset articles are posted, when free access is provided to everyone (subject to the applicable ASM license terms and conditions). Supplemental material intended, and accepted, for publication is not posted until publication of the final, typeset article.

The ASM embargo policy allows a press release to be issued as soon as the accepted manuscript is posted on the AAC Accepts page. To be notified as soon as your manuscript is posted, please sign up for e-Alerts at http://aac.asm.org/cgi/alerts.

Instructions on how to cite such manuscripts may be found in “References.”

Page Proofs

Page proofs, together with a query sheet and instructions for handling proofs, will be made available to the corresponding author electronically. Queries must be answered on the query page, and any changes related to the queries, as well as any additional changes, must be indicated on the proofs. Note that the copy editor does not query at every instance where a change has been made. Queries are written only to request necessary information or clarification of an unclear passage or to draw attention to edits that may have altered the sense. It is the author's responsibility to read the entire text, tables, and figure legends, not just items queried. Corrected proofs must be returned within two business days after notification of availability.

The proof stage is not the time to make extensive corrections, additions, or deletions. Figures as they appear in the proofs are for validation of content and placement, not quality of reproduction or color accuracy. Print output of figures in the PDF page proofs will be of lower quality than the same figures viewed on a monitor. Please avoid making changes to figures based on quality of color or reproduction in proof.

Important new information that has become available between acceptance of the manuscript and receipt of the proofs may be inserted as an addendum in proof with the permission of the editor. If references to unpublished data or personal communications are added, it is expected that written assurance granting permission for the citation will be included. Limit changes to corrections of spelling errors, incorrect data, and grammatical errors and updated information for references to articles that have been submitted or are in press. If URLs have been provided in the article, recheck the sites to ensure that the addresses are still accurate and the material that you expect the reader to find is indeed there.

Questions about late proofs and problems with the proofs should be directed to the ASM Journals Department (email, nlin@asmusa.org.; telephone, 202-942-9231).

PDF Files

A corresponding author who has included an e-mail address in his/her "corresponding author" footnote will have limited access (10 downloads, total) to the PDF file of his/her published article. An e-mail alert will automatically be sent to him/her on the day the issue is posted. It will provide a URL, which will be required to obtain access, and instructions. An article may be viewed, printed, or stored, provided that it is for the author's own use.

Should coauthors or colleagues be interested in viewing the paper for their own use, the corresponding author may provide them with the URL; a copy of the article may not be forwarded electronically. However, they must be made aware of the terms and conditions of the ASM copyright. (For details, go to http://www.journals.asm.org/site/misc/terms.xhtml.) Note that each such download will count toward the corresponding author's total of 10. After 10 downloads, access will be denied and can be obtained only through a subscription to the journal (either individual or institutional) or after the standard access control has been lifted (i.e., 6 months after publication).

Year Published: 

2013