Editorial Policy and 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 December 2014.
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.
Use of Microbiological Information
The Council on Microbial Sciences (COMS) 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 COMS resolution mentioned above. Members of the ASM Journals Committee will evaluate the rare manuscript that might raise such issues during the evaluation process. However, as indicated elsewhere in these Instructions, 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 Agents and Toxins List on the CDC website and the U.S. Government Policy for Oversight of Life Sciences Dual Use Research of Concern (March 2012).
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, and/or the "International Guiding Principles for Biomedical Research Involving Animals," as revised by the International Council for Laboratory Animal Science (ICLAS) and the Councils for International Organizations of Medical Sciences (CIOMS) in 2012. A statement of IRB or IACUC approval or waiver (and reason for waiver) or a statement of adherence to the Declaration of Helsinki as revised in 2013, and/or the “International Guiding Principles for Biomedical Research Involving Animals,” as revised by the International Council for Laboratory Animal Science (ICLAS) and the Councils for International Organizations of Medical Sciences (CIOMS) in 2012. A statement of IRB or IACUC approval or waiver (and reason for waiver) or a statement of adherence to the Declaration of Helsinki and/or Guiding Principles must be included in the text. The sex of research subjects and animals, and of materials derived directly from them (e.g., primary cell lines and clinical samples), should be included if these data are available.
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, 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.
Publishing Ethics
Authorship. 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 (“Defining the Role of Authors and Contributors”). 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.
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.
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.
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.
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 (e.g., writing assistance, technical editing, language editing, or proofreading) must be disclosed.
Nonauthor contributions. Contributions from individuals who do not meet the ICMJE criteria for authorship should be acknowledged in the Acknowledgments section. Those who 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.
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.
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 eJournalPress (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.
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 Office of Research Integrity 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 journal-wide submission 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 disclose 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. ASM encourages authors to consult COPE’s "Code of Conduct and Best Practice Guidelines for Journal Editors." 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.
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. Publication of an announcement does not preclude a later publication (e.g., a full comparative analysis) on the same organism in an ASM journal. 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 a related manuscript file. Whether the material constitutes the substance of a paper and therefore renders the manuscript unacceptable for publication is an editorial decision.
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 (but see “Preprint policy,” below)
- 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
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 Sources section of the submission form (see "Acknowledgments" below). In addition, if a manuscript concerns a commercial product, the manufacturer’s name must be indicated in the text in an obvious manner.
Data and Materials
Availability of data and materials. By publishing in MRA, the authors agree that, subject to requirements or limitations imposed by local and/or U.S. Government laws and regulations, any materials and data that are reasonably requested by others are available from a publicly accessible collection or will be made available in a timely fashion, at reasonable cost, and in limited quantities to members of the scientific community for noncommercial purposes. Similarly, the authors agree to make available computer programs and/or code, originating in the authors' laboratory, reported in the article but that is 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 form on a suitable medium. 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. ASM asks authors to assert this in a "Data availability" paragraph at the end of the text of their submitted manuscript. Therefore, a condition of publication in MRA is that authors make data fully available and without restriction, except in rare circumstances. Data availability will be confirmed at submission. See our Data Policy.
Authors should provide the following in a "Data availability" paragraph at the end of the text of their submitted manuscript: data description, name(s) of the repositories, and digital object identifiers (DOIs) or accession numbers.
Data citation. To promote reproducibility, ASM expects researchers to identify and cite data sets and/or code used in their experiments and studies. These may be large or complex data sets that can include, but are not limited to, data from microarray, genomic, structural, proteomic, or video imaging analyses. Authors should cite both the data set repository and the published article in which the data set and/or code was originally described. Citations of data should be included in the reference list with persistent unique identifiers (e.g., active URLs, accession numbers, etc.). If computer code or software was created to generate results or interpret data, then a statement to that effect should be included in the “Data availability” paragraph. For cases in which the software is publicly available (e.g., FigTree to generate phylogenetic trees), the URL of the software informational page should be provided. It is preferred that authors use established, publicly available data type-specific repositories. If there is no appropriate repository available, general publicly available repositories should be used (e.g., Dryad, figshare, etc.). Examples of proper data citation are included in the "References" section of these Instructions to Authors.
Culture deposition. MRA expects authors, where possible, to deposit important strains 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.
Nucleotide and amino acid sequences. Newly determined nucleotide sequence data must be deposited in one of the following publicly available databases: DNA Data Bank of Japan (DDBJ), http://www.ddbj.nig.ac.jp/; European Nucleotide Archive (ENA), http://www.ebi.ac.uk/ena/; or GenBank, National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/nucleotide. GenBank/ENA/DDBJ accession numbers must be included in the Genome Announcement at the time of submission. It is expected that the sequence data will be released to the public at the time of submission. Communication from the relevant database confirming public data availability must be included with the initial submission as a Data Release Email file. Announcements will not be considered for publication until the availability of the data or of the sequence(s) in GenBank/ENA/DDBJ has been verified. The accession number(s) should be included in a separate paragraph at the end of the announcement.
It is expected that, when previously published sequence accession numbers are cited in a manuscript, the original published article(s), as well as a citation of the database where the accession number is deposited, will be included in the References section.
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 INSD, and new locus tag prefixes must be assigned in cooperation with INSD to ensure that they conform to the agreed-upon criteria.
Copyright
Copyright of all material published in MRA remains with the authors. The authors grant the American Society for Microbiology a nonexclusive license to publish their work if it is accepted. Upon publication, the work becomes available to the public to copy, distribute, or display under a Creative Commons Attribution 4.0 International license (CC BY 4.0). Please contact the corresponding author to obtain permission for reuse of MRA content.
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 content (in whole or in part) from previous publications. Reprinted text must be enclosed in quotation marks, and the permission statement must be included as running text or incorporated parenthetically.
It is expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted.
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.