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Organization and Format

Instructions to Authors (PDF)

Summary and Text

On receipt at ASM, the electronic file of an accepted manuscript undergoes an automated preediting, cleanup, and tagging process specific to the particular article type. To optimize this process, manuscripts must be supplied in the correct format and with the appropriate section headings. Consult a recent issue of CMR for format and style.

The title page must include the title, the running title (not to exceed 54 characters and spaces), the name of each author, all authors' affiliations at the time the work was performed, the name(s) and e-mail address(es) of the corresponding author(s), and a footnote indicating the present address of any author no longer at the institution where the work was performed. Place a number sign (#) in the byline after the affiliation letter(s) of the author to whom inquiries regarding the paper should be directed (see “Correspondent footnote”). Indicate each author's affiliation with a superscript lowercase letter placed after the author's surname in the byline (separate multiple affiliation letters with commas but no space). Each affiliation should have its own line and its own superscript affiliation letter preceding it. Do not consolidate different departments at one institution into one address with a single affiliation letter, even if all affected authors belong to all of those departments. Please review this sample title page for guidance. A table of contents showing the major headings and subheadings of the text should follow the title page. Headings and subheadings have the following format:

LEVEL 1 HEAD (flush left, all caps, boldface)

Level 2 Head (flush left, initial caps, boldface)

   Level 3 head. (boldface paragraph lead-in, sentence capitalization)

   (i) Level 4 head. (boldface subparagraph lead-in, sentence capitalization)

   (a) Level 5 head. (lightface italic sub-subparagraph lead-in, sentence capitalization)

The summary, which will be included in the issue table of contents and must be no longer than 250 words, should be placed at the beginning of the electronic file (before the Introduction) with the heading “SUMMARY.” Clinical Microbiology Best Practices articles will have a structured summary without word limitation.

Type every portion of the manuscript double-spaced (a minimum of 6 mm between lines), including figure legends, table footnotes, and References, and number all pages in sequence, including the author biographies, figure legends, and tables. Place the last two items after the References section. Manuscript pages should have continuous line numbers; manuscripts without line numbers may be editorially rejected by the editor, with a suggestion of resubmission after line numbers are added. The font size should be no smaller than 12 points. It is recommended that the following sets of characters be easily distinguishable in the manuscript: the numeral zero (0) and the letter "oh" (O); the numeral one (1), the letter "el" (l), and the letter "eye" (I); and a multiplication sign (×) and the letter “ex.” (x). Do not create symbols as graphics or use special fonts that are external to your word processing program; use the "insert symbol" function. Set the page size to 8.5 by 11 inches (ca. 21.6 by 28 cm). Italicize any words that should appear in italics, and indicate paragraph lead-ins in boldface type (unless they are level 5 heads). Please note that ASM uses the serial comma.

Manuscripts may be editorially rejected, without review, on the basis of poor English or lack of conformity to the standards set forth in these Instructions.

Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language or engage a professional language editing service for help.

Acknowledgments. Statements regarding sources of direct financial support (e.g., grants, fellowships, and scholarships, etc.) should appear in the Acknowledgments. A funding statement indicating what role, if any, the funding agency had in your study (for example, “The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.”) may be included. Funding agencies may have specific wording requirements, and compliance with such requirements is the responsibility of the author. In cases in which research is not funded by any specific project grant, funders need not be listed, and the following statement may be used: “This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.” Statements regarding indirect financial support (e.g., commercial affiliations, consultancies, stock or equity interests, and patent-licensing arrangements) are also allowed. It is the responsibility of authors to provide a general statement disclosing financial or other relationships that are relevant to the study. (See the “Conflict of interest” section.)

References. In the reference list, 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 (see section ii below).

(i) References listed in the References section. The following types of references must be listed in the References section:

  • Journal articles (both print and online)
  • Books (both print and online)
  • Book chapters (publication title is required)
  • Patents
  • Theses and dissertations
  • Published conference proceedings
  • Meeting abstracts (from published abstract books or journal supplements)
  • Letters (to the editor)
  • Company publications
  • In-press journal articles, books, and book chapters
  • Data sets
  • Code

Provide the names of all the authors and/or editors for each reference; long bylines should not be abbreviated with “et al.” All listed references must be cited in the text. Abbreviate journal names according to the PubMed Journals Database (National Library of Medicine, National Institutes of Health), the primary source for ASM style. Do not use periods with abbreviated words. The EndNote output style for ASM Journals’ current reference style can be found http://journals.asm.org/sites/default/files/additional_assets/thumbs/ASM_Journals.ens; click “Open” and then “Download and Install” to save it to your EndNote Styles folder (it should replace any earlier output styles for ASM journals [all ASM journals use the same reference style]). Note that DOIs are not needed for most references. ASM copy editors will automatically insert DOIs on all references in the CrossRef and PubMed databases during copyediting. URLs for government reports and other references not indexed in these databases should be provided if desired; URLs for citations of database accession numbers and code/software should be provided by you.

Follow the styles shown in the examples below.

  1. Caserta E, Haemig HAH, Manias DA, Tomsic J, Grundy FJ, Henkin TM, Dunny GM. 2012. In vivo and in vitro analyses of regulation of the pheromone-responsive prgQ promoter by the PrgX pheromone receptor protein. J Bacteriol 194:3386–3394.
  2. Johnson J, Robinson VR. 2016. Cleavage of JPS-1 in cells infected with human rhinovirus. mSystems 1:e00001-15.
  3. Winnick S, Lucas DO, Hartman AL, Toll D. 2005. How do you improve compliance? Pediatrics 115:e718–e724.
  4. Falagas ME, Kasiakou SK. 2006. Use of international units when dosing colistin will help decrease confusion related to various formulations of the drug around the world. Antimicrob Agents Chemother 50:2274–2275. (Letter.) {“Letter” or “Letter to the editor” is allowed but not required at the end of such an entry.}
  5. Cox CS, Brown BR, Smith JC. J Gen Genet, in press. * {Article title is optional; journal title is mandatory.}
  6. Forman MS, Valsamakis A. 2003. Specimen collection, transport, and processing: virology, p 1227–1241. In Murray PR, Baron EJ, Pfaller MA, Jorgensen JH, Yolken RH (ed), Manual of clinical microbiology, 8th ed. ASM Press, Washington, DC.
  7. da Costa MS, Nobre MF, Rainey FA. 2001. Genus I. Thermus Brock and Freeze 1969, 295,AL emend. Nobre, Trüper and da Costa 1996b, 605, p 404–414. In Boone DR, Castenholz RW, Garrity GM (ed), Bergey’s manual of systematic bacteriology, 2nd ed, vol 1. Springer, New York, NY.
  8. Fitzgerald G, Shaw D. In Waters AE (ed), Clinical microbiology, in press. EFH Publishing Co, Boston, MA. * {Chapter title is optional.}
  9. Green PN, Hood D, Dow CS. 1984. Taxonomic status of some methylotrophic bacteria, p 251–254. In Crawford RL, Hanson RS (ed), Microbial growth on C1 compounds. Proceedings of the 4th International Symposium. American Society for Microbiology, Washington, DC.
  10. Rotimi VO, Salako NO, Mohaddas EM, Philip LP. 2005. Abstr 45th Intersci Conf Antimicrob Agents Chemother, abstr D-1658. {Abstract title is optional.}
  11. Smith D, Johnson C, Maier M, Maurer JJ. 2005. Distribution of fimbrial, phage and plasmid associated virulence genes among poultry Salmonella enterica serovars, abstr P-038, p 445. Abstr 105th Gen Meet Am Soc Microbiol. American Society for Microbiology, Washington, DC. {Abstract title is optional.}
  12. Garcia CO, Paira P, Burgos R, Molina J, Molina JF, Calvo C. 1996. Detection of salmonella DNA in synovial membrane and synovial fluid from Latin American patients. Arthritis Rheum 39(Suppl):S185. {Meeting abstract published in journal supplement.}
  13. O’Malley DR. 1998. PhD thesis. University of California, Los Angeles, CA. {Title is optional.}
  14. Stratagene. 2006. Yeast DNA isolation system: instruction manual. Stratagene, La Jolla, CA. {Use the company name as the author if none is provided for a company publication.}
  15. Odell JC. April 1970. Process for batch culturing. US patent 484,363,770. {Include the name of the patented item/process if possible; the patent number is mandatory.}
  16. Harrison F, Roberts AEL, Gabrilska R, Rumbaugh KP, Lee C, Diggle SP. 2015. A 1,000-year-old antimicrobial remedy with antistaphylococcal activity. mBio 6:e01129-15. {Original article that describes how data submitted to a database were generated.}
  17. Harrison F, Roberts AEL, Gabrilska R, Rumbaugh KP, Lee C, Diggle SP. 2015. Data from "A 1,000-year-old antimicrobial remedy with antistaphylococcal activity." Dryad Digital Repository https://doi.org/10.5061/dryad.mn17p. {Citation for the database where the data in the previous reference were deposited; the URL is necessary.}
  18. Wang Y, Rozen D. 2016. Colonization and transmission of the gut microbiota of the burying beetle, Nicrophorus vespilloides, through development. bioRxiv https://doi.org/10.1101/091702.

*A reference to an in-press ASM publication should state the control number (e.g., CMR00123-18) if it is a journal article or the name of the publication if it is a book.

In some online journal articles, posting or revision dates may serve as the year of publication, and a DOI (preferred) or URL is required for articles with nontraditional page numbers or electronic article identifiers.

Magalon A, Mendel R. 2015. Biosynthesis and insertion of the molybdenum cofactor. EcoSal Plus 2015 doi:10.1128/ecosalplus.ESP-0006-2013.

Note: a posting or accession date is required for any online reference that is periodically updated or changed.

Citations of ASM Accepts manuscripts (articles from other, issue-based ASM journals that are published ahead of the issue) should look like the following example.

Wang GG, Pasillas MP, Kamps MP. 15 May 2006. Persistent transactivation by Meis1 replaces Hox function in myeloid leukemogenesis models: evidence for cooccupancy of Meis1-Pbx and Hox-Pbx complexes on promoters of leukemia-associated genes. Mol Cell Biol doi:10.1128/MCB.00586-06.

Other journals may use different styles for their publish-ahead-of-print manuscripts, but citation entries must include the following information: author name(s), posting date, title, journal title, and volume and page numbers and/or DOI. The following is an example:

Zhou FX, Merianos HJ, Brunger AT, Engelman DM. 13 February 2001, posting date. Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci U S A doi:10.1073/pnas.041593698.

To encourage data sharing and reuse, ASM recommends reporting data sets and/or code both in a dedicated “Data availability” paragraph and in References. The components of a complete data citation include the

  • responsible party (senior author, collector, agency),
  • publication year,
  • complete name of a data set, including the name of the database or repository and its URL, or the name of the analysis software (if appropriate), including the version and project,
  • publisher (if appropriate), and
  • persistent unique identifier(s) (e.g., URL[s] or accession number[s]).

The following templates might be helpful.

Author. Year. Description of study topic. Retrieved from Database URL (accession no. ••••••). {Unpublished raw data.}
Author. Year. Description or title of software (version). Repository URL. Retrieved day month year. {Software or code.}

Examples follow.

Christian SL, McDonough J, Liu C-Y, Shaikh S, Vlamakis V, Badner JA, Chakravarti A, Gershon ES. 2002. Data from “An evaluation of the assembly of an approximately 15-Mb region on human chromosome 13q32-q33 linked to bipolar disorder and schizophrenia.” GenBank https://www.ncbi.nlm.nih.gov/nuccore/AF339794 (accession no. AF339794). {Accession number.}
Sun Z. 2013. Reprocessed: in-depth membrane proteomic study of breast cancer tissues. ProteomeXchange http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=RPXD000665 (accession number requested). {Unassigned accession number.}
Hogle S. 2015. Supplemental material for Hogle et al. 2015 mBio. figshare https://doi.org/10.6084/m9.figshare.1533034.v1. Retrieved 16 March 2017. {Code and/or software.}
Nesbitt HK, Moore JW. 2016. Data from “Species and population diversity in Pacific salmon fisheries underpin indigenous food security.” Dryad Digital Repository https://doi.org/10.5061/dryad.ng8pf. {Data set in repository.}

Manuscript submissions that have appeared in preprint archives should cite the preprint in References, and the fact that a paper has appeared online before should be mentioned parenthetically at the end of the introductory section: (This article was submitted to an online preprint archive [1].) The reference should take the form noted above in reference 18.

(ii) References cited in the text. References that should be cited in the text include the following:

  • Unpublished data
  • Manuscripts submitted for publication
  • Unpublished conference presentations (e.g., a report or poster that has not appeared in published conference proceedings)
  • Personal communications
  • Patent applications and patents pending
  • Computer software, databases, and websites (home pages)

These references should be made parenthetically in the text as follows:

. . . similar results (R. B. Layton and C. C. Weathers, unpublished data).

. . . system was used (J. L. McInerney, A. F. Holden, and P. N. Brighton, submitted for publication).

. . . as described previously (M. G. Gordon and F. L. Rattner, presented at the Fourth Symposium on Food Microbiology, Overton, IL, 13 to 15 June 1989). {For nonpublished abstracts and posters, etc.}

. . . this new process (V. R. Smoll, 20 June 1999, Australian Patent Office). {For non-U.S. patent applications, give the date of publication of the application.}

. . . available in the GenBank database (http://www.ncbi.nlm.nih.gov/Genbank/index.html).

. . . using ABC software (version 2.2; Department of Microbiology, State University [http://www.state.micro.edu]).

URLs for companies that produce any of the products mentioned in your study or for products being sold may not be included in the article. However, company URLs that permit access to scientific data related to the study or to shareware used in the study are permitted.

(iii) Citations in abstracts. Since the abstract must be able to stand apart from the article, references cited in it should be clear without recourse to the References section. Use an abbreviated form of citation, omitting the article title, as follows.

(M. J. Fraser, G. E. Smith, and M. D. Summers, J Virol 47:287–300, 1983)

(J. Scholefield, R. Manson, R. J. Johnston, R. Scott, and M. Spinell, p. 179–183, in R. C. Tilton, ed., Rapid Methods and Automation in Microbiology, 1981)

“. . . the recent report of A. K. Datta and J. S. Pagano (Antimicrob Agents Chemother 24:10–14, 1983) . . .”

When necessary, this style should also be used for references cited in legends for supplemental material and in Addenda in Proof.

(iv) References related to supplemental material. If references must be cited in the supplemental material, list them in a separate References section within the supplemental material and cite them by those numbers; do not simply include citations of numbers from the reference list of the associated article. If the same reference(s) is to be cited in both the article itself and the supplemental material, then that reference would be listed in both References sections.

Author Biographies

Corresponding authors should submit a short biographical sketch and photo for each author for publication with the article. Biographical information should be submitted at the modification stage.

  • The text limit is 150 words for each author and should include WHO you are (your name), WHERE you received your education, WHAT positions you have held and at WHICH institutions, WHERE you are now (your current institution), WHY you have this interest, and HOW LONG you have been in this field.
  • The photo should be a black-and-white head shot of passport size. Photos will be reduced to approximately 1.125 inches wide by 1.375 inches high. Photos must meet the production criteria for regular figures and should be checked for production quality by using Rapid Inspector, provided at the following URL: http://rapidinspector.cadmus.com/RapidInspector/zmw/index.jsp.
  • To submit, upload the text and photos with your modified manuscript in the eJP online manuscript submission and peer review system. Include the biographical text after the References section of your manuscript, in the same file. Upload the head shots in the submission system as “Bio Photo” files; include the author’s name or enough of it for identification in each photo’s file name.

Contact the scientific editor if you have questions about what to write. Contact the production editor if you have questions about submitting your files.

Correspondent Footnote

The e-mail address for the corresponding author should be included on the title page of the manuscript. This information will be published in the article as a footnote to facilitate communication and will be used to notify the corresponding author of the availability of proofs and, later, of the PDF file of the published article. No more than two authors may be designated corresponding authors.