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JOURNAL OF CLINICAL MICROBIOLOGY

2006 INSTRUCTIONS TO AUTHORS*

SCOPE

The Journal of Clinical Microbiology (JCM) is devotedto the dissemination of new knowledge concerning themicrobiological aspects of human and animal infectionsand infestations, particularly their etiological agents, di-agnosis, and epidemiology. Case Reports will be consid-ered if they are novel, add to existing knowledge, and areoriented toward microbiology. (See p. 10 for a descrip-tion of the two different types of Case Reports pub-lished.) Manuscripts which describe members of the‘‘normal’’ human microbiota which become involved indisease production or complication and manuscriptsdealing with the interactions of hospitalized patients andthe microbial environment of the hospital may also besubmitted for consideration.

ASM publishes a number of different journals cover-ing various aspects of the field of microbiology. Eachjournal has a prescribed scope which must be consid-ered in determining the most appropriate journal foreach manuscript. The following guidelines may be ofassistance.

(i) JCM will consider manuscripts (a) that describe theuse of antimicrobial, antiparasitic, or anticancer agentsas tools in the isolation, identification, or epidemiologyof microorganisms associated with disease; (b) that areconcerned with quality control procedures for diffusion,elution, or dilution tests for determining susceptibilitiesto antimicrobial agents in clinical laboratories; and (c)that deal with applications of commercially preparedtests or kits to assays performed in clinical laboratoriesto measure the activities of established antimicrobialagents or their concentrations in body fluids. Manu-scripts on all other aspects of antimicrobial or antipar-asitic agents, including reports concerned with develop-ment or modification of assay methods and validation oftheir sensitivity and specificity, will be considered forpublication in Antimicrobial Agents and Chemotherapy.

(ii) JCM will consider manuscripts dealing with theisolation or identification of viral agents from humansand animals, with viral pathogenesis and immunity, andwith the etiology and diagnosis of viral diseases. Inaddition, epidemiological studies of viral diseases orthose involving the use of bacteriophages as a typingsystem or to identify bacteria will be considered. How-ever, papers on the biology of phages and other virusesare more appropriate for the Journal of Virology or theJournal of Bacteriology.

(iii) Reports of clinical microbiology investigations orstudies of the hospital population and the environmentas they relate to nosocomial infections should be sub-mitted to JCM. Manuscripts dealing with ecology or

environmental studies or with the application of micro-organisms to agricultural or industrial processes aremore appropriate for Applied and EnvironmentalMicrobiology.

(iv) Papers involving clinical immunology, vaccines, orassessment and laboratory diagnostic aspects of immu-nologic diseases (e.g., autoimmune diseases and primaryimmunodeficiencies) are more appropriate for Clinicaland Vaccine Immunology (formerly Clinical and Diagnos-tic Laboratory Immunology). Manuscripts dealing withmechanisms of pathogenicity are appropriate for Infec-tion and Immunity.

(v) Manuscripts that describe detection of infectiousagents by using already well described techniques (e.g.,RT-PCR, RAPD, PFGE, real-time PCR, etc.) will notbe considered for publication unless application of thetechnique substantially improves the diagnostic process.It is expected that such manuscripts will compare sensitiv-ity, specificity, and accuracy data with data obtained frommore conventional methods using clinical specimens.

(vi) JCM will consider manuscripts that describe di-agnostic microbiology assays and those that compareassay performance. To improve the accuracy and ensurethe completeness of their studies, authors should referto the Standards for Reporting of Diagnostic Accuracy(STARD) for guidance. The entire set of guidelines,including checklists, may be found at http://www.consort-statement.org/stardstatement.htm.

Questions about these guidelines may be directed tothe editor in chief of the journal being considered.

If transfer to another ASM journal is recommendedby an editor, the corresponding author will be contacted.

Note that a manuscript rejected by one ASM journalon scientific grounds or on the basis of its general suit-ability for publication is considered rejected by all otherASM journals.

EDITORIAL POLICY

Use of Microbiological Information

The Council Policy Committee (CPC) of the Ameri-can Society for Microbiology affirms the long-standingposition of the Society that microbiologists will work forthe proper and beneficent application of science and willcall to the attention of the public or the appropriateauthorities misuses of microbiology or of informationderived from microbiology. ASM members are obligatedto discourage any use of microbiology contrary to thewelfare of humankind, including the use of microbes asbiological weapons. Bioterrorism violates the fundamen-tal principles expressed in the Code of Ethics of theSociety and is abhorrent to ASM and its members.

ASM recognizes that there are valid concerns regard-ing the publication of information in scientific journals

* Shading indicates material that has been added or significantlyupdated.

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JOURNAL OF CLINICAL MICROBIOLOGY, Jan. 2006, p. 1–19 Vol. 44, No. 10095-1137/06/$08.00�0 doi:10.1128/JCM.44.1.1–19.2006Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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that could be put to inappropriate use as described in theCPC resolution mentioned above. Members of the ASMPublications Board will evaluate the rare manuscriptthat might raise such issues during the review process.However, as indicated elsewhere in these Instructions,research articles must contain sufficient detail, and ma-terial/information must be made available, to permit thework to be repeated by others. Supply of materialsshould be in accordance with laws and regulations gov-erning the shipment, transfer, possession, and use ofbiological materials and must be for legitimate, bona fideresearch needs. Links to, and information regarding,these laws and regulations can be found at http://www.asm.org/Policy/index.asp.

General Requirements

Manuscripts submitted to the journal must representreports of original research, and the original data mustbe available for review by the editor if necessary.

All authors of a manuscript must have agreed to itssubmission and are responsible for its content (initialsubmission and any subsequent versions), including ap-propriate citations and acknowledgments, and must alsohave agreed that the corresponding author has the au-thority to act on their behalf in all matters pertaining topublication of the manuscript. The corresponding au-thor is responsible for obtaining such agreements andfor informing the coauthors of the manuscript’s statusthroughout the submission, review, and publication pro-cess. For Authors’ Corrections and Retractions, signedletters of agreement from all of the authors must besubmitted (see p. 12).

By submission of a manuscript to the journal, theauthors guarantee that they have the authority to pub-lish the work and that the manuscript, or one withsubstantially the same content, was not published pre-viously, is not being considered or published elsewhere,and was not rejected on scientific grounds by anotherASM journal.

It is expected that the authors will provide writtenassurance that permission to cite unpublished data orpersonal communications has been granted.

By publishing in the journal, the authors agree thatany DNAs, viruses, microbial strains, mutant animalstrains, cell lines, antibodies, and similar materialsnewly described in the article are available from a na-tional collection or will be made available in a timelyfashion, at reasonable cost, and in limited quantities tomembers of the scientific community for noncommercialpurposes. The authors guarantee that they have theauthority to comply with this policy either directly or bymeans of material transfer agreements through theowner.

Similarly, the authors agree to make available com-puter programs, originating in the authors’ laboratory,that are the only means of confirming the conclusionsreported in the article but that are not available com-mercially. The program(s) and suitable documentationregarding its (their) use may be provided by any of the

following means: (i) as a program transmitted via theInternet, (ii) as an Internet server-based tool, or (iii) asa compiled or assembled form on a suitable medium(e.g., magnetic or optical). It is expected that the mate-rial will be provided in a timely fashion and at reason-able cost to members of the scientific community fornoncommercial purposes. The authors guarantee thatthey have the authority to comply with this policy eitherdirectly or by means of material transfer agreementsthrough the owner.

Primary Publication

A scientific paper or its substance published in a serial,periodical, book, conference report, symposium pro-ceeding, or technical bulletin, posted on a nonpersonalwebsite, or made available through any other retrievablesource, including CD-ROM and other electronic forms,is unacceptable for submission to an ASM journal ongrounds of prior publication.

Posting of a method/protocol on a nonpersonal web-site should not interfere with the author’s ability to havea manuscript utilizing that technique considered for pub-lication in an ASM journal; however, ultimately, it is aneditorial decision whether the method constitutes thesubstance of a paper.

Posting of a limited amount of original data on apersonal/university/company website or websites ofsmall collaborative groups working on a problem doesnot preclude subsequent submission to, and publicationby, an ASM journal. The posted data, however, may notconstitute the substance of the submission. Specificquestions about this policy may be referred to the Pub-lications Board chairman on a case-by-case basis. Post-ing of theses and dissertations on a personal/university-hosted website does not preclude subsequent submissionto, and publication by, an ASM journal.

Posting of unpublished sequence data on the Internetis usually not considered prior publication; however, theaddress (URL) of the source of the sequence should beincluded in the text.

Preliminary disclosures of research findings webcastas meeting presentations or published in abstract formas adjuncts to a meeting, e.g., part of a program, are notconsidered prior publication.

It is incumbent upon the author to acknowledge anyprior publication, including his own articles, of the datacontained in a manuscript submitted to an ASM journal.A copy of the relevant work should be submitted withthe paper as supporting material.

Ultimately, it is an editorial decision whether the ma-terial constitutes the substance of a paper.

Permissions

The corresponding author is responsible for obtainingpermission from both the original author and the originalpublisher (i.e., the copyright owner) to reproduce ormodify figures (including maps) and tables and to repro-duce text (in whole or in part) from previous publications.

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The original signed permission(s) must be submitteddirectly to the editor, outside the Rapid Review system,no later than the modification stage and should be iden-tified as to the relevant item in the ASM manuscript(e.g., ‘‘permissions for Fig. 1 in JCM00123-06’’). In ad-dition, a statement indicating that the material is beingreprinted with permission must be included in the rele-vant figure legend or table footnote of the manuscript.Reprinted text must be enclosed in quotation marks, andthe permission statement must be included as runningtext or indicated parenthetically.

For supplemental material intended for posting byASM (see p. 5), if the authors of the JCM manuscriptare not also the owner of the supplemental material, thecorresponding author must send to ASM signed permis-sion from the copyright owner that allows posting of thematerial, as a supplement to the article, by ASM. Thecorresponding author is also responsible for incorporat-ing in the supplemental material any copyright noticesrequired by the owner.

Authorship

An author is one who made a substantial contributionto the overall design and execution of the experiments;therefore, ASM considers all authors responsible forthe entire paper. Individuals who provided assistance,e.g., supplied strains or reagents or critiqued the paper,need not be listed as authors but may be recognized inthe Acknowledgments section.

A study group, surveillance team, working group, con-sortium, or the like (e.g., the Active Bacterial Core Sur-veillance Team) may be listed as a coauthor in the bylineif its contributing members satisfy the requirements forauthorship and accountability as described in these In-structions. The names (and institutional affiliations ifdesired) of the contributing members only may be givenin a footnote keyed to the study group name in the bylineor as a separate paragraph in the Acknowledgmentssection.

If the contributing members of the group associatedwith the work do not fulfill the criteria of substantialcontribution to and responsibility for the paper, thegroup may not be listed in the author byline. Instead, itand the names of its contributing members may be listedin the Acknowledgments section.

All authors must agree to the order in which theirnames are listed in the byline. Statements regardingequal contributions by two or more authors (e.g., X.J.and Y.S. contributed equally to . . .) are permitted asfootnotes to bylines. Other statements of attribution maybe included in the Acknowledgments section.

A change in authorship (order of listing or addition ordeletion of a name) after submission of the manuscriptwill be implemented only after receipt of signed state-ments of agreement from all parties involved. Disputesabout authorship may delay review and/or publication ofthe manuscript.

Conflict of Interest

All authors are expected to disclose, in the manuscriptsubmittal letter, any commercial affiliations as well asconsultancies, stock or equity interests, and patent-licensing arrangements that could be considered to posea conflict of interest regarding the submitted article.(Inclusion of a company name in the author addresslines of the manuscript does not constitute disclosure.)Details of the disclosure to the editor will remain con-fidential. However, it is the responsibility of authors toprovide, in the Acknowledgments section, a generalstatement disclosing financial or other relationships thatare relevant to the study. Examples of potentially con-flicting interests that should be disclosed include rela-tionships that might detract from an author’s objectivityin presentation of study results, and interests whosevalue would be enhanced by the results presented. Allfunding sources for the project, institutional and corpo-rate, should be credited in the Acknowledgments sec-tion, as described below. In addition, if a manuscriptconcerns a commercial product, the manufacturer’sname must be indicated in the Materials and Methodssection or elsewhere in the text, as appropriate, in anobvious manner.

Copyright

To maintain and protect the Society’s ownership andrights and to continue to afford scientists the opportunityto publish in high-quality journals, ASM requires thecorresponding author to sign a copyright transfer agree-ment on behalf of all the authors. This agreement is sentto the corresponding author when the manuscript is ac-cepted and scheduled for publication. Unless this agree-ment is executed (without changes and/or addenda),ASM will not publish the manuscript.

In the copyright transfer agreement signed by an au-thor, ASM grants to that author (and coauthors) theright to republish discrete portions of his (their) article inany other publication (print, CD-ROM, and other elec-tronic forms) of which he is (they are) the author(s) oreditor(s), on the condition that appropriate credit is givento the original ASM publication. This republication rightalso extends to posting on a host computer to whichthere is access via the Internet. Except as indicated be-low, significant portions of the article may not be reprint-ed/posted without ASM’s prior written permission, how-ever, as this would constitute duplicate publication.

Authors may post their own published articles on theirpersonal or university-hosted (but not corporate, govern-ment, or similar) websites without ASM’s prior writtenpermission provided that appropriate credit is given (i.e.,either the copyright lines shown on the top of the firstpage of the PDF version or “Copyright © AmericanSociety for Microbiology, [insert journal name, volumenumber, page numbers, and year]” for the HTML version).

The copyright transfer agreement asks that authorswho were U.S. Government employees and who wrotethe article as part of their employment duties be identi-

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fied. This is because works authored solely by such U.S.Government employees are not subject to copyright pro-tection, so there is no copyright to be transferred. Theother provisions of the copyright transfer agreement,such as author representations of originality and author-ity to enter into the agreement, apply to U.S. Govern-ment employee-authors as well as to other authors.

Copyright for supplemental material (see p. 5) re-mains with the author, but a license permitting the post-ing by ASM will be sent, along with the article copyrighttransfer agreement, to the corresponding author forsigning at the acceptance stage. (If the author of thearticle is not also the copyright owner of the supplemen-tal material, the corresponding author must send toASM signed permission from the owner that allows post-ing of the material, as a supplement to the article, byASM. The corresponding author is also responsible forincorporating into the supplemental material any copy-right notices required by the owner.)

Funding Agency Repositories

The National Institutes of Health (NIH) requests thatits grantee and intramural authors provide copies oftheir accepted manuscripts to PubMed Central (PMC)for posting in the PMC Public Access Repository. ASMallows such JCM authors to do so. ASM also allows JCMauthors whose work was supported by similar fundingagencies that have public access requirements like thoseof NIH (e.g., the Wellcome Trust) to post their acceptedmanuscripts in publicly accessible electronic reposito-ries maintained by those funding agencies. If a fundingagency does not itself maintain such a site, then ASMallows the author to fulfill that requirement by deposit-ing the manuscript (not the typeset article) in an appro-priate institutional or subject-based open repository es-tablished by a government or noncommercial entity.

Since ASM makes the final, typeset articles from itsprimary-research journals available free of charge on theASM Journals and PMC websites 6 months after finalpublication, ASM recommends that when submitting theaccepted manuscript to PMC or similar public accesssite, the author specify that the posting release date forthe manuscript be no earlier than 6 months after pub-lication of the typeset article by ASM.

Use of Human Subjects or Animals in Research

The use of human subjects or other animals for re-search purposes is regulated by the federal governmentand individual institutions. Manuscripts containing in-formation related to human or animal use should clearlystate that the research has complied with all relevantfederal guidelines and institutional policies. Copies ofthese guidelines and policy statements must be availablefor review by the editor if necessary.

Patient Identification

To protect the privacy of individuals mentioned inclinical studies, in case histories, and as sources of iso-

lates, do not identify them by their initials, even as partof a strain designation. Change the initials to numeralsor use randomly chosen letters. Do not give hospital unitnumbers; if a designation is needed, use only the last twodigits of the unit. (Note: Established designations ofsome viruses and cell lines, although they consist ofinitials, are acceptable [e.g., JC virus, BK virus, andHeLa cells].)

Nucleotide and Amino Acid Sequences

It is expected that newly determined nucleotideand/or amino acid sequence data will be deposited andGenBank/EMBL/DDBJ accession numbers will be in-cluded in the manuscript no later than the modificationstage of the review process. It is also expected that thesequence data will be released to the public no later thanthe publication date of the article. The accession num-bers should be included in a separate paragraph at theend of the Materials and Methods section for full-lengthpapers or at the end of the text for Notes. If conclusionsin a manuscript are based on the analysis of sequencesand a GenBank/EMBL/DDBJ accession number is notprovided at the time of the review, authors should pro-vide the sequence data as supplemental material.

It is expected that, when previously published se-quence accession numbers are cited in a manuscript,the original citations (e.g., journal articles) will beincluded in the References section when possible orreasonable.

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

Analyses should specify the database, and the date ofeach analysis should be indicated in the format MM/YY.If relevant, the version of the software used should bespecified.

See p. 14 for nucleic acid sequence formatting instruc-tions.

The URLs of the databases mentioned above are asfollows: DNA Data Bank of Japan (DDBJ), http://www.ddbj.nig.ac.jp; EMBL Nucleotide Sequence Submission(EMBL), http://www.ebi.ac.uk; and GenBank, NationalCenter for Biotechnology Information (GenBank), http://www.ncbi.nlm.nih.gov.

Structural Determinations

It is expected that coordinates for new structures ofmacromolecules will be deposited in the Protein DataBank and that assigned identification codes will be in-cluded in the manuscript no later than the modificationstage of the review process. It is also expected that thecoordinates will be released to the public no later thanthe publication date of the article. Authors are encour-aged to send coordinates with their original submission,however, so that reviewers can examine them along withthe manuscript. The accession number(s) should be



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listed in a separate paragraph at the end of the Materialsand Methods section for full-length papers or at the endof the text for Notes.

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

Microarray Data

It is expected that the entire set of supporting mi-croarray data will be deposited in the appropriate publicdatabase (e.g., GEO, ArrayExpress, or CIBEX) and thatthe assigned accession number(s) will be included in themanuscript no later than the modification stage of thereview process. It is also expected that the data will bereleased to the public no later than 6 months after pub-lication of the typeset article. Authors are encouraged tosend the relevant data with their original submission,however, so that reviewers can examine them along withthe manuscript. The accession number(s) should belisted in a separate paragraph at the end of the Materialsand Methods section for full-length papers or at the endof the text for Notes.

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

Culture Deposition

JCM expects authors to deposit important strains inpublicly accessible culture collections and to refer to thecollections and strain numbers in the text. Since theauthenticity of subcultures of culture collection speci-mens that are distributed by individuals cannot be en-sured, authors should indicate laboratory strain designa-tions and donor sources as well as original culturecollection identification numbers.

Supplemental MaterialSupplemental material intended for posting by ASM

may not include additional figures or tables that simplysupport the authors’ conclusions. It must be restricted tolarge or complex data sets or results that cannot bereadily displayed in printed form because of space ortechnical limitations. Such material may include datafrom microarray, structural, biochemical, or video imag-ing analyses. In such cases, the manuscript submitted forreview should include a distillation of the results so thatthe principal conclusions are fully supported withoutreferral to the supplemental material.

Supplemental material intended for posting by ASMmust be uploaded in Rapid Review and will be reviewedalong with the manuscript. The decision to publish (i.e.,post online only) the material with the article if it isaccepted will be made by the editor and conveyed to thecorresponding author in the acceptance e-mail. Note,therefore, it is possible that an article will be accepted

but that the supplemental material will not be.If the software required for users to view/use the sup-

plemental material is not embedded in the file, you areurged to use shareware or generally available/easily ac-cessible programs.

Unlike the article, supplemental material will not beedited by the ASM Journals staff and proofs will not bemade available.

Supplemental material will always remain associatedwith its article and is not subject to any modificationsafter publication. Material that has been published pre-viously (print or online) is not acceptable for posting assupplemental data. Instead, the appropriate reference(s)to the original publication should be made in the articletext.

Copyright for the supplemental material remains withthe author, but a license permitting the posting by ASMwill be sent, along with the article copyright transferagreement, to the corresponding author for signing. Ifyou are not the copyright owner, you must provide toASM signed permission from the owner that allows post-ing of the material, as a supplement to your article, byASM. You are responsible for including in the supple-mental material any copyright notices required by theowner.

A one-time charge (amount not yet determined) maybe levied for posting of supplemental material. Wheninstituted, the charge will be indicated in the ASM ac-ceptance letter.

Compliance

Failure to comply with the policies described in theseInstructions may result in a letter of reprimand, a sus-pension of publishing privileges in ASM journals, and/ornotification of the authors’ institutions.

Warranties and Exclusions

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

Page Charges

Authors whose research was supported by grants, spe-cial funds (including departmental and institutional), orcontracts (including governmental) or whose researchwas done as part of their official duties (government,corporate, etc.) are required to pay page charges.

For a corresponding author who is an ASM member,page charges are currently $65 per page for the first sixpages and $200 per page for each page in excess of six(subject to change without notice). To obtain the mem-ber rate, the corresponding author must be an ASMmember.



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For a nonmember corresponding author, pagecharges are currently $75 per page for the first six pagesand $250 for each page in excess of six. A correspondingauthor who is not an ASM member may join ASM toobtain the member rate.

If the research was not supported by any of the meansdescribed above, a request to waive the charges may bemailed (Journals Department, ASM, 1752 N St., N.W.,Washington, DC 20036-2904, USA) or faxed (202-942-9355) to the Journals Department. This request mustindicate how the work was supported and should beaccompanied by copies of the title page and Acknowl-edgments section.

Minireviews, Guest Commentaries, and CommentLetters to the Editor are not subject to page charges.New-Data Letters to the Editor and fast-track articlesare subject to page charges.

Editorial Style

The editorial style of ASM journals conforms to theASM Style Manual for Journals (American Society forMicrobiology, 2006, in-house document) and How ToWrite and Publish a Scientific Paper, 5th ed. (Oryx Press,1998), as interpreted and modified by the editors and theASM Journals Department.

The editors and the Journals Department reserve theprivilege of editing manuscripts to conform with thestylistic conventions set forth in the aforesaid publica-tions and in these Instructions.

Review Process

All manuscripts are considered to be confidential andare reviewed by the editors, members of the editorialboard, or qualified ad hoc reviewers. To expedite thereview process, authors should recommend at least tworeviewers who are not members of their institution(s)and have never been associated with them or their labo-ratory(ies); please provide their contact informationwhere indicated on the submission form.

Copies of in-press and submitted manuscripts that are im-portant for judgment of the present manuscript should beincluded as supporting material to facilitate the review.

When a manuscript is submitted to the journal, it isgiven a number (e.g., JCM00047-06 version 1) and as-signed to one of the editors. (Always refer to this num-ber in communications with the editor and the JournalsDepartment.) It is the responsibility of the correspondingauthor to inform the coauthors of the manuscript’s statusthroughout the submission, review, and publication pro-cesses. The reviewers operate under strict guidelines setforth in “Guidelines for the Reviewers” (http://www.journals.asm.org/misc/reviewguide.shtml) and are ex-pected to complete their reviews expeditiously.

The corresponding author is notified, generally within4 to 6 weeks after submission, of the editor’s decision toaccept, reject, or require modification. When modifica-tion is requested, the corresponding author must eithersubmit the modified version within 2 months or with-

draw the manuscript. A point-by-point response to thereviews must be provided in the Rebuttal section of theRapid Review submission form for the revised manu-script, and a compare copy of the manuscript (withoutfigures) should be included as supporting material if theeditor requested one.

Manuscripts that have been rejected, or withdrawnafter being returned for modification, may be resubmit-ted if the major criticisms have been addressed. (Note: Amanuscript rejected by one ASM journal on scientificgrounds or on the basis of its general suitability forpublication is considered rejected by all other ASMjournals.) The cover letter must state that the manu-script is a resubmission, and the former manuscript num-ber should be provided in the appropriate field on thesubmission form. A point-by-point response to the re-views and a compare copy of the revised manuscriptshowing the changes must be included as supportingmaterial (the Rebuttal section appears in the submissionform only if the manuscript is a modification). Resub-mitted manuscripts are normally handled by the originaleditor.

Rejected manuscripts may be resubmitted only onceunless permission has been obtained from the originaleditor or from the editor in chief.

Notification of Acceptance

When an editor has decided that a manuscript is ac-ceptable for publication on the basis of scientific merit,the author and the Journals Department are notified.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 beenprepared according to the criteria set forth in theseInstructions and those in Rapid Review, the acceptanceprocedure will be completed successfully. If there areproblems that would cause extensive corrections to bemade at the copyediting stage or if the files are notacceptable for production, ASM Journals staff will con-tact the corresponding author.

Once all the material intended for publication hasbeen determined to be adequate, the manuscript isscheduled for the next available issue and an acceptanceletter indicating the month of publication, approximatepage proof dates, and table of contents section is mailedto the corresponding author; a copyright transfer agree-ment is also included, as is a license to permit posting ofsupplemental material (if applicable). The editorial staffof the ASM Journals Department completes the editingof the manuscript to bring it into conformity with pre-scribed standards.

Page Proofs

Page proofs, together with a query sheet and instruc-tions for handling proofs, will be made available to thecorresponding author electronically via a PDF file thatcan be accessed through a unique password. Since cor-responding authors will be notified of the availability of



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their PDF proofs, instructed how to access informationabout page charges, reprints, and color figure charges (ifapplicable), and assigned their unique password via e-mail, an e-mail address must be supplied in the corre-spondent footnote. Failure to do so may result in a delayin publication. The PDF page proofs must be printedout, and corrections must be written on the hard copy.Queries must be answered on the query page or on aseparate sheet of paper, and any changes related to thequeries must be indicated on the proofs. Note that thecopy editor does not query at every instance where achange has been made. Queries are written only to re-quest necessary information or clarification of an un-clear passage or to draw attention to edits that may havealtered the sense. It is the author’s responsibility to readthe entire text, tables, and figure legends, not just itemsqueried. As soon as the page proofs are corrected andsigned by the person who proofread them (within 48 h),they should be mailed or sent by a courier service suchas FedEx, not faxed or sent as an e-mail attachment, tothe ASM Journals Department.

The proof stage is not the time to make extensivecorrections, additions, or deletions. Important new in-formation that has become available between accep-tance of the manuscript and receipt of the proofs may beinserted as an addendum in proof with the permission ofthe editor. If references to unpublished data or personalcommunications are added, it is expected that writtenassurance granting permission for the citation will beincluded. Limit changes to correction of spelling errors,incorrect data, and grammatical errors and updated in-formation for references to articles that have been sub-mitted or are in press. If URLs have been provided inthe article, recheck the sites to ensure that the addressesare still accurate and the material that you expect thereader to find is indeed there.

Questions about late proofs and problems in the proofsshould be directed to the ASM Journals Department(telephone, 202-942-9215). Questions about accessing orviewing your PDF proofs should be directed to Katie Gayof Cadmus Professional Communications at 804-261-3155 or [email protected].

Reprints

Reprints (in multiples of 100) may be purchased by allcoauthors. In the proof notification e-mail, the corre-sponding author will be instructed how to access infor-mation about reprints.

The corresponding authors of Minireviews and GuestCommentaries will receive 100 free reprints of their con-tribution; additional reprints (in multiples of 100) maybe purchased if desired. As for regular articles, the cor-responding author will be instructed, in the proof noti-fication e-mail, how to access information about re-prints.

PDF Files

A corresponding author who has included an e-mailaddress in his “corresponding author” footnote will have

limited access (10 downloads, total) to the PDF file ofhis published article. An e-mail alert will automaticallybe sent to him on the day the issue is posted. It willprovide a URL, which will be required to obtain access,and instructions. An article may be viewed, printed, orstored, provided that it is for the author’s own use.

Should coauthors or colleagues be interested in view-ing the paper for their own use, the corresponding au-thor may provide them with the URL; a copy of thearticle may not be forwarded electronically. However,they must be made aware of the terms and conditionsof the ASM copyright. (For details, go to http://www.journals.asm.org/misc/terms.shtml.) Note that each suchdownload will count toward the corresponding author’stotal of 10. After 10 downloads, access will be deniedand can be obtained only through a subscription to thejournal (either individual or institutional) or after thestandard access control has been lifted (i.e., 6 monthsafter publication).

HOW TO SUBMIT MANUSCRIPTS

All submissions to JCM must be made electronicallyvia the Rapid Review online submission and peer reviewsystem at the following URL: www.rapidreview.com/ASM2/author.html. (E-mailed submissions will not beaccepted.) First-time users must create an Author ac-count, which may be used for submitting to all ASMjournals. Instructions for creating an Author accountare available at the above URL under the CreateAccount button. The person from whose account asubmission is made will be recorded as the corre-sponding author, and any correspondence will be sentto the e-mail address in that account. Step-by-stepinstructions for submitting a manuscript via RapidReview are available from the account holder’s MyManuscripts page. Information on file types accept-able for electronic submission can be found under theMore About File Formats button.

ORGANIZATION AND FORMAT

On receipt at ASM, an accepted manuscript under-goes an automated preediting, cleanup, and tagging pro-cess specific to the particular article type. To optimizethis process, manuscripts must be supplied in the correctformat and with the appropriate sections and headings.

Type every portion of the manuscript double spaced(a minimum of 6 mm between lines), including figurelegends, table footnotes, and References, and numberall pages in sequence, including the abstract, figure leg-ends, and tables. Place the last two items after the Ref-erences section. Manuscript pages should have linenumbers; manuscripts without line numbers may beeditorially rejected by the editor, with a suggestion ofresubmission after line numbers are added. The fontsize should be no smaller than 12 points. It is recom-mended that the following sets of characters be easily



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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 asgraphics or use special fonts that are external to yourword processing program; use the “insert symbol” func-tion. Set the page size to 81⁄2 by 11 inches (ca. 21.6 by 28cm). Italicize or underline any words that should appearin italics, and indicate paragraph lead-ins in bold type.

Authors who are unsure of proper English usageshould have their manuscripts checked by someone pro-ficient in the English language.

Manuscripts may be editorially rejected, without re-view, on the basis of poor English or lack of conformityto the standards set forth in these Instructions.

Full-Length Papers

Full-length papers include the elements described inthis section.

Title, running title, and byline. Each manuscriptshould present the results of an independent, cohesivestudy; thus, numbered series titles are not permitted.Exercise care in composing a title. Avoid the main title/subtitle arrangement, complete sentences, and unneces-sary articles. On the title page include the title, runningtitle (not to exceed 54 characters and spaces), name ofeach author, address(es) of the institution(s) at whichthe work was performed, each author’s affiliation, and afootnote indicating the present address(es) of any au-thor(s) no longer at the institution where the work wasperformed. Place an asterisk after the name of the au-thor to whom inquiries regarding the paper should bedirected (see “Correspondent footnote” below).

Study group in byline. A study group, surveillanceteam, working group, consortium, or the like (e.g., theActive Bacterial Core Surveillance Team) may be listedas a coauthor in the byline if its contributing memberssatisfy the requirements for authorship and accountabil-ity as described in these Instructions. The names (andinstitutional affiliations if desired) of the contributingmembers may be given in a footnote keyed to the studygroup name in the byline or as a separate paragraph inAcknowledgments.

If the contributing members of the group associatedwith the work do not fulfill the criteria of substantialcontribution to and responsibility for the paper, thegroup may not be listed in the author byline. Instead, itand the names of its contributing members may be listedin the Acknowledgments section.

Correspondent footnote. The complete mailing ad-dress, a single telephone number, a single fax number,and a single e-mail address for the corresponding authorshould be included on the title page of the manuscript.This information will be published in the article as afootnote to facilitate communication, and the e-mail ad-dress will be used to notify the corresponding author of

availability of proofs and, later, of the PDF file of thepublished article.

Abstract. Limit the abstract to 250 words or fewer andconcisely summarize the basic content of the paper with-out presenting extensive experimental details. Avoid ab-breviations and references, and do not include diagrams.When it is essential to include a reference, use the sameformat as shown for the References section but omit thearticle title. Conclude the abstract with a summary state-ment. Because the abstract will be published separatelyby abstracting services, it must be complete and under-standable without reference to the text.

Introduction. The introduction should supply suffi-cient background information to allow the reader tounderstand and evaluate the results of the present studywithout referring to previous publications on the topic.The introduction should also provide the hypothesis thatwas addressed or the rationale for the present study.Choose references carefully to provide the most salientbackground rather than an exhaustive review of thetopic.

Case Report. The Case Report section, placed afterthe introduction and before Materials and Methods, isoptional and gives relevant clinical information aboutone or more patients while being incidental to the rest ofthe paper. (If the Case Report constitutes the entirearticle, the paper must be presented in Case Reportformat [see p. 11], which differs from that used for afull-length text or a Note.)

Materials and Methods. The Materials and Methodssection must include sufficient technical information toallow the experiments to be repeated. The sources of allmedia (i.e., name and location of manufacturer) or com-ponents of a new formulation must be provided. Whencentrifugation conditions are critical, give enough infor-mation to enable another investigator to repeat the pro-cedure: make of centrifuge, model of rotor, tempera-ture, time at maximum speed, and centrifugal force (� grather than revolutions per minute). For commonly usedmaterials and methods (e.g., media and protein concen-tration determinations), a simple reference or specifi-cally recommended product or procedure is sufficient. Ifseveral alternative methods are commonly used, it ishelpful to identify the method briefly as well as to citethe reference. For example, it is preferable to state ‘‘cellswere broken by ultrasonic treatment as previously de-scribed (9)’’ rather than to state ‘‘cells were broken aspreviously described (9).’’ The reader should be allowedto assess the method without constant reference to pre-vious publications. Describe new methods completely,and give sources of unusual chemicals, reagents, equip-ment, or microbial strains. When large numbers of mi-crobial strains or mutants are used in a study, includetables identifying the immediate sources (i.e., sourcesfrom whom the strains were obtained) and properties ofthe strains, mutants, bacteriophages, plasmids, etc.



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A method, strain, etc., used in only one of severalexperiments reported in the paper may be described inthe Results section or very briefly (one or two sentences)in a table footnote or figure legend. It is expected thatthe sources from whom the strains were obtained will beidentified.

Results. In the Results section, include the rationaleor design of the experiments as well as the results;reserve extensive interpretation of the results for theDiscussion section. Present the results as concisely aspossible in one of the following: text, table(s), or fig-ure(s). Avoid extensive use of graphs to present datawhich might be more concisely presented in the text ortables. For example, except in unusual cases, double-reciprocal plots used to determine apparent Km valuesshould not be presented as graphs; instead, the valuesshould be stated in the text. Similarly, graphs illustratingother methods commonly used to derive kinetic or phys-ical constants (e.g., reduced-viscosity plots and plotsused to determine sedimentation velocity) need not beshown except in unusual circumstances. All tabular datamust be accompanied by either standard deviation val-ues or standard errors of the means. The number ofreplicate determinations (or animals) used for makingsuch calculations must also be included. All statementsconcerning the significance of the differences observedshould be accompanied by probability values given inparentheses. The statistical procedure used should bestated in Materials and Methods. Limit illustrations(particularly photomicrographs and electron micro-graphs) to those that are absolutely necessary to showthe experimental findings. Number figures and tables inthe order in which they are cited in the text, and be sureto cite all figures and tables.

Discussion. The Discussion section should provide aninterpretation of the results in relation to previouslypublished work and to the experimental system at hand.It must not contain extensive repetition of the Resultssection or reiteration of the introduction. In short pa-pers, the Results and Discussion sections may be com-bined.

Acknowledgments. The source of any financial sup-port received for the work being published must beindicated in the Acknowledgments section. (It will beassumed that the absence of such an acknowledgment isa statement by the authors that no support was re-ceived.) The usual format is as follows: ‘‘This work wassupported by Public Health Service grant CA-01234from the National Cancer Institute.’’

Recognition of personal assistance should be given asa separate paragraph, as should any statements disclaim-ing endorsement or approval of the views reflected in thepaper or of a product mentioned therein.

Appendixes. Appendixes, which contain additional ma-terial to aid the reader, are permitted. Titles, authors,

and References sections that are distinct from those ofthe primary article are not allowed. If it is not feasible tolist the author(s) of the appendix in the byline or theAcknowledgments section of the primary article, rewritethe appendix so that it can be considered for publicationas an independent article, either full-length or Notestyle. Equations, tables, and figures should be labeledwith the letter ‘‘A’’ preceding the numeral to distinguishthem from those cited in the main body of the text.

References. (i) Works listed in References. The Ref-erences section must include all journal articles (bothprint and online), books and book chapters (both printand online), patents, theses and dissertations, and pub-lished conference proceedings (not abstracts; see be-low), as well as in-press journal articles, book chapters,and books (publication title must be given). Arrange thecitations in alphabetical order (letter by letter, ignoringspaces and punctuation) by first author and numberconsecutively. Provide the names of all the authors foreach reference. All listed references must be cited par-enthetically by number in the text. Since title and bylineinformation that is downloaded from PubMed does notshow accents, italics, or special characters, authorsshould refer to the PDF files or hard-copy versions ofthe articles and incorporate the necessary corrections inthe submitted manuscript. Abbreviate journal names ac-cording to BIOSIS Serial Sources (BIOSIS, Philadelphia,Pa., 2005).

Follow the styles shown in the examples below.

Print references:

1. Arendsen, A. F., M. Q. Solimar, and S. W. Ragsdale.1999. Nitrate-dependent regulation of acetate biosyn-thesis and nitrate respiration by Clostridium ther-moaceticum. J. Bacteriol. 181:1489–1495.

2. Cox, C. S., B. R. Brown, and J. C. Smith. J. Gen.Genet., in press.* {Article title is optional; journal titleis mandatory.}

3. da Costa, M. S., M. F. Nobre, and F. A. Rainey. 2001.Genus I. Thermus Brock and Freeze 1969, 295,AL

emend. Nobre, Truper and da Costa 1996b, 605, p.404–414. In D. R. Boone, R. W. Castenholz, andG. M. Garrity (ed.), Bergey’s manual of systematicbacteriology, 2nd ed., vol. 1. Springer, New York,N.Y.

4. Elder, B. L., and S. E. Sharp. 2003. Cumitech 39,Competency assessment in the clinical laboratory.Coordinating ed., S. E. Sharp. ASM Press, Washing-ton, D.C.

5. Fitzgerald, G., and D. Shaw. In A. E. Waters (ed.),Clinical microbiology, in press. EFH Publishing Co.,Boston, Mass.* {Chapter title is optional.}

6. Forman, M. S., and A. Valsamakis. 2003. Specimencollection, transport, and processing: virology, p.1227–1241. In P. R. Murray, E. J. Baron, M. A.Pfaller, J. H. Jorgensen, and R. H. Yolken (ed.),Manual of clinical microbiology, 8th ed. ASM Press,Washington, D.C.



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7. Green, P. N., D. Hood, and C. S. Dow. 1984. Taxo-nomic status of some methylotrophic bacteria, p. 251–254. In R. L. Crawford and R. S. Hanson (ed.), Mi-crobial growth on C1 compounds. Proceedings of the4th International Symposium. American Society forMicrobiology, Washington, D.C.

8. Odell, J. C. April 1970. Process for batch culturing.U.S. patent 484,363,770. {Include the name of thepatented item/process if possible.}

9. O’Malley, D. R. 1998. Ph.D. thesis. University of Cal-ifornia, Los Angeles. {Title is optional.}

*A reference to an in-press ASM publication shouldstate the control number (e.g., JCM00577-06) if it is ajournal article or the name of the publication if it is abook.

Online references:

1. Charlier, D., and N. Glansdorff. September 2004,posting date. Biosynthesis of arginine and poly-amines. In R. Curtiss III et al. (ed.), EcoSal—Esche-richia coli and Salmonella: cellular and molecular bi-ology, chapter 3.6.1.10. [Online.] http://www.ecosal.org. ASM Press, Washington, D.C. {For online-onlybooks or continually updated Web resources [for thelatter, posting or accession date is required, but publish-er’s name and location are optional].}.

2. Dimick, J. B., H. G. Welch, and J. D. Birkmeyer. 18August 2004, posting {or revision} date. Surgicalmortality as an indicator of hospital quality. JAMA292. [Online.] http://jama.ama-assn.org/cgi/content/short/292/7/847. {For online journals; page numbersmay not be available.}

3. Sullivan, C. J. (ed.). 1999–2001. Fungi: an evolvingelectronic resource for the microbiological commu-nity. ASM Press. [Online.] http://link.asmusa.de/link/service/books/91090. Accessed 7 September 2001.{For online-only books.}

4. Zellnitz, F., and P. M. Foley. 2 October 1998, posting{or revision} date. History of virology. Am. Virol. J.1:30–50. [Online.] http://www.avj.html. {For online-only journals; page numbers may not be available.}

5. Zheng, Z., and J. Zou. 5 September 2001. The initialstep of the glycerolipid pathway: identification of glyc-erol-3-phosphate/dihydroxyacetone phosphate dualsubstrate acyltransferases in Saccharomyces cerevi-siae. J. Biol. Chem. doi:10.1074/jbc.M104749200. {Forpapers published online in manuscript form.}

NOTE: A URL or DOI is necessary for each online-onlyreference; a posting or accession date is required for anyonline reference that is periodically updated or changed.

(ii) Items cited in the text. References to unpublisheddata, articles submitted for publication, meeting ab-stracts (including those published in journal supple-ments), personal communications, letters (irrespectiveof type) and authors’ replies to letters, company publi-cations, patent applications and patents pending, com-

puter software, databases, and websites should be madeparenthetically 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, andP. N. Brighton, submitted for publication).

. . . in mitochondria (S. De Wit, C. Thioux, and N.Clumeck, Abstr. 34th Intersci. Conf. Antimicrob. AgentsChemother., abstr. 114, 1994).

. . . for other bacteria (A. X. Jones, personal communi-cation.)

. . . discussed previously (L. B. Jensen, A. M. Ham-merum, R. L. Poulsen, and H. Westh, Letter, Antimi-crob. Agents Chemother. 43:724–725, 1999).

. . . discussed previously (S. L. W. On and P. A. R. Van-damme, Authors’ Reply to Letter, J. Clin. Microbiol.39:2751–2752, 2001).

. . . the manufacturer (Sigma manual, Sigma ChemicalCo., St. Louis, Mo.).

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

. . . information found at the XYZ website (http://cbx_iou.pgr).

. . . the ABC program (version 2.2; Department of Mi-crobiology, State University [http://www.stu.micro]).

URLs for companies that produce any of the productsmentioned in your study or for products being sold mayNOT be included in the article. However, companyURLs that permit access to scientific data related to thestudy or to shareware used in the study are permitted.

Notes

The Note format is intended for the presentation ofbrief observations that do not warrant full-length papers.However, Notes should contain firm data; observationsalone are not acceptable. Submit Notes in the same wayas full-length papers. They receive the same review, theyare not published more rapidly than full-length papers, andthey are not considered preliminary communications.

Each Note must have an abstract of no more than 50words. Do not use section headings in the body of theNote; combine methods, results, and discussion in a sin-gle section. Paragraph lead-ins are permissible. The textshould be kept to a minimum and if possible should notexceed 1,000 words; the number of figures and tablesshould also be kept to a minimum. Materials and meth-ods should be described in the text, not in figure legendsor table footnotes. Acknowledgments should be pre-sented as in full-length papers, but no separate headingis used. The References section is identical to that offull-length papers.



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Minireviews

Minireviews are expected to be focused discussions ofdefined topics relevant to clinical microbiologists. Ingeneral, they are to be submitted only after invitation byone of the JCM editors. Unsolicited Minireviews arediscouraged. The cover letter should state whether thearticle was solicited and by whom.

Minireviews are not expected to be comprehensivereviews of the literature but rather very directed discus-sions of specific issues, with emphasis on the views of theauthor(s). Thus, they may not exceed 12 double-spacedmanuscript pages in length, inclusive of illustrations, ta-bles, and references. References should be limited to 20or fewer. Minireviews do not have abstracts. In the Ab-stract section of the submission form, put “Not applica-ble.” The body of the Minireview may either have sec-tion headings or be set up like a Note (see above).Minireviews should be submitted via Rapid Review.

Minireviews will be reviewed by two JCM editors, withthe aim of expedited processing. In general, it is hopedthat, barring the necessity of major revisions, acceptedMinireviews will appear in print within 3 months of theirsubmission.

Guest Commentaries

Guest Commentaries are invited communications con-cerning relevant topics in clinical microbiology that arenot necessarily covered by Minireviews. They are in-tended to engender discussion and stimulate consensusstatements by such organizations as the American Acad-emy of Microbiology, Clinical and Laboratory StandardsInstitute, etc. Reviews of the literature, methods andother how-to papers, and responses targeted at a specificpublished paper are not appropriate. Guest Commen-taries are subject to review.

The length may not exceed 4 printed pages, and theformat is like that of a Minireview (see above). Com-mentaries should be submitted via Rapid Review.

Case Reports

While a full-length article or a Note may contain acase report section when the report is incidental to therest of the paper, a specific Case Report format must beused when the report constitutes the entire article.

A Case Report must include an abstract of no morethan 50 words. The text starts with presentation of thecase under the section heading “Case Report”; there isno introductory text before the Case Report heading.After the case is presented, the rest of the text follows ina separate section after a ruled line to separate thesections. No separate head is used for this short discus-sion section, but paragraph lead-ins are permitted. Thetotal number of tables and figures (combined) must notexceed 3. For a recent example of a correctly format-ted Case Report, see J. Clin. Microbiol. 39:1678–1679,2001.

Letters to the Editor

Two types of Letters to the Editor may be submitted.The first type (Comment Letter) is intended for com-ments on the articles published previously in the journaland must cite published references to support the writ-er’s argument. The second type (New-Data Letter) mayreport new, concise findings that are not appropriate forpublication as full-length papers or Notes.

Letters may be no more than 500 words long and mustbe typed double spaced. Refer to a recently publishedLetter for correct formatting. Note that authors andaffiliations are listed at the foot of the Letter. Provideonly the primary affiliation for each author.

All Letters to the Editor must be submitted electron-ically, and the type of Letter (New Data or Comment)must be selected from the drop-down list in the submis-sion form. For Letters commenting on published arti-cles, the cover letter should state the volume and issue inwhich the article was published, the title of the article,and the last name of the first author. In the Abstractsection of the submission form, put “Not applicable.”Letters to the Editor do not have abstracts. Both types ofLetter must have a title, which must appear on themanuscript and on the submission form. Figures andtables should be kept to a minimum.

If the Letter is related to a published article, it will besent to the editor who handled the article in question. Ifthe editor believes that publication is warranted, he willsolicit a reply from the corresponding author of thearticle and give approval for publication.

New-Data Letters will be assigned to an editor accord-ing to subject matter and will be reviewed by that editorand/or a reviewer.

Please note that some indexing/abstracting servicesdo not include Letters to the Editor in their databases.

Fast-Track Communications

The fast-track route is intended for accelerated reviewof short communications that are of significant interest toclinical microbiologists. Manuscripts are limited to 750words, one figure, one table, and 10 or fewer references.The format should be the same as that of a new-dataletter (see Letters to the Editor, above). Fast-track arti-cles should be submitted via Rapid Review.

A fast-track submission is subject to approval as suchby the editor in chief. If approved for the fast-trackroute, the manuscript will be assigned to an appropriateJCM editor and reviewed, according to the same stan-dards applied for traditional manuscripts, within 1 week.If accepted, the manuscript will be scheduled for thenext available issue and edited. An acceptance letter andcopyright agreement will be mailed to the correspondingauthor. Proofs will be made available electronically asfor regular articles.

A fast-track submission that is not approved for thefast-track route will be handled as a New-Data Letteraccording to normal procedures.



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Errata

The Erratum section provides a means of correctingerrors that occurred during the writing, typing, editing,or printing (e.g., a misspelling, a dropped word or line,or mislabeling in a figure) of a published article. SendErrata directly to the ASM Journals Department (1752N St., N.W., Washington, DC 20036-2904, USA), bothon disk and in hard copy (only one hard copy is neces-sary). Please see a recent issue for correct formatting.

Authors’ Corrections

The Author’s Correction section provides a means ofcorrecting errors of omission (e.g., author names or cita-tions) and errors of a scientific nature that do not alter theoverall basic results or conclusions of a published article.

For omission of an author’s name, the authors of thearticle and the author whose name was inadvertentlyomitted must agree, in writing, to publication of theCorrection. For other issues involving authorship, in-cluding contributions and use or ownership of dataand/or materials, all disputing parties must agree, inwriting, to publication of the Correction. Copies of theagreement letters must accompany the Correction andbe sent directly to the Journals Department. Send theCorrection both on disk and in hard copy (only one hardcopy is necessary). Please see a recent issue for correctformatting.

Corrections of a scientific nature (e.g., an incorrectunit of measurement or order of magnitude usedthroughout; contamination of one of numerous cultures;or misidentification of a mutant strain, causing errone-ous data for only a portion [noncritical] of the study)must be sent, both on disk and in hard copy, directly tothe editor who handled the article and must be accom-panied by signed letters of agreement from all of the au-thors of the article. If the editor believes that publicationis warranted, he will send the Correction to the JournalsDepartment for publication. Note that the addition of newdata is not permitted.

Retractions

Retractions are reserved for major errors or breachesof ethics that, for example, may call into question thesource of the data or the validity of the results andconclusions of an article. Send a Retraction and an ac-companying explanatory letter signed by all of the authorsdirectly to the editor in chief of the journal. The editorwho handled the paper and the chairman of the ASMPublications Board will be consulted. If all parties agreeto the publication and content of the Retraction, it willbe sent to the Journals Department for publication.

ILLUSTRATIONS AND TABLES

Digital files that are acceptable for production (seebelow) must be provided for all illustrations on returnof the modified manuscript. (On initial submission, the

entire paper may be submitted in PDF format.)We strongly recommend that before returning their

modified manuscripts, authors check the acceptability oftheir digital images for production by running their filesthrough Rapid Inspector, a tool provided at the follow-ing URL: http://rapidinspector.cadmus.com/mw/. RapidInspector is an easy-to-use Web-based application thatidentifies file characteristics that may render the imageunusable for production.

Illustrations may be continuous-tone images, linedrawings, or composites. Color graphics may be submit-ted, but the cost of printing in color must be borne by theauthor. Suggestions about how to reduce costs and en-sure accurate color reproduction are given below.

The preferred format for tables is MS Word; however,

Macintosh

ApplicationFile type

Black and white Color (CMYK)a

Adobe Illustrator 6.0, 7.0,8.0, 9.0, 10.0, 11.0 CS

EPS EPS

Adobe InDesign 1.0 EPS EPSAdobe PageMaker 6.5 EPS EPSAdobe Photoshop 4.0, 5.0,

5.5, 6.0, 7.0, 8.0 CSTIFF TIFF

Adobe Photoshop 5.0 LE TIFF N/Ab

ChemDraw Pro 5.0 EPS/TIFF EPS/TIFFCorel Photo-Paint 8.0 TIFF EPSCorelDRAW 6.0, 8.0 EPS/TIFF EPSDeneba Canvas 6.0, 7.0,

8.0EPS/TIFF EPS

Macromedia FreeHand7.0, 8.0, 9.0

EPS EPS

PowerPoint 98, 2001 PPTc N/Ab

Prism 3 by GraphPad TIFF N/Ab

Synergy Kaleidagraph3.08, 3.51

EPS N/Ab

a Color graphics must be saved and printed in the CMYK mode, not RGB.b ASM accepts only black-and-white, not color, graphics created with Kalei-

dagraph, Adobe Photoshop 5.0 LE, Prism 3 by GraphPad, and PowerPoint.c For instructions on saving PowerPoint files, refer to the Cadmus digital art

website at http://cjs.cadmus.com/da/index.asp.

Windows

Application

File type

Black andwhite

Color(CMYK)a

Adobe Illustrator 7.0, 8.0, 9.0, 10.0, 11.0 CS EPS EPSAdobe InDesign 1.0 EPS EPSAdobe PageMaker 6.5 EPS EPSAdobe Photoshop 4.0, 5.0, 5.5, 6.0, 7.0,

8.0 CSTIFF TIFF

Adobe Photoshop 5.0 LE TIFF N/Ab

ChemDraw Pro 5.0 EPS/TIFF EPS/TIFFCorel Photo-Paint 8.0, 9.0 TIFF EPSCorelDRAW 7.0, 8.0, 9.0 EPS/TIFF EPSDeneba Canvas 6.0, 7.0 EPS/TIFF EPSMacromedia FreeHand 7.0, 8.0, 9.0 EPS EPSPowerPoint 97, 2000, XP PPTc N/Ab

Prism 3 by GraphPad TIFF N/Ab

SigmaPlot 8.01 EPS EPS

a Color graphics must be saved and printed in the CMYK mode, not RGB.b ASM accepts only black-and-white, not color, graphics created with Adobe

Photoshop 5.0 LE, Prism 3 by GraphPad, and PowerPoint.c For instructions on saving PowerPoint files, refer to the Cadmus digital art

website at http://cjs.cadmus.com/da/index.asp.



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WordPerfect and Acrobat PDF are also acceptable (seethe section on Tables below).

Since the contents of computer-generated images canbe manipulated for better clarity, the Publications Boardat its May 1992 meeting mandated that a description ofthe software/hardware used should be put in the figurelegend(s).

Illustrations

File types and formats. As mentioned above, illustra-tions may be supplied as PDF files for reviewing pur-poses only on initial submission; in fact, we recommendthis option to minimize file upload time. At the modifi-cation stage, production quality digital files must besubmitted: TIFF or EPS files from supported applica-tions or PowerPoint files (black and white only). Exceptfor figures produced in PowerPoint, all graphics submit-ted with modified manuscripts must be bitmap, gray-scale, or CMYK (not RGB). Acceptable file types andformats for production are given in the charts above.More-detailed instructions for preparing illustrations areavailable on the World Wide Web at http://cjs.cadmus.com/da. Please review this information before preparingyour files. If you require additional information, pleasesend an e-mail inquiry to [email protected].

Minimum resolution. It is extremely important that ahigh enough resolution is used. Any imported imagesmust be at the correct resolution before they are placed.Note, however, that the higher the resolution, the largerthe file and the longer the upload time. Publication qual-ity will not be improved by using a resolution higher thanthe minimum. Minimum resolutions are as follows:

300 dpi for grayscale and color600 dpi for lettering1,200 dpi for line art600 dpi for combination art (lettering and images)

Size. All graphics MUST be submitted at their in-tended publication size; that is, the image uploadedshould be 100% of its print dimensions so that no re-duction or enlargement is necessary. Resolution must beat the required level at the submitted size. Include onlythe significant portion of an illustration. White spacemust be cropped from the image, and excess space be-tween panel labels and the image must be eliminated.

Maximum width for a 1-column figure: 35⁄16 inches(ca. 8.4 cm)

Maximum width for a 2-column figure: 67⁄8 inches(ca. 17.4 cm)

Minimum width for a 2-column figure: 41⁄4 inches(10.8 cm)

Maximum height: 91⁄16 inches (23.0 cm)

Contrast. Illustrations must contain sufficient contrastto withstand the inevitable loss of contrast and detail

inherent in the printing process. See also the section oncolor illustrations below.

Labeling and assembly. All final lettering, labeling,tooling, etc., MUST be incorporated into the figures. Itcannot be added at a later date. If a figure number isincluded, it must appear well outside the boundaries ofthe image itself. (Numbering may need to be changed atthe copyediting stage.) Each figure must be uploaded asa separate file, and any multipanel figures must be as-sembled into one file; i.e., rather than uploading a sep-arate file for each panel in a figure, assemble all panelsin one piece and supply them as one file.

Fonts. To avoid font problems, set all type in one ofthe following fonts: Helvetica, Times Roman, EuropeanPI, Mathematical PI, or Symbol. All fonts other thanthese five must be converted to paths (or outlines) in theapplication with which they were created. For font use inPowerPoint images, refer to the Cadmus digital art web-site, http://cjs.cadmus.com/da.

Compression. Images created with Macintosh appli-cations may be compressed with Stuffit. Images createdwith Windows applications may be compressed withWINZIP or PKZIP.

Color illustrations. Because the process of placingink on paper by using printing presses is different fromthat used to produce a photo print or a laser print andthe color rendition on images viewed on a monitor de-pends to some extent on monitor resolution, some dif-ferences in color and contrast between the image yousubmit and the image printed in the journal or publishedonline will be evident. (Figures showing red or greenfluorescence and those with a significant range of colorsmay be difficult or impossible to reproduce exactly.)Color illustrations must be saved as either TIFF or EPSfiles, according to the application used (see chartsabove). The mode of the TIFF or EPS file must beCMYK, not RGB. Graphics in the RGB color space areintended for display on a monitor only and will notseparate correctly for printing.

The cost of printing in color must be borne by the author.The current color costs may be accessed from the sub-mission form in Rapid Review and, for accepted manu-scripts, will be included in the acceptance letter sent outby ASM. Adherence to the following guidelines, in ad-dition to the general ones above, will help to minimizecosts and to ensure color reproduction that is as accurateas possible.

Include only the significant portions of illustrations sothat the number of printed pages containing color fig-ures is minimized. The individual panels of a single fig-ure must be assembled in a single file, including anynecessary labels. Optimal color reproduction will be ob-tained if the composites comprise panels containing similarcolors of similar lightness or darkness. If necessary, make



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unlike panels into separate figures/files; this will increasethe cost, but the color rendition will be more accurate sincethe two panels will be “scanned” separately.

Drawings

Submit graphs, charts, complicated chemical or math-ematical formulas, diagrams, and other drawings as fin-ished products not requiring additional artwork or type-setting. No part of the graph or drawing may behandwritten. All elements, including letters, numbers,and symbols, must be easily readable, and both axes of agraph must be labeled. Keep in mind that the journal ispublished both in print and online and that the sameelectronic files submitted by the authors are used toproduce both.

When creating line art, please use the following guide-lines:

1. All art MUST be submitted at its intended publica-tion size. For acceptable dimensions, see the Sizesection above.

2. Avoid using screens (i.e., shading) in line art. It canbe difficult and time-consuming to reproduce theseimages without moire patterns. Various pattern back-grounds are preferable to screens as long as the pat-terns are not imported from another application. Ifyou must use images containing screens,

• Generate the image at line screens of 85 lines perinch or lower.

• When applying multiple shades of gray, differenti-ate the gray levels by at least 20%.

• Never use levels of gray below 20% or above 70%as they will fade out or become totally black uponscanning and reduction.

3. Use thick, solid lines that are no finer than 1 point inthickness.

4. No type should be smaller than 6 points at the finalpublication size.

5. Avoid layering type directly over shaded or texturedareas.

6. Avoid the use of reversed type (white lettering on ablack background).

7. Avoid heavy letters, which tend to close up, and un-usual symbols, which the printer may not be able toreproduce in the legend.

8. If colors are used, avoid using similar shades of thesame color and avoid very light colors.

In figure ordinate and abscissa scales (as well as tablecolumn headings), avoid the ambiguous use of numberswith exponents. Usually, it is preferable to use the ap-propriate Systeme International d’Unites (SI) symbols(� for 10�6, m for 10�3, k for 103, M for 106, etc.). Acomplete listing of SI symbols can be found in the In-ternational Union of Pure and Applied Chemistry (IU-

PAC) “Manual of Symbols and Terminology for Physi-cochemical Quantities and Units’’ (Pure Appl. Chem.21:3–44, 1970). Thus, a representation of 20,000 cpm ona figure ordinate should be made by the number 20accompanied by the label kcpm.

When powers of 10 must be used, the journal requiresthat the exponent power be associated with the numbershown. In representing 20,000 cells per ml, the numeralof the ordinate would be ‘‘2’’ and the label would be ‘‘104

cells per ml’’ (not ‘‘cells per ml � 10�4’’). Likewise, anenzyme activity of 0.06 U/ml would be shown as 6 ac-companied by the label 10�2 U/ml. The preferred des-ignation would be 60 mU/ml (milliunits per milliliter).

Presentation of Nucleic Acid Sequences

Nucleic acid sequences of limited length which are theprimary subject of a study may be presented freestyle in themost effective format. Longer nucleic acid sequences mustbe presented as figures in the following format to conservespace. Print the sequence in lines of approximately 100 to120 nucleotides in a nonproportional (monospace) fontthat is easily legible when published with a line length of 6inches (ca. 15.2 cm). If possible, lines of nucleic acid se-quence should be further subdivided into blocks of 10 or 20nucleotides by spaces within the sequence or by marksabove it. Uppercase and lowercase letters may be used todesignate the exon-intron structure, transcribed regions,etc., if the lowercase letters remain legible at a 6-inch (ca.15.2-cm) line length. Number the sequence line by line;place numerals, representing the first base of each line, tothe left of the lines. Minimize spacing between lines ofsequence, leaving room only for annotation of the se-quence. Annotation may include boldface, underlining,brackets, boxes, etc. Encoded amino acid sequences may bepresented, if necessary, immediately above or below the firstnucleotide of each codon, by using the single-letter amino acidsymbols. Comparisons of multiple nucleic acid sequencesshould conform as nearly as possible to the same format.

Figure Legends

Legends should provide enough information so thatthe figure is understandable without frequent referenceto the text. However, detailed experimental methodsmust be described in the Materials and Methods section,not in a figure legend. A method that is unique to one ofseveral experiments may be reported in a legend only ifthe discussion is very brief (one or two sentences). De-fine all symbols used in the figure and define all abbre-viations that are not used in the text.

Tables

Tables that contain artwork, chemical structures, orshading must be submitted as illustrations in an acceptableformat at the modification stage. The preferred format forregular tables is MS Word; however, WordPerfect andAcrobat PDF are also acceptable. Note that a straightExcel file is not currently an acceptable format. Excel files



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must be either embedded in a Word or WordPerfect doc-ument or converted to PDF before being uploaded. If yourmodified manuscript contains PDF tables, select “for re-viewing purposes only” at the beginning of the file uploadprocess.

Tables should be formatted as follows. Arrange thedata so that columns of like material read down, notacross. The headings should be sufficiently clear so thatthe meaning of the data is understandable without ref-erence to the text. See the Abbreviations section (p. 17)of these Instructions for those that should be used intables. Explanatory footnotes are acceptable, but moreextensive table “legends” are not. Footnotes should notinclude detailed descriptions of the experiment. Tables

must include enough information to warrant table for-mat; those with fewer than six pieces of data will beincorporated into the text by the copy editor. Table 1 isan example of a well-constructed table.

NOMENCLATURE

Chemical and Biochemical Nomenclature

The recognized authority for the names of chemicalcompounds is Chemical Abstracts (CAS, Columbus,Ohio) and its indexes. The Merck Index, 13th ed.(Merck & Co., Inc., Whitehouse Station, N.J., 2001),is also an excellent source. For biochemical terminol-ogy, including abbreviations and symbols, consult Bio-chemical Nomenclature and Related Documents (1978;reprinted for The Biochemical Society, London, En-gland) and the instructions to authors of the Journal ofBiological Chemistry and the Archives of Biochemistry andBiophysics (first issues of each year).

Do not express molecular weight in daltons; molecularweight is a unitless ratio. Molecular mass is expressed indaltons.

For enzymes, use the recommended (trivial) nameassigned by the Nomenclature Committee of the Inter-national Union of Biochemistry (IUB) as described in En-zyme Nomenclature (Academic Press, Inc., New York,N.Y., 1992) and at http://www.chem.qmul.ac.uk/iubmb

/enzyme/. If a nonrecommended name is used, place theproper (trivial) name in parentheses at first use in theabstract and text. Use the EC number when one hasbeen assigned, and express enzyme activity either inkatals (preferred) or in the older system of micromolesper minute.

For nomenclature of restriction enzymes, DNA meth-yltransferases, homing endonucleases, and their genes,refer to the article by Roberts et al. (Nucleic Acids Res.31:1805–1812, 2003).

Drugs

Whenever possible, use generic names of drugs; theuse of trade names is not permitted.

Nomenclature of Microorganisms

Binary names, consisting of a generic name and aspecific epithet (e.g., Escherichia coli), must be used forall microorganisms. Names of categories at or above thegenus level may be used alone, but specific and subspe-cific epithets may not. A specific epithet must be pre-ceded by a generic name, written out in full the firsttime it is used in a paper. Thereafter, the generic nameshould be abbreviated to the initial capital letter (e.g., E.coli), provided there can be no confusion with othergenera used in the paper. Names of all taxa (kingdoms,phyla, classes, orders, families, genera, species, and sub-species) are printed in italics and should be underlined(or italicized) in the manuscript; strain designations andnumbers are not. Vernacular (common) names shouldbe in lowercase roman type (e.g., streptococcus, bru-cella). For Salmonella, genus, species, and subspeciesnames should be rendered in standard form: Salmonellaenterica at first use, S. enterica thereafter; Salmonellaenterica subsp. arizonae at first use, S. enterica subsp.arizonae thereafter. Names of serovars should be in ro-man type with the first letter capitalized: Salmonellaenterica serovar Typhimurium. After the first use, theserovar may also be given without a species name: Sal-monella serovar Typhimurium. For other informationregarding serovar designations, see Identification and Se-rotyping of Salmonella and an Update of the Kaufmann-White Scheme (A. C. McWhorter-Murlin and F. W.Hickman-Brenner, Centers for Disease Control and Pre-vention, Atlanta, Ga., 1994) and Antigenic Formulas ofthe Salmonella Serovars (M. Y. Popoff and L. Le Minor,WHO Collaborating Centre for Reference and Re-search on Salmonella, Institute Pasteur, Paris, France,1997). For a summary of the current standards for Sal-monella nomenclature and the Kaufmann-White crite-ria, see the articles by Brenner et al. (J. Clin. Microbiol.38:2465–2467, 2000) and McQuiston et al. (J. Clin. Mi-crobiol. 42:1923–1932, 2004).

The spelling of bacterial names should follow the Ap-proved Lists of Bacterial Names (Amended) & Index of theBacterial and Yeast Nomenclatural Changes (V. B. D.Skerman et al., ed., ASM Press, Washington, D.C., 1989)and the validation lists and notification lists published in

TABLE 1. Correlation between detection of V-Z viral antibody byneutralization and by EIA and IAHAa

Antibody

No. of samples with V-Zvirus-neutralizing antibody Correlation

(%)Positiveb Negative

EIAPositive 50 4Negative 3 64 94

IAHAPositivec 37 0 87Negative 16 68

a Sera from individuals without evidence of a current V-Z virus infection.b Titer � 1:4.c Titer � 1:8.



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the International Journal of Systematic and EvolutionaryMicrobiology (formerly the International Journal of System-atic Bacteriology) since January 1989. In addition, two siteson the World Wide Web list current approved bacterialnames: Bacterial Nomenclature Up-to-Date (http://www.dsmz.de/microorganisms/main.php?contentleft_id�14)and List of Prokaryotic Names with Standing in Nomen-clature (http://www.bacterio.cict.fr). If there is reason touse a name that does not have standing in nomenclature,the name should be enclosed in quotation marks in the titleand at its first use in the abstract and the text and anappropriate statement concerning the nomenclatural statusof the name should be made in the text. “Candidatus”species should always be set in quotation marks.

For guidelines regarding new names and descriptionsof new genera and species, see the articles by Tindall(Int. J. Syst. Bacteriol. 49:1309–1312, 1999) and Stacke-brandt et al. (Int. J. Syst. Evol. Microbiol. 52:1043–1047,2002). To validate new names and/or combinations, au-thors must submit three copies of their published articleto the International Journal of Systematic and Evolution-ary Microbiology.

It is recommended that a strain be deposited in atleast two recognized culture collections in differentcountries when that strain is necessary for the descrip-tion of a new taxon (Int. J. Syst. Evol. Microbiol. 50:2239–2244, 2000).

Since the classification of fungi is not complete, it isthe responsibility of the author to determine the ac-cepted binomial for a given organism. Sources for thesenames include The Yeasts: a Taxonomic Study, 4th ed. (C.P. Kurtzman and J. W. Fell, ed., Elsevier Science Pub-lishers B.V., Amsterdam, The Netherlands, 1998), andAinsworth and Bisby’s Dictionary of the Fungi, 9th ed.(P. M. Kirk, P. F. Cannon, J. C. David, and J. A. Stalp-ers, ed., CABI Publishing, Wallingford, Oxfordshire,United Kingdom, 2001).

Names used for viruses should be those approved bythe International Committee on Taxonomy of Viruses(ICTV) and published in Virus Taxonomy: Classificationand Nomenclature of Viruses, Seventh Report of the Inter-national Committee on Taxonomy of Viruses (M. H. V.van Regenmortel et al., ed., Academic Press, San Diego,Calif., 2000). In addition, the recommendations of theICTV regarding the use of species names should gener-ally be followed: when the entire species is discussed asa taxonomic entity, the species name, like other taxa, isitalic and has the first letter and any proper nouns cap-italized (e.g., Tobacco mosaic virus, Murray Valley enceph-alitis virus). When the behavior or manipulation of individ-ual viruses is discussed, the vernacular (e.g., tobaccomosaic virus, Murray Valley encephalitis virus) should beused. If desired, synonyms may be added parentheticallywhen the name is first mentioned. Approved generic (orgroup) and family names may also be used.

Microorganisms, viruses, and plasmids should be giv-en designations consisting of letters and serial numbers.It is generally advisable to include a worker’s initials ora descriptive symbol of locale, laboratory, etc., in the

designation. Each new strain, mutant, isolate, or deriv-ative should be given a new (serial) designation. Thisdesignation should be distinct from those of the geno-type and phenotype, and italicized genotypic and phe-notypic symbols should not be included. Plasmids arenamed with a lowercase “p” followed by the designationin uppercase letters and numbers. To avoid the use ofthe same designation as that of a widely used strain orplasmid, check the designation against a publication da-tabase such as Medline.

Genetic Nomenclature

To facilitate accurate communication, it is importantthat standard genetic nomenclature be used wheneverpossible and that deviations or proposals for new nam-ing systems be endorsed by an appropriate authoritativebody. Review and/or publication of submitted manu-scripts that contain new or nonstandard nomenclaturemay be delayed by the editor or the Journals Depart-ment so that they may be reviewed by the Genetics andGenomics Committee of the ASM Publications Board.

Before submission of manuscripts, authors may directquestions on genetic nomenclature to the committee’schairman: Maria Costanzo (e-mail: [email protected]). Such a consultation should be mentionedin the manuscript submission letter.

Bacteria. The genetic properties of bacteria are de-scribed in terms of phenotypes and genotypes. The phe-notype describes the observable properties of an organ-ism. The genotype refers to the genetic constitution ofan organism, usually in reference to some standard wildtype. Use the recommendations of Demerec et al. (Ge-netics 54:61–64, 1966) as a guide to the use of theseterms. If your manuscript contains information includinggenetic nomenclature, please refer to the Instructions toAuthors in the January issue of the Journal of Bacteriology.

‘‘Mutant’’ vs. ‘‘mutation.’’ Keep in mind the distinctionbetween a mutation (an alteration of the primary se-quence of the genetic material) and a mutant (a straincarrying one or more mutations). One may speak aboutthe mapping of a mutation, but one cannot map a mu-tant. Likewise, a mutant has no genetic locus, only aphenotype.

“Homology” versus “similarity.” For use of termsthat describe relationships between genes, consult thearticles by Theissen (Nature 415:741, 2002) and Fitch(Trends Genet. 16:227–231, 2000). “Homology” impliesa relationship between genes that share a common evo-lutionary origin; partial homology is not recognized.When sequence comparisons are discussed, it is moreappropriate to use the term “percent sequence similar-ity” or “percent sequence identity,” as appropriate.

Tetracycline resistance determinants. The nomencla-ture for tetracycline resistance determinants is based onthe proposal of Levy et al. (Antimicrob. Agents Chemo-



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ther. 43:1523–1524, 1999). The style for such determi-nants is, e.g., Tet B; the space helps distinguish thedeterminant designation from that for phenotypes andproteins (TetB). The above-referenced article also givesthe correct format for genes, proteins, and determinantsin this family.

Viruses. The genetic nomenclature for viruses differsfrom that for bacteria. In most instances, viruses have nophenotype, since they have no metabolism outside hostcells. Therefore, distinctions between phenotype and ge-notype cannot be made. Superscripts are used to indi-cate hybrid genomes. Genetic symbols may be one, two,or three letters.

Eukaryotes. For information about the genetic no-menclature of eukaryotes, see the Instructions to Au-thors for Eukaryotic Cell and Molecular and Cellular Bi-ology.

ABBREVIATIONS AND CONVENTIONS

Verb Tense

ASM strongly recommends that for clarity you use thepast tense to narrate particular events in the past, in-cluding the procedures, observations, and data of thestudy that you are reporting. Use the present tense foryour own general conclusions, the conclusions of previ-ous researchers, and generally accepted facts. Thus, mostof the abstract, Materials and Methods, and Results willbe in the past tense, and most of the introduction andsome of the Discussion will be in the present tense.

Be aware that it may be necessary to vary the tense ina single sentence. For example, it is correct to say‘‘White (30) demonstrated that XYZ cells grow at pH6.8,’’ ‘‘Figure 2 shows that ABC cells failed to grow atroom temperature,’’ and ‘‘Air was removed from thechamber and the mice died, which proves that mice re-quire air.’’ In reporting statistics and calculations, it iscorrect to say ‘‘The values for the ABC cells are statis-tically significant, indicating that the drug inhibited. . . .’’

For an in-depth discussion of tense in scientific writ-ing, see p. 207–209 in How To Write and Publish a Sci-entific Paper, 5th ed.

Abbreviations

General. Abbreviations should be used as an aid to thereader, rather than as a convenience for the author, andtherefore their use should be limited. Abbreviations oth-er than those recommended by the IUPAC-IUB (Bio-chemical Nomenclature and Related Documents, 1978)should be used only when a case can be made for ne-cessity, such as in tables and figures.

It is often possible to use pronouns or to paraphrase along word after its first use (e.g., ‘‘the drug’’ or ‘‘thesubstrate’’). Standard chemical symbols and trivial namesor their symbols (folate, Ala, Leu, etc.) may also be used.

It is strongly recommended that all abbreviations ex-cept those listed below be introduced in the first para-graph in Materials and Methods. Alternatively, defineeach abbreviation and introduce it in parentheses thefirst time it is used; e.g., ‘‘Cultures were grown in Eagleminimal essential medium (MEM).’’ Generally, elimi-nate abbreviations that are not used at least three timesin the text (including tables and figure legends).

Not requiring introduction. In addition to abbrevia-tions for Systeme International d’Unites (SI) units ofmeasurement, other common units (e.g., bp, kb, andDa), and chemical symbols for the elements, the follow-ing should be used without definition in the title, ab-stract, text, figure legends, and tables: DNA (deoxyri-bonucleic acid); cDNA (complementary DNA); RNA(ribonucleic acid); cRNA (complementary RNA);RNase (ribonuclease); DNase (deoxyribonuclease);rRNA (ribosomal RNA); mRNA (messenger RNA);tRNA (transfer RNA); AMP, ADP, ATP, dAMP,ddATP, GTP, etc. (for the respective 5� phosphates ofadenosine and other nucleosides) (add 2�-, 3�-, or 5�-when needed for contrast); ATPase, dGTPase, etc.(adenosine triphosphatase, deoxyguanosine triphospha-tase, etc.); NAD (nicotinamide adenine dinucleotide);NAD� (nicotinamide adenine dinucleotide, oxidized);NADH (nicotinamide adenine dinucleotide, reduced);NADP (nicotinamide adenine dinucleotide phosphate);NADPH (nicotinamide adenine dinucleotide phosphate,reduced); NADP� (nicotinamide adenine dinucleotidephosphate, oxidized); poly(A), poly(dT), etc. (polyade-nylic acid, polydeoxythymidylic acid, etc.); oligo(dT), etc.(oligodeoxythymidylic acid, etc.); UV (ultraviolet); PFU(plaque-forming units); CFU (colony-forming units);MIC (minimal inhibitory concentration); Tris [tris(hy-droxymethyl)aminomethane]; DEAE (diethylaminoethyl);EDTA (ethylenediaminetetraacetic acid); EGTA [ethyl-ene glycol-bis(�-aminoethyl ether)-N,N,N�,N�-tetraaceticacid]; HEPES (N-2-hydroxyethylpiperazine-N�-2-eth-anesulfonic acid); PCR (polymerase chain reaction); andAIDS (acquired immunodeficiency syndrome). Abbrevia-tions for cell lines (e.g., HeLa) also need not be defined.

The following abbreviations should be used withoutdefinition in tables:

amt (amount) SE (standard error)approx (approximately) SEM (standard error of theavg (average) mean)concn (concentration) sp act (specific activity)diam (diameter) sp gr (specific gravity)expt (experiment) temp (temperature)exptl (experimental) tr (trace)ht (height) vol (volume)mo (month) vs (versus)mol wt (molecular weight) wk (week)no. (number) wt (weight)prepn (preparation) yr (year)SD (standard deviation)

Drugs. Should an author decide to abbreviate the



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names of antimicrobial agents in a manuscript, the fol-lowing standard abbreviations are strongly recom-mended.

Antibacterial agents. Amikacin, AMK; amoxicillin,AMX; amoxicillin-clavulanic acid, AMC; ampicillin,AMP; ampicillin-sulbactam, SAM; azithromycin, AZM;azlocillin, AZL; aztreonam, ATM; carbenicillin, CAR;cefaclor, CEC; cefadroxil, CFR; cefamandole, FAM; ce-fazolin, CFZ; cefdinir, CDR; cefditoren, CDN; cefepime,FEP; cefetamet, FET; cefixime, CFM; cefmetazole, CMZ;cefonicid, CID; cefoperazone, CFP; cefotaxime, CTX;cefotetan, CTT; cefoxitin, FOX; cefpodoxime, CPD; cef-prozil, CPR; ceftazidime, CAZ; ceftibuten, CTB; cefti-zoxime, ZOX; ceftriaxone, CRO; cefuroxime (axetil)and cefuroxime (sodium), CXM; cephalexin, LEX;cephalothin, CEF; cephapirin, HAP; cephradine, RAD;chloramphenicol, CHL; cinoxacin, CIN; ciprofloxacin,CIP; clarithromycin, CLR; clinafloxacin, CLX; clinda-mycin, CLI; daptomycin, DAP; dicloxacillin, DCX;dirithromycin, DTM; doxycycline, DOX; enoxacin,ENX; erythromycin, ERY; fleroxacin, FLE; fosfomy-cin, FOF; gatifloxacin, GAT; gentamicin, GEN; grepa-floxacin, GRX; imipenem, IPM; kanamycin, KAN; levo-floxacin, LVX; linezolid, LZD; lomefloxacin, LOM;loracarbef, LOR; meropenem, MEM; methicillin, MET;mezlocillin, MEZ; minocycline, MIN; moxalactam,MOX; moxifloxacin, MXF; nafcillin, NAF; nalidixicacid, NAL; netilmicin, NET; nitrofurantoin, NIT; nor-floxacin, NOR; ofloxacin, OFX; oxacillin, OXA; penicil-lin, PEN; piperacillin, PIP; piperacillin-tazobactam,TZP; quinupristin-dalfopristin (Synercid), Q-D; rifabu-tin, RFB; rifampin, RIF; rifapentine, RFP; sparfloxacin,SPX; spectinomycin, SPT; streptomycin, STR; teicoplanin,TEC; telithromycin, TEL; tetracycline, TET; ticarcillin,TIC; ticarcillin-clavulanic acid, TIM; tobramycin, TOB;trimethoprim, TMP; trimethoprim-sulfamethoxazole,SXT; trovafloxacin, TVA; and vancomycin, VAN.

�-Lactamase inhibitors. Clavulanic acid, CLA; sulbac-tam, SUL; and tazobactam, TZB.

Antifungal agents. Amphotericin B, AMB; clotrim-azole, CLT; flucytosine, 5FC; fluconazole, FLC; itracon-azole, ITC; ketoconazole, KTC; nystatin, NYT; terbin-afine, TRB; and voriconazole, VRC.

Antiviral agents. Acyclovir, ACV; cidofovir, CDV;famciclovir, FCV; foscarnet, FOS; ganciclovir, GCV;penciclovir, PCV; valaciclovir, VCV; and zidovudine,AZT.

Reporting Numerical Data

Standard metric units are used for reporting length,weight, and volume. For these units and for molarity, usethe prefixes m, �, n, and p for 10�3, 10�6, 10�9, and10�12, respectively. Likewise, use the prefix k for 103.Avoid compound prefixes such as m� or ��. Use �g/ml

or �g/g in place of the ambiguous ppm. Units of tem-perature are presented as follows: 37°C or 324 K.

When fractions are used to express units such as enzy-matic activities, it is preferable to use whole units, such as‘‘g’’ or ‘‘min,’’ in the denominator instead of fractional ormultiple units, such as �g or 10 min. For example, ‘‘pmol/min’’ is preferable to ‘‘nmol/10 min,’’ and ‘‘�mol/g’’ is pref-erable to ‘‘nmol/�g.’’ It is also preferable that anunambiguous form such as exponential notation be used;for example, ‘‘�mol g�1 min�1’’ is preferable to ‘‘�mol/g/min.’’ Always report numerical data in the appropriate SIunits.

Representation of data as accurate to more than twosignificant figures must be justified by presentation ofappropriate statistical analyses.

For a review of some common errors associated withstatistical analyses and reports, plus guidelines on how toavoid them, see the article by Olsen (Infect. Immun.71:6689–6692, 2003).

For a review of basic statistical considerations for vi-rology experiments, see the article by Richardson andOverbaugh (J. Virol. 79:669–676, 2005).

Statistics

Statistical analysis of data is a crucial component ofscientific publication. Authors who are unsure of properstatistical analysis should have their manuscriptschecked by a qualified statistician.

The following is a list of important items that must beconsidered before manuscript submission. Deficienciesin any of these areas may delay review and/or publica-tion.

• Statistical analyses were performed on all quanti-tative data regardless of how significant the differ-ences look in the tables or figures.

• Data were appropriately analyzed as parametric(normally distributed) or nonparametric data.

• Parametric and nonparametric data are presentedappropriately. Means and standard deviations orstandard errors are appropriate means of present-ing data analyzed by parametric analyses (i.e., t testand analysis of variance [ANOVA]), but only me-dians and surrounding levels (quartiles, quintiles,10th and 90th percentiles, etc.) are appropriate fornonparametric statistics (Mann-Whitney test,Kruskal-Wallis test, etc.). Means have no meaningin nonparametric analyses.

• For any data in which there are more than twocomparisons (i.e., between one control and morethan one experimental group), an analysis must bedone for multigroup comparisons. Such an analysiswould usually be an ANOVA for parametric dataor a Kruskal-Wallis test for nonparametric data. ttests cannot be used when more than two groupsare being compared (except as indicated below).Failure to use multigroup tests generates type 1



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errors: concluding that two data sets within theoverall data set being compared are different whenin fact they are not. Exception: Some statisticiansargue that two-group comparisons can be used onmultigroup data if the expected outcomes are appro-priately anticipated before the experiment. For exam-ple, data generated by individually testing two unre-lated factors for their effects on a target with only asingle, untreated target as a control could be appro-priately analyzed by t tests instead of ANOVA.

• For all appropriate multigroup comparisons, two Pvalues must be generated and provided in themanuscript. The main P value applies to the overalldata set and indicates that within that data set atleast two groups differ from each other. The overallP value does not indicate which two groups aredifferent. The main P value and the overall P valueshould be computed by using a post hoc test. ForANOVA, these post hoc tests are usually Dunnett’stest (used to compare multiple experimental groupsto a single control), the Fisher protected least sig-nificant difference (PLSD) test, the Tukey-Kramertest, and the Games-Howell test. Others may beused. Note that each post hoc test has certain un-derlying assumptions that may not be applicable tothe data under analysis. For a Kruskal-Wallis non-parametric ANOVA, the Dunn procedure is appro-priate to generate P values for two-group compar-isons.

• Data presented as endpoints (i.e., LD50, ID50, etc.)contain both the calculated value and a confidenceinterval with a statistical significance associatedwith it (95%, 99%, or similar confidence interval),calculated by logit or probit analysis. Simple LD50values such as Reed-Muench calculations may notbe used alone.

• When samples are taken multiple times from oneexperimental entity (i.e., multiple serum samplesfrom one animal, gross pathological scores mea-sured for the same animal over time, growth curves,etc.), one cannot use analyses such as t tests,ANOVA, the Mann-Whitney test, etc., becausethese tests assume that each measure is indepen-dent. An entity with a high score on day 1 is morelikely to have a high score on day 2 than is an entitywith a low score. It is likely that some expert sta-tistical help will be needed for these situations, usu-

ally involving regression analysis, survival analysis,etc.

• Statistical significance and biological significanceare not the same. There is nothing magic about a Pvalue of 0.05. When results from small sample sizesare compared, a P value of 0.05 will often beobtained, but it may be dependent on the outcomeof a single experimental value. If sample sizes aresmall, then more-vigorous (i.e., smaller) P valuesmay be necessary. If sample sizes are large, P valuesof �0.05 may be important. There should be bothstatistical and biological significance to the resultsand conclusions in the manuscript.

For a review of some common errors associated withstatistical analyses and reports, plus guidelines on how toavoid them, see the article by Olsen (Infect. Immun.71:6689–6692, 2003).

For a review of basic statistical considerations for vi-rology experiments, see the article by Richardson andOverbaugh (J. Virol. 79:669–676, 2005).

Isotopically Labeled Compounds

For simple molecules, labeling is indicated in thechemical formula (e.g., 14CO2, 3H2O, and H2

35SO4).Brackets are not used when the isotopic symbol isattached to the name of a compound that in its naturalstate does not contain the element (e.g., 32S-ATP) orto a word that is not a specific chemical name (e.g.,131I-labeled protein, 14C-amino acids, and 3H-ligands).

For specific chemicals, the symbol for the isotope in-troduced is placed in square brackets directly precedingthe part of the name that describes the labeled entity.Note that configuration symbols and modifiers precedethe isotopic symbol. The following examples illustratecorrect usage:

[14C]urea UDP-[U-14C]glucoseL-[methyl-14C]methionine E. coli [32P]DNA[2,3-3H]serine fructose 1,6-[1-32P]bisphosphate[-14C]lysine [�-32P]ATP

JCM follows the same conventions for isotopic label-ing as the Journal of Biological Chemistry, and more-detailed information can be found in the instructions toauthors of that journal (first issue of each year).



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