JOURNAL OF CLINICAL MICROBIOLOGY: 2008 INSTRUCTIONS TO AUTHORS

The Journal of Clinical Microbiology (JCM) is devoted to thedissemination of new knowledge concerning the microbiologicalaspects of human and animal infections and infestations, particularlytheir etiological agents, diagnosis, and epidemiology. CaseReports will be considered if they are novel, add to existingknowledge, and are oriented toward microbiology. (See p. 12for a description of the two different types of Case Reportspublished.) Manuscripts describing members of the "normal" humanmicrobiota that become involved in disease production or complicationand manuscripts dealing with the interactions of hospitalizedpatients and the microbial environment of the hospital may alsobe submitted for consideration.

ASM publishes a number of different journals covering variousaspects of the field of microbiology. Each journal has a prescribedscope which must be considered in determining the most appropriatejournal for each manuscript. The following guidelines may beof assistance.

(i) JCM will consider manuscripts (a) that describe the useof antimicrobial, antiparasitic, or anticancer agents as toolsin the isolation, identification, or epidemiology of microorganismsassociated with disease; (b) that are concerned with qualitycontrol procedures for diffusion, elution, or dilution testsfor determining susceptibilities to antimicrobial agents inclinical laboratories; and (c) that deal with applications ofcommercially prepared tests or kits to assays performed in clinicallaboratories to measure the activities of established antimicrobialagents or their concentrations in body fluids. Manuscripts onall other aspects of antimicrobial or antiparasitic agents,including reports concerned with development or modificationof assay methods and validation of their sensitivity and specificity,will be considered for publication in Antimicrobial Agents andChemotherapy.

(ii) JCM will consider manuscripts dealing with the isolationor identification of viral agents from humans and animals, withviral pathogenesis and immunity, and with the etiology and diagnosisof viral diseases. In addition, epidemiological studies of viraldiseases or those involving the use of bacteriophages as a typingsystem or to identify bacteria will be considered. However,papers on the biology of phages and other viruses are more appropriatefor the Journal of Virology or the Journal of Bacteriology.

(iii) Reports of clinical microbiology investigations or studiesof the hospital population and the environment as they relateto nosocomial infections should be submitted to JCM. Manuscriptsdealing with ecology or environmental studies or with the applicationof microorganisms to agricultural or industrial processes aremore appropriate for Applied and Environmental Microbiology.

(iv) Papers involving clinical immunology, vaccines, or assessmentand laboratory diagnostic aspects of immunologic diseases (e.g.,autoimmune diseases and primary immunodeficiencies) are moreappropriate for Clinical and Vaccine Immunology (formerly Clinicaland Diagnostic Laboratory Immunology). Manuscripts dealing withmechanisms of pathogenicity are appropriate for Infection andImmunity.

(v) Manuscripts that describe detection of infectious agentsby using already well described techniques (e.g., RT-PCR, RAPD,PFGE, real-time PCR, etc.) will not be considered for publicationunless application of the technique substantially improves thediagnostic process. It is expected that such manuscripts willcompare sensitivity, specificity, and accuracy data with dataobtained from more conventional methods using clinical specimens.

(vi) JCM will consider manuscripts that describe diagnosticmicrobiology assays and those that compare assay performances.To improve the accuracy and ensure the completeness of theirstudies, authors should refer to the Standards for Reportingof Diagnostic Accuracy (STARD) for guidance. The entire setof guidelines, including checklists, may be found at http://www.consort-statement.org/stardstatement.htm.

Questions about these guidelines may be directed to the editorin chief of the journal being considered.

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

Note that a manuscript rejected by one ASM journal on scientificgrounds or on the basis of its general suitability for publicationis considered rejected by all other ASM journals.

EDITORIAL POLICY

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EDITORIAL POLICY

Use of Microbiological Information

The Council Policy Committee (CPC) of the American Society forMicrobiology affirms the long-standing position of the Societythat microbiologists will work for the proper and beneficentapplication of science and will call to the attention of thepublic or the appropriate authorities misuses of microbiologyor of information derived from microbiology. ASM members areobligated to discourage any use of microbiology contrary tothe welfare of humankind, including the use of microbes as biologicalweapons. Bioterrorism violates the fundamental principles expressedin the Code of Ethics of the Society and is abhorrent to ASMand its members.

ASM recognizes that there are valid concerns regarding the publicationof information in scientific journals that could be put to inappropriateuse as described in the CPC resolution mentioned above. Membersof the ASM Publications Board will evaluate the rare manuscriptthat might raise such issues during the review process. However,as indicated elsewhere in these Instructions, research articlesmust contain sufficient detail, and material/information mustbe made available, to permit the work to be repeated by others.Supply of materials should be in accordance with laws and regulationsgoverning the shipment, transfer, possession, and use of biologicalmaterials and must be for legitimate, bona fide research needs.Links to, and information regarding, these laws and regulationscan be found at http://www.asm.org/Policy/index.asp.

General Requirements

Manuscripts submitted to the journal must represent reportsof original research, and the original data must be availablefor review by the editor if necessary.

All authors of a manuscript must have agreed to its submissionand are responsible for its content (initial submission andany subsequent versions), including appropriate citations andacknowledgments, and must also have agreed that the correspondingauthor has the authority to act on their behalf in all matterspertaining to publication of the manuscript. The correspondingauthor is responsible for obtaining such agreements and forinforming the coauthors of the manuscript's status throughoutthe submission, review, and publication process. For Authors’Corrections and Retractions, signed letters of agreement fromall of the authors must be submitted (see p. 13).

By submission of a manuscript to the journal, the authors guaranteethat they have the authority to publish the work and that themanuscript, or one with substantially the same content, wasnot published previously, is not being considered or publishedelsewhere, and was not rejected on scientific grounds by anotherASM journal.

It is expected that the authors will provide written assurancethat permission to cite unpublished data or personal communicationshas been granted.

By publishing in the journal, the authors agree that, subjectto requirements or limitations imposed by laws or governmentalregulations of the United States, any DNAs, viruses, microbialstrains, mutant animal strains, cell lines, antibodies, andsimilar materials newly described in the article are availablefrom a national collection or will be made available in a timelyfashion, at reasonable cost, and in limited quantities to membersof the scientific community for noncommercial purposes. Theauthors guarantee that they have the authority to comply withthis policy either directly or by means of material transferagreements through the owner.

Similarly, the authors agree to make available computer programs,originating in the authors’ laboratory, that are the onlymeans of confirming the conclusions reported in the articlebut that are not available commercially. The program(s) andsuitable documentation regarding its (their) use may be providedby any of the following means: (i) as a program transmittedvia the Internet, (ii) as an Internet server-based tool, or(iii) as a compiled or assembled form on a suitable medium (e.g.,magnetic or optical). It is expected that the material willbe provided in a timely fashion and at reasonable cost to membersof the scientific community for noncommercial purposes. Theauthors guarantee that they have the authority to comply withthis policy either directly or by means of material transferagreements through the owner.

Primary Publication

A scientific paper or its substance published in a serial, periodical,book, conference report, symposium proceeding, or technicalbulletin, posted on a nonpersonal website, or made availablethrough any other retrievable source, including CD-ROM and otherelectronic forms, is unacceptable for submission to an ASM journalon grounds of prior publication. Work, or its substance, presentedas a meeting poster and subsequently reproduced or distributedas a "company white paper" is also unacceptable for submissionon grounds of prior publication.

Posting of a method/protocol on a nonpersonal website shouldnot interfere with the author's ability to have a manuscriptutilizing that technique considered for publication in an ASMjournal; however, ultimately, it is an editorial decision whetherthe method constitutes the substance of a paper.

Posting of a limited amount of original data on a personal/university/companywebsite or websites of small collaborative groups working ona problem does not preclude subsequent submission to, and publicationby, an ASM journal. The posted data, however, may not constitutethe substance of the submission. Specific questions about thispolicy may be referred to the Publications Board chairman ona case-by-case basis.

Posting of theses and dissertations on a personal/university-hostedwebsite does not preclude subsequent submission to, and publicationby, an ASM journal. Similarly, posting for sale on a commercialor similar website of an original, unmodified thesis or dissertation(i.e., as submitted to, and accepted by, the thesis/dissertationcommittee) does not preclude subsequent submission to, and publicationby, an ASM journal.

Posting of unpublished sequence data on the Internet is usuallynot considered prior publication; however, the address (URL)of the source of the sequence should be included in the text.

Preliminary disclosures of research findings webcast as meetingpresentations or published in abstract form as adjuncts to ameeting, e.g., part of a program, are not considered prior publication.

It is incumbent upon the author to acknowledge any prior publication,including his own articles, of the data contained in a manuscriptsubmitted to an ASM journal. A copy of the relevant work shouldbe submitted with the paper as supplemental material.

Ultimately, it is an editorial decision whether the materialconstitutes the substance of a paper.

Permissions

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

The original signed permission(s) must be submitted directlyto the editor, outside the Rapid Review system, no later thanthe modification stage and should be identified as to the relevantitem in the ASM manuscript (e.g., "permissions for Fig. 1 inJCM00123-08"). In addition, a statement indicating that thematerial is being reprinted with permission must be includedin the relevant figure legend or table footnote of the manuscript.Reprinted text must be enclosed in quotation marks, and thepermission statement must be included as running text or indicatedparenthetically.

For supplemental material intended for posting by ASM (see p.5), if the authors of the JCM manuscript are not also the ownersof the supplemental material, the corresponding author mustsend to ASM signed permission from the copyright owner thatallows posting of the material, as a supplement to the article,by ASM. The corresponding author is also responsible for incorporatingin the supplemental material any copyright notices requiredby the owner.

Authorship

An author is one who made a substantial contribution to theoverall design and execution of the experiments; therefore,ASM considers all authors responsible for the entire paper.Individuals who provided assistance, e.g., supplied strainsor reagents or critiqued the paper, need not be listed as authorsbut may be recognized in the Acknowledgments section.

A study group, surveillance team, working group, consortium,or the like (e.g., the Active Bacterial Core Surveillance Team)may be listed as a coauthor in the byline if its contributingmembers satisfy the requirements for authorship and accountabilityas described in these Instructions. The names (and institutionalaffiliations if desired) of the contributing members only maybe given in a footnote keyed to the study group name in thebyline or as a separate paragraph in the Acknowledgments section.

If the contributing members of the group associated with thework do not fulfill the criteria of substantial contributionto and responsibility for the paper, the group may not be listedin the author byline. Instead, it and the names of its contributingmembers may be listed in the Acknowledgments section.

All authors must agree to the order in which their names arelisted in the byline. Statements regarding equal contributionsby two or more authors (e.g., X.J. and Y.S. contributed equallyto ...) are permitted as footnotes to bylines and must be agreedto by all of the authors. Other statements of attribution maybe included in the Acknowledgments section.

A change in authorship (order of listing, addition or deletionof a name, or corresponding author designation) after submissionof the manuscript will be implemented only after receipt ofsigned statements of agreement from all parties involved.

Disputes about authorship may delay or prevent review and/orpublication of the manuscript. Should the individuals involvedbe unable to reach an accord, review and/or publication of themanuscript can proceed only after the matter is investigatedand resolved by the authors’ institution(s) and an officialreport of such and signed statements of agreement are providedto ASM.

Conflict of Interest

All authors are expected to disclose, in the manuscript submittalletter, any commercial affiliations as well as consultancies,stock or equity interests, and patent-licensing arrangementsthat could be considered to pose a conflict of interest regardingthe submitted manuscript. (Inclusion of a company name in theauthor address lines of the manuscript does not constitute disclosure.)Details of the disclosure to the editor will remain confidential.However, it is the responsibility of authors to provide, inthe Acknowledgments section, a general statement disclosingfinancial or other relationships that are relevant to the study.Examples of potentially conflicting interests that should bedisclosed include relationships that might detract from an author'sobjectivity in presentation of study results, and interestswhose value would be enhanced by the results presented. Allfunding sources for the project, institutional and corporate,should be credited in the Acknowledgments section, as describedbelow. In addition, if a manuscript concerns a commercial product,the manufacturer's name must be indicated in the Materials andMethods section or elsewhere in the text, as appropriate, inan obvious manner.

Copyright

To maintain and protect the Society's ownership and rights andto continue to afford scientists the opportunityto publish inhigh-quality journals, ASM requires the corresponding authorto sign a copyright transfer agreement on behalf of all theauthors. This agreement is sent to the corresponding authorwhen the manuscript is accepted and scheduled for publication.Unless this agreement is executed (without changes and/or addenda),ASM will not publish the article.

In the copyright transfer agreement signed by an author, ASMgrants to that author (and coauthors) the right to republishdiscrete portions of his (their) article in any other publication(print, CD-ROM, and other electronic forms) of which he is (theyare) the author(s) or editor(s), on the condition that appropriatecredit is given to the original ASM publication. This republicationright also extends to posting on a host computer to which thereis access via the Internet. Except as indicated below, significantportions of the article may not be reprinted/posted withoutASM's prior written permission, however, as this would constituteduplicate publication.

Authors may post their own published articles on their personalor university-hosted (but not corporate, government, or similar)websites without ASM's prior written permission provided thatappropriate credit is given (i.e., either the copyright linesshown on the top of the first page of the PDF version or "Copyright\C American Society for Microbiology, [insert journal name,volume number, page numbers, and year]" for the HTML version).

The copyright transfer agreement asks that authors who wereU.S. government employees and who wrote the article as partof their employment duties be identified. This is because worksauthored solely by such U.S. government employees are not subjectto copyright protection, so there is no copyright to be transferred.The other provisions of the copyright transfer agreement, suchas author representations of originality and authority to enterinto the agreement, apply to U.S. government employee-authorsas well as to other authors.

Copyright for supplemental material (see p. 5) remains withthe author, but a license permitting the posting by ASM willbe sent, along with the article copyright transfer agreement,to the corresponding author for signing at the acceptance stage.(If the author of the article is not also the copyright ownerof the supplemental material, the corresponding author mustsend to ASM signed permission from the owner that allows postingof the material, as a supplement to the article, by ASM. Thecorresponding author is also responsible for incorporating intothe supplemental material any copyright notices required bythe owner.)

Funding Agency Repositories

The National Institutes of Health (NIH) requests that its granteeand intramural authors provide copies of their accepted manuscriptsto PubMed Central (PMC) for posting in the PMC Public AccessRepository. ASM allows such JCM authors to do so. ASM also allowsJCM authors whose work was supported by similar funding agenciesthat have public access requirements like those of the NIH (e.g.,the Wellcome Trust) to post their accepted manuscripts in publiclyaccessible electronic repositories maintained by those fundingagencies. If a funding agency does not itself maintain sucha site, then ASM allows the author to fulfill that requirementby depositing the manuscript (not the typeset article) in anappropriate institutional or subject-based open repository establishedby a government or noncommercial entity.

Since ASM makes the final, typeset articles from its primary-researchjournals available free of charge on the ASM Journals and PMCwebsites 4 months after final publication, ASM recommends thatwhen submitting the accepted manuscript to PMC or a similarpublic access site, the author specify that the posting releasedate for the manuscript be no earlier than 4 months after publicationof the typeset article by ASM.

Use of Human Subjects or Animals in Research

The use of human subjects or other animals for research purposesis regulated by the federal government and individual institutions.Manuscripts containing in-formation related to human or animaluse should clearly state that the research has complied withall relevant federal guidelines and institutional policies.Copies of these guidelines and policy statements must be availablefor review by the editor if necessary.

Patient Identification

To protect the privacy of individuals mentioned in clinicalstudies, in case histories, and as sources of isolates, do notidentify them by their initials, even as part of a strain designation.Change the initials to numerals or use randomly chosen letters.Do not give hospital unit numbers; if a designation is needed,use only the last two digits of the unit. (Note: Establisheddesignations of some viruses and cell lines, although they consistof initials, are acceptable [e.g., JC virus, BK virus, and HeLacells].)

Nucleotide and Amino Acid Sequences

It is expected that newly determined nucleotide and/or aminoacid sequence data will be deposited and GenBank/EMBL/DDBJ accessionnumbers will be included in the manuscript no later than themodification stage of the review process. It is also expectedthat the sequence data will be released to the public no laterthan the publication (online posting) date of the accepted manuscript.The accession numbers should be included in a separate paragraphat the end of the Materials and Methods section for full-lengthpapers or at the end of the text for Notes. If conclusions ina manuscript are based on the analysis of sequences and a GenBank/EMBL/DDBJaccession number is not provided at the time of the review,authors should provide the sequence data as supplemental material.

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

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

Analyses should specify the database, and the date of each analysisshould be indicated as, e.g., January 2008. If relevant, theversion of the software used should be specified.

See p. 16 for nucleic acid sequence formatting instructions.

The URLs of the databases mentioned above are as follows: DNAData Bank of Japan (DDBJ), http://www.ddbj.nig.ac.jp/; EMBLNucleotide Sequence Database (EMBL), http://www.ebi.ac.uk/embl/;and GenBank, National Center for Biotechnology Information (GenBank),http://www.ncbi.nlm.nih.gov/.

Structural Determinations

It is expected that coordinates for new structures of macromoleculeswill be deposited in the Protein Data Bank and that assignedidentification codes will be included in the manuscript no laterthan the modification stage of the review process. It is alsoexpected that the coordinates will be released to the publicno later than the publication (online posting) date of the acceptedmanuscript. Authors are encouraged to send coordinates withtheir original submission, however, so that reviewers can examinethem along with the manuscript. The accession number(s) shouldbe listed in a separate paragraph at the end of the Materialsand Methods section for full-length papers or at the end ofthe text for Notes.

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

Microarray Data

It is expected that the entire set of supporting microarraydata will be deposited in the appropriate public database (e.g.,GEO, ArrayExpress, or CIBEX) and that the assigned accessionnumber(s) will be included in the manuscript no later than themodification stage of the review process. It is also expectedthat the data will be released to the public no later than thepublication (online posting) date of the accepted manuscript.Authors are encouraged to send the relevant data with theiroriginal submission, however, so that reviewers can examinethem along with the manuscript. The accession number(s) shouldbe listed in a separate paragraph at the end of the Materialsand Methods section for full-length papers or at the end ofthe text for Notes.

The URLs of the databases mentioned above are as follows: GeneExpression Omnibus (GEO), http://www.ncbi.nlm.nih.gov/projects/geo/;ArrayExpress, http://www.ebi.ac.uk/arrayexpress/?#ae=main[0];and Center for Information Biology Gene Expression Database(CIBEX), http://cibex.nig.ac.jp/index.jsp.

Culture Deposition

JCM expects authors to deposit important strains in publiclyaccessible culture collections and to refer to the collectionsand strain numbers in the text. Since the authenticity of subculturesof culture collection specimens that are distributed by individualscannot be ensured, authors should indicate laboratory straindesignations and donor sources as well as original culture collectionidentification numbers.

Supplemental Material

Supplemental material intended for posting by ASM may not includeadditional figures or tables that simply support the authors’conclusions. It must be restricted to large or complex datasets or results that cannot readily be displayed in printedform because of space or technical limitations. Such materialmay include data from microarray, structural, biochemical, orvideo imaging analyses. In such cases, the manuscript submittedfor review should include a distillation of the results so thatthe principal conclusions are fully supported without referralto the supplemental material.

Supplemental material intended for posting by ASM must be uploadedin Rapid Review and will be reviewed along with the manuscript.The maximum size permitted for an individual file is 25 MB.If your file exceeds this size, you must use a file compressionutility (e.g., WinZip or Stuffit) to reduce the size below 25MB. The decision to publish (i.e., post online only) the materialwith the article if it is accepted will be made by the editorand conveyed to the corresponding author in the acceptance e-mail.Therefore, it is possible that a manuscript will be acceptedbut that the supplemental material will not be.

If the software required for users to view/use the supplementalmaterial is not embedded in the file, you are urged to use sharewareor generally available/easily accessible programs.

Unlike the manuscript, supplemental material will not be editedby the ASM Journals staff and proofs will not be made available.References related to supplemental material only should notbe listed in the References section of an article; instead,include them with the supplemental material hosted by ASM orposted on a personal/institutional website.

Supplemental material will always remain associated with itsarticle and is not subject to any modifications after publication.

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

Copyright for the supplemental material remains with the author,but a license permitting the posting by ASM will be sent, alongwith the article copyright transfer agreement, to the correspondingauthor for signing. If you are not the copyright owner, youmust provide to ASM signed permission from the owner that allowsposting of the material, as a supplement to your article, byASM. You are responsible for including in the supplemental materialany copyright notices required by the owner.

A one-time charge (amount not yet determined) may be leviedfor posting of supplemental material. When instituted, the chargewill be indicated in the ASM acceptance letter.

Compliance

Failure to comply with the policies described in these Instructionsmay result in a letter of reprimand, a suspension of publishingprivileges in ASM journals, and/or notification of the authors’institutions. Authors employed by companies whose policies donot permit them to comply with the ASM policies may be sanctionedas individuals and/or ASM may refuse to consider manuscriptshaving authors from such companies.

Warranties and Exclusions

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

Page Charges

Authors whose research was supported by grants, special funds(including departmental and institutional), or contracts (includinggovernmental) or whose research was done as part of their officialduties (government, corporate, etc.) are required to pay pagecharges (based on the number of typeset pages, including illustrations,in the article).

For a corresponding author who is an ASM member, page chargesare currently $65 per page for the first eight pages and $200per page for each page in excess of eight (subject to changewithout notice). To obtain the member rate, the correspondingauthor must be an ASM member.

For a nonmember corresponding author, page charges are currently$75 per page for the first eight pages and $250 for each pagein excess of eight (subject to change without notice). A correspondingauthor who is not an ASM member may join ASM to obtain the memberrate.

If the research was not supported by any of the means describedabove, a request to waive the charges may be mailed (JournalsDepartment, ASM, 1752 N St., N.W., Washington, DC 20036-2904,USA) or faxed (202-942-9355) to the Journals Department. Thisrequest must indicate how the work was supported and shouldbe accompanied by copies of the title page and Acknowledgmentssection.

Minireviews, Guest Commentaries, and Comment Letters to theEditor are not subject to page charges. New-Data Letters tothe Editor and fast-track articles are subject to page charges.

Editorial Style

The editorial style of ASM journals conforms to the ASM StyleManual for Journals (American Society for Microbiology, 2008,in-house document) and How To Write and Publish a ScientificPaper, 6th ed. (Greenwood Press, Westport, CT, 2006), as interpretedand modified by the editors and the ASM Journals Department.

The editors and the Journals Department reserve the privilegeof editing manuscripts to conform with the stylistic conventionsset forth in the aforesaid publications and in these Instructions.

Review Process

All manuscripts are considered to be confidential and are reviewedby the editors, members of the editorial board, or qualifiedad hoc reviewers.

To expedite the review process, authors must recommend at leastthree editorial board members who have expertise in the field,who are not members of their institution(s), who have not recentlybeen associated with their laboratory(ies), and who could nototherwise be considered to pose a conflict of interest regardingthe submitted manuscript.

Copies of in-press and submitted manuscripts that are importantfor judgment of the present manuscript should be included assupplemental material to facilitate the review.

When a manuscript is submitted to the journal, it is given anumber (e.g., JCM00047-08 version 1) and assigned to one ofthe editors. (Always refer to this number in communicationswith the editor and the Journals Department.) It is the responsibilityof the corresponding author to inform the coauthors of the manuscript'sstatus throughout the submission, review, and publication processes.The reviewers operate under strict guidelines set forth in "Guidelinesfor the Reviewers" (http://www.journals.asm.org/misc/reviewguide.shtml)and are expected to complete their reviews expeditiously.

The corresponding author is notified, generally within 4 to6 weeks after submission, of the editor's decision to accept,reject, or require modification. When modification is requested,the corresponding author must either submit the modified versionwithin 2 months or withdraw the manuscript. A point-by-pointresponse to the reviews must be provided in the designated sectionof the Rapid Review submission form for the revised manuscript,and a compare copy of the manuscript (without figures) shouldbe included as supplemental material if the editor requestedone.

Manuscripts that have been rejected, or withdrawn after beingreturned for modification, may be resubmitted to the same ASMjournal if the major criticisms have been addressed. A manuscriptrejected by one ASM journal on scientific grounds or on thebasis of its general suitability for publication is consideredrejected by all other ASM journals; however, a manuscript rejectedsolely on the basis of scope may be "resubmitted" to a moreappropriate ASM journal. A manuscript is considered a resubmissionno matter how much (or little) it differs from the rejectedor withdrawn manuscript and regardless of how much time haspassed.

For all resubmissions (to the same or a different journal, andirrespective of the extent of the revisions and irrespectiveof the amount of time between rejection and resubmission), thecover letter must state that the manuscript is a resubmission,and the former manuscript number must be provided in the appropriatefield on the submission form. A point-by-point response to thereview(s) and a compare copy of the revised manuscript showingall changes must be included as supplemental material (the Rebuttalsection appears in the submission form only if the manuscriptis a modification). Manuscripts resubmitted to the same journalare normally handled by the original editor.

Rejected manuscripts may be resubmitted only once unless permissionhas been obtained from the original editor or from the editorin chief.

Notification of Acceptance

When an editor has decided that a manuscript is acceptable forpublication on the basis of scientific merit, the author andthe Journals Department are notified. A PDF version of the acceptedmanuscript is posted online as soon as possible (see below).

The text files undergo an automated preediting, cleanup, andtagging process specific to the particular article type, andthe illustrations are examined. If all files have been preparedaccording to the criteria set forth in these Instructions andthose in Rapid Review, the acceptance procedure will be completedsuccessfully. If there are problems that would cause extensivecorrections to be made at the copyediting stage or if the filesare not acceptable for production, ASM Journals staff will contactthe corresponding author. Once all the material intended forpublication has been determined to be adequate, the manuscriptis scheduled for the next available issue and an acceptanceletter indicating the month of publication, approximate pageproof dates, and table of contents section is mailed to thecorresponding author; a copyright transfer agreement is alsoincluded, as is a license to permit posting of supplementalmaterial (if applicable). The editorial staff of the ASM JournalsDepartment completes the editing of the manuscript to bringit into conformity with prescribed standards.

Publish ahead of Print

For its primary-research journals, ASM posts online PDF versionsof manuscripts that have been peer reviewed and accepted butnot yet copyedited. This feature is called "[journal acronym]Accepts" (e.g., JCM Accepts) and is accessible from the Journalswebsite. The manuscripts are published online as soon as possibleafter acceptance, on a weekly basis, before the copyedited,typeset articles are published. They are posted "as is" (i.e.,as submitted by the authors at the modification stage) and donot reflect ASM editorial changes. No corrections/changes tothe PDF manuscripts are accepted. Accordingly, there likelywill be differences between the JCM Accepts manuscripts andthe final, typeset articles. The manuscripts remain listed onthe JCM Accepts page until the final, typeset articles are posted.At that point, the manuscripts are removed from the JCM Acceptspage and become available only through links from the final,typeset articles. The manuscripts are under subscription accesscontrol until 4 months after the typeset articles are posted,when free access is provided to everyone (subject to the applicableASM license terms and conditions). Supplemental material intended,and accepted, for publication is not posted until publicationof the final, typeset article.

Instructions on how to cite such manuscripts may be found inthe "References" section below (p. 10).

Page Proofs

Page proofs, together with a query sheet and instructions forhandling proofs, will be made available to the correspondingauthor electronically via a PDF file that can be accessed througha unique password. Since corresponding authors will be notifiedof the availability of their PDF proofs, instructed how to accessinformation about page charges, reprints, and color figure charges(if applicable), and assigned their unique password via e-mail,an e-mail address must be supplied in the correspondent footnote.Failure to do so may result in a delay in publication. The PDFpage proofs must be printed out, and corrections must be writtenon the hard copy. Queries must be answered on the query pageor on a separate sheet of paper, and any changes related tothe queries must be indicated on the proofs. Note that the copyeditor does not query at every instance where a change has beenmade. Queries are written only to request necessary informationor clarification of an unclear passage or to draw attentionto edits that may have altered the sense. It is the author'sresponsibility to read the entire text, tables, and figure legends,not just items queried. As soon as the page proofs are correctedand signed by the person who proofread them (within 48 h), theyshould be mailed or sent by a courier service such as FedEx,not faxed or sent as an e-mail attachment, to the ASM JournalsDepartment.

The proof stage is not the time to make extensive corrections,additions, or deletions. Important new information that hasbecome available between acceptance of the manuscript and receiptof the proofs may be inserted as an addendum in proof with thepermission of the editor. If references to unpublished dataor personal communications are added, it is expected that writtenassurance granting permission for the citation will be included.Limit changes to correction of spelling errors, incorrect data,and grammatical errors and updated information for referencesto articles that have been submitted or are in press. If URLshave been provided in the article, recheck the sites to ensurethat the addresses are still accurate and the material thatyou expect the reader to find is indeed there.

Questions about late proofs and problems in the proofs shouldbe directed to the ASM Journals Department (telephone, 202-942-9384).Questions about accessing or viewing your PDF proofs shouldbe directed to Katie Gay of Cadmus Communications at 804-261-3155or gayk{at}cadmus.com.

Reprints

Reprints (in multiples of 100) may be purchased by all coauthors.In the proof notification e-mail, the corresponding author willbe instructed how to access information about reprints.

The corresponding authors of Minireviews and Guest Commentariesmay receive 100 free reprints of their contribution; additionalreprints (in multiples of 100) may be purchased if desired.As for regular articles, the corresponding author will be instructed,in the proof notification e-mail, how to access informationabout reprints.

PDF Files

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

Should coauthors or colleagues be interested in viewing thepaper for their own use, the corresponding author may providethem with the URL; a copy of the article may not be forwardedelectronically. However, they must be made aware of the termsand conditions of the ASM copyright. (For details, go to http://www.journals.asm.org/misc/terms.shtml.)Note that each such download will count toward the correspondingauthor's total of 10. After 10 downloads, access will be deniedand can be obtained only through a subscription to the journal(either individual or institutional) or after the standard accesscontrol has been lifted (i.e., 4 months after publication).

HOW TO SUBMIT MANUSCRIPTS

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HOW TO SUBMIT MANUSCRIPTS

All submissions to JCM must be made electronically via the RapidReview online submission and peer review system at the followingURL: https://www.rapidreview.com/ASM2/CALogon.jsp. (E-mailedsubmissions will not be accepted.) First-time users must createan Author account, which may be used for submitting to all ASMjournals. Instructions for creating an Author account are availableat the above URL under the Create Account button. Step-by-stepinstructions for submitting a manuscript via Rapid Review areavailable from the account holder's My Manuscripts page. Informationon file types acceptable for electronic submission can be foundunder the More About File Formats button.

PDFs of submitted manuscripts are retained in Rapid Review for1 to 2 years, after which they are deleted.

ORGANIZATION AND FORMAT

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ORGANIZATION AND FORMAT

On receipt at ASM, an accepted manuscript undergoes an automatedpreediting, cleanup, and tagging process specific to the particulararticle type. To optimize this process, manuscripts must besupplied in the correct format and with the appropriate sectionsand headings.

Type every portion of the manuscript double spaced (a minimumof 6 mm between lines), including figure legends, table footnotes,and References, and number all pages in sequence, includingthe abstract, figure legends, and tables. Place the last twoitems after the References section. Manuscript pages shouldhave line numbers; manuscripts without line numbers may be editoriallyrejected by the editor, with a suggestion of resubmission afterline numbers are added. The font size should be no smaller than12 points. It is recommended that the following sets of charactersbe easily distinguishable in the manuscript: the numeral zero(0) and the letter "oh" (O); the numeral one (1), the letter"el" (l), and the letter "eye" (I); and a multiplication sign(x) and the letter "ex" (x). Do not create symbols as graphicsor use special fonts that are external to your word processingprogram; use the "insert symbol" function. Set the page sizeto 8 $1/2$ by 11 inches (ca. 21.6 by 28 cm). Italicize or underlineany words that should appear in italics, and indicate paragraphlead-ins in bold type.

Authors who are unsure of proper English usage should have theirmanuscripts checked by someone proficient in the English language.

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

Full-Length Papers

Full-length papers include the elements described in this section.

Title, running title, and byline.

Each manuscript should present the results of an independent,cohesive study; thus, numbered series titles are not permitted.Exercise care in composing a title. Avoid the main title/subtitlearrangement, complete sentences, and unnecessary articles. Onthe title page include the title, running title (not to exceed54 characters and spaces), name of each author, address(es)of the institution(s) at which the work was performed, eachauthor's affiliation, and a footnote indicating the presentaddress(es) of any author(s) no longer at the institution wherethe work was performed. Place an asterisk after the name ofthe author to whom inquiries regarding the paper should be directed(see "Correspondent footnote" below).

Study group in byline.

A study group, surveillance team, working group, consortium,or the like (e.g., the Active Bacterial Core Surveillance Team)may be listed as a coauthor in the byline if its contributingmembers satisfy the requirements for authorship and accountabilityas described in these Instructions. The names (and institutionalaffiliations if desired) of the contributing members may begiven in a footnote keyed to the study group name in the bylineor as a separate paragraph in Acknowledgments.

Correspondent footnote.

The complete mailing address, a single telephone number, a singlefax number, and a single e-mail address for the correspondingauthor should be included on the title page of the manuscript.This information will be published in the article as a footnoteto facilitate communication, and the e-mail address will beused to notify the corresponding author of the availabilityof proofs and, later, of the PDF file of the published article.

Abstract.

Limit the abstract to 250 words or fewer and concisely summarizethe basic content of the paper without presenting extensiveexperimental details. Avoid abbreviations and references, anddo not include diagrams. When it is essential to include a reference,use the same format as shown for the References section butomit the article title. Conclude the abstract with a summarystatement. Because the abstract will be published separatelyby abstracting services, it must be complete and understandablewithout reference to the text.

Introduction.

The introduction should supply sufficient background informationto allow the reader to understand and evaluate the results ofthe present study without referring to previous publicationson the topic. The introduction should also provide the hypothesisthat was addressed or the rationale for the present study. Choosereferences carefully to provide the most salient backgroundrather than an exhaustive review of the topic.

Case Report.

The Case Report section, placed after the introduction and beforeMaterials and Methods, is optional and gives relevant clinicalinformation about one or more patients while being incidentalto the rest of the paper. (If the Case Report constitutes theentire article, the paper must be presented in Case Report format[see p. 12], which differs from that used for a full-lengthtext or a Note.)

Materials and Methods.

The Materials and Methods section must include sufficient technicalinformation to allow the experiments to be repeated. The sourcesof all media (i.e., name and location of manufacturer) or componentsof a new formulation must be provided. When centrifugation conditionsare critical, give enough information to enable another investigatorto repeat the procedure: make of centrifuge, model of rotor,temperature, time at maximum speed, and centrifugal force (xg rather than revolutions per minute). For commonly used materialsand methods (e.g., media and protein concentration determinations),a simple reference or specifically recommended product or procedureis sufficient. If several alternative methods are commonly used,it is helpful 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 described(9)" rather than to state "cells were broken as previously described(9)." This allows the reader to assess the method without constantreference to previous publications. Describe new methods completely,and give sources of unusual chemicals, reagents, equipment,or microbial strains. When large numbers of microbial strainsor mutants are used in a study, include tables identifying theimmediate sources (i.e., sources from whom the strains wereobtained) and properties of the strains, mutants, bacteriophages,plasmids, etc.

A method, strain, etc., used in only one of several experimentsreported in the paper may be described in the Results sectionor very briefly (one or two sentences) in a table footnote orfigure legend. It is expected that the sources from whom thestrains were obtained will be identified.

Results.

In the Results section, include the rationale or design of theexperiments as well as the results; reserve extensive interpretationof the results for the Discussion section. Present the resultsas concisely as possible in one of the following: text, table(s),or figure(s). Avoid extensive use of graphs to present datawhich might be more concisely presented in the text or tables.For example, except in unusual cases, double-reciprocal plotsused to determine apparent K_m values should not be presentedas graphs; instead, the values should be stated in the text.Similarly, graphs illustrating other methods commonly used toderive kinetic or physical constants (e.g., reduced-viscosityplots and plots used to determine sedimentation velocity) neednot be shown except in unusual circumstances. All tabular datamust be accompanied by either standard deviation values or standarderrors of the means. The number of replicate determinations(or animals) used for making such calculations must also beincluded. All statements concerning the significance of thedifferences observed should be accompanied by probability valuesgiven in parentheses. The statistical procedure used shouldbe stated in Materials and Methods. Limit illustrations (particularlyphotomicrographs and electron micrographs) to those that areabsolutely necessary to show the experimental findings. Numberfigures and tables in the order in which they are cited in thetext, and be sure to cite all figures and tables.

Discussion.

The Discussion section should provide an interpretation of theresults in relation to previously published work and to theexperimental system at hand. It must not contain extensive repetitionof the Results section or reiteration of the introduction. Inshort papers, the Results and Discussion sections may be combined.

Acknowledgments.

The source of any financial sup-port received for the work beingpublished must be indicated in the Acknowledgments section.(It will be assumed that the absence of such an acknowledgmentis a statement by the authors that no support was re-ceived.)The usual format is as follows: "This work was supported byPublic Health Service grant CA-01234 from the National CancerInstitute."

Recognition of personal assistance should be given as a separateparagraph, as should any statements disclaiming endorsementor approval of the views reflected in the paper or of a productmentioned therein.

Appendixes.

Appendixes, which contain additional material to aid the reader,are permitted. Titles, authors, and References sections thatare distinct from those of the primary article are not allowed.If it is not feasible to list the author(s) of the appendixin the byline or the Acknowledgments section of the primaryarticle, rewrite the appendix so that it can be considered forpublication as an independent article, either full-length orNote style. Equations, tables, and figures should be labeledwith the letter "A" preceding the numeral to distinguish themfrom those cited in the main body of the text.

References.

(i) References listed in the References section. The Referencessection must include all journal articles (both print and online),books and book chapters (both print and online), patents, thesesand dissertations, published conference proceedings, meetingabstracts from published abstract books or journal supplements,letters (to the editor), and company publications, as well asin-press journal articles, book chapters, and books (publicationtitle must be given). Arrange the citations in alphabeticalorder (letter by letter, ignoring spaces and punctuation) byfirst author and number consecutively. Provide the names ofall the authors for each reference. All listed references mustbe cited parenthetically by number in the text. Since titleand byline information that is downloaded from PubMed does notalways show accents, italics, or special characters, authorsshould refer to the PDF files or hard-copy versions of the articlesand incorporate the necessary corrections in the submitted manuscript.Abbreviate journal names according to the List of Journals Indexedfor Medline (National Library of Medicine, National Institutesof Health, 2007; available at ftp://nlmpubs.nlm.nih.gov/online/journals/ljiweb.pdf),the primary source for ASM style.

Follow the styles shown in the examples below for print references.

Arendsen, A. F., M. Q. Solimar, and S. W. Ragsdale. 1999. Nitrate-dependentregulation of acetate biosynthesis and nitrate respiration byClostridium thermoaceticum. J. Bacteriol. 181:1489-1495.
Cox,C. S., B. R. Brown, and J. C. Smith. J. Gen. Genet., inpress.*{Article title is optional; journal title is mandatory.}
daCosta, M. S., M. F. Nobre, and F. A. Rainey. 2001. GenusI.Thermus Brock and Freeze 1969, 295,^AL emend. Nobre, Trüperand da Costa 1996b, 605, p. 404-414. In D. R. Boone, R. W. Castenholz,and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology,2nd ed., vol. 1. Springer, New York, NY.
Elder, B. L., andS. E. Sharp. 2003. Cumitech 39, Competencyassessment in theclinical laboratory. Coordinating ed., S.E. Sharp. ASM Press,Washington, DC.
Falagas, M. E., and S. K. Kasiakou. 2006.Use of internationalunits when dosing colistin will help decreaseconfusion relatedto various formulations of the drug aroundthe world. Antimicrob.Agents Chemother. 50:2274-2275. (Letter.){"Letter" or "Letterto the editor" is allowed but not requiredat the end of suchan entry.}
Fitzgerald, G., and D. Shaw.In A. E. Waters (ed.), Clinicalmicrobiology, in press. EFHPublishing Co., Boston, MA.* {Chaptertitle is optional.}
Forman,M. S., and A. Valsamakis. 2003. Specimen collection,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. ASMPress, Washington,DC.
Garcia, C. O., S. Paira, R. Burgos, J. Molina, J. F. Molina,and C. Calvo. 1996. Detection of salmonella DNA in synovialmembrane and synovial fluid from Latin American patients. ArthritisRheum. 39(Suppl.):S185. {Meeting abstract published in journalsupplement.}
Green, P. N., D. Hood, and C. S. Dow. 1984. Taxonomicstatusof some methylotrophic bacteria, p. 251-254. In R. L.Crawfordand R. S. Hanson (ed.), Microbial growth on C₁ compounds.Proceedingsof the 4th International Symposium. American Societyfor Microbiology,Washington, DC.
Odell, J. C. April 1970.Process for batch culturing. U.S. patent484,363,770. {Includethe name of the patented item/processif possible; the patentnumber is mandatory.}
O'Malley, D. R. 1998. Ph.D. thesis.University of California,Los Angeles. {Title is optional.}
Rotimi, V. O., N. O. Salako, E. M. Mohaddas, and L. P. Philip.2005. Abstr. 45th Intersci. Conf. Antimicrob. Agents Chemother.,abstr. D-1658. {Abstract title is optional.}
Smith, D., C.Johnson, M. Maier, and J. J. Maurer. 2005. Distributionof fimbrial,phage and plasmid associated virulence genes amongpoultry Salmonellaenterica serovars, abstr. P-038, p. 445.Abstr. 105th Gen. Meet.Am. Soc. Microbiol. American Societyfor Microbiology, Washington,DC. {Abstract title is optional.}
Stratagene. 2006. YeastDNA isolation system: instruction manual.Stratagene, La Jolla,CA. {Use the company name as the authorif none is providedfor a company publication.}

*A reference to an in-press ASM publication should state thecontrol number (e.g., JCM00577-08) if it is a journal articleor the name of the publication if it is a book.

Online references must provide the same information that printreferences do, but some variation is allowed. For online journalarticles, posting or revision dates may replace the year ofpublication, and a DOI or URL may be provided in addition toor in lieu of volume and page numbers. Some examples follow.

Charlier, D., and N. Glansdorff. September 2004, posting date.Chapter 3.6.1.10, Biosynthesis of arginine and polyamines. InR. Curtiss III et al. (ed.), EcoSal—Escherichia coli andSalmonella: cellular and molecular biology. ASM Press, Washington,DC. http://www.ecosal.org/ecosal/index.jsp. {Note that eachchapter has its own posting date.}
Dionne, M. S., and D. S.Schneider. 2002. Screen-ing the fruitflyimmune system. GenomeBiol. 3:REVIEWS1010. http://genomebiology.com/2002/3/4/reviews/1010.
Smith, F. X., H. J. Merianos, A. T. Brunger, and D. M. Engelman.2001. Polar residues drive association of polyleucine transmembranehelices. Proc. Natl. Acad. Sci. USA 98:2250-2255. doi:10.1073/pnas.041593698.
Winnick, S., D. O. Lucas, A. L. Hartman, and D. Toll. 2005.How do you improve compliance? Pediatrics 115:e718-e724.

NOTE: A posting or accession date is required for any onlinereference that is periodically updated or changed.

(ii) References cited in the text. References to unpublisheddata, manuscripts submitted for publication, unpublished conferencepresentations (e.g., a report or poster that has not appearedin published conference proceedings), personal communications,patent applications and patents pending, computer software,databases, and websites (home pages) should be made parentheticallyin the text as follows.

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

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

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

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

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

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

URLs for companies that produce any of the products mentionedin your study or for products being sold may NOT be includedin the article. However, company URLs that permit access toscientific data related to the study or to shareware used inthe study are permitted.

(iii) References related to supplemental material. Referencesthat are related only to supplemental material hosted by ASMor posted on a personal/institutional website should not belisted in the References section of an article; include themwith the supplemental material itself.

(iv) Referencing publish-ahead-of-print manuscripts. Citationsof ASM Accepts manuscripts should look like the following example.

Wang, G. G., M. P. Pasillas, and M. P. Kamps. 15 May 2006. Persistenttransactivation by Meis1 replaces Hox function in myeloid leukemogenesismodels: evidence for co-occupancy of Meis1-Pbx and Hox-Pbx complexeson promoters of leukemia-associated genes. Mol. Cell. Biol.doi:10.1128/MCB.00586-06.

If an author of an article cites an ASM Accepts manuscript inhis paper but wishes at the proof stage to change the referenceentry to that for the published article, the following styleshould be used:

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

Zhou, F. X., H. J. Merianos, A. T. Brunger, and D. M. Engelman.13 February 2001, posting date. Polar residues drive associationof polyleucine transmembrane helices. Proc. Natl. Acad. Sci.USA doi:10.1073/pnas.041593698.

Notes

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Notes

The Note format is intended for the presentation of brief observationsthat do not warrant full-length papers. However, Notes shouldcontain firm data; observations alone are not acceptable. SubmitNotes in the same way as full-length papers. They receive thesame review, they are not published more rapidly than full-lengthpapers, and they are not considered preliminary communications.

Each Note must have an abstract of no more than 50 words. Donot use section headings in the body of the Note; combine methods,results, and discussion in a single section. Paragraph lead-insare permissible. The text should be kept to a minimum and ifpossible should not exceed 1,000 words; the number of figuresand tables should also be kept to a minimum. Materials and methodsshould be described in the text, not in figure legends or tablefootnotes. Acknowledgments should be presented as in full-lengthpapers, but no separate heading is used. The References sectionis identical to that of full-length papers.

Minireviews

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Minireviews

Minireviews are expected to be focused discussions of definedtopics relevant to clinical microbiologists. In general, theyare to be submitted only after invitation by one of the JCMeditors. Unsolicited Minireviews are discouraged. The coverletter should state whether the article was solicited and bywhom.

Minireviews are not expected to be comprehensive reviews ofthe literature but rather very directed discussions of specificissues, with emphasis on the views of the author(s). Thus, theymay not exceed 12 double-spaced manuscript pages in length,inclusive of illustrations, tables, and references. Referencesshould be limited to 20 or fewer. Minireviews do not have abstracts.In the Abstract section of the submission form, put "Not Applicable."The body of the Minireview may either have section headingsor be set up like a Note (see above). Minireviews should besubmitted via Rapid Review.

Minireviews will be reviewed by two JCM editors, with the aimof expedited processing. In general, it is hoped that, barringthe necessity of major revisions, accepted Minireviews willappear in print within 3 months of their submission.

Guest Commentaries

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Guest Commentaries

Guest Commentaries are invited communications concerning relevanttopics in clinical microbiology that are not necessarily coveredby Minireviews. They are intended to engender discussion andstimulate consensus statements by such organizations as theAmerican Academy of Microbiology, Clinical and Laboratory StandardsInstitute, etc. Reviews of the literature, methods and otherhow-to papers, and responses targeted at a specific publishedpaper are not appropriate. Guest Commentaries are subject toreview.

The length may not exceed 4 printed pages, and the format islike that of a Minireview (see above). Commentaries should besubmitted via Rapid Review.

Case Reports

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Case Reports

While a full-length article or a Note may contain a case reportsection when the report is incidental to the rest of the paper,a specific Case Report format must be used when the report constitutesthe entire article.

A Case Report must include an abstract of no more than 50 words.The text starts with presentation of the case under the sectionheading "Case Report"; there is no introductory text beforethe Case Report heading. After the case is presented, the restof the text follows in a separate section after a ruled lineto separate the sections. No separate head is used for thisshort discussion section, but paragraph lead-ins are permitted.The total number of tables and figures (combined) must not exceed3. For an example of a correctly formatted Case Report, seeJ. Clin. Microbiol. 39:1678-1679, 2001.

Letters to the Editor

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Letters to the Editor

Two types of Letters to the Editor may be submitted. The firsttype (Comment Letter) is intended for comments on final, typesetarticles published in the journal (not on publish-ahead-of-printmanuscripts) and must cite published references to support thewriter's argument. The second type (New-Data Letter) may reportnew, concise findings that are not appropriate for publicationas full-length papers or Notes.

Letters may be no more than 500 words long and must be typeddouble spaced. Refer to a recently published Letter for correctformatting. Note that authors and affiliations are listed atthe foot of the Letter. Provide only the primary affiliationfor each author.

All Letters to the Editor must be submitted electronically,and the type of Letter (New Data or Comment) must be selectedfrom the drop-down list in the submission form. For Letterscommenting on published articles, the cover letter should statethe volume and issue in which the article was published, thetitle of the article, and the last name of the first author.In the Abstract section of the submission form, put "Not applicable."Letters to the Editor do not have abstracts. Both types of Lettermust have a title, which must appear on the manuscript and onthe submission form. Figures and tables should be kept to aminimum.

If the Letter is related to a published article, it will besent to the editor who handled the article in question. If theeditor believes that publication is warranted, he will solicita reply from the corresponding author of the article and giveapproval for publication.

New-Data Letters will be assigned to an editor according tosubject matter and will be reviewed by that editor and/or areviewer.

Please note that some indexing/abstracting services do not includeLetters to the Editor in their databases.

Fast-Track Communications

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Fast-Track Communications

The fast-track route is intended for accelerated review of shortcommunications that are of significant interest to clinicalmicrobiologists. Manuscripts are limited to 750 words, one figure,one table, and 10 or fewer references. The format should bethe same as that of a new-data letter (see Letters to the Editor,above). Fast-track articles should be submitted via Rapid Review.

A fast-track submission is subject to approval as such by theeditor in chief. If approved for the fast-track route, the manuscriptwill be assigned to an appropriate JCM editor and reviewed,according to the same standards applied for traditional manuscripts,within 1 week. If accepted, the manuscript will be scheduledfor the next available issue and edited. An acceptance letterand copyright agreement will be mailed to the correspondingauthor. Proofs will be made available electronically as forregular articles.

A fast-track submission that is not approved for the fast-trackroute will be handled as a New-Data Letter according to normalprocedures.

Errata

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Errata

The Erratum section provides a means of correcting errors thatoccurred 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. Submit Errata via Rapid Review (see"How To Submit Manuscripts," above). In the Abstract sectionof the submission form (a required field), put "Not Applicable."Upload the text of your Erratum as an MS Word file. Please seea recent issue for correct formatting.

Authors’ Corrections

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Authors’ Corrections

The Author's Correction section provides a means of correctingerrors of omission (e.g., author names or citations) and errorsof a scientific nature that do not alter the overall basic resultsor conclusions of a published article (e.g., an incorrect unitof measurement or order of magnitude used throughout, contaminationof one of numerous cultures, or misidentification of a mutantstrain, causing erroneous data for only a portion [noncritical]of the study). Note that the addition of new data is not permitted.

For corrections of a scientific nature or issues involving authorship,including contributions and use or ownership of data and/ormaterials, all disputing parties must agree, in writing, topublication of the Correction. For omission of an author's name,letters must be signed by the authors of the article and theauthor whose name was omitted. The editor who handled the articlewill be consulted if necessary.

Submit an Author's Correction via Rapid Review (see "How ToSubmit Manuscripts," above). In the submission form, selectErratum as the manuscript type; there is no separate selectionin Rapid Review for Authors’ Corrections, but your Correctionwill be published as such if appropriate. In the Abstract sectionof the submission form (a required field), put "Not Applicable."Upload the text of your Author's Correction as an MS Word file.Please see a recent issue for correct formatting. Signed lettersof agreement must be supplied as supplemental material (scannedPDF files).

Retractions

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Retractions

Retractions are reserved for major errors or breaches of ethicsthat, for example, may call into question the source of thedata or the validity of the results and conclusions of an article.Submit Retractions via Rapid Review (see "How To Submit Manuscripts,"above). In the Abstract section of the submission form (a requiredfield), put "Not Applicable." Upload the text of your Retractionas an MS Word file. Letters of agreement signed by all of theauthors must be supplied as supplemental material (scanned PDFfiles). The Retraction will be assigned to the editor in chiefof the journal, and the editor who handled the paper and thechairman of the ASM Publications Board will be consulted. Ifall parties agree to the publication and content of the Retraction,it will be sent to the Journals Department for publication.

ILLUSTRATIONS AND TABLES

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ILLUSTRATIONS AND TABLES

Digital files that are acceptable for production (see below)must be provided for all illustrations on return of the modifiedmanuscript. (On initial submission, the entire paper may besubmitted in PDF format.)

We strongly recommend that before returning their modified manuscripts,authors check the acceptability of their digital images forproduction by running their files through Rapid Inspector, atool provided at the following URL: http://rapidinspector.cadmus.com/RapidInspector/zmw/index.jsp.Rapid Inspector is an easy-to-use Web-based application thatidentifies file characteristics that may render the image unusablefor production.

Illustrations may be continuous-tone images, line drawings,or composites. Color graphics may be submitted, but the costof printing in color must be borne by the author. Suggestionsabout how to reduce costs and ensure accurate color reproductionare given below.

The preferred format for tables is MS Word; however, WordPerfectand Acrobat PDF are also acceptable (see the section on tables below).

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Image Manipulation

Computer-generated images may be processed only minimally. Processing(e.g., changing contrast, brightness, or color balance) is acceptableonly if applied to all parts of the image, as well as to thecontrols, equally, and descriptions of all such adjustmentsand the tools used (both hardware and software) must be providedin the manuscript. Unprocessed data and files must be retainedby the authors and be provided to the editor on request.

Illustrations

File types and formats. As mentioned above, illustrations maybe supplied as PDF files for reviewing purposes only on initialsubmission; in fact, we recommend this option to minimize fileupload time. At the modification stage, production quality digitalfiles must be submitted: TIFF or EPS files from supported applicationsor PowerPoint files (black and white only). Except for figuresproduced in PowerPoint, all graphics submitted with modifiedmanuscripts must be bitmap, grayscale, or CMYK (not RGB). Halftoneimages (those with various densities or shades) must be grayscale,not bitmap.

Color PowerPoint files are not accepted because the application,designed for developing on-screen computer presentations, usesthe RGB color mode whereas the printing process uses the CMYKcolor mode. Colors that are represented in a PowerPoint imagemay not be reproducible on a printing press. Although black-and-whiteMicrosoft PowerPoint files are accepted, we do not recommenduse of PowerPoint. PowerPoint requires users to pay close attentionto the fonts used in their images (see the section on fontsbelow). If instructions for fonts are not followed exactly,images prepared for publication are subject to missing characters,improperly converted characters, or shifting/obscuring of elementsor text in the figure. Use of PowerPoint is therefore not recommendedfor either color or black-and-white illustrations.

Acceptable file types and formats for production are given inthe charts above. More-detailed instructions for preparing illustrationsare available at http://art.cadmus.com/da/index.jsp. Pleasereview this information before preparing your files. If yourequire additional information, please send an e-mail inquiryto digitalart{at}cadmus.com.

Minimum resolution. It is extremely important that a high enoughresolution is used. Any imported images must be at the correctresolution before they are placed. Note, however, that the higherthe resolution, the larger the file and the longer the uploadtime. Publication quality will not be improved by using a resolutionhigher than the minimum. Minimum resolutions are as follows:

300 dpi for grayscale and color

600 dpi for lettering

1,200dpi for line art

600 dpi for combination art (lettering andimages)

Size. All graphics MUST be submitted at their intended publicationsize; that is, the image uploaded should be 100% of its printdimensions so that no reduction or enlargement is necessary.Resolution must be at the required level at the submitted size.Include only the significant portion of an illustration. Whitespace must be cropped from the image, and excess space betweenpanel labels and the image must be eliminated.

Maximum widthfor a 1-column figure: 3 Formula

inches (ca. 8.4 cm)

Maximum width for a 2-column figure: 6 $7/8$ inches(ca. 17.4 cm)

Minimum width for a 2-column figure: 4 $1/4$ inches(10.8 cm)

Maximum height: 9 Formula

inches (23.0 cm)

Contrast. Illustrations must contain sufficient contrast towithstand the inevitable loss of contrast and detail inherentin the printing process. See also "Color illustrations" below.

Labeling and assembly. All final lettering, labeling, tooling,etc., must be incorporated into the figures. It cannot be addedat a later date. If a figure number is included, it must appearwell outside the boundaries of the image itself. (Numberingmay need to be changed at the copyediting stage.) Each figuremust be uploaded as a separate file, and any multipanel figuresmust be assembled into one file; i.e., rather than uploadinga separate 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 of the followingfonts: Helvetica, Times Roman, European PI, Mathematical PI,or Symbol. All fonts other than these five must be convertedto paths (or outlines) in the application with which they werecreated. For proper font use in PowerPoint images, refer tothe Cadmus digital art website, http://art.cadmus.com/da/instructions/ppt_disclaimer.jsp.

Compression. Images created with Macintosh applications maybe compressed with Stuffit. Images created with Windows applicationsmay be compressed with WinZip or PKZIP.

Color illustrations. The cost of printing in color must be borneby the author. The current color cost per figure may be accessedfrom the submission form in Rapid Review. For accepted manuscripts,the total cost of the color will be included in the acceptanceletter sent out by ASM. Adherence to the following guidelines,in addition to the general ones below, will help to minimizecosts and to ensure color reproduction that is as accurate aspossible.

Because of the requirements of print production, color illustrationsmust be in the CMYK (cyan, magenta, yellow, black) color space.The "normal" color mode for most computer software is RGB (red,green, blue), which is also the color space of your computermonitor. Since CMYK is a smaller color space (meaning it candefine fewer colors), colors often shift when an RGB file isconverted to CMYK. In particular, figures showing red or greenfluorescence and those with a significant range of colors maybe difficult or impossible to reproduce during the printingprocess.

Color illustrations must be supplied in the CMYK color mode,as either (i) CMYK TIFF images with a resolution of at least300 pixels per inch (raster files, consisting of pixels) or(ii) Illustrator-compatible EPS files with CMYK color elements(vector files, consisting of lines, fonts, fills, and images).See the charts above for a list of supported applications.

We cannot accept any Microsoft Office files (PowerPoint, Word,Excel) for color illustrations because they are restricted tothe RGB color space.

Drawings

Submit graphs, charts, complicated chemical or mathematicalformulas, diagrams, and other drawings as finished productsnot requiring additional artwork or typesetting. No part ofthe graph or drawing may be handwritten. All elements, includingletters, numbers, and symbols, must be easily readable, andboth axes of a graph must be labeled. Keep in mind that thejournal is published both in print and online and that the sameelectronic files submitted by the authors are used to produceboth.

When creating line art, please use the following guidelines:

All art MUST be submitted at its intended publication size.For acceptable dimensions, see "Size" above.
Avoid using screens(i.e., shading) in line art. It can be difficultand time-consumingto reproduce these images without moirépatterns. Variouspattern backgrounds are preferable to screensas long as thepatterns are not imported from another application.If you mustuse images containing screens,
- Generate the imageat line screensof 85 lines per inch or lower.
- When applyingmultiple shadesof gray, differentiate the graylevels by atleast 20%.
- Neveruse levels of gray below 20% or above 70%as they willfadeout or become totally black upon scanningand reduction.
Use thick, solid lines that are no finer than 1 point in thickness.
No type should be smaller than 6 points at the final publicationsize.
Avoid layering type directly over shaded or texturedareas.
Avoid the use of reversed type (white lettering ona black background).
Avoid heavy letters, which tend to closeup, and unusual symbols,which the printer may not be able toreproduce in the legend.
If colors are used, avoid using similarshades of the same colorand avoid very light colors.

In figure ordinate and abscissa scales (as well as table columnheadings), avoid the ambiguous use of numbers with exponents.Usually, it is preferable to use the appropriate SystèmeInternational d'Unités (SI) symbols (µ for 10^–6,m for 10^–3, k for 10³, M for 10⁶, etc.). A complete listingof SI symbols can be found in the International Union of Pureand Applied Chemistry (IUPAC) publication Quantities, Unitsand Symbols in Physical Chemistry (Blackwell Science, Oxford,United Kingdom, 1993); an abbreviated list is available at http://www.iupac.org/reports/1993/homann/index.html.Thus, a representation of 20,000 cpm on a figure ordinate shouldbe made by the number 20 accompanied by the label kcpm.

When powers of 10 must be used, the journal requires that theexponent power be associated with the number shown. In representing20,000 cells per ml, the numeral of the ordinate would be "2"and the label would be "10⁴ cells per ml" (not "cells per mlx 10^–4"). Likewise, an enzyme activity of 0.06 U/ml wouldbe shown as 6 accompanied by the label 10^–2 U/ml. Thepreferred designation would be 60 mU/ml (milliunits per milliliter).

Presentation of Nucleic Acid Sequences

Nucleic acid sequences of limited length which are the primarysubject of a study may be presented freestyle in the most effectiveformat. Longer nucleic acid sequences must be presented as figuresin the following format to conserve space. Print the sequencein lines of approximately 100 to 120 nucleotides in a nonproportional(monospace) font that is easily legible when published witha line length of 6 inches (ca. 15.2 cm). If possible, linesof nucleic acid sequence should be further subdivided into blocksof 10 or 20 nucleotides by spaces within the sequence or bymarks above it. Uppercase and lowercase letters may be usedto designate 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; placenumerals, representing the first base of each line, to the leftof the lines. Minimize spacing between lines of sequence, leavingroom only for annotation of the sequence. Annotation may includeboldface, underlining, brackets, boxes, etc. Encoded amino acidsequences may be presented, if necessary, immediately aboveor below the first nucleotide of each codon, by using the single-letteramino acid symbols. Comparisons of multiple nucleic acid sequencesshould conform as nearly as possible to the same format.

Figure Legends

Legends should provide enough information so that the figureis understandable without frequent reference to the text. However,detailed experimental methods must be described in the Materialsand Methods section, not in a figure legend. A method that isunique to one of several experiments may be reported in a legendonly if the discussion is very brief (one or two sentences).Define all symbols used in the figure and define all abbreviationsthat are not used in the text.

Tables

Tables that contain artwork, chemical structures, or shadingmust be submitted as illustrations in an acceptable format atthe modification stage. The preferred format for regular tablesis MS Word; however, WordPerfect and Acrobat PDF are also acceptable.Note that a straight Excel file is not currently an acceptableformat. Excel files must be either embedded in a Word or WordPerfectdocument or converted to PDF before being uploaded. If yourmodified manuscript contains PDF tables, select "for reviewingpurposes only" at the beginning of the file upload process.

Tables should be formatted as follows. Arrange the data so thatcolumns of like material read down, not across. The headingsshould be sufficiently clear so that the meaning of the datais understandable without reference to the text. See the "Abbreviations"section (p. 18) of these Instructions for those that shouldbe used in tables. Explanatory footnotes are acceptable, butmore extensive table "legends" are not. Footnotes should notinclude detailed descriptions of the experiment. Tables mustinclude enough information to warrant table format; those withfewer than six pieces of data will be incorporated into thetext by the copy editor. Table 1 is an example of a well-constructedtable.

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TABLE 1. Correlation between detection of V-Z viral antibody by neutralization and by EIA and IAHA^a

NOMENCLATURE

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NOMENCLATURE

Chemical and Biochemical Nomenclature

The recognized authority for the names of chemical compoundsis Chemical Abstracts (CAS, Columbus, OH) and its indexes. TheMerck Index, 14th ed. (Merck & Co., Inc., Whitehouse Station,NJ, 2006), is also an excellent source. For biochemical terminology,including abbreviations and symbols, consult Biochemical Nomenclatureand Related Documents (Portland Press, London, United Kingdom,1992), available at http://www.chem.qmul.ac.uk/iupac/bibliog/white.html,and the instructions to authors of the Journal of BiologicalChemistry and the Archives of Biochemistry and Biophysics (firstissues of each year).

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

For enzymes, use the recommended (trivial) name assigned bythe Nomenclature Committee of the International Union of Biochemistry(IUB) as described in Enzyme Nomenclature (Academic Press, Inc.,New York, NY, 1992) and at http://www.chem.qmul.ac.uk/iubmb/enzyme/.If a nonrecommended name is used, place the proper (trivial)name in parentheses at first use in the abstract and text. Usethe EC number when one has been assigned, and express enzymeactivity either in katals (preferred) or in the older systemof micromoles per minute.

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

Drugs

Whenever possible, use generic names of drugs; the use of tradenames is not permitted.

Nomenclature of Microorganisms

Binary names, consisting of a generic name and a specific epithet(e.g., Escherichia coli), must be used for all microorganisms.Names of categories at or above the genus level may be usedalone, but specific and subspecific epithets may not. A specificepithet must be preceded by a generic name, written out in fullthe first time it is used in a paper. Thereafter, the genericname should be abbreviated to the initial capital letter (e.g.,E. coli), provided there can be no confusion with other generaused in the paper. Names of all taxa (kingdoms, phyla, classes,orders, families, genera, species, and subspecies) are printedin italics and should be italicized (or underlined) in the manuscript;strain designations and numbers are not. Vernacular (common)names should be in lowercase roman type (e.g., streptococcus,brucella). For Salmonella, genus, species, and subspecies namesshould be rendered in standard form: Salmonella enterica atfirst use, S. enterica thereafter; Salmonella enterica subsp.arizonae at first use, S. enterica subsp. arizonae thereafter.Names of serovars should be in roman type with the first lettercapitalized: Salmonella enterica serovar Typhimurium. Afterthe first use, the serovar may also be given without a speciesname: Salmonella serovar Typhimurium. For other informationregarding serovar designations, see Antigenic Formulas of theSalmonella Serovars, 8th ed. (M. Y. Popoff, WHO CollaboratingCentre for Reference and Research on Salmonella, Institut Pasteur,Paris, France, 2001). For a summary of the current standardsfor Salmonella nomenclature and the Kaufmann-White criteria,see the article by Brenner et al. (J. Clin. Microbiol. 38:2465-2467,2000), the opinion of the Judicial Commission of the InternationalCommittee on Systematics of Prokaryotes (Int. J. Syst. Evol.Microbiol. 55:519-520, 2005), and the article by Tindall etal. (Int. J. Syst. Evol. Microbiol. 55:521-524, 2005).

The spelling of bacterial names should follow the Approved Listsof Bacterial Names (Amended) & Index of the Bacterial andYeast Nomenclatural Changes (V. B. D. Skerman et al., ed., ASMPress, Washington, DC, 1989) and the validation lists and notificationlists published in the International Journal of Systematic andEvolutionary Microbiology (formerly the International Journalof Systematic Bacteriology) since January 1989. In addition,two sites on 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 Nomenclature(http://www.bacterio.cict.fr/). If there is reason to use aname that does not have standing in nomenclature, the name shouldbe enclosed in quotation marks in the title and at its firstuse in the abstract and the text and an appropriate statementconcerning the nomenclatural status of the name should be madein the text. "Candidatus" species should always be set in quotationmarks.

For guidelines regarding new names and descriptions of new generaand species, see the articles by Tindall (Int. J. Syst. Bacteriol.49:1309-1312, 1999) and Stackebrandt et al. (Int. J. Syst. Evol.Microbiol. 52:1043-1047, 2002). To validate new names and/orcombinations, authors must submit three copies of their publishedarticle to the International Journal of Systematic and EvolutionaryMicrobiology.

It is recommended that a strain be deposited in at least tworecognized culture collections in different countries when thatstrain is necessary for the description of a new taxon (Int.J. Syst. Evol. Microbiol. 50:2239-2244, 2000).

Since the classification of fungi is not complete, it is theresponsibility of the author to determine the accepted binomialfor a given organism. Sources for these names include The Yeasts:a Taxonomic Study, 4th ed. (C. P. Kurtzman and J. W. Fell, ed.,Elsevier Science Publishers B.V., Amsterdam, The Netherlands,1998), and Ainsworth and Bisby's Dictionary of the Fungi, 9thed. (P. M. Kirk, P. F. Cannon, J. C. David, and J. A. Stalpers,ed., CABI Publishing, Wallingford, Oxfordshire, United Kingdom,2001); see also http://www.speciesfungorum.org/Names/Fundic.asp.

Names used for viruses should be those approved by the InternationalCommittee on Taxonomy of Viruses (ICTV) and published in VirusTaxonomy: Eighth Report of the International Committee on Taxonomyof Viruses (C. M. Fauquet et al., ed., Elsevier Academic Press,San Diego, CA, 2005). In addition, the recommendations of theICTV regarding the use of species names should generally befollowed: when the entire species is discussed as a taxonomicentity, the species name, like other taxa, is italic and hasthe first letter and any proper nouns capitalized (e.g., Tobaccomosaic virus, Murray Valley encephalitis virus). When the behavioror manipulation of individual viruses is discussed, the vernacular(e.g., tobacco mosaic virus, Murray Valley encephalitis virus)should be used. If desired, synonyms may be added parentheticallywhen the name is first mentioned. Approved generic (or group)and family names may also be used.

Microorganisms, viruses, and plasmids should be given designationsconsisting of letters and serial numbers. It is generally advisableto include a worker's initials or a descriptive symbol of locale,laboratory, etc., in the designation. Each new strain, mutant,isolate, or derivative should be given a new (serial) designation.This designation should be distinct from those of the genotypeand phenotype, and italicized genotypic and phenotypic symbolsshould not be included. Plasmids are named with a lowercase"p" followed by the designation in uppercase letters and numbers.To avoid the use of the same designation as that of a widelyused strain or plasmid, check the designation against a publicationdatabase such as Medline.

Genetic Nomenclature

To facilitate accurate communication, it is important that standardgenetic nomenclature be used whenever possible and that deviationsor proposals for new naming systems be endorsed by an appropriateauthoritative body. Review and/or publication of submitted manuscriptsthat contain new or nonstandard nomenclature may be delayedby the editor or the Journals Department so that they may bereviewed by the Genetics and Genomics Committee of the ASM PublicationsBoard.

Before submission of manuscripts, authors may direct questionson genetic nomenclature to the com-mittee's chairman: MariaCostanzo (e-mail: maria{at}genome.stanford.edu). Such a consultationshould be mentioned in the manuscript submission letter.

Bacteria. The genetic properties of bacteria are described interms of phenotypes and genotypes. The phenotype describes theobservable properties of an organism. The genotype refers tothe genetic constitution of an organism, usually in referenceto some standard wild type. Use the recommendations of Demerecet al. (Genetics 54:61-64, 1966) as a guide to the use of theseterms. If your manuscript contains information including geneticnomenclature, please refer to the Instructions to Authors inthe January issue of the Journal of Bacteriology.

"Mutant" vs. "mutation." Keep in mind the distinction betweena mutation (an alteration of the primary sequence of the geneticmaterial) and a mutant (a strain carrying one or more mutations).One may speak about the mapping of a mutation, but one cannotmap a mutant. Likewise, a mutant has no genetic locus, onlya phenotype.

"Homology" versus "similarity." For use of terms that describerelationships between genes, consult the articles by Theissen(Nature 415:741, 2002) and Fitch (Trends Genet. 16:227-231,2000). "Homology" implies a relationship between genes thatshare a common evolutionary origin; partial homology is notrecognized. When sequence comparisons are discussed, it is moreappropriate to use the term "percent sequence similarity" or"percent sequence identity," as appropriate.

Tetracycline resistance determinants. The nomenclature for tetracyclineresistance determinants is based on the proposal of Levy etal. (Antimicrob. Agents Chemother. 43:1523-1524, 1999). Thestyle for such determinants is, e.g., Tet B; the space helpsdistinguish the determinant designation from that for phenotypesand proteins (TetB). The above-referenced article also givesthe correct format for genes, proteins, and determinants inthis family.

Viruses. The genetic nomenclature for viruses differs from thatfor bacteria. In most instances, viruses have no phenotype,since they have no metabolism outside host cells. Therefore,distinctions between phenotype and genotype cannot be made.Superscripts are used to indicate hybrid genomes. Genetic symbolsmay be one, two, or three letters.

Eukaryotes. For information about the genetic nomenclature ofeukaryotes, see the Instructions to Authors for Eukaryotic Celland Molecular and Cellular Biology.

ABBREVIATIONS AND CONVENTIONS

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