Instructions for Authors

General Considerations
Article Classification
Manuscript Preparation
Finalizing Submission
Author Inquiries

Avicenna Journal of Clinical Microbiology and Infection (AJCMI) is an open access, international and multidisciplinary peer-reviewed journal that considers subjects on medical biochemistry, novel information leading to a better understanding of biological mechanisms of human diseases, their prevention, diagnosis, and treatment. Articles on normal metabolic processes or with constituents of normal cells or reports of experimental or clinical studies in animals which are relevant to human disease are also welcomed. Please observe a detailed list on diverse fields at Aim and Scope of the journal.

The submission procedure in conducted through the online submission system. In order to start the submitting author, is required to create an account and login. This author is responsible to provide full details including names and email addresses on behalf of all co-authors. Please keep in mind that academic or institutional email addresses are preferred when submitting. Result of initial evaluations, request for minor/major revision, Editor's decision on rejection or acceptance, etc., will all be visible at the author's personal account in addition to informing the corresponding author via email provided upon submission.

General Considerations

1- Open Access License, Copyright and Fees

• AJCMI is an open access journal and the Vice Chancellor for Research and Technology of Hamadan University of Medical Sciences supports all submission and publication costs of Avicenna Journal of Clinical Microbiology and Infection. Thus, there is no submission fee, article processing charge or any other publication expenses in AJCMI for authors.

• The AJCMI articles are under Creative Commons Attribution License. It is mandatory that authors for each submission complete and upload the Exclusive License Agreement form during the online submission. Please observe our Open Access and Copyright Policy for more information.

2- Cover Letter

A cover letter must be uploaded for your article. The corresponding author must refer and confirm the following items including:

• Provide the type and title of your publication and an explanation on novelty of the research, and reasons on why this work will be interesting for AJCMI authors.

• State that the submitted article is original, and is not under consideration for publication or already published elsewhere (Editorial Policies on duplicate publication); and that the accuracy and integrity of the research is approved by all authors (ICMJE) and responsible authorities where the research was carried out.

• Declare any potential conflict of interests or any explanation on issues relating to journal ethical or editorial policies.

• The submitting author must take responsibility for the submission of the manuscript on behalf of all authors as the corresponding author.

3- Authorship and Language

• The corresponding author is required to complete the Authorship and Conflict of Interest Statement and upload during the online submission.

• Any changes in authorship of the article after submission must be approved by all authors. In this regard AJCMI follows the COPE guidelines for any changes in order, addition, or deletion of authors of the manuscript.

• Authors are encouraged to prepare the language of their manuscripts with the utmost care. AJCMI uses the CrossCheck  iThenticate Plagiarism detector to screen submitted manuscripts for originality.

• The language editors will check the language and grammar of your submitted manuscript. Beware that manuscripts in poor English will not be sent for review. We recommend having your manuscript professionally edited by a qualified English-speaking researcher in your field prior to submission.

Article Classification

AJCMI publishes diverse categories of articles. All types of articles are subject to peer-review. The journal publishes the following types of articles including Original Article, Brief Reports/Short Communication, Review Articles, Editorial, and Letter to Editor.

1- Editorial

Editorials are the message of the AJCMI and are written in-house by the journal's Editorial Board members. Editorials are preferably no more than 1000 words. These provide state of the art discussions on the AJCMI main scopes. No abstract is required for these articles.

2- Original Article

These articles must be of primary original, methodologically accurate, and relevant to experimental or clinical studies in fields of clinical microbiology. They should contain no more than 4000 words excluding structured abstract, tables, and references. Tables, table legends and figure legends should be inserted subsequent to references. Figures and supplementary files should be uploaded separately during submission. Each manuscript should clearly state an objective or hypothesis; the design of study and methodology; data analysis and interpretations; the main results of the study, discussing the results; addressing study limitations and the conclusion. All original articles require a structured abstract.

3- Review Article

These articles consist of literature reviews, systematic reviews, meta-analyses, and meta-syntheses. These articles may be up to 7000 words excluding abstract, tables, and references. The specific type of study or analysis, intervention, population, exposure, outcomes or tests should be described for each data source or article. Authors are to clearly cover the following topics in the method section: search strategy and selection criteria, data extraction, quality assessment, and data analysis. An unstructured abstract is required.

4- Brief Report/Policy Brief

Brief report articles are not intended to publish preliminary results, but the results which are of exceptional interest and are particularly topical and relevant. Policy brief articles as a summary report offer a practical and evidence-based investigation of policy-related issues. These articles should be no more than 2000 words including up to three figures or tables, references and the main text. A structured abstract is required for these types of articles.

5- Letter to Editor

We welcome short letters with topics of interest to the AJCMI readership. These letters should not exceed 1000 words including only one table or figure, references and the main text. No abstract is required for these articles.

* Please insert the type of your manuscript on top of the Title Page and Main Manuscript.

Manuscript Preparation

1- Manuscript Format

• During submitting you are required to upload files of Title Page, Main Document (without title page details), Cover Letter, Figure, and Supplementary files, Exclusive License Agreement form, Authorship and Conflict of Interest Statement.

• Acceptable manuscripts' file format is Microsoft Word (DOC, DOCX). Do not submit your main document in PDF format. Manuscript text should be prepared in 12 point Times New Roman font with double line spacing at an A4 size paper with clear margins (2.5 cm) on both sides. Use page number for your manuscript.

• Based on the type of your research, manuscripts should be prepared into sections (main headings) of Title, Abstract, Background, Materials and Methods, Results, Discussion, Conclusion, and References. Please check the Article Classification for an abstract type your article requires. A structured abstract consists of Background, Objectives, Methods, Results, Conclusion, and Keywords. The maximum word number for all types of abstracts is 300.

• Headings should not be in all capital. Only the first letter of all headings must be capital. Title, Main Headings and Headings should be in Bold whereas the subheading should only be written in italic.

• Following Conclusion your manuscript must include Additional Statements of Acknowledgements, Authors’ Contribution, Conflict of Interests, Ethical Issues, and Funding/Support.

2- Title Page:

The title page should contain the following components:

• Manuscript Title; Please keep it as precise and concise as possible and ensure it reflects the subject matter

• Running Title

• Full name of all authors with their affiliations (including Department, Faculty, University, City, Country). You may use number superscripts to indicate authors with their affiliations.

• The Corresponding Author must include an email address and a telephone number. Use asterisk (*) to clearly indicate the corresponding author.

3- Main Document:

• The main document must not include the author’s names and affiliations.

• The first page of the main document should consist of Article Title, Article Type, and Abstract (if required or structured/unstructured).

• Abstract: It should state briefly and clearly the purpose and setting of the research, the principal findings and major conclusions, and the article's contribution to knowledge. The maximum word number for all types of abstracts is 300. Please minimize the use of abbreviations and do not cite references in the abstract. A structured abstract consists of Background, Objectives, Methods, Results, Conclusion, and Keywords.
• Keywords: Up to 6 keywords are entered separately into the online system during submission,   which should accurately reflect the content of the article. These keywords should be selected from the Medical Subject Headings (MeSH) list. Abbreviations/acronyms could be used with their expansions. The keywords will be used for indexing purposes. As you add keywords within the online submission system, please insert these within the Main Document as well.   

• Following abstract, the main text should be arranged in Background, Materials and Methods, Results, Discussion, Conclusion, Acknowledgements, Authors’ Contribution, Conflict of Interests, Ethical Issues, Funding/Support, and References.

• Background: The Background summarizes a concise review of the subject area and the rationale for the study. It should neither review the subject extensively nor should it contain detailed comparisons to previous research, data or conclusions.

• Materials and Methods: This should include a clear description of the experimental design and sampling procedures and sufficient details of the methods, instruments, analytic processes, software version selected, and statistical analyses performed. If an apparatus is used, its manufacturer’s name and address should be given in parenthesis. If the method is established, provide references but if the method is novel, present detailed information to allow the work to be reproduced. In cases where a study involves the use of live animals or human subjects, the author should include a statement that all experiments were performed in compliance with the relevant laws and institutional guidelines, and also state the institutional committee(s) that has approved the experiments. They should also include a statement that informed consent was obtained for any experimentation with human subjects. All abbreviations must be spelled out the first time used, followed by the abbreviated form in parentheses. Units of measurement must be complied with the International System of Units (SI).

• Results: It must be written in the text format. Tables and figures must be referenced sequentially in the same order as in the text. Repetition of table contents should be avoided. Total number of tables and figures should not exceed 5 in number. Tables, table caption and figure legends should be inserted subsequent to References and not within the text. Figures and Supplementary files should be uploaded separately during submission. Table captions should be typed above the tables while table footnote should be placed below. Figure legends should be indicated below the figures. The following provides a detailed description for Formulas/Equations, Tables and Figures:

1. Formulas/Equations
• Equations should be typed only in Math Type

(Download the software from http://www.dessci.com/en/products/mathtype/).

• Graphical objects should not be used.
• Your equations should be editable.
• If you have used built-in equation editing tool in Microsoft Word, the equations will become unusable during the typesetting process. To resolve this problem, please re-key your equations using Math Type.
• Long equations should be set off from the text and numbered sequentially.
• If you cannot avoid using many equations or schemes, you can collect them in a table of equations and shot them as a framed figure to avoid typesetting errors.
  
  
1. Tables
• All tables should be inserted within the text as close as possible to where they are referenced. Authors should not upload them as separate tables.
• Tables should be cited in numerical order within the main text.
• Tables must be prepared left to right and cell-based.
• Should be editable and upright on the page, not on sideways.
• Should be prepared with real rows and columns and not aligned with tabs, returns, or spaces.
• Should be plain with NO colors, shading, or graphics.
• Should not contain inserted text boxes, tables within tables or cells within cells.
• Symbols and abbreviations should be defined immediately below the table, followed by essential brief description.
2. Figures

• All figures/images must be placed numerically in one file and uploaded separately from the main text into the online submission system. Please do not include figures in the article text.
• All figures/images must be cited within the main manuscript in numerical order (Figure 1, Figure 2, etc.).
• Figure numbers and legends must be inserted below each figure.
• Multi-panel figures should be labeled in A, B, C, D, etc.
• Histograms must be arranged in a simple, two-dimensional format, with no background grid.
• All specific patient or hospital details must be removed or blacked out (including X-rays, MRI scans, etc.).
• If photographs of patients are used, they should not be identifiable.
• Original data from which the images were prepared should be available, as the editors may request to see these data (e.g., Office, SPSS and other line art images).
• Lettering in figures (for example, labeling of axes) should be in lower-case type, with the first letter capitalized and no full stop. All text should be in a sans-serif typeface, preferably Arial with appropriate font size to be easily read.
• Avoid using the touch-up tools, such as cloning and healing tools in Photoshop, or any feature that deliberately obscures manipulations.
• In order to publish all figures as open access, authors must have permission from the rights holder if they wish to include images that have been published elsewhere in non-open-access journals. Graphics downloaded from Web pages should not be used unless the author has a right to re-publish those as open access. The original source and the permission should be indicated in the figure legend, and a citation should be included in the reference list.
• Figures and images must be of high resolutions of at least 300 dpi for color figures, 600 dpi for grayscales and 1200 dpi for line arts. Acceptable files containing figures/images include: Adobe Portable Document Format (PDF) for photography or microscopy, Encapsulated PostScript (EPS) for illustrations or diagrams, Tagged Image File Format (TIFF), EPS, or PS. Files prepared with Adobe Illustrator, Corel Draw or Adobe Photoshop should be uploaded in these native file formats. Please consider the notes below:
  1. PDF and EPS formats are preferred over TIFF when exporting graphs, diagrams or line art from any software applied; specifically, PDF as it's more compact than EPS files.
  2. Vector drawing data is absent from JPEG, PNG, TIFF, or BMP file formats. Therefore, resaving any of these files as a PDF or EPS will not produce a vector drawing in these files. Please provide the original EPS or PDF file versions of artwork.
  3. JPEG or TIFF format should be used for photographs, histological slides, radiographs, etc.
  4. Utilize image editing software such as Adobe Photoshop to insert labels, arrows and other marks on photographs, histological slides, radiographs, etc. in order to produce a high quality JPEG or TIFF file. Please prevent using Microsoft Word or Power Point for inserting any marks on images.
  5. Acceptable digital formats include: Corel Draw, Adobe Illustrator, Unlocked PDFs created from a vector program, Microsoft PowerPoint, Excel, and Word as long as graphs are not placed into these programs as rasterized (pixel-based) images. Not acceptable file formats are Canvas, Delta Graph, Tax, Sigma Plot. Convert these files to PDFs, EPS, or postscript formats before submission.

• Discussion: This section should emphasize on the significant results of the present study results, in addition to its' limitations/similarities in comparison with other relevant studies. But detailed data should not be repeated in the discussion again and should consist of novel implications of the study. It must be mentioned that the initially considered hypothesis is accepted or declined here. Implications for future developments are also proposed in this section.

• Conclusion: It should state clear and precise interpretation from the results and demonstrating the importance of ideas and introducing possible new or expanded ways of thinking about the research problem.

• Acknowledgements: All contributors who do not meet the criteria for authorship should be covered in the acknowledgement section. It should include persons who provided technical help, writing assistance and departmental head that only provided general support. The authors should obtain permission to acknowledge from all those mentioned in the Acknowledgments section.

• Authors’ Contribution: The contributions of all authors must be clearly described. The corresponding author is responsible for completing this information at submission, and it is expected that all authors will have reviewed, discussed, and agreed to their individual contributions ahead of this time. Each author’s individual contribution(s) to the study must be stated based on the author statement provided by CRediT, which is a classification system consisting of 14 roles that describe the typical contributions made by authors to research outputs.
• CRediT roles are defined as follows:

• Conceptualization
  Ideas; formulation or evolution of overarching research goals and aims

  Data curation

  Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later reuse.

  Formal analysis

  Application of statistical, mathematical, computational, or other formal techniques to analyze or synthesize study data

  Funding acquisition

  Acquisition of the financial support for the project leading to this publication

  Investigation
  Conducting a research and investigation process, specifically performing the experiments, or data/evidence collection

  Methodology

  Development or design of methodology; creation of models

  Project administration

  Management and coordination responsibility for the research activity planning and execution

  Resources

  Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools

  Software

  Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components

  Supervision

  Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team

  Validation

  Verification, whether as a part of the activity or separate, of the overall replication/ reproducibility of results/experiments and other research outputs

  Visualization

  Preparation, creation and/or presentation of the published work, specifically visualization/ data presentation

  Writing-original draft

  Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation)

  Writing - review & editing

  Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre-or post publication stages

• Conflict of Interest: Authors must make sure that they have declared any actual or potential conflicts of interest in their manuscript when submitting their work. The corresponding author is responsible for confirming with the co-authors whether they have any financial and non-financial conflicts with regards to the publication of their work (ICMJE). If there is no conflict of interest, it should be stated that “The author(s) declare(s) that they have no conflict of interests”.

• Ethical Issues: All authors, reviewers, and editors should consider COPE, ICMJE and Equator Network reporting guidelines in medical ethics and scientific writings.  

• Funding/Support: All funding sources (internal or external/ grant ID, name of grant-receiving researcher, grant provider) from any institution/university supporting the research must be declared in this section.

• Supplementary Files: Additional files such as datasets, large tables, figures, or other information can be submitted as Supplementary files. These files must be cited within the main manuscript in numerical order (Supplementary file 1, etc.). Each Supplementary file must be submitted separately. Please provide a short title/caption for each file during submission. Note that documents including patient consent forms, etc., must not be uploaded as Supplementary files; if such files are required by the editor, we request from the author to be send via email.

• References: All manuscripts should be accompanied by relevant references and the Uniform Vancouver style is required.

1. References must each be numbered, ordered sequentially as they appear in the text, tables, boxes and figures. Arrange references as a simple list at the end of your manuscript in Endnote software.
2. Please ensure that every reference cited in the text is also present in the reference list (and vice versa).
3. Authors are responsible for the accuracy of cited references and these should be checked before the manuscript is submitted.
4. Only one publication can be listed for each number.
5. Within text insert reference numbers inside parenthesis. Separate two or more reference in parenthesis with commas.
6. Please note that if references are not in Vancouver style or are not cited in order the manuscript may be returned for amendment before it is passed on to the Editor for assessment.
7. The author should ensure reference to locally published studies by doing proper literature search. It may not be possible for the editor and reviewers to check the accuracy of all reference citations. Specifically make sure that to duplicate reference is present within your list. To minimize such errors author should verify references against the original documents.
8. The titles of journals and books should be abbreviated according to the list of journals indexed in “Journal Database” available from: http://www.pubmed.gov and http://cassi.cas.org/search.jsp.
9. All authors should be listed when six or less; when seven or more, only the first six should be listed and followed by et al.
10. Insert Digital Object Identifier (DOI) at the end of each reference if available.
11. Please download via Vancouver Style. You may also observe the link for more information on this reference style. An example is provided below:

Journal Article: Vasoo S, Barreto JN, Tosh PK. Emerging issues in gram-negative bacterial resistance: an update for the practicing clinician. Mayo Clin Proc. 2015;90(3):395-403. doi: 10.1016/j.mayocp.2014.12.002.3. 

Reviewers

• Authors are required to suggest a potential peer reviewer for their manuscript. At the on-line submission provide full name and institutional email address (observe Editorial Policies for suggesting peer reviewers). Be advised that false information will result in rejection of article and further investigation based on theMisconduct Policy. Note that the Editor-in-Chief retains the sole right to decide whether or not the suggested reviewer is invited.

Proofs

• The galley proof (as PDF file) will be sent to the corresponding author via email. Authors must read the proof thoroughly, answer any comments in the PDF file and send approval of for all corrections in due time. We will do everything possible to get your article published quickly and accurately. Therefore, it is important to ensure that all of your corrections are sent back to us in one communication. Not meeting the deadline and a long delay to respond could lead to withdraw of paper at this stage.

Finalizing Submission

Make sure that you have uploaded the required files in the File Upload section of the online submission. These files include:

• Title Page
• Main Document (without title page)
• Cover Letter
• Figure
• Supplementary
• Ethical Approval
• Exclusive License Agreement
• Authorship and Conflict of Interest Statement

Before completing the process, the submitting author is required to review the submission proof (PDF), which will be automatically generated. The submitting author may go back and correct any sections as necessary, review the submission proof again, and then submit your manuscript using the “Submit” button.

Author Inquiries

For further assistance or any inquiries relating to the submission please contact the editorial office at:

• ajcmi@umsha.ac.ir
• ajcmicrob@gmail.com

Or you may submit a message at this link.