MetaResistome

1. About the Journal & Scope Validation

MetaResistome is an international scholarly forum dedicated to advancing world-class scientific research in antimicrobial resistance (AMR), whole-genome sequencing (WGS), and environmental pathogen intelligence. We publish high-impact empirical investigations, bioinformatics methodology reports, and critical reviews that decipher the emergence, dissemination, and mitigation of resistant pathogens.

Before submitting, authors must ensure their manuscript directly addresses two fundamental scope criteria:

1. Is the biological focus directly tied to antimicrobial resistance, pathogen genomics, or microbial surveillance? Studies that investigate benign environmental commensals without relevance to AMR, pathogenicity, mobile genetic elements, or public health surveillance fall outside MetaResistome's scope.
2. Is the study conducted under biologically or environmentally realistic conditions? Metagenomic surveillance, wastewater monitoring, and phenotypic resistance assays must reflect realistic ecological or clinical exposure levels. In computational papers, bioinformatic workflows must be benchmarked against standard reference databases.

2. Article Categories

Original Research Articles

Full-length primary empirical studies presenting original scientific discoveries within the journal's scope. Contributions must not be submitted in multiple parts (i.e., Part I and Part II); they must be consolidated into a single comprehensive manuscript. Recommended length: 3,500 to 6,500 words (excluding references), with up to 8 publication-grade figures/tables.

Review Articles

Critical, authoritative evaluations of defined topics, emerging resistome challenges, or innovative surveillance methodologies. Review articles must synthesize current knowledge, identify unresolved paradoxes, and outline future research trajectories. In their cover letter, authors of Review Articles must provide: (1) a clear rationale for the timeliness and novelty of the review compared to existing literature; (2) a summary of the authors' domain expertise; and (3) a list of their recent relevant publications.

Methodology & Bioinformatic Protocol Reports

Detailed reports validating novel computational algorithms, machine learning models for resistance gene annotation, wet-lab extraction protocols for complex environmental matrices (e.g. sewage/sludge), or benchmarking studies. All computational code, software packages, or scripts must be open source and deposited in a public repository with an immutable DOI (Zenodo, Figshare, or GitHub).

Perspectives & Short Genome Announcements

Concise communications presenting critical perspectives by experienced researchers on emerging AMR policies, or brief reports announcing complete, closed genomes of high-threat multidrug-resistant clinical or wastewater isolates. Length: up to 2,000 words, up to 2 display items.

3. Peer Review Process

MetaResistome adheres to a single-anonymized peer review process. Every submitted manuscript is initially assessed by the Founding Editor-in-Chief or a Handling Section Editor for scientific scope, formatting compliance, and ethical standards.

Submissions passing initial triage are assigned to a minimum of two independent, active expert reviewers. The final editorial decision (Accept, Minor Revision, Major Revision, or Reject) rests with the responsible Editor. Editorial board members are recused from decisions concerning papers:

• Which they have authored or co-authored.
• Authored by current or recent departmental colleagues or close scientific collaborators.
• In which they have a personal, professional, or commercial conflict of interest.

Authors may submit a formal appeal regarding an editorial rejection provided it presents factual, substantive scientific counter-evidence. Only one appeal per manuscript will be considered, and the appeal ruling is final.

4. Hybrid Publishing Model, Open Access & Copyright

MetaResistome operates as a Hybrid Journal. Upon manuscript acceptance, corresponding authors can select their preferred publishing pathway:

• Option A - Gold Open Access (CC BY 4.0): Published under the Creative Commons Attribution 4.0 International license. Immediate, permanent worldwide open access for researchers and public health authorities. Authors retain unrestricted copyright. (Inaugural Volume Waiver: zero APC fees apply for manuscripts submitted to Volume 1).
• Option B - Subscription Publishing (Zero APC): Traditional publishing model with no author-facing publication charges, supported by institutional subscriptions and standard archiving.
• Data Sharing Mandate: Regardless of publishing route, all empirical genomic data and code must comply with MetaResistome's FAIR data accessibility requirements.

5. Ethics and Publishing Policies

Submission Declaration

Submission of an article implies that:

• The work described has not been published previously (except in the form of an academic thesis, published lecture, conference abstract, or recognized preprint).
• The manuscript is not under active consideration for publication elsewhere.
• Publication has been approved by all listed co-authors and by the responsible authorities at the institution where the work was performed.

Authorship Criteria & Accountability

Authorship credit must be grounded in the International Committee of Medical Journal Editors (ICMJE) guidelines. All listed authors must meet all four criteria:

1. Substantial contributions to the conception or design of the study, or the acquisition, analysis, or interpretation of data.
2. Drafting the work or critically revising it for vital intellectual content.
3. Final approval of the version submitted and published.
4. Agreement to be accountable for all aspects of the work ensuring accuracy and integrity.

Contributors who do not meet all four criteria (such as technical assistants, language editors, or laboratory heads who provided general supervision) should be recognized in the Acknowledgments section.

Declaration of Competing Interests

Authors must declare any financial, commercial, or personal relationships with individuals or organizations that could inappropriately influence or bias their research. If no competing interests exist, authors must explicitly state:

Funding Sources Disclosure

Authors must disclose all sources of financial support. Please format funding disclosures in the following standardized manner to ensure funder compliance:

Declaration of Generative AI in Manuscript Preparation

Authors must disclose any use of generative artificial intelligence (GenAI) technologies in the writing or preparation of the manuscript upon submission.

• AI tools must never be listed or cited as an author or co-author. Authorship implies legal and scientific accountability that can only be assumed by humans.
• AI tools may only be used with direct human oversight. Authors remain 100% accountable for verifying the factual accuracy, citations, and authenticity of all text and data.
• Prohibition: Use of AI tools to generate, alter, or synthesize primary experimental data, microscopy micrographs, gel bands, or clinical images is strictly forbidden.

Preprints & Open Science

MetaResistome encourages preprint posting on recognized community servers such as bioRxiv, medRxiv, and arXiv. Sharing a preprint prior to or during peer review does not constitute prior publication. Authors should notify the editorial desk of the preprint DOI upon submission so that upon publication, MetaResistome can link the preprint directly to the final Version of Record.

Image Manipulation & Integrity Standards

Scientific images - including agarose gels, western blots, pulsed-field gel electrophoresis (PFPE), transmission electron microscopy (TEM), and clinical micrographs - represent primary observational evidence. No specific feature within an image may be enhanced, obscured, introduced, moved, or deleted.

• Linear brightness and contrast adjustments are acceptable only if applied uniformly across the entire image and do not obscure genuine background information.
• All splices or grouped lanes in gel figures must be clearly delineated with dividing black or white lines and fully explained in the figure legend.
• Authors must retain all original, uncropped, unprocessed raw image files. Editors may request raw data files during peer review.

6. Writing and Formatting Guidelines

File Formats

Manuscripts should be submitted as editable documents: Microsoft Word (.docx) or LaTeX (with compiled .pdf and bundled .tex source files). Use standard margins (2.5 cm / 1 inch), double line spacing, and continuous line numbering throughout the text.

Title Page Requirements

The title page must include:

• Article Title: Informative, concise, avoiding acronyms and hyperbolic words like "First", "Novel", or "Paradigm-shifting".
• Author Names & Affiliations: Full given names and family names; institutional addresses with department, institution, city, and country.
• Corresponding Author: Clearly indicated with an asterisk (*), providing active institutional email address and telephone number.
• ORCID iDs: Authors are strongly encouraged to provide their 16-digit ORCID identifier.

Highlights & Abstract

• Highlights: 3 to 5 core bullet points (maximum 85 characters per bullet point including spaces) capturing the novel empirical findings of the study.
• Abstract: Maximum 250 words summarizing the rationale, methodology, primary results, and biological implications. Avoid literature citations in the abstract.
• Keywords: 4 to 6 specific keywords separated by semicolons (e.g. Wastewater surveillance; Metagenomic NGS; Extended-spectrum beta-lactamase; One Health; Mobile resistome).

Graphical Abstract

Authors of Original Research and Review Articles are strongly encouraged to submit a Graphical Abstract upon final acceptance. This visual summary appears in the table of contents and social feeds to help researchers quickly grasp the study's central premise.

• Preferred dimensions: minimum 1200 × 675 pixels (16:9 aspect ratio) or 1000 × 1000 pixels.
• Resolution: 300 DPI minimum; clear, uncluttered visual flow; legible font sizes (minimum 10 pt at display size).

Manuscript Structure

Original Research papers must be subdivided into numbered sections (e.g. 1. Introduction, 2. Materials and methods, 3. Results, 4. Discussion, 5. Conclusions):

• 1. Introduction: Clear statement of the global AMR or pathogen surveillance context, review of pertinent literature, and study objectives.
• 2. Materials and Methods: Detailed procedures allowing complete reproduction. Specify strain identifiers, sampling coordinates, sequencing library preparation kits, sequencing platform (e.g., Illumina NovaSeq, Oxford Nanopore), software versions, and bioinformatic parameters.
• 3. Results: Objective, logical presentation supported by figures and tables. Avoid redundant duplication of tabular data in narrative text.
• 4. Discussion: Critical interpretation of findings in relation to global literature, biological significance, mechanism of resistance dissemination, limitations, and future outlook.
• 5. Conclusions: Clear summary of the primary insights derived from the investigation.

Tables, Figures and Artwork

• Figures: Submit high-resolution TIFF, EPS, or vector PDF files. Line art: 600–1000 DPI; photographic micrographs: 300–600 DPI. Number figures consecutively using Arabic numerals (Figure 1, Figure 2).
• Legends: Each figure must have a self-contained legend explaining all symbols, abbreviations, and scale bars.
• Tables: Create tables using Word's table editor (do not embed tables as non-editable pictures). Place footnotes below the table body using superscript lowercase letters.

Mandatory Research Data Availability Statement

In accordance with MetaResistome's open science commitment, all raw sequencing reads and assembled genomic contigs must be publicly accessible in an International Nucleotide Sequence Database Collaboration (INSDC) repository (NCBI SRA/GenBank, ENA, or DDBJ) prior to publication.

Reference Style & Formatting

MetaResistome uses the numbered NLM / Vancouver citation style. Citations should be numbered consecutively in the text using bracketed numerals (e.g., [1], [2,3], [4-7]). Include complete author lists (up to 6 authors before using et al.) and DOIs for all cited literature.

7. Pre-Submission Checklist

Before transmitting your files to the editorial desk, please ensure that you have fulfilled all items on this checklist: