NCBI AMRFinderPlus抗性基因检测工具结构化详解 (Guide to NCBI AMRFinderPlus for Antimicrobial Resistance Gene Detection)

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一、工具概述

• NCBI AMRFinderPlus 是由美国国家生物技术信息中心（NCBI）开发的微生物耐药性和相关基因检测工具。
• Identifies not just acquired AMR genes but also point mutations, virulence, metal, biocide, and stress genes by leveraging curated reference data and Hidden Markov Models (HMMs) from NCBI.

二、数据库与依赖资源

• 核心数据库为“细菌抗菌药物耐药基因参考数据库”（Bacterial AMR Reference Gene Database），BioProject号：PRJNA313047，包含人工整理的耐药基因/HMM模型与命名体系(https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047/)。
• NCBI BioProject: PRJNA313047 — the official umbrella record for resistance genes, supporting scholarly citation and comparative studies.

三、功能支持与检测范围

• 支持蛋白序列和装配后的基因组（核酸序列）输入，可检测：
  • 获得性耐药基因
  • 关键点突变
  • 毒力因子/金属/应激/生物杀灭剂耐受基因（通过 --plus 选项）
• Detects both acquired resistance genes and resistance-associated point mutations; the “Plus” option includes stress, metal, and virulence determinants.

四、安装与更新

• 推荐用 Bioconda 或 GitHub 安装，定期更新数据库：
  • Bioconda: mamba install ncbi-amrfinderplus / mamba update ncbi-amrfinderplus
  • Check version: amrfinder -V

五、使用流程（命令结构）

• 典型命令与输入选项：
  • 装配基因组核酸序列： amrfinder -n assembly.fna -o amr.tsv --plus
  • 预测蛋白序列： amrfinder -p proteins.faa -o amr.tsv --plus
  • 需要突变规则的物种（如大肠杆菌、沙门氏菌等），可添加 --organism Escherichia
• If your input is protein (for specificity): amrfinder -p proteins.faa -o amr.tsv --plus
• Add --organism for species-specific detection rules (e.g., Salmonella, E. coli).

六、输出结果解读

• 输出结果包括：
  • 基因/等位基因名称
  • 类别
  • 检测方法（Exact / BLAST / HMM）
  • Percent identity \& coverage
• Reference Gene Hierarchy explains why HMM hits may be mapped to gene families.

七、与ResFinder工具对比

• AMRFinderPlus 强调数据库人工整理、层级命名与HMM深度，支持点突变/毒力因子类别；
• ResFinder primarily uses BLAST for acquired resistance genes; both are widely used.
• 两者结果可互补，建议在关键案例均报告并比较结论。

八、β-内酰胺酶检测相关

• AMRFinderPlus 能精准识别各类 β-内酰胺酶以及特定等位基因（KPC、NDM、OXA-48等），但药物抑制剂敏感性需结合表型MIC和人工比对。

九、实践建议与数据管理

• 分析前应QC（覆盖度、污染、N50等），优先用蛋白输入以降低假阳性；务必记录运行软件与数据库版本。
• Reference all results and analyses to your BioProject for project transparency and reproducibility.

十、数据提交与BioProject关联

• 强烈推荐提交数据到NCBI，关联BioProject，实验报告/论文需标明引用。合规数据将进入 Pathogen Detection/Isolate Browser，便于下游标准化分析与溯源。
• Follow NCBI pathogen/AMR submission guidelines for maximum interoperability and future-proofing.

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主要优点总结

• 全面覆盖AMR基因、点突变至毒力因子，有权威数据库与持续更新支持，多模式比对结果提升准确率。适用于宏/微生物组耐药基因监测、临床感染溯源、研究数据管理等多场景。

Citation: Reference Database: BioProject PRJNA313047 Official tool page: https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/

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This structured guide is suitable for scientific communication, teaching, or lab documentation. Please cite the BioProject and include the official tool URL when republishing.

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What AMRFinderPlus is good for

• Detects acquired AMR genes and key resistance-associated point mutations from assembled genomes (protein or nucleotide).
• It also optionally reports virulence, stress/biocide/metal genes (“Plus”).
  国家生物技术信息中心+1

Powered by NCBI’s curated Bacterial AMR Reference Gene Database (with HMMs and a naming hierarchy), used in NCBI’s Pathogen Detection pipeline.
journals.asm.org+2国家生物技术信息中心+2

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Database you’ll cite/use

Bacterial Antimicrobial Resistance Reference Gene Database
BioProject accession: PRJNA313047. Keep this in methods/notes.
国家生物技术信息中心

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Install & update (typical options)

• Bioconda or GitHub.
• After install, update DB regularly.
• Check versions with amrfinder -V.
  GitHub+2bioconda.github.io+2

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Minimal commands you’ll actually run

On an assembly (nucleotide FASTA): amrfinder -n assembly.fna -o amr.tsv --plus

If you have predicted proteins (often best for specificity): amrfinder -p proteins.faa -o amr.tsv --plus

Add organism when supported for point-mutation rules (e.g., Salmonella, E. coli, Campylobacter, S. aureus): amrfinder -n assembly.fna --organism Escherichia -o amr.tsv 国家生物技术信息中心+1

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Reading the output (what to look for)

• You’ll get gene/allele names, class, method (Exact/Blast/HMM), and % identity/coverage.
• Use the Reference Gene Hierarchy for how borderline hits are named and why an HMM hit maps to a family.
  国家生物技术信息中心

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How it complements (and differs from) ResFinder

• AMRFinderPlus: includes a curated hierarchy, extensive HMMs, and point-mutation rules for several taxa; “Plus” genes beyond classic AMR.
  国家生物技术信息中心+1

• ResFinder: strong for acquired genes via BLAST rules.
  Both are widely used; results can differ slightly by database scope and curation. Consider running both for critical cases and reconciling (multiple reviews/benchmarks discuss trade-offs).
  PubMed Central+1

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β-lactamase & BLI angle (important in the context)

• AMRFinderPlus will identify β-lactamase families and many specific alleles (e.g., KPC, OXA-48-like, NDM, CTX-M).
• Neither AMRFinderPlus nor ResFinder guarantees inhibitor efficacy (e.g., avibactam, vaborbactam) because allele-specific substitutions, expression, porins/efflux affect phenotype.
• Use the call to narrow likely classes (KPC vs OXA-48 vs MBL) and confirm with MICs.
  国家生物技术信息中心+1

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Tie-in with BioProject

• BioProject is the umbrella record linking all your project’s sequence data (assemblies, SRA reads, BioSamples).

• Create one for your study; reference it in your reports.
  国家生物技术信息中心

• If you submit to NCBI (recommended), follow the Pathogen/AMR submission guidance so your data appear in Pathogen Detection/Isolate Browser and benefit from standardized pipelines.
  国家生物技术信息中心+1

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Practical checkpoints / best practices

• QC first (coverage, contamination, N50); subpar assemblies yield spurious or missed hits.

• Run with proteins when available (often fewer false positives); still keep nucleotide run if you lack annotation.
  国家生物技术信息中心

• Record software & DB versions in your methods (e.g., “AMRFinderPlus vX.Y; database YYYY-MM-DD; PRJNA313047”).
  biocontainer-doc.readthedocs.io

• Corroborate critical clinical calls (e.g., suspected KPC escape mutants) with phenotypic MICs and, if needed, manual allele review.
  PubMed Central

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Run through an interpretation plan (what AMR genes/mutations to report, and how to summarize likely β-lactam/BLI implications).