ArticlePLoS genetics2022
HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.Bioinformatics (Oxford, England) · 2026Article
- Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh.Microorganisms · 2026Review
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Leveraging the microbiome to combat antibiotic resistant gynecological infections.npj antimicrobials and resistance · 2025Review
- Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system.Animal microbiome · 2025Article
- Detection of rare plasmid hosts using a targeted Hi-C approach.ISME communications · 2025Article
- Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era.Nature reviews. Microbiology · 2024Review
- The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs.Animal microbiome · 2023Article
- Resistome expansion in disease-associated human gut microbiomes.Microbiome · 2023Article
- Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts.Microbial genomics · 2023Article
- Identifying ways of producing pigs more sustainably: tradeoffs and co-benefits in land and antimicrobial use.Scientific reports · 2023Article
- Impact of microbial genome completeness on metagenomic functional inference.ISME communications · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.