Academic Journal
HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.
| العنوان: | HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. |
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| المؤلفون: | Kalmar, L, Gupta, S, Kean, IRL, Ba, X, Hadjirin, N, Lay, EM, de Vries, SPW, Bateman, M, Bartlet, H, Hernandez-Garcia, J, Tucker, AW, Restif, O, Stevens, MP, Wood, JLN, Maskell, DJ, Grant, AJ, Holmes, MA |
| المساهمون: | Didelot, X |
| بيانات النشر: | Public Library of Science (PLoS) |
| سنة النشر: | 2022 |
| المجموعة: | The University of Melbourne: Digital Repository |
| الوصف: | 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. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| تدمد: | 1553-7390 1553-7404 |
| Relation: | pii: PGENETICS-D-21-00617; Kalmar, L., Gupta, S., Kean, I. R. L., Ba, X., Hadjirin, N., Lay, E. M., de Vries, S. P. W., Bateman, M., Bartlet, H., Hernandez-Garcia, J., Tucker, A. W., Restif, O., Stevens, M. P., Wood, J. L. N., Maskell, D. J., Grant, A. J. & Holmes, M. A. (2022). HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. PLoS Genet, 18 (3), pp.e1009776-. https://doi.org/10.1371/journal.pgen.1009776.; http://hdl.handle.net/11343/307133 |
| الاتاحة: | http://hdl.handle.net/11343/307133 |
| Rights: | CC BY ; https://creativecommons.org/licenses/by/4.0 |
| رقم الانضمام: | edsbas.8B0D841B |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 15537390 15537404 |
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