Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.
PLoS Genet. 2022 Mar 14;18(3):e1009776. doi: 10.1371/journal.pgen.1009776. eCollection 2022 Mar.
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.
shotgun 宏基因组学是一种强大的工具，可用于鉴定微生物组中的抗生素耐药性 (AMR) 基因，但它有一个局限性，即无法将质粒等染色体外 DNA 与宿主细菌染色体联系起来。在这里，我们提出了一种全面的实验室和生物信息学管道 HAM-ART（Hi-C 辅助宏基因组学用于抗生素耐药性追踪），该管道经过优化，可用于生成包括染色体和染色体外 AMR 基因在内的宏基因组组装基因组。我们在一项比较低抗菌药物使用和高抗菌药物使用猪（有机和常规农场）的 100 个猪粪便微生物组的研究中展示了该管道的性能。我们发现低抗菌药物使用和高抗菌药物使用农场之间的 AMR 基因分布存在显著差异，包括三种乳杆菌中仅存在于高抗菌药物使用农场的质粒携带林可酰胺类耐药基因。生物信息学管道代码可在 https://github.com/lkalmar/HAM-ART 上获得。
