Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India.
The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, United Kingdom.
J Glob Antimicrob Resist. 2022 Dec;31:167-174. doi: 10.1016/j.jgar.2022.08.017. Epub 2022 Aug 30.
The use of antibiotics in human medicine and livestock production has contributed to the widespread occurrence of Antimicrobial Resistance (AMR). Recognizing the relevance of AMR to human and livestock health, it is important to assess the occurrence of genetic determinants of resistance in medical, veterinary, and public health settings in order to understand risks of transmission and treatment failure. Advances in next-generation sequencing technologies have had a significant impact on research in microbial genetics and microbiome analyses. The aim of the present study was to compare the Illumina MiSeq and Ion Torrent S5 Plus sequencing platforms for the analysis of AMR genes in a veterinary/public health setting.
All samples were processed in parallel for the two sequencing technologies, subsequently following a common bioinformatics workflow to define the occurrence and abundance of AMR gene sequences. The Comprehensive Antibiotic Resistance Database (CARD), QIAGEN Microbial Insight - Antimicrobial Resistance, Antimicrobial resistance database, and Comprehensive Antibiotic Resistance Database developed by CLC bio (CARD-CLC) databases were compared for analysis, with the most genes identified using CARD.
Drawing on these results, we described an end-to-end workflow for the analysis of AMR genes a using advances in next-generation sequencing. No statistically significant differences were observed among any other genes except the tet-(40) gene between two sequencing platforms, which may be due to the short amplicon length.
Irrespective of sequencing chemistry and platform used, comparative analysis of AMR genes and candidate host organism suggest that the Illumina MiSeq and Ion Torrent platforms performed almost equally. Regardless of sequencing platform, the results were closely comparable with minor differences.
人类医学和畜牧业生产中抗生素的使用导致了抗菌药物耐药性（AMR）的广泛发生。鉴于 AMR 与人类和牲畜健康的相关性，评估医学、兽医和公共卫生环境中耐药遗传决定因素的发生情况，以了解传播和治疗失败的风险非常重要。下一代测序技术的进步对微生物遗传学和微生物组分析的研究产生了重大影响。本研究的目的是比较 Illumina MiSeq 和 Ion Torrent S5 Plus 测序平台在兽医/公共卫生环境中分析 AMR 基因的性能。
所有样本均同时进行两种测序技术的处理，随后遵循共同的生物信息学工作流程来定义 AMR 基因序列的发生和丰度。比较了 Comprehensive Antibiotic Resistance Database (CARD)、QIAGEN Microbial Insight - Antimicrobial Resistance、Antimicrobial resistance database 和由 CLC bio 开发的 Comprehensive Antibiotic Resistance Database (CARD-CLC) 数据库进行分析，其中使用 CARD 识别出最多的基因。
根据这些结果，我们描述了使用下一代测序技术分析 AMR 基因的端到端工作流程。除了两种测序平台之间的 tet-(40) 基因外，其他任何基因之间均未观察到统计学上的显著差异，这可能是由于扩增子长度较短。
无论测序化学和平台如何，对 AMR 基因和候选宿主生物体的比较分析表明，Illumina MiSeq 和 Ion Torrent 平台的性能几乎相当。无论测序平台如何，结果都非常接近，只有微小差异。
