PDF(Pubmed)
Abstract：
Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.
摘要：
宏基因组学提供了来自复杂食物和水微生物群的细菌病原体的最高水平的菌株区分。随着装配算法的快速发展,根据食源性和水性病原体的宏基因组鉴定中的性能来定义最佳组装者是必要的。我们的目标是使用模拟细菌群落对食源性和水性病原体进行宏基因组鉴定的短阅读组装者进行基准测试。通过生成IlluminaHiSeq的配对末端短读数来模拟新鲜菠菜和地表水中的细菌群落，MiSeq,和NovaSeq在不同的测序深度。在新鲜菠菜和地表水中的模拟群落中包括耐多药的印第安纳沙门氏菌SI43和铜绿假单胞菌PAO1，分别。ABYSS,IDBA-UD,MaSuRCA,MEGAHIT,metaSPA,和RayMeta在装配质量方面进行了基准测试，质粒的鉴定，毒力基因，沙门氏菌致病性岛，抗菌素抗性基因，染色体点突变,血清分型,多位点序列分型,和全基因组系统发育。总的来说,MEGHIT,metaSPA,和RayMeta对宏基因组鉴定更有效。当使用分类为沙门氏菌或铜绿假单胞菌的提取读段进行下游基因组分析时，我们没有获得最佳的汇编程序。但是当与沙门氏菌或铜绿假单胞菌菌株进行比对时，提取的读数显示出与参考基因组一致的系统发育拓扑结构。在大多数情况下,HiSeq,MiSeq,和NovaSeq在相同的测序深度下具有可比性，而更高的测序深度通常导致更准确的结果。随着装配算法的进步和成熟,对装配工的评估应该是一个连续的过程。
