Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities.
Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities.
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DOI：
10.3390/microorganisms10122416
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发表时间：
2022-12-06
期刊：
影响因子：
4.5
通讯作者：
中科院分区：
文献类型：
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作者：
元基因组学提供了对来自复杂的食物和水微生物群的细菌病原体的最高水平的菌株识别。随着组装算法的快速发展，在食源性和水性病原菌的元基因组鉴定中，根据性能定义一个最优的组装器是必要的。我们的目标是利用模拟细菌群落对短读汇编器进行基准测试，以用于食源性和水源性病原体的元基因组鉴定。通过在不同测序深度产生Illumina HiSeq、MiSeq和NovaSeq的成对末端短读数来模拟新鲜菠菜和地表水中的细菌群落。多药耐药的印第安纳沙门氏菌SI43和铜绿假单胞菌PAO1分别被纳入新鲜菠菜和地表水的模拟群落中。Abyss、IDBA-UD、Masurca、MegaHit、MetaSPAdes和Ray Meta在组装质量、质粒鉴定、毒力基因、沙门氏菌致病岛、抗菌素耐药基因、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等方面进行了基准测试。总体而言，MEGHIT、MetaSPAdes和Ray Meta对元基因组鉴定更为有效。当我们使用被归类为沙门氏菌或铜绿假单胞菌的提取片段进行下游基因组分析时，我们没有获得最佳的组装器，但当提取的片段与沙门氏菌或铜绿假单胞菌菌株比对时，它们与参考基因组显示出一致的系统发育拓扑。在大多数情况下，HiSeq、MiSeq和NovaSeq在相同的测序深度上具有可比性，而更高的测序深度通常会导致更准确的结果。随着汇编算法的发展和成熟，对汇编者的评价应该是一个连续的过程。
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.
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影响因子：
2.2
作者：
Forouzan, Esmaeil;Shariati, Parvin;Yakhchali, Bagher
通讯作者：
Yakhchali, Bagher
影响因子：
5.4
作者：
BECKERS, HJ;DANIELSBOSMAN, MSM;BIJKERK, H
通讯作者：
BIJKERK, H
影响因子：
3.7
作者：
Kaas RS;Leekitcharoenphon P;Aarestrup FM;Lund O
通讯作者：
Lund O
影响因子：
7
作者：
Nurk S;Meleshko D;Korobeynikov A;Pevzner PA
通讯作者：
Pevzner PA
DOI：
10.1093/bioinformatics/bty630
发表时间：
2019-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gourlé H;Karlsson-Lindsjö O;Hayer J;Bongcam-Rudloff E
通讯作者：
Bongcam-Rudloff E