Metagenomics data provides rich information for the detection of foodborne pathogens from food and environmental samples that are mixed with complex background bacteria strains. While pathogen detection from metagenomic sequencing data has become an activity of increasing interest, shotgun sequencing of uncultured food samples typically produces data that contains reads from many different organisms, making accurate strain typing a challenging task. Particularly, as many pathogens may contain a common set of genes that are highly similar to those from normal bacteria in food samples, traditional strain-level abundance profiling approaches do not perform well at detecting pathogens of very low abundance levels. To overcome this limitation, we propose an abundance correction method based on species-specific genomic regions to achieve high sensitivity and high specificity in target pathogen detection at low abundance.

中文翻译：

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狙击：从宏基因组测序数据中高度敏感的病原体检测

元基因组学数据为从与复杂背景细菌菌株混合的食品和环境样品中检测食源性病原体提供了丰富的信息。尽管从宏基因组测序数据中检测病原体已成为人们越来越感兴趣的活动，但未培养食品样本的shot弹枪测序通常会产生包含来自许多不同生物体的读数的数据，这使得准确的菌株分类成为一项艰巨的任务。特别是，由于许多病原体可能包含与食品样本中正常细菌的基因高度相似的一组通用基因，因此传统的菌株级丰度分析方法在检测极低丰度水平的病原体时效果不佳。为了克服此限制，