Quasimetagenomics refers to the sequencing of a modified food microbiome to facilitate combined detection and subtyping of targeted pathogens in a single workflow. Through quasimetagenomic sequencing, pathogens are detected and subtyped in a shortened time frame compared to traditional culture enrichment and whole genome sequencing-based analyses. While this method was previously used to detect and subtype Salmonella enterica from chicken, iceberg lettuce, and black pepper, it has not been applied to investigate multiple pathogens in one workflow. A quasimetagenomic method to concertedly detect and subtype Salmonella enterica and Escherichia coli O157:H7 from artificially contaminated romaine lettuce in a single workflow was developed. All quasimetagenomic samples with initial target pathogen inoculum levels of ~1 CFU/g were detected and serotyped after co-enrichment of the two pathogens for 12 h. Single nucleotide polymorphism typing was achievable for some initial pathogen inoculum levels as low as ~0.1 CFU/g. Our results suggest that this method can be used for concerted detection and subtyping of multiple bacterial pathogens from romaine lettuce even at low contamination levels.

准基因组学是指修饰的食品微生物组的测序，以促进在单个工作流程中对目标病原体的组合检测和亚型化。与传统的培养物富集和基于全基因组测序的分析相比，通过准基因组测序，可以在较短的时间内检测到病原体并将其亚型化。尽管此方法以前曾用于检测鸡，卷心莴苣和黑胡椒中的肠炎沙门氏菌并对其进行亚型化，但尚未应用于在一个工作流程中研究多种病原体的方法。准基因组学方法共同检测肠炎沙门氏菌和大肠杆菌并亚型通过单一工作流程开发了来自人工污染的生菜的O157：H7。共富集两种病原体12 h后，检测到所有初始目标病原体接种水平为〜1 CFU / g的拟染色体组学样品并进行血清分型。对于某些低至约0.1 CFU / g的初始病原体接种水平，可实现单核苷酸多态性分型。我们的结果表明，即使在低污染水平下，该方法也可用于协同检测和鉴别生菜中多种细菌病原体。