Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, CF10 3AX, UK.
Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
Microb Genom. 2022 Nov;8(11). doi: 10.1099/mgen.0.000884.
The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.
家居和个人护理（HPC）行业通常依赖于初始培养和随后的生化测试来识别污染产品中的微生物。这个过程很慢（培养需要几天），劳动强度大，而且会错过那些无法从保存的消费品恶劣环境中恢复的微生物。由于 HPC 行业的制造过程是高通量的，因此微生物污染的鉴定过程可以受益于已经开发出的多种与培养无关的方法，这些方法用于检测和分析微生物。我们描述了一种从 HPC 产品中直接进行自动化 DNA 提取，然后应用宏基因组学方法进行细菌种属和菌株水平鉴定的新工作流程。该工作流程通过应用于一种通用清洁剂（GPC）的历史微生物污染进行了验证。在产品中通过宏基因组学检测到了单一的 菌株。该宏基因组与通过传统培养方法平行分离的污染物的基因组相似。通过对污染样品的稀释系列进行检测，我们还提供了证据表明，该工作流程能够检测到产品中低至 100 CFU/ml 的污染生物。据我们所知，这是宏基因组学分析首次提供传统分离污染物生物的确认证据的实例，涉及 HPC 产品。
