MAY 20239 its root cause" (pg 146). USP <1113> also explains the utility and benefit of strain typing.If the microbial contaminant is the same as a laboratory QC strain, it's important to first eliminate laboratory error. This can also be done through strain typing. For example, Staphylococcus aureus can be typed through the spaA gene and Pseudomonas aeruginosa can be typed through the ascA, guaA, mutL, and nuoD genes. The genes are sequenced, and then phylogenetic trees are generated and interpreted. In the example below, the laboratory QC strain Pseudomonas aeruginosa ATCC# 9027 was different from the product contaminant and thus the contamination was not due to lab error.Figure 1. The genetic differences in the ascA, guaA, mutL, and nuoD genes indicate that the laboratory QC strain is different from the product contaminant. After laboratory error is ruled out, a review of environmental monitoring data is required. Some additional sampling may also be required. If the same species is recovered, strain typing can identify the source. In the case of a media fill failure, the microbial contaminant was identified as Micrococcus luteus. The species-level identification provided direction to focus the investigation on operators since Micrococcus is a common skin flora. A review of EM trends found recent hits on personnel monitoring as well as some surface sampling. By strain typing the gsp, prfA, and sahH genes, the isolates can be compared. In this case, the strain from Operator A was identical to the media fill strain, indicating that Operator A was likely the source. Operator B contaminated the Pass Through, and all the other isolates were different strains.Figure 2. Micrococcus luteus isolates that were strain typed using the gsp, prfA, and sahH genes. The phylogenetic trees represent the relatedness of the isolates to each other and are interpreted to make conclusions.Strain typing can provide beneficial information to quickly locate the root cause of microbial contamination. The primary drawback is that since strain typing is a comparison of different isolates, multiple isolates must first be found and identified. If the same species is not discovered through environmental monitoring, then no definitive root cause can be determined.While strain typing can be an intensive and technical undertaking, it is become more widely available through contract labs and in core laboratories. The technology has advanced rapidly with results becoming faster and less expensive. The adoption of whole genome sequencing for strain typing is not just a valuable tool for public outbreaks, but also for pharmaceutical manufacturers in investigations. Given the regulatory and business pressure for thorough root cause analysis, microbiologists need to utilize every tool available to quickly remediate contamination events. When contamination investigations are required, it is important for microbiologists to use all available tools to quickly find the source of the contamination
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