Culture independent bacterial identification in post-mortem samples

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Investigation of post-mortem samples for a bacterial aetiology is challenging. There may be pathological signs of inflammation and infection, but not always. Further complications arise via detection of organisms derived from agonal or post-mortem translocation from the colonised mucous membranes and contamination artificially introduced by collection processes. Attributing a terminal outcome to the finding of specific bacteria ranges from high certainty for pathogens not associated with the human microbiome, to low certainty when observing mixed bacterial species including normal flora. Clinical features of infection, known individual risk factors, particular bacterial virulence genes, and case histories are important pieces of the puzzle. Treatment with antimicrobials, peculiar nutritional and atmospheric requirements of bacteria, and delays in sample collection can all reduce the ability of traditional culture methods to recover causative organisms. In those circumstances recovery and specific identification of bacterial DNA has been an effective diagnostic augmentation for post-mortem bacteriology. Use of DNA encoding the bacterial ribosomes has been the primary culture independent approach. This technique will be discussed and local cases will be presented. The diagnostic value of 2 nd and 3 rd generation DNA sequencing instrument output and resultant bioinformatically reconstructed microbial genome content from clinical samples will be discussed.