Implementation of clinical metagenomics for pathogen identification in intra-abdominal sepsis: A case report

Clinical metagenomics methods significantly expand diagnostic capabilities, especially in cases where pathogens cannot be identified using traditional methods. This study describes a clinical case of acute gangrenous-perforated appendicitis complicated by severe sepsis and multiple organ failure. Blood cultures were negative throughout hospitalization, which served as the basis for metagenomic sequencing of whole blood and plasma obtained from the patient on the first and seventh days of illness. Two sequencing platforms were used: MGI and Oxford Nanopore (ONT). A total of 28.2 million to 58.6 million paired reads were obtained on the MGI platform, and 0.54 to 5.1 million reads on the ONT platform. The ratio of Homo sapiens DNA fragments to microbial DNA fragments was 99% and <1%, respectively. Cell-free DNA (cfDNA) fragments of anaerobes Bacteroides thetaiotaomicron, Phocaeicola vulgatus, and Barnesiella intestinihominis, which are part of the human intestinal microbiota but can cause severe sepsis with high mortality, were detected in blood plasma samples. Many DNA fragments of the herpes virus Roseolovirus human beta 6a were detected in all samples, likely indicating its reactivation and possible role in the severity of the infection. Information on potential pathogens obtained through metagenomic sequencing methods can be used to inform etiotropic treatment strategies.

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