Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing

Abstract

Importance Transfusion-related sepsis remains a major hospital infection control issue due to challenges with diagnosis, prevention and management. Novel, unbiased, culture-independent diagnostic approaches are needed. Objective To present a case series of septic transfusion events in which culture-independent metagenomic next generation sequencing (mNGS) of blood products afforded rapid and actionable assessment of pathogen identity, abundance and genetic relatedness. Design, Setting and Participants In this series of three septic transfusion cases, mNGS of direct clinical blood specimens was performed in addition to standard culture-based approaches for clinical investigation. Cases involved Gram-negative sepsis and stemmed from hospital infection control investigations at two tertiary care hospitals in Northern California. Pathogen detection leveraged ID-Seq, a new open-access bioinformatics portal. Novel approaches to distinguish environmental microbiota from relevant pathogens were developed. Phylogenetic analysis was performed to assess microbial relatedness and understand transmission events. Main Outcomes and Measures Detection of pathogens from patient blood samples and transfused products using culture-independent mNGS. Assessment of microbial genomic relatedness to verify transmission events using a combination of mNGS and sequencing of cultured bacterial isolates. Results mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis, and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture, or that failed to grow due to prior antibiotic administration. In addition, we developed new methodology to enhance the accuracy of mNGS-based assessment of transfusion-related pathogens that share taxonomic similarity to background microbial contaminants commonly found in metagenomic sequencing assays. Conclusions and Relevance In each case, culture-independent metagenomic sequencing of blood products afforded rapid and actionable assessment of pathogen identity, abundance and genetic relatedness. Together, these challenging cases demonstrated the potential for mNGS to advance existing methods for investigating transfusion-transmitted infections. Key Points Question Can the assessment and prevention of transfusion-transmitted infections be enhanced by incorporating clinical metagenomic next generation sequencing? Findings We describe three septic transfusion cases, two of which involved fatalities, where culture-independent metagenomic sequencing of blood products afforded rapid and actionable assessment of pathogen identity, abundance and genetic relatedness. Meaning Transfusion-transmitted infections continue to result in significant morbidity and are challenging to prevent and diagnose. We found that culture-independent metagenomic sequencing enhanced traditional hospital infection control strategies used to investigate septic transfusion events.