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Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, Derisi JL, Tato CM, Langelier C. Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing. Clin Infect Dis 2021; 71:1179-1185. [PMID: 31563940 PMCID: PMC7442849 DOI: 10.1093/cid/ciz960] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Transfusion-related sepsis remains an important hospital infection control challenge. Investigation of septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration. METHODS In 3 gram-negative septic transfusion cases, we performed metagenomic next-generation sequencing (mNGS) of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events. 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. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens that share taxonomic similarity to contaminants commonly found in mNGS library preparations. CONCLUSIONS Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance, and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.
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Affiliation(s)
- Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Microbiology and Immunology, University of California-San Francisco, San Francisco, California, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Deborah Yokoe
- Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA.,Department of Hospital Epidemiology and Infection Prevention, University of California-San Francisco, San Francisco, California, USA
| | - Amy Nichols
- Department of Hospital Epidemiology and Infection Prevention, University of California-San Francisco, San Francisco, California, USA
| | - Nam K Tran
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Sarah E Barnard
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Peter M Conner
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Ashok Nambiar
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Matt S Zinter
- Division of Pulmonary and Critical Care Medicine, Department of Pediatrics, University of California-San Francisco, San Francisco, California, USA
| | - Morvarid Moayeri
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Paula Hayakawa Serpa
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Brian C Prince
- Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Jenai Quan
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Joseph L Derisi
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA
| | | | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
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