Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients.

Autor: Birdsell DN; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. Dawn.Birdsell@nau.edu., Özsürekci Y; Department of Pediatric Infectious Disease Unit in Ankara, Hacettepe University Faculty of Medicine, Ankara, Turkey., Rawat A; Translational Genomics Research Institute, Flagstaff, AZ, USA.; Present Address: Division of Biomedical Informatics Research, Sidra Medical & Research Center, Doha, Qatar., Aycan AE; Department of Pediatric Infectious Disease Unit in Ankara, Hacettepe University Faculty of Medicine, Ankara, Turkey., Mitchell CL; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.; Present Address: Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA., Sahl JW; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Johansson A; Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden., Colman RE; Translational Genomics Research Institute, Flagstaff, AZ, USA.; Present address: Department of Medicine, University of California, San Diego, California, USA., Schupp JM; Translational Genomics Research Institute, Flagstaff, AZ, USA., Ceyhan M; Department of Pediatric Infectious Disease Unit in Ankara, Hacettepe University Faculty of Medicine, Ankara, Turkey., Keim PS; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.; Translational Genomics Research Institute, Flagstaff, AZ, USA., Wagner DM; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Jazyk: angličtina
Zdroj: BMC infectious diseases [BMC Infect Dis] 2018 Jul 11; Vol. 18 (1), pp. 319. Date of Electronic Publication: 2018 Jul 11.
DOI: 10.1186/s12879-018-3218-2
Abstrakt: Background: Underlying coinfections may complicate infectious disease states but commonly go unnoticed because an a priori clinical suspicion is usually required so they can be detected via targeted diagnostic tools. Shotgun metagenomics is a broad diagnostic tool that can be useful for identifying multiple microbes simultaneously especially if coupled with lymph node aspirates, a clinical matrix known to house disparate pathogens. The objective of this study was to analyze the utility of this unconventional diagnostic approach (shotgun metagenomics) using clinical samples from human tularemia cases as a test model. Tularemia, caused by the bacterium Francisella tularensis, is an emerging infectious disease in Turkey. This disease commonly manifests as swelling of the lymph nodes nearest to the entry of infection. Because swollen cervical nodes are observed from many different types of human infections we used these clinical sample types to analyze the utility of shotgun metagenomics.
Methods: We conducted an unbiased molecular survey using shotgun metagenomics sequencing of DNA extracts from fine-needle aspirates of neck lymph nodes from eight tularemia patients who displayed protracted symptoms. The resulting metagenomics data were searched for microbial sequences (bacterial and viral).
Results: F. tularensis sequences were detected in all samples. In addition, we detected DNA of other known pathogens in three patients. Both Hepatitis B virus (HBV) and Human Parvovirus B-19 were detected in one individual and Human Parvovirus B-19 alone was detected in two other individuals. Subsequent PCR coupled with Sanger sequencing verified the metagenomics results. The HBV status was independently confirmed via serological diagnostics, despite evading notice during the initial assessment.
Conclusion: Our data highlight that shotgun metagenomics of fine-needle lymph node aspirates is a promising clinical diagnostic strategy to identify coinfections. Given the feasibility of the diagnostic approach demonstrated here, further steps to promote integration of this type of diagnostic capability into mainstream clinical practice are warranted.
Databáze: MEDLINE
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