title: Massive parallel sequencing provides new perspectives on bacterial brain abscesses.
abstract: Rapid development within the field of massive parallel sequencing (MPS) is about to bring this technology within reach for diagnostic microbiology laboratories. We wanted to explore its potential for improving diagnosis and understanding of polymicrobial infections, using bacterial brain abscesses as an example. We conducted a prospective nationwide study on bacterial brain abscesses. Fifty-two surgical samples were included over a 2-year period. The samples were categorized as either spontaneous intracerebral, spontaneous subdural, or postoperative. Bacterial 16S rRNA genes were amplified directly from the specimens and sequenced using Ion Torrent technology, with an average of 500,000 reads per sample. The results were compared to those from culture- and Sanger sequencing-based diagnostics. Compared to culture, MPS allowed for triple the number of bacterial identifications. Aggregatibacter aphrophilus, Fusobacterium nucleatum, and Streptococcus intermedius or combinations of them were found in all spontaneous polymicrobial abscesses. F. nucleatum was systematically detected in samples with anaerobic flora. The increased detection rate for Actinomyces spp. and facultative Gram-negative rods further revealed several species associations. We suggest that A. aphrophilus, F. nucleatum, and S. intermedius are key pathogens for the establishment of spontaneous polymicrobial brain abscesses. In addition, F. nucleatum seems to be important for the development of anaerobic flora. MPS can accurately describe polymicrobial specimens when a sufficient number of reads is used to compensate for unequal species concentrations and principles are defined to discard contaminant bacterial DNA in the subsequent data analysis. This will contribute to our understanding of how different types of polymicrobial infections develop.
authors.affiliation: Department of Microbiology, Haukeland University Hospital, Bergen, Norway oyvind.kommedal@helse-bergen.no.
authors.forename: Øyvind
authors.initials: Ø
authors.lastname: Kommedal
authors.affiliation: Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
authors.forename: Marianne Thulin
authors.initials: MT
authors.lastname: Wilhelmsen
authors.affiliation: Department of Medicine, Haukeland University Hospital, Bergen, Norway Department of Clinical Science, University of Bergen, Bergen, Norway.
authors.forename: Steinar
authors.initials: S
authors.lastname: Skrede
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
authors.forename: Roger
authors.initials: R
authors.lastname: Meisal
authors.affiliation: Department of Microbiology, St. Olav's University Hospital, Trondheim, Norway.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Jakovljev
authors.affiliation: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
authors.forename: Peter
authors.initials: P
authors.lastname: Gaustad
authors.affiliation: Department of Microbiology, Oslo University Hospital, Oslo, Norway.
authors.forename: Nils Olav
authors.initials: NO
authors.lastname: Hermansen
authors.affiliation: Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
authors.forename: Einar
authors.initials: E
authors.lastname: Vik-Mo
authors.affiliation: Department of Neurosurgery, St. Olav's University Hospital, Trondheim, Norway Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Ole
authors.initials: O
authors.lastname: Solheim
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
authors.forename: Ole Herman
authors.initials: OH
authors.lastname: Ambur
authors.affiliation: Isentio, Inc., Palo Alto, California, USA.
authors.forename: Øystein
authors.initials: Ø
authors.lastname: Sæbø
authors.affiliation: Department of Neurosurgery, University of North Norway, Tromsø, Norway.
authors.forename: Christina Teisner
authors.initials: CT
authors.lastname: Høstmælingen
authors.affiliation: Department of Neurosurgery, Haukeland University Hospital, Bergen, Norway Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors.forename: Christian
authors.initials: C
authors.lastname: Helland
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001424:Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology*; D001922:Brain Abscess / Q000175:diagnosis* / Q000382:microbiology*; D060085:Coinfection / Q000175:diagnosis / Q000382:microbiology; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S