title: Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: microbial constituents of empyema, liver abscess, and intracerebral abscess.
abstract: The polymicrobial nature of invasive pyogenic infections may be underestimated by routine culture practices, due to the fastidious nature of many organisms and the loss of viability during transport or from prior antibacterials. Pyrosequencing was performed on brain and liver abscesses and pleural fluid and compared to routine culture data. Forty-seven invasive pyogenic infection samples from 44 patients [6 intracerebral abscess (ICA), 21 pyogenic liver abscess (PLA), and 18 pleural fluid (PF) samples] were assayed. Pyrosequencing identified an etiologic microorganism in 100 % of samples versus 45 % by culture, p <0.01. Pyrosequencing was also more likely than traditional cultures to classify infections as polymicrobial, 91 % versus 17 %, p <0.001. The median number of genera identified by pyrosequencing compared to culture was 1 [interquartile range (IQR) 1-3] versus 0 (IQR 0-1) for ICA, 7 (IQR 1-15) versus 1 (IQR 0-1) for PLA, and 15 (IQR 9-19) versus 0 (IQR 0-1) for PF. Where organisms were cultured, they typically represented the numerically dominant species identified by pyrosequencing. Complex microbial communities are involved in invasive pyogenic infection of the lung, liver, and brain. Defining the polymicrobial nature of invasive pyogenic infections is the first step towards appreciating the clinical and diagnostic implications of these complex communities.
authors.affiliation: Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive NW, Calgary Laboratory Services, Calgary, AB, T2N 4N, Canada.
authors.forename: C D
authors.initials: CD
authors.lastname: Sibley
authors.forename: D L
authors.initials: DL
authors.lastname: Church
authors.forename: M G
authors.initials: MG
authors.lastname: Surette
authors.forename: S E
authors.initials: SE
authors.lastname: Dowd
authors.forename: M D
authors.initials: MD
authors.lastname: Parkins
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D058491:Bacterial Load; D015373:Bacterial Typing Techniques / Q000379:methods*; D001922:Brain Abscess / Q000382:microbiology*; D002648:Child; D002675:Child, Preschool; D046508:Culture Techniques; D004269:DNA, Bacterial / Q000235:genetics; D004653:Empyema / Q000382:microbiology*; D006090:Gram-Negative Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D046290:Liver Abscess, Pyogenic / Q000382:microbiology*; D008875:Middle Aged; D010996:Pleural Effusion / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013290:Streptococcal Infections / Q000382:microbiology; D013291:Streptococcus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S