The Expansion of the Microbiological Spectrum of Brain Abscesses with Use of Multiple 16S Ribosomal DNA Sequencing

Abstract

Background. Brain abscess is commonly treated using empirically prescribed antibiotics. Thus, a comprehensive study of bacterial organisms associated with brain abscess is essential to define the best empirical treatment for this life-threatening condition. Methods. We prospectively compared cultures to single and multiple sequenced 16S ribosomal DNA polymerase chain reaction amplifications (by cloning and/or pyrosequencing) of cerebral abscesses in 20 patients from 2 hospitals in Marseilles, France, during the period January 2005 through December 2007. Results. The obtained cultures identified significantly fewer types of bacteria (22 strains) than did molecular testing (72 strains; P = .017, by analysis of variance test). We found that a patient could exhibit as many as 16 different bacterial species in a single abscess. The obtained cultures identified 14 different species already known to cause cerebral abscess. Single sequencing performed poorly, whereas multiple sequencing identified 49 species, of which 27 had not been previously reported in brain abscess investigations and 15 were completely unknown. Interestingly, we observed 2 patients who harbored Mycoplasma hominis (an emerging pathogen in this situation) and 3 patients who harbored Mycoplasma faucium, which, to our knowledge, has never been reported in literature. Conclusions. Molecular techniques dramatically increased the number of identified agents in cerebral abscesses. Mycoplasma species are common and should be detected in this situation. These findings led us to question the accuracy of the current empirical treatment of brain abscess.

Massive Parallel Sequencing Provides New Perspectives on Bacterial Brain Abscesses

“…Campylobacter gracilis (previously Bacteroides gracilis) and Campylobacter rectus are the most dominant Campylobacter species in the oral cavity and represent another long-acknowledged genus in intracranial infections rarely recovered by culture (1,4,30). In this study, C. gracilis (n ϭ 8) was found exclusively in samples positive for Actinomyces spp.…”

“…Recent investigations of bacterial brain abscesses using universal amplification of the bacterial 16S rRNA gene, followed by Sanger sequencing of cloned amplicons, have revealed that only a fraction of the bacteria present are identified by culture (1,2). Nevertheless, this approach has limitations when it comes to detecting smaller subpopulations in a multispecies community, unless very high numbers of clones are sequenced (3).…”

Identification of Rare Pathogenic Bacteria in a Clinical Microbiology Laboratory: Impact of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

“…The number of newly described bacteria has risen impressively during the past few decades (1,2). Notably, the identification of new pathogens in clinical microbiology has been spectacularly improved during previous decades by the use of molecular identification, especially 16S rRNA gene sequencing (3)(4)(5)(6)(7)(8). Molecular identification is one of the most useful techniques but remains expensive and requires a workload that is not adapted for routine use.…”

Direct 16S rRNA Gene Sequencing from Clinical Specimens, with Special Focus on Polybacterial Samples and Interpretation of Mixed DNA Chromatograms

“…A review of the literature confirms the role of Campylobacter gracilis in certain extra-oro-intestinal abscesses and empyemata (6,11). Most recently, it was discovered by broad-range amplification and cloning in three polybacterial brain abscesses (1). The blood culture results were included mainly to get a comparison between culture and sequencing, unaffected by antibiotics, sample collection procedures, or transportation.…”