Molecular Techniques Yield Many More Strains Than Culturing

John G. Bartlett, MD


November 13, 2009

Isolation of bacteria by conventional cultures detects many fewer strains than found with molecular techniques. In this viewpoint, analysis of brain abscesses from 20 patients totaled 22 strains of bacteria for conventional culture and 72 strains with single and multiple sequencing, raising questions regarding the accuracy of current empirical treatment choices.

The Expansion of the Microbiological Spectrum of Brain Abscess With Use of Multiple 16S Ribosomal DNA Sequencing

Al Masalma M, Armougom F, Scheld WM, et al
Clin Infect Dis. 2009;48:1169-1178


The goal was to define the bacteriology of cerebral abscess using molecular techniques for comparison with conventional culture techniques.

The study was done prospectively on cerebral abscesses in 20 patients from 2 hospitals in Marseilles, France, from 2005 to 2007. Conventional cultures were done as routine with both aerobic and anaerobic techniques. For molecular definition, the investigators used amplified bacterial 16S ribosomal DNA sequencing with progressive techniques, including: (1) the "traditional" Sanger sequencing with 1 sequence/sample; (2) similar sequencing of clones from libraries with about 100 sequences per sample; and (3) pyrosequencing of molecules within polymerase chain reaction products.

The conventional culture method yielded 22 strains of bacteria, whereas the molecular tests yielded 72 strains. In terms of species, 14 were noted in the conventional culture technique, which was increased by 4 with the "traditional" Sanger sequencing; the total of 18 recognized species was increased to 44 with the "deeper analysis" techniques.

The study authors reported that the number of bacterial species detected in brain abscesses from 20 patients totaled 22 strains of bacteria for conventional culture and 72 strains with single and multiple sequencing. They concluded by questioning the accuracy of current empirical treatment based on conventional cultures.


Didier Raoult and colleagues, who are well respected for high-quality work using molecular methods to detect microbes, especially difficult-to-grow microbes, did the work reported here in Marseilles, France. Of note, their conventional cultures failed to yield any anaerobes despite the fact that anaerobes are well known to cause most brain abscesses, so there may be some serious question about the adequacy of the standard cultures. The molecular methods used yielded anaerobes but actually had large numbers of mycoplasma and a large number of bacteria from the Ribosomal Database Project II that most clinicians will not recognize.

It is well known that conventional culture techniques cannot detect many bacteria and that this is particularly true of the human colon, which is packed with bacteria, most of which have never been cultivated. The importance of this paper on brain abscess concerns the relevance of the observations. Specifically, is this more than we need to know, or is this an important message for the future of infectious disease study and treatment? Assuming the latter, this is a very important observation that merits full attention.