Clinical use for direct 16S sequencing

Detection and identification of bacteria directly from clinical samples by broad-range PCR targeting the 16S rRNA gene and DNA sequencing (Direct 16S rDNA sequencing) gives the possibility to identify bacteria that died during transportation or as a consequence of antibiotic treatment, and to uncover bacteria with special growth requirements. The latest advances in PCR and sequencing technology also offer a more rapid identification compared to standard phenotypical methods that depend on bacterial growth.

The single strongest reason to consider direct 16S rDNA sequencing as a supplement to culture should be the administration of antibiotics prior to sample collection. In hospitals that do not have dedicated transport systems for anaerobic bacteria, it should also be considered for important samples like brain abscesses regardless of antimicrobial status. There has been a tendency to await culture results, and eventually proceed to direct sequencing only in culture negative samples. This policy fails to take into consideration that in samples affected by antibiotics some species can still be able to grow, whereas others are not. An incomplete microbiological answer can be misleading and result in insufficient antimicrobial coverage, especially in patients where standard empiric therapy cannot be used or in patients that are transferred to per oral treatment.

In specimens containing more than one bacterium, direct 16S sequencing will generate mixed DNA chromatograms that complicate further interpretation. Consequently the use of this valuable diagnostic tool has been limited to infections that are predominantly mono-bacterial (e.g. CSF and synovial fluids). RipSeq Mixed  is an algorithm able to directly analyze these ambiguous chromatograms. The use of direct 16S rDNA sequencing can therefore be expanded into a number of typical poly-microbial specimens. It has been found to be of particular value in internal abscesses (e.g. brain, liver and pancreas), pleural fluids and bile.
 
In many cases this can save lives and in most cases decrease patient pain, drug side effects and number of days in hospital.