16S Pathogen Diagnosis of Culture-Negative Infections

Stavnsbjerg et al. [1] collected 76 culture-negative samples from 46 patients who were suspicious of an infection. Specimens comprised of various tissues, bones, heart valves, joint and other body fluids, E-swabs and other samples. The samples were analysed by two commercial broad-range 16S rRNA gene PCR assays. The MicroSeq® ID system (Applied Biosystems, USA) uses total DNA extracts from the samples for broad-range 16S rRNA gene PCR and sequencing. The other system used in the study, UMD-SelectNA™ (Molzym, Germany), removes human DNA in samples before automated extraction of potentially present microbial DNA which is analysed by broad-range Real-Time 16S rRNA gene PCR and sequencing.

The UMD-SelectNA™ found bacterial DNA in 22 samples (29% positive), whereas only 11 samples were positive with MicroSeq® ID (14%). Ten samples from 8 patients with endocarditis, abscesses, infected joint and cancer were positive with both methods. Pathogens were identical by the two assays, except for a mixed infection in a pus sample from a cerebral abscess where the compositions of species were different but regarded relevant with both methods. UMD-SelectNA™ was further positive with 12 samples that were MicroSeq® ID-negative. Among these, other findings from the patients supported the results of 7 positive samples, whereas 5 samples gave ambiguous results.

The authors concluded that UMD-SelectNA™ found significantly more pathogens in culture-negative samples and thus proved more sensitive than MicroSeq® ID. Because of the increased sensitivity special care has to be taken to avoid contamination during handling. Clinical evaluation of the patients' history needs to be performed to assess the relevance of findings.