Comparison of 16S Ribosomal RNA Targeted Sequencing and Culture for Bacterial Identification in Normally Sterile Body Fluid Samples: Report of a 10-Year Clinical Laboratory Review

Abstract

As 16S ribosomal RNA (rRNA)-targeted sequencing can detect DNA from non-viable bacteria, it can be used to identify pathogens from clinical samples even in patients pretreated with antibiotics. We compared the results of 16S rRNA-targeted sequencing and culture for identifying bacterial species in normally sterile body fluid (NSBF): cerebrospinal, pericardial, peritoneal and pleural fluids. Over a 10-year period, a total of 312 NSBF samples were evaluated simultaneously using 16S rRNA-targeted sequencing and culture. Results were concordant in 287/312 (92.0%) samples, including 277 (88.8%) negative and 10 (3.2%) positive samples. Of the 16 sequencing-positive, culture-negative samples, eight showed clinically relevant isolates that included Fusobacterium nucleatum subsp. nucleatum, Streptococcus pneumoniae, and Staphylococcus spp. All these samples were obtained from the patients pretreated with antibiotics. The diagnostic yield of 16S rRNA-targeted sequencing combined with culture was 11.2%, while that of culture alone was 6.1%. 16S rRNA-targeted sequencing in conjunction with culture could be useful for identifying bacteria in NSBF samples, especially when patients have been pretreated with antibiotics and when anaerobic infection is suspected.

Keywords: 16S ribosomal RNA; Culture; Diagnostic yield; Normally sterile body fluid; Sequencing.

Fig. 1. Direct 16S ribosomal RNA sequencing versus culture for identifying bacteria in normally sterile body fluid samples (N=312). Clinically relevant isolates are indicated in bold.