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. 2024 Jun 21;14(13):1318.
doi: 10.3390/diagnostics14131318.

Performance of 16S rRNA Gene Next-Generation Sequencing and the Culture Method in the Detection of Bacteria in Clinical Specimens

Alexandru Botan  1 , Giuseppina Campisciano  2   3 , Verena Zerbato  4 , Stefano Di Bella  3 , Omar Simonetti  4 , Marina Busetti  5 , Dan Alexandru Toc  6 , Roberto Luzzati  3 , Manola Comar  2   3
Affiliations

Performance of 16S rRNA Gene Next-Generation Sequencing and the Culture Method in the Detection of Bacteria in Clinical Specimens

Alexandru Botan et al. Diagnostics (Basel). .

Abstract

Effective treatment of infectious diseases requires prompt and accurate bacterial identification and tailored antimicrobial treatments. Traditional culture methods are considered the gold standard, but their effectiveness diminishes for fastidious and hard-to-grow microorganisms. In recent years, molecular diagnostic tools such as 16S rRNA gene next-generation sequencing (16S NGS) have gained popularity in the field. We analysed data from samples submitted for 16S NGS between July 2022 and July 2023 at the Department of Advanced Translational Microbiology in Trieste, Italy. The study included samples submitted for both culture-based identification and 16S NGS. Conventional media were used for culture, and bacterial identification was performed using MALDI-TOF mass spectrometry. The V3 region of the 16S rRNA gene was sequenced using the Ion PGM platform. Among the 123 samples submitted, drainage fluids (38%) and blood (23%) were the most common, with requests predominantly from the Infectious Diseases (31.7%) and Orthopedic (21.13%) Units. In samples collected from patients with confirmed infections, 16S NGS demonstrated diagnostic utility in over 60% of cases, either by confirming culture results in 21% or providing enhanced detection in 40% of instances. Among the 71 patients who had received antibiotic therapies before sampling (mean 2.3 prior antibiotic days), pre-sampling antibiotic consumption did not significantly affect the sensitivity of 16S NGS. In routine microbiology laboratories, combining 16S NGS with culture method enhances the sensitivity of microbiological diagnostics, even when sampling is conducted during antibiotic therapy.

Keywords: 16S NGS; culture-based diagnosis; diagnosis; diagnostic microbiology.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Surgical (blue) and medical departments (red) requesting 16S NGS examination.
Figure 2
Figure 2
Impact of 16S NGS results in samples from patients with a confirmed infection.
Figure 3
Figure 3
Effects of antibiotic administration on culture and 16S NGS results.
See this image and copyright information in PMC

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