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. 2023 Aug 1;23(1):505.
doi: 10.1186/s12879-023-08472-w.

Concordance between culture, Molecular Culture and Illumina 16S rRNA gene amplicon sequencing of bone and ulcer bed biopsies in people with diabetic foot osteomyelitis

Meryl Cinzía Tila Tamara Gramberg  1   2   3   4   5 , Carmen Knippers  6 , Rimke Sabine Lagrand  7   8   9 , Jarne Marijn van Hattem  10 , Marcus Christofoor de Goffau  11   12   13 , Andries Edward Budding Budding  14 , Mark Davids  11 , Sebastien Matamoros  10 , Max Nieuwdorp  9   11 , Vincent de Groot  7   8   9 , Martin den Heijer  15 , Louise Willy Elizabeth Sabelis  7   8   9 , Edgar Josephus Gerardus Peters  16   17   18   19
Affiliations

Concordance between culture, Molecular Culture and Illumina 16S rRNA gene amplicon sequencing of bone and ulcer bed biopsies in people with diabetic foot osteomyelitis

Meryl Cinzía Tila Tamara Gramberg et al. BMC Infect Dis. .

Abstract

Background: In clinical practice the diagnosis of diabetic foot osteomyelitis (DFO) relies on cultures of bone or ulcer bed (UB) biopsies, of which bone biopsy is reference standard. The slow growth or fastidious nature of some bacteria, hamper expeditious detection and identification. Rapid molecular techniques may solve both issues, but their additional value for everyday practice is unknown. We investigated the concordance between conventional culture, the molecular techniques Molecular Culture (MC), and illumina 16S rRNA gene amplicon (16S) sequencing in people with DFO.

Methods: In the BeBoP trial, bone and UB biopsies were obtained from people with DFO who visited Amsterdam UMC. These biopsies were analysed using 1) conventional culture, 2)MC, a rapid broad range PCR analysing the 16S-23S ribosomal-interspace-region, and 3) 16S sequencing, and evaluated concordance among these techniques.

Results: We analysed 20 samples (11 bone and 9 UB) of 18 people. A total of 84 infectious agents were identified, 45 (54%) by all techniques, an additional 22 (26.5%, overall 80.5%) by both MC and 16S, and the remaining 16 species by culture and MC or 16S, or by a single method only. MC and 16S identified anaerobes not detected by culturing in 5 samples, and the presence of bacteria in 7 of 8 culture-negative (6 bone, 2 UB) samples.

Conclusion: The high level of concordance between MC and 16S and the additional ability of molecular techniques to detect various bacteria not detected by culturing opens up prospects for routine use of fast molecular techniques, in clinical settings including DFO.

Trial registration: The BeBoP trial is retrospectively registered on 05-03-2019 in Netherlands Trial Register: NL 7582.

Keywords: 16S rRNA gene amplicon sequencing; Bone and ulcer bed biopsy; Culture; Diabetic foot osteomyelitis; Molecular culture.

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Conflict of interest statement

All authors state that they have no conflicts of interest, except for dr. AE Budding (owner of InBiome).

Figures

Fig. 1
Fig. 1
Reciprocal process of analysing results of culturing, Molecular Culture (MC) and Illumina 16S sequencing (16S)
Fig. 2
Fig. 2
Overview of the concordance between diagnostic strategies in the detection bacterial species: 84 pathogens represented by 29 different bacterial species were detected. MC Molecular Culture, 16S Illumina 16S sequencing
See this image and copyright information in PMC

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