Exploring the Microbiota of Diabetic Foot Infections With Culturomics

Abstract

The purpose of this prospective observational study was to evaluate the richness and diversity of bacteria in samples from diabetic foot infections using a culturomics approach. Bacterial culture findings from wound samples were analyzed together with clinical characteristics and treatment outcomes. We included 43 patients admitted to a French referral center with a moderate to severe diabetic foot infection. The 30,000 colonies identified yielded 53 different bacterial species. The global α-Shannon diversity was 3.34 and the bacterial richness per patient was 4 ± 2. Of all the identified bacterial species, 19 (35.8%) had never been previously cultured or identified by molecular methods from diabetic foot ulcers. Most of the samples were polymicrobial (N = 38; 88.3%). Of all the isolated species, the most prevalent were Staphylococcus aureus (N = 28; 52.8%), Enterococcus faecalis (N = 24; 45.2%), Enterobacter cloacae (N = 12; 22.6%), Staphylococcus lugdunensis (N = 10; 18.7%), Staphylococcus epidermidis (N = 6; 11.3%), Proteus mirabilis (N = 6; 11.3%), and Finegoldia magna (N = 5; 9.4%). The only factor associated with wound improvement after a 1-month follow-up was the presence of E. faecalis (p = 0.012) when compared with patients without wound improvement. This study confirms the complementary role of culturomics in the exploration of complex microbiota. Further studies on a larger scale are needed to fully understand the clinical importance of the microbiota of diabetic foot infections.

Keywords: bacterial species; culturomics; diabetes; foot infection; microbiota.

Figure 1

Bacterial species isolated from wound samples from 43 patients (blue circles), analyzed using culturomics. In purple, the most prevalent bacterial species; in red, the bacterial species isolated in five or more patients; in orange, the bacterial species isolated in more than one patient; in yellow, species isolated in only one patient.

Figure 2

Link between patients and wound characteristics, bacterial composition and clinical outcome at 1-month follow-up appointment and following standardized treatment. Principal component analysis using XLSTAT-2017 (Addinsoft, Paris, France) was performed on species' raw data (presence on each patient's wound sample) obtained by culturomics. The first (F1), and second (F2) components accounted for 17.5 and 11.7%, respectively, of the overall variability.Y, years; F, female; M, male; DFU, diabetic foot ulcer; S. aureus, Staphylococcus aureus; S. lugdunensis, Staphylococcus lugdunensis; S. epidermidid, Staphylococcus epidermidis; E. faecalis, Enterococcus faecalis; E. cloacae, Enterobacter cloacae; F. magna, Finegoldia magna; P. mirabilis, Proteus mirabilis.