Impact on the Gut Microbiota of Intensive and Prolonged Antimicrobial Therapy in Patients With Bone and Joint Infection

Abstract

There is a growing interest in the potentially deleterious impact of antibiotics on gut microbiota. Patients with bone and joint infection (BJI) require prolonged treatment that may impact significantly the gut microbiota. We collected samples from patients with BJI at baseline, end of antibiotics (EOT), and 2 weeks after antibiotic withdrawal (follow-up, FU) in a multicenter prospective cohort in France. Microbiota composition was determined by shotgun metagenomic sequencing. Fecal markers of gut permeability and inflammation as well as multi-drug-resistant bacteria (MDRB) and Clostridioides difficile carriage were assessed at each time point. Sixty-two patients were enrolled: 27 native BJI, 14 osteosynthesis-related BJI, and 21 prosthetic joint infections (PJI). At EOT, there was a significant loss of alpha-diversity that recovered at FU in patients with native BJI and PJI, but not in patients with osteosynthesis-related BJI. At EOT, we observed an increase of Proteobacteria and Bacteroidetes that partially recovered at FU. The principal component analysis (PCoA) of the Bray-Curtis distance showed a significant change of the gut microbiota at the end of treatment compared to baseline that only partially recover at FU. Microbiota composition at FU does not differ significantly at the genus level when comparing patients treated for 6 weeks vs. those treated for 12 weeks. The use of fluoroquinolones was not associated with a lower Shannon index at the end of treatment; however, the PCoA of the Bray-Curtis distance showed a significant change at EOT, compared to baseline, that fully recovered at FU. Levels of fecal neopterin were negatively correlated with the Shannon index along with the follow-up (r ² = 0.17; p < 0.0001). The PCoA analysis of the Bray-Curtis distance shows that patients with an elevated plasma level of C-reactive protein (≥5 mg/L) at EOT had a distinct gut microbial composition compared to others. MDRB and C. difficile acquisition at EOT and FU represented 20% (7/35) and 37.1% (13/35) of all MDRB/C. difficile-free patients at the beginning of the study, respectively. In patients with BJI, antibiotics altered the gut microbiota diversity and composition with only partial recovery, mucosal inflammation, and permeability and acquisition of MDRB carriage. Microbiome interventions should be explored in patients with BJI to address these issues.

Keywords: antibiotics; antimicrobial therapy; bone and joint infection; dysbiosis; gut microbiota.

Figure 1

Types of antibiotics and treatment duration in the OSIRIS cohort. (A) Distribution of the different types of antibiotics used. (B) Distribution of the antibiotic durations used.

Figure 2

Effect of antibiotics on the gut microbiota in bone joint infection (BJI). (A) Shannon index (genus level) at three times of sampling; Wilcoxon test. (B) Richness (genus level) at three times of sampling; Wilcoxon test. (C) Shannon index at three times of sampling according to the type of BJI; Wilcoxon test for paired comparison, Mann–Whitney analysis for inter-group comparisons. (D) Global composition of bacterial microbiota at the phylum level. (E) Beta diversity. Principal coordinate analysis of Bray–Curtis distance at three different times of sampling; permutational multivariate analysis of variance. B, baseline; EOT, end of treatment; FU, follow-up. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.

Figure 3

Impact of antibiotic duration on the gut microbiota composition. (A) Shannon index distribution (genus level) at the end of treatment and at follow-up (15 days after antibiotic withdrawal) according to antibiotic duration; Wilcoxon test for paired comparison and, Mann-Whitney test for inter-group comparisons. (B) Richness distribution (genus level) at the end of treatment and at follow-up (15 days after antibiotic withdrawal) according to antibiotic duration; Wilcoxon test for paired comparison and, Mann-Whitney test for inter-group comparisons. (C) Correlation between the Shannon index and antibiotic duration at EOT and FU; simple linear regression. Principal coordinate analysis of Bray–Curtis distance at three different times of sampling for (D) patients treated for 6 weeks with antibiotics (41 to 60 days) or (E) 12 weeks with antibiotics (81 to 100 days); permutational multivariate analysis of variance. B, baseline; EOT, end of treatment; FU, follow-up. *p < 0.05; **p < 0.01; ***p < 0.001.

Figure 4

Impact of the use of fluoroquinolone (FQ) on gut microbiota composition. (A) Shannon index distribution (genus level) at the end of treatment and at follow-up (15 days after antibiotic withdrawal) according to exposition to FQ; Wilcoxon test for paired comparison and, Mann-Whitney test for inter-group comparisons. (B) Richness (genus level) at the end of treatment and at follow-up (15 days after antibiotic withdrawal) according to exposition to FQ; Wilcoxon test for paired comparison and, Mann-Whitney test for inter-group comparisons. Principal coordinate analysis of Bray–Curtis distance at three different times of sampling for (C) patients treated with FQ or (D) without FQ; permutational multivariate analysis of variance. B, baseline; EOT, end of treatment; FU, follow-up. *p < 0.05; **p < 0.01; ***p < 0.001.

Figure 5

Correlation between markers of gut inflammation, permeability, and microbiota alpha-diversity. Values of fecal neopterin (A), fecal calprotectin (B), fecal zonulin (C), fecal immunoglobulin A (D) at different time points; Wilcoxon test. (E) Correlation between fecal neopterin and the Shannon index (genus level) all along the study; simple linear regression. B, baseline; EOT, end of treatment; FU, follow-up. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.

Figure 6

Correlation between systemic and mucosal markers of inflammation. (A) Evolution of the plasmatic level of C-reactive protein (CRP) at different time points. (B) Correlation between fecal neopterin and plasmatic CRP; simple linear regression. (C) Principal coordinate analysis of Bray–Curtis distance between patients with each sample colored according to plasmatic CRP level at the end of treatment; permutational multivariate analysis of variance. B, baseline; EOT, end of treatment; FU, follow-up. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.

Figure 7

Fecal multi-drug-resistant bacteria (MDRB) and Clostridioides difficile carriage. (A) Proportion of patients with a positive fecal carriage (culture) at different time points. (B) EBSL as percentage of the total of all Gram-negative bacteria (aerobic culture). (C) Bray Curtis distance between baseline and 15 days after antibiotic withdrawal (FU) according to the carriage of MDRB; Mann–Whitney test. (D) Fecal neopterin at baseline and 15 days after antibiotic withdrawal (FU) according to the carriage of MDRB; Mann–Whitney test. B, baseline; EOT, end of treatment; FU, follow-up; ESBL, extended-spectrum beta-lactamases; MRSA, methicillin-resistant Staphylococcus aureus. *p < 0.05; **p < 0.01; ***p < 0.001.