Taxonomic and phenotypic analysis of bifidobacteria isolated from IBD patients as potential probiotic strains.

BACKGROUND: Inflammatory Bowel Diseases (IBD) are a major public health issue with unclear aetiology. Changes in the composition and functionality of the intestinal microbiota are associated with these pathologies, including the depletion of strict anaerobes such as Feacalibacterium prausnitzii. Less evidence is observed for depletion in other anaerobes, among which bifidobacteria. This study characterized the taxonomic and functional diversity of bifidobacteria isolated from the human intestinal microbiota in active and non-active IBD patients by a culturomics approach and evaluated if these bifidobacteria might be used as probiotics for gut health. RESULTS: A total of 341 bifidobacteria were isolated from the intestinal microbiota of IBD patients (52 Crohn's disease and 26 ulcerative colitis patients), with a high proportion of Bifidobacterium dentium strains (28% of isolated bifidobacteria). In ulcerative colitis, the major species identified was B. dentium (39% of isolated bifidobacteria), in active and non-active ulcerative colitis. In Crohn's disease, B. adolescentis was the major species isolated from non-active patients (40%), while similar amounts of B. dentium and B. adolescentis were found in active Crohn's disease patients. The relative abundance of B. dentium was increased with age, both in Crohn's disease and ulcerative colitis and active and non-active IBD patients. Antibacterial capacities of bifidobacteria isolated from non-active ulcerative colitis against Escherichia coli LF82 and Salmonella enterica ATCC 14028 were observed more often compared to strains isolated from active ulcerative colitis. Finally, B. longum were retained as strains with the highest probiotic potential as they were the major strains presenting exopolysaccharide synthesis, antibacterial activity, and anti-inflammatory capacities. Antimicrobial activity and EPS synthesis were further correlated to the presence of antimicrobial and EPS gene clusters by in silico analysis. CONCLUSIONS: Different bifidobacterial taxonomic profiles were identified in the microbiota of IBD patients. The most abundant species were B. dentium, mainly associated to the microbiota of ulcerative colitis patients and B. adolescentis, in the intestinal microbiota of Crohn's disease patients. Additionally, the relative abundance of B. dentium significantly increased with age. Furthermore, this study evidenced that bifidobacteria with probiotic potential (antipathogenic activity, exopolysaccharide production and anti-inflammatory activity), especially B. longum strains, can be isolated from the intestinal microbiota of both active and non-active Crohn's disease and ulcerative colitis patients.

High hydrostatic pressure is similar to Holder pasteurization in preserving donor milk antimicrobial activity.

BACKGROUND: The microbiological safety of donor milk (DM) is commonly ensured by Holder pasteurization (HoP, 62.5 °C for 30 min) in human milk banks despite its detrimental effects on bioactive factors. We compared the antimicrobial properties of DM after Holder pasteurization treatment or High Hydrostatic Pressure processing (HHP, 350 MPa at 38 °C), a non-thermal substitute for DM sterilization. METHODS: We assessed lactoferrin and lysozyme concentrations in raw, HHP- and HoP-treated pools of DM (n = 8). The impact of both treatments was evaluated on the growth of Escherichia coli and Group B Streptococcus in comparison with control media (n = 4). We also addressed the effect of storage of HHP treated DM over a 6-month period (n = 15). RESULTS: HHP milk demonstrated similar concentrations of lactoferrin compared with raw milk, while it was significantly decreased by HoP. Lysozyme concentrations remained stable regardless of the condition. Although a bacteriostatic effect was observed against Escherichia coli at early timepoints, a sharp bactericidal effect was observed against Group B Streptococcus. Unlike HoP, these results were significant for HHP compared to controls. Stored DM was well and safely preserved by HHP. CONCLUSION: Our study demonstrates that this alternative sterilization method shows promise for use with DM in human milk banks. IMPACT: Antimicrobial activity of donor milk after High Hydrostatic Pressure treatment has not been clearly evaluated. Donor milk lactoferrin is better preserved by High Hydrostatic Pressure than conventional Holder pasteurization, while lysozyme concentration is not affected by either treatment. As with Holder pasteurization, High Hydrostatic Pressure preserves donor milk bacteriostatic activity against E. coli in addition to bactericidal activity against Group B Streptococcus. Donor milk treated by High Hydrostatic Pressure can be stored safely for 6 months.

Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.

The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.

Accuracy of the GeneXpert® MRSA/SA SSTI test to diagnose methicillin-resistant Staphylococcus spp. infection in bone fixation and fusion and management of infected non-unions.

INTRODUCTION: The GeneXpert® MRSA/SA SSTI (Methicillin Resistant Staphylococcus aureus/S. aureus skin and soft tissue infection) PCR test allows early detection of methicillin resistance in staphylococci. This test was developed for skin infections and has been evaluated for prosthetic joint infections but, to our knowledge, has not been evaluated for hardware infections outside of arthroplasties. Furthermore, we conducted a retrospective study in patients with non-prosthetic osteosynthesis hardware aiming: (1) to identify the diagnostic values of the PCR test compared to conventional cultures and the resulting rate of appropriate antibiotic therapy; (2) to identify the rate of false negative (FN) results; (3) to identify and compare the rates of failure of infectious treatment (FN versus others); (4) to search for risk factors for FN of the PCR test. HYPOTHESIS: The PCR test allowed early and appropriate targeting of antibiotic therapy. MATERIAL AND METHODS: The results of PCR tests and conventional cultures for osteoarticular infections of non-prosthetic hardware over four years (2012-2016) were compared to identify the diagnostic values of using the results of conventional culture as a reference and the rate of appropriate antibiotic therapies. Infectious management failures between the results of the FN group and the others were compared, and variables associated with a FN of the PCR test were identified. RESULTS: The analysis of 419 PCR tests allowed us to establish a sensitivity of 42.86%, a specificity of 96.82%, a positive predictive value of 60% and a negative predictive value of 93.83%. Using the results of the PCR test for the targeting of postoperative antibiotic therapy, it was suitable for staphylococcal coverage in 90.94% (381/419). The rates of patients for whom infectious treatment failed were not significantly different between the FN group and the other patients (20.8% versus 17.7%, respectively; Hazard Ratio=1.12 (95%CI 0.47-2.69, p=0.79)). A skin opening during the initial trauma (p=0.005) and a polymicrobial infection were significantly associated with a risk of FN from the PCR test (p<0.001). CONCLUSION: The PCR test makes it possible to reduce the duration of empirical broad-spectrum antibiotic therapy during the treatment of an infection of osteosynthesis hardware but causes a lack of antibiotic coverage in 9.06% of cases. LEVEL OF EVIDENCE: III; diagnostic case control study.

Macrophage-induced reduction of bacteriophage density limits the efficacy of in vivo pulmonary phage therapy.

The rise of antimicrobial resistance has led to renewed interest in evaluating phage therapy. In murine models highly effective treatment of acute pneumonia caused by Pseudomonas aeruginosa relies on the synergistic antibacterial activity of bacteriophages with neutrophils. Here, we show that depletion of alveolar macrophages (AM) shortens the survival of mice without boosting the P. aeruginosa load in the lungs. Unexpectedly, upon bacteriophage treatment, pulmonary levels of P. aeruginosa were significantly lower in AM-depleted than in immunocompetent mice. To explore potential mechanisms underlying the benefit of AM-depletion in treated mice, we developed a mathematical model of phage, bacteria, and innate immune system dynamics. Simulations from the model fitted to data suggest that AM reduce bacteriophage density in the lungs. We experimentally confirmed that the in vivo decay of bacteriophage is faster in immunocompetent compared to AM-depleted animals. These findings demonstrate the involvement of feedback between bacteriophage, bacteria, and the immune system in shaping the outcomes of phage therapy in clinical settings.