Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study.

Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 (n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia-Shigella (p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution (n = 6) (p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound-colonizing microorganisms.

Role of gut microbiota and bacterial translocation in acute intestinal injury and mortality in patients admitted in ICU for septic shock.

Introduction: Sepsis is a life-threatening organ dysfunction with high mortality rate. The gut origin hypothesis of multiple organ dysfunction syndrome relates to loss of gut barrier function and the ensuing bacterial translocation. The aim of this study was to describe the evolution of gut microbiota in a cohort of septic shock patients over seven days and the potential link between gut microbiota and bacterial translocation. Methods: Sixty consecutive adult patients hospitalized for septic shock in intensive care units (ICU) were prospectively enrolled. Non-inclusion criteria included patients with recent or scheduled digestive surgery, having taken laxatives, pre- or probiotic in the previous seven days, a progressive digestive neoplasia, digestive lymphoma, chronic inflammatory bowel disease, moribund patient, and pregnant and lactating patients. The primary objective was to evaluate the evolution of bacterial diversity and richness of gut microbiota during seven days in septic shock. Epidemiological, clinical and biological data were gathered over seven days. Gut microbiota was analyzed through a metagenomic approach. 100 healthy controls were selected among healthy blood donors for reference basal 16S rDNA values. Results: Significantly lower bacterial diversity and richness was observed in gut microbiota of patients at Day 7 compared with Day 0 (p<0.01). SOFA score at Day 0, Acute Gastrointestinal Injury (AGI) local grade, septic shock origin and bacterial translocation had an impact on alpha diversity. A large increase in Enterococcus genus was observed at Day 7 with a decrease in Enterobacterales, Clostridiales, Bifidobacterium and other butyrate-producing bacteria. Discussion: This study shows the importance of bacterial translocation during AGI in septic shock patients. This bacterial translocation decreases during hospitalization in ICUs in parallel to the decrease of microbiota diversity. This work highlights the role of gut microbiota and bacterial translocation during septic shock.

Impact of Infection Control on Prevalence of Surgical Site Infections in a Large Tertiary Care Hospital in Haiphong City.

Few point prevalence surveys (PPS) have been conducted in Vietnam on Surgical Site Infections (SSI) or antimicrobial use in surgery. The objective of this study was to evaluate the PPSs of SSI before and after implementation of antibiotic stewardship programs (ASP) and infection control (IC) in a Vietnamese tertiary care hospital. ASP and IC practices were implemented in operating rooms and the orthopedic department, including antibiotic training, skin preparation, hand hygiene, gloves and sterile instruments, and SSIs risk factors. A PPS of SSIs and antimicrobial use was performed in January 2016 according to methods from the Centers for Disease Control and Prevention, before ASP and IC, and in December 2019. Information recorded included surgical data, antibiotic prophylaxis, microorganisms, and SSI risk factors. Skin preparation compliance assessed preoperative washing and antisepsis. SSI prevalence was 7.8% in 2016 versus 5.4% in 2019 (p = 0.7). The use of prophylactic antibiotics decreased from 2016 to 2019. A third-generation cephalosporin was prescribed more than 48 h after surgery for most patients. Skin preparation compliance increased from 54.4% to 70.5% between assessments. The decreased SSI, although non-statistically significant, warrants continuing this program. Vietnamese hospitals must provide comprehensive IC education to healthcare workers to address the prevention of SSI and establish IC policies.

Biofilm Formation in Methicillin-Resistant Staphylococcus aureus Isolated in Cystic Fibrosis Patients Is Strain-Dependent and Differentially Influenced by Antibiotics.

Cystic fibrosis (CF) is a genetic disease with lung abnormalities making patients particularly predisposed to pulmonary infections. Staphylococcus aureus is the most frequently identified pathogen, and multidrug-resistant strains (MRSA, methicillin-resistant S. aureus) have been associated with more severe lung dysfunction leading to eradication recommendations. Diverse bacterial traits and adaptive skills, including biofilm formation, may, however, make antimicrobial therapy challenging. In this context, we compared the ability of a collection of genotyped MRSA isolates from CF patients to form biofilm with and without antibiotics (ceftaroline, ceftobiprole, linezolid, trimethoprim, and rifampicin). Our study used standardized approaches not previously applied to CF MRSA, the BioFilm Ring test® (BRT®), the Antibiofilmogram®, and the BioFlux™ 200 system which were adapted for use with the artificial sputum medium (ASM) mimicking conditions more relevant to the CF lung. We included 63 strains of 10 multilocus sequence types (STs) isolated from 35 CF patients, 16 of whom had chronic colonization. The BRT® showed that 27% of the strains isolated in 37% of the patients were strong biofilm producers. The Antibiofilmogram® performed on these strains showed that broad-spectrum cephalosporins had the lowest minimum biofilm inhibitory concentrations (bMIC) on a majority of strains. A focus on four chronically colonized patients with inclusion of successively isolated strains showed that ceftaroline, ceftobiprole, and/or linezolid bMICs may remain below the resistance thresholds over time. Studying the dynamics of biofilm formation by strains isolated 3years apart in one of these patients using BioFlux™ 200 showed that inhibition of biofilm formation was observed for up to 36h of exposure to bMIC and ceftaroline and ceftobiprole had a significantly greater effect than linezolid. This study has brought new insights into the behavior of CF MRSA which has been little studied for its ability to form biofilm. Biofilm formation is a common characteristic of prevalent MRSA clones in CF. Early biofilm formation was strain-dependent, even within a sample, and not only observed during chronic colonization. Ceftaroline and ceftobiprole showed a remarkable activity with a long-lasting inhibitory effect on biofilm formation and a conserved activity on certain strains adapted to the CF lung environment after years of colonization.

In-Host Emergence of Linezolid Resistance in a Complex Pattern of Toxic Shock Syndrome Toxin-1-Positive Methicillin-Resistant Staphylococcus aureus Colonization in Siblings with Cystic Fibrosis.

Methicillin-resistant Staphylococcus aureus (MRSA) can cause chronic lung infections in patients with Cystic Fibrosis (CF). One option for managing them is the use of linezolid. We hereby report the in-host emergence of linezolid resistance (LR) in MRSA in CF siblings via a population analysis. A collection of 171 MRSA strains from 68 samples were characterized by determining their linezolid Minimal Inhibitory Concentrations (MICs), analyzing the locus of staphylococcal protein A (spa) and whole genome sequencing. Courses of linezolid were retraced. Strains belonged to three spa types (t002, t045, t127) and two sequence types (ST1, ST5). Emergence of LR occurred under treatment, one year apart in both siblings, in the CC5-MRSA-I Geraldine clone harboring the toxic shock syndrome toxin-1-encoding gene. Resistance was related to a G2576T substitution present in a variable number of 23S rRNA gene copies. Susceptible and resistant strains were co-isolated within samples. Single Nucleotide Polymorphism-based analysis revealed complex colonizations by highly diversified, clonally related populations. LR remains rare in MRSA and there are very few longitudinal analyses documenting its emergence. Analyzing a large MRSA collection revealed new aspects of LR emergence: it emerges in specific subclonal lineages resulting from adaptive diversification of MRSA in the CF lung and this heterogeneity of intra-sample resistance may contribute to compromising antibiotic management.

Abnormal vaginal microbiome associated with vaginal mesh complications.

AIMS: To identify differences in the vaginal microbiomes of women after transvaginal mesh (TVM) surgery for pelvic organ prolapse with and without mesh-associated complications. METHODS: Patients with complications were eligible as cases, patients without as controls. DNA was isolated and the V1-2 region of the 16S ribosomal RNA gene was amplified and sequenced. Overall richness was quantified using Chao1. Overall diversity was expressed as Shannon diversity and screened for group differences using analysis of variance. Multivariate differences among groups were evaluated with functions from R. RESULTS: We recruited 14 patients after mesh exposure, 5 after contraction, and 21 as controls. The average number of operational taxonomic unit was 74.79 (SD ± 63.91) for controls, 57.13 (SD ± 58.74) after exposures, and 92.42 (SD ± 50.01) after contractions. Total 89.6% of bacteria in controls, 86.4% in previous exposures, and 81.3% in contractions were classified as either Firmicutes, Proteobacteria, or Actinobacteria (P < .001). Veillonella spp. was more abundant in patients after contraction (P = .045). The individual microbiomes varied, and we did not detect any significant differences in richness but a trend towards higher diversity with complications. CONCLUSIONS: The presence of Veillonella spp. could be associated with mesh contraction. Our study did not identify vaginal microbiotic dysbiosis as a factor associated with exposure. Larger cohort studies would be needed to distinguish the vaginal microbiome of women predisposed to mesh-related complications for targeted phenotyping of patients who could benefit from TVM surgery.

Multiple stir bar sorptive extraction combined with gas chromatography-mass spectrometry analysis for a tentative identification of bacterial volatile and/or semi-volatile metabolites.

We propose a new approach combining the principles and advantages of stir bar sorptive extraction (SBSE) and headspace sorptive extraction (HSSE). Stir bars have so far never been used for the extraction of volatile/semi-volatile bacterial compounds. The effectiveness of two stir bars with polydimethylsiloxane (PDMS) or ethylene glycol/silicone (EGS) as sorbent was tested by performing sample extraction directly in gas chromatography (GC) vials containing bacterial cultures. Several combinations of desorption and extraction were tested at different growth times. When the extraction was carried out simultaneously with the EGS stir bar in headspace and the PDMS in the bacterial culture, the number of extracted compounds was significantly increased. Using both twisters increased the polarity range of the compounds found, and extraction at the end of the exponential phase of growth generated the best yields. This method was successfully applied to determine the production of 17 molecules by a strain of Staphylococcus aureus. In conclusion, this study paves the way for a new method for determining the volatile metabolite profile of bacteria, which can provide a promising innovative alternative in the identification of biomarkers.

Performance of a new in-house medium Carba MTL-broth for the rapid detection of carbapenemase-producing Enterobacteriaceae.

INTRODUCTION: The spread of carbapenemase-producing Enterobacteriaceae (CPE) represents a major public health issue. Methods allowing rapid detection of carbapenemases in developing countries are therefore urgently needed. In the current study, we developed a new in-house medium for the rapid detection of CPE isolates, especially OXA-48 producers. METHODOLOGY: A panel of 144 clinical strains previously characterized was tested on in-house Carba MTL-broth medium using four different concentrations of ertapenem (0.5 to 2 mg/L), and compared to chromID® OXA-48 and chromID® CARBA (BioMérieux) media. RESULTS: Comparative evaluation of the Carba MTL-broth with chromID® OXA-48 and chromID® CARBA showed that chromID® OXA-48 and Carba MTL-broth had the highest sensitivity for detection of OXA-48 producers (93.9% and 100%, respectively) comparatively to chromID® CARBA (21.2%). The chromID® OXA-48 had the highest specificity (100%), as compared to the Carba MTL-broth (65.5%) and chromID® CARBA (84.4%) for the detection of OXA-48 producers. CONCLUSIONS: The in-house Carba MTL-broth developed in this study is sensitive, inexpensive, an easy-to-use phenotypic method for the detection of OXA-48-producing enterobacteria. Given the burden of pan-drug resistance, its implementation in the microbiology laboratory of developing countries could be a useful tool for rapid detection of these bacteria.

[Micro-inflammation and digestive bacterial translocation in chronic kidney disease]. / Micro-inflammation et translocation bactérienne d'origine digestive dans la maladie rénale chronique.

Micro-inflammation has been recognized as a major factor associated with the poor prognosis of patients with chronic kidney disease. Those patients have an increased rate of pro-inflammatory markers like interleukin 6, C-Reactive protein, Tumor Necrosis Factor α and fibrinogen. Among multiple and complex causes of micro-inflammation the gut microbiota could be an important actor considering the dysbiosis in chronic kidney disease which would enhance the synthesis of uremic toxins with cardiovascular toxicity and the bacterial translocation. This review details the role of the gut microbiota in human pathology and in chronic kidney disease focusing on the bacterial translocation that could occur because of an impaired digestive permeability. This bacterial translocation could induce a chronic immune response and could take part in the raise of pro-inflammatory markers in chronic kidney disease. New therapeutic strategies aiming at preventing metabolic and cardiovascular complications could emerge from the understanding of the relationships between gut microbiota and host in this particular pathology.

The Rational Design, Synthesis, and Antimicrobial Properties of Thiophene Derivatives That Inhibit Bacterial Histidine Kinases.

The emergence of multidrug-resistant bacteria emphasizes the urgent need for novel antibacterial compounds targeting unique cellular processes. Two-component signal transduction systems (TCSs) are commonly used by bacteria to couple environmental stimuli to adaptive responses, are absent in mammals, and are embedded in various pathogenic pathways. To attenuate these signaling pathways, we aimed to target the TCS signal transducer histidine kinase (HK) by focusing on their highly conserved adenosine triphosphate-binding domain. We used a structure-based drug design strategy that begins from an inhibitor-bound crystal structure and includes a significant number of structurally simplifiying "intuitive" modifications to arrive at the simple achiral, biaryl target structures. Thus, ligands were designed, leading to a series of thiophene derivatives. These compounds were synthesized and evaluated in vitro against bacterial HKs. We identified eight compounds with significant inhibitory activities against these proteins, two of which exhibited broad-spectrum antimicrobial activity. The compounds were also evaluated as adjuvants for the treatment of resistant bacteria. One compound was found to restore the sensivity of these bacteria to the respective antibiotics.

Elevated IP10 levels are associated with immune activation and low CD4⁺ T-cell counts in HIV controller patients.

BACKGROUND: Although HIV controllers (HICs) achieve long-term control of viremia in the absence of antiretroviral therapy (ART), they display marked immune activation. The levels of inflammatory biomarkers in HICs and the biomarkers' relationships with immunologic and virologic status have yet to be fully characterized. DESIGN: A cohort study. METHODS: Plasma levels of seven biomarkers [tumor necrosis factor (TNF)α, interleukin (IL)6, IL10, interferon gamma-induced protein 10 (IP10), monocyte chemoattractant protein-1 (MCP1), soluble CD14 (sCD14), soluble CD163 (sCD163)] were compared in 70 HICs, 33 HIV-1-infected, treatment-naive noncontrollers (viremic patients), 30 ART-treated patients and 40 healthy donors. In HICs, we investigated the interplay between biomarkers, cell activation and the CD4⁺ T-cell count. RESULTS: HICs had higher levels of IP10, TNFα and sCD14 than healthy donors did (P < 0.01 for each). Also, TNFα and sCD14 levels of the HICs were similar to those measured in viremic and ART-treated patients. However, the levels of IL6 and IL10 were significantly lower in HICs than in viremic or ART-treated patients. In HICs, only IP10 levels differed significantly from those in both healthy donors and viremic patients, and were positively correlated with the expression of CD8⁺ and CD4⁺ T-cell activation markers. The IP10 levels of HICs were still elevated 12 and 24 months after the initial assay. Lastly, IP10 levels at enrollment were negatively correlated with the CD4⁺ T-cell count at enrollment and 12 months later. CONCLUSION: HICs display a number of inflammatory features associated with persistent T-cell immune activation.