Gut microbiota dynamics in a 1-year follow-up after adult liver transplantation in Northeast China

Background: Liver transplantation (LTx) is the most effective treatment for end-stage liver diseases. Gut microorganisms influence the host physiology. We aim to profile the dynamics of gut microbiota in the perioperative period and a 1-year follow-up of LTx recipients in Northeast China. Methods: A total of 257 fecal samples were longitudinally collected from 85 LTx patients using anal swabs from pre-LTx to 1-year post-LTx. A total of 48 fecal samples from end-stage liver disease patients without LTx served as the control. 16S rRNA sequencing was used to analyze gut microbiota diversity, bacterial genera, phenotype classification, and metabolic pathways. Results: The diversity of gut microbiota decreased significantly after transplantation, accompanied by a profound change in the microbial structure, which is characterized by increased abundance of facultative anaerobic bacteria dominated by g_Enterococcus and reduced anaerobic bacteria composition. Predicted functional analysis also revealed disturbances in the metabolic pathway of the gut microbiota. After LTx, the diversity of microbiota gradually recovered but to a less preoperative level after 1 year of recovery. Compared with pre-transplantation, the microbiome structure was characterized by an increase in Acidaminococcus and Acidithiobacillus after 1 year of transplantation. Conclusion: LTx and perioperative treatment triggered gut microbial dysbiosis. The gut microbiota was restructured after LTx to near to but significantly differed from that of pre-LTx.

Effect of sub-inhibitory concentrations of antibiotics on biofilm formation and expression of virulence genes in penicillin-resistant, ampicillin-susceptible Enterococcus faecalis

Biofilm formation is a key factor in the pathogenesis of enterococcal infections. Thus, the biofilm-forming ability and frequency of biofilm-related genes in penicillin-resistant, ampicillin-susceptible Enterococcus faecalis (PRASEF) compared to penicillin- and ampicillin-susceptible E. faecalis (PSASEF) were assessed in the present study. In addition, the effect of sub-inhibitory concentrations (sub-MICs) of antibiotics on biofilm formation and expression of virulence genes was evaluated. Twenty PRASEF and 21 PSASEF clinical isolates were used to determine the effect of sub-MICs of antibiotics (ampicillin, penicillin, and gentamicin) on biofilm formation, and ten selected isolates were subjected to RT-qPCR to detect the transcript levels of virulence genes (efaA, asa1, esp, and ace). Antibiotic susceptibility was evaluated by the microdilution broth method. Biofilm formation assay was performed using the microtiter plate method. All PSASEF and PRASEF isolates produced biofilms in vitro. Most isolates had three or four virulence genes. Sub-MICs of ampicillin significantly decreased biofilm production and expression of ace and asa1 genes, although the transcript levels were significantly lower (−350% and −606.2%, respectively) among the PSASEF isolates only. Sub-MICs of gentamicin did not have any significant effect on biofilm formation, but slightly increased the transcript levels of efaA. In conclusion, this study showed that the biofilm-forming ability and frequency of the evaluated virulence genes were similar among the PRASEF and PSASEF isolates. Further, in vitro antibiotic sub-MICs were confirmed to interfere with the expression pattern of virulence genes and biofilm formation by E. faecalis. However, further studies are required to clarify the role of sublethal doses of antibiotics on enterococcal biofilms.

Hidden agenda of Enterococcus faecalis lifestyle transition: planktonic to sessile state

Enterococcus faecalis, a human gastrointestinal tract commensal, is known to cause nosocomial infections. Interestingly, the pathogen's host colonization and persistent infections are possibly linked to its lifestyle changes from planktonic to sessile state. Also, the multidrug resistance and survival fitness acquired in the sessile stage of E. faecalis has challenged treatment regimes. This situation exists because of the critical role played by several root genes and their molecular branches, which are part of quorum sensing, aggregation substance, surface adhesions, stress-related response and sex pheromones in the sessile state. It is therefore imperative to decode the hidden agenda of E. faecalis and understand the significant factors influencing biofilm formation. This would, in turn, augment the development of novel strategies to tackle E. faecalis infections.

Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections

The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.

Subinhibitory Antibiotic Concentrations Enhance Biofilm Formation of Clinical Enterococcus faecalis Isolates

Enterococcus faecalis is a microorganism that can be found in the oral cavity, especially in secondary endodontic infections, with a prevalence ranging from 24-70%. The increase in the ability to form biofilms in the presence of subinhibitory antibiotic concentrations is a phenomenon that is observed for a wide variety of bacterial pathogens and is associated with increased resistance. In this study, therefore, six E. faecalis isolates from an endodontic environment and two control strains were exposed to subinhibitory concentrations of Penicillin G, Amoxicillin, Doxycycline, Fosfomycin, Tetracycline and Vancomycin and examined for their biofilm formation abilities. The minimum inhibitory concentration (MIC) was determined for all E. faecalis isolates. A culture of the isolate was mixed with a serial dilution series of the respective antibiotic, incubated overnight and the biofilm formation was analyzed using a microtiter plate assay. All isolates were able to form biofilms in the absence of an antibiotic. A significant increase in biofilm formation of up to more than 50% was found in the isolates exposed to subinhibitory concentrations of various antibiotics. Most isolates showed a significant increase in Fosfomycin (7/8), Doxycycline (6/8) and Tetracycline (6/8). Three endodontic isolates showed a significant increase in five of the antibiotics examined at the same time. On exposure to Vancomycin, three endodontic isolates and the two control strains showed an increase. The increase in the ability to form biofilms extended over a concentration range from 1/2 to 1/64 of the MIC concentration. Antibiotics may reach certain niches in the oral cavity at subinhibitory concentrations only. This can increase the biofilm formation by enterococci, and in turn lead to decreased susceptibility of these taxa to antibiotics.

Effect of kitasamycin and nitrofurantoin at subinhibitory concentrations on quorum sensing regulated traits of Chromobacterium violaceum

Quorum sensing (QS) is a mechanism of intercellular communication in bacteria that received substantial attention as alternate strategy for combating bacterial resistance and the development of new anti-infective agents. The present investigation reports on the assessment of using subinhibitory concentrations of antibiotics for the inhibition of QS-regulated phenotypes in Chromobacterium violaceum. Primarily, the minimum inhibitory concentrations of a series of antibiotics were determined by a microdilution method. Subsequently, the inhibitory effects of selected antibiotics on QS-regulated traits, namely violacein and chitinase production, biofilm formation and motility were evaluated using C. violaceum CV026 and C. violaceum ATCC 12472. Results revealed that kitasamycin and nitrofurantoin exhibited the highest quorum sensing inhibitory (QSI) activity. The amount of violacein produced by C. violaceum was significantly reduced in the presence of either kitasamycin or nitrofurantoin. Moreover, the chitinolytic activity, biofilm formation, and motility were also impaired in kitasamycin or nitrofurantoin-treated cultures. We further confirmed QSI effects at the molecular level using molecular docking and real-time quantitative polymerase chain reaction (RT-qPCR). Results of molecular docking suggested that both antibiotics can interact with CviR transcriptional regulator of C. violaceum. Furthermore, RT-qPCR revealed the suppressive effect of kitasamycin and nitrofurantoin on five genes under the control of the CviI/CviR system: cviI, cviR, vioB, vioC, and vioD. Giving that kitasamycin and nitrofurantoin are being safely used for decades, this study emphasizes their potential application as antivirulence agents to disarm resistant bacterial strains, making their removal an easier task for the immune system or for another antibacterial agent.

Effects of sub-inhibitory concentrations of meropenem and tigecycline on the expression of genes regulating pili, efflux pumps and virulence factors involved in biofilm formation by Acinetobacter baumannii

Background: Sub-minimal inhibitory concentrations of antibiotics have been indicated to affect the biofilm formation in pathogens of nosocomial infections. This study aimed to investigate the effects of meropenem and tigecycline at their sub-minimum inhibitory concentrations (MICs) on the biofilm formation capacity of Acinetobacter baumannii (A. baumannii), as well as the expression levels of genes involved in biofilm formation, quorum sensing, pili assembly and efflux pumps. Materials and methods: In this study, four non-clonal strains (AB10, AB13, AB32 and AB55), which were different from the aspects of antibiotic susceptibility and biofilm formation from each other were selected for the evaluation of antimicrobial susceptibility, biofilm inducibility at sub-MICs of meropenem and tigecycline and the gene expression levels (the abaI, abaR, bap, pgaA, csuE, bfmS, bfmR, ompA, adeB, adeJ and adeG genes). Result: A significant increase in the MICs of all antibiotics was demonstrated in the biofilm cells in each four strains. The biofilm formation was significantly decreased in all the representative strains exposed to tigecycline. However, the biofilm inducibility at sub-MICs of meropenem was dependent on strain genotype. In concordance with these results, Pearson correlation analysis indicated a positive significant correlation between the biofilm formation capacity and the mRNA levels of genes encoding efflux pumps except adeJ, the genes involved in biofilm formation, pili assembly and quorum sensing following exposure to meropenem and tigecycline at their sub-MICs. Conclusion: These results revealed valuable data into the correlation between the gene transcription levels and biofilm formation, as well as quorum sensing and their regulation at sub-MICs of meropenem and tigecycline.

Bactericidal ZnO glass-filled thermoplastic polyurethane and polydimethyl siloxane composites to inhibit biofilm-associated infections

This study investigates a novel approach to controlling biofilms of the most frequent pathogens implicated in the etiology of biomaterials-associated infections. New bactericidal filler based on a non-toxic glass, belonging to B2O3-SiO2-Al2O3-Na2O-ZnO system, was used to formulate composites of the most widely used polymers in biomedical applications [i.e. thermoplastic polyurethane (TPU) and polydimethyl siloxane (PDMS)], with varying percentage by weight of the bactericidal glass (5, 15, 25, 35, 50%). Glass-filled polymer composites show dramatically restricted bacterial colonisation and biofilm formation. They exhibit time- and dose-dependent killing, with maximal action at 5 days. The highest activity was found against S.epidermidis biofilm (99% of reduction), one of the most common cause of nosocomial infections. The tensile properties of the obtained glass-filled composites are comparable with the literature data concerning polymeric biomaterials for medical implants and devices. In addition, all the materials presented in this research, revealed an excellent biocompatibility. This was disclosed by cell viability values above 70%, none alteration on erythrocyte membrane or cell functionality in contact with materials (haemolytic index 0-2%), and absence of interferences in blood coagulation (intrinsic, extrinsic and final pathways).

Interplay between Antibiotic Efficacy and Drug-Induced Lysis Underlies Enhanced Biofilm Formation at Subinhibitory Drug Concentrations

Subinhibitory concentrations of antibiotics have been shown to enhance biofilm formation in multiple bacterial species. While antibiotic exposure has been associated with modulated expression of many biofilm-related genes, the mechanisms of drug-induced biofilm formation remain a focus of ongoing research efforts and may vary significantly across species. In this work, we investigate antibiotic-induced biofilm formation in Enterococcus faecalis, a leading cause of nosocomial infections. We show that biofilm formation is enhanced by subinhibitory concentrations of cell wall synthesis inhibitors but not by inhibitors of protein, DNA, folic acid, or RNA synthesis. Furthermore, enhanced biofilm is associated with increased cell lysis, increases in extracellular DNA (eDNA) levels, and increases in the density of living cells in the biofilm. In addition, we observe similar enhancement of biofilm formation when cells are treated with nonantibiotic surfactants that induce cell lysis. These findings suggest that antibiotic-induced biofilm formation is governed by a trade-off between drug toxicity and the beneficial effects of cell lysis. To understand this trade-off, we developed a simple mathematical model that predicts changes in antibiotic-induced biofilm formation due to external perturbations, and we verified these predictions experimentally. Specifically, we demonstrate that perturbations that reduce eDNA (DNase treatment) or decrease the number of living cells in the planktonic phase (a second antibiotic) decrease biofilm induction, while chemical inhibitors of cell lysis increase relative biofilm induction and shift the peak to higher antibiotic concentrations. Overall, our results offer experimental evidence linking cell wall synthesis inhibitors, cell lysis, increased eDNA levels, and biofilm formation in E. faecalis while also providing a predictive quantitative model that sheds light on the interplay between cell lysis and antibiotic efficacy in developing biofilms.

Biofilm-related disease

INTRODUCTION

Biofilm formation represents a protected mode of growth that renders bacterial cells less susceptible to antimicrobials and to killing by host immune effector mechanisms and so enables the pathogens to survive in hostile environments and also to disperse and colonize new niches. Biofilm disease includes device-related infections, chronic infections in the absence of a foreign body, and even malfunction of medical devices. Areas covered: This review puts forward a new medical entity that represents a major public health issue, which we have named 'biofilm-related disease'. We highlight the characteristics of biofilm disease including its pathogenesis, microbiological features, clinical presentation, and treatment challenges. Expert commentary: The diversity of biofilm-associated infections is increasing over time and its impact may be underestimated. This peculiar form of development endows associated bacteria with a high tolerance to conventional antimicrobial agents. A small percentage of persister cells developing within the biofilm is known to be highly tolerant to antibiotics and has typically been involved in causing relapse of infections. Knowledge of the pivotal role played by biofilm-growing microorganisms in related infections will provide new treatment dynamics for this biofilm-related disease.

Biofilm formation in enterococci: genotype-phenotype correlations and inhibition by vancomycin

Enterococci are nosocomial pathogens that can form biofilms, which contribute to their virulence and antibiotic resistance. Although many genes involved in biofilm formation have been defined, their distribution among enterococci has not been comprehensively studied on a genome scale, and their diagnostic ability to predict biofilm phenotypes is not fully established. Here, we assessed the biofilm-forming ability of 90 enterococcal clinical isolates. Major patterns of virulence gene distribution in enterococcal genomes were identified, and the differentiating virulence genes were screened by polymerase chain reaction (PCR) in 31 of the clinical isolates. We found that detection of gelE in Enterococcus faecalis is not sufficient to predict gelatinase activity unless fsrAB, or fsrB alone, is PCR-positive (P = 0.0026 and 0.0012, respectively). We also found that agg is significantly enriched in isolates with medium and strong biofilm formation ability (P = 0.0026). Additionally, vancomycin, applied at sub minimal inhibitory concentrations, inhibited biofilm in four out of five strong biofilm-forming isolates. In conclusion, we suggest using agg and fsrB genes, together with the previously established gelE, for better prediction of biofilm strength and gelatinase activity, respectively. Future studies should explore the mechanism of biofilm inhibition by vancomycin and its possible use for antivirulence therapy.

Subinhibitory Concentrations of Ciprofloxacin Enhance Antimicrobial Resistance and Pathogenicity of Enterococcus faecium

Enterococcus faecium has emerged as a major opportunistic pathogen for 2 decades with the spread of hospital-adapted multidrug-resistant clones. As members of the intestinal microbiota, they are subjected to numerous bacterial stresses, including antibiotics at subinhibitory concentrations (SICs). Since fluoroquinolones are extensively prescribed, SICs are very likely to occur in vivo, with potential effects on bacterial metabolism with subsequent modulation of opportunistic traits. The aim of this study was to evaluate globally the impact of SICs of ciprofloxacin on antimicrobial resistance and pathogenicity of E. faecium Transcriptomic analysis was performed by RNA sequencing (RNA-seq) (HiSeq 2500; Illumina) using the vanB-positive reference strain E. faecium Aus0004 in the absence or presence of ciprofloxacin SIC (0.38 mg/liter, i.e., 1/8 of the MIC). Several genetic and phenotypic tests were used for validation. In the presence of ciprofloxacin SIC, 196 genes were significantly induced, whereas 286 genes were significantly repressed, meaning that 16.8% of the E. faecium genome was altered. Among upregulated genes, EFAU004_02294 (fold change, 14.3) encoded a protein (Qnr of E. faecium [EfmQnr]) homologue of Qnr proteins involved in quinolone resistance in Gram-negative bacilli. Its implication in intrinsic and adaptive fluoroquinolone (FQ) resistance in E. faecium was experimentally ascertained. Moreover, EFAU004_02292, coding for the collagen adhesin Acm, was also induced by the SIC of ciprofloxacin (fold change, 8.2), and higher adhesion capabilities were demonstrated phenotypically. Both EfmQnr and Acm determinants may play an important role in the transition from a commensal to a pathogenic state of E. faecium that resides in the gut of patients receiving fluoroquinolone therapy.

Effect of the Medium Composition on the Zn2+ Lixiviation and the Antifouling Properties of a Glass with a High ZnO Content

The dissolution of an antimicrobial ZnO-glass in the form of powder and in the form of sintered pellets were studied in water, artificial seawater, biological complex media such as common bacterial/yeast growth media (Luria Bertani (LB), yeast extract, tryptone), and human serum. It has been established that the media containing amino acids and proteins produce a high lixiviation of Zn²⁺ from the glass due to the ability of zinc and zinc oxide to react with amino acids and proteins to form complex organic compounds. The process of Zn²⁺ lixiviation from the glass network has been studied by X-ray photoelectron spectroscopy (XPS). From these results we can state that the process of lixiviation of Zn²⁺ from the glass network is similar to the one observed in sodalime glasses, where Na⁺ is lixiviated to the media first and the fraction of Zn that acts as modifiers (~2/3) is lixiviated in second place. After the subsequent collapse of the outer surface glass layer (about 200-300 nm thick layer) the dissolution process starts again. Antifouling properties against different bacteria (S. epidermidis, S. aureus, P. aeruginosa, E. coli, and M. lutea) have also been established for the glass pellets.

Emodin affects biofilm formation and expression of virulence factors in Streptococcus suis ATCC700794

Streptococcus suis (S. suis) is a swine pathogen and also a zoonotic agent. In this study, the effects of subinhibitory concentrations (sub-MICs) of emodin on biofilm formation by S. suis ATCC700794 were evaluated. As quantified by crystal violet staining, biofilm formation by S. suis ATCC700794 was dose-dependently decreased after growth with 1/2 MIC, 1/4 MIC, or 1/8 MIC of emodin. By scanning electron microscopy, the structural architecture of the S. suis ATCC700794 biofilms was examined following growth in culture medium supplemented with 1/2 MIC, 1/4 MIC, 1/8 MIC, or 1/16 MIC of emodin. Scanning electron microscopy analysis revealed the potential effect of emodin on biofilm formation by S. suis ATCC700794. The expression of luxS gene and virulence genes in S. suis ATCC700794 was investigated by quantitative RT-PCR. It was found that sub-MICs of emodin significantly decreased the expression of gapdh, sly, fbps, ef, and luxS. However, it was found that sub-MICs of emodin significantly increased the expression of cps2J, mrp, and gdh. These findings showed that sub-MICs of emodin could cause the difference in the expression level of the virulence genes.