Proteomic comparison of biofilm vs. planktonic Staphylococcus epidermidis cells suggests key metabolic differences between these conditions

PFAS inhibited sulfamethoxazole removal by regulating biofilm metabolisms on biological activated carbon

Activated carbon (AC) filtration is an effective technique to remove emerging contaminants in drinking water treatment plants. Adsorption onto AC and biodegradation by biofilm are two main mechanisms for the removal of emerging contaminants such as antibiotics. However, the effects of highly bioaccumulative and toxic poly- and perfluoroalkyl substances (PFAS) on antibiotic removal by AC filtration have not been well-understood. In this work, two AC columns were built and operated for 434 days to study the effects of ng-level PFAS on the removal of sulfamethoxazole (SMX). The results showed that 100 ng/L PFAS significantly decreased the removal rate of 1 μg/L SMX from 78.8 % to 71.7 %. Trace PFAS decreased the abundances of ammonia monooxygenase and nitrite-oxidizing bacteria, thus repressing nitrification co-metabolism process. Meanwhile, trace PFAS inhibited tricarboxylic acid (TCA) cycle by preventing pyruvate from generating acetyl-CoA, reducing energy supply for co-metabolism process. On the other hand, inhibiting TCA cycle led to a redirection of carbon from growth into polysaccharide intercellular adhesin biosynthesis. Trace PFAS also increased glutamate synthase and glutamine synthetase abundances, which promoted biofilm formation and then hindered SMX adsorption by AC. This study provides new insights into the adverse role of PFAS in antibiotic removal by AC filtration.

Comparative metabolic study of planktonic and sessile cells in Salmonella Enteritidis ATCC 13076: Elucidating metabolic pathways driving biofilm formation

Microorganisms tend to accumulate on surfaces, forming aggregates such as biofilms, which grant them resistance to various environmental stressors and antimicrobial agents. This ability has hindered the effective treatment of diseases caused by pathogenic microorganisms, including Salmonella, which is responsible for a significant number of deaths worldwide. This study aimed to compare the metabolic profiles of planktonic and sessile cells of Salmonella Enteritidis using a metabolomics approach. The metabolites extracted from the bacterial cells were analyzed by LC/MS approach. Raw data were analyzed using Thermo Xcalibur v 3.1 software. For data processing, XCMS was used for feature detection, retention time, correction and alignment. The data matrix was analyzed by uni- and multivariate statistical methods (PCA, PLS-DA, Heatmap) in MetaboAnalyst software v 6.0. A total of 121 metabolites were presumptively identified as differential metabolic characteristics between the two bacterial states, and they were associated with their corresponding metabolic pathways. Among the metabolites that exhibited positive modulation in planktonic cells were proline, phenylalanine, which act as precursors of essential metabolites and part of the stress adaptation mechanisms. In addition, putrescine and cadaverine, play crucial roles in growth, stress response, and cell stability In contrast, the most representative metabolites in sessile cells included lysine, adenosine, purines, pyrimidines, and citrate, mainly associated with maintaining cellular homeostasis, stress response and metabolic regulation. Finally, pathway enrichment analysis identified metabolic changes in 11 pathways, predominantly involving purine and pyrimidine metabolism, arginine and proline metabolism, and vitamin B6 metabolism. These findings facilitated the identification of potential metabolic pathways associated with biofilm formation in the sessile cells of Salmonella Enteritidis.

A novel multiplex fluorescent-labeling method for the visualization of mixed-species biofilms in vitro

In nature, bacteria usually exist as mixed-species biofilms, where they engage in a range of synergistic and antagonistic interactions that increase their resistance to environmental challenges. Biofilms are a major cause of persistent infections, and dispersal from initial foci can cause new infections at distal sites thus warranting further investigation. Studies of development and spatial interactions in mixed-species biofilms can be challenging due to difficulties in identifying the different bacterial species in situ. Here, we apply CellTrace dyes to studies of biofilm bacteria and present a novel application for multiplex labeling, allowing identification of different bacteria in mixed-species, in vitro biofilm models. Oral bacteria labeled with CellTrace dyes (far red, yellow, violet, and CFSE [green]) were used to create single- and mixed-species biofilms, which were analyzed with confocal spinning disk microscopy (CSDM). Biofilm supernatants were studied with flow cytometry (FC). Both Gram-positive and Gram-negative bacteria were well labeled and CSDM revealed biofilms with clear morphology and stable staining for up to 4 days. Analysis of CellTrace labeled cells in supernatants using FC showed differences in the biofilm dispersal between bacterial species. Multiplexing with different colored dyes allowed visualization of spatial relationships between bacteria in mixed-species biofilms and relative coverage by the different species was revealed through segmentation of the CSDM images. This novel application, thus, offers a powerful tool for studying structure and composition of mixed-species biofilms in vitro.IMPORTANCEAlthough most chronic infections are caused by mixed-species biofilms, much of our knowledge still comes from planktonic cultures of single bacterial species. Studies of formation and development of mixed-species biofilms are, therefore, required. This work describes a method applicable to labeling of bacteria for in vitro studies of biofilm structure and dispersal. Critically, labeled bacteria can be multiplexed for identification of different species in mixed-species biofilms using confocal spinning disk microscopy, facilitating investigation of biofilm development and spatial interactions under different environmental conditions. The study is an important step in increasing the tools available for such complex and challenging studies.

Staphylococcus epidermidis biofilms undergo metabolic and matrix remodeling under nitrosative stress

Staphylococcus epidermidis is a commensal skin bacterium that forms host- and antibiotic-resistant biofilms that are a major cause of implant-associated infections. Most research has focused on studying the responses to host-imposed stresses on planktonic bacteria. In this work, we addressed the open question of how S. epidermidis thrives on toxic concentrations of nitric oxide (NO) produced by host innate immune cells during biofilm assembly. We analyzed alterations of gene expression, metabolism, and matrix structure of biofilms of two clinical isolates of S. epidermidis, namely, 1457 and RP62A, formed under NO stress conditions. In both strains, NO lowers the amount of biofilm mass and causes increased production of lactate and decreased acetate excretion from biofilm glucose metabolism. Transcriptional analysis revealed that NO induces icaA, which is directly involved in polysaccharide intercellular adhesion (PIA) production, and genes encoding proteins of the amino sugar pathway (glmM and glmU) that link glycolysis to PIA synthesis. However, the strains seem to have distinct regulatory mechanisms to boost lactate production, as NO causes a substantial upregulation of ldh gene in strain RP62A but not in strain 1457. The analysis of the matrix components of the staphylococcal biofilms, assessed by confocal laser scanning microscopy (CLSM), showed that NO stimulates PIA and protein production and interferes with biofilm structure in a strain-dependent manner, but independently of the Ldh level. Thus, NO resistance is attained by remodeling the staphylococcal matrix architecture and adaptation of main metabolic processes, likely providing in vivo fitness of S. epidermidis biofilms contacting NO-proficient macrophages.

Evaluation of the antimicrobial function of Ginkgo biloba exocarp extract against clinical bacteria and its effect on Staphylococcus haemolyticus by disrupting biofilms

ETHNOPHARMACOLOGICAL RELEVANCE

The fruit of Ginkgo biloba L. (Ginkgo nuts) has been used for a long time as a critical Chinese medicine material to treat cough and asthma, as well as a disinfectant. Similar records were written in the Compendium of Materia Medica (Ben Cao Gang Mu, pinyin in Chinese) and Sheng Nong's herbal classic (Shen Nong Ben Cao Jing, pinyin in Chinese). Recent research has shown that Ginkgo biloba exocarp extract (GBEE) has the functions of unblocking blood vessels and improving brain function, as well as antitumour activity and antibacterial activity. GBEE was shown to inhibit methicillin-resistant Staphylococcus aureus (MRSA) biofilm formation as a traditional Chinese herb in our previous report in this journal. AIM OF THE STUD: yThe antibiotic resistance of clinical bacteria has recently become increasingly serious. Thus, this study aimed to investigate the Ginkgo biloba exocarp extract (GBEE) antibacterial lineage, as well as its effect and mechanism on S. haemolyticus biofilms. This study will provide a new perspective on clinical multidrug resistant (MDR) treatment with ethnopharmacology herbs.

METHODS

The microbroth dilution assay was carried out to measure the antibacterial effect of GBEE on 13 types of clinical bacteria. Bacterial growth curves with or without GBEE treatment were drawn at different time points. The potential targets of GBEE against S. haemolyticus were screened by transcriptome sequencing. The effects of GBEE on bacterial biofilm formation and mature biofilm disruption were determined by crystal violet staining and scanning electron microscopy. The metabolic activity of bacteria inside the biofilm was assessed by colony-forming unit (CFU) counting and (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2HY-tetrazolium bromide (MTT) assay. Quantitative polymerase chain reaction (qPCR) was used to measure the gene expression profile of GBEE on S. haemolyticus biofilm-related factors.

RESULTS

The results showed that GBEE has bacteriostatic effects on 3 g-positive (G⁺) and 2 g-negative (G^-) bacteria among 13 species of clinical bacteria. The antibacterial effect of GBEE supernatant liquid was stronger than the antibacterial effect of GBEE supernviaould-like liquid. GBEE supernatant liquid inhibited the growth of S. epidermidis, S. haemolyticus, and E. faecium at shallow concentrations with minimum inhibitory concentrations (MICs) of 2 μg/ml, 4 μg/ml and 8 μg/ml, respectively. Genes involved in quorum sensing, two-component systems, folate biosynthesis, and ATP-binding cassette (ABC) transporters were differentially expressed in GBEE-treated groups compared with controls. Crystal violet, scanning electron microscopy (SEM) and MTT assays showed that GBEE suppressed S. haemolyticus biofilm formation in a dose-dependent manner. Moreover, GBEE supernatant liquid downregulated cidA, cidB and atl, which are involved in cell lysis and extracellular DNA (eDNA) release, as well as downregulated the cbp, ebp and fbp participation in encoding cell-surface binding proteins.

CONCLUSIONS

GBEE has an excellent antibacterial effect on gram-positive bacteria and also inhibits the growth of gram-negative bacteria, such as A. baumannii (carbapenem-resistant Acinetobacter baumannii) CRABA and S. maltophilia. GBEE inhibits the biofilm formation of S. haemolyticus by altering the regulation and biofilm material-related genes, including the release of eDNA and cell-surface binding proteins.

Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis

Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.

Evaluation of immune effect of Streptococcus suis biofilm-associated protein PDH

As a zoonotic pathogen, Streptococcus suis(S. suis) takes pigs as the main host and is mainly colonizes in the upper respiratory tract and tonsil of pigs, causing septicemia, endocarditis and meningitis in pigs. Pyruvate dehydrogenase (PDH) is an enzyme that catalyzes the conversion of pyruvate to acetyl-CoA. As an immunogenic membrane-associated protein in S. suis, it has been found to be closely related to the formation of biofilm. In this study, the recombinant PDH (rPDH) of S. suis ZY05719 (serotype 2) was expressed and purified in E. coli by His affinity chromatography. Western blotting analysis showed that there was a strong specific reaction between PDH protein and PDH antiserum. Mice were immunized with recombinant PDH and inactivated bacteria, and the relative survival rates were 70 % and 60 %, respectively. In addition, mice immunized with PDH caused high levels of antibodies and high expression of immune-related genes in the spleen, which significantly protected the liver, brain and spleen from pathological damage. In addition, PDH antiserum could significantly inhibit the growth of S. suis and the formation of S. suis biofilm in vitro. These results further suggest that PDH is a promising candidate for S. suis biofilm-related subunit vaccine.

Targeting antibiotic tolerance in anaerobic biofilms associated with oral diseases: Human antimicrobial peptides LL-37 and lactoferricin enhance the antibiotic efficacy of amoxicillin, clindamycin and metronidazole

Antimicrobial peptides are receiving increasing attention as potential therapeutic agents for treating biofilm-related infections of the oral cavity. Many bacteria residing in biofilms exhibit an enhanced antibiotic tolerance, which grants intrinsically susceptible microorganisms to survive lethal concentrations of antibiotics. In this study, we examined the effects of two endogenous human antimicrobial peptides, LL-37 and human Lactoferricin, on the antibiotic drug efficacy of amoxicillin, clindamycin and metronidazole in two types of polymicrobial biofilms, which aimed to represent frequent oral diseases: (1) facultative anaerobic (Streptococcus mutans, Streptococcus sanguinis, Actinomyces naeslundii) and (2) obligate anaerobic biofilms (Veillonella parvula, Parvimonas micra, Fusobacterium nucleatum). LL-37 and Lactoferricin enhanced the anti-biofilm effect of amoxicillin and clindamycin in facultative anaerobic biofilms. Metronidazole alone was ineffective against facultative anaerobic biofilms, but the presence of LL-37 and Lactoferricin led to a greater biofilm reduction. Obligate anaerobic biofilms showed an increased drug tolerance to amoxicillin and clindamycin, presumably due to metabolic downshifts of the bacteria residing within the biofilm. However, when combined with LL-37 or Lactoferricin, the reduction of obligate anaerobic biofilms was markedly enhanced for all antibiotics, even for amoxicillin and clindamycin. Furthermore, our results suggest that antimicrobial peptides enhance the dispersion of matured biofilms, which may be one of their mechanisms for targeting biofilms. In summary, our study proves that antimicrobial peptides can serve as an auxiliary treatment strategy for combatting enhanced antibiotic tolerance in bacterial biofilms.