Ureolytic Biomineralization Reduces Proteus mirabilis Biofilm Susceptibility to Ciprofloxacin

The roles of calcium signaling and calcium deposition in microbial multicellularity

Calcium signaling is an essential mediator of signal-controlling gene expression in most developmental systems. In addition, calcium has established extracellular functions as a structural component of biogenic minerals found in complex tissues. In bacteria, the formation of calcium carbonate structures is associated with complex colony morphology. Genes promoting the formation of biogenic minerals are essential for proper biofilm development and protection against antimicrobial solutes and toxins. Here we review recent findings on the role of calcium and calcium signaling as emerging regulators of biofilm formation in beneficial bacteria, as well as essential mediators of biofilm formation and virulence in human pathogens. The presented analysis concludes that the new understanding of calcium signaling may help to improve the performance of beneficial strains for sustainable agriculture, microbiome manipulation, and sustainable construction. Unraveling the roles of calcium may also promote the development of novel therapies against biofilm infections that target calcium uptake, calcium sensors, and calcium carbonate deposition.

Recent Advances in the Control of Clinically Important Biofilms

Biofilms are complex structures formed by bacteria, fungi, or even viruses on biotic and abiotic surfaces, and they can be found in almost any part of the human body. The prevalence of biofilm-associated diseases has increased in recent years, mainly because of the frequent use of indwelling medical devices that create opportunities for clinically important bacteria and fungi to form biofilms either on the device or on the neighboring tissues. As a result of their resistance to antibiotics and host immunity factors, biofilms have been associated with the development or persistence of several clinically important diseases. The inability to completely eradicate biofilms drastically increases the burden of disease on both the patient and the healthcare system. Therefore, it is crucial to develop innovative ways to tackle the growth and development of biofilms. This review focuses on dental- and implant-associated biofilm infections, their prevalence in humans, and potential therapeutic intervention strategies, including the recent advances in pharmacology and biomedical engineering. It lists current strategies used to control the formation of clinically important biofilms, including novel antibiotics and their carriers, antiseptics and disinfectants, small molecule anti-biofilm agents, surface treatment strategies, and nanostructure functionalization, as well as multifunctional coatings particularly suitable for providing antibacterial effects to the surface of implants, to treat either dental- or implant-related bacterial infections.

The roles of intracellular and extracellular calcium in Bacillus subtilis biofilms

In nature, bacteria reside in biofilms– multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation—mineral-forming cells—that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes.

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The orchestrated formation of calcite scaffolds supports the morphogenesis of microbial biofilms

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A novel subpopulation—mineral-forming cells—is essential for biofilm formation

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This subpopulation contains an intracellular calcium-accumulating niche, supporting the formation of calcium carbonate

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Intracellular calcium homeostasis and calcium export are associated with a functional biofilm macrostructure

Calcium carbonate mineralization is essential for biofilm formation and lung colonization

Biofilms are differentiated microbial communities held together by an extracellular matrix. μCT X-ray revealed structured mineralized areas within biofilms of lung pathogens belonging to two distant phyla - the proteobacteria Pseudomonas aeruginosa and the actinobacteria Mycobacterium abscessus. Furthermore, calcium chelation inhibited the assembly of complex bacterial structures for both organisms with little to no effect on cell growth. The molecular mechanisms promoting calcite scaffold formation were surprisingly conserved between the two pathogens as biofilm development was similarly impaired by genetic and biochemical inhibition of calcium uptake and carbonate accumulation. Moreover, chemical inhibition and mutations targeting mineralization significantly reduced the attachment of P. aeruginosa to the lung, as well as the subsequent damage inflicted by biofilms to lung tissues, and restored their sensitivity to antibiotics. This work offers underexplored druggable targets for antibiotics to combat otherwise untreatable biofilm infections.

A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms

In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.

Preoperative antibiotic therapy exceeding 7 days can minimize infectious complications after percutaneous nephrolithotomy in patients with positive urine culture

PURPOSE

To explore an appropriate duration of antibiotic therapy before percutaneous nephrolithotomy (PCNL) in patients with positive urine culture.

METHODS

From March 2016 to May 2018, consecutive patients with positive urine culture undergoing PCNL were prospectively registered. Initial preoperative antibiotics were given empirically. If needed, antibiotics were upgraded or adjusted to susceptible antibiotic after obtaining antibiotic-sensitivity test. Postoperative systemic inflammatory response syndrome (SIRS) was the primary outcome.

RESULTS

Among the 220 participants, the incidence of positive stone culture and SIRS were 85.5% and 36.8%. Escherichia coli (53.6%, 44.5%) and Proteus mirabilis (8.2%, 10.0%) were the top two bacteria in urine and stones. In univariable analysis, patients with postoperative SIRS had a higher rate of stone culture positivity (97.5% VS 78.4%, P < 0.001) and a shorter duration of preoperative antibiotics therapy (3.4 ± 2.7 days versus 4.2 ± 2.8 days, P = 0.037). The landscape of SIRS showed a declining trend as the elongation of preoperative antibiotics (P = 0.039). In a day-by-day comparison, SIRS was less prevalent in patients treated by pre-PCNL antibiotics ≥ 7 days than in those with antibiotics ≤ 6 days (21.7% VS 40.8%, P = 0.017). Multivariable logistic regression confirmed positive stone culture (P = 0.001, OR 11.115) as an independent risk factor and pre-PCNL antibiotics ≥ 7 days (P = 0.048, OR 0.449) as an independent protective factor for SIRS. Preoperative antibiotic ≥ 7 days decreased SIRS from 45.4 to 27.8% and from 9.1 to 0% in patients with a positive and negative stone culture, respectively.

CONCLUSION

Exceeding seven days should be appropriate duration of antibiotic therapy before PCNL in patients with positive urine cultures.

Photothermal nanoparticles for ablation of bacteria associated with kidney stones

OBJECTIVE

To determine whether photothermal polymer nanoparticles (NPs) can interface with bacteria associated with kidney stones, generate heat when stimulated with near infrared (NIR) light, and aid in reducing bacterial burden.

METHODS

Two types of kidney stones, artificial, and those removed during percutaneous nephrolithotomy (PCNL), were inoculated with Escherichia coli (E. coli) and then incubated with NPs composed of FITC-labeled Poly[4,4-bis(2-ethylhexyl)-cyclopenta[2,1-b;3,4-b']-dithiophene-2,6-diyl-alt-2,1,3-benzoselenadiazole-4,7-diyl] (PCPDTBSe). Association of the PCPDTBSe NPs was evaluated using fluorescence microscopy. Infected stones were incubated with NPs and exposed to 800 nm light to generate temperature increases from 25.4 to 68.6 °C on the stones. Following photothermal treatment, the stones were homogenized and the bacteria was enumerated via colony counting assays to evaluate the bactericidal effect. The photothermal effect was also evaluated using scanning electron microscopy of the treated biofilms.

RESULTS

Both kidney stone types sequestered E. coli. Control stones and stones treated with laser only had growth of numerous bacterial colonies, while stones exposed to NPs and laser grew significantly less, or none (p = 0.02).

CONCLUSIONS

The polymer NPs interface with E. coli on artificial and patient-derived kidney stones, and they can impart a bactericidal effect, when stimulated with NIR to generate heat. This technique may possibly be extended to treating infected kidney stones in patients.

Enhanced antibiotic treatment based on positive urine dipstick infection test before percutaneous nephrolithotomy did not prevent postoperative infection in patients with negative urine culture

INTRODUCTION

Urinary tract infection (UTI) should be treated before percutaneous nephrolithotomy (PCNL). However, the most appropriate treatment strategy in patients with negative urine culture but positive urine dipstick infection test (positive urinary leukocyte or nitrite reaction) remains unclear.

METHODS

From August 2016 to February 2018, 806 consecutive patients who had undergone the first-stage PCNL with negative urine culture were included. Preoperative urinalysis, antibiotic treatment, intraoperative stone culture, and postoperative systemic inflammatory response syndrome (SIRS) were prospectively recorded. The primary outcome was SIRS. The impact of preoperative antibiotics on preoperative urinary tract infection, stone culture, and postoperative SIRS was studied.

RESULTS

Among the 806 participants, the rate of positive urine dipstick infection test and SIRS were 26.8% and 7.2%, respectively. In univariable analysis, positive urinary nitrite (p<0.001), positive urinary leukocytes (p<0.001), positive urine dipstick infection test (p<0.001), longer duration of pre-PCNL antibiotics (p=0.001), higher level of pre-PCNL antibiotics (p=0.010), infection stones (p=0.001), and positive stone culture (p<0. 001) were risk factors for SIRS. However, multivariable analysis showed that positive stone culture (p=0.004) and prolonged preoperative treatment with antibiotics (p=0.021) were independent risk factors for SIRS. Although preoperative antibiotics reduced the incidence of positive urine leukocyte (p<0.001) or nitrite reactions (p<0.001), prolonged or upgraded preoperative antibiotics did not affect the incidence of positive stone culture. Whether stone culture was positive (p=0.023) or negative (p=0.025), prolonged preoperative treatment with antibiotics was associated with a higher incidence of SIRS.

CONCLUSIONS

Enhanced preoperative antibiotic treatment based on positive urine dipstick infection tests was insufficient to reduce the incidence of positive stone culture but increased the risk of SIRS after PCNL in patients with negative urine cultures.

Malonate utilization by Pseudomonas aeruginosa affects quorum-sensing and virulence and leads to formation of mineralized biofilm-like structures

Pseudomonas aeruginosa is an opportunistic pathogen that uses malonate among its many carbon sources. We recently reported that, when grown in blood from trauma patients, P. aeruginosa expression of malonate utilization genes was upregulated. In this study, we explored the role of malonate utilization and its contribution to P. aeruginosa virulence. We grew P. aeruginosa strain PA14 in M9 minimal medium containing malonate (MM9) or glycerol (GM9) as a sole carbon source and assessed the effect of the growth on quorum sensing, virulence factors, and antibiotic resistance. Growth of PA14 in MM9, compared to GM9, reduced the production of elastases, rhamnolipids, and pyoverdine; enhanced the production of pyocyanin and catalase; and increased its sensitivity to norfloxacin. Growth in MM9 decreased extracellular levels of N-acylhomoserine lactone autoinducers, an effect likely associated with increased pH of the culture medium; but had little effect on extracellular levels of PQS. At 18 hr of growth in MM9, PA14 formed biofilm-like structures or aggregates that were associated with biomineralization, which was related to increased pH of the culture medium. These results suggest that malonate significantly impacts P. aeruginosa pathogenesis by influencing the quorum sensing systems, the production of virulence factors, biofilm formation, and antibiotic resistance.

Proteus mirabilis Biofilm: Development and Therapeutic Strategies

Proteus mirabilis is a Gram negative bacterium that is a frequent cause of catheter-associated urinary tract infections (CAUTIs). Its ability to cause such infections is mostly related to the formation of biofilms on catheter surfaces. In order to form biofilms, P. mirabilis expresses a number of virulence factors. Such factors may include adhesion proteins, quorum sensing molecules, lipopolysaccharides, efflux pumps, and urease enzyme. A unique feature of P. mirabilis biofilms that build up on catheter surfaces is their crystalline nature owing to their ureolytic biomineralization. This leads to catheter encrustation and blockage and, in most cases, is accompanied by urine retention and ascending UTIs. Bacteria embedded in crystalline biofilms become highly resistant to conventional antimicrobials as well as the immune system. Being refractory to antimicrobial treatment, alternative approaches for eradicating P. mirabilis biofilms have been sought by many studies. The current review focuses on the mechanism by which P. mirabilis biofilms are formed, and a state of the art update on preventing biofilm formation and reduction of mature biofilms. These treatment approaches include natural, and synthetic compounds targeting virulence factors and quorum sensing, beside other strategies that include carrier-mediated diffusion of antimicrobials into biofilm matrix. Bacteriophage therapy has also shown successful results in vitro for combating P. mirabilis biofilms either merely through their lytic effect or by acting as facilitators for antimicrobials diffusion.

A Novel Method to Reveal a Ureolytic Biofilm Attachment and In Situ Growth Monitoring by Electrochemical Impedance Spectroscopy

The formation of biofilms capable of efficiently carrying out ureolysis is of fundamental importance in several biotechnological systems such as urinary tract infections, building materials and municipal wastewater treatment. This work proposes a straightforward method for the formation of a ureolytic biofilm attached to graphite. The proposed strategy reduced the time needed to complete ureolysis to 3 days instead of 16 days required in suspension culture. To confirm the formation of a ureolytic biofilm, scanning electron microscopy and confocal laser scanning microscopy studies were employed ex situ. However, it is imperative to analyse the biofilm by direct non-invasive techniques. Accordingly, open circuit potential (OCP) and electrochemical impedance spectroscopy (EIS) were used as in situ monitoring techniques. The reduction in OCP from - 0.01 to - 0.2 V vs. Ag/AgCl and the increase in capacitance from 200 to 260 μF cm^-2 were related to biofilm attachment. To the best of our knowledge, this is the first time in which a ureolytic biofilm attachment has been analysed by EIS. The increase in the biomass from 0.04 to 2.81 μm³ μm^-2 and in average thickness from 10.19 to 32.78 μm was related to biofilm maturation.

Current insights into the mechanisms and management of infection stones

Infection stones are complex aggregates of crystals amalgamated in an organic matrix that are strictly associated with urinary tract infections. The management of patients who form infection stones is challenging owing to the complexity of the calculi and high recurrence rates. The formation of infection stones is a multifactorial process that can be driven by urine chemistry, the urine microenvironment, the presence of modulator substances in urine, associations with bacteria, and the development of biofilms. Despite decades of investigation, the mechanisms of infection stone formation are still poorly understood. A mechanistic understanding of the formation and growth of infection stones - including the role of organics in the stone matrix, microorganisms, and biofilms in stone formation and their effect on stone characteristics - and the medical implications of these insights might be crucial for the development of improved treatments. Tools and approaches used in various disciplines (for example, engineering, chemistry, mineralogy, and microbiology) can be applied to further understand the microorganism-mineral interactions that lead to infection stone formation. Thus, the use of integrated multidisciplinary approaches is imperative to improve the diagnosis, prevention, and treatment of infection stones.

Magnesium-doped zinc oxide nanoparticles alter biofilm formation of Proteus mirabilis

Aim: Proteus mirabilis biofilms colonize medical devices, and their role in microbial pathogenesis is well established. Magnesium-doped zinc oxide nanoparticles (ZnO:MgO NPs) have potential antimicrobial properties; thus, we aimed at evaluating the antibiofilm activity of ZnO:MgO NPs against P. mirabilis biofilm. Materials & methods: After synthesis and characterization of ZnO:MgO NPs and their addition to a polymer film, we evaluated the stages of P. mirabilis biofilm development over glass coverslip covered by different concentrations of ZnO:MgO NPs. Results: Low concentrations of ZnO:MgO NPs affect the development of P. mirabilis biofilm. Descriptors showed reduced values in bacterial number, bacterial volume and extracellular material. Conclusion: Our results highlight this new application of ZnO:MgO NPs as a potential antibiofilm strategy in medical devices.

Bacterial biofilm formation on indwelling urethral catheters

Urethral catheters are the most commonly deployed medical devices and used to manage a wide range of conditions in both hospital and community care settings. The use of long-term catheterization, where the catheter remains in place for a period >28 days remains common, and the care of these patients is often undermined by the acquisition of infections and formation of biofilms on catheter surfaces. Particular problems arise from colonization with urease-producing species such as Proteus mirabilis, which form unusual crystalline biofilms that encrust catheter surfaces and block urine flow. Encrustation and blockage often lead to a range of serious clinical complications and emergency hospital referrals in long-term catheterized patients. Here we review current understanding of bacterial biofilm formation on urethral catheters, with a focus on crystalline biofilm formation by P. mirabilis, as well as approaches that may be used to control biofilm formation on these devices. SIGNIFICANCE AND IMPACT OF THE STUDY: Urinary catheters are the most commonly used medical devices in many healthcare systems, but their use predisposes to infection and provide ideal conditions for bacterial biofilm formation. Patients managed by long-term urethral catheterization are particularly vulnerable to biofilm-related infections, with crystalline biofilm formation by urease producing species frequently leading to catheter blockage and other serious clinical complications. This review considers current knowledge regarding biofilm formation on urethral catheters, and possible strategies for their control.

Micro-CT X-ray imaging exposes structured diffusion barriers within biofilms

In nature, bacteria predominantly exist as highly structured biofilms, which are held together by extracellular polymeric substance and protect their residents from environmental insults, such as antibiotics. The mechanisms supporting this phenotypic resistance are poorly understood. Recently, we identified a new mechanism maintaining biofilms - an active production of calcite minerals. In this work, a high-resolution and robust µCT technique is used to study the mineralized areas within intact bacterial biofilms. µCT is a vital tool for visualizing bacterial communities that can provide insights into the relationship between bacterial biofilm structure and function. Our results imply that dense and structured calcium carbonate lamina forms a diffusion barrier sheltering the inner cell mass of the biofilm colony. Therefore, µCT can be employed in clinical settings to predict the permeability of the biofilms. It is demonstrated that chemical interference with urease, a key enzyme in biomineralization, inhibits the assembly of complex bacterial structures, prevents the formation of mineral diffusion barriers and increases biofilm permeability. Therefore, biomineralization enzymes emerge as novel therapeutic targets for highly resistant infections.

Architects of nature: growing buildings with bacterial biofilms

In his text 'On Architecture', Vitruvius suggested that architecture is an imitation of nature. Here we discuss what happens when we begin using nature in architecture. We describe recent developments in the study of biofilm structure, and propose combining modern architecture and synthetic microbiology to develop sustainable construction approaches. Recently, Kolodkin-Gal laboratory and others revealed a role for precipitation of calcium carbonate in the maturation and assembly of bacterial communities with complex structures. Importantly, they demonstrated that different secreted organic materials shape the calcium carbonate crystals formed by the bacterial cells. This provides a proof-of-concept for a potential use of bacteria in designing rigid construction materials and altering crystal morphology and function. In this study, we discuss how these recent discoveries may change the current strategies of architecture and construction. We believe that biofilm communities enhanced by synthetic circuits may be used to construct buildings and to sequester carbon dioxide in the process.

From Catheter to Kidney Stone: The Uropathogenic Lifestyle of Proteus mirabilis

Proteus mirabilis is a model organism for urease-producing uropathogens. These diverse bacteria cause infection stones in the urinary tract and form crystalline biofilms on indwelling urinary catheters, frequently leading to polymicrobial infection. Recent work has elucidated how P. mirabilis causes all of these disease states. Particularly exciting is the discovery that this bacterium forms large clusters in the bladder lumen that are sites for stone formation. These clusters, and other steps of infection, require two virulence factors in particular: urease and MR/P fimbriae. Highlighting the importance of MR/P fimbriae is the cotranscribed regulator, MrpJ, which globally controls virulence. Overall, P. mirabilis exhibits an extraordinary lifestyle, and further probing will answer exciting basic microbiological and clinically relevant questions.