Type 1 fimbriae contribute to catheter-associated urinary tract infections caused by Escherichia coli

Tyrosol blocks E. coli anaerobic biofilm formation via YbfA and FNR to increase antibiotic susceptibility

Bacteria within mature biofilms are highly resistant to antibiotics than planktonic cells. Oxygen limitation contributes to antibiotic resistance in mature biofilms. Nitric oxide (NO) induces biofilm dispersal; however, low NO levels stimulate biofilm formation, an underexplored process. Here, we introduce a mechanism of anaerobic biofilm formation by investigating the antibiofilm activity of tyrosol, a component in wine. Tyrosol inhibits E. coli and Pseudomonas aeruginosa biofilm formation by enhancing NO production. YbfA is identified as a target of tyrosol and its downstream targets are sequentially determined. YbfA activates YfeR, which then suppresses the anaerobic regulator FNR. This suppression leads to decreased NO production, elevated bis-(3'-5')-cyclic dimeric GMP levels, and finally stimulates anaerobic biofilm formation in the mature stage. Blocking YbfA with tyrosol treatment renders biofilm cells as susceptible to antibiotics as planktonic cells. Thus, this study presents YbfA as a promising antibiofilm target to address antibiotic resistance posed by biofilm-forming bacteria, with tyrosol acting as an inhibitor.

Medical Device-Associated Biofilm Infections and Multidrug-Resistant Pathogens

Medical devices such as venous catheters (VCs) and urinary catheters (UCs) are widely used in the hospital setting. However, the implantation of these devices is often accompanied by complications. About 60 to 70% of nosocomial infections (NIs) are linked to biofilms. The main complication is the ability of microorganisms to adhere to surfaces and form biofilms which protect them and help them to persist in the host. Indeed, by crossing the skin barrier, the insertion of VC inevitably allows skin flora or accidental environmental contaminants to access the underlying tissues and cause fatal complications like bloodstream infections (BSIs). In fact, 80,000 central venous catheters-BSIs (CVC-BSIs)-mainly occur in intensive care units (ICUs) with a death rate of 12 to 25%. Similarly, catheter-associated urinary tract infections (CA-UTIs) are the most commonlyhospital-acquired infections (HAIs) worldwide.These infections represent up to 40% of NIs.In this review, we present a summary of biofilm formation steps. We provide an overview of two main and important infections in clinical settings linked to medical devices, namely the catheter-asociated bloodstream infections (CA-BSIs) and catheter-associated urinary tract infections (CA-UTIs), and highlight also the most multidrug resistant bacteria implicated in these infections. Furthermore, we draw attention toseveral useful prevention strategies, and advanced antimicrobial and antifouling approaches developed to reduce bacterial colonization on catheter surfaces and the incidence of the catheter-related infections.

Surface-enhanced Raman spectroscopy for studying the interaction of organometallic compound bis(1,3-dihexylimidazole-2-yl) silver(i) hexafluorophosphate (v) with the biofilm of Escherichia coli

Escherichia coli biofilms are a major cause of gastrointestinal tract diseases, such as esophageal, stomach and intestinal diseases. Nowadays, these are the most commonly occurring diseases caused by consuming contaminated food. In this study, we evaluated the efficacy of probiotics in controlling multidrug-resistant E. coli and reducing its ability to form biofilms. Our results substantiate the effective use of probiotics as antimicrobial alternatives and to eradicate biofilms formed by multidrug-resistant E. coli. In this research, surface enhanced Raman spectroscopy (SERS) was utilized to identify and evaluate Escherichia coli biofilms and their response to the varying concentrations of the organometallic compound bis(1,3-dihexylimidazole-2-yl) silver(i) hexafluorophosphate (v). Given the escalating challenge of antibiotic resistance in bacteria that form biofilms, understanding the impact of potential antibiotic agents is crucial for the healthcare sector. The combination of SERS with principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) enabled the detection and characterization of the biofilm, providing insights into the biochemical changes induced by the antibiotic candidate. The identified SERS spectral features served as indicators for elucidating the mode of action of the potential drug on the biofilm. Through PCA and PLS-DA, metabolic variations allowing the differentiation and classification of unexposed biofilms and biofilms exposed to different concentrations of the synthesized antibiotic were successfully identified, with 95% specificity, 96% sensitivity, and a 0.75 area under the curve (AUC). This research underscores the efficiency of surface enhanced Raman spectroscopy in differentiating the impact of potential antibiotic agents on E. coli biofilms.

Factors influencing initial bacterial adhesion to antifouling surfaces studied by single-cell force spectroscopy

Biofilm formation, a major concern for healthcare systems, is initiated when bacteria adhere to surfaces. Escherichia coli adhesion is mediated by appendages, including type-1 fimbriae and curli amyloid fibers. Antifouling surfaces prevent the adhesion of bacteria to combat biofilm formation. Here, we used single-cell force-spectroscopy to study the interaction between E. coli and glass or two antifouling surfaces: the tripeptide DOPA-Phe(4F)-Phe(4F)-OMe and poly(ethylene glycol) polymer-brush. Our results indicate that both antifoulants significantly deter E. coli initial adhesion. By using two mutant strains expressing no type-1 fimbriae or curli amyloids, we studied the adhesion mechanism. Our results suggest that the bacteria adhere to different antifoulants via separate mechanisms. Finally, we show that some bacteria adhere much better than others, illustrating how the variability of bacterial cultures affects biofilm formation. Our results emphasize how additional study at the single-cell level can enhance our understanding of bacterial adhesion, thus leading to novel antifouling technologies.

Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy

Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.

Biofilm Formation by Escherichia coli Isolated from Urinary Tract Infections from Aguascalientes, Mexico

Uropathogenic Escherichia coli (UPEC) strains are among the leading causes of urinary tract infections (UTIs) worldwide. They can colonize the urinary tract and form biofilms that allow bacteria to survive and persist, causing relapses of infections and life-threatening sequelae. Here, we analyzed biofilm production, antimicrobial susceptibility, virulence factors, and phylogenetic groups in 74 E. coli isolated from diagnosed patients with UTIs to describe their microbiological features and ascertain their relationship with biofilm capabilities. High levels of ceftazidime resistance are present in hospital-acquired UTIs. Isolates of multidrug resistance strains (p = 0.0017) and the yfcV gene (p = 0.0193) were higher in male patients. All the strains tested were able to form biofilms. Significant differences were found among higher optical densities (ODs) and antibiotic resistance to cefazolin (p = 0.0395), ceftazidime (p = 0.0302), and cefepime (p = 0.0420). Overall, the presence of fimH and papC coincided with strong biofilm formation by UPEC. Type 1 fimbriae (p = 0.0349), curli (p = 0.0477), and cellulose (p = 0.0253) production was significantly higher among strong biofilm formation. Our results indicated that high antibiotic resistance may be related to male infections as well as strong and moderate biofilm production. The ability of E. coli strains to produce biofilm is important for controlling urinary tract infections.

Antimicrobial Potency and E. coli β-Carbonic Anhydrase Inhibition Efficacy of Phenazone-Based Molecules

In this investigation, 4-antipyrinecarboxaldhyde was reacted with methyl hydrazinecarbodithioate to afford the carbodithioate derivative 3. The as-prepared carbodithioate derivative 3 is considered to be a key molecule for the preparation of new antipyrine-1,3,4-thiadiazole-based molecules (4-9) through its reaction with the appropriate hydrazonoyl halides. Furthermore, a typical Biginelli three-component cyclocondensation reaction involving ethyl acetoacetate, 4-antipyrinecarboxaldhyde, and thiourea under the standard conditions is carried out in the presence of sulfuric acid to afford the corresponding antipyrine-pyrimidine hybrid molecule (10). The latter was submitted to react with hydrazine monohydrate to provide the corresponding hydrazide derivative (11) which, under reaction with ethyl acetoacetate in refluxing ethanol containing catalytic amount of acetic acid, afforded the corresponding derivative (12). The structure of the newly synthesized compounds was affirmed by their spectral and microanalytical data. We also screened for their antimicrobial potential (ZOI and MIC) and conducted a kinetic study. Additionally, the mechanism of biological action was assessed by a membrane leakage assay and SEM imaging technique. Moreover, the biological activities and the binding modes of these compounds were further supplemented by an in silico docking study against E. coli β-carbonic anhydrase. The amount of cellular protein released by E. coli is directly correlated to the concentration of compound 9, which was found to be 177.99 µg/mL following treatment with 1.0 mg/mL of compound 9. This finding supports compound 9's antibacterial properties and explains how the formation of holes in the E. coli cell membrane results in the release of proteins from the cytoplasm. The newly synthesized compounds represent acceptable antimicrobial activities with potential action against E. coli β-carbonic anhydrase. The docking studies and antimicrobial activity test proved that compound (9) declared a greater activity than the other synthesized compounds.

Quorum sensing N-acyl homoserine lactones-SdiA enhances the biofilm formation of E. coli by regulating sRNA CsrB expression

As an important virulence phenotype of Escherichia coli, the regulation mechanism of biofilm by non-coding RNA and quorum sensing system has not been clarified. Here, by transcriptome sequencing and RT-PCR analysis, we found CsrB, a non-coding RNA of the carbon storage regulation system, was positively regulated by the LuxR protein SdiA. Furthermore, β-galactosidase reporter assays showed that SdiA enhanced promoter transcriptional activity of csrB. The consistent dynamic expression levels of SdiA and CsrB during Escherichia coli growth were also detected. Moreover, curli assays and biofilm assays showed sdiA deficiency in Escherichia coli SM10λπ or BW25113 led to a decreased formation of biofilm, and was significantly restored by over-expression of CsrB. Interestingly, the regulations of SdiA on CsrB in biofilm formation were enhanced by quorum sensing signal molecules AHLs. In conclusion, SdiA plays a crucial role in Escherichia coli biofilm formation by regulating the expression of non-coding RNA CsrB. Our study provides new insights into SdiA-non-coding RNA regulatory network involved in Escherichia coli biofilm formation.

Multidrug-resistant Escherichia coli isolated from patients and surrounding hospital environments in Bangladesh: A molecular approach for the determination of pathogenicity and resistance

Extended spectrum β-lactamase producing Escherichia coli (ESBL E. coli) is a primary concern for hospital and community healthcare settings, often linked to an increased incidence of nosocomial infections. This study investigated the characteristics of ESBL E. coli isolated from hospital environments and clinical samples. In total, 117 ESBL E. coli isolates were obtained. The isolates were subjected to molecular analysis for the presence of resistance and virulence genes, antibiotic susceptibility testing, quantitative adherence assay, ERIC-PCR for phylogenetic analysis and whole genome sequencing of four highly drug resistant isolates. Out of the 117 isolates, 68.4% were positive for blaCTX-M, 39.3% for blaTEM, 30.8% for blaNDM-1, 13.7% for blaOXA and 1.7% for blaSHV gene. Upon screening for diarrheagenic genes, no isolates were found to harbour any of the tested genes. In the case of extraintestinal pathogenic E. coli (ExPEC) virulence factors, 7.6%, 11%, 5.9%, 4.3% and 21.2% of isolates harbored the focG, kpsMII, sfaS, afa and iutA genes, respectively. At a temperature of 25°C, 14.5% of isolates exhibited strong biofilm formation with 21.4% and 28.2% exhibiting moderate and weak biofilm formation respectively, whereas 35.9% were non-biofilm formers. On the other hand at 37°C, 2.6% of isolates showed strong biofilm formation with 3.4% and 31.6% showing moderate and weak biofilm formation respectively, whereas, 62.4% were non-biofilm formers. Regarding antibiotic susceptibility testing, all isolates were found to be multidrug-resistant (MDR), with 30 isolates being highly drug resistant. ERIC-PCR resulted in 12 clusters, with cluster E-10 containing the maximum number of isolates. Hierarchical clustering and correlation analysis revealed associations between environmental and clinical isolates, indicating likely transmission and dissemination from the hospital environment to the patients. The whole genome sequencing of four highly drug resistant ExPEC isolates showed the presence of various antimicrobial resistance genes, virulence factors and mobile genetic elements, with isolates harbouring the plasmid incompatibility group IncF (FII, FIB, FIA). The sequenced isolates were identified as human pathogens with a 93.3% average score. This study suggests that ESBL producing E. coli are prevalent in the healthcare settings of Bangladesh, acting as a potential reservoir for AMR bacteria. This information may have a profound effect on treatment, and improvements in public healthcare policies are a necessity to combat the increased incidences of hospital-acquired infections in the country.

Reduction of biofilm formation of Escherichia coli by targeting quorum sensing and adhesion genes using the CRISPR/Cas9-HDR approach, and its clinical application on urinary catheter

BACKGROUND

Escherichia coli is a common cause of biofilm-associated urinary tract infections (UTIs). Biofilm formation in E. coli is responsible for various indwelling medical device-associated infections, including catheter-associated urinary tract infections (CAUTIs). This study aimed to reduce biofilm formation of E. coli ATCC 25922 by knocking out genes involved in quorum sensing (QS) (luxS) and adhesion (fimH and bolA) using the CRISPR/Cas9-HDR approach.

METHOD

Single-guide RNAs (sgRNAs) were designed to target luxS, fimH and bolA genes. Donor DNA for homologous recombination was constructed to provide accurate repairs of double-strand breaks (DSBs). A biofilm quantification assay (crystal violet assay) was performed to quantify the biofilm formation of mutant and wild-type strains. Morphological changes in biofilm architecture were confirmed by scanning electron microscopy (SEM). Further application of the biofilm formation of mutant and wild-type strains on urinary catheter was tested.

RESULTS

Crystal violet assay showed that the biofilm formation of ΔfimH, ΔluxS, and ΔbolA strains was significantly reduced compared to the wild-type strain (P value < 0.001). The percentage of biofilm reduction of mutant strains was as follows: ΔluxS1 77.51 %, ΔfimH1 78.37 %, ΔfimH2 84.17 %, ΔbolA1 78.24 %, and ΔbolA2 75.39 %. Microscopic analysis showed that all mutant strains lack extracellular polymeric substances (EPS) production compared to the wild-type strain, which was embedded in its EPS matrix. The adherence, cell aggregation, and biofilm formation of wild-type strain on urinary catheters were significantly higher compared to ΔfimH, ΔluxS and ΔbolA strains.

CONCLUSION

Altogether, our results demonstrated that the knockout of luxS, fimH, and bolA genes reduced EPS matrix production, which is considered the main factor in the development, maturation, and maintenance of the integrity of biofilm. This pathway could be a potential strategy to disrupt E. coli biofilm-associated UTIs. This study suggests that CRISPR/Cas9-HDR system may provide an efficient and site-specific gene editing approach that exhibits a possible antibiofilm strategy through intervention with the QS mechanism and adhesion property to suppress biofilm formation associated with UTI catheter infections.

Synthesis, Antimicrobial, and Antibiofilm Activities of Some Novel 7-Methoxyquinoline Derivatives Bearing Sulfonamide Moiety against Urinary Tract Infection-Causing Pathogenic Microbes

A new series of 4-((7-methoxyquinolin-4-yl) amino)-N-(substituted) benzenesulfonamide 3(a-s) was synthesized via the reaction of 4-chloro-7-methoxyquinoline 1 with various sulfa drugs. The structural elucidation was verified based on spectroscopic data analysis. All the target compounds were screened for their antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria, and unicellular fungi. The results revealed that compound 3l has the highest effect on most tested bacterial and unicellular fungal strains. The highest effect of compound 3l was observed against E. coli and C. albicans with MIC = 7.812 and 31.125 µg/mL, respectively. Compounds 3c and 3d showed broad-spectrum antimicrobial activity, but the activity was lower than that of 3l. The antibiofilm activity of compound 3l was measured against different pathogenic microbes isolated from the urinary tract. Compound 3l could achieve biofilm extension at its adhesion strength. After adding 10.0 µg/mL of compound 3l, the highest percentage was 94.60% for E. coli, 91.74% for P. aeruginosa, and 98.03% for C. neoformans. Moreover, in the protein leakage assay, the quantity of cellular protein discharged from E. coli was 180.25 µg/mL after treatment with 1.0 mg/mL of compound 3l, which explains the creation of holes in the cell membrane of E. coli and proves compound 3l's antibacterial and antibiofilm properties. Additionally, in silico ADME prediction analyses of compounds 3c, 3d, and 3l revealed promising results, indicating the presence of drug-like properties.

Influence of Metal Cations on the Viscoelastic Properties of Escherichia coli Biofilms

Biofilms frequently cause complications in various areas of human life, e.g., in medicine and in the food industry. More recently, biofilms are discussed as new types of living materials with tunable mechanical properties. In particular, Escherichia coli produces a matrix composed of amyloid-forming curli and phosphoethanolamine-modified cellulose fibers in response to suboptimal environmental conditions. It is currently unknown how the interaction between these fibers contributes to the overall mechanical properties of the formed biofilms and if extrinsic control parameters can be utilized to manipulate these properties. Using shear rheology, we show that biofilms formed by the E. coli K-12 strain AR3110 stiffen by a factor of 2 when exposed to the trivalent metal cations Al(III) and Fe(III), while no such response is observed for the bivalent cations Zn(II) and Ca(II). Strains producing only one matrix component did not show any stiffening response to either cation or even a small softening. No stiffening response was further observed when strains producing only one type of fiber were co-cultured or simply mixed after biofilm growth. These results suggest that the E. coli biofilm matrix is a uniquely structured composite material when both matrix fibers are produced from the same bacterium. While the exact interaction mechanism between curli, phosphoethanolamine-modified cellulose, and trivalent metal cations is currently not known, our results highlight the potential of using extrinsic parameters to understand and control the interplay between biofilm structure and mechanical properties. This will ultimately aid in the development of better strategies for controlling biofilm growth.

CRISPR-Cas System: A Tool to Eliminate Drug-Resistant Gram-Negative Bacteria

Rapidly emerging drug-resistant superbugs, especially Gram-negative bacteria, pose a serious threat to healthcare systems all over the globe. Newer strategies are being developed to detect and overcome the arsenal of weapons that these bacteria possess. The development of antibiotics is time-consuming and may not provide full proof of action on evolving drug-resistant pathogens. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are promising in curbing drug-resistant bacteria. This review focuses on the pathogenesis of Gram-negative bacteria, emergence of antimicrobial drug resistance, and their treatment failures. It also draws attention to the present status of the CRISPR-Cas system in diagnosisand treatment of Gram-negative bacterial infections.

Antimicrobial Properties of Plant Fibers

Healthcare-associated infections (HAI), or nosocomial infections, are a global health and economic problem in developed and developing countries, particularly for immunocompromised patients in their intensive care units (ICUs) and surgical site hospital areas. Recurrent pathogens in HAIs prevail over antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa. For this reason, natural antibacterial mechanisms are a viable alternative for HAI treatment. Natural fibers can inhibit bacterial growth, which can be considered a great advantage in these applications. Moreover, these fibers have been reported to be biocompatible and biodegradable, essential features for biomedical materials to avoid complications due to infections and significant immune responses. Consequently, tissue engineering, medical textiles, orthopedics, and dental implants, as well as cosmetics, are fields currently expanding the use of plant fibers. In this review, we will discuss the source of natural fibers with antimicrobial properties, antimicrobial mechanisms, and their biomedical applications.

Formulation of Cinnamon (Cinnamomum verum) oil loaded solid lipid nanoparticles and evaluation of its antibacterial activity against Multi-drug Resistant Escherichia coli

Today, the increment in microbial resistance has guided the researches focus into new antimicrobial compounds or transmission systems. Escherichia coli (E. coli) is an opportunistic pathogen, producing a biofilm responsible for a wide range of nosocomial infections which are often difficult to eradicate with available antibiotics. On the other hand, Cinnamomum verum (cinnamon oil) (CO) is widely used as a natural antibacterial agent and Solid lipid nanoparticles (SLNs) are promising carriers for antibacterial compounds due to their lipophilic nature and ease of transmission through the bacterial cell wall. In this study, nanoparticles containing cinnamon oil (CO-SLN) were prepared by dual emulsion method and evaluated in terms of particle size, shape, entrapment efficiency (EE), transmission electron microscopy (TEM), oil release kinetics, and cell compatibility. The antibacterial activity of CO-SLN and CO against 10 drug-resistant E. coli strains was investigated. The anti-biofilm activity of CO-SLN on the selected pathogen was also investigated. Nanoparticles with an average size of 337.6 nm, and zeta potential of -26.6 mV were fabricated and their round shape was confirmed by TEM images. The antibacterial effects of CO-SLN and CO were reported with MIC Value of 60–75 µg/mL and 155–165 µg/mL and MBC value of 220–235 µg/ml and 540–560 µg/ml, respectively. On the other hand, CO-SLN with 1/2 MIC concentration had the greatest inhibition of biofilm formation in 24 h of incubation (55.25%). The data presented indicate that the MIC of CO-SLN has significantly reduced and it seems that SLN has facilitated and promoted CO transmission through the cell membrane.

The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA

In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.

Modular 3D-Printed Peg Biofilm Device for Flexible Setup of Surface-Related Biofilm Studies

Medical device-related biofilms are a major cause of hospital-acquired infections, especially chronic infections. Numerous diverse models to study surface-associated biofilms have been developed; however, their usability varies. Often, a simple method is desired without sacrificing throughput and biological relevance. Here, we present an in-house developed 3D-printed device (FlexiPeg) for biofilm growth, conceptually similar to the Calgary Biofilm device but aimed at increasing ease of use and versatility. Our device is modular with the lid and pegs as separate units, enabling flexible assembly with up- or down-scaling depending on the aims of the study. It also allows easy handling of individual pegs, especially when disruption of biofilm populations is needed for downstream analysis. The pegs can be printed in, or coated with, different materials to create surfaces relevant to the study of interest. We experimentally validated the use of the device by exploring the biofilms formed by clinical strains of Escherichia coli and Klebsiella pneumoniae, commonly associated with device-related infections. The biofilms were characterized by viable cell counts, biomass staining, and scanning electron microscopy (SEM) imaging. We evaluated the effects of different additive manufacturing technologies, 3D printing resins, and coatings with, for example, silicone, to mimic a medical device surface. The biofilms formed on our custom-made pegs could be clearly distinguished based on species or strain across all performed assays, and they corresponded well with observations made in other models and clinical settings, for example, on urinary catheters. Overall, our biofilm device is a robust, easy-to-use, and relevant assay, suitable for a wide range of applications in surface-associated biofilm studies, including materials testing, screening for biofilm formation capacity, and antibiotic susceptibility testing.

Temperature-Dependent Influence of FliA Overexpression on PHL628 E. coli Biofilm Growth and Composition

Biofilm growth and survival pose a problem in both medical and industrial fields. Bacteria in biofilms are more tolerant to antibiotic treatment due to the inability of antibiotics to permeate to the bottom layers of cells in a biofilm and the creation of altered microenvironments of bacteria deep within the biofilm. Despite the abundance of information we have about E. coli biofilm growth and maturation, we are still learning how manipulating different signaling pathways influences the formation and fitness of biofilm. Understanding the impact of signaling pathways on biofilm formation may narrow the search for novel small molecule inhibitors or activators that affect biofilm production and stability. Here, we study the influence of the minor sigma transcription factor FliA (RpoF, sigma-28), which controls late-stage flagellar assembly and chemotaxis, on biofilm production and composition at various temperatures in the E. coli strain PHL628, which abundantly produces the extracellular structural protein curli. We examined FliA's influence on external cellular structures like curli and flagella and the biomolecular composition of the biofilm's extracellular polymeric substance (EPS) using biochemical assays, immunoblotting, and confocal laser scanning microscopy (CLSM). At 37°C, FliA overexpression results in the dramatic growth of biofilm in polystyrene plates and more modest yet significant biofilm growth on silica slides. We observed no significant differences in curli concentration and carbohydrate concentration in the EPS with FliA overexpression. Still, we did see significant changes in the abundance of EPS protein using CLSM at higher growth temperatures. We also noticed increased flagellin concentration, a major structural protein in flagella, occurred with FliA overexpression, specifically in planktonic cultures. These experiments have aided in narrowing our focus to FliA's role in changing the protein composition of the EPS, which we will examine in future endeavors.

Questioning the source of identified non-foodborne pathogens from food-contact wooden surfaces used in Hong Kong's urban wet markets

In this study, a phylogenic analysis was performed on pathogens previously identified in Hong Kong wet markets' cutting boards. Phylogenetic comparisons were made between phylotypes obtained in this study and environmental and clinical phylotypes for establishing the possible origin of selected bacterial species isolated from wet market cutting board ecosystems. The results reveal a strong relationship between wet market bacterial assemblages and environmental and clinically relevant phylotypes. However, our poor knowledge of potential cross-contamination sources within these wet markets is further exacerbated by failing to determine the exact or presumed origin of its identified pathogens. In this study, several clinically relevant bacterial pathogens such as Klebsiella pneumoniae, Streptococcus suis and Streptococcus porcinus were linked to cutting boards associated with pork; Campylobacter fetus, Staphylococcus aureus, Escherichia coli, and A. caviae in those associated with poultry; and Streptococcus varanii, A. caviae, Vibrio fluvialis, and Vibrio parahaemolyticus in those associated with seafood. Identifying non-foodborne clinically relevant pathogens in wet market cutting boards in this study confirms the need for safety approaches for wet market meat, including cold storage. The presented study justifies the need for future systematic epidemiological studies to determine identified microbial pathogens. Such studies should bring about significant improvements in the management of hygienic practices in Hong Kong's wet markets and work towards a One Health goal by recognizing the importance of wet markets as areas interconnecting food processing with animal and clinical environments.

A Novel Device-Integrated Drug Delivery System for Local Inhibition of Urinary Tract Infection

Background: Catheter-associated urinary tract infection (CAUTI) is a frequent community-acquired infection and the most common nosocomial infection. Here, we developed a novel antimicrobial catheter concept that utilizes a silicone-based interpenetrating polymer network (IPN) as balloon material to facilitate a topical slow-release prophylaxis of antibacterial agents across the balloon to the urinary bladder.

Methods: The balloon material was achieved by modifying low shore hardness silicone tubes with a hydrogel interpenetrating polymer in supercritical CO₂ using the sequential method. Release properties and antibacterial efficacy of the IPN balloon treatment concept was investigated in vitro and in a porcine CAUTI model developed for the study. In the latter, Bactiguard Infection Protection (BIP) Foley catheters were also assessed to enable benchmark with the traditional antimicrobial coating principle.

Results: Uropathogenic Escherichia coli was undetectable in urinary bladders and on retrieved catheters in the IPN treatment group as compared to control that revealed significant bacteriuria (>10⁵ colony forming units/ml) as well as catheter-associated biofilm. The BIP catheters failed to prevent E. coli colonization of the bladder but significantly reduced catheter biofilm formation compared to the control.

Conclusion: The IPN-catheter concept provides a novel, promising delivery route for local treatment in the urinary tract.

Novel Plasmid-Borne Fimbriae-Associated Gene Cluster Participates in Biofilm Formation in Escherichia coli

This study reported the involvement of a gene cluster from a conjugative plasmid in the biofilm formation of Escherichia coli. We used a novel EZ-Tn5 transposon technique to generate a transposon library and used arbitrarily primed PCR to detect the insertion sites in biofilm formation-deficient mutants. To validate the function of candidate biofilm formation genes, the genes were cloned into plasmid pBluescript II SK (+) and transformed into E. coil DH5α. Biofilm production from the transformants was then assessed by phenotypic biofilm formation using Crystal Violet staining and microscopy. A total of 3,000 transposon mutants of E. coli DH5α-p253 were screened, of which 28 were found to be deficient in biofilm formation. Further characterization revealed that 24/28 mutations were detected with their insertions in chromosome, while the remaining 4 mutations were evidenced that the functional genes for biofilm formation were harbored in the plasmid. Interestingly, the plasmid sequencing showed that these four transposon mutations were all inserted into a fimbriae-associated gene cluster (fim-cluster). This fim-cluster is a hybrid segment spanning a 7,949 bp sequence, with a terminal inverted repeat sequence and two coding regions. In summary, we performed a high-efficiency screening to a library constructed with the EZ-Tn5-based transposon approach and identified the gene clusters responsible for the biofilm production of E. coli, especially the genes harbored in the plasmid. Further studies are needed to understand the spread of this novel plasmid-mediated biofilm formation gene in clinical E. coli isolates and the clinical impacts.

Tuning surface topographies on biomaterials to control bacterial infection

Microbial contamination and subsequent formation of biofilms frequently cause failure of surgical implants and a good understanding of the bacteria-surface interactions is vital to the design and safety of biomaterials. In this review, the physical and chemical factors that are involved in the various stages of implant-associated bacterial infection are described. In particular, topographical modification strategies that have been employed to mitigate bacterial adhesion via topographical mechanisms are summarized and discussed comprehensively. Recent advances have improved our understanding about bacteria-surface interactions and have enabled biomedical engineers and researchers to develop better and more effective antibacterial surfaces. The related interdisciplinary efforts are expected to continue in the quest for next-generation medical devices to attain the ultimate goal of improved clinical outcomes and reduced number of revision surgeries.

Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation

Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.

Biofilm-Producing Bacteria and Risk Factors (Gender and Duration of Catheterization) Characterized as Catheter-Associated Biofilm Formation

Background

A catheter-associated urinary tract infection (CA-UTI) is preceded by biofilm formation, which is related to several risk factors such as gender, age, diabetic status, duration of catheterization, bacteriuria before catheterization, virulence gene factor, and antibiotic usage.

Aims

This study aims to identify the microbial composition of catheter samples, including its corresponding comparison with urine samples, to determine the most important risk factors of biofilm formation and characterize the virulence gene factors that correlate with biofilm formation.

Methods

A longitudinal cross-sectional study was conducted on 109 catheterized patients from September 2017 to January 2018. The risk factors were obtained from the patients' medical records. All catheter and urine samples were cultured after removal, followed by biomass quantification. Isolate identification and antimicrobial susceptibility testing were performed using the Vitex2 system. Biofilm-producing bacteria were identified by the Congo Red Agar (CRA) method. A PCR test characterized the virulence genes of dominant bacteria (E. coli). All data were collected and processed for statistical analysis.

Results

Out of 109 catheterized patients, 78% of the catheters were culture positive, which was higher than those of the urine samples (37.62%). The most common species isolated from the catheter cultures were Escherichia coli (28.1%), Candida sp. (17.8%), Klebsiella pneumoniae (15.9%), and Enterococcus faecalis (13.1%). E. coli (83.3%) and E. faecalis (78.6%) were the main isolates with a positive CRA. A statistical analysis showed that gender and duration prior to catheterization were associated with an increased risk of biofilm formation (p < 0.05).

Conclusion

E. coli and E. faecalis were the most common biofilm-producing bacteria isolated from the urinary catheter. Gender and duration are two risk factors associated with biofilm formation, therefore determining the risk of CAUTI. The presence of PapC as a virulence gene encoding pili correlates with the biofilm formation. Biofilm-producing bacteria, female gender, duration of catheterization (more than five days), and PapC gene presence have strong correlation with the biofilm formation. To prevent CAUTI, patients with risk factors should be monitored by urinalysis tests to detect earlier the risk of biofilm formation.

Phenotypic and Genetic Determination of Biofilm Formation in Heat Resistant Escherichia coli Possessing the Locus of Heat Resistance

Despite the effectiveness of thermal inactivation processes, Escherichiacoli biofilms continue to be a persistent source of contamination in food processing environments. E. coli strains possessing the locus of heat resistance are a novel food safety threat and raises the question of whether these strains can also form biofilms. The objectives of this study were to determine biofilm formation in heat resistant E. coli isolates from clinical and environmental origins using an in-house, two-component apparatus and to characterize biofilm formation-associated genes in the isolates using whole genome sequencing. Optimal conditions for biofilm formation in each of the heat resistant isolates were determined by manipulating inoculum size, nutrient concentration, and temperature conditions. Biofilm formation in the heat resistant isolates was detected at temperatures of 24 °C and 37 °C but not at 4 °C. Furthermore, biofilm formation was observed in all environmental isolates but only one clinical isolate despite shared profiles in biofilm formation-associated genes encoded by the isolates from both sources. The circulation of heat resistant E. coli isolates with multi-stress tolerance capabilities in environments related to food processing signify that such strains may be a serious food safety and public health risk.

Adhesion of Escherichia Coli to Nanostructured Surfaces and the Role of Type 1 Fimbriae

Bacterial fimbriae are an important virulence factor mediating adhesion to both biotic and abiotic surfaces and facilitating biofilm formation. The expression of type 1 fimbriae of Escherichia coli is a key virulence factor for urinary tract infections and catheter-associated urinary tract infections, which represent the most common nosocomial infections. New strategies to reduce adhesion of bacteria to surfaces is therefore warranted. The aim of the present study was to investigate how surfaces with different nanotopography-influenced fimbriae-mediated adhesion. Surfaces with three different nanopattern surface coverages made in polycarbonate were fabricated by injection molding from electron beam lithography nanopatterned templates. The surfaces were constructed with features of approximately 40 nm width and 25 nm height with 100 nm, 250 nm, and 500 nm interspace distance, respectively. The role of fimbriae type 1-mediated adhesion was investigated using the E. coli wild type BW25113 and ΔfimA (with a knockout of major pilus protein FimA) and ΔfimH (with a knockout of minor protein FimH) mutants. For the surfaces with nanotopography, all strains adhered least to areas with the largest interpillar distance (500 nm). For the E. coli wild type, no difference in adhesion between surfaces without pillars and the largest interpillar distance was observed. For the deletion mutants, increased adhesion was observed for surfaces without pillars compared to surfaces with the largest interpillar distance. The presence of a fully functional type 1 fimbria decreased the bacterial adhesion to the nanopatterned surfaces in comparison to the mutants.

Chemotaxis and cyclic-di-GMP signalling control surface attachment of Escherichia coli

Attachment to surfaces is an important early step during bacterial infection and during formation of submerged biofilms. Although flagella-mediated motility is known to be important for attachment of Escherichia coli and other bacteria, implications of motility regulation by cellular signalling remain to be understood. Here, we show that motility largely promotes attachment of E. coli, including that mediated by type 1 fimbriae, by allowing cells to reach, get hydrodynamically trapped at and explore the surface. Inactivation or inhibition of the chemotaxis signalling pathway improves attachment by suppressing cell reorientations and thereby increasing surface residence times. The attachment is further enhanced by deletion of genes encoding the cyclic diguanosine monophosphate (c-di-GMP)-dependent flagellar brake YcgR or the diguanylate cyclase DgcE. Such increased attachment in absence of c-di-GMP signalling is in contrast to its commonly accepted function as a positive regulator of the sessile state. It is apparently due to the increased swimming speed of E. coli in absence of YcgR-mediated motor control, which strengthens adhesion mediated by the type 1 fimbriae. Thus, both signalling networks that regulate motility of E. coli also control its engagement with both biotic and abiotic surfaces, which has likely implications for infection and biofilm formation.

Genome rearrangements induce biofilm formation in Escherichia coli C - an old model organism with a new application in biofilm research

BACKGROUND

Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced.

RESULTS

Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for lipopolysaccharide (LPS) synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the - 35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene. And finally, E. coli C encodes an additional sigma70 subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway in E. coli.

CONCLUSIONS

Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.

Risk Factors Analysis for Catheter-Associated Urinary Tract Infection in Medan, Indonesia

BACKGROUND

Catheter-associated urinary tract infection (CAUTI) is one of the most common infections in health care caused by several risk factors.

AIM

This study aims at analysing the risky factors triggering CAUTI.

METHODS

This research was designed by applying prospective study. It was conducted from July to November 2018 by involving 82 patients attached to the catheter and treated in the General Hospital of Medan as the sample. The study instrument used observational sheets by measuring the occurrence of urinary tract infection using urine culture analysis ≥ 105 CFU/ml.

RESULTS

The results showed that there was a relationship (p < 0.05) amongs age (p = 0.01; RR = 0.51), diabetes mellitus (p = 0.00; RR = 7.61), duration of catheterization (p = 0.00; RR = 0.01), indications for catheter use (p = 0.00; RR = 0.34) with CAUTI, and there were not significant relationship (p > 0.05) amongs genre (p = 0.06; RR = 1.72), drainage system (p = 0.43; RR = 0.43) and catheter care (p = 0.08; RR = 0.50) with CAUTI. Diabetes mellitus (p = 0.00; OR = 8.92 95% CI = 1.02-11.83) and duration of catheterization (p = 0, 00; OR = 32.84 95% CI = 3.81-322.74) were the most significant factor related to CAUTI.

CONCLUSION

CAUTI is influenced by various factors, and it can be controlled by understanding those factors so that the right interventions to prevent the infections can be taken and the quality of nursing care can be increased as well.

Disperse red 15 (DR15) impedes biofilm formation of uropathogenic Escherichia coli

Catheter associated urinary tract infection (CAUTI) is a highly prevalent hospital-acquired infection that is predominantly caused by uropathogenic Escherichia coli (UPEC). It adheres on catheter surface using type I pili as the initial step of pathogenesis that progresses to form biofilm. In this study, potential inhibitors against FimH adhesin of type I pili were screened computationally that yielded ten compounds. These were further validated in vitro against adhesion and biofilm formation. The compounds, 1-Amino-4-hydroxyanthraquinone (Disperse Red 15 or DR15) and 4-(4'-chloro-4-biphenylylsulfonylamino) benzoic acid (CB1) impaired adhesion and biofilm formation without inhibiting the planktonic growth. Also, both compounds inhibited cell assemblages like autoaggregation and swarming motility by unknown mechanisms. DR15 was further derivatised into N-(4-hydroxy-9,10-dioxo-9,10-dihydroanthracen-1-yl) undec-10-enamide that self-assembled with linseed oil, which was used as the coating material on urinary Foley catheters. The thin-film coating on the catheter did not leach when incubated in artificial urine and effectively restricted biofilm formation of UPEC. Altogether, the thin-film coating of urinary catheter with DR15 inhibited biofilm formation of UPEC and this application could potentially help to reduce CAUTI incidents in healthcare facilities.

Biofilm formation by multidrug resistant Enterobacteriaceae strains isolated from solid organ transplant recipients

Solid organ transplant (SOT) recipients are especially at risk of developing infections by multidrug resistant bacteria (MDR). In this study, the biofilm-forming capability of 209 MDR strains (Escherichia coli n = 106, Klebsiella pneumoniae n = 78, and Enterobacter spp. n = 25) isolated from rectal swabs in the first 48 hours before or after kidney (93 patients), liver (60 patients) or kidney/pancreas transplants (5 patients) were evaluated by using a microplate assay. Thirty-nine strains were isolated before transplant and 170 strains were isolated post-transplant. Overall, 16% of E. coli strains, 73% of K. pneumoniae strains and 4% Enterobacter strains showed moderate or strong biofilm production. Nine strains isolated from infection sites after transplantation were responsible of infections in the first month. Of these, 4 K. pneumoniae, 1 E. coli and 1 Enterobacter spp. strains isolated pre-transplant or post-transplant as colonizers caused infections in the post-transplant period. Our results suggest that in vitro biofilm formation could be an important factor for adhesion to intestine and colonization in MDR K. pneumoniae strains in SOT recipients, but this factor appears to be less important for MDR E. coli and Enterobacter spp.

The association of surface adhesin genes and the biofilm formation among Klebsiella oxytoca clinical isolates

Bacterial adhesins mediate the attachment and biofilm production leading to the persistence of colonized strains. The aim of this study was evaluation of the association of surface adhesin genes with the biofilm formation among Klebsiella oxytoca isolates. Among 50 isolates of K. oxytoca from patients with antibiotic-associated diarrhoea, the susceptibility test, MIC (according to CLSI 2016) and phenotypic biofilm formation (with microtitre tissue-plate assay) were performed. The presence of adhesins was investigated using PCR. Thirty-three (66%) isolates produced moderate-level biofilms, but none of them exhibited strong biofilm formation. The presence of adhesins was as follows: fimA, 60% (n = 30), mrkA, 42% (n = 21), matB, 96% (n = 48) and pilQ, 92% (n = 46). The biofilm formation was related to the presence of fimA (odds ratio (OR) 0.8571, 95% CI 1.733–6.267, p <0.0001), mrkA (OR 0.2462, 95% CI 2.723–4.622, p 0.001), matB (OR 0.4521, 95% CI 1.353–5.332, p 0.008) and pilQ (OR 0.1481, 95% CI 1.691–6.117, p <0.0001). The npsB toxin-encoding gene was detected among 46 (92%) isolates. Resistance to non-β-lactam antibiotics was significantly associated with the presence of adhesin-encoding genes. The presence of adhesins and the capsular encoding gene was significantly associated with biofilm formation among K. oxytoca isolates. The presence of surface adhesin-encoding genes was significantly associated with the biofilm formation and also with resistance to non-β-lactam antibiotics among K. oxytoca clinical isolates. In addition, biofilm production was not significantly associated with β-lactam resistance among the isolates.

Nanoscience-Based Strategies to Engineer Antimicrobial Surfaces

Microbial contamination and biofilm formation of medical devices is a major issue associated with medical complications and increased costs. Consequently, there is a growing need for novel strategies and exploitation of nanoscience-based technologies to reduce the interaction of bacteria and microbes with synthetic surfaces. This article focuses on surfaces that are nanostructured, have functional coatings, and generate or release antimicrobial compounds, including "smart surfaces" producing antibiotics on demand. Key requirements for successful antimicrobial surfaces including biocompatibility, mechanical stability, durability, and efficiency are discussed and illustrated with examples of the recent literature. Various nanoscience-based technologies are described along with new concepts, their advantages, and remaining open questions. Although at an early stage of research, nanoscience-based strategies for creating antimicrobial surfaces have the advantage of acting at the molecular level, potentially making them more efficient under specific conditions. Moreover, the interface can be fine tuned and specific interactions that depend on the location of the device can be addressed. Finally, remaining important challenges are identified: improvement of the efficacy for long-term use, extension of the application range to a large spectrum of bacteria, standardized evaluation assays, and combination of passive and active approaches in a single surface to produce multifunctional surfaces.

Activation of the NLRP3 Inflammasome Pathway by Uropathogenic Escherichia coli Is Virulence Factor-Dependent and Influences Colonization of Bladder Epithelial Cells

The NLRP3 inflammasome and IL-1β release have recently been suggested to be important for the progression of urinary tract infection (UTI). However, much is still unknown regarding the interaction of UPEC and the NLRP3 inflammasome. The purpose of this study was to elucidate what virulence factors uropathogenic Escherichia coli (UPEC) use to modulate NLRP3 inflammasome activation and subsequent IL-1β release and the role of NLRP3 for UPEC colonization of bladder epithelial cells. The bladder epithelial cell line 5637, CRISPR/Cas9 generated NLRP3, caspase-1 and mesotrypsin deficient cell lines and transformed primary bladder epithelial cells (HBLAK) were stimulated with UPEC isolates and the non-pathogenic MG1655 strain. We found that the UPEC strain CFT073, but not MG1655, induced an increased caspase-1 activity and IL-1β release from bladder epithelial cells. The increase was shown to be mediated by α-hemolysin activation of the NLRP3 inflammasome in an NF-κB-independent manner. The effect of α-hemolysin on IL-1β release was biphasic, initially suppressive, later inductive. Furthermore, the phase-locked type-1-fimbrial ON variant of CFT073 inhibited caspase-1 activation and IL-1β release. In addition, the ability of CFT073 to adhere to and invade NLRP3 deficient cells was significantly reduced compare to wild-type cells. The reduced colonization of NLRP3-deficient cells was type-1 fimbriae dependent. In conclusion, we found that the NLRP3 inflammasome was important for type-1 fimbriae-dependent colonization of bladder epithelial cells and that both type-1 fimbriae and α-hemolysin can modulate the activity of the NLRP3 inflammasome.

Role of nutrient limitation in the competition between uropathogenic strains of Klebsiella pneumoniae and Escherichia coli in mixed biofilms

Klebsiella pneumoniae and Escherichia coli form mixed species biofilms in catheter-associated urinary tract infections. Recently, a detrimental effect of K. pneumoniae over E. coli was observed in mixed species biofilms grown in an artificial urine medium. The mechanism behind this competitive interaction was studied. K. pneumoniae partially outcompeted E. coli in early-stage batch-fed biofilms, whereas both microorganisms co-exist at longer times (K. pneumoniae:E. coli ratio, 55:1), as shown by cell counts and confocal microscopy. E. coli cells were scattered along the K. pneumoniae biofilm. Biofilm supernatants did not appear to contain either antimicrobial or anti-biofilm activities against E. coli. Biofilms grown under continuous flow prevented interspecies competition. K. pneumoniae showed both increased siderophore production and better growth in iron-limited media compared to E. coli. In summary, these results indicate the importance of nutrient (particularly iron) competition in the modulation of the bacterial composition of mixed species biofilms formed by uropathogenic K. pneumoniae and E. coli.

A Method for Quantification of Epithelium Colonization Capacity by Pathogenic Bacteria

Most bacterial infections initiate at the mucosal epithelium lining the gastrointestinal, respiratory, and urogenital tracts. At these sites, bacterial pathogens must adhere and increase in numbers to effectively breach the outer barrier and invade the host. If the bacterium succeeds in reaching the bloodstream, effective dissemination again requires that bacteria in the blood, reestablish contact to distant endothelium sites and form secondary site foci. The infectious potential of bacteria is therefore closely linked to their ability to adhere to, colonize, and invade epithelial and endothelial surfaces. Measurement of bacterial adhesion to epithelial cells is therefore standard procedure in studies of bacterial virulence. Traditionally, such measurements have been conducted with microtiter plate cell cultures to which bacteria are added, followed by washing procedures and final quantification of retained bacteria by agar plating. This approach is fast and straightforward, but yields only a rough estimate of the adhesive properties of the bacteria upon contact, and little information on the ability of the bacterium to colonize these surfaces under relevant physiological conditions. Here, we present a method in which epithelia/endothelia are simulated by flow chamber-grown human cell layers, and infection is induced by seeding of pathogenic bacteria on these surfaces under conditions that simulate the physiological microenvironment. Quantification of bacterial adhesion and colonization of the cell layers is then performed by in situ time-lapse fluorescence microscopy and automatic detection of bacterial surface coverage. The method is demonstrated in three different infection models, simulating Staphylococcus aureus endothelial infection and Escherichia coli intestinal- and uroepithelial infection. The approach yields valuable information on the fitness of the bacterium to successfully adhere to and colonize epithelial surfaces and can be used to evaluate the influence of specific virulence genes, growth conditions, and antimicrobial treatment on this process.

CRISPR Interference (CRISPRi) Inhibition of luxS Gene Expression in E. coli: An Approach to Inhibit Biofilm

Biofilm is a sessile bacterial accretion embedded in self-producing matrix. It is the root cause of about 80% microbial infections in human. Among them, E. coli biofilms are most prevalent in medical devices associated nosocomial infections. The objective of this study was to inhibit biofilm formation by targeting gene involved in quorum sensing, one of the main mechanisms of biofilm formation. Hence we have introduced the CRISPRi, first time to target luxS gene. luxS is a synthase, involved in the synthesis of Autoinducer-2(AI-2), which in turn guides the initial stage of biofilm formation. To implement CRISPRi system for luxS gene suppression, we have synthesized complementary sgRNA to target gene sequence and co-expressed with dCas9, a mutated form of an endonuclease. Suppression of luxS expression was confirmed through qRT-PCR. The effect of luxS gene on biofilm inhibition was studied through crystal violet assay, XTT reduction assay and scanning electron microscopy. We conclude that CRISPRi system could be a potential strategy to inhibit bacterial biofilm through mechanism base approach.

CRISPR-based genome editing of clinically important Escherichia coli SE15 isolated from indwelling urinary catheters of patients

Urinary tract infections (UTIs) are clinically important problems that lead to serious morbidity and mortality, and indwelling urinary catheters are a major factor of UTIs. In this study, we applied clustered regularly interspaced short palindromic repeats (CRISPR) genome editing to generate ΔluxS mutant strains from clinical isolates of Escherichiacoli SE15, which is one of major pathogens and can cause colonization and biofilm formation in the catheter. A major regulatory pathway of such biofilm formation on medical devices is the quorum sensing mechanism via small molecule autoinducer-2 synthesized by LuxS enzyme. Here, we used the CRISPR-Cas9 system for precise deletion of luxS gene in clinical isolate E. coli SE15. To this end, we constructed a donor DNA for homologous recombination to delete 93 bases in the chromosomal target (luxS) and observed the success rate of luxS deletion to be 22.7 %. We conducted biofilm assay to observe decreased biofilm formation in the E. coil SE15 ΔluxS mutants compared to wild-type E. coil SE15. Quantitative real-time PCR analysis of E. coil SE15 ΔluxS mutants showed that the expression of luxS was below detection level. We also observed that the relative mRNA levels of biofilm-formation-related genes, such as mqsR, pgaBC and csgEF, were significantly decreased in E. coil SE15 ΔluxS mutants compared to wild-type. We conclude that genome editing by CRISPR-Cas9 system is an effective tool to dissect the molecular mechanism of biofilm formation in medically important strains, and the study may serve as a basis for developing novel medical intervention against UTIs caused by biofilm.

DamX Controls Reversible Cell Morphology Switching in Uropathogenic Escherichia coli

The ability to change cell morphology is an advantageous characteristic adopted by multiple pathogenic bacteria in order to evade host immune detection and assault during infection. Uropathogenic Escherichia coli (UPEC) exhibits such cellular dynamics and has been shown to transition through a series of distinct morphological phenotypes during a urinary tract infection. Here, we report the first systematic spatio-temporal gene expression analysis of the UPEC transition through these phenotypes by using a flow chamber-based in vitro infection model that simulates conditions in the bladder. This analysis revealed a novel association between the cell division gene damX and reversible UPEC filamentation. We demonstrate a lack of reversible bacterial filamentation in a damX deletion mutant in vitro and absence of a filamentous response by this mutant in a murine model of cystitis. While deletion of damX abrogated UPEC filamentation and secondary surface colonization in tissue culture and in mouse infections, transient overexpression of damX resulted in reversible UPEC filamentation. In this study, we identify a hitherto-unknown damX-mediated mechanism underlying UPEC morphotypical switching. Murine infection studies showed that DamX is essential for establishment of a robust urinary tract infection, thus emphasizing its role as a mediator of virulence. Our study demonstrates the value of an in vitro methodology, in which uroepithelium infection is closely simulated, when undertaking targeted investigations that are challenging to perform in animal infection models.

IMPORTANCE

Urinary tract infections (UTIs) are most often caused by uropathogenic Escherichia coli (UPEC) and account for a considerable health care burden. UPEC exhibits a dynamic lifestyle in the course of infection, in which the bacterium transiently adopts alternative morphologies ranging from rod shaped to coccoid and filamentous, rendering it better at immune evasion and host epithelium adhesion. This penchant for morphotype switching might in large measure account for UPEC's success as a pathogen. In aiming to uncover genes underlying the phenomenon of UPEC morphotype switching, this study identifies damX, a cell division gene, as a mediator of reversible filamentation during UTI. DamX-mediated filamentation represents an additional pathway for bacterial cell shape control, an alternative to SulA-mediated FtsZ sequestration during E. coli uropathogenesis, and hence represents a potential target for combating UTI.

The global regulatory effect of Edwardsiella tarda Fur on iron acquisition, stress resistance, and host infection: A proteomics-based interpretation

Ferric uptake regulator (Fur) is an important transcriptional regulator of Gram-negative bacteria. Edwardsiella tarda is a severe fish bacterial pathogen with a broad host range that includes humans. In this study, we examined the regulatory function of Fur in E. tarda via a proteomic approach. Compared to the wild type TX01, the fur mutant TX01Δfur exhibited (i) retarded growth, (ii) enhanced siderophore production, (iii) increased acid tolerance, which is in contrast to observations in other bacterial species, (iv) decreased survival against oxidative stress and host serum, (v) impaired ability to inhibit host immune response, (vi) attenuated tissue infectivity and overall virulence. The deficiency of TX01Δfur was rescued by introduction of an exogenous fur gene. iTRAQ-based comparative proteomic analysis of TX01Δfur and TX01 identified 89 differentially expressed proteins that cover a wide range of functional categories including those affected by fur mutation. In addition, 16 proteins were identified for the first time to be regulated by Fur in Gram-negative bacteria. These results provide the first protein-based interpretation of the global impact of Fur on the physiology and infectivity of E. tarda.

SIGNIFICANCE

This study demonstrates that in E. tarda, Fur controls multiple aspects of bacterial life, including growth, metabolism, iron acquisition, stress response, and host infection. In line with these observations, proteomics analysis identified a large amount of proteins affected in expression by Fur, which are involved in bacterial physiology and infectivity. Hence, these results link for the first time the pleiotropic effect of Fur with global protein expression and shed new light on the function and regulatory mechanism of Fur in pathogenic bacteria.

Escherichia coli biofilm: development and therapeutic strategies

Escherichia coli biofilm consists of a bacterial colony embedded in a matrix of extracellular polymeric substances (EPS) which protects the microbes from adverse environmental conditions and results in infection. Besides being the major causative agent for recurrent urinary tract infections, E. coli biofilm is also responsible for indwelling medical device-related infectivity. The cell-to-cell communication within the biofilm occurs due to quorum sensors that can modulate the key biochemical players enabling the bacteria to proliferate and intensify the resultant infections. The diversity in structural components of biofilm gets compounded due to the development of antibiotic resistance, hampering its eradication. Conventionally used antimicrobial agents have a restricted range of cellular targets and limited efficacy on biofilms. This emphasizes the need to explore the alternate therapeuticals like anti-adhesion compounds, phytochemicals, nanomaterials for effective drug delivery to restrict the growth of biofilm. The current review focuses on various aspects of E. coli biofilm development and the possible therapeutic approaches for prevention and treatment of biofilm-related infections.

Strengths and Limitations of Model Systems for the Study of Urinary Tract Infections and Related Pathologies

Urinary tract infections (UTIs) are some of the most common bacterial infections worldwide and are a source of substantial morbidity among otherwise healthy women. UTIs can be caused by a variety of microbes, but the predominant etiologic agent of these infections is uropathogenic Escherichia coli (UPEC). An especially troubling feature of UPEC-associated UTIs is their high rate of recurrence. This problem is compounded by the drastic increase in the global incidence of antibiotic-resistant UPEC strains over the past 15 years. The need for more-effective treatments for UTIs is driving research aimed at bettering our understanding of the virulence mechanisms and host-pathogen interactions that occur during the course of these infections. Surrogate models of human infection, including cell culture systems and the use of murine, porcine, avian, teleost (zebrafish), and nematode hosts, are being employed to define host and bacterial factors that modulate the pathogenesis of UTIs. These model systems are revealing how UPEC strains can avoid or overcome host defenses and acquire scarce nutrients while also providing insight into the virulence mechanisms used by UPEC within compromised individuals, such as catheterized patients. Here, we summarize our current understanding of UTI pathogenesis while also giving an overview of the model systems used to study the initiation, persistence, and recurrence of UTIs and life-threatening sequelae like urosepsis. Although we focus on UPEC, the experimental systems described here can also provide valuable insight into the disease processes associated with other bacterial pathogens both within the urinary tract and elsewhere within the host.

Uropathogenic Escherichia coli Express Type 1 Fimbriae Only in Surface Adherent Populations Under Physiological Growth Conditions

BACKGROUND

Most uropathogenic Escherichia coli (UPEC) strains harbor genes encoding adhesive type 1 fimbria (T1F). T1F is a key factor for successful establishment of urinary tract infection. However, UPEC strains typically do not express T1F in the bladder urine, and little is understood about its induction in vivo.

METHODS

A flow chamber infection model was used to grow UPEC under conditions simulating distinct infection niches in the bladder. Type 1 fimbriation on isolated UPEC was subsequently determined by yeast cell agglutination and immunofluorescence microscopy, and the results were correlated with the ability to adhere to and invade cultured human bladder cells.

RESULTS

Although inactive during planktonic growth in urine, T1F expression occurs when UPEC settles on and infects bladder epithelial cells or colonizes catheters. As a result, UPEC in these sessile populations enhances bladder cell adhesion and invasion potential. Only T1F-negative UPEC are subsequently released to the urine, thus limiting T1F expression to surface-associated UPEC alone.

CONCLUSIONS

Our results demonstrate that T1F expression is strictly regulated under physiological growth conditions with increased expression during surface growth adaptation and infection of uroepithelial cells. This leads to separation of UPEC into low-expression planktonic populations and high-expression sessile populations.

Presence of Virulence-Associated Genes and Ability to Form Biofilm among Clinical Isolates of Escherichia coli Causing Urinary Infection in Domestic Animals

Background:

Urinary tract infection caused by Escherichia coli is a frequently observed condition both in humans and animals. Uropathogenic E. coli (UPEC) has been shown to have a pathogenicity island that enables them to infect the urinary tract. Because there is little information about the presence of UPEC-associated virulent genes in animal isolates this work was carried out with the intent to enhance the understanding about the strains of E.coli that cause infections in animals.

Results:

We screened 21 E. coli strains isolated causing urinary tract infection in domestic animals. Primers were designed to amplify urinary infection-associated genes. Nine genes, papA, tcpC, fyuA, tpbA, Lma, hylA, picU, tonB, and flicC were then amplified and sequenced. Different from the human isolate CFT073, all the animals E. coli lack some of the pathogenesis-associated genes. Genes encoding for proteins used to scavenge iron appear not to be so necessary during animal infections as they are in human infection. In further investigation of phenotypic properties, it was observed that animal UPECs have significantly more impaired ability to form biofilms than human UPEC strain.

Conclusions:

This study identified significant differences between human and animal UPECs. This may have its roots in the fact that it is difficult to determine if an animal has symptoms. Future studies will focus on some of the observations.

Relationship of biofilm formation and different virulence genes in uropathogenic Escherichia coli isolates from Northwest Iran

Background and objectives: The Escherichia coli (E. coli) bacterium is one of the main causative agents of urinary tract infections (UTI) worldwide. The ability of this bacterium to form biofilms on medical devices such as catheters plays an important role in the development of UTI. The aim of the present study was to investigate the possible relationship between virulence factors and biofilm formation of E. coli isolates responsible for urinary tract infection.

Materials and methods: A total of 100 E. coli isolates isolated from patients with UTI were collected and characterized by routine bacteriological methods. In vitro biofilm formation by these isolates was determined using the 96-well microtiter-plate test, and the presence of fimA, papC, and hly virulence genes was examined by PCR assay. Data analysis was performed using SPSS 16.0 software.

Results: From 100 E. coli isolates isolated from UTIs, 92% were shown to be biofilm positive. The genes papC, fimA, and hly were detected in 43%, 94% and 26% of isolates, respectively. Biofilm formation in isolates that expressed papC, fimA, and hly genes was 100%, 93%, and 100%, respectively. A significant relationship was found between presence of the papC gene and biofilm formation in E. coli isolates isolated from UTI (P<0.01), but there was no statistically significant correlation between presence of fimA and hly genes with biofilm formation (P<0.072, P<0.104).

Conclusion: Results showed that fimA and hly genes do not seem to be necessary or sufficient for the production of biofilm in E. coli, but the presence of papC correlates with increased biofilm formation of urinary tract isolates. Overall, the presence of fimA, papC, and hly virulence genes coincides with in vitro biofilm formation in uropathogenic E. coli isolates.

In vitro Dynamic Model of a Catheterized Bladder and Biofilm Assay

Biofilm formation on catheters is thought to contribute to persistence of catheter-associated urinary tract infections (CAUTI) which represent the most frequent nosocomial infections. Understanding of factors relevant for CAUTI pathogenesis and evaluation of new therapeutics or interference strategies requires a model system that mirrors the physico-chemical conditions prevailing in a catheterized human bladder. The described in vitro dynamic model of a catheterized bladder enables to emulate many of the characteristics of a catheterized human bladder albeit in the absence of a bladder epithelium. A minor modification compared to the original model system (Stickler, et al., 1999) allows temperature maintenance of the top 10 cm of the catheter, thereby enabling reproducible monitoring of biofilm formation on the internal catheter surface.

Nosocomial urinary tract infections: A review

Nosocomial urinary tract infections are a common complication in healthcare systems worldwide. A review of the literature was performed in June 2014 using the Medical Literature Analysis and Retrieval System Online (MEDLINE) database, through either PubMed or Ovid as a search engine, to identify publications regarding nosocomial urinary tract infections (NUTIs) definition, epidemiology, etiology and treatment.According to current definitions, more than 30% of nosocomial infections are urinary tract infections (UTIs). A UTI is defined 'nosocomial' (NUTI) when it is acquired in any healthcare institution or, more generally, when it is related to patient management. The origin of nosocomial bacteria is endogenous (the patient's flora) in two thirds of the cases. Patients with indwelling urinary catheters, those undergoing urological surgery and manipulations, long-stay elderly male patients and patients with debilitating diseases are at high risk of developing NUTIs. All bacterial NUTIs should be treated, whether the patient is harboring a urinary catheter or not. The length of treatment depends on the infection site. There is abundance of important guidance which should be considered to reduce the risk of NUTIs (hand disinfection with instant hand sanitizer, wearing non-sterile gloves permanently, isolation of infected or colonized catheterized patients). Patients with asymptomatic bacteriuria can generally be treated initially with catheter removal or catheter exchange, and do not necessarily need antimicrobial therapy. Symptomatic patients should receive antibiotic therapy. Resistance of urinary pathogens to common antibiotics is currently a topic of concern.