Role of Capsular Polysaccharides in Biofilm Formation: An AFM Nanomechanics Study

Co-existence of antibiotic resistance and virulence factors in carbapenem resistant Klebsiella pneumoniae clinical isolates from Alexandria, Egypt

BACKGROUND

The emergence and spread of carbapenem resistance among Enterobacteriaceae, particularly Klebsiella pneumoniae, constitute a serious threat to public health, since carbapenems are the last line of defense in the treatment of life-threatening infections caused by drug-resistant Enterobacteriaceae. The current study investigated the co-existence of different virulence factors and carbapenemases in carbapenem-resistant Klebsiella pneumoniae clinical isolates from Alexandria, Egypt.

RESULTS

Phenotypic characterization of virulence factors indicated that 41.5% of the isolates were strong biofilm producers, while hypermucoviscosity was detected in 14.9% of the isolates. All isolates harbored five or more virulence factor encoding genes. entB, ycfM, mrkD and fimH were detected in all isolates, while only one isolate was negative for ybtS. uge, iutA, rmpA and kpn were detected in 61 (64.8%), 55 (58.5%), 41 (43.6%) and 27 (28.7%) isolates, respectively, while all isolates lacked magA and k2A. Phenotypic detection of carbapenemases was explored by performing CarbaNP and mCIM/eCIM. CarbaNP test showed positive results in 98.9% of the isolates and positive mCIM tests were observed in all isolates, while 68 (72.3%) isolates showed positive eCIM tests. blaNDM was the most prevalent carbapenemase encoding gene (92.5%) followed by the blaOXA-48 (51.1%), while blaKPC was detected in only one (1.06%) isolate. blaVIM, blaIMP and blaGES were not detected in any of the tested isolates.

CONCLUSIONS

The widespread of carbapenem-resistant Klebsiella pneumoniae represents a major problem in health care settings. A significant association between certain virulence factors and carbapenemase-encoding genes was observed. Antibiotic stewardship programs and infection control policies should be effectively implemented especially in hospitals to limit the spread of such highly virulent pathogens.

capD deletion in the Elizabethkingia miricola capsular locus leads to capsule production deficiency and reduced virulence

Elizabethkingia miricola is a multidrug-resistant pathogen that can cause life-threatening infections in immunocompromised humans and outbreaks in amphibians. However, the specific virulence factors of this microorganism have not been described. In this study, we identified the polysaccharide biosynthesis protein-encoding gene capD, which is located in the conserved region of the Wzy-dependent capsule synthesis gene cluster in the E. miricola strain FL160902, and investigated its role in the pathogenesis of E. miricola. Our results revealed that the capD deletion strain (ΔcapD) lost its typical encapsulated structure, with a 45% reduction in cell wall thickness. CapD affects wza expression in the capsule polysaccharide synthesis pathway. Furthermore, the survival rates were significantly reduced in ΔcapD in response to complement-mediated killing, desiccation stress, and macrophage phagocytosis, whereas biofilm formation, surface hydrophobicity, and adherence to both endothelial and epithelial cells were increased. Additionally, the deletion of capD sharply attenuated the virulence of E. miricola in a frog infection model. Complementation of the capD gene restored the biological properties and virulence to wild-type levels. Overall, these findings suggest that CapD contributes to polysaccharide synthesis and plays a crucial role in the pathogenesis of E. miricola.

Transcriptomic characterization of recombinant Clostridium beijerinckii NCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase from Clostridium pasteurianum ATCC 6013

Bioconversion of abundant lactose-replete whey permeate to value-added chemicals holds promise for valorization of this expanding food processing waste. Efficient conversion of whey permeate-borne lactose requires adroit microbial engineering to direct carbon to the desired chemical. An engineered strain of Clostridium beijerinckii NCIMB 8052 (C. beijerinckii_mgsA+mgR) that produces 87% more butanol on lactose than the control strain was assessed for global transcriptomic changes. The results revealed broadly contrasting gene expression patterns in C. beijerinckii_mgsA+mgR relative to the control strain. These were characterized by widespread decreases in the abundance of mRNAs of Fe-S proteins in C. beijerinckii_mgsA+mgR, coupled with increased differential expression of lactose uptake and catabolic genes, iron uptake genes, two-component signal transduction and motility genes, and genes involved in the biosynthesis of vitamins B5 and B12, aromatic amino acids (particularly tryptophan), arginine, and pyrimidines. Conversely, the mRNA patterns suggest that the L-aspartate-dependent de novo biosynthesis of NAD as well as biosynthesis of lysine and asparagine and metabolism of glycine and threonine were likely down-regulated. Furthermore, genes involved in cysteine and methionine biosynthesis and metabolism, including cysteine desulfurase-a central player in Fe-S cluster biosynthesis-equally showed reductions in mRNA abundance. Genes involved in biosynthesis of capsular polysaccharides and stress response also showed reduced mRNA abundance in C. beijerinckii_mgsA+mgR. The results suggest that remodeling of cellular and metabolic networks in C. beijerinckii_mgsA+mgR to counter anticipated effects of methylglyoxal production from heterologous expression of methylglyoxal synthase led to enhanced growth and butanol production in C. beijerinckii_mgsA+mgR.

IMPORTANCE

Biological production of commodity chemicals from abundant waste streams such as whey permeate represents an opportunity for decarbonizing chemical production. Whey permeate remains a vastly underutilized feedstock for bioproduction purposes. Thus, enhanced understanding of the cellular and metabolic repertoires of lactose-mediated production of chemicals such as butanol promises to identify new targets that can be fine tuned in recombinant and native microbial strains to engender stronger coupling of whey permeate-borne lactose to value-added chemicals. Our results highlight new genetic targets for future engineering of C. beijerinckii for improved butanol production on lactose and ultimately in whey permeate.

A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD

Many bacteria are protected by different types of polysaccharide capsules, structures formed of long repetitive glycan chains that are sometimes free and sometimes anchored to the outer membrane via lipid tails. One type, called group 4 capsule, results from the expression of the gfcABCDE-etp-etk operon in Escherichia coli. Of the proteins encoded in this operon, GfcE is thought to provide the export pore for free polysaccharide chains, but none of the proteins has been implicated in the export of chains carrying a lipid anchor. For this function, GfcD has been a focus of attention as the only outer membrane β-barrel encoded in the operon. AlphaFold predicts two β-barrel domains in GfcD, a canonical N-terminal one of 12 strands and an unusual C-terminal one of 13 strands, which features a large lateral aperture between strands β1 and β13. This immediately suggests a lateral exit gate for hydrophobic molecules into the membrane, analogous to the one proposed for the lipopolysaccharide export pore LptD. Here, we report an unsteered molecular dynamics study of GfcD embedded in the bacterial outer membrane, with the common polysaccharide anchor, lipid A, inserted in the pore of the C-terminal barrel. Our results show that the lateral aperture does not collapse during simulations and membrane lipids nevertheless do not penetrate the barrel but the lipid chains of the lipid A molecule readily exit into the membrane.

Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica

The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.

IMPORTANCE

Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.

Effect of the polysaccharide capsule and its heptose on the resistance of Campylobacter jejuni to innate immune defenses

Campylobacter jejuni is a commensal in many animals but causes diarrhea in humans. Its polysaccharide capsule contributes to host colonization and virulence in a strain- and model-specific manner. We investigated if the capsule and its heptose are important for interactions of strain NCTC 11168 with various hosts and their innate immune defenses. We determined that they support bacterial survival in Drosophila melanogaster and enhance virulence in Galleria mellonella. We showed that the capsule had limited antiphagocytic activity in human and chicken macrophages, decreased adherence to chicken macrophages, and decreased intracellular survival in both macrophages. In contrast, the heptose increased uptake by chicken macrophages and supported adherence to human macrophages and survival within them. While the capsule triggered nitric oxide production in chicken macrophages, the heptose mitigated this and protected against nitrosative assault. Finally, the C. jejuni strain NCTC 11168 elicited strong cytokine production in both macrophages but quenched ROS production independently from capsule and heptose, and while the capsule and heptose did not protect against oxidative assault, they favored growth in biofilms under oxidative stress. This study shows that the wild-type capsule with its heptose is optimized to resist innate defenses in strain NCTC 11168 often via antagonistic effects of the capsule and its heptose.

Simultaneous Visualization of Microscopic Conductivity and Deformation in Conductive Elastomers

Conductive elastomers are promising for a wide range of applications in many fields due to their unique mechanical and electrical properties, and an understanding of the conductive mechanisms of such materials under deformation is crucial. However, revealing the microscopic conduction mechanism of conductive elastomers is a challenge. In this study, we developed a method that combines in situ deformation nanomechanical atomic force microscopy (AFM) and conductive AFM to successfully and simultaneously characterize the microscopic deformation and microscopic electrical conductivity of nanofiller composite conductive elastomers. With this approach, we visualized the conductive network structure of carbon black and carbon nanotube composite conductive elastomers at the nanoscale, tracked their microscopic response under different compressive strains, and revealed the correlation between microscopic and macroscopic electrical properties. This technique is important for understanding the conductive mechanism of conductive elastomers and improving the design of conductive elastomers.

Acquisition of regulator on virulence plasmid of hypervirulent Klebsiella allows bacterial lifestyle switch in response to iron

Hypervirulent Klebsiella pneumoniae causes liver abscess and potentially devastating metastatic complications. The majority of Klebsiella-induced liver abscess are caused by the CG23-I sublineage of hypervirulent Klebsiella pneumoniae. This and some other lineages possess a >200-kb virulence plasmid. We discovered a novel protein IroP nestled in the virulence plasmid-encoded salmochelin operon that cross-regulates and suppresses the promoter activity of chromosomal type 3 fimbriae (T3F) gene transcription. IroP is itself repressed by iron through the ferric uptake regulator. Iron-rich conditions increase T3F and suppress capsule mucoviscosity, leading to biofilm formation and cell adhesion. Conversely, iron-poor conditions cause a transcriptional switch to hypermucoid capsule production and T3F repression. The likely acquisition of iroP on mobile genetic elements and successful adaptive integration into the genetic circuitry of a major lineage of hypervirulent K. pneumoniae reveal a powerful example of plasmid chromosomal cross talk that confers an evolutionary advantage. Our discovery also addresses the conundrum of how the hypermucoid capsule that impedes adhesion could be regulated to facilitate biofilm formation and colonization. The acquired ability of the bacteria to alternate between a state favoring dissemination and one that favors colonization in response to iron availability through transcriptional regulation offers novel insights into the evolutionary success of this pathogen. IMPORTANCE Hypervirulent Klebsiella pneumoniae contributes to the majority of monomicrobial-induced liver abscess infections that can lead to several other metastatic complications. The large virulence plasmid is highly stable in major lineages, suggesting that it provides survival benefits. We discovered a protein IroP encoded on the virulence plasmid that suppresses expression of the type 3 fimbriae. IroP itself is regulated by iron, and we showed that iron regulates hypermucoid capsule production while inversely regulating type 3 fimbriae expression through IroP. The acquisition and integration of this inverse transcriptional switch between fimbriae and capsule mucoviscosity shows an evolved sophisticated plasmid-chromosomal cross talk that changes the behavior of hypervirulent K. pneumoniae in response to a key nutrient that could contribute to the evolutionary success of this pathogen.

Nanomechanical Profiling of Aβ42 Oligomer-Induced Biological Changes in Single Hippocampus Neurons

Understanding how Aβ42 oligomers induce changes in neurons from a mechanobiological perspective has important implications in neuronal dysfunction relevant to neurodegenerative diseases. However, it remains challenging to profile the mechanical responses of neurons and correlate the mechanical signatures to the biological properties of neurons given the structural complexity of cells. Here, we quantitatively investigate the nanomechanical properties of primary hippocampus neurons upon exposure to Aβ42 oligomers at the single neuron level by using atomic force microscopy (AFM). We develop a method termed heterogeneity-load-unload nanomechanics (HLUN), which exploits the AFM force spectra in the whole loading-unloading cycle, allowing comprehensive profiling of the mechanical properties of living neurons. We extract four key nanomechanical parameters, including the apparent Young's modulus, cell spring constant, normalized hysteresis, and adhesion work, that serve as the nanomechanical signatures of neurons treated with Aβ42 oligomers. These parameters are well-correlated with neuronal height increase, cortical actin filament strengthening, and calcium concentration elevation. Thus, we establish an HLUN method-based AFM nanomechanical analysis tool for single neuron study and build an effective correlation between the nanomechanical profile of the single neurons and the biological effects triggered by Aβ42 oligomers. Our finding provides useful information on the dysfunction of neurons from the mechanobiological perspective.

Surface Energy and Viscoelastic Characteristics of Staphylococcus epidermidis and Cutibacterium acnes Biofilm on Commercial Skin Constructs versus agar

Biofilms are recalcitrant to both study and infectious disease treatment as it requires not only the study or management of single organism behavior, but also many dynamical interactions including but not limited to bacteria-bacteria, bacteria-host, bacteria-nutrients, and bacteria-material across multiple time scales. This study performs comparative and quantitative research of two materials used in biofilm research, TSA agar and skin epidermal, to reveal how adhesion effects viscoelastic properties of biofilms at long time scales. We show that the host surface stressors, such as wettability and surface energy, impact the biofilm's mechanical integrity and viscoelastic properties. While it is known that the bacteria-material interface influences initial biofilm formation and external stress influences mature biofilm function, this study examines the influence of the bacteria-material interface on mature biofilms. These mechanical viscoelastic properties have the potential to determine metabolite and pathogenesis pathways which means that the platform researchers use to study impacts the outcome.

Disarm The Bacteria: What Temperate Phages Can Do

In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.

Interspecies relationships between nosocomial pathogens associated to preterm infants and lactic acid bacteria in dual-species biofilms

The nasogastric enteral feeding tubes (NEFTs) used to feed preterm infants are commonly colonized by bacteria with the ability to form complex biofilms in their inner surfaces. Among them, staphylococci (mainly Staphylococcus epidermidis and Staphylococcus aureus) and some species belonging to the Family Enterobacteriaceae are of special concern since they can cause nosocomial infections in this population. NETF-associated biofilms can also include lactic acid bacteria (LAB), with the ability to compete with pathogenic species for nutrients and space. Ecological interactions among the main colonizers of these devices have not been explored yet; however, such approach could guide future strategies involving the pre-coating of the inner surfaces of NEFTs with well adapted LAB strains in order to reduce the rates of nosocomial infections in neonatal intensive care units (NICUs). In this context, this work implied the formation of dual-species biofilms involving one LAB strain (either Ligilactobacillus salivarius 20SNG2 or Limosilactobacillus reuteri 7SNG3) and one nosocomial strain (either Klebsiella pneumoniae 9SNG3, Serratia marcescens 10SNG3, Staphylococcus aureus 45SNG3 or Staphylococcus epidermidis 46SNG3). The six strains used in this study had been isolated from the inner surface of NEFTs. Changes in adhesion ability of the pathogens were characterized using a culturomic approach. Species interactions and structural changes of the resulting biofilms were analyzed using scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). No aggregation was observed in dual-species biofilms between any of the two LAB strains and either K. pneumoniae 9SNG3 or S. marcescens 10SNG3. In addition, biofilm thickness and volume were reduced, suggesting that both LAB strains can control the capacity to form biofilms of these enterobacteria. In contrast, a positive ecological relationship was observed in the combination L. reuteri 7SNG3-S. aureus 45SNG3. This relationship was accompanied by a stimulation of S. aureus matrix production when compared with its respective monospecies biofilm. The knowledge provided by this study may guide the selection of potentially probiotic strains that share the same niche with nosocomial pathogens, enabling the establishment of a healthier microbial community inside NEFTs.

LPS O Antigen Plays a Key Role in Klebsiella pneumoniae Capsule Retention

Despite the importance of encapsulation in bacterial pathogenesis, the biochemical mechanisms and forces that underpin retention of capsule by encapsulated bacteria are poorly understood. In Gram-negative bacteria, there may be interactions between lipopolysaccharide (LPS) core and capsule polymers, between capsule polymers with retained acyl carriers and the outer membrane, and in some bacteria, between the capsule polymers and Wzi, an outer membrane protein lectin. Our transposon studies in Klebsiella pneumoniae B5055 identified additional genes that, when insertionally inactivated, resulted in reduced encapsulation. Inactivation of the gene waaL, which encodes the ligase responsible for attaching the repeated O antigen of LPS to the LPS core, resulted in a significant reduction in capsule retention, measured by atomic force microscopy. This reduction in encapsulation was associated with increased sensitivity to human serum and decreased virulence in a murine model of respiratory infection and, paradoxically, with increased biofilm formation. The capsule in the WaaL mutant was physically smaller than that of the Wzi mutant of K. pneumoniae B5055. These results suggest that interactions between surface carbohydrate polymers may enhance encapsulation, a key phenotype in bacterial virulence, and provide another target for the development of antimicrobials that may avoid resistance issues associated with growth inhibition. IMPORTANCE Bacterial capsules, typically comprised of complex sugars, enable pathogens to avoid key host responses to infection, including phagocytosis. These capsules are synthesized within the bacteria, exported through the outer envelope, and then secured to the external surface of the organism by a force or forces that are incompletely described. This study shows that in the important hospital pathogen Klebsiella pneumoniae, the polysaccharide capsule is retained by interactions with other surface sugars, especially the repeated sugar molecule of the LPS molecule in Gram-negative bacteria known as "O antigen." This O antigen is joined to the LPS molecule by ligation, and loss of the enzyme responsible for ligation, a protein called WaaL, results in reduced encapsulation. Since capsules are essential to the virulence of many pathogens, WaaL might provide a target for new antimicrobial development, critical to the control of pathogens like K. pneumoniae that have become highly drug resistant.

Transcriptomic Analysis Reveals That Municipal Wastewater Effluent Enhances Vibrio vulnificus Growth and Virulence Potential

Vibrio vulnificus is an opportunistic pathogen indigenous to estuarine and marine environments and associated with aquatic organisms. Vibrio vulnificus is of utmost importance because it causes 95% of the seafood-related deaths in the United States due to rapid progression of septicemia. Changes in environmental parameters associated with climate change and coastal population expansion are altering geographical constraints, resulting in increased Vibrio spread, exposure, and rates of infection. In addition, coastal population expansion is resulting in increased input of treated municipal sewage into areas that are also experiencing increased Vibrio proliferation. This study aimed to better understand the influence of treated sewage effluent on effluent-receiving microbial communities using Vibrio as a model of an opportunistic pathogen. Integrated transcriptomic approaches were used to analyze the changes in overall gene expression of V. vulnificus NBRC 15645 exposed to wastewater treatment plant (WWTP) effluent for a period of 6h using a modified seawater yeast extract media that contained 0, 50, and 100% filtered WWTP effluent. RNA-seq reads were mapped, annotated, and analyzed to identify differentially expressed genes using the Pathosystems Resource Integration Center analysis tool. The study revealed that V. vulnificus responds to wastewater effluent exposure by activating cyclic-di-GMP-influenced biofilm development. Also, genes involved in crucial functions, such as nitrogen metabolism and bacterial attachment, were upregulated depending on the presence of treated municipal sewage. This altered gene expression increased V. vulnificus growth and proliferation and enhanced genes and pathways involved in bacterial survival during the early stages of infection in a host. These factors represent a potential public health risk due to exposure to environmental reservoirs of potentially Vibrio strains with enhanced virulence profiles in coastal areas.

pH-Responsive Smart Wettability Surface with Dual Bactericidal and Releasing Properties

Biomaterial-associated infections caused by pathogenic bacteria have important implications on human health. This study presents the design and preparation of a smart surface with pH-responsive wettability. The smart surface exhibited synergistic antibacterial function, with high liquid repellency against bacterial adhesion and highly effective bactericidal activity. The wettability of the surface can switch reversibly between superhydrophobicity and hydrophobicity in response to pH; this controls bacterial adhesion and release. Besides, the deposited silver nanoparticles of the surface were also responsible for bacterial inhibition. Benefiting from the excellent liquid repellency, the surface could highly resist bacterial adhesion after immersing in a bacterial suspension for 10 s (85%) and 1 h (71%). Adhered bacteria can be easily eliminated using deposited silver nanoparticles during the subsequent treatment of alkaline bacterial suspension, and the ratio of deactivated bacteria was above 75%. After the pH returned to neutral, the deactivated bacteria can be easily released from the surface. This antibacterial surface showed an improved bacterial removal efficiency of about 99%. The results shed light on future antibacterial applications of the smart surface combining both bactericidal and adhesion-resistant functionalities.

Dismantling the bacterial glycocalyx: Chemical tools to probe, perturb, and image bacterial glycans

The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.

AFM-Based Correlative Microscopy Illuminates Human Pathogens

Microbes have an arsenal of virulence factors that contribute to their pathogenicity. A number of challenges remain to fully understand disease transmission, fitness landscape, antimicrobial resistance and host heterogeneity. A variety of tools have been used to address diverse aspects of pathogenicity, from molecular host-pathogen interactions to the mechanisms of disease acquisition and transmission. Current gaps in our knowledge include a more direct understanding of host-pathogen interactions, including signaling at interfaces, and direct phenotypic confirmation of pathogenicity. Correlative microscopy has been gaining traction to address the many challenges currently faced in biomedicine, in particular the combination of optical and atomic force microscopy (AFM). AFM, generates high-resolution surface topographical images, and quantifies mechanical properties at the pN scale under physiologically relevant conditions. When combined with optical microscopy, AFM probes pathogen surfaces and their physical and molecular interaction with host cells, while the various modes of optical microscopy view internal cellular responses of the pathogen and host. Here we review the most recent advances in our understanding of pathogens, recent applications of AFM to the field, how correlative AFM-optical microspectroscopy and microscopy have been used to illuminate pathogenicity and how these methods can reach their full potential for studying host-pathogen interactions.

Measurement of the interconnected turgor pressure and envelope elasticity of live bacterial cells

Turgor pressure and envelope elasticity of bacterial cells are two mechanical parameters that play a dominant role in cellular deformation, division, and motility. However, a clear understanding of these two properties is lacking because of their strongly interconnected mechanisms. This study established a nanoindentation method to precisely measure the turgor pressure and envelope elasticity of live bacteria. The indentation force-depth curves of Klebsiella pneumoniae bacteria were recorded with atomic force microscopy. Through combination of dimensional analysis and numerical simulations, an explicit expression was derived to decouple the two properties of individual bacteria from the nanoindentation curves. We show that the Young's modulus of bacterial envelope is sensitive to the external osmotic environment, and the turgor pressure is significantly dependent on the external osmotic stress. This method can not only quantify the turgor pressure and envelope elasticity of bacteria, but also help resolve the mechanical behaviors of bacteria in different environments.

Pili and other surface proteins influence the structure and the nanomechanical properties of Lactococcus lactis biofilms

Lactic acid bacteria, in particular Lactococcus lactis, are widely used in the food industry, for the control and/or the protection of the manufacturing processes of fermented food. While L. lactis has been reported to form compact and uniform biofilms it was recently shown that certain strains able to display pili at their surface form more complex biofilms exhibiting heterogeneous and aerial structures. As the impact of those biofilm structures on the biomechanical properties of the biofilms is poorly understood, these were investigated using AFM force spectroscopy and imaging. Three types of strains were used i.e., a control strain devoid of pili and surface mucus-binding protein, a strain displaying pili but no mucus-binding proteins and a strain displaying both pili and a mucus-binding protein. To identify potential correlations between the nanomechanical measurements and the biofilm architecture, 24-h old biofilms were characterized by confocal laser scanning microscopy. Globally the strains devoid of pili displayed smoother and stiffer biofilms (Young Modulus of 4-100 kPa) than those of piliated strains (Young Modulus around 0.04-0.1 kPa). Additional display of a mucus-binding protein did not affect the biofilm stiffness but made the biofilm smoother and more compact. Finally, we demonstrated the role of pili in the biofilm cohesiveness by monitoring the homotypic adhesion of bacteria to the biofilm surface. These results will help to understand the role of pili and mucus-binding proteins withstanding external forces.

Discovery of Welcome Biopolymers in Surface Water: Improvements in Drinking Water Production

The presence of biopolymers in surface waters and their significance for potable water supply have received little attention previously owing to their low concentrations. In this paper, we present the results of an extensive study that has investigated the role and benefits of biopolymers during the purification of surface water with reference to their specific biological and physico-chemical properties. Using samples collected from two representative surface waters in China and the United Kingdom, macromolecular biopolymers were separated and concentrated for subsequent investigation of their role in coagulation, metal ion adsorption, and membrane separation. Our results show that biopolymers significantly improve the antifouling capability of membrane nanofiltration, in combination with the enhanced conventional coagulation performance and additional security against several unhealthy metal pollutants (e.g., Fe, Al, and Cr). We believe this is the first study that reveals the versatile benefits and the fate of natural biopolymers in surface water purification processes.

Effects of Curcumin and Its Analogues on Infectious Diseases

Infectious diseases (IDs) are life-threatening illnesses, which result from the spread of pathogenic microorganisms such as bacteria, viruses, fungi, and parasites. IDs are a major challenge for the healthcare systems around the world, leading to a wide variety of clinical manifestations and complications. Despite the capability of frontline-approved medications to partially prevent or mitigate the invasion and subsequent damage of IDs to host tissues and cells, problems such as drug resistance, insufficient efficacy, unpleasant side effects, and high expenses stand in the way of their beneficial applications. One strategy is to evaluate currently explored and available bioactive compounds as possible anti-microbial agents. The natural polyphenol curcumin has been postulated to possess various properties including anti-microbial activities. Studies have shown that it possess pleiotropic effects against bacterial- and parasitic-associating IDs including drug-resistant strains. Curcumin can also potentiate the efficacy of available anti-bacterial and anti-parasitic drugs in a synergistic fashion. In this review, we summarize the findings of these studies along with reported controversies of native curcumin and its analogues, alone and in combination, toward its application in future studies as a natural anti-bacterial and anti-parasitic agent.

Biofilm Production by Carbapenem-Resistant Klebsiella pneumoniae Significantly Increases the Risk of Death in Oncological Patients

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a prominent cause of nosocomial infections associated with high rates of morbidity and mortality, particularly in oncological patients. The hypermucoviscous (HMV) phenotype and biofilm production are key factors for CRKP colonization and persistence in the host. This study aims at exploring the impact of CRKP virulence factors on morbidity and mortality in oncological patients. A total of 86 CRKP were collected between January 2015 and December 2019. Carbapenem resistance-associated genes, antibiotic susceptibility, the HMV phenotype, and biofilm production were evaluated. The median age of the patients was 71 years (range 40–96 years). Clinically infected patients were 53 (61.6%), while CRKP colonized individuals were 33 (38.4%). The most common infectious manifestations were sepsis (43.4%) and pneumonia (18.9%), while rectal surveillance swabs were the most common site of CRKP isolation (81.8%) in colonized patients. The leading mechanism of carbapenem resistance was sustained by the KPC gene (96.5%), followed by OXA-48 (2.3%) and VIM (1.2%). Phenotypic CRKP characterization indicated that 55.8% of the isolates were strong biofilm-producers equally distributed between infected (54.2%) and colonized (45.8%) patients. The HMV phenotype was found in 22.1% of the isolates, which showed a significant (P<0.0001) decrease in biofilm production as compared to non-HMV strains. The overall mortality rate calculated on the group of infected patients was 35.8%. In univariate analysis, pneumoniae significantly correlated with death (OR 5.09; CI 95% 1.08–24.02; P=0.04). The non-HMV phenotype (OR 4.67; CI 95% 1.13–19.24; P=0.03) and strong biofilm-producing strains (OR 5.04; CI95% 1.39–18.25; P=0.01) were also associated with increased CRKP infection-related mortality. Notably, the multivariate analysis showed that infection with strong biofilm-producing CRKP was an independent predictor of mortality (OR 6.30; CI 95% 1.392–18.248; P=0.004). CRKP infection presents a high risk of death among oncological patients, particularly when pneumoniae and sepsis are present. In infected patients, the presence of strong biofilm-producing CRKP significantly increases the risk of death. Thus, the assessment of biofilm production may provide a key element in supporting the clinical management of high-risk oncological patients with CRKP infection.

3D micromorphology evaluation of kefir microbial films loaded with extract of Amazon rainforest fruit Cupuaçu

We performed qualitative and quantitative analysis of surfaces of kefir biofilms loaded with Amazon rainforest fruit extract. Scanning electron microscopy and atomic force microscopy were used to evaluate the micromorphology of the biofilms. The films surface displayed a lower density of microorganisms (∼ 0.061 microorganisms/μm²) for the lowest concentration of fruit extract, however, a greater density (∼0.220 microorganisms/μm²) was observed for the higher concentration. Height stereometric parameters revealed that the biofilms with the highest concentration presented the highest roughness. However, almost all the stereometric parameters related to texture showed no significant difference. Furthermore, the Hurst coefficients of the average power spectrum density were similar for all biofilms. Fractal parameters confirmed that higher concentrations of fruit extract induced a superior topographic irregularity. However, fractal lacunarity does not show any significant difference confirming the similarity of the microtextures. Moreover, fractal succolarity and surface entropy exhibited values that suggested ideal percolation and strong topographic uniformity, respectively, indicating that these films can uniformly adhere to other surfaces. Our results confirm that the stereometric and fractal parameters can be relevant for the surface characterization of microbial films, which can be of great importance to the biomedical field.

Quantitative analysis of the surficial and adhesion properties of the Gram-negative bacterial species Comamonas testosteroni modulated by c-di-GMP

Cyclic diguanylate monophosphate (c-di-GMP) is a ubiquitous intracellular secondary messenger which governs the transition from a bacterial cell's planktonic state to biofilm formation by stimulating the production of a variety of exopolysaccharide material by the bacterial cell. A range of genes involved in c-di-GMP signaling in the Gram-negative species Comamonas testosteroni have been identified previously, yet the physical-chemical properties of the produced extracellular polymeric substances (EPS) and the bacterial adhesion characteristics regulated by c-di-GMP are not well understood. Here, we modulated the in vivo c-di-GMP levels of Comamonas testosteroni WDL7 through diguanylate cyclase (YedQ) and phosphodiesterase (YhjH) gene editing. The strains and their adhesion properties were characterized by Fourier-transform infrared and two-dimensional correlation spectroscopy analysis (FTIR-2D CoS), contact angle and zeta potential measurements, atomic force microscopy (AFM) and extended-Derjaguin-Landau-Verwey-Overbeek (ExDLVO) analysis. Our results show that high c-di-GMP levels promoted the secretion of long-chain hydrophobic and electroneutral extracellular polysaccharides and proteins. The protein molecules on WDL7/pYedQ2 promoted the bacterial self-aggregation and adhesion onto negatively charged surfaces. In contrast, the reduction of intracellular c-di-GMP concentrations resulted in a nearly 80 % decrease in the adhesion of bacterial cells, although little change in the surface hydrophobicity or surface charge properties were observed for these cells relative to the wild type. These results indicate that the reduced adsorption of WDL7/YhjH that we observed may be caused by the flagellum-accelerated mobility at low c-di-GMP concentrations. Taken together, these results improve our mechanistic understanding of the effects of c-di-GMP in controlling bacterial physical-chemical properties and initial biofilm development.

Physics Comes to the Aid of Medicine-Clinically-Relevant Microorganisms through the Eyes of Atomic Force Microscope

Despite the hope that was raised with the implementation of antibiotics to the treatment of infections in medical practice, the initial enthusiasm has substantially faded due to increasing drug resistance in pathogenic microorganisms. Therefore, there is a need for novel analytical and diagnostic methods in order to extend our knowledge regarding the mode of action of the conventional and novel antimicrobial agents from a perspective of single microbial cells as well as their communities growing in infected sites, i.e., biofilms. In recent years, atomic force microscopy (AFM) has been mostly used to study different aspects of the pathophysiology of noninfectious conditions with attempts to characterize morphological and rheological properties of tissues, individual mammalian cells as well as their organelles and extracellular matrix, and cells’ mechanical changes upon exposure to different stimuli. At the same time, an ever-growing number of studies have demonstrated AFM as a valuable approach in studying microorganisms in regard to changes in their morphology and nanomechanical properties, e.g., stiffness in response to antimicrobial treatment or interaction with a substrate as well as the mechanisms behind their virulence. This review summarizes recent developments and the authors’ point of view on AFM-based evaluation of microorganisms’ response to applied antimicrobial treatment within a group of selected bacteria, fungi, and viruses. The AFM potential in development of modern diagnostic and therapeutic methods for combating of infections caused by drug-resistant bacterial strains is also discussed.

Differential expression of vvhA and CPS operon allele 1 genes in Vibrio vulnificus under biofilm and planktonic conditions

Examination of genes encoding for the virulence factors, hemolysin/cytolysin (vvhA) and capsular polysaccharide (CPS allele 1), during biofilm formation revealed that their expression was influenced by the maturity of the biofilm as well as by temperature. At 24 °C, expression of vvhA during biofilm formation was low between 4 and 12 h but increased 10-fold by 24 h to (5.1 × 10⁴ ± 6.3 × 10³mRNA copies/ml) as the biofilm matured. Compared to planktonic cells, expression of vvhA during biofilm formation at 24 °C was initially up-regulated at 4 h (1.07 ± 0.00-fold) but then was down-regulated almost four-fold during the intermediate and mature stages of biofilm formation. In contrast, vvhA expression at 37 °C was up-regulated almost four-fold in the early stages (4 and 6 h) of biofilm formation and remained two-fold up-regulated by 24 h even as the biofilm was deteriorating. CPS allele 1 expression at 24 °C during biofilm formation was up-regulated (1.50 ± 0.18-fold) during the initial attachment phase of the cells but was strongly down-regulated during the intermediate phases at 8 and 10 h (74.42 ± 42.16-fold and 453.76 ± 193.32-fold, respectively), indicating that capsular polysaccharide (CPS) is not important to intermediate biofilm architecture. Interestingly, as the biofilm matured by 24 h, expression of CPS allele 1 was again up-regulated (1.88 ± 1.07), showing that CPS plays a role in mature biofilm. At 37 °C, CPS allele 1 expression was significantly up-regulated (up to 10⁵) during biofilm formation, indicating that the biofilm form of V. vulnificus may be preferred over the planktonic form in the human host.

Investigation of LuxS-mediated quorum sensing in Klebsiella pneumoniae

Introduction

Autoinducer-2 (AI-2) quorum sensing is a bacterial communication system that responds to cell density. The system requires luxS activity to produce AI-2, which can regulate gene expression and processes such as biofilm formation.

Aim

To investigate the role of luxS in biofilm formation and gene expression in the nosocomial pathogen Klebsiella pneumoniae.

Methodology

A ΔluxS gene deletion was made in K. pneumoniae KP563, an extensively drug-resistant isolate. AI-2 production was assessed in wild-type and ΔluxS strains grown in media supplemented with different carbohydrates. Potential roles of luxS in biofilm formation were investigated using a microtiter plate biofilm assay and scanning electron microscopy. Quantitative RT-PCR evaluated the expression of lipopolysaccharide (wzm and wbbM), polysaccharide (pgaA), and type 3 fimbriae (mrkA) synthesis genes in wild-type and ΔluxS mutant biofilm extracts.

Results

AI-2 production was dependent on the presence of luxS. AI-2 accumulation was highest during early stationary phase in media supplemented with glucose, sucrose or glycerol. Changes in biofilm architecture were observed in the ΔluxS mutant, with less surface coverage and reduced macrocolony formation; however, no differences in biofilm formation between the wild-type and ΔluxS mutant using a microtiter plate assay were observed. In ΔluxS mutant biofilm extracts, the expression of wzm was down-regulated, and the expression of pgaA, which encodes a porin for poly-β−1,6-N-acetyl-d-glucosamine (PNAG) polysaccharide secretion, was upregulated.

Conclusion

Relationships among AI-2-mediated quorum sensing, biofilm formation and gene expression of outer-membrane components were identified in K. pneumoniae. These inter-connected processes could be important for bacterial group behaviour and persistence.

Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems

Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.

The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by Chloroflexi populations. Additionally, we present evidence for metabolically diverse, formate-utilizing Sulfurovum populations and new genomic and phylogenetic insights into the unique Lost City Methanosarcinales.

IMPORTANCE Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.

In Vivo Relationship between the Nano-Biomechanical Properties of Streptococcal Polysaccharide Capsules and Virulence Phenotype

In common with many bacterial pathogens, Streptococcus pneumoniae has a polysaccharide capsule which facilitates immune evasion and determines virulence. Recent data have shown that the closely related Streptococcus mitis also expresses polysaccharide capsules including those with an identical chemical structure to S. pneumoniae capsular serotypes. We utilized atomic force microscopy (AFM) techniques to investigate the biophysical properties of S. mitis and S. pneumoniae strains expressing the same capsular serotypes that might relate to differences in virulence potential. When comparing S. mitis and S. pneumoniae strains with identical capsule serotypes, S. mitis strains were susceptible to neutrophil killing, and electron microscopy and AFM demonstrated significant morphological differences. Force-volume mapping using AFM showed distinct force-curve profiles for the center and edge areas of encapsulated streptococcal strains. This "edge effect" was not observed in unencapsulated bacteria and therefore was a direct representation of the mechanical properties of the bacterial capsule. When two strains of S. mitis and S. pneumoniae expressed an identical capsular serotype, they presented similar biomechanical characteristics. This infers a potential relationship between capsule biochemistry and nanomechanics, independent of bacterial strain. Overall, this study demonstrates that it is possible to investigate reproducibly the mechanistic, structural, and mechanical properties of both the capsule and the body of individual living bacterial cells and relate the data to virulence phenotypes. We have demonstrated that using nanomechanics to investigate individual bacterial cells we can now begin to identify the surface properties bacterial pathogens require to avoid host-mediated immunity.

Hypervirulent Klebsiella pneumoniae serotype K1 clinical isolates form robust biofilms at the air-liquid interface

The prevalence of a new hypervirulent and hypermucoviscous K. pneumoniae phenotype (Hmv) is increasing worldwide, mainly linked to serotypes K1 and K2. Since capsular thickness can directly affect the capability to form biofilms, we aimed to evaluate the association between the Hmv phenotype with adhesion and biofilm formation in a collection of clinical K. pneumoniae isolates.

We selected 38 Hmv clinical isolates [15 serotype K1; 9 serotype K2; 3 non-K1/K2 (rmpA⁺); 11 non-K1/K2 (rmpA^-)] and 7 non-Hmv clinical isolates. The Hmv phenotype was assessed through the mucoviscosity test. Serum resistance was determined by bacterial viability tests in pooled human serum. Adhesion was evaluated with the Biofilm Ring Test^®, and biofilm formation was identified by crystal violet staining (Solid-Liquid, SLI-biofilm) or visual examination (Air-Liquid, ALI-biofilm).

This study linked for the first time the formation of robust ALI-biofilm plugs by K. pneumoniae to the capsular serotype K1, a group of hypervirulent strains which are generally highly susceptible to the antimicrobial agents. Among all the studied isolates, the capsular serotype K1 presented lower initial adhesion despite having the adhesins mrkD and fimH but higher ALI-biofilm formation than isolates with other capsular serotypes (K2 or non-K1/K2). This structure might confer increased resistance to a group of hypervirulent K. pneumoniae serotype K1.

Super-Resolution Fluorescence Microscopy Study of the Production of K1 Capsules by Escherichia coli: Evidence for the Differential Distribution of the Capsule at the Poles and the Equator of the Cell

The production of Escherichia coli K1 serotype capsule was investigated using direct stochastic optical reconstruction microscopy with live bacteria and graphene oxide-coated coverslips, overcoming many morphological artifacts found in other high-resolution imaging techniques. Super-resolution fluorescence images showed that the K1 capsular polysaccharide is not uniformly distributed on the cell surface, as previously thought. These studies demonstrated that on the cell surfaces the K1 capsule at the poles had bimodal thicknesses of 238 ± 41 and 323 ± 62 nm, whereas at the equator, there was a monomodal thickness of 217 ± 29 nm. This bimodal variation was also observed in high-pressure light-scattering chromatography measurements of purified K1 capsular polysaccharide. Particle tracking demonstrated that the formation of the capsule was dominated by the expansion of lyso-phosphatidylglycerol (lyso-PG) rafts that anchor the capsular polysaccharide in the outer membrane, and the expansion of these rafts across the cell surface was driven by new material transported through the capsular biosynthesis channels. The discovery of thicker capsules at the poles of the cell will have implications in mediating interactions between the bacterium and its immediate environment.

Revealing the Effects of Curcumin on SH-SY5Y Neuronal Cells: A Combined Study from Cellular Viability, Morphology, and Biomechanics

In this work, the effects of curcumin on the viability, morphology, and nanomechanics of SH-SY5Y neuronal cells were investigated using a conventional cell viability test kit (CCK-8) and sophisticated AFM imaging and force measurement techniques. CCK-8 tests show that SH-SY5Y neuronal cells have a dose-response to curcumin in terms of viability that is dependent on the exposure durations. When exposed to a maximum dosage of 32 μg/mL used in the present study for 4 h, 24 h, and 48 h, the cell viability dropped to 73.4 ± 4.5%, 9.1 ± 3.2%, and 2.5 ± 1.2% of the control, correspondingly. AFM studies show that curcumin can induce the disappearance of synapses of the cells and the change of biomechanics. After exposure for 24 h at the concentration of 16 μg/mL, the viscous deformation of the cells decreased from 2.15 ± 0.02 to 1.58 ± 0.03 (×10^-15 N·m), the elastic deformation increased from 1.26 ± 0.04 to 1.72 ± 0.07 (×10^-15 N·m), and adhesion work decreased from 0.56 ± 0.07 to 0.39 ± 0.04 (×10^-16 N·m). The morphological and mechanical changes obtained using AFM can be interpreted from optically observed cellular structural changes. The present study provides insights into the effects of curcumin on neuronal cells from both biological and biophysical aspects, which can help more comprehensively understand the interactions between curcumin and SH-SY5Y cells. The demonstrated techniques can be potentially used to assess the efficacy of bioactive constituents on cells or help screen drugs.

Extracellular polymeric substances of biofilms: Suffering from an identity crisis

Microbial biofilms can be both cause and cure to a range of emerging societal problems including antimicrobial tolerance, water sanitation, water scarcity and pollution. The identities of extracellular polymeric substances (EPS) responsible for the establishment and function of biofilms are poorly understood. The lack of information on the chemical and physical identities of EPS limits the potential to rationally engineer biofilm processes, and impedes progress within the water and wastewater sector towards a circular economy and resource recovery. Here, a multidisciplinary roadmap for addressing this EPS identity crisis is proposed. This involves improved EPS extraction and characterization methodologies, cross-referencing between model biofilms and full-scale biofilm systems, and functional description of isolated EPS with in situ techniques (e.g. microscopy) coupled with genomics, proteomics and glycomics. The current extraction and spectrophotometric characterization methods, often based on the principle not to compromise the integrity of the microbial cells, should be critically assessed, and more comprehensive methods for recovery and characterization of EPS need to be developed.

A Patterned Butyl Methacrylate-co-2-Hydroxyethyl Acrylate Copolymer with Softening Surface and Swelling Capacity

The tunable swelling and mechanical properties of nanostructures polymers are crucial parameters for the creation of adaptive devices to be used in diverse fields, such as drug delivery, nanomedicine, and tissue engineering. We present the use of anodic aluminum oxide templates as a nanoreactor to copolymerize butyl methacrylate and 2-hydroxyethyl acrylate under radical conditions. The copolymer obtained under confinement showed significant differences with respect to the same copolymer obtained in bulk conditions. Molecular weights, molecular weight dispersities, Young's modulus, and wetting behaviors were significantly modified. The combination of selected monomers allowed us to obtain nanopillar structures with an interesting softening surface and extraordinary swelling capacity that could be of special interest to surface science and specifically, cell culture.

The Effects of β-Lactam Antibiotics on Surface Modifications of Multidrug-Resistant Escherichia coli: A Multiscale Approach

Possible multidrug-resistant (MDR) mechanisms of four resistant strains of Escherichia coli to a model β-lactam, ampicillin, were investigated using contact angle measurements of wettability, crystal violet assays of permeability, biofilm formation, fluorescence imaging, and nanoscale analyses of dimensions, adherence, and roughness. Upon exposure to ampicillin, one of the resistant strains, E. coli A5, changed its phenotype from elliptical to spherical, maintained its roughness and biofilm formation abilities, decreased its length and surface area, maintained its cell wall integrity, increased its hydrophobicity, and decreased its nanoscale adhesion to a model surface of silicon nitride. Such modifications are suggested to allow these cells to conserve energy during metabolic dormancy. In comparison, resistant strains E. coli D4, A9, and H5 elongated their cells, increased their roughness, increased their nanoscale adhesion forces, became more hydrophilic, and increased their biofilm formation upon exposure to ampicillin. These results suggest that these strains resisted ampicillin through biofilm formation that possibly introduces diffusion limitations to antibiotics. Investigations of how MDR bacterial cells modify their surfaces in response to antibiotics can guide research efforts aimed at designing more effective antibiotics and new treatment strategies for MDR bacterial infections.

Effect of copper on diesel degradation in Pseudomonas extremaustralis

Environments co-contaminated with heavy metals and hydrocarbons have become an important problem worldwide, especially due to the effect of metals on hydrocarbon degrading microorganisms. Pseudomonas extremaustralis, a bacterium isolated from a pristine pond in Antarctica, showed high capabilities to cope with environmental stress and a very versatile metabolism that includes alkane degradation under microaerobic conditions. In this work, we analyzed P. extremaustralis' capability to resist high copper concentrations and the effect of copper presence in diesel biodegradation. We observed that P. extremaustralis resisted up to 4 mM CuSO₄ in a rich medium such as LB. This copper resistance is sustained by the presence of the cus and cop operons together with other efflux systems and porins located in a single region in P. extremaustralis genome. When copper was present, diesel degradation was negatively affected, even though copper enhanced bacterial attachment to hydrocarbons. However, when a small amount of glucose (0.05% w/v) was added, the presence of CuSO₄ enhanced alkane degradation. In addition, atomic force microscopy analysis showed that the presence of glucose decreased the negative effects produced by copper and diesel on the cell envelopes.

Nanotoxicity of Silver Nanoparticles on HEK293T Cells: A Combined Study Using Biomechanical and Biological Techniques

Human embryonic kidney 293T cells (HEK293T cells) before and after treatment with silver nanoparticles (AgNPs) were measured using advanced atomic force microscopy (AFM) force measurement technique, and the biomechanical property of cells was analyzed using a theoretical model. The biomechanical results showed that the factor of viscosity of untreated HEK293T cells reduced from 0.65 to 0.40 for cells exposure to 40 μg/mL of AgNPs. Comet assay indicated that significant DNA damage occurred in the treated cells, measured as tail DNA% and tail moment. Furthermore, gene expression analysis showed that for the cells treated with 40 μg/mL of AgNPs, the antiapoptosis genes Bcl2-t and Bclw were, respectively, downregulated to 0.65- and 0.66-fold of control, and that the proapoptosis gene Bid was upregulated to 1.55-fold of control, which indicates that apoptosis occurred in cells exposed to AgNPs. Interestingly, excellent negative correlations were found between the factor of viscosity and tail DNA%, and tail moment, which suggest that the biomechanical property can be correlated with genotoxicity of nanoparticles on the cells. Based on the above results, we conclude that (1) AgNPs can lead to biomechanical changes in HEK293T cells, concomitantly with biological changes including cell viability, DNA damage, and cell apoptosis; (2) the factor of viscosity can be exploited as a promising label-free biomechanical marker to assess the nanotoxicity of nanoparticles on the cells; and (3) the combination of AFM-based mechanical technique with conventional biological methods can provide more comprehensive understanding of the nanotoxicity of nanoparticles than merely by using the biological techniques.

Novel role of the LPS core glycosyltransferase WapH for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis

Psychrotroph microorganisms have developed cellular mechanisms to cope with cold stress. Cell envelopes are key components for bacterial survival. Outer membrane is a constituent of Gram negative bacterial envelopes, consisting of several components, such as lipopolysaccharides (LPS). In this work we investigated the relevance of envelope characteristics for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis by analyzing a mini Tn5 wapH mutant strain, encoding a core LPS glycosyltransferase. Our results showed that wapH strain is impaired to grow under low temperature but not for cold survival. The mutation in wapH, provoked a strong aggregative phenotype and modifications of envelope nanomechanical properties such as lower flexibility and higher turgor pressure, cell permeability and surface area to volume ratio (S/V). Changes in these characteristics were also observed in the wild type strain grown at different temperatures, showing higher cell flexibility but lower turgor pressure under cold conditions. Cold shock experiments indicated that an acclimation period in the wild type is necessary for cell flexibility and S/V ratio adjustments. Alteration in cell-cell interaction capabilities was observed in wapH strain. Mixed cells of wild type and wapH strains, as well as those of the wild type strain grown at different temperatures, showed a mosaic pattern of aggregation. These results indicate that wapH mutation provoked marked envelope alterations showing that LPS core conservation appears as a novel essential feature for active growth under cold conditions.

Effects of stimulated aggrecanolysis on nanoscale morphological and mechanical properties of wild-type and aggrecanase-resistant mutant mice cartilages

A key event in arthritis pathogenesis is the degradation of aggrecan, the major component in articular cartilage. In this work, we investigate the effects of stimulated aggrecanolysis on the morphological and nanomechanical properties of cartilage harvested from wild-type mice and aggrecanase-resistant mutant mice named "Jaffa". The cartilages were native or were subjected to stimulated aggrecanolysis by interleukin-1[Formula: see text] (IL-1[Formula: see text]) treatment. The nanoscale morphological and mechanical properties of the sectioned cartilages were measured by using a sharp probe by atomic force microscopy (AFM). The IL-1[Formula: see text] treatment resulted in a higher nanoroughess and stiffness of the cartilage from wild-type mice. However, the same treatment did not lead to any measurable change in the nanoroughness or stiffness of the cartilage from mutant mice Jaffa. This suggests that blocking aggrecanolysis by genetic modification has created the stability in the structures and mechanical properties of the cartilage at nanoscale. The present study provides insight into the mechanism of aggrecan degradation, which can complement the examination by biochemical and histological techniques.

Dynamics of mono- and dual-species biofilm formation and interactions between Staphylococcus aureus and Gram-negative bacteria

Microorganisms are not commonly found in the planktonic state but predominantly form dual- and multispecies biofilms in almost all natural environments. Bacteria in multispecies biofilms cooperate, compete or have neutral interactions according to the involved species. Here, the development of mono- and dual-species biofilms formed by Staphylococcus aureus and other foodborne pathogens such as Salmonella enterica subsp. enterica serovar Enteritidis, potentially pathogenic Raoultella planticola and non-pathogenic Escherichia coli over the course of 24, 48 and 72 h was studied. Biofilm formation was evaluated by the crystal violet assay (CV), enumeration of colony-forming units (CFU cm-2 ) and visualization using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). In general, Gram-negative bacterial species and S. aureus interacted in a competitive manner. The tested Gram-negative bacteria grew better in mixed dual-species biofilms than in their mono-species biofilms as determined using the CV assay, CFU ml-2 enumeration, and CLSM and SEM visualization. In contrast, the growth of S. aureus biofilms was reduced when cultured in dual-species biofilms. CLSM images revealed grape-like clusters of S. aureus and monolayers of Gram-negative bacteria in both mono- and dual-species biofilms. S. aureus clusters in dual-species biofilms were significantly smaller than clusters in S. aureus mono-species biofilms.

Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages

Background

Bifidobacterium longum 105-A produces markedly high amounts of capsular polysaccharides (CPS) and exopolysaccharides (EPS) that should play distinct roles in bacterial–host interactions. To identify the biological function of B. longum 105-A CPS/EPS, we carried out an informatics survey of the genome and identified the EPS-encoding genetic locus of B. longum 105-A that is responsible for the production of CPS/EPS. The role of CPS/EPS in the adaptation to gut tract environment and bacteria-gut cell interactions was investigated using the ΔcpsD mutant.

Results

A putative B. longum 105-A CPS/EPS gene cluster was shown to consist of 24 putative genes encoding a priming glycosyltransferase (cpsD), 7 glycosyltransferases, 4 CPS/EPS synthesis machinery proteins, and 3 dTDP-L-rhamnose synthesis enzymes. These enzymes should form a complex system that is involved in the biogenesis of CPS and/or EPS. To confirm this, we constructed a knockout mutant (ΔcpsD) by a double cross-over homologous recombination. Compared to wild-type, the ∆cpsD mutant showed a similar growth rate. However, it showed quicker sedimentation and formation of cell clusters in liquid culture. EPS was secreted by the ∆cpsD mutant, but had altered monosaccharide composition and molecular weight. Comparison of the morphology of B. longum 105-A wild-type and ∆cpsD by negative staining in light and electron microscopy revealed that the formation of fimbriae is drastically enhanced in the ∆cpsD mutant while the B. longum 105-A wild-type was coated by a thick capsule. The fimbriae expression in the ∆cpsD was closely associated with the disappearance of the CPS layer. The wild-type showed low pH tolerance, adaptation, and bile salt tolerance, but the ∆cpsD mutant had lost this survivability in gastric and duodenal environments. The ∆cpsD mutant was extensively able to bind to the human colon carcinoma Caco-2 cell line and was phagocytosed by murine macrophage RAW 264.7, whereas the wild-type did not bind to epithelial cells and totally resisted internalization by macrophages.

Conclusions

Our results suggest that CPS/EPS production and fimbriae formation are negatively correlated and play key roles in the survival, attachment, and colonization of B. longum 105-A in the gut.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-017-0177-x) contains supplementary material, which is available to authorized users.

Modeling and Identification of the Rate-Dependent Hysteresis of Piezoelectric Actuator Using a Modified Prandtl-Ishlinskii Model

Piezoelectric actuator (PEA) is an ideal microscale and nanoscale actuator because of its ultra-precision positioning resolution. However, the inherent hysteretic nonlinearity significantly degrades the PEA’s accuracy. The measured hysteresis of PEA exhibits strong rate-dependence and saturation phenomena, increasing the difficulty in the hysteresis modeling and identification. In this paper, a modified Prandtl-Ishlinskii (PI) hysteresis model is proposed. The weights of the backlash operators are updated according to the input rates so as to account for the rate-dependence property. Subsequently, the saturation property is realized by cascading a polynomial operator with only odd powers. In order to improve the efficiency of the parameter identification, a special control input consisting of a superimposition of multiple sinusoidal signals is utilized. Because the input rate of such a control input covers a wide range, all the parameters of the hysteresis model can be identified through only one set of experimental data, and no additional curve-fitting is required. The effectiveness of the hysteresis modeling and identification methodology is verified on a PEA-driven flexure mechanism. Experimental results show that the modeling accuracy is on the same order of the noise level of the overall system.

Influence of Fimbriae on Bacterial Adhesion and Viscoelasticity and Correlations of the Two Properties with Biofilm Formation

The surface polymers of bacteria determine the ability of bacteria to adhere to a substrate for colonization, which is an essential step for a variety of microbial processes, such as biofilm formation and biofouling. Capsular polysaccharides and fimbriae are two major components on a bacterial surface, which are critical for mediating cell-surface interactions. Adhesion and viscoelasticity of bacteria are two major physical properties related to bacteria-surface interactions. In this study, we employed atomic force microscopy (AFM) to interrogate how the adhesion work and the viscoelasticity of a bacterial pathogen, Klebsiella pneumoniae, influence biofilm formation. To do this, the wild-type, type 3 fimbriae-deficient, and type 3 fimbriae-overexpressed K. pneumoniae strains have been investigated in an aqueous environment. The results show that the measured adhesion work is positively correlated to biofilm formation; however, the viscoelasticity is not correlated to biofilm formation. This study indicates that AFM-based adhesion measurements of bacteria can be used to evaluate the function of bacterial surface polymers in biofilm formation and to predict the ability of bacterial biofilm formation.

Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain

For several decades, many bacteria, among which A. baumannii, have shown their ability to colonize the upper surface of static liquids, forming a biofilm at the air-liquid interface named pellicle. Despite the ubiquity of these pellicles in both natural and artificial environments, few studies have investigated this biofilm type. The present data set provides the first description of the whole proteome of A. baumannii cells grown as pellicle, using a label-free mass spectrometry approach. Results are in accord with the general findings reporting that sessile bacteria are far more resistant to detrimental conditions than their planktonic counterparts, by the accumulation of stress proteins. The present investigation also confirmed previous studies suggesting a correlation between the pellicle forming ability and the bacterial virulence. Indeed, we showed the up-regulation of numerous virulence factors during the pellicle growth, e.g. phospholipases, adhesion factors, as well as those of the GacAS Two-Component System (TCS) and Type 6 Secretion System (T6SS). We also highlighted that Bam and Tam systems, both related to the OM insertion machinery, play a critical role during pellicle biogenesis. Moreover, sessile bacteria activate several pathways, e.g. iron, magnesium, phosphate pathways, which allows for increasing the panel of nutrient sources.

Atomic Force Microscopy Studies of the Interaction of Antimicrobial Peptides with Bacterial Cells

Antimicrobial peptides (AMPs) are promising therapeutic alternatives to conventional antibiotics. Many AMPs are membrane-active but their mode of action in killing bacteria or in inhibiting their growth remains elusive. Recent studies indicate the mechanism of action depends on peptide structure and lipid components of the bacterial cell membrane. Owing to the complexity of working with living cells, most of these studies have been conducted with synthetic membrane systems, which neglect the possible role of bacterial surface structures in these interactions. In recent years, atomic force microscopy has been utilized to study a diverse range of biological systems under non-destructive, physiologically relevant conditions that yield in situ biophysical measurements of living cells. This approach has been applied to the study of AMP interaction with bacterial cells, generating data that describe how the peptides modulate various biophysical behaviours of individual bacteria, including the turgor pressure, cell wall elasticity, bacterial capsule thickness, and organization of bacterial adhesins.

Interrogation of drug effects on HeLa cells by exploiting new AFM mechanical biomarkers

New AFM mechanical biomarkers including cell brush length, adhesion work and the factor of viscosity are discovered for drug assays.