Comparison of computer resources needed for FDM, FEM and BEM modeling of cantilever beam structure.
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Barely three months into the new year and we are happy to announce a monumental milestone reached - 150 million downloads.
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Design of several devices and their measurements aspects are introduced. Topics related to microwave region as well as Terahertz and quasi-optical region are considered. Bi-isotropic metamaterial in optical region is investigated. Interesting numerical methods in frequency domain and time domain for scattering, radiation, forward as well as reverse problems and microwave imaging are summarized. 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Venkateswarlu",coverURL:"https://cdn.intechopen.com/books/images_new/371.jpg",editedByType:"Edited by",editors:[{id:"58592",title:"Dr.",name:"Arun",surname:"Shanker",slug:"arun-shanker",fullName:"Arun Shanker"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"72",title:"Ionic Liquids",subtitle:"Theory, Properties, New Approaches",isOpenForSubmission:!1,hash:"d94ffa3cfa10505e3b1d676d46fcd3f5",slug:"ionic-liquids-theory-properties-new-approaches",bookSignature:"Alexander Kokorin",coverURL:"https://cdn.intechopen.com/books/images_new/72.jpg",editedByType:"Edited by",editors:[{id:"19816",title:"Prof.",name:"Alexander",surname:"Kokorin",slug:"alexander-kokorin",fullName:"Alexander Kokorin"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"314",title:"Regenerative Medicine and Tissue Engineering",subtitle:"Cells and Biomaterials",isOpenForSubmission:!1,hash:"bb67e80e480c86bb8315458012d65686",slug:"regenerative-medicine-and-tissue-engineering-cells-and-biomaterials",bookSignature:"Daniel Eberli",coverURL:"https://cdn.intechopen.com/books/images_new/314.jpg",editedByType:"Edited by",editors:[{id:"6495",title:"Dr.",name:"Daniel",surname:"Eberli",slug:"daniel-eberli",fullName:"Daniel Eberli"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"57",title:"Physics and Applications of Graphene",subtitle:"Experiments",isOpenForSubmission:!1,hash:"0e6622a71cf4f02f45bfdd5691e1189a",slug:"physics-and-applications-of-graphene-experiments",bookSignature:"Sergey Mikhailov",coverURL:"https://cdn.intechopen.com/books/images_new/57.jpg",editedByType:"Edited by",editors:[{id:"16042",title:"Dr.",name:"Sergey",surname:"Mikhailov",slug:"sergey-mikhailov",fullName:"Sergey Mikhailov"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"1373",title:"Ionic Liquids",subtitle:"Applications and Perspectives",isOpenForSubmission:!1,hash:"5e9ae5ae9167cde4b344e499a792c41c",slug:"ionic-liquids-applications-and-perspectives",bookSignature:"Alexander Kokorin",coverURL:"https://cdn.intechopen.com/books/images_new/1373.jpg",editedByType:"Edited by",editors:[{id:"19816",title:"Prof.",name:"Alexander",surname:"Kokorin",slug:"alexander-kokorin",fullName:"Alexander Kokorin"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}}]},chapter:{item:{type:"chapter",id:"70854",title:"Boundary Element Mathematical Modelling and Boundary Element Numerical Techniques for Optimization of Micropolar Thermoviscoelastic Problems in Solid Deformable Bodies",doi:"10.5772/intechopen.90824",slug:"boundary-element-mathematical-modelling-and-boundary-element-numerical-techniques-for-optimization-o",body:'\n
The classical thermo-elasticity (CTE) theory which was introduced by Duhamel [1] and Neumann [2] characterized the strain-temperature gradients equations in an elastic body, but it has two shortcomings contrary to physical observations: First, the heat conduction equation of this theory does not include any elastic terms. Second, the heat conduction equation is of a parabolic type predicting infinite speeds of thermal waves. Biot [3] developed the classical coupled thermo-elasticity (CCTE) theory to overcome the first shortcoming in CTE. However, both theories share the second shortcoming. So, several generalized thermoelasticity theories that predict finite speeds of propagation for heat waves have been developed such as extended thermo-elasticity (ETE) theory of Lord and Shulman [4], temperature-rate-dependent thermo-elasticity (TRDTE) theory of Green and Lindsay [5], three linear generalized thermoelasticity theories (type I, II and III) of Green and Naghdi [6, 7], low-temperature thermoelasticity (LTTE) model of Hetnarski and Ignaczak [8], the dual phase-lag (DPL) heat conduction equation of Tzou [9, 10] which has been developed taking into consideration the phonons-electrons interactions to obtain dual phase-lag thermoelasticity (DPLTE) [11, 12], and three-phase-lag thermoelasticity (TPLTE) model of Choudhuri [13] who takes into consideration the phase-lags of heat flux, temperature gradient and thermal displacement gradient. Chen and Gurtin [14], introduced the theory of two-temperatures (conductive temperature and thermodynamic temperature) heat conduction in the context of elastic bodies, then Youssef [15] extended this theory to generalized thermoelasticity. Fahmy [16] introduced three-temperature nonlinear generalized micropolar-magneto-thermoelasticity theory and developed a new boundary element technique for Modeling and Simulation of complex problems associated with this theory. Theory of micropolar elasticity [17, 18] has been developed for studying the mechanical behavior of polymers and elastomers and applied in many applications [19, 20, 21, 22, 23, 24]. Then, Eringen [25] and Nowacki [26] extended it to micropolar thermoelasticity, and then implemented in various applications [27, 28, 29]. Because of strong nonlinearity of three-temperatures radiative heat conduction equations, the numerical solution and simulation of such problems are always difficult and require the development of new numerical schemes [30, 31]. In comparison with other numerical methods [32, 33, 34], the boundary element method has been successfully applied and performed for solving various applications [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]. The boundary element technique has been formulated in the context of micropolar thermoelasticity by Sladek and Sladek [61, 62, 63] and Huang and Liang [64]. Through the current paper, the term three-temperatures introduced for the first time in the field of nonlinear generalized micropolar thermoviscoelasticity. Recently, evolutionary algorithms [65, 66] have received much attention of researchers. The genetic algorithm (GA) can deal with the multi-objective and complex shapes problems. Also, it could reach an optimal solution with highly reduced computational cost.
\nThe main aim of this article is to introduce a new theory called nonlinear generalized micropolar thermoviscoelasticity involving three temperatures. Because of strong nonlinearity, it is very difficult to solve the problems related to this theory analytically. Therefore, we propose a new boundary element model for simulation and optimization of three temperatures nonlinear generalized micropolar thermoviscoelastic problems associated with this theory. The genetic algorithm (GA) was implemented based on free form deformation (FFD) technique and nonuniform rational B-spline (NURBS) curve as an optimization technique for the considered problems. The numerical results demonstrate the validity and accuracy of our proposed model.
\nThe governing equations for three-temperature anisotropic generalized micropolar thermoviscoelasticity problems can be expressed as [58]
\nwhere
\nThe two-dimension three-temperature (2D-3T) radiative heat conduction equations can be expressed as [53]
\nWith reference to a Cartesian coordinate system \n
The 2D-3T radiative heat conduction Eqs. (6)–(8) can be expressed as [53]
\nwhere
\nand
\nwhere parameters \n
The total energy of unit mass can be described by
\nInitial and boundary conditions can be written as
\nwe use the time-dependent fundamental solution which is a solution of the following differential equation
\nIn which the points \n
The boundary integral equation corresponding to our considered heat conduction can be written as in Fahmy [46, 47, 48] as follows
\nwhich can be expressed in the following form [53].
\nThe time derivative of temperature \n
where \n
Also, we assume that \n
Thus, Eq. (18) results in the following boundary integral equation [53]
\nwhere
\nand
\nIn which the entries of \n
The boundary integral discretization scheme has been applied to (21) with the use of (23), we get [53]
\nwhere \n
The diffusion matrix can be defined as
\nwith
\nFor solving (25) numerically, we interpolate the functions \n
where \n
The time derivative of (29) can be expressed as
\nBy substituting from Eqs. (29)–(31) into Eq. (25), we obtain
\nMaking use of initial conditions and boundary conditions at \n
The Adaptive Smoothing and Prolongation Algebraic Multigrid (aSP-AMG) method, which uses an adaptive Factorized Sparse Approximate Inverse (aFSAI) [67] preconditioner as high performance technique that has been implemented efficiently in Matlab (R2018a) for solving the resulting simultaneous linear algebraic systems (33).
\nAccording to the weighted residual method, we can write the differential Eqs. (1) and (2) in the following integral form
\nwhere
\nThe boundary conditions are
\nBy integrating by parts the first term of Eqs. (34) and (35), we obtain
\nOn the basis of Huang and Liang [64], we can write
\nBy integrating by parts, the left-hand side of (43) can be written as
\nAccording to Eringen [68], the elastic and couple stresses can be written in the following form
\nwhere \n
Hence, Eq. (44) can be re-expressed as [53]
\nBy applying integration by parts again, the left-hand side of (46) can be written as [53]
\nThe obtained weighting functions for \n
According to Dragos [69], the fundamental solutions can be written as
\nThe obtained weighting functions for \n
The fundamental solutions that have been obtained analytically by Dragos [69] can be written as
\nUsing the above two sets of weighting functions into (47) we have
\nThus, we can write
\nwhere
\nIn order to solve (56) numerically, we construct the following functions
\nsubstituting above functions into (56) and discretizing the boundary, we obtain
\nEquation after integration may be expressed as
\nwhich can be expressed as
\nwhere
\nThus, we can write the following system of matrix equation as
\nHence, we get the following system of linear algebraic equations
\nIn order to solve (63), we apply adaptive smoothing and prolongation algebraic multigrid (aSP-AMG) based on adaptive Factorized Sparse Approximate Inverse (aFSAI) as described in [67] for solving the resulting simultaneous linear algebraic system (63) in Matlab (R2018a).
\nB-spline basis functions are used as weights in the same manner as Bézier basis functions. Spline curves can be expressed in terms of \n
The efficiency of our numerical modeling technique has been improved using a nonuniform rational B-spline curve (NURBS) to decrease the computation time and model optimized boundary where it reduces the number of control points and provides the flexibility to design a large variety of shapes.
\nThe considered NURBS can be defined as follows
\nwhere \n
The genetic algorithm greatly reduces computing time and computer memory of achieving an optimum solution, so, it can be used for solving multi-objective problems without needing to calculate the sensitivities. The profiles of the considered objects are represented based on the free form deformation (FFD) technique, where the FFD control points are considered as the genes and then the profiles of chromosomes are defined by the sequence of genes. The population is constructed by many individuals (chromosomes), where the fitness functions are evaluated by using the BEM.
\nTwo criteria can be implemented during shape optimization of the solid bodies [70]
\nI. The minimum global compliance:
\nII. The minimum boundary equivalent stresses
\n\n\n
In order to find the optimal boundary conditions for temperature the following functional can be applied
\nwhere \n
In order to identify unknown inner boundary, we use the following functional
\nwhere \n
For illustration of the theoretical results of our proposed technique from the preceding sections, two numerical examples are analyzed below. The first example is the cantilever beam with inferior corner load, the second is the Michell-type structure, where the material has the following physical data [58]:
\nThe elasticity tensor
\n\n\n
As a practical example, the proposed algorithm is applied on the cantilever beam with inferior corner load \n
Cantilever beam structure geometry.
Initial boundary of the cantilever beam structure.
Cantilever beam optimization process from initial to final structure for different iterations.
The present measured boundary element method (BEM) optimization results of the first example are compared in Figure 4 with measured finite difference method (FDM) optimization results obtained by Itzá et al. [71] and measured finite element method (FEM) optimization results obtained using the software package COMSOL Multiphysics, version 5.4. It is clear from this figure that the BEM results obtained by the proposed technique are in excellent agreement with the FDM results [71] and FEM results of the COMSOL Multiphysics.
\nFinal cantilever beam structure for BEM, FDM and FEM.
\nTable 1 shows that our proposed BEM modeling of cantilever beam with inferior corner load drastically reduces the manpower needed for modeling and computer resources needed for the calculation in comparison with the calculated results based on the FDM and FEM.
\nComparison of computer resources needed for FDM, FEM and BEM modeling of cantilever beam structure.
As application example, we use a beam with a mid-span load \n
Michel-type structure geometry.
Initial boundary of the Michel-type structure.
\nFigure 7 shows the cantilever beam optimization process from initial to final structure for different iterations.
\nMichell-type structure optimization process from initial to final structure for different iterations.
The optimization results of the second example obtained with the proposed BEM are compared in Figure 8 with FDM optimization results [71] and FEM optimization results of COMSOL Multiphysics software, version 5.4. It is clear from this figure that our BEM results obtained by the proposed technique are in excellent agreement with the FDM and FEM results.
\nFinal Michell-type structure for BEM, FDM and FEM.
\nTable 2 shows that our proposed BEM modeling of Michell-type structure dramatically reduces the computer resources necessary to calculate our proposed modeling in comparison with the calculated results based on the FDM and FEM.
\nComparison of computer resources needed for FDM, FEM and BEM modeling of Michell-type structure.
In the present paper, we propose a new theory called nonlinear micropolar thermoviscoelasticity involving three temperatures. A new mathematical modeling of nonlinear generalized micropolar thermoviscoelasticity problem. A new boundary element technique for simulation and optimization problems of mechanics of solid deformable bodies is implemented based on genetic algorithm (GA), free form deformation (FFD) method and nonuniform rational B-spline curve (NURBS) as the global optimization technique for solving complex simulation and optimization problems associated with the proposed theory. FFD is an efficient and versatile parameterization technique for treating shape optimization problems with complex shapes. It is implemented for simulation and optimization of the shape. In the formulation of the considered problem, solutions are obtained for specific arbitrary parameters which are the control points positions in the considered problem, the profiles of the considered objects are determined by FFD method, where the FFD control points positions are treated as genes, and then the chromosomes profiles are defined with the genes sequence. The population is founded by a number of individuals (chromosomes), where the objective functions of individuals are determined by the boundary element method (BEM). Due to the large amount of computer resources required by the FDM and FEM, our proposed BEM model can be applied to a wide range of simulation and optimization problems related with our proposed theory. The numerical results demonstrate the validity, accuracy and efficiency of our proposed technique.
\n\n\n\nα\n,\n\nα\n¯\n\n,\nα\n̿\n,\nα\nˇ\n\n\n | micro-polar constants |
\n\n\n\nβ\nij\n\n\n\n | stress–temperature coefficients |
\n\n\n\nδ\nij\n\n\n\n | Kronecker delta \n\n\ni\n\nj\n=\n1\n\n2\n\n\n\n |
\n\n\nδ\n\n, \n\nη\n\n\n | weight coefficients |
\n\n\n\nε\nij\n\n\n\n | strain tensor |
\n\n\n\nε\nijk\n\n\n\n | alternate tensor |
\n\n\n\nϵ\nij\n\n\n\n | micro-strain tensor |
\n\n\nλ\n\n\n | tractions |
\n\n\n\nϑ\n0\n\n\n\n | viscoelastic relaxation time |
\n\n\nϖ\n\n\n | weights of control points |
\n\n\nρ\n\n\n | material density |
\n\n\n\nσ\nij\n\n\n\n | force stress tensor |
\n\n\n\nσ\n0\n\n\n\n | reference stress |
\n\n\nτ\n\n\n | time |
\n\n\n\nτ\n0\n\n,\n\nτ\n1\n\n,\n\nτ\n2\n\n\n\n | relaxation times |
\n\n\n\nω\ni\n\n\n\n | micro-rotation vector |
\n\n\nℵ\n\n\n | \n\n\n=\n\n\n1\n+\n\nϑ\n0\n\n\n∂\n\n∂\nτ\n\n\n\n\n\n viscoelastic constant |
\n\n\nb\n\n\n | internal heat generation vector |
\n\n\nc\n\n\n | specific heat capacity |
\n\n\n\nC\nijkl\n\n\n\n | constant elastic moduli |
\n\n\ne\n\n\n | \n\n\n=\n\nε\nkk\n\n=\n\nϵ\nkk\n\n\n dilatation |
\n\n\n\ne\nlij\n\n\n\n | piezoelectric tensor |
\n\n\n\nF\ni\n\n\n\n | mass force vector |
\n\n\nJ\n\n\n | micro-inertia coefficient |
\n\n\nJ\n\n\n | current density vector |
\n\n\n\nK\ne\n\n\n\n | electron conductive coefficients |
\n\n\n\nK\ni\n\n\n\n | ion conductive coefficients |
\n\n\n\nK\nr\n\n\n\n | phonon conductive coefficients |
\n\n\nk\n\n, \n\nl\n\n\n | boundary points |
\n\n\nM\n,\nN\n\n\n | sensors numbers |
\n\n\n\nM\ni\n\n\n\n | mass couple vector |
\n\n\n\nm\nij\n\n\n\n | couple stress tensor |
\n\n\nP\n\n\n | total energy of unit mass |
\n\n\n\nP\ne\n\n\n\n | \n\n\n=\n\nc\ne\n\n\nT\ne\n\n\n Electron energy |
\n\n\n\nP\ni\n\n\n\n | \n\n\n=\n\nc\ni\n\n\nT\ni\n\n\n Ion energy |
\n\n\n\nP\nr\n\n\n\n | \n\n\n=\n\n1\nρ\n\n\nc\nr\n\n\nT\nr\n4\n\n\n Phonon energy |
\n\n\nℙ\n\n\n | values vector of tractions and couple stress |
\n\n\n\np\ni\n\n\n\n | singular points |
\n\n\nQ\n\n\n | heat flux vectors |
\n\n\nℚ\n\n\n | values vector of displacements and microrotations |
\n\n\nR\n\n\n | problem’s boundary |
\n\n\nS\n\n\n | problem’s domain |
\n\n\n\nT\ne\n\n\n\n | electron temperature |
\n\n\n\nT\ni\n\n\n\n | ion temperature |
\n\n\n\nT\nr\n\n\n\n | phonon temperature |
\n\n\nu\n\n\n | boundary displacement |
\n\n\n\nu\ni\n\n\n\n | displacement vector |
\n\n\n\nu\n0\n\n\n\n | reference displacement |
\n\n\n\nu\nk\n\n\n\n | computed displacements |
\n\n\n\n\nu\n̂\n\nk\n\n\n\n | measured displacements |
\n\n\n\nW\nei\n\n\n\n | electron-ion energy coefficient |
\n\n\n\nW\ner\n\n\n\n | electron–phonon energy coefficient |
UTI affects approximately 150 million people worldwide, which is most common infection with female predominance [1]. Around 15–25% hospitalized patients receiving indwelling urinary catheter develops CAUTI with prolonged catheterization and in among 40% nosocomial UTI, 80% is due to CAUTI [2]. CAUTI causes about 20% of episodes of health-care acquired bacteraemia in intensive care facilities and over 50% in long term care facilities [3]. The microbiology of biofilm on an indwelling catheter is dynamic with continuing turnover of organisms in the biofilm. Patients continue to acquire new organisms at a rate of about 3–7%/day. In long term catheterization that is by the end of 30 days CAUTI develops in 100% patients usually with 2 or more symptoms or clinical sign of haematuria, fever, suprapubic or loin pain, visible biofilm in character or catheter tube and acute confusion all state [4]. In CAUTI the incidence of infection is
It is recommended that urine specimens be obtained through the catheter port using aseptic technique or, if a port is not present, puncturing the catheter tubing with a needle and syringe in patients with short term catheterization [11]. In long term indwelling catheterization, the ideal method of obtaining urine for culture is to replace the catheter and collect the specimen from the freshly placed catheter. In a symptomatic patient, this should be done immediately prior to initiating antimicrobial therapy. Culture specimens from the urine beg should not be obtained [10, 12]. Urine sample can be collected from suprapubic puncture also. Biofilm can be cultured from the catheter, for this swab is taken from inner side of catheter.
Catheter Associated Asymptomatic Bacteriuria (CA-ASB) is diagnosed when one or more organisms are present at quantitative counts ≥105 cfu/mL from an appropriately collected urine specimen in a patient with no symptoms [13]. Lower quantitative counts may be isolated from urine specimens prior to ≥105 cfu/mL being present, but these lower counts likely reflect the presence of organisms in biofilm forming along the catheter, rather than bladder bacteriuria [14]. Thus, it is recommended that the catheter be removed and a new catheter inserted, with specimen collection from the freshly placed catheter, before antimicrobial therapy is initiated for symptomatic infection [13]. In biofilm culture, most biofilm contains mixed bacterial communities meaning polymicrobial colonization.
Patients who remain catheterized without having antimicrobial therapy and who have colony counts ≥10 2 cfu/mL (or even lower colony counts), the level of bacteriuria or candiduria uniformly increases to >105 cfu/mL within 24–48 h [14]. Given that colony counts in bladder urine as low as 102 cfu/mL are associated with symptomatic UTI in non-catheterized patients [15], untreated catheterized patients and those who have colony counts ≥102 cfu/mL or even lower, the level of bacteriuria or candiduria uniformly increases to >105 cfu/mL within 24–48 h [10, 16]. Colony counts as low as 102 cfu/mL in bladder urine may be associated with symptomatic UTI in non-catheterized patients. Whereas low colony counts in catheter urine specimens are likely to be contaminated by periurethral flora, and the colony counts will increase rapidly if untreated. Low colony counts in catheter urine specimens are also reflective of significant bacteriuria in patients with intermittent catheterization [14].
Pyuria is usually present in CA-UTI, as well as in CA-ASB. The sensitivity of pyuria for detecting infections due to enterococci or yeasts appears to be lower than that for gram-negative bacilli. Dipstick testing for nitrites and leukocyte esterase was also shown to be unhelpful in establishing a diagnosis in catheterized patients hospitalized in the ICU [17].
It is the most common cause of CAUTI in 24–60% patients [5, 18]. In CAUTI the source of this organism is usually patients own colonic flora.
It has three antigens O-cell was antigen, H- flagella antigen and k- Capsular antigen. It has pili—a capsule, fimbriae, endotoxins and exotoxins also. Uropathogenic
Gram stain picture and morphology of
Diagnosis of
Proteus species, member of the Enterobacteriaceae family of gram-negative bacilli are distinguishable from most other genera by their ability to swarm across an agar surface [23, 24]. Proteus species are most widely distributed in environment and as other enterobacteriaceae, this bacteria is part of intestinal flora of human being [25, 26]. Proteus also found in multiple environmental habitats, including long-term care facilities and hospitals. In hospital setting, it is not unusual for proteus species to colonize both the skin and mucosa of hospitalized patient and causing opportunistic nosocomial infections. It is one of the common causes of UTI in hospitalized patients undergoing urinary catheterization [26, 27].
UTIs are the most common manifestation of Proteus infection. Proteus infection accounts for 1–2% of UTIs in healthy women and 5% of hospital acquired UTIs. Catheters associated UTI have a prevalence of 20–45%. Proteus mirabilis causes 90% of proteus infection and proteus vulgaris and proteus penneri also isolated from long-term care facilities and hospital and from patients with underlying disease or specialized care. Most common age group is 20–50 years. More common in female group and the ratio between male female begins to decline after 50 years. UTI in men younger than 50 are usually caused by urologic abnormalities. Patients with recurrent infections, those with structural abnormalities of the urinary tract, those who have had urethral instrumentation or catheterization have an increase frequency of infection caused by proteus species [28].
Proteus mirabilis produces an acidic capsular polysaccharide which was shown from glycose analysis, carboxyl reduction, methylation, periodate oxidation and the application high resolution nuclear magnetic resonance techniques. Proteus species possess an extracytoplasmic outer membrane, a common feature shared with other gram-negative bacteria. Infection depends upon the interacting organism and the host defense mechanism. Various component of the membrane interplay with the host to determine virulence. Virulence factors associated with adhesion, motility, biofilm formation, immunoavoidance, nutrient acquisition and as well as factors that cause damage to the host [29, 30] (Figure 2).
Gram stain picture and morphology of Proteus. Adapted from CCBC faculty web. BIOL 230 Lab Manual: gram stain of Proteus mirabilis and Proteus vulgaris bacteria (SEM) | Macro & Micro: Up Close and Personal | Pinterest | Microbiology, Bacteria shapes and Fungi.
Certain virulence factors such as adhesin, motility and biofilm formation have been identified in Proteus species that has a positive correlation with risk of infection. After attachment of Proteus with urothelial cells, interleukin 6 and interleukin 8 secreted from the urothelial cells causes apoptosis and mucosal endothelial cell desquamation. Urease production of proteus also augments the risk of UTI. Urease production, together with the presence of bacterial motility and fimbriae or pili, as well as adhesins anchored directly within bacterial cell membrane may favor the upper urinary tract infection. Once firmly attached on the uroepithelium or catheter surface, bacteria begin to phenotypically change, producing exopolysaccharides that entrap and protect bacteria. These attached bacteria replicate and form microcolonies that eventually mature into biofilms [31, 32]. Once established, biofilms inherently protect uropathogens from antibiotic and the host immune response [33, 34]. Proteus mirabilis as with other uropathogens is capable of adapting to the urinary tract environment and acquiring nutrients. And this is accomplished by the production of degradative enzymes such urease and proteases, toxins such as Haemolysin Hpm A and iron nutrient acquisition proteins.
The infection with Proteus can be diagnosed by taking a urine sample for microscopy and culture which is sufficient in most of the cases except in few cases where advanced diagnostic tools are used. If the urine is alkaline, it is suggestive of infection with Proteus sp. The diagnosis of Proteus is made on swarming motility on media, unable to metabolized lactose and has a distinct fishy door. Ultrasound or CT scan to identify renal stone (Struvite stone) or to visualized kidneys or surrounding structures. It will allow to exclude other possible problems, mimicking symptoms of urinary tract infection [35, 36].
Pseudomonas is a gram-negative bacteria belonging to the family Pseudomonadaceae and containing 191 validly described species [37]. Because of their widespread occurrence in water and plant seeds, the pseudomonas was observed in early history of microbiology. Pseudomonas is flagellated, motile, aerobic organism with Catalase and oxidase-positive. Pseudomonas may be the most common nuclear or of ice crystals in clouds, thereby being of utmost importance to the formation of snow and rain around the world [38]. All species of Pseudomonas are strict aerobes, and a significant number of organisms can produce exopolysaccharides associated with biofilm formation [39]. Pseudomonas is an opportunistic human pathogen that is especially adept at forming surface associated biofilms. Pseudomonas causes catheter associated urinary tract infection(CAUTIs) through biofilm formation on the surface of indwelling catheters, and biofilm mediated infection including ventilator associated pneumonia, infections related to mechanical heart valves, stents, grafts, sutures, and contract lens associated corneal infection [40].
Pseudomonas is third ranking causes nosocomial UTI about 12%, where
Pseudomonas aeruginosa is a gram-negative, rod shaped, asporogenous and monoflagellated, noncapsular bacterium but many strains have a mucoid slime layer. Pseudomonas has an incredible nutritional versatility. Pseudomonas can catabolize a wide range of organic molecule including organic compounds such as benzoate. This, then make Pseudomonas a very ubiquitous microorganism and Pseudomonas is the most abundant organism on earth [43] (Figure 3).
Gram stain picture and morphology of Pseudomonas aeroginosa. Adapted from Science News. A new antibiotic uses sneaky tactics to kill drug-resistant Pseudomonas aeruginosa illustration and Pseudomonas Aeruginosa Stock Photos & Pseudomonas Aeruginosa Stock Images—Alams.
Pseudomonas is widely distributed in nature and is commonly present in moist environment of hospitals. It is pathogenic only when introduce into areas devoid of normal defense such as disruption of mucous membrane and skin, usage of intravenous or urinary catheters and neutropenia due to cancer or in cancer therapy. Its pathogenic activity depends on its antigenic structure, enzymes and toxins [44]. Among the enzymes Catalase, Pyocyanin, Proteases, elastase, haemolysin, Phospholipase C, exoenzyme S and T and endotoxin and endotoxin A play role in disease process and as well as immunosuppression. Pseudomonas can infect almost any organ or external site. Pseudomonas in invasive and toxigenic. It attached to and colonized the mucous membrane of skin. Pseudomonas can invade locally to produce systemic disease and septicemia. Pseudomonal UTs are usually hospital acquired and are associated with catheterization, instrumentation and surgery. These infections can involve the urinary tract through an ascending infection or through bacteriuria spread. These UTIs may be a source of bacteraemia or septicemia [45].
Identification of bacterium with microscopy is simple method of identification of pseudomonas. Culture and antibiotic sensitivity pattern can be done in most laboratory media commonly on blood agar or eosin-methylthionine blue agar. Pseudomonas has inability to ferment lactose and has a positive oxidase reaction. Fluorescence under UV light is helpful in early identification of colonies. Fluorescence is also used to suggest the presence of pseudomonas in wounds [46].
Urinary catheters are standard medical devices utilized in both hospital and nursing home settings are associated with a high frequency of catheter-associated urinary tract infections (CAUTI). The contribution of Klebsiella spp. in CAUTI is near about 7.7% [47].
Gram stain picture and morphology of Klebsiella pneumonie. Adapted from studyblue.com. Microbio Lab Practical I—Microbiology 101 with Johnson at University of Vermont—StudyBlue. Study 368 Microbio Lab Practical I flashcards from Tess H. on StudyBlue and Klebsiella Pneumoniae Stock Photos and Pictures. Getty Images
The source of Klebsiella causing CAUTI can be endogenous typically via meatal, rectal, or vaginal colonization or exogenous, such as via equipment or contaminated hands of healthcare personnel. They typically migrate along the outer surface of the indwelling urethral catheter, until they enter the urethra.
Migration of the Klebsiella along the inner surface of the indwelling urethral catheter occurs much less frequently, compared with along the outer surface Internal (intraluminal) bacterial ascension occurs by Klebsiella tend to be introduced when opening the otherwise closed urinary drainage system, ascend from the urine collection bag into the bladder via reflux, biofilm formation occurs.
A critical step in progression to CAUTI by Klebsiella is to adhere to host surfaces, which is frequently achieved using pili (fimbriae) [49]. Pili are filamentous structures extending from the surface of Klebsiella. They can be as long as 10 μm and between 1 and 11 nm in diameter. Among the two types of pili—type 1 (fim) pili and type 3 (mrk) pili, type 1 aids virulence by their ability to adhere with mucosal surfaces and type 3 pili strongly associated with biofilm production [50]. Both fim and mrk pili are considered part of the core genome [51]. It is thought that both types of pili play a role in colonization of urinary catheters, leading to CAUTI [52]. In addition to fim and mrk pili, a number of additional usher-type pili have been identified in Klebsiella with an average of ~8 pili clusters per strain. Based on varying gene frequencies, some of these appear to be part of the accessory genome. Immediately after catheterization Klebsiella starts biofilm production on the inner as well as outer surface of the catheter and on urothelium. Biofilm augments migration of Klebsiella into urethra and urinary bladder. Biofilm formation on the catheter surface by
Modifiable risk factor are prolonged catheterization, lack of adherence to aseptic catheter care, insertion of the indwelling urethral catheter in a location other than an operating room, presence of a urethral stent, feecal incontinence. Non-modifiable risk factor—renal disease (i.e., serum creatinine >2 mg/dL), diabetes mellitus, older age (i.e., age > 50 years old), female sex, malnutrition and severe underlying illness [53]. For infection several virulence factors such as surface factors (fimbriae, adhesins, and P and type 1 pili) and extracellular factors toxins, siderophores, enzymes, and polysaccharide coatings are necessary for initial adhesion with colonization of host mucosal surfaces for tissue invasion overcoming the host defense mechanisms, and causing chronic infections [55].
Diagnosis of klebsiella infection is by isolation and laboratory identification of bacterium from urine or biofilm. Laboratory diagnosis can be done by culture of specimen—urine or catheter biofilm in blood agar, MacConkey’s agar. Specific ELISA, latex agglutination tests, PCR and other immunological-based detection methods are sophisticated alternatives for diagnosis of klebsiella. Determination of a gene on capsule of Klebsiella is rapid and simple method for the determination of the K types of most
Enterobacter species, particularly Enterobacter cloacae and
Enterobacter bacteria are motile, rod-shaped cells, facultative anaerobic, non-spore-forming, some of which are encapsulated belonging to the family Enterobacteriaceae. They are important opportunistic and multi-resistant bacterial pathogens. As facultative anaerobes, some Enterobacter bacteria ferment both glucose and lactose as a carbon source, presence of ornithine decarboxylase (ODC) activity and the lack of urease activity. In biofilms they secrete various cytotoxins (enterotoxins, hemolysins, pore-forming toxins. Though it is microflora in the intestine of humans, it is pathogens in plants and insects. Amp C β-lactamase production by
Gram stain picture and morphology of Enterobacter species. Adapted from Gram Stain Kit | Microorganism Stain | abcam.comAdwww.abcam.com/ and Science Prof Online. Gram-negative Bacteria Images: photos of
The most important test to document Enterobacter infections is culture. Direct gram staining of the specimen is also useful. In the laboratory, growth of Enterobacter isolates is occurs in 24 h or less; Enterobacter species grow rapidly on selective (i.e., MacConkey) and nonselective (i.e., sheep blood) agars.
Enterococci are gram-positive facultative anaerobic cocci, two species are common commensal organisms in the intestines of humans: Enterococcus faecalis (90–95%) and Enterococcus faecium (5–10%) [60]. Though normally a gut commensal, these organisms are commonly responsible for nosocomial infection of urinary tract, biliary tract and blood, particularly in intensive care units (ICU) [61].
The most important cause of bacteriuria is the formation of biofilm along the catheter surface [64]. Enterococcus is gram positive bacteria often found in pairs or short chains. Broadly, Enterococcus is in two groups—faecalis and non-faecalis (
Morphology of Enterococcus. Adapted from Science Photo Library/Alamy Stock Photo Image ID: F6YBC3.
Urine sample and biofilm microscopy can identify this gram positive organism. Culture yields the growth of
One of the common causes of catheter associated urinary tract infection is fungal infection. Bacterial infections are accounted for 70.9% of catheter associated urinary infection.
Morphology of Candida albicans. Adapted from biomedik8888, Aug 24, 2011.
Urine and materials removed from catheter are needed. Microscopic examinations of gram-stained specimen showed pseudohyphae and budding cells. Culture on Sabouraud’s agar at room temperature and at 37°C showed typical colonies and budding pseudomycelia [79].
It is facultative anaerobic bacilli gram-negative rod of Enterobacteriaceae family considered opportunistic human pathogen but not a component of human facial flora. It is capable of producing a pigment called prodigiosin, which ranges in color from dark red to pale pink. It is ubiquitously spent in nature and has preference for damp conditions. Though previously known as nonpathogenic, but since 1970s it is associated with multi drug resistant infection due to presence of R factor—a plasmid. A study in Japan showed 6.8% incidence of UTI with this organism [80]. It also causes bacteraemia rarely. Diagnosis is confirmed by culture of the urine specimen or catheter biofilm. Automated bacterial identification systems and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is the other modality for diagnosis of serratia as well as other enterobacteriaceae [81].
This non-fermentative gram-negative rod discovered as plant growth-promoting bacterium and potential biocontrol agent against plant pathogens. Infection with this uncommon organism in CAUTI occurs in combination with commonest bacteria
Achromobacter denitrificans is gram negative bacterium formerly known as
In polymicrobial biofilm,
Staphylococci (methicillin-sensitive
The incidence of Staphylococcal UTI as well as CAUTI is increasing and the organisms carry wide variety of multidrug-resistant genes on plasmids, which augment spread of resistance among other species [86].
Diagnosis is easy, gram stain of the sample, culture is sufficient. Advanced techniques rarely needed (Figure 8).
Morphology of Staphylococcus aureus. Adapted from abcam.comAdwww.abcam.com/ pharmacist-driven intervention improves care of patients with S aureus Bacteremia/Staph aureus. Nebraska Medicine
CAUTI is one of the most nosocomial Infection worldwide resulting from rational as well as sometimes irrational use of indwelling urinary catheter. Cause of CAUTI is formation of pathogenic biofilm commonly due to UPEC, Proteus, Klebsiella, Pseudomonas, Enterobacter rarely Candida and other uncommon opportunistic organisms. CAUTI has got high impact on morbidity and mortality as biofilm producing organisms are more antibiotic resistant. Antibiotic resistance is a global problem. Early detection of CAUTI is simple by examination of urine and catheter biofilm with microscopy as well as culture with antibiogram. It is easy and cost effective with early diagnosis and treatment for good clinical outcome. Advanced and sophisticated methods like Immunomagnetic separation, specific ELISA, colony immunoblot assays and PCR for diagnosis of CAUTI is seldom necessary.
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