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Standard Particle Swarm Optimization on the CEC2013 Real‐Parameter Optimization Benchmark Functions
Abstract
A revised version updates an ERROR in the used code. Please see https://www.researchgate.net/publication/259643271_Standard_Particle_Swarm_Optimization_on_the_CEC2013_RealParameter_Optimization_Benchmark_Functions_--_revised
Results for an implementation of Standard Particle Swarm Optimization on the CEC2013 Real-Parameter Optimization Benchmark Functions
This revised version is based on fixing a code error in the previous version. See the Appendix for more details.
Source code:
https://www.researchgate.net/publication/259643342_Source_code_for_an_implementation_of_Standard_Particle_Swarm_Optimization_--_revised?ev=prf_pub
Single objective optimization algorithms are the basis of the more complex optimization algorithms such as multi-objective optimizations algorithms, niching algorithms, constrained optimization algorithms and so on. Research on the single objective optimization algorithms influence the development of these optimization branches mentioned above. In the recent years various kinds of novel optimization algorithms have been proposed to solve real-parameter optimization problems. Eight years have passed since the CEC’05 Special Session on Real-Parameter Optimization[1]. Considering the comments on the CEC’05 test suite received by us, we propose to organize a new competition on real parameter single objective optimization. In the CEC’13 test suite, the previously proposed composition functions[2] are improved and additional test functions are included. This special session is devoted to the approaches, algorithms and techniques for solving real parameter single objective optimization without making use of the exact equations of the test functions. We encourage all researchers to test their algorithms on the CEC’13 test suite which includes 28 benchmark functions. The participants are required to send the final results in the format specified in the technical report to the organizers. The organizers will present an overall analysis and comparison based on these results. We will also use statistical tests on convergence performance to compare algorithms that eventually generate similar final solutions. Papers on novel concepts that help us in understanding problem characteristics are also welcome. The C and Matlab codes for CEC’13 test suite can be downloaded from the website given below:
http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC2013/CEC2013.htm
In this work we benchmark, for the first time, the latest Standard Particle Swarm Optimisation algorithm (SPSO-2011) against the 28 test functions designed for the Special Session on Real-Parameter Single Objective Optimisation at CEC-2013. SPSO-2011 is a major improvement over previous PSO versions, with an adaptive random topology and rotational invariance constituting the main advancements. Results showed an outstanding performance of SPSO-2011 for the family of unimodal and separable test functions, with a fast convergence to the global optimum, while good performance was observed for four rotated multimodal functions. Conversely, SPSO-2011 showed the weakest performance for all composition problems (i.e. highly complex functions specially designed for this competition) and certain multimodal test functions. In general, a fast convergence towards the region of the global optimum was achieved, requiring less than 10E+03 function evaluations. However, for most composition and multimodal functions SPSO-2011 showed a limited capability to “escape” from sub-optimal regions. Despite this limitation, a desirable feature of SPSO-2011 was its scalable behaviour, which observed up to 50-dimensional problems, i.e. keeping a similar performance across dimensions with no need for increasing the population size. Therefore, it seems advisable that future PSO improvements be focused on enhancing the algorithm's ability to solve non-separable and asymmetrical functions, with a large number of local minima and a second global minimum located far from the true optimum. This work is the first effort towards providing a baseline for a fair comparison of future PSO improvements.
Many practical optimization problems are con-strained, and have a bounded search space. In this paper, we pro-pose and compare a wide variety of bound handling techniques for particle swarm optimization. By examining their performance on flat landscapes, we show that many bound handling techniques introduce a significant search bias. Furthermore, we compare the performance of many bound handling techniques on a variety of test problems, demonstrating that the bound handling technique can have a huge impact on the algorithm performance, and that the method recently proposed as standard is generally not performing well.
A pneumococcal serotyping/genotyping system (PSGS) was developed based upon targeted PCR, followed by electrospray ionization
mass spectrometry and amplicon base composition analysis. Eight multiplex PCRs, 32 targeting serotype-determining capsular
biosynthetic loci, and 8 targeting multilocus sequence typing (MLST) loci were employed for each of 229 highly diverse Streptococcus pneumoniae isolates. The most powerful aspect of the PSGS system was the identification of capsular serotypes accounting for the majority
of invasive and carried pneumococcal strains. Altogether, 45 different serotypes or serogroups were correctly predicted among
the 196 resolvable isolates, with only 2 unexpected negative results. All 33 isolates that represented 23 serotypes not included
in the PSGS yielded negative serotyping results. A genotyping database was constructed using the base compositions of 65-
to 100-bp sections of MLST alleles compiled within http://www.mlst.net. From this database, one or more MLST sequence types (STs) that comprised a PSGS genotype were identified. The end result
of more PSGS genotypes (163) than conventional STs actually tested (155) was primarily due to amplification failures of 1
to 3 targets. In many instances, the PSGS genotype could provide resolution of single- and double-locus variants. This molecular
serotyping/genotyping scheme is well suited to rapid characterization of large sets of pneumococcal isolates.
Background: Respiratory tract infections caused by influenza A and B viruses often present nonspecifically, and a rapid, high-throughput laboratory technique that can identify influenza viruses is clinically and epidemiologically desirable. The PLEX-ID Flu Assay (Abbott Molecular Inc., Des Plaines, IL) incorporates multi-locus PCR and electrospray ionization/mass spectrometry to detect and differentiate influenza A 2009 H1N1 (H1N1-p), seasonal H1N1 (H1N1-s), influenza A H3N2, and influenza B in nasopharyngeal swab (NPS) specimens.Methods: The clinical performance characteristics of the PLEX-ID Flu Assay in symptomatic patients were determined in this multicenter trial. A total of 2,617 prospectively and retrospectively collected NPS specimens from patients with influenza-like illness between February 2008 and May 28, 2010, were eligible for inclusion in the study. Each specimen was tested in parallel by the PLEX-ID Flu Assay and by the Prodesse® ProFLU™+ Assay (Prodesse, Inc., Madison, WI), to detect influenza A and B. Specimens testing positive for influenza A by ProFLU+ were subtyped as H1N1-p, H1N1-s, or H3N2 using the ProFAST™+ Assay (Gen-Probe Prodesse, Inc.).Results: Reproducibility of the PLEX-ID Flu Assay ranged from 98.3-100.0% as determined by testing a nine-specimen panel at three clinical sites on each of five days. Positive percent agreements (PPA) and negative percent agreements (NPA) of the PLEX-ID Flu assay were 94.5% and 99.0% for Flu A and 96.0% and 99.9% for Flu B. For the Flu A subtyping characterization, the PLEX-ID Flu assay had PPA and NPA of 98.3 % and 97.5 % for H1N1-p, 88.6% and 100.0% for H1N1-s and 98.0% and 99.9% for H3N2. The overall agreement between the PLEX-ID and Prodesse ProFLU™+/ProFAST+ assays were 97.1-100.0%. Bi-directional Sanger sequencing analysis revealed that 87.5% of 96 discrepant results between the PLEX-ID Flu and ProFLU™+/ProFAST+ assays were on Flu A detection and H1N1-p subtyping.Conclusions: The PLEX-ID Flu Assay demonstrated high accuracy for simultaneous detection and identification of influenza A and B in patient specimens, providing a new laboratory tool for rapid diagnosis and management of influenza A and B infections.
Detection of pathogens in bloodstream infections is important for directing antimicrobial treatment, but current culture-based
approaches can be problematic. Broad-range PCR assays which target conserved genomic motifs for postamplification amplicon
analysis permit detection of sepsis-causing pathogens. Comparison of different broad-range assays is important for informing
future implementation strategies. In this study, we compared positive-blood-culture bottles processed by PCR coupled to high-resolution
melting curve analysis (PCR/HRMA) and PCR coupled to electrospray ionization-mass spectrometry (PCR/ESI-MS) to microbiology
culture results. Genus-level concordance was 90% (confidence interval [CI], 80 to 96%) for PCR/HRMA and 94% (CI, 85 to 98%)
for PCR/ESI-MS. Species-level concordance was 90% (CI, 80 to 96%) for PCR/HRMA and 86% (CI, 75 to 93%) for PCR/ESI-MS. Unlike
PCR/HRMA, PCR/ESI-MS was able to resolve polymicrobial samples. Our results demonstrated that the two assays have similar
overall concordance rates but may have different roles as potential adjunctive tests with standard blood culture, since each
method has different capabilities, advantages, and disadvantages.
Emerging technologies for rapid identification of microbes demonstrate a shift from traditional biochemical and molecular testing algorithms toward methods using mass spectrometry (MS) for the semiquantitative analysis of microbial proteins and genetic elements. This study was performed to assess the diagnostic accuracy of 2 such technologies, PCR-electrospray ionization (ESI)/MS and MALDI-TOF/MS, with respect to phenotypic and biochemical profiling as a reference standard method. A positive challenge set of blood culture bottles was used to compare PCR-ESI/MS and MALDI-TOF/MS performance on a matched set of samples.
We performed characterization of bloodstream infections from blood cultures using the Ibis T5000 PCR-ESI/MS and the Bruker MALDI Biotyper 2.0 (MALDI-TOF/MS) platforms for microbial identification. Diagnostic accuracy was determined by independent comparison of each method to phenotypic and biochemical characterization with Vitek2 analysis as the reference standard identification.
The diagnostic accuracy, represented as positive agreement, at the genus level was 0.965 (0.930-0.984) for PCR-ESI/MS and 0.969 (0.935-0.987) for MALDI-TOF/MS, and at the species level was 0.952 (0.912-0.974) with PCR-ESI/MS and 0.943 (0.902-0.968) for MALDI-TOF/MS. No statistically significant difference was found between PCR-ESI/MS and MALDI-TOF/MS in the ability to rapidly identify microorganisms isolated from blood culture.
Our results demonstrate that PCR-ESI/MS and MALDI-TOF/MS are equivalent in their ability to characterize bloodstream infections with respect to the reference standard, and highlight key differences in the methods that allow for each method to have a unique niche as a tool for rapid identification of microbes in blood cultures.
Sepsis is among the top 10 causes of mortality in the United States. Rapid administration of antibiotics is one of the most important contributors to patient survival, yet only a limited number of methods exist for rapid identification of microbes cultivated from bloodstream infections, which can lead to sepsis. While traditional single-target molecular methods have been shown to greatly improve survival for septic patients by enabling rapid deescalation of broad-spectrum antibiotics, multiplex methods offer even greater possibilities. A novel multiplex method, PCR coupled to electrospray ionization mass spectrometry (PCR/ESI-MS), was used to identify the genus and species of microorganisms found to cause human bloodstream infections. DNA was directly extracted from 234 BacT-Alert blood culture bottles, and results were compared to those obtained by clinical reference standard methods. The study results demonstrated 98.7% and 96.6% concordance at the genus and species levels, respectively. Mixtures of microbes were identified in 29 blood culture bottles, including mixed species of the same genus, as well as mixtures containing Gram-positive and Gram-negative organisms, exemplifying the PCR/ESI-MS capability to identify multiple organisms simultaneously without the need for cultivation. This study demonstrates high analytical accuracy in comparison to routine subculture of blood culture bottles and phenotypic identification of microbes. Without foreknowledge of the microorganisms potentially present, the PCR/ESI-MS methods can deliver accurate results in as little as 5 to 6 h after a positive alarm from the automated blood culture system; however, current batch mode testing limits the method's clinical utility at this time.
A gram-negative, rod-shaped microorganism was detected in a 69-year-old man suffering from chronic back pain but otherwise exhibiting no signs of infection. The bacterium could not be identified using any routine diagnostic modality. A research use only application utilizing PCR and Mass Spectrometry was performed on nucleic acid extracted from the tissue sample. These studies resulted in the implication of Bartonella quintana as the underlying cause of the infection. B. quintana is not a well-known cause of an abdominal aortic mycotic aneurysm. This article will discuss the B. quintana infection, its diagnosis and treatment, and reinforce the potential of B. quintana as a possible etiology in mycotic aneurysms that show no apparent indications of infection. It will also explore the potential use of polymerase chain reaction detected by electrospray ionization mass spectrometry (PCR/ESI-MS) to help identify B. quintana in a situation where other conventional methods prove non-informative.
Echocardiography plays a key role in the assessment of infective endocarditis (IE). It is useful for the diagnosis of endocarditis, the assessment of the severity of the disease, the prediction of short- and long-term prognosis, the prediction of embolic events, and the follow-up of patients under specific antibiotic therapy. Echocardiography is also useful for the diagnosis and management of the complications of IE, helping the physician in decision-making, particularly when a surgical therapy is considered. Finally, intraoperative echocardiography must be performed in IE to help the surgeon in the assessment and management of patients with IE during surgery. The current 'recommendations for the practice of echocardiography in infective endocarditis' aims to provide both an updated summary concerning the value and limitations of echocardiography in IE, and clear and simple recommendations for the optimal use of both transthoracic and transoesophageal echocardiography in IE.
We describe a new Bartonella species for which we propose the name Candidatus Bartonella mayotimonensis. It was isolated from native aortic valve tissue of a person with infective endocarditis. The new species was identified by using PCR amplification and sequencing of 5 genes (16S rRNA gene, ftsZ, rpoB, gltA, and internal transcribed spacer region).
The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay
that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black
Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41%) samples were positive for V. cholerae, and 5 (0.8%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected.
A duplex PCR (dPCR) assay was developed to simultaneously detect and differentiate Bartonella quintana, Bartonella henselae, and Coxiella burnetii from surgical heart valve tissue specimens with an analytic sensitivity of 10 copies/reaction. Among 17 specimens collected
from patients with a clinical diagnosis of culture-negative endocarditis, 2, 4, and 2 were positive for B. quintana, B. henselae, and C. burnetii, respectively, by the dPCR assay, which matched the results obtained by universal bacterial 16S rRNA gene amplification and
sequencing.
We describe a new technology for the molecular genotyping of microbes using a platform known commercially as the Ibis T5000. The technology couples multilocus polymerase chain reaction (PCR) to electrospray ionization/mass spectrometry (PCR/ESI-MS) and was developed to provide rapid, high-throughput, and precise digital analysis of either isolated colonies or original patient specimens on a platform suitable for use in hospital or reference diagnostic laboratories or public health settings. The PCR/ESI-MS method measures digital molecular signatures from microbes, enabling real-time epidemiological surveillance and outbreak investigation. This technology will facilitate understanding of the pathways by which infectious organisms spread and will enable appropriate interventions on a time frame not previously achievable.
Tropheryma whipplei is a bacterium commonly found in people with Whipple's disease, a rare systemic chronic infection. In the present study, we hypothesized that bacterium glycosylation may impair the immune response.
Bacterial extracts were analyzed by glycostaining, and reactive proteins, identified by matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectometry, were purified to generate antibodies that could be used in immunofluorescence studies. The reactivity of serum samples obtained from patients and asymptomatic carriers was tested against native or deglycosylated bacteria, for which the fate in macrophages was also investigated.
To our knowledge, we evidenced, for the first time in T. whipplei, a 110-kDa glycoprotein containing sialic acid. This protein, identified as an Wnt1-inducible signaling pathway (WiSP) protein, is associated with periodic acid-Schiff (PAS) staining in infected intramacrophage biofilm. Consistent with the lack of enzymes required for the glycosylation pathway in this bacterium, the glycoproteins disappear during in vitro axenic subcultures, whereas human transcriptome analysis reveals the up-regulation of corresponding genes within infected macrophages. Proteic antigens are not recognized by the serum samples obtained from patients compared with those obtained from nonsick carriers, and T. whipplei that exhibits a low glycosylation profile does not efficiently multiply in macrophages in vitro.
T. whipplei glycosylation is likely to impair antibody-mediated immune recognition in patients. Such an intracellular antigen masking system in bacteria has not previously been described.
Although the sensitivity and specificity of the Duke criteria for the diagnosis of infective endocarditis (IE) have been validated
by investigators from Europe and the United States, several shortcomings of this schema remain. The Duke IE database contains
records collected prospectively on >800 cases of definite and possible IE since 1984. Databases on echo-cardiograms and on
patients with Staphylococcus aureus bacteremia at Duke University Medical Center are also maintained. Analyses of these databases, our experience with the Duke
criteria in clinical practice, and analysis of the work of others have led us to propose the following modifications of the
Duke schema. The category “possible IE” should be defined as having at least 1 major criterion and 1 minor criterion or 3
minor criteria. The minor criterion “echocardiogram consistent with IE but not meeting major criterion” should be eliminated,
given the widespread use of transesophageal echocardiography (TEE). Bacteremia due to S. aureus should be considered a major criterion, regardless of whether the infection is nosocomially acquired or whether a removable
source of infection is present. Positive Q-fever serology should be changed to a major criterion.
To determine the effect of human immunodeficiency virus (HIV) infection and other factors on infective endocarditis (IE) among
injection drug users (IDUs), the incidence of IE was determined according to HIV status in a cohort of IDUs. A nested case-control
study assessed IE risk factors. IE incidence (117 cases) was higher among HIV-seropositive than HIV-seronegative IDUs (13.8
vs. 3.3 cases/1000 person-years) during 1988–1998. Multivariate analysis of HIV-infected case patients revealed an inverse
association between IE and CD4 lymphocyte count (odds ratio [OR] for 200–499 cells/mm3, 2.01; OR for < 200 cells/mm3, 3.61) and with alcohol intake (OR for 1–21 drinks/week, 0.43; OR for > 21 drinks/week, 0.32). Women had an increased risk
of IE (OR, 3.26), as did persons with increasing injection drug use frequency (OR for less than daily use, 3.15; OR for at
least daily use, 6.07). This study confirms that IE is more common among IDUs with advanced HIV immunosuppression even after
accounting for injection drug use behaviors.
Epidemic respiratory infections are responsible for extensive morbidity and mortality within both military and civilian populations. We describe a high-throughput method to simultaneously identify and genotype species of bacteria from complex mixtures in respiratory samples. The process uses electrospray ionization mass spectrometry and base composition analysis of PCR amplification products from highly conserved genomic regions to identify and determine the relative quantity of pathogenic bacteria present in the sample. High-resolution genotyping of specific species is achieved by using additional primers targeted to highly variable regions of specific bacterial genomes. This method was used to examine samples taken from military recruits during respiratory disease outbreaks and for follow up surveillance at several military training facilities. Analysis of respiratory samples revealed high concentrations of pathogenic respiratory species, including Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pyogenes. When S. pyogenes was identified in samples from the epidemic site, the identical genotype was found in almost all recruits. This analysis method will provide information fundamental to understanding the polymicrobial nature of explosive epidemics of respiratory disease.
A real-time PCR method using the LightCycler (Roche Applied Science, Indianapolis, IN) was compared to a conventional PCR
assay for the detection of Tropheryma whipplei in 321 clinical specimens. The LightCycler method had sensitivity and specificity comparable to the conventional method but
required considerably less labor and time (3 h versus 3 to 5 days).
We applied 16S rRNA gene sequencing to identify bacterial species present in formalin-fixed, paraffin-embedded heart valve
tissue. In 40% (12/30) of the cases, we were able to identify the bacterium to the species-genus level. For more recent cases
(≤4 years), the success rate was significantly improved, to 70% (P < 0.001).
Since its birth in 1995, particle swarm optimization (PSO) has been well studied and successfully applied. While a better understanding of PSO and particle behaviors have been obtained through theoretical and empirical analysis, some issues about the beavior of particles remain unanswered. One such issue is how velocities should be initialized. Though zero initial velocities have been advocated, a popular initialization strategy is to set initial weights to random values within the domain of the optimization problem. This article first illustrates that particles tend to leave the boundaries of the search space irrespective of the initialization approach, resulting in wasted search effort. It is also shown that random initialization increases the number of roaming particles, and that this has a negative impact on convergence time. It is also shown that enforcing a boundary constraint on personal best positions does not help much to address this problem. The main objective of the article is to show that the best approach is to initialize particles to zero, or random values close to zero, without imposing a personal best bound.
The diagnosis of periprosthetic joint infection poses many challenges, one of which is the difficulty of isolating the infecting organism. Recently, a sophisticated modality (the Ibis Biosciences T5000 biosensor system) has been introduced that uses pan-domain primers in a series of polymerase chain reactions (PCRs) to identify and speciate essentially all bacteria and fungi as well as to identify key antibiotic resistance genes. We investigated the role of the Ibis in identifying infecting organisms in cases of known and suspected periprosthetic joint infection.
Synovial fluid specimens were collected prospectively from eighty-two patients undergoing eighty-seven arthroplasty procedures (sixty-five knee revisions, fifteen hip revisions, and seven primary knee arthroplasties) and were sent for both conventional culture and Ibis analysis. The surgeon's clinical determination of the cause for revision arthroplasty was failure due to infection in twenty-three cases and noninfectious failure in fifty-seven cases.
In the twenty-three cases that were considered on clinical grounds to involve a periprosthetic joint infection, the Ibis detected the same pathogen isolated by conventional culture in seventeen of eighteen cases and also detected one or more organisms in four of the five culture-negative cases. In addition, the Ibis detected organisms in fifty (88%) of the fifty-seven cases in which revision arthroplasty was performed for a presumed noninfectious failure.
The Ibis technology was not only effective at detecting organisms in cases of suspected periprosthetic joint infection in which cultures were negative, but it also suggested that many of the revision arthroplasty cases that have previously been considered to be purely aseptic may have a component of unrecognized, subclinical infection.
Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
In this work, we describe a strategy for the detection and characterization of microorganisms associated with a potential biological warfare attack or a natural outbreak of an emerging infectious disease. This approach, termed TIGER (Triangulation Identification for the Genetic Evaluation of Risks), relies on mass spectrometry-derived base composition signatures obtained from PCR amplification of broadly conserved regions of the microbial genome(s) in a sample. The sample can be derived from air filtration devices, clinical samples, or other sources. Core to this approach are “intelligent PCR primers” that target broadly conserved regions of microbial genomes that flank variable regions. This approach requires that high-performance mass measurements be made on PCR products in the 80–140 bp size range in a high-throughput, robust modality. As will be demonstrated, the concept is equally applicable to bacteria and viruses and could be further applied to fungi and protozoa. In addition to describing the fundamental strategy of this approach, several specific examples of TIGER are presented that illustrate the impact this approach could have on the way biological weapons attacks are detected and the way that the etiologies of infectious diseases are determined. The first example illustrates how any bacterial species might be identified, using Bacillus anthracis as the test agent. The second example demonstrates how DNA-genome viruses are identified using five members of Poxviridae family, whose members includes Variola virus, the agent responsible for smallpox. The third example demonstrates how RNA-genome viruses are identified using the Alphaviruses (VEE, WEE, and EEE) as representative examples. These examples illustrate how the TIGER technology can be applied to create a universal identification strategy for all pathogens, including those that infect humans, livestock, and plants.
Despite improvements in medical and surgical therapies, infective endocarditis is associated with poor prognosis and remains a therapeutic challenge. Many factors affect the outcome of this serious disease, including virulence of the microorganism, characteristics of the patients, presence of underlying disease, delays in diagnosis and treatment, surgical indications, and timing of surgery. We review the strengths and limitations of present therapeutic strategies and propose future directions for better management of endocarditis according to the most recent research. Novel perspectives on the management of endocarditis are emerging and offer hope for decreasing the rate of residual deaths by accelerating the process of diagnosis and risk stratification, reducing delays in starting antimicrobial therapy, rapid transfer of high-risk patients to specialised medico-surgical centres, development of new surgical methods, and close long-term follow-up.
The aim was to evaluate 16S rDNA sequencing in heart valves in patients with infective endocarditis undergoing surgery.
Fifty-seven patients with infective endocarditis were examined in this prospective study by analysing heart valves with 16S rDNA sequencing and culturing methods and comparing the results to blood cultures. As controls, heart valves from 61 patients without any signs of endocarditis were examined.
All together 77% of the endocarditis patients were positive for 16S rDNA, 84% had positive blood cultures and 23% had positive cultures from heart valves, whereas only 16% of the cultures from heart valves were concordant with results from blood cultures or 16S rDNA. Concordant results between 16S rDNA sequencing and blood cultures were found in 75% patients. All controls were negative for 16S rDNA. In 4 out of 9 patients with negative blood cultures, the aetiology was established by 16S rDNA alone, i.e. viridans group streptococci.
In this Swedish study, 16S rDNA sequencing of valve material was shown to be a valuable addition in blood culture-negative cases. The value of heart valve culture was low. Molecular diagnosis using 16S rDNA sequencing should be recommended in patients undergoing valve replacement for infective endocarditis.
Infective endocarditis (IE) is lethal if not aggressively treated with antibiotics alone or in combination with surgery. The epidemiology of this condition has substantially changed over the past four decades, especially in industrialized countries. Once a disease that predominantly affected young adults with previously well-identified valve disease--mostly chronic rheumatic heart disease--IE now tends to affect older patients and new at-risk groups, including intravenous-drug users, patients with intracardiac devices, and patients exposed to healthcare-associated bacteremia. As a result, skin organisms (for example, Staphylococcus spp.) are now reported as the pathogen in these populations more often than oral streptococci, which still prevail in the community and in native-valve IE. Moreover, progress in molecular diagnostics has helped to improve the diagnosis of poorly cultivable pathogens, such as Bartonella spp. and Tropheryma whipplei, which are responsible for blood-culture-negative IE more often than expected. Epidemiological data indicate that IE mostly occurs independently of medico-surgical procedures, and that circumstantial antibiotic prophylaxis is likely to protect only a minute proportion of individuals at risk. Therefore, new strategies to prevent IE--including improvement of dental hygiene, decontamination of carriers of Staphylococcus aureus, vaccination, and, possibly, antiplatelet therapy--must be explored.
Polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS, previously known as “TIGER”) utilizes PCR with broad-range primers to amplify products from a wide array of organisms within a taxonomic group, followed by analysis of PCR amplicons using mass spectrometry. Computer analysis of precise masses allows for calculations of base compositions for the broad-range PCR products, which can then be compared to a database for identification. PCR/ESI-MS has the benefits of PCR in sensitivity and high-throughput capacity, but also has the distinct advantage of being able to detect and identify organisms with no prior characterization or sequence data. Existing broad range PCR primers, designed with an emphasis on human pathogens, were tested for their ability to amplify DNA of well characterized phytobacterial strains, as well as to populate the existing PCR/ESI-MS bacterial database with base counts. In a blinded panel study, PCR/ESI-MS successfully identified 93% of unknown bacterial DNAs to the genus level and 73% to the species/subspecies level. Additionally, PCR/ESI-MS was capable of detecting and identifying multiple bacteria within the same sample. The sensitivity of PCR/ESI-MS was consistent with other PCR based assays, and the specificity varied depending on the bacterial species. Preliminary tests with real life samples demonstrate a high potential for using PCR/ESI-MS systems for agricultural diagnostic applications.
Polymerase chain reaction electrospray ionization mass spectrometry (PCR/ESI-MS) was tested for its ability to accurately identify a blinded panel of 156 diverse bacterial isolates, mostly human and/or animal pathogens. Here, 142/156 (91%) isolates were correctly identified to the genus level and 115/156 (74%) were correctly identified to the species level. Only 9% were misidentified. This study shows that multilocus PCR/ESI-MS has the potential to be a useful technique for identifying a broad range of bacteria.
A retrospective study of 69 cases of infective endocarditis in 68 children (group I: 1971–1981; 34 children; group II: 1982–1992; 34 children) disclosed the following features: a moderate increase in the global incidence of infective endocarditis (0.5% of children hospitalized in paediatric cardiology units) and of its incidence in the very young (proportion of children less than 1 year of age: 9% in group I and 17% in group II); no rheumatic heart disease amongst predisposing heart diseases in children living in France; a major causal role of congenital heart diseases (72%), with an increasing incidence previous operation (group I:42%; group II: 56%); an increase in associated complex congenital heart diseases (group I: 11%; group II: 20%); no change in related mitral valve prolapse (5% in both groups); positive blood cultures in 76% of cases, with similar rates of Staphylococci (group I:27%; group II: 30%) and of unusual microorganisms (15% in both groups); a major diagnostic role for echocardiography (vegetations in group II: 64%). Complications occurred in 75% of cases in both groups (pulmonary or systemic emboli, mycotic aneurysms, valvar regurgitation), leading to heart failure in 29% of group I patients and in 32% of group II patients.
Mortality has decreased, from 12% in group I to 3% in group II, as a result of more frequent cardiovascular surgery (group I: II cases; group II: 15 cases), problems due to restrictive prostheses, and severe consequences: only 27% of group II children were cured without deterioration of their cardiac condition.
These data confirm that the natural history of infective endocarditis has changed over the last two decades.
The etiologic diagnosis of infective endocarditis is easily made in the presence of continuous bacteremia with gram-positive cocci. However, the blood culture may contain a bacterium rarely associated with endocarditis, such as Lactobacillus spp., Klebsiella spp., or nontoxigenic Corynebacterium, Salmonella, Gemella, Campylobacter, Aeromonas, Yersinia, Nocardia, Pasteurella, Listeria, or Erysipelothrix spp., that requires further investigation to establish the relationship with endocarditis, or the blood culture may be uninformative despite a supportive clinical evaluation. In the latter case, the etiologic agents are either fastidious extracellular or intracellular bacteria. Fastidious extracellular bacteria such as Abiotrophia, HACEK group bacteria, Clostridium, Brucella, Legionella, Mycobacterium, and Bartonella spp. need supplemented media, prolonged incubation time, and special culture conditions. Intracellular bacteria such as Coxiella burnetii cannot be isolated routinely. The two most prevalent etiologic agents of culture-negative endocarditis are C. burnetti and Bartonella spp. Their diagnosis is usually carried out serologically. A systemic pathologic examination of excised heart valves including periodic acid-Schiff (PAS) staining and molecular methods has allowed the identification of Whipple's bacillus endocarditis. Pathologic examination of the valve using special staining, such as Warthin-Starry, Gimenez, and PAS, and broad-spectrum PCR should be performed systematically when no etiologic diagnosis is evident through routine laboratory evaluation.
Gemella morbillorum (G. morbillorum) is part of the commensal flora of the oropharynx and intestinal tract, and on rare occasions causes infective endocarditis. A 55-year-old man with massive aortic regurgitation caused by recurrent infective endocarditis with G. morbillorum had a history of prior endocarditis caused by alpha-hemolytic streptococcus and multiple antibiotic allergies 5 years prior, and was successfully treated by aortic valve replacement. Almost all the reported cases of endocarditis caused by G. morbillorum have been bacteriologically cured with antibiotics and this is the first reported case of recurrent endocarditis caused by G. morbillorum in which the initial infection was bacteriologically cured by antibiotics and the secondary infection treated with valve replacement. This organism can be one of the causes of infective endocarditis and prompt surgical repair is mandatory if the infection is refractory or there is progression of congestive heart failure under antibiotic cover.
Clinical and molecular medicines are undergoing a revolution based on the accelerated advances in biotechnology such as DNA microarrays and proteomics. Answers to fundamental questions such as how does the DNA sequence differ between individuals and what makes one individual more prone for a certain disease are eagerly being sought in this postgenomic era. Several government and nonprofit organizations provide the researchers access to human tissues for molecular studies. The tissues procured by the different organizations may differ with respect to fixation and processing parameters that may affect significantly the molecular profile of the tissues. It is imperative that a prospective investigator be aware of the potential contributing factors before designing a project. The purpose of this review is to provide an overview of the methods of human tissue acquisition, fixation, and preservation. In addition, the parameters of procurement and fixation that affect the quality of the tissues at the molecular level are discussed.
IE is a serious, life-threatening disease. Because treatment must often be adapted to the pathogen involved, rapid identification of the etiologic agent is critical to successful management of each patient. When difficult-to-culture pathogens are involved, routine microbiologic tests, including blood culture, may remain negative. Because such cases may account for up to 31% of all IE cases, alternative diagnostic approaches are necessary. Among the etiologic agents of culture-negative endocarditis, C burnetii and Bartonella spp play a major role; each is responsible for up to 3% of episodes of IE. The authors therefore recommend the systematic use of specific serologies in all cases of clinically suspected endocarditis. The cross-reactivity between C burnetii, Bartonella spp, and Chlamydia spp is of diagnostic importance because all are potential etiologic agents of endocarditis. However, given that the levels of specific antibodies observed in Bartonella endocarditis are extremely high, low-level cross-reactions with other antigens should not lead to misdiagnosis, provided serology for all suspected agents is performed. When serologic test results are negative for both Bartonella spp and C burnetii, special staining by the Gram, Giemsa, Gimenez, PAS, Warthin-Starry, and Grocott methods may guide the use of new diagnostic tools such as PCR and tissue culture for isolation and identification of the causative agent. Such novel approaches may lead to more comprehensive patient evaluations and the discovery of new etiologic agents of IE.
The introduction of molecular methods into biomedical science, particularly nucleic acid amplification techniques including the polymerase chain reaction, has significantly improved the diagnosis of several diseases. Likewise, the adoption of such molecular techniques to aid in the detection and identification of causal organisms in patients with infective endocarditis (IE) has been particularly beneficial in cases of difficult, atypical or culture-negative IE. Several different molecular approaches have been suggested for the diagnosis of IE, including variations in the type of cardiological specimens examined, nucleic acid extraction, gene target and molecular platform, each presenting their own advantages and disadvantages. This review examines the molecular approach to the detection and identification of causal agents of IE and provides details and a discussion of the application of such methods, particularly those implemented over the last 7 years.
To identify the current etiologies of blood culture-negative infective endocarditis and to describe the epidemiologic, clinical, laboratory, and echocardiographic characteristics associated with each etiology, as well as with unexplained cases, we tested samples from 348 patients suspected of having blood culture-negative infective endocarditis in our diagnostic center, the French National Reference Center for Rickettsial Diseases, between 1983 and 2001. Serology tests for Coxiella burnettii, Bartonella species, Chlamydia species, Legionella species, and Aspergillus species; blood culture on shell vial; and, when available, analysis of valve specimens through culture, microscopic examination, and direct PCR amplification were performed. Physicians were asked to complete a questionnaire, which was computerized. Only cases of definite infective endocarditis, as defined by the modified Duke criteria, were included. A total of 348 cases were recorded-to our knowledge, the largest series reported to date. Of those, 167 cases (48%) were associated with C. burnetii, 99 (28%) with Bartonella species, and 5 (1%) with rare, fastidious bacterial agents of endocarditis (Tropheryma whipplei, Abiotrophia elegans, Mycoplasma hominis, Legionella pneumophila). Among 73 cases without etiology, 58 received antibiotic drugs before the blood cultures. Six cases were right-sided endocarditis and 4 occurred in patients who had a permanent pacemaker. Finally, no explanatory factor was found for 5 remaining cases (1%), despite all investigations.Q fever endocarditis affected males in 75% of cases, between 40 and 70 years of age. Ninety-one percent of patients had a previous valvulopathy, 32% were immunocompromised, and 70% had been exposed to animals. Our study confirms the improved clinical presentation and prognosis of the disease observed during the last decades. Such an evolution could be related to earlier diagnosis due to better physician awareness and more sensitive diagnostic techniques. As for Bartonella species, B. quintana was recorded more frequently than B. henselae (53 vs 17 cases). For 18 patients with Bartonella endocarditis, the responsible species was not identified. Species determination was achieved through culture and/or PCR in 49 cases and through Western immunoblotting in 22. Comparison of B. quintana and B. henselae endocarditis revealed distinct epidemiologic patterns. The 2 cases due to T. whipplei reflect the emerging role of this agent as a cause of infective endocarditis. Because identification of the bacterium was possible only through analysis of excised valves by histologic examination, PCR, and culture on shell vial, the prevalence of the disease might be underestimated. Among patients who received antibiotic drugs before blood cultures, 4 cases (7%) were found to be associated with Streptococcus species (2 S. bovis and 2 S. mutans) through 16S rDNA gene amplification directly from the valve, which shows the usefulness of this technique in overcoming the limitations of previous antibiotic treatment. Right-sided endocarditis occurred classically in young patients (mean age, 36 yr), intravenous drug users in 50% of cases, and suffering more often from embolic complications. Finally, 5 cases without etiology or explaining factors were all immunocompetent male patients with previous aortic valvular lesions, and 3 of the 5 presented with an aortic abscess. Further investigations should be focused on this group to identify new agents of infective endocarditis.
Granulicatella elegans is a fastidious organism that is rarely implicated as a cause of infective endocarditis. Here, we describe a patient with mitral valve prolapse who developed G. elegans endocarditis. The organism was isolated from blood cultures and the patient had mitral valvuloplasty and repair, and completed a course of 6 weeks of intravenous antibiotics with no sequela.
This report describes a successful operative case of tricuspid infective endocarditis in an IV drug user. Despite cessation of IV drug use, there were further recurrences. Six different microorganisms with multiple portals of entry were identified, including one episode of fungal endocarditis, To our knowledge, this is the first case of recurrent infective endocarditis involving Candida dubliniensis in an HIV-negative patient.
Particle swarm optimization has become a common heuristic technique in the optimization community, with many researchers exploring the concepts, issues, and applications of the algorithm. In spite of this attention, there has as yet been no standard definition representing exactly what is involved in modern implementations of the technique. A standard is defined here which is designed to be a straightforward extension of the original algorithm while taking into account more recent developments that can be expected to improve performance on standard measures. This standard algorithm is intended for use both as a baseline for performance testing of improvements to the technique, as well as to represent PSO to the wider optimization community
Standard Particle Swarm Optimisation 2011 at CEC-2013: A baseline for future PSO improvementsProblem Definitions and Evaluation Criteria for the CEC 2013 Special Session on Real-Parameter Optimization
- M J J Zambrano-Bigiarini
- B Y Liang
- P N Qu
- A G Suganthan
- Hernández-Díaz
M. Zambrano-Bigiarini, etal, "Standard Particle Swarm Optimisation 2011 at CEC-2013: A
baseline for future PSO improvements," IEEE CEC, 2013, pp. 2337-2344.
[6]
J.J. Liang, B.Y. Qu, P.N. Suganthan, A.G. Hernández-Díaz, "Problem Definitions and
Evaluation Criteria for the CEC 2013 Special Session on Real-Parameter Optimization," Technical
Report, Nanyang Technological University, Singapore, January 2013
[7]
https://www.researchgate.net/publication/248082703_PSO_results_-_CEC2013_RealParameter_Optimization_Benchmark_Functions?ev=prf_pub
- J A Al-Tawfiq
- G Kiwan
- H Murrar
Al-Tawfiq JA, Kiwan G, Murrar H. 2007. Granulicatella elegans native
valve infective endocarditis: case report and review. Diagn. Microbiol.
Infect. Dis. 57:439 -441.