Application of chemical attribution in matching OPNAs-exposed biological samples with exposure sources- based on the impurity profiles via GC × GC-TOFMS analysis

Chemical attribution is a vital tool to attribute chemicals or related materials to their origins in chemical forensics via various chemometric methods. Current progress related to organophosphorus nerve agents (OPNAs) has mainly focused on the attribution of chemical sources and synthetic pathways. It has not yet been applied in matching exposed biological samples to their sources. This work used chemical attribution to explore organic impurity profiles in biological samples exposed to various OPNAs. Chemical attribution was first used to identify the exposure source of biological samples based on the full-scan data via comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometer (GC × GC-TOFMS). Taking peak area as the only variable, it can quickly match exposed samples to their sources by applying unsupervised or supervised models, screen difference compounds via one-way ANOVA or t-tests, and then identify valuable impurities that can distinguish different types of exposed samples. To further obtain the impurity profile only applicable to a certain weapon' samples, the irrelevant components were removed via conventional methods. The findings showed there were 53 impurities that can promote distinguishing six groups of OPNA exposed samples, as well as 42 components that can be used as valuable impurities to distinguish class G and class V samples. These were all unique impurities that appear in a certain weapon' samples. The outcomes can be a reference for tracing the source for OPNA-exposed samples, which was beneficial to the further development in source matching of forensic samples. Moreover, the chemical attribution for impurity profiles in biological samples after weapons exposure may inspire research into the characteristics of impurity profile in biological samples as well as practical applications of chemical attribution for OPNA-exposed samples, that may expand potential biomarkers and break the limits of existing markers in the future.

Physician-directed microbiological testing versus syndromic multiplex PCR in gastroenteritis

INTRODUCTION

Syndromic multiplex PCR testing is an alternative to conventional stool testing based on physician-directed request forms. The objective of this study was to compare the etiologic yield of conventional microbiological testing based on physician-directed request forms with that of rapid syndromic testing. In addition, the adequacy of the clinician ordering, which is an important piece of the diagnostic stewardship, was evaluated.

MATERIALS AND METHODS

Physician-directed conventional microbiological testing and extensive molecular syndromic testing with the Fast Track Diagnostics Gastroenteritis Kit were performed in parallel on 1238 samples to evaluate the contribution of a multiplex panel to the diagnostic process of gastroenteritis.

RESULTS

A potential causative pathogen was identified in 18.4% of stool samples by standard microbiological testing and in 41.3% of stool samples tested using the syndromic panel. Only 15.1% of the request forms could be considered successful of which 88.2% were labeled inadequate. Conventional physician-directed based testing missed the etiologic diagnosis in 32.3% of the specimens (excluding sapovirus and astrovirus). Bacterial infections were theoretically not missed as bacterial stool culture was requested on all stool samples, but in 28.6% of the cases, no isolate could be recovered. In 36.9% of the samples testing positive for a viral pathogen, no viral testing was requested. In addition, 72.5% of all samples positive for a parasite were clinically suspected by the physician.

CONCLUSION

This study suggests that syndromic multiplex PCR assays are a better strategy for pathogen detection in patients with gastroenteritis than physician-directed laboratory testing based on the clinical presentation.

Biosensors; nanomaterial-based methods in diagnosing of Mycobacterium tuberculosis

Diagnosis of Mycobacterium tuberculosis (Mtb) before the progression of pulmonary infection can be very effective in its early treatment. The Mtb grows so slowly that it takes about 6-8 weeks to be diagnosed even using sensitive cell culture methods. The main opponent in tuberculosis (TB) and nontuberculous mycobacterial (NTM) epidemiology, like in all contagious diseases, is to pinpoint the source of infection and reveal its transmission and dispersion ways in the environment. It is crucial to be able to distinguish and monitor specific mycobacterium strains in order to do this. In food analysis, clinical diagnosis, environmental monitoring, and bioprocess, biosensing technologies have been improved to manage and detect Mtb. Biosensors are progressively being considered pioneering tools for point-of-care diagnostics in Mtb discoveries. In this review, we present an epitome of recent developments of biosensing technologies for M. tuberculosis detection, which are categorized on the basis of types of electrochemical, Fluorescent, Photo-thermal, Lateral Flow, Magneto-resistive, Laser, Plasmonic, and Optic biosensors.

A hypothetical model of multi-layered cost-effective wastewater treatment plant integrating microbial fuel cell and nanofiltration technology: A comprehensive review on wastewater treatment and sustainable remediation

Wastewater management has emerged as an uprising concern that demands immediate attention from environmentalists worldwide. Indiscriminate and irrational release of industrial and poultry wastes, sewage, pharmaceuticals, mining, pesticides, fertilizers, dyes and radioactive wastes, contribute immensely to water pollution. This has led to the aggravation of critical health concerns as evident from the uprising trends of antimicrobial resistance, and the presence of xenobiotics and pollutant traces in humans and animals due to the process of biomagnification. Therefore, the development of reliable, affordable and sustainable technologies for the supply of fresh water is the need of the hour. Conventional wastewater treatment often involves physical, chemical, and biological processes to remove solids from the effluent, including colloids, organic matter, nutrients, and soluble pollutants (metals, organics). Synthetic biology has been explored in recent years, incorporating both biological and engineering concepts to refine existing wastewater treatment technologies. In addition to outlining the benefits and drawbacks of the current technologies, this review addresses novel wastewater treatment techniques, especially those using dedicated rational design and engineering of organisms and their constituent parts. Furthermore, the review hypothesizes designing a multi-bedded wastewater treatment plant that is highly cost-efficient, sustainable and requires easy installation and handling. The novel setup envisages removing all the major wastewater pollutants, providing water fit for household, irrigation and storage purposes.

Recent advances in diagnostic approaches for orf virus

Orf virus (ORFV), the prototype species of the Parapoxvirus genus, is an important zoonotic virus, causing great economic losses in livestock production. At present, there are no effective drugs for orf treatment. Therefore, it is crucial to develop accurate and rapid diagnostic approaches for ORFV. Over decades, various diagnostic methods have been established, including conventional methods such as virus isolation and electron microscopy; serological methods such as virus neutralization test (VNT), immunohistochemistry (IHC) assay, immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA); and molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and recombinase-aided amplification (RAA) assay. This review provides an overview of currently available diagnostic approaches for ORFV and discusses their advantages and limitations and future perspectives, which would be significantly helpful for ORFV early diagnosis and surveillance to prevent outbreak of orf. KEY POINTS: • Orf virus emerged and reemerged in past years • Rapid and efficient diagnostic approaches are needed and critical for ORFV detection • Novel and sensitive diagnostic methods are required for ORFV detection.

Conventional methods and future trends in antimicrobial susceptibility testing

Antimicrobial susceptibility testing is an essential task for selecting appropriate antimicrobial agents to treat infectious diseases. Constant evolution has been observed in methods used in the diagnostic microbiology laboratories. Disc diffusion or broth microdilution are classical and conventional phenotypic methods with long turnaround time and labour-intensive but still widely practiced as gold-standard. Scientists are striving to develop innovative, novel and faster methods of antimicrobial susceptibility testing to be applicable for routine microbiological laboratory practice and research. To meet the requirements, there is an increasing trend towards automation, genotypic and micro/nano technology-based innovations. Automation in detection systems and integration of computers for online data analysis and data sharing are giant leaps towards versatile nature of automated methods currently in use. Genotypic methods detect a specific genetic marker associated with resistant phenotypes using molecular amplification techniques and genome sequencing. Microfluidics and microdroplets are recent addition in the continuous advancement of methods that show great promises with regards to safety and speed and have the prospect to identify and monitor resistance mechanisms. Although genotypic and microfluidics methods have many exciting features, however, their applications into routine clinical laboratory practice warrant extensive validation. The main impetus behind the evolution of methods in antimicrobial susceptibility testing is to shorten the overall turnaround time in obtaining the results and to enhance the ease of sample processing. This comprehensive narrative review summarises major conventional phenotypic methods and automated systems currently in use, and highlights principles of some of the emerging genotypic and micro/nanotechnology-based methods in antimicrobial susceptibility testing.

Diagnosis of female urethral diverticulum using pelvic floor ultrasound and comparison with voiding cystourethrogram (imaging study)

INTRODUCTION AND HYPOTHESIS

The purpose of this study was to evaluate the sensitivity and specificity of pelvic floor ultrasound (PFUS) in the diagnostic work-up of female urethral diverticulum (UD) and to compare results of PFUS with voiding cystourethrogram (VCUG).

METHODS

We retrospectively reviewed our database of patients, who received VCUG and PFUS for the diagnosis of UD. A total of 196 consecutive female patients with a minimum of one symptom, such as a lower urinary tract symptom (LUTS), postmicturition dribble, dyspareunia and recurrent urinary tract infection (UTI) who underwent initial diagnostics with VCUG and PFUS were selected. Diagnostic performance of both procedures, which included size, complexity, echogenicity. and content were compared.

RESULTS

Recurrent UTI and LUTS were the most common symptoms, which were present in 165 (84%) and 163 patients (83%) respectively. Final diagnosis of UD was based on PFUS and VCUG findings in 69 (35%) and 58 (30%) cases respectively. Based on our study cohort, the sensitivity of PFUS in detecting UD was significantly higher than that of VCUG: 94% (IQR: 89-97) versus 78% (IQR: 73-85, p<0.01), with a trend toward higher specificity: 100% (IQR: 94-100) versus 84% (IQR: 78-84, p=0.05). Enabling direct UD visualisation, PFUS was associated with a positive predictive value (PPV) of 100% (IQR: 97-100) and a negative predictive value (NPV) of 88% (IQR: 78-95), whereas VCUG had an inferior accuracy with a PPV of 84 (IQR: 80-84) and a NPV of 68 (IQR: 62-79).

CONCLUSIONS

In clinical practice, VCUG has a lower sensitivity than PFUS. Based on these results, we recommend the usage of dynamic PFUS as part of a non-invasive work-up.

Conventional and advanced detection approaches of fluoride in water: a review

Fluorine is a naturally occurring element found in soil, water, food materials, and natural minerals such as fluorapatite, sellaite, and cryolite and exists as fluoride compounds with other elements because of high reactivity. The exposure of fluoride to the environment and human beings are industrial factors, food, water, and geogenic factors that impact the health of millions of human beings worldwide. Overexposure to fluoride exceeding the permissible limit (1.5 mg/l as per WHO) causes several diseases in human beings, such as teeth mottling, thyroid inflammation, dental fluorosis, skeletal fluorosis, lesions in the kidney, and other organs. To overcome the deleterious impact of fluoride, its detection at an early stage is very much required. Therefore, feeling the importance of the same, immense efforts have been made to the selective and sensitive determination of fluoride in water by numerous researchers. This review paper summarizes the various conventional methods such as spectroscopic, ion chromatography, ICP-OES, and gas chromatography-mass spectrometry, their advantages, and drawbacks leading to the development of advanced ready-to-use detection strategies such as stamartphones for on-the-spot fluoride detection. This review paper also discusses future directions, which will assist scientists in achieving a new benchmark in developing a reliable, cost-effective, and user-friendly fluoride detector.

Systematic Review of Comparison of use of Ultrasonic Scalpel Versus Conventional Haemostatic Techniques in Performing Thyroid Surgery

Haemostasis during any surgical procedure is fundamental for attaining a positive patient outcome. Safe thyroid surgery requires meticulous attention for careful control of bleeding and safe guarding important structures like recurrent laryngeal nerve. Many methods such as ligation and suturing, electro ligation sealing, coagulation, and ultrasonic coagulation have been put to use for achieving haemostasis. The objective of this systemic review was to compare and review the surgical outcomes between harmonic (ultrasonic) scalpel and conventional ligature techniques in performing thyroid surgery. The systematic review was performed in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement and checklist with a total of 11 studies selected for qualitative analysis. The statistical software Review Manager 5.4.1 provided by the Cochrane Collaboration was used for performing the analysis on the two groups. It was concluded that the use of harmonic scalpel for thyroid surgery is useful for reducing operative time, postoperative pain, drainage volume and transient hypocalcemia, hence can be a reliable and a safe tool compared to conventional techniques often used for surgery.

Automated 2D Slice-Based Skull Stripping Multi-View Ensemble Model on NFBS and IBSR Datasets

This study proposed and evaluated a two-dimensional (2D) slice-based multi-view U-Net (MVU-Net) architecture for skull stripping. The proposed model fused all three TI-weighted brain magnetic resonance imaging (MRI) views, i.e., axial, coronal, and sagittal. This 2D method performed equally well as a three-dimensional (3D) model of skull stripping. while using fewer computational resources. The predictions of all three views were fused linearly, producing a final brain mask with better accuracy and efficiency. Meanwhile, two publicly available datasets-the Internet Brain Segmentation Repository (IBSR) and Neurofeedback Skull-stripped (NFBS) repository-were trained and tested. The MVU-Net, U-Net, and skip connection U-Net (SCU-Net) architectures were then compared. For the IBSR dataset, compared to U-Net and SC-UNet, the MVU-Net architecture attained better mean dice score coefficient (DSC), sensitivity, and specificity, at 0.9184, 0.9397, and 0.9908, respectively. Similarly, the MVU-Net architecture achieved better mean DSC, sensitivity, and specificity, at 0.9681, 0.9763, and 0.9954, respectively, than the U-Net and SC-UNet for the NFBS dataset.

Accurate laboratory diagnosis of human intestinal and extra-intestinal amoebiasis

Accurate diagnosis of Entamoeba histolytica is important, as it is known as a causative agent for both invasive intestinal and extra-intestinal amoebiasis. Amoebiasis has a worldwide distribution, especially in developing countries, and it is responsible for up to 100,000 fatal cases annually. A number of diagnostic methods, including microscopy, culture, antigen detection, molecular based methods, and serological assays have been proposed to assist in diagnosing amoebiasis. The present study aimed to gather new data and review the available diagnostic tests of both intestinal and extra-intestinal amoebiasis and to highlight pitfalls and challenges of each of them. A broad literature of electronic databases was conducted and covered articles published up to March 2022. For laboratory diagnosis of intestinal amoebiasis, direct microscopy stool examinations and cultures should be held as the high-performance diagnostic strategies. Molecular and immunological-based assays are also recommended as complementary tests. To diagnose extra-intestinal infection, the use of serological tests is still considered the method of choice. However, serodiagnosis requires further improvement for the accurate differential diagnosis of active infection from past infections.

FTIR microspectroscopic study of biomacromolecular changes in As2O3 induced MGC803 cells apoptosis

It is well-known that As₂O₃ has significant anticancer effects, however, little is known regarding its mechanism for treating gastric cancer. Thus, we investigated biomacromolecular (DNA, proteins and lipids) changes of human gastric cancer cell line MGC803 to further understand As₂O₃-induced apoptosis. Conventional methods showed the increase of the apoptosis rate, the decrease of mitochondrial membrane potential (MMP), the accumulation of reactive oxygen species (ROS) and the changes of apoptotic proteins, etc. Fourier transform infrared (FTIR) microspectroscopy sensitively recognized overall biomacromolecular changes caused by the above: Peak-area ratios indicated the content/structure changes in DNA, proteins and lipids. Principle component analysis (PCA) revealed significant changes in intracellular DNA concentration and structure. This study suggests that As₂O₃ may exert anti-gastric cancer effect by altering intracellular biomacromolecules especially DNA.

Biosensors promising bio-device for pandemic screening "COVID-19"

Undoubtedly, the coronavirus pandemic is one of the most influential events not only in medicine but also in the economic field in the world. Rapid transmission and high mortality rates, as well as prolonged and asymptomatic communal periods, are the most important reasons for the global panic due to coronavirus. Since coronavirus treatment and specific vaccines are not yet available, early detection of the virus is critical. A rapid and accurate diagnosis can play a crucial role in the treatment and control of the COVID 19 disease. Serological, ELISA, and molecular-based tests, including PCR and RT-PCR, are among the most important routine methods for detecting coronaviruses. False-positive/negative results, low sensitivity and specificity, and the need for advanced equipment are among the disadvantages and problems of routine methods. To eliminate the drawbacks of routine methods, new technologies are being developed. Biosensors are one of the most important ones. This paper is a summary of the up-to-date states of innovative bio-sensing tools for the ultrasensitive detection of coronaviruses (COVID 19) with encouraging uses for future challenges in disease diagnosis.

Magnetite nanoparticles: Synthesis methods - A comparative review

Iron oxide-based nanoparticles have gathered tremendous scientific interest towards their application in a variety of fields. Magnetite has been particularly investigated due to its readily availability, versatility, biocompatibility, biodegradability, and special magnetic properties. As the behavior of nano-scale magnetite is in direct relation to its shape, size, and surface chemistry, accurate control over the nanoparticle synthesis process is essential in obtaining quality products for the intended end uses. Several chemical, physical, and biological methods are found in the literature and implemented in the laboratory or industrial practice. However, non-conventional methods emerged in recent years to bring unprecedented synthesis performances in terms of better-controlled morphologies, sizes, and size distribution. Particularly, microfluidic methods represent a promising technology towards smaller reagent volume use, waste reduction, precise control of fluid mixing, and ease of automation, overcoming some of the major drawbacks of conventional bulk methods. This review aims to present the main properties, applications, and synthesis methods of magnetite, together with the newest advancements in this field.

Sterilization methods of liposomes: Drawbacks of conventional methods and perspectives

Liposomes are targeted drug delivery systems that are of great pharmaceutical and therapeutic interest. Parenteral route is the main way used for liposome administration. In this case, their sterility is a requirement. However, due to the particular sensitivity of liposomes and their tendency to physicochemical alterations, their sterilization remains a real challenge. Conventional sterilization methods such as heat, ethylene oxide, ultraviolet and gamma irradiations are considered as unsuitable for liposome sterilization and the recommended methods for obtaining sterility of liposomes are filtration and aseptic manufacturing. Unfortunately, these recommended methods are not without limitations. This review outlines the difficulties associated with the use of these different classical methods for obtaining liposome sterility. The effects on liposome physicochemical and biopharmaceutical characteristics as well as efficacy, toxicity and practical problems of these sterilization techniques have been discussed. The search for an alternative method being therefore necessary, the applicability of supercritical carbon dioxide (ScCO₂) technology, which is nowadays a promising strategy for the sterilization of sensitive products such as liposomes, is also examined. It appears from this analysis that ScCO₂ could effectively be an interesting alternative to achieve sterility of liposomes, but for this, sterilization assays including challenge tests and optimization studies are needed.

Assessment of erosion: use of nuclear techniques and conventional methods-case of the Fergoug watershed, Algeria

The importance of the soil degradation in the Mediterranean area, more particularly in Algeria, has revealed the need for a diagnosis of the erosion processes' dynamism. In this context, the present work discusses the results obtained by different approaches (conventional methods, Revised Universal Soil Loss Equation (RUSLE), and fallout radionuclides (use of FRNs)). The use of nuclear techniques (FRNs) such as Cesium-137, Lead-210, and Beryllium-7 as tracers can provide an invaluable amount of information on rates of soil loss that is associated with sheet and rill erosion as well as on the redistribution and transfer of that sediment within the landscape. This work mainly presents the results obtained by the application of nuclear isotopes. In the Fergoug watershed study, the use of conventional and nuclear methods has led to converging results. The latter can be summarized as follows: sheet erosion from 1.5 to 10 t·ha^-1·year^-1 for bare soil and 0.1 to 4 t·ha^-1·year^-1 for cultivated soil. The use of the RUSLE method has shown that erosion is medium to very high (1 to 33 t·ha^-1·year^-1). Estimates of erosion by Cesium-137 (¹³⁷Cs) provided a good understanding of the distribution of the isotope at the slope level and therefore of erosion. The erosion rate is from 26 to 42 t·ha^-1·year^-1, depending on the models used. On the other hand, sedimentation reached 35 and 55 t·ha^-1·year^-1 downstream of the slopes. The variation of ¹³⁷Cs between transects and along the same transect is linked to erosion. The ¹³⁷Cs method has provided a great deal of information and thus constitutes, by its accuracy and speed, an effective and valuable tool for assessing erosion for medium term (50 years) and monitoring the impacts of land use. It can enable one to overcome the various constraints and limits encountered in the various conventional approaches. It thus appears to be an essential alternative or an effective tool to supplement the conventional methods.

Intelligent systems for additive manufacturing-based repair in remanufacturing: a systematic review of its potential

The conventional component repair in remanufacturing involves human decision making that is influenced by several factors such as conditions of incoming cores, modes of failure, severity of damage, features and geometric complexities of cores and types of reparation required. Repair can be enhanced through automation using additive manufacturing (AM) technology. Advancements in AM have led to the development of directed energy deposition and laser cladding technology for repair of damaged parts and components. The objective of this systematic literature review is to ascertain how intelligent systems can be integrated into AM-based repair, through artificial intelligence (AI) approaches capable of supporting the nature and process of decision making during repair. The integration of intelligent systems in AM repair is expected to enhance resource utilization and repair efficiency during remanufacturing. Based on a systematic literature review of articles published during 2005-2021, the study analyses the activities of conventional repair in remanufacturing, trends in the applications of AM for repair using the current state-of-the-art technology and how AI has been deployed to facilitate repair. The study concludes with suggestions on research areas and opportunities that will further enhance the automation of component repair during remanufacturing using intelligent AM systems.

Comparison of performances of conventional and deep learning-based methods in segmentation of lung vessels and registration of chest radiographs

Conventional machine learning-based methods have been effective in assisting physicians in making accurate decisions and utilized in computer-aided diagnosis for more than 30 years. Recently, deep learning-based methods, and convolutional neural networks in particular, have rapidly become preferred options in medical image analysis because of their state-of-the-art performance. However, the performances of conventional and deep learning-based methods cannot be compared reliably because of their evaluations on different datasets. Hence, we developed both conventional and deep learning-based methods for lung vessel segmentation and chest radiograph registration, and subsequently compared their performances on the same datasets. The results strongly indicated the superiority of deep learning-based methods over their conventional counterparts.

Efficacy of Computer-Aided Design and Manufacturing Versus Computer-Aided Design and Finite Element Modeling Technologies in Brace Management of Idiopathic Scoliosis: A Narrative Review

The efficiency and design quality of scoliosis braces produced by the conventional casting method depends highly on the orthotist's experience. Recently, advanced engineering techniques have been used with the aim of improving the quality of brace design and associated clinical outcomes. Numerically controlled machine tools have provided enormous opportunities for reducing the manufacturing time and saving material. However, the effectiveness of computer-aided brace manufacturing for scoliosis curve improvement is controversial. This narrative review is aimed at comparing the efficacy of braces made by the conventional method with those made by two computer-aided methods: computer-aided design and manufacturing (CAD-CAM), and computer-aided design and finite element modeling (CAD-FEM). The comparison was performed on scoliosis parameters in coronal, sagittal, and transverse planes. Scientific databases were searched, and 11 studies were selected for this review. Because of the diversity of study designs, it was not possible to decisively conclude which brace-manufacturing method is most effective. Similar effectiveness in curve correction was found in the coronal plane for braces made by using advanced manufacturing and conventional methods. In the sagittal plane, modern braces seem to be more effective than traditional braces, but there is an ongoing debate among clinicians, about which CAD-CAM and CAD-FEM brace provides a better treatment outcome. The relative effectiveness of modern and conventional methods in correcting deformities in the transverse plane is also a controversial subject. Overall, advanced engineering design and production methods can be proposed as time- and cost-efficient approaches for scoliosis management. However, there is insufficient evidence yet to conclude that CAD-CAM, and CAD-FEM methods provide significantly better clinical outcomes than those of conventional methods in the treatment of scoliosis curve. Moreover, for some factors, such as molding and the patient's posture during the data acquisition, in brace curve-correction plan, the orthotist's experience and scoliosis curve flexibility should be explored to confidently compare the outcomes of conventional, CAD-CAM, and CAD-FEM methods.

Analytical techniques for the detection of glycated haemoglobin underlining the sensors

The increase in concentrations of blood glucose results arise in the proportion of glycated haemoglobin. Therefore, the percentage of glycated haemoglobin in the blood could function as a biomarker for the average glucose level over the past three months and can be used to detect diabetes. The study of glycated haemoglobin tends to be complex as there are about three hundred distinct assay techniques available for evaluating glycated haemoglobin which contributes to some differences in the recorded values from the similar samples. This review outlines distinct analytical methods that have evolved in the recent past for precise recognition of the glycated - proteins.

Molecular and culture based assessment of bacterial pathogens in subjects with diabetic foot ulcer

INTRODUCTION

Expeditious and precise discerning of bacterial pathogens is a fundamental grail, of clinical diagnostic microbiology. Genotypic detection is a budding substitute to recognize phenotypic culture based processes in bacterial identification.

AIMS

We report a comparative evaluation of biochemical and genomic-based assays for exploring the commonest bacterial flora of infected diabetic foot ulcers along with clinical variables of subjects enrolled.

METHODS

The pathogens selected (i) Staphylococcus aureus ii) Pseudomonas aeruginosa, iii) Escherichia coli and iv) Klebsiella pneumonia, stood for the most frequent isolates of diabetic foot infection in previous studies from Northern India. Identification of these pathogens were done by conventional assays and polymerase chain reaction.

RESULTS

Of 50 specimens obtained from infected DFUs, 74% of cases were affirmative by bacteriological assays and 90% showed positivity via polymerase chain reaction (PCR). Among processed samples 44 isolates were detectable through phenotypic analysis and 65 bacteria by species-specific PCR. Thirteen samples and 21 isolates could not be scrutinized by phenotypic identification systems. The most prevalent pathogens identifiable were Klebsiella pneumonia, followed by Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli.

CONCLUSIONS

We have shown that PCR-based diagnostic methods improved the identification compared to conventional methods and highlight the incorporation of PCR due to shorten turnaround time translating into improved clinical outcomes.

A broad-range PCR technique for the diagnosis of infective endocarditis

Infective endocarditis (IE) remains a severe and potentially fatal disease demanding sophisticated diagnostic strategies for detection of the causative microorganisms. The aim of the present study was to develop a broad-range 16S ribosomal RNA gene polymerase chain reaction in the routine diagnostic of IE for the early diagnosis of fatal disease. A broad-range PCR technique was selected and evaluated in terms of its efficiency in the diagnosis of endocarditis using 19 heart valves from patients undergoing cardiovascular surgeries at the Habib Bourguiba Hospital of Sfax, Tunisia, on the grounds of suspected IE. The results demonstrated the efficiency of this technique particularly in cases involving a limited number of bacteria since it helped to increase detection sensitivity. The technique proved to be efficient, particularly, in the bacteriological diagnosis of IE in contexts involving negative results from conventional culture methods and other contexts involving bacterial species that were not amenable to identification by phenotypic investigations. Indeed, the sequencing of the partial 16S ribosomal RNA gene revealed the presence of Bartonella henselae, Enterobacter sp., and Streptococcus pyogenes in three heart valves with the negative culture. It should be noted that the results obtained from the polymerase chain reaction-sequencing identification applied to the heart valve and the strain isolated from the same tissue were not consistent with the ones found by the conventional microbiological methods in the case of IE caused by Gemella morbillorum. In fact, the results from the molecular identification revealed the presence of Lactobacillus jensenii. Overall, the results have revealed that the proposed method is sensitive, reliable and might open promising opportunities for the early diagnosis of IE.

Clinical evaluation of a multi-parameter customized respiratory TaqMan(®) array card compared to conventional methods in immunocompromised patients

BACKGROUND

Respiratory viral infections can cause significant morbidity and mortality in immunocompromised patients. Conventional tests routinely available at most institutions are limited by the number of detectable pathogens, by a poor sensitivity and/or a long turnaround time.

OBJECTIVES

To compare the performance of routine conventional testing with direct fluorescent antibody assays and viral culture to a customized TaqMan® array card (TAC) real-time PCR method, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously.

STUDY DESIGN

We collected 143 respiratory samples from 120 symptomatic immunocompromised patients. Samples for which conventional and TAC results were discordant underwent further verification testing.

RESULTS

The TAC assay identified viral pathogens in more samples than did conventional testing (77/143 versus 27/143; McNemar P<0.0001), even when TAC results for viruses that could not be detected by conventional testing were excluded from analysis (59/143 versus 26/143; P<0.0001). In addition, the TAC assay identified 18 samples with non-viral pathogens. Verification testing confirmed positive TAC results for 50 out of 55 samples for which conventional testing was negative. Two out of three samples with a positive conventional test but negative TAC result were confirmed positive. A viral and a total pathogen co-infection rate of 5.6% and 11.8% were found, respectively.

CONCLUSIONS

The customized TAC assay resulted in a significantly increased identification of respiratory viruses. This study provides a practical real-life assessment of the performance of the TAC assay in a population for whom rapid and accurate diagnosis of viral and atypical pathogens is crucial for appropriate clinical management.

Detection of Vancomycin Resistant Enterococci from Rectal Swab Samples by Becton-Dickinson GeneOhm VanR assay and Culture at ICU of a Tertiary Care Center in Turkey

Objectives: Vancomycin resistance is due to change in ligase enzyme that destroys the binding of the drug. The gold standard is culture; but now molecular methods have also been developed. The aim was to detect the VRE rate at ICUs by culture and BD GeneOhm™ VanR and compare the results of both assays.

Methodology: 135 perianal swabs were taken from the patients at ICUs between January 1^st 2009 and April 30^th 2009. Samples were identified by conventional methods and BD GeneOhm VanR assay.

Results: In newborn ICU, 41 patients (74.6%) were negative by both methods. Two (3.6%) were positive by both methods. Twelve (21.8%) of them were culture negative and PCR positive. In adult ICU, 73 (91.3%) patients were negative by both methods. Seven patients (8.8%) were positive by molecular method only.

Conclusion: This study showed low VRE positivity due to factors like inhibition in PCR or culture negativity due low inoculum for bacterial growth. Early detection of VRE is an important issue especially in ICUs and molecular techniques are important tools; but against all, we still need to confirm this method with culture based techniques and in order to do this further studies with higher number of patients with VRE colonisation are required.