In-vitro diagnosis of single and poly microbial species targeted for diabetic foot infection using e-nose technology

Volatile organic compounds (VOCs) detection for the identification of bacterial infections in clinical wound samples

Early detection of wound infections is critical for timely intervention and prevention of possible complications since prompt treatment can help lower pathogen spread and enhance faster healing. Early detection also helps reduce the risk of serious infections requiring extensive medical interventions or life-threatening diseases such as sepsis. Culture-based approaches currently used for bacterial identification have limited sensitivity and specificity. At the same time, they are time-consuming, resulting in delays in therapy and, therefore, having a negative impact on the treatment outcomes. Quantifying the volatile organic compounds (VOCs) released by bacteria residing in wounds is a promising, non-invasive option for detecting infections at early stages. This method allows for continuous monitoring without requiring invasive procedures, thereby reducing patient discomfort and the risk of further complications. Spectroscopy methods and sensors are the primary VOC detection and quantification approaches, but sensors are more rapid, cost-effective, non-invasive, and precise. This review highlights the significance of the early detection of wound infection to enable timely intervention and prevent complications, emphasizing the limitations of culture-based approaches. It also explores the potential of quantifying VOCs using different methods and discusses the correlation between their levels and the rate of bacterial infections in wounds. Additionally, the review evaluates current VOC-based monitoring methods for wound management, identifies gaps in the field, and advocates for further research to advance wound care and enhance patient outcomes.

The Detection of Bacteria in the Maxillary Sinus Secretion of Patients With Acute Rhinosinusitis Using an Electronic Nose: A Pilot Study

OBJECTIVE

Detecting bacteria as a causative pathogen of acute rhinosinusitis (ARS) is a challenging task. Electronic nose technology is a novel method for detecting volatile organic compounds (VOCs) that has also been studied in association with the detection of several diseases. The aim of this pilot study was to analyze maxillary sinus secretion with differential mobility spectrometry (DMS) and to determine whether the secretion demonstrates a different VOC profile when bacteria are present.

METHODS

Adult patients with ARS symptoms were examined. Maxillary sinus contents were aspirated for bacterial culture and DMS analysis. k-Nearest neighbor and linear discriminant analysis were used to classify samples as positive or negative, using bacterial cultures as a reference.

RESULTS

A total of 26 samples from 15 patients were obtained. After leave-one-out cross-validation, k-nearest neighbor produced accuracy of 85%, sensitivity of 67%, specificity of 94%, positive predictive value of 86%, and negative predictive value of 84%.

CONCLUSIONS

The results of this pilot study suggest that bacterial positive and bacterial negative sinus secretion release different VOCs and that DMS has the potential to detect them. However, as the results are based on limited data, further conclusions cannot be made. DMS is a novel method in disease diagnostics and future studies should examine whether the method can detect bacterial ARS by analyzing exhaled air.

Machine learning algorithms in microbial classification: a comparative analysis

This research paper presents an overview of contemporary machine learning methodologies and their utilization in the domain of healthcare and the prevention of infectious diseases, specifically focusing on the classification and identification of bacterial species. As deep learning techniques have gained prominence in the healthcare sector, a diverse array of architectural models has emerged. Through a comprehensive review of pertinent literature, multiple studies employing machine learning algorithms in the context of microbial diagnosis and classification are examined. Each investigation entails a tabulated presentation of data, encompassing details about the training and validation datasets, specifications of the machine learning and deep learning techniques employed, as well as the evaluation metrics utilized to gauge algorithmic performance. Notably, Convolutional Neural Networks have been the predominant selection for image classification tasks by machine learning practitioners over the last decade. This preference stems from their ability to autonomously extract pertinent and distinguishing features with minimal human intervention. A range of CNN architectures have been developed and effectively applied in the realm of image classification. However, addressing the considerable data requirements of deep learning, recent advancements encompass the application of pre-trained models using transfer learning for the identification of microbial entities. This method involves repurposing the knowledge gleaned from solving alternate image classification challenges to accurately classify microbial images. Consequently, the necessity for extensive and varied training data is significantly mitigated. This study undertakes a comparative assessment of various popular pre-trained CNN architectures for the classification of bacteria. The dataset employed is composed of approximately 660 images, representing 33 bacterial species. To enhance dataset diversity, data augmentation is implemented, followed by evaluation on multiple models including AlexNet, VGGNet, Inception networks, Residual Networks, and Densely Connected Convolutional Networks. The results indicate that the DenseNet-121 architecture yields the optimal performance, achieving a peak accuracy of 99.08%, precision of 99.06%, recall of 99.00%, and an F1-score of 98.99%. By demonstrating the proficiency of the DenseNet-121 model on a comparatively modest dataset, this study underscores the viability of transfer learning in the healthcare sector for precise and efficient microbial identification. These findings contribute to the ongoing endeavors aimed at harnessing machine learning techniques to enhance healthcare methodologies and bolster infectious disease prevention practices.

Artificial Intelligence Methodologies Applied to Technologies for Screening, Diagnosis and Care of the Diabetic Foot: A Narrative Review

Diabetic foot syndrome is a multifactorial pathology with at least three main etiological factors, i.e., peripheral neuropathy, peripheral arterial disease, and infection. In addition to complexity, another distinctive trait of diabetic foot syndrome is its insidiousness, due to a frequent lack of early symptoms. In recent years, it has become clear that the prevalence of diabetic foot syndrome is increasing, and it is among the diabetes complications with a stronger impact on patient's quality of life. Considering the complex nature of this syndrome, artificial intelligence (AI) methodologies appear adequate to address aspects such as timely screening for the identification of the risk for foot ulcers (or, even worse, for amputation), based on appropriate sensor technologies. In this review, we summarize the main findings of the pertinent studies in the field, paying attention to both the AI-based methodological aspects and the main physiological/clinical study outcomes. The analyzed studies show that AI application to data derived by different technologies provides promising results, but in our opinion future studies may benefit from inclusion of quantitative measures based on simple sensors, which are still scarcely exploited.

An Experimental Apparatus for E-Nose Breath Analysis in Respiratory Failure Patients

Background: Non-invasive, bedside diagnostic tools are extremely important for tailo ring the management of respiratory failure patients. The use of electronic noses (ENs) for exhaled breath analysis has the potential to provide useful information for phenotyping different respiratory disorders and improving diagnosis, but their application in respiratory failure patients remains a challenge. We developed a novel measurement apparatus for analysing exhaled breath in such patients. Methods: The breath sampling apparatus uses hospital medical air and oxygen pipeline systems to control the fraction of inspired oxygen and prevent contamination of exhaled gas from ambient Volatile Organic Compounds (VOCs) It is designed to minimise the dead space and respiratory load imposed on patients. Breath odour fingerprints were assessed using a commercial EN with custom MOX sensors. We carried out a feasibility study on 33 SARS-CoV-2 patients (25 with respiratory failure and 8 asymptomatic) and 22 controls to gather data on tolerability and for a preliminary assessment of sensitivity and specificity. The most significant features for the discrimination between breath-odour fingerprints from respiratory failure patients and controls were identified using the Boruta algorithm and then implemented in the development of a support vector machine (SVM) classification model. Results: The novel sampling system was well-tolerated by all patients. The SVM differentiated between respiratory failure patients and controls with an accuracy of 0.81 (area under the ROC curve) and a sensitivity and specificity of 0.920 and 0.682, respectively. The selected features were significantly different in SARS-CoV-2 patients with respiratory failure versus controls and asymptomatic SARS-CoV-2 patients (p < 0.001 and 0.046, respectively). Conclusions: the developed system is suitable for the collection of exhaled breath samples from respiratory failure patients. Our preliminary results suggest that breath-odour fingerprints may be sensitive markers of lung disease severity and aetiology.

Use of GC-IMS for detection of volatile organic compounds to identify mixed bacterial culture medium

In order to explore the possibility to identify common wound infection bacteria in mixed culture with gas chromatograph-ion migration spectroscopy (GC-IMS), the headspace gas of single and mixed cultures of Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa were detected and analyzed by GC-IMS system. The bacteria were cultured in thioglycolate medium tubes then transferred to the sampling bottles (indirect method), or directly cultured in the sampling bottles (direct method) to allow accumulation of volatile compounds and facilitate automation. The specific microorganism volatile organic compounds (mVOCs) of the three bacteria were obtained. Some of them have been known to certain substance, for example, ethanol, isoamyl acetate, Phenylacetaldehyde, 2-heptanone etc., while others have not. Principal component analysis (PCA) showed that a higher separability can be achieved with direct method than indirect method. This work indicated that it is possible to identify compound bacteria by detecting specific mVOCs with GC-IMS, and the specific mVOCs should be medium-dependent.

Real-Time In-Vehicle Air Quality Monitoring System Using Machine Learning Prediction Algorithm

This paper presents the development of a real-time cloud-based in-vehicle air quality monitoring system that enables the prediction of the current and future cabin air quality. The designed system provides predictive analytics using machine learning algorithms that can measure the drivers’ drowsiness and fatigue based on the air quality presented in the cabin car. It consists of five sensors that measure the level of CO₂, particulate matter, vehicle speed, temperature, and humidity. Data from these sensors were collected in real-time from the vehicle cabin and stored in the cloud database. A predictive model using multilayer perceptron, support vector regression, and linear regression was developed to analyze the data and predict the future condition of in-vehicle air quality. The performance of these models was evaluated using the Root Mean Square Error, Mean Squared Error, Mean Absolute Error, and coefficient of determination (R²). The results showed that the support vector regression achieved excellent performance with the highest linearity between the predicted and actual data with an R² of 0.9981.

Machine learning in the clinical microbiology laboratory: has the time come for routine practice?

BACKGROUND

Machine learning (ML) allows the analysis of complex and large data sets and has the potential to improve health care. The clinical microbiology laboratory, at the interface of clinical practice and diagnostics, is of special interest for the development of ML systems.

AIMS

This narrative review aims to explore the current use of ML In clinical microbiology.

SOURCES

References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, biorXiv, arXiV, ACM Digital Library and IEEE Xplore Digital Library up to November 2019.

CONTENT

We found 97 ML systems aiming to assist clinical microbiologists. Overall, 82 ML systems (85%) targeted bacterial infections, 11 (11%) parasitic infections, nine (9%) viral infections and three (3%) fungal infections. Forty ML systems (41%) focused on microorganism detection, identification and quantification, 36 (37%) evaluated antimicrobial susceptibility, and 21 (22%) targeted the diagnosis, disease classification and prediction of clinical outcomes. The ML systems used very diverse data sources: 21 (22%) used genomic data of microorganisms, 19 (20%) microbiota data obtained by metagenomic sequencing, 19 (20%) analysed microscopic images, 17 (18%) spectroscopy data, eight (8%) targeted gene sequencing, six (6%) volatile organic compounds, four (4%) photographs of bacterial colonies, four (4%) transcriptome data, three (3%) protein structure, and three (3%) clinical data. Most systems used data from high-income countries (n = 71, 73%) but a significant number used data from low- and middle-income countries (n = 36, 37%). Performance measures were reported for the 97 ML systems, but no article described their use in clinical practice or reported impact on processes or clinical outcomes.

IMPLICATIONS

In clinical microbiology, ML has been used with various data sources and diverse practical applications. The evaluation and implementation processes represent the main gap in existing ML systems, requiring a focus on their interpretability and potential integration into real-world settings.

A Novel Subspace Alignment-Based Interference Suppression Method for the Transfer Caused by Different Sample Carriers in Electronic Nose

A medical electronic nose (e-nose) with 31 gas sensors is used for wound infection detection by analyzing the bacterial metabolites. In practical applications, the prediction accuracy drops dramatically when the prediction model established by laboratory data is directly used in human clinical samples. This is a key issue for medical e-nose which should be more worthy of attention. The host (carrier) of bacteria can be the culture solution, the animal wound, or the human wound. As well, the bacterial culture solution or animals (such as: mice, rabbits, etc.) obtained easily are usually used as experimental subjects to collect sufficient sensor array data to establish the robust predictive model, but it brings another serious interference problem at the same time. Different carriers have different background interferences, therefore the distribution of data collected under different carriers is different, which will make a certain impact on the recognition accuracy in the detection of human wound infection. This type of interference problem is called "transfer caused by different sample carriers". In this paper, a novel subspace alignment-based interference suppression (SAIS) method with domain correction capability is proposed to solve this interference problem. The subspace is the part of space whose dimension is smaller than the whole space, and it has some specific properties. In this method, first the subspaces of different data domains are gotten, and then one subspace is aligned to another subspace, thereby the problem of different distributions between two domains is solved. From experimental results, it can be found that the recognition accuracy of the infected rat samples increases from 29.18% (there is no interference suppression) to 82.55% (interference suppress by SAIS).

An E-Nose for the Monitoring of Severe Liver Impairment: A Preliminary Study

Biologically inspired to mammalian olfactory system, electronic noses became popular during the last three decades. In literature, as well as in daily practice, a wide range of applications are reported. Nevertheless, the most pioneering one has been (and still is) the assessment of the human breath composition. In this study, we used a prototype of electronic nose, called Wize Sniffer (WS) and based it on an array of semiconductor gas sensor, to detect ammonia in the breath of patients suffering from severe liver impairment. In the setting of severely impaired liver, toxic substances, such as ammonia, accumulate in the systemic circulation and in the brain. This may result in Hepatic Encephalopathy (HE), a spectrum of neuro-psychiatric abnormalities which include changes in cognitive functions, consciousness, and behaviour. HE can be detected only by specific but time-consuming and burdensome examinations, such as blood ammonia levels assessment and neuro-psychological tests. In the presented proof-of-concept study, we aimed at investigating the possibility of discriminating the severity degree of liver impairment on the basis of the detected breath ammonia, in view of the detection of HE at its early stage.

A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections

With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.

Wound odor: current methods of treatment and need for objective measures

Chronic wounds are an enormous burden to society, costing billions of dollars annually in the USA alone. Despite the extensive research into methods to heal chronic wounds, many remain unhealed for months to years. There is a need to focus on patient reported outcomes to improve quality of life in patients with non-healing wounds. Wound odor has a significant impact on patient quality of life; however, relatively little information is available on the management of wound odor. We review the current data available on wound odor and discuss the need for standardized objective measures of odor to improve research quality. An independent search of the PubMed and Embase databases was conducted using combinations of the following words or phrases: "wounds," "chronic wounds," "diabetic ulcers," "venous leg ulcers (VLUs)," "malignant ulcers," "odor," "odour," "smell," "malodor," "artificial olfaction," "electronic nose," and "e-nose." Article references were also searched for significance. There are few overall studies on wound odor, and fewer randomized controlled trials. Current trials on odor have consistent weaknesses such as subjective measures and poor methodology. No single odor treatment modality has been demonstrated to be widely effective for wound odor or superior to other methods. Future research should incorporate objective measures of odor such as electronic noses into clinical trials.

A study on volatile organic compounds emitted by in-vitro lung cancer cultured cells using gas sensor array and SPME-GCMS

Background

Volatile organic compounds (VOCs) emitted from exhaled breath from human bodies have been proven to be a useful source of information for early lung cancer diagnosis. To date, there are still arguable information on the production and origin of significant VOCs of cancer cells. Thus, this study aims to conduct in-vitro experiments involving related cell lines to verify the capability of VOCs in providing information of the cells.

Method

The performances of e-nose technology with different statistical methods to determine the best classifier were conducted and discussed. The gas sensor study has been complemented using solid phase micro-extraction-gas chromatography mass spectrometry. For this purpose, the lung cancer cells (A549 and Calu-3) and control cell lines, breast cancer cell (MCF7) and non-cancerous lung cell (WI38VA13) were cultured in growth medium.

Results

This study successfully provided a list of possible volatile organic compounds that can be specific biomarkers for lung cancer, even at the 24th hour of cell growth. Also, the Linear Discriminant Analysis-based One versus All-Support Vector Machine classifier, is able to produce high performance in distinguishing lung cancer from breast cancer cells and normal lung cells.

Conclusion

The findings in this work conclude that the specific VOC released from the cancer cells can act as the odour signature and potentially to be used as non-invasive screening of lung cancer using gas array sensor devices.

Electronic Nose in the Detection of Wound Infection Bacteria from Bacterial Cultures: A Proof-of-Principle Study

BACKGROUND

Soft tissue infections, including postoperative wound infections, result in a significant burden for modern society. Rapid diagnosis of wound infections is based on bacterial stains, cultures, and polymerase chain reaction assays, and the results are available earliest after several hours, but more often not until days after. Therefore, antibiotic treatment is often administered empirically without a specific diagnosis.

METHODS

We employed our electronic nose (eNose) system for this proof-of-concept study, aiming to differentiate the most relevant bacteria causing wound infections utilizing a set of clinical bacterial cultures on identical blood culture dishes, and established bacterial lines from the gaseous headspace.

RESULTS

Our eNose system was capable of differentiating both methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, Escherichia coli, Pseudomonas aeruginosa, and Clostridium perfringens with an accuracy of 78% within minutes without prior sample preparation. Most importantly, the system was capable of differentiating MRSA from MSSA with a sensitivity of 83%, a specificity of 100%, and an overall accuracy of 91%.

CONCLUSIONS

Our results support the concept of rapid detection of the most relevant bacteria causing wound infections and ultimately differentiating MRSA from MSSA utilizing gaseous headspace sampling with an eNose.

Machine Learning and Data Mining Methods in Diabetes Research

The remarkable advances in biotechnology and health sciences have led to a significant production of data, such as high throughput genetic data and clinical information, generated from large Electronic Health Records (EHRs). To this end, application of machine learning and data mining methods in biosciences is presently, more than ever before, vital and indispensable in efforts to transform intelligently all available information into valuable knowledge. Diabetes mellitus (DM) is defined as a group of metabolic disorders exerting significant pressure on human health worldwide. Extensive research in all aspects of diabetes (diagnosis, etiopathophysiology, therapy, etc.) has led to the generation of huge amounts of data. The aim of the present study is to conduct a systematic review of the applications of machine learning, data mining techniques and tools in the field of diabetes research with respect to a) Prediction and Diagnosis, b) Diabetic Complications, c) Genetic Background and Environment, and e) Health Care and Management with the first category appearing to be the most popular. A wide range of machine learning algorithms were employed. In general, 85% of those used were characterized by supervised learning approaches and 15% by unsupervised ones, and more specifically, association rules. Support vector machines (SVM) arise as the most successful and widely used algorithm. Concerning the type of data, clinical datasets were mainly used. The title applications in the selected articles project the usefulness of extracting valuable knowledge leading to new hypotheses targeting deeper understanding and further investigation in DM.

Development and mining of a volatile organic compound database

Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases. Information on VOCs is scattered in the literature until now; however, there is still no available database describing VOCs and their biological activities. To attain this purpose, we have developed KNApSAcK Metabolite Ecology Database, which contains the information on the relationships between VOCs and their emitting organisms. The KNApSAcK Metabolite Ecology is also linked with the KNApSAcK Core and KNApSAcK Metabolite Activity Database to provide further information on the metabolites and their biological activities. The VOC database can be accessed online.