Review of Telemicrobiology

The Use of Machine Learning for Image Analysis Artificial Intelligence in Clinical Microbiology

The growing transition to digital microbiology in clinical laboratories creates the opportunity to interpret images using software. Software analysis tools can be designed to use human-curated knowledge and expert rules, but more novel artificial intelligence (AI) approaches such as machine learning (ML) are being integrated into clinical microbiology practice. These image analysis AI (IAAI) tools are beginning to penetrate routine clinical microbiology practice, and their scope and impact on routine clinical microbiology practice will continue to grow. This review separates the IAAI applications into 2 broad classification categories: (i) rare event detection/classification or (ii) score-based/categorical classification. Rare event detection can be used for screening purposes or for final identification of a microbe including microscopic detection of mycobacteria in a primary specimen, detection of bacterial colonies growing on nutrient agar, or detection of parasites in a stool preparation or blood smear. Score-based image analysis can be applied to a scoring system that classifies images in toto as its output interpretation and examples include application of the Nugent score for diagnosing bacterial vaginosis and interpretation of urine cultures. The benefits, challenges, development, and implementation strategies of IAAI tools are explored. In conclusion, IAAI is beginning to impact the routine practice of clinical microbiology, and its use can enhance the efficiency and quality of clinical microbiology practice. Although the future of IAAI is promising, currently IAAI only augments human effort and is not a replacement for human expertise.

The Critical Value of Telepathology in the COVID-19 Era

Background

Telepathology, which includes the use of telecommunication links, helps enable transmission of digital pathology images for primary diagnosis, quality assurance, education, research, or second opinion diagnoses.

Observations

This review covers all aspects of telepathology implementation, including the selection of platforms, budgets and regulations, validation, implementation, education, quality monitoring, and the potential to improve practice. Considering the long-term trends, the lessons of the COVID-19 pandemic, and the potential for future pandemics or other disasters, the validation and implementation of telepathology remains a reasonable choice for laboratories looking to improve their practice.

Conclusions

Though barriers to implementation exist, there are potential benefits, such as the wide spectrum of uses like frozen section, telecytology, primary diagnosis, and second opinions. Telepathology represents an innovation that may transform the future of pathology practice.

Development of Automatic Portable Pathology Scanner and Its Evaluation for Clinical Practice

Digital pathological scanners transform traditional glass slides into whole slide images (WSIs), which significantly improve the efficiency of pathological diagnosis and promote the development of digital pathology. However, the huge economic burden limits the spread and application of general WSI scanners in relatively remote and backward regions. In this paper, we develop an automatic portable cytopathology scanner based on mobile internet, Landing-Smart, to avert the above problems. Landing-Smart is a tiny device with a size of 208 mm × 107 mm × 104 mm and a weight of 1.8 kg, which integrates four main components including a smartphone, a glass slide carrier, an electric controller, and an optical imaging unit. By leveraging a simple optical imaging unit to substitute the sophisticated but complex conventional light microscope, the cost of Landing-Smart is less than $3000, much cheaper than general WSI scanners. On the one hand, Landing-Smart utilizes the built-in camera of the smartphone to acquire field of views (FoVs) in the section one by one. On the other hand, it uploads the images to the cloud server in real time via mobile internet, where the image processing and stitching method is implemented to generate the WSI of the cytological sample. The practical assessment of 209 cervical cytological specimens has demonstrated that Landing-Smart is comparable to general digital scanners in cytopathology diagnosis. Landing-Smart provides an effective tool for preliminary cytological screening in underdeveloped areas.

Next Generation Digital Pathology: Emerging Trends and Measurement Challenges for Molecular Pathology

Digital pathology is revolutionising the analysis of histological features and is becoming more and more widespread in both the clinic and research. Molecular pathology extends the tissue morphology information provided by conventional histopathology by providing spatially resolved molecular information to complement the structural information provided by histopathology. The multidimensional nature of the molecular data poses significant challenge for data processing, mining, and analysis. One of the key challenges faced by new and existing pathology practitioners is how to choose the most suitable molecular pathology technique for a given diagnosis. By providing a comparison of different methods, this narrative review aims to introduce the field of molecular pathology, providing a high-level overview of many different methods. Since each pixel of an image contains a wealth of molecular information, data processing in molecular pathology is more complex. The key data processing steps and variables, and their effect on the data, are also discussed.

Teleclinical Microbiology: An Innovative Approach to Providing Web-Enabled Diagnostic Laboratory Services in Syria

OBJECTIVES

Telemedicine can compensate for the lack of health care specialists in response to protracted humanitarian crises. We sought to assess the usability of a teleclinical microbiology (TCM) program to provide diagnostic services in a hard-to-reach region of Syria.

METHODS

A semimobile station was equipped with conventional micrograph and macrograph digital imaging systems. An electronic platform (Telemicrobiology in Humanitarian Crises, TmHC) was created to facilitate sharing, interpreting, and storing the results. A pilot study was conducted to identify the bacterial species and antimicrobial susceptibility pattern of 74 urinary clinical isolates. An experience survey was conducted to capture the feedback of 8 participants in the program.

RESULTS

The TmHC platform (https://sdh.ngo/tmhc/) enabled systematic transmission of the laboratory records and co-interpretation of the results. The isolates were identified as Escherichia coli (n = 61), Klebsiella pneumoniae (n = 12), and Proteus mirabilis(n = 1). All the isolates were multidrug resistant. The performance of our TCM module was rated 4 (satisfying) and 5 (very satisfying) by 6 and 2 users, respectively. Data security of and cost-effectiveness were the main perceived concerns.

CONCLUSIONS

Although we encountered several context-related obstacles, our TCM program managed to reach a highly vulnerable population of 4 million people confined in the northwest region of Syria.

Eye Tracking-An Innovative Tool in Medical Parasitology

The innovative Eye Movement Modelling Examples (EMMEs) method can be used in medicine as an educational training tool for the assessment and verification of students and professionals. Our work was intended to analyse the possibility of using eye tracking tools to verify the skills and training of people engaged in laboratory medicine on the example of parasitological diagnostics. Professionally active laboratory diagnosticians working in a multi-profile laboratory (non-parasitological) (n = 16), laboratory diagnosticians no longer working in this profession (n = 10), and medical analyst students (n = 56), participated in the study. The studied group analysed microscopic images of parasitological preparations made with the cellSens Dimension Software (Olympus) system. Eye activity parameters were obtained using a stationary, video-based eye tracker Tobii TX300 which has a 3-ms temporal resolution. Eye movement activity parameters were analysed along with time parameters. The results of our studies have shown that the eye tracking method is a valuable tool for the analysis of parasitological preparations. Detailed quantitative and qualitative analysis confirmed that the EMMEs method may facilitate learning of the correct microscopic image scanning path. The analysis of the results of our studies allows us to conclude that the EMMEs method may be a valuable tool in the preparation of teaching materials in virtual microscopy. These teaching materials generated with the use of eye tracking, prepared by experienced professionals in the field of laboratory medicine, can be used during various training, simulations and courses in medical parasitology and contribute to the verification of education results, professional skills, and elimination of errors in parasitological diagnostics.

Immune contexture analysis in immuno-oncology: applications and challenges of multiplex fluorescent immunohistochemistry

The tumor microenvironment is an integral player in cancer initiation, tumor progression, response and resistance to anti-cancer therapy. Understanding the complex interactions of tumor immune architecture (referred to as 'immune contexture') has therefore become increasingly desirable to guide our approach to patient selection, clinical trial design, combination therapies, and patient management. Quantitative image analysis based on multiplexed fluorescence immunohistochemistry and deep learning technologies are rapidly developing to enable researchers to interrogate complex information from the tumor microenvironment and find predictive insights into treatment response. Herein, we discuss current developments in multiplexed fluorescence immunohistochemistry for immune contexture analysis, and their application in immuno-oncology, and discuss challenges to effectively use this technology in clinical settings. We also present a multiplexed image analysis workflow to analyse fluorescence multiplexed stained tumor sections using the Vectra Automated Digital Pathology System together with FCS express flow cytometry software. The benefit of this strategy is that the spectral unmixing accurately generates and analyses complex arrays of multiple biomarkers, which can be helpful for diagnosis, risk stratification, and guiding clinical management of oncology patients.

Essential role of laboratory physicians in transformation of laboratory practice and management to a value-based patient-centric model

The laboratory is a vital part of the continuum of patient care. In fact, there are few programs in the healthcare system that do not rely on ready access and availability of complex diagnostic laboratory services. The existing transactional model of laboratory "medical practice" will not be able to meet the needs of the healthcare system as it rapidly shifts toward value-based care and precision medicine, which demands that practice be based on total system indicators, clinical effectiveness, and patient outcomes. Laboratory "value" will no longer be focused primarily on internal testing quality and efficiencies but rather on the relative cost of diagnostic testing compared to direct improvement in clinical and system outcomes. The medical laboratory as a "business" focused on operational efficiency and cost-controls must transform to become an essential clinical service that is a tightly integrated equal partner in direct patient care. We would argue that this paradigm shift would not be necessary if laboratory services had remained a "patient-centric" medical practice throughout the last few decades. This review is focused on the essential role of laboratory physicians in transforming laboratory practice and management to a value-based patient-centric model. Value-based practice is necessary not only to meet the challenges of the new precision medicine world order but also to bring about sustainable healthcare service delivery.

A Systematic Overview of Zoonotic Helminth Infections in North America

Zoonotic helminths are frequent human parasites that generally complete their natural life cycle in the absence of humans. This review encompasses 30 common or clinically relevant zoonotic helminth infections that are endemic to North America. For each organism or disease, the following information is briefly reviewed: taxonomy, biology, and life cycle, epidemiology, route of transmission for the human host, clinical manifestations, pathologic features, treatment, and laboratory diagnosis. Illustrations are provided for select parasites.

Implementation of Whole Slide Imaging for Clinical Purposes: Issues to Consider From the Perspective of Early Adopters

CONTEXT

- There is growing interest in the use of digital pathology, especially whole slide imaging, for diagnostic purposes. Many issues need to be considered when incorporating this technology into a clinical laboratory. The College of American Pathologists (CAP) established a Digital Pathology Committee to support the development of CAP programs related to digital pathology. One of its many initiatives was a panel discussion entitled "Implementing Whole-Slide Imaging for Clinical Use: What to Do and What to Avoid," given for 3 years at the CAP annual meetings starting in 2014.

OBJECTIVES

- To review major issues to consider when implementing whole slide imaging for clinical purposes as covered during the panel discussion.

DESIGN

- The views expressed and recommendations given are based primarily on the personal experience of the authors as early adopters of this technology. It is not intended to be an exhaustive review of digital pathology.

RESULTS

- Implementation is best approached in phases. Early efforts are directed toward identifying initial clinical applications and assembling an implementation team. Scanner selection should be based on intended use and budget. Recognizing pathologist concerns over the use of digital pathology for diagnostic purposes, ensuring adequate training, and performing appropriate validation studies will enhance adoption. Once implemented, the transition period from glass slide to image-based diagnostics will be associated with challenges, especially those related to a hybrid glass slide-digital slide workflow.

CONCLUSIONS

- With appropriate preparation, planning, and stepwise implementation, whole slide imaging can be used safely and reliably for frozen sections, consultation, quality assurance, and primary diagnosis.

Update on Malaria Diagnostics and Test Utilization

Malaria is a potentially life-threatening disease requiring rapid diagnosis and treatment. Although microscopic examination of thick and thin blood films remains the gold standard for laboratory diagnosis, rapid antigen tests and nucleic acid amplification methods may also play a useful role in detection of acute infection. This review discusses the advantages and disadvantages of the commonly used diagnostic methods and provides important practice points for optimal malaria test utilization.