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AI, The Next Frontier In Full Microbiology Laboratory Automation

AI, The Next Frontier In Full Microbiology Laboratory Automation

AI in the clinical microbiology laboratory amplifies human ingenuity and is the next frontier in full laboratory automation as it focuses on algorithms to automatically read and interpret growth on plates, count colonies, and recognize colony morphology.

Laboratories have been practicing clinical microbiology the same way for decades; however, over the last several years, things have started to change. Change is necessary as microbiology faces big challenges such as increased workload due to screening and diagnosing agents of hospital-acquired infections and multiple drug resistant organisms, along with the pressure of producing faster results. Timeliness and accuracy in the diagnosis of microbial infections are associated with decreased mortality and reduced length of hospitalization, especially for severe, life-threatening infections. Every hour of delay in administrating the targeted antibiotics to septic shock patients decreases their chances of survival by 7.6 percent. Tools and instruments available in the clinical microbiology labs for analysis of patient samples and diagnosis are thus constantly evolving. The main motivation behind this is to decrease the overall time taken to obtain the results from the instruments, enhance the ease of sample processing, and increase the sample turnaround time with the ultimate goal of earlier patient treatment and better recovery rates.

Clinical chemistry, hematology, and immunology laboratories perform much of their work on large automated lines containing instrument after instrument, which perform patient testing 24/7 and report a vast majority of results with no intervention by laboratory staff. Of course, they have the advantage of having their specimens largely submitted in blood tubes of all the same size, which makes automation possible. In microbiology, on the other hand, laboratorians handle a multitude of specimen types with many varying consistencies making automation more difficult. But advances in specimen collection devices for clinical microbiology have made automation a reality. Additionally, with the advent of new innovative collection devices, various specimen types can now be collected into a similar sized tube and be ready for placement onto automated processing platforms.

Microbiology is an ever expending branch in laboratory diagnosis, not only in terms of the variety of investigation that it serves but also techniques that are being incorporated to improve the accuracy of results. Development of kit-based rapid techniques is a major achievement in last three decades. As the techniques are ever changing, the requirement of equipment and reagents also changes accordingly. Newer platforms have significantly replaced the conventional microbiological methods. Direct detection of microorganisms from patient specimens is an area of great interest because of the potential benefits of rapid identification of patient care, antimicrobial stewardship, and healthcare cost. Liquid-based microbiology specimen collection devices opened the door to automated specimen processing, which has in turn opened the door to full microbiology laboratory automation. And now that full laboratory automation has digitized reading of cultures, artificial intelligence (AI) will allow innovative algorithms and specialized software to automatically report culture results, similar to core-laboratories. AI in the clinical microbiology laboratory amplifies human ingenuity and is the next frontier in full laboratory automation as it focuses on algorithms to automatically read and interpret growth on plates, count colonies, and recognize colony morphology.

Additionally, algorithms are available that will determine not only growth/no growth from cultures, but also use segregation software along with chromogenic agars to sort these cultures into user-defined groups of insignificant growth, mixed growth, and those that are of significant counts that would need identifications and susceptibilities performed. The software was shown to decrease the turnaround time for culture results, improve workflow and quality, and allow for cost savings. AI software eliminates mundane tasks for staff, allowing them to concentrate their efforts on the more difficult cultures and laboratory testing. AI also has a role in assisting in the interpretation of growth from traditional media (non-chromogenic agars). Investigators have shown a reduction of approximately 50 percent in the time necessary to perform specific tasks in the laboratory when using full laboratory automation and AI algorithms. For example, when assessing the tasks of urine screening and reading, picking of colonies for further analysis, and screening of MRSA cultures, it was shown that these three tasks took approximately 17 hours daily before the implementation of full laboratory automation and AI algorithms; after implementation, these same three tasks took approximately nine hours per day.

As microbiology labs continue to face unprecedented challenges, microbiology laboratory automation, AI, and innovative reading algorithms can help to fill these vacancies by relieving workload, decreasing errors, and reducing the repetitive motion injuries associated with specimen processing and culture work up/reporting. Thus, globally, the clinical microbiology market is expected to reach USD 4.95 billion by 2023 from USD 3.63 billion in 2018, growing at a CAGR of 6.4 percent, predicts MarketsandMarkets. Technological advancements in the field of infectious disease diagnostics, rising incidence, and prevalence of infectious diseases and growing outbreak of epidemics, and increased funding and public–private investments for the development of novel products for infectious disease diagnosis are major factors driving growth of the clinical microbiology market. Other factors leading to market growth include rapid growth in geriatric population and increasing number of clinical researches. Furthermore, improving healthcare infrastructure across emerging countries, and demand for advanced molecular diagnostic products are creating new opportunities for the market. However, reimbursement concerns and an unfavorable regulatory scenario restrain market growth.

Indian market dynamics

The Indian market for microbiology instruments and reagents in 2017 is estimated at Rs 400 crore. Biomerieux and BD India continue to dominate the market.

The market is moving toward automation. However, the classical microbiology analyzers continue to be popular in selected government and municipal hospitals. Blood culture tests, which have now  been completely automated, are the exception.

The identification and antibiotic susceptibility analyzers and reagents have a 50 percent market share in their respective segments. The blood culture and tuberculosis analyzers and reagents combined have a 50 percent share in their respective segments. 

The NABH has a very large responsibility as India is going through a very dangerous phase with antibiotics easily available and easily prescribed. The patients are gradually becoming drug-resistant and with not many antibiotics being introduced by the pharma industry, it is leading to a very serious situation for the patients. Also, with the huge gap in prescriptions written and tests actually done, the segment has a long way to go. Over the last couple of years, it has been observed that the recovering patients in the hospitals, especially in ICUs, are falling prey to infection contracted from other patients or, more often, the caregiver staff. With immunity levels low, the patient is highly susceptible to carriers of infection. The increase in demand for the identification and antibiotic susceptibility analyzers and reagents may be explained by this new trend.

Outlook

According to the World Health Organization (WHO), antibiotic resistance is among the major threats to global health, food security, and development. This in turn, leads to higher medical costs, prolonged hospital stays, and increased mortality. The growing burden of infectious diseases in India is amongst the highest worldwide. Rapid reporting of microbiology culture results is of utmost importance in the management of infectious diseases and is essential for patient care. Antimicrobial resistance is a growing concern in India, with several government initiatives beginning to fund R&D in this space; for instance, the government has notified governance mechanisms to develop a National Action Plan for AMR and to oversee AMR containment activities. The health ministry is constantly engaged in activities for containment of AMR in the country. Laboratories have been able to initiate data reporting system in WHONET, the software for AMR surveillance data reporting. Labs have also been assessed for building capacity for quality testing. Laboratory automation in clinical microbiology has the potential to revolutionize laboratory operations. The future of clinical microbiology will be improved detection of all pathogens including new ones with rapidity and reduced cost, making them reach the smallest market for improved infectious disease diagnostics.

Microbiology market in India is rapidly transforming with renewed interests in recent years on health and disease awareness. Liquid-based microbiology specimen collection devices, automated specimen processing, and digital imaging with AI reading algorithms are adding value to microbiology laboratories now and will do so in the future as well as clinicians and manufacturers work together to conquer the challenges. Manufacturers are also focusing on reducing the time to results, developing new reagents to expand the range of bacteria that can be detected by new systems, and identify resistant bacteria, creating tests to analyze the susceptibility of bacteria to new antibiotics launched by the pharmaceutical industry, automating the microbiology lab, and strengthening connectivity within laboratories. The next decade, and particularly the next few years, should prove intriguing as manufactures strive to further impact clinical decision-making for infectious diseases by technological advances in clinical microbiology instruments.

Industry Speak
Microbiome Today

The human microbiome consists of large, but still undetermined, microbes. We have often come across the terms good bacteria and bad bacteria in human gut. The gut microbiota in humans evolves throughout the life. They play a very important role in both health and disease. Good bacteria help in digesting food, produce certain vitamins, regulate the immune system, and maintain health by preventing infection. Bad gut bacteria (or an imbalanced microbiome) often cause digestion related disorders. Their role has led this subject to extensive research.

An international project -The Human Microbiome Project (HMP) was launched by NIH in 2007 to characterize organisms in different regions of human body that served as an initiative and a roadmap for biomedical research. In order to study host-microbe interactions, several approaches of culture dependent and independent methods have been developed. Classical culturing, cultoromics, phylogenetic approach, metagenomics studies are a useful tool to map genetic material of the gut microbes. Other novel approaches for their cultivation such as encapsulation into microdroplets or gel particles, diffusion chambers simulating natural environment, microfabricated cultivation chips have been reported which require access to microfluidic or microfabricated technology.

Classical cultivation procedures are adapted to cultivate specific anaerobic microorganisms. Majority of the gut flora are anaerobic or microaerophilic. GMM media, Gifu anaerobic media are commonly used for their isolation. Customized selective media combined with selective bioactive agents are also used for isolation. The most common phyla in the human gut are firmicutes, bacteroidetes, actinobacteria, and proteobacteria. ATCC provides reference standards for microbiome research work. ATCC microbiome standards are fully sequenced, characterized, and authenticated mock microbial communities that mimic mixed metagenomics samples. Each community is prepared from authenticated strains that have been selected for relevant phenotypic and genomic attributes.

Recent gut microbiota cultivation approaches arise through the integration of phylogenetic profiling methods with new cultivation conditions to mimic biological niches. Cultivation of gut bacteria are coupled to rapid taxonomic identification, cultivation based multiplex phenotyping.

Chromogenic media can be used for selective cultivation and enumeration of bacteria such as bifidobacteria, lactobacilli, clostridium, and other gut species.

Gut Microbiota and Probiotic Science Foundation of India registered in 2011 has been created to perpetuate the science of gut microbiota and probiotics in the country. In India many premier research institutes such as National Centre for Cell Science (NCCS), Indian Institute of Science (IISc) and others have embarked in to the microbiome research. Hope soon our good bacteria would be better substitutes for current antibiotics.

Dr G. M. Warke
Founder and CMD,
HiMedia Laboratories Pvt. Ltd.

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