Fast Track Diagnostics and UgenTec Announce New Interpretation Software for All FTD Real-Time PCR Multiplex Kits

Fast Track Diagnostics S.à.r.l., one of the leading global suppliers of syndromic real-time PCR multiplexing kits, has been partnering for several months with UgenTec NV, an innovative European medical device software company that develops artificially intelligent PCR interpretation software.

From the first of January 2018, all Fast Track Diagnostics´ kits will be available on UgenTec´s FastFinder, a fully automated real-time PCR interpretation platform. This module will allow technicians to fully automate and standardise analysis of FTD´s kits with Applied Biosystems 7500 and LightCycler® 480 PCR platforms. The software will be developed for nearly all other clinical PCR machines by end of Q2 2018 and rolled out to users over that period.

The combination of Fast Track Diagnostics' kits and FastFinder’s artificial intelligence will considerably improve the processes within laboratories. The software is developed under ISO13485 standards and is CE IVD-certified.

“Fast Track Diagnostics strives constantly to deliver concrete and high quality solutions to healthcare specialists for the benefit of patients” said Bill Carman, Chief Executive Officer of Fast Track Diagnostics, “UgenTec´s knowledge on overcoming PCR interpretation challenges has brought the analysis time of FTD´s kits down to few minutes, bringing considerable efficiencies to the laboratory workflow.”

“Partnering with Fast Track Diagnostics will result in a strong increase in customer value” said Dr. Tom Martens, Managing Director at UgenTec “Their years of experience in manufacturing syndromic real-time PCR multiplexing kits combined with our IVD software knowledge will allow laboratories across the globe to decrease their eyes-on time drastically”.

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GenePOC Launches its GenePOC™ CDiff Test in the United States

GenePOC Inc. (GenePOC), a member of the Debiopharm Group™, is proud to announce the launch of its 2nd FDA cleared assay in less than 6 months, GenePOC™ CDiff, for use on the revogene™ instrument. The GenePOC CDiff test targets the toxin B gene of toxigenic C. difficile strains in unformed stool specimens obtained from patients suspected of having C. difficile infection (CDI). The test provides a novel and highly flexible alternative to assist clinicians in rapidly identifying, isolating and treating patients having CDI. Consequently, rapid management of patients having CDI will aid in preventing the spread of the bacteria - identified as an urgent threat in healthcare settings by the center for disease control (CDC).

About C. difficile infection in the US 

In the United States, CDI is the leading cause of infectious antibiotic-associated diarrhea with 293 000 infections per year[i] representing $4.8 billion in additional healthcare cost per year[ii]. CDI poses many challenges to health institutions, among which is being able to efficiently test the patients at risk.

Traditional testing methods for identification of toxigenic C. difficile, such as toxigenic culture and enzyme immunoassays (EIA), have been found to be labor intensive, to increase delays and, to have limited sensitivity[iii].

There exists a need for a faster and simpler testing algorithm. According to the 2010 guidance from the American Society for Microbiology, nucleic acid amplification tests detecting C. difficile toxin genes may be used as a stand-alone test[iv]. In fact, those molecular tests provide sensitive, specific and timely identification of patients with toxigenic C. difficile infection, and exhibit better performance than toxin EIAs[v].

According to Dr Nathan Ledeboer from the Medical College of Wisconsin, in Milwaukee: "It all starts with timely diagnosis of C. difficile infections to critically impact patient management and ensure proper implementation of infection control practices". Dr Nathan Ledeboer participated in a multicentric clinical trial, evaluating GenePOC CDiff test for use on the revogene instrument.

About GenePOC CDiff test 

The GenePOC CDiff assay is a qualitative in vitro diagnostic test to detect the toxin B (tcdB) gene of toxigenic C. difficile in unformed (liquid or soft) stool specimens obtained from patients suspected of having CDI. Performing this test enables healthcare professionals to detect the presence of toxigenic C. difficile within 70 minutes after loading the patient sample in the test cartridge or PIE. Early and accurate detection can lead to better control and management of CDI, which in turn can improve patient management and reduce the risk of transmission.

"A simple one-step algorithm to detect toxigenic C. difficile, using a clinical test with excellent performance, will inevitably contribute to better control the spread of CDI and reduce outbreaks" says Dr Patrice Allibert, CEO of GenePOC. "What makes our assay so unique is its right balance between sensitivity and specificity. This translates into the ability to identify patients with CDI from a single GenePOC CDiff test, a molecular test with less than 1% unresolved rate according to clinical trial results. Our test is performed on the affordable, user-friendly revogene instrument which can be directly connected to the hospital and laboratory information systems (LIS/HIS), for seamless transmission and communication of actionable results", Patrice Allibert continued.

References

i. Dubberke et al. Clin Infect Dis 2012; 55: S88-92.
ii. Lessa et al. N Engl J Med 2015; 372(9):825-834.
iii. Carroll KC. Tests for the diagnosis of Clostridium difficile infection: the next generation Anaerobe. 2011 Aug;17(4):170-4.
iv. Cohen SH, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infect Control Hosp Epidemiol 2010; 31:431-55.
v. Wilcox MH, Planche T, Fang FC. What is the current role of algorithmic approaches for diagnosis of Clostridium difficile infection? J Clin Microbiol, 2010, vol. 48 (pg. 4347-4353).

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University of Queensland Researchers Develop Rapid, Cheap Nucleic Acid Extraction Technology

Researchers at the University of Queensland have developed a rapid nucleic acid purification technology that obtains amplification-ready genetic material from difficult biological samples in less than 30 seconds.

In a study published in PLOS Biology, the researchers initially investigated the ability of certain chemicals to capture anionic DNA and RNA by spotting them on a piece of cellulose-based paper. While none of the chemical treatments produced reproducible amplification, the team found that the nucleic acids almost instantly bound to the untreated paper.

In addition, the cellulose-based paper retained the genetic material during a short washing step to remove contaminants, and they then eluted the material directly into an amplification reaction chamber.

"We used the adsorbing solvency of the paper to suck up a certain amount of the genetic sample, as determined by the size of the nucleic acid binding site," Michael Mason, a University of Queensland senior postdoctoral research fellow and co-first author on the paper, said in an interview.

Mason's team adapted the cellulose filter to develop an equipment-free nucleic acid extraction process that uses a dipstick made from the paper, with a small 8-mm2 DNA-binding surface and a long water-repellent handle made by filling the filter paper with paraplast wax.

The process involves homogenizing tissue in a tube containing appropriate lysis buffer and ball bearings to help break down the tissue, then using the dipstick to capture nucleic acids by dipping it into the lysate three times. The dipstick is then dipped up and down in a wash solution three times. Finally, the bound nucleic acids are eluted from the cellulose by putting the dipstick directly into the amplification mix three times.

While researchers have used other types of membranes to induce rapid nucleic acid extraction, including aluminum oxide and silica-based filters, the methods require relatively complex fabrication, multiple pipetting steps, or electrical equipment to help purify the nucleic acids.

To validate the new nucleic acid purification method, Mason's team matched the test against AMPure, a popular commercial rapid paramagnetic bead DNA extraction method sold by Beckman Coulter. They saw that the cellulose method purified amplifiable DNA significantly faster, in under 30 seconds compared to 14.5 minutes for AMPure purification.

While techniques like AMPure only take 10 minutes and do not require electrical equipment, Mason's team believes the tools required are too costly for external applications such as field-based point-of-need assays.  

"Importantly, the method achieves this speed and simplicity without the need for any pipetting, [and is] significantly cheaper, with consumables costing four times less than those required by the AMPure system, and does not require the initial investment of $685-$876 for the specialized magnet plate," the authors stated in the paper.    

According to the study, AMPure's paramagnetic beads cost $0.65 per sample, whereas the team's cellulose dipstick purification method costs $0.15 per sample, including plasticware and reagents. Mason explained that if the ball bearings used to homogenize the tissue are washed and reused, the cost for the cellulose dipstick purification could be further reduced to $0.06 per sample.

Mason and his team have filed a patent for the cellulose disc extraction method through UniQuest, a commercialization company for the University of Queensland. Mason said that UniQuest is currently in discussions with firms interested in commercializing the technology, but did not disclose them at this time.

"We haven't found [any] limitations, but we are looking into new uses for this technology, and we might find that we do need to increase the amount of DNA that binds onto the dipstick," Mason said.

Mason envisions the cellulose-based technology to be used in a wide range of situations, including clinical care and high school science classes. He also plans to use the technology to detect food pathogens, and his team is currently working with food-based molecular diagnostic projects in Papua New Guinea.

"You can have situations in the near future, like in hospitals, if a doctor suspects you have some sort of blood pathogen, he could actually take a drop of blood and perform the test right next to the bedside," Mason said.

In addition, Mason built an electronic amplification device that cost about A$30 ($23) using parts purchased on Ebay. He explained that this device "takes the tube out of the dipstick, performs the reactions, and returns the results quickly." Mason said that "doctors would know within an hour what's wrong with the patient."

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New Salmonella Multiplex PCR Solution offers First Validated Assay for Simultaneous Detection of Three Salmonella Targets in One Rapid Test

Poultry and pork producers can now rapidly screen for 3 Salmonella targets with one rapid PCR test. The new Thermo Scientific RapidFinder Salmonella Multiplex PCR System is the first validated multiplex PCR assay for simultaneous detection of Salmonella species, Typhimurium and Enteritidis.

Thermo Fisher Scientific, a market leader in culture media, microbiology, molecular and mass spectrometry systems, has been awarded AOAC-RI Performance Tested MethodsSM certification for its RapidFinder Salmonella Multiplex PCR Detection Workflow. Validated for use on the Applied Biosystems Food Safety 7500 Fast System and the Applied Biosystems Food Safety QuantStudio 5 System, the workflow features simple sample preparation and results in as few as 16 hours from raw and cooked poultry and pork as well as production environment samples.

"Salmonella serovars Typhimurium and Enteritidis are most commonly associated with the disease in humans. As a result there are multiple strategies and regulations targeting a reduction in the contamination level of these serovars in the poultry and pork industries," said Bernd Hofmann, vice president, global marketing, microbiology, Thermo Fisher Scientific. "Identifying the serovar of any Salmonella strain quickly can bring substantial economic benefits to pork and poultry producers. To be able to detect three targets in as few as 16 hours now means product may be released two or three days sooner than when using conventional tests."

Many rapid methods are available to detect all Salmonella species but not all are capable of providing the serovar identity of a Salmonella strain if detected. To get that information the laboratory must run additional rapid tests, which can prove very expensive, or use a series of conventional biochemical and serological tests that can take several days to complete.

The RapidFinder Salmonella Multiplex PCR Solution offers:

• Simple sample enrichment and PCR preparation protocols – fast & scalable for small to higher-throughput laboratories
• Multiplexed, simultaneous detection of Salmonella species, Typhimurium and Enteritidis facilitating one-well screening and identification for maximum efficiency
• TaqMan-based PCR probe technology for excellent sensitivity, specificity and reliability as evidenced through AOAC-RI Performance Tested MethodsSM (PTM) studies
• Confidence in results – AOAC-RI PTM certification as part of an extensive validation program to address salmonella testing needs at all stages of the poultry and pork production process

In addition to the RapidFinder Salmonella Multiplex PCR Solution, Thermo Fisher Scientific provides real-time PCR-based workflow solutions and other methods to test for a broad range of food safety and quality indicators including other bacterial pathogens, meat species identification and GMO markers, as well as an expanding range of custom developed assays. All of our PCR solutions are designed to run on the Applied Biosystems 7500 Fast Real-Time PCR System which provides expansive molecular capability and streamlined testing processes which may reduce overall costs.

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Sekisui Diagnostics Enters Strategic Alliance with Mesa Biotech Inc. for Molecular POC Testing System

Sekisui Diagnostics and Mesa Biotech Inc. announce a strategic alliance, to distribute the Mesa Biotech POC molecular system for Flu A/Flu B.   Sekisui Diagnostics will assume exclusive distribution of the Mesa Biotech POC system in the U.S. and Canada, pending FDA clearance.

The Mesa Biotech molecular dock and test cassette system provides physicians with rapid infectious disease diagnosis at the point of care with increased sensitivity and specificity over most rapid tests currently on the market by using nucleic acid PCR (polymerase chain reaction)amplification technology. The first test cassette will test for Flu A/Flu B with additional tests to be added over time.

"Sekisui Diagnostics is pleased to announce our new relationship with Mesa Biotech which will complement our existing rapid test portfolio," said Robert Schruender, President and COO of Sekisui Diagnostics. "This system is highly compatible with our business channels and relationships with distributors. It also offers the potential to strengthen our flu portfolio in the mid-to-long term by offering physicians the simplicity, convenience and procedural familiarity of traditional POC rapid immunoassays, while providing the superior sensitivity, specificity and information content of laboratory-based PCR testing."

"We are extremely excited to partner with Sekisui Diagnostics for the commercialization of Mesa Biotech's point of care PCR platform in North America," said Dr. Hong Cai, co-founder and CEO of Mesa Biotech. "Our PCR platform solution and pipeline coupled with Sekisui's Diagnostics commercial and supply chain expertise as well as their unparalleled field sales relationships brings tremendous synergy opportunities for both organizations."

About Sekisui Diagnostics

Sekisui Diagnostics is a global diagnostics company committed to improving patient's lives by providing innovative medical diagnostics to physicians and laboratories through a global commercial network.  Product lines include clinical chemistry and coagulation systems, reagents, point-of-care systems and rapid tests, as well as enzymes and specialty bio-chemicals.

About Mesa Biotech Inc.

Mesa Biotech designs, develops and manufactures next generation molecular diagnostic tests, bringing the superior diagnostic performance of nucleic acid PCR amplification to the point-of-care (POC). Mesa Biotech's System consists of a portable, palm-sized dock and a disposable, assay-specific test cassette. This patented system will allow healthcare professionals to access actionable, laboratory-quality results at the POC with greater sensitivity and specificity than current infectious disease rapid immunodiagnostic tests. Mesa Biotech's technology development has been funded to date by a series of grants and private equity investments.

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Qvella Progresses on Rapid Sepsis Testing Platform With BioMérieux as New Investor

Toronto-based molecular diagnostics firm Qvella announced this week that it received $20 million in Series B funding, including support from a surprising new investor: BioMérieux.

A potential competitor in the rapid multiplex PCR diagnostics space, BioMérieux said that it will now explore collaborative opportunities in complementary markets around Qvella's field-activated sample treatment, or FAST technology.

BioMérieux sees Qvella's technology as an accompaniment to the BioFire FilmArray diagnostic platform, Frédéric Sweeney, vice president of corporate development and strategic financing said in an email, adding, "Technology that will help to advance microbiology and in vitro diagnostics is a strategic priority for BioMérieux."

Sweeney explained that BioMérieux has a dedicated team of business development professionals who explore and monitor companies, like Qvella, in order to make advancements in addressing growing healthcare threats, such as antimicrobial resistance.

Qvella has primarily focused its development on the fundamental problem of sample preparation, Sweeney further said, including automating the isolation, concentration, and lysis of a small number of pathogens in a whole blood sample.

BioFire FilmArray sample prep, meanwhile, uses silica beads to free the cell components, and magnetic beads to capture the DNA or RNA.

Overall, Qvella's technology "can be seen as a nice complement to many of BioMérieux’s other ranges of microbiology, immunoassay, or molecular biology products," Sweeney further said.

Qvella recently presented preliminary data and announced an updated timeline for the launch of its PCR-based, multiplex blood stream infection (BSI) panel.

The firm noted during a corporate workshop at the Association of Molecular Pathology meeting last month that its BSI test in development requires no extraction or purification. The test uses a fully integrated instrument with an easy-to-use graphical interface and disposable cartridges, and relies on a number of innovative core technologies to detect pathogens directly from whole blood in around 45 minutes.

Firstly, it employs a ribosomal target at the family or genus level to cast a wider net in capturing sepsis-causing pathogens, Qvella's CEO, Tino Alavie, said in a follow-up interview. The firm has balanced this, considering a treatment perspective as well as something that is manageable from a multiplexing perspective, in order "to give the most impactful response to clinicians," Alavie added.

At the AMP workshop, Qvella's scientific administrator Susan Novak reported that a version of the test with 16 reaction wells could detect up to 84 sepsis-causing species. These fit under one family-level, five genus-level, and 10 species-level categories, and covered greater than 90 percent of sepsis cases, according to Novak. The test was also able to identify polymicrobial cases in spiked-in samples.

Qvella's technology also uses a proprietary method for pathogenic cell isolation which involves a hemolysis step followed by centrifugal field and wash steps to generate a cell suspension, Alavie said. Qvella's FAST method is used to treat and lyse cells, after which pathogen nucleic acids can be subjected to array-based multiplex RT-PCR.

One person dies of sepsis every two minutes in the US and delays in initiation of appropriate antimicrobial therapies increase mortality, according to a 2011 review. A presentation at Qvella's workshop highlighted a gap in "rapid" sepsis diagnostics, namely that tests that rely on blood cultures are generally too slow to help in initial treatment decisions.

In the presentation, Larissa May, an emergency room physician who is also an antibiotic steward at the University of California, Davis, said that, from a stewardship perspective, the typical four days to identify a sepsis-causing pathogen is "frankly, unacceptable."

May highlighted that patients are often placed on early empiric, broad-spectrum antibiotic therapy while clinicians wait for lab results that can show the exact pathogen or pathogens that causing the infection. And, in patients with an unknown source of infection, certain pathogens may not be considered in the initial diagnosis, May said in a follow-up interview.

Narrowing of antibiotic spectrum does not occur as early as needed due to current practice patterns and physician behavior, May said, including time constraints of traditional microbiologic testing and a reluctance among prescribers to switch therapies.

"Truly fast tests that [provide results] in less than an hour with high accuracy — with the caveat that this would not obviate the need for confirmatory culture — would enable a much-needed paradigm shift, moving from empiric to initial targeting therapy, earlier de-escalation, and ultimately improved patient outcomes due to more appropriate therapy and improved antibiotic stewardship in healthcare, including for critically ill patients," May said.

BioMérieux, meanwhile, has a company-wide focus on antibiotic stewardship. It's BacT/ALERT Virtuo blood culture platform was cleared by the US Food and Drug Administration earlier this year, and the firm has obtained new indications for its procalcitonin (PCT) diagnostic immunoassay which was recently cleared to guide antibiotic management in suspected sepsis and lower respiratory tract infections.

Subsidiary BioFire manufactures the FilmArray Blood Culture Identification (BCID) assay which was cleared by the FDA in 2013 and tests for 27 pathogens that can cause sepsis, including three common antibiotic resistance markers, in about one hour.

The BCID test has been demonstrated to have clinical benefits. For example, a study in 2015 showed it could lead to reduced use of broad-spectrum antimicrobials as well as earlier de-escalation. And a recent study of pediatric patients with sepsis showed clinical benefits of resistance testing in particular. Both studies also suggested that the clinical benefits of rapid diagnostic microbiological tools are enhanced with a concurrent antibiotic stewardship program, particularly one that includes things like templated comments to guide physician prescribing based on test results. However, although the BCID is faster than conventional culture methods — which can take days and require subculture and phenotypic susceptibility testing — the test still requires a positive blood culture.

Qvella has now lined up all the clinical trial sites for the BSI test, according to Novak.

The firm's timeline to launch includes: US pre-clinical trials from Q2 to Q3 2018; clinical trials, CE mark, and European launch from Q3 to Q4 2018; and FDA submission in Q1 2019.

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PathoQuest and Mayo Clinic Enter into an Agreement to Conduct Study of iDTECT™ Blood in Patients with Febrile Neutropenia

PathoQuest, a life sciences leader focused on improving pathogen identification in biological samples, today announced that it will conduct research with Mayo Clinic to study the company’s proprietary iDTECT™ Blood test. Mayo Clinic will explore the use of iDTECT Blood in the context of a prospective study designed to confirm the utility of a next generation sequencing-based metagenomic approach to identify pathogens in patients with neutropenic fever. PathoQuest will work with Robin Patel, M.D., Chair, Division of Clinical Microbiology and Director of the Infectious Disease Research Laboratory at the Mayo Clinic to conduct the study.

PathoQuest, a life sciences leader focused on improving pathogen identification in biological samples, today announced that it will conduct research with Mayo Clinic to study the company’s proprietary iDTECT™ Blood test. Mayo Clinic will explore the use of iDTECT Blood in the context of a prospective study designed to confirm the utility of a next generation sequencing-based metagenomic approach to identify pathogens in patients with neutropenic fever. PathoQuest will work with Robin Patel, M.D., Chair, Division of Clinical Microbiology and Director of the Infectious Disease Research Laboratory at the Mayo Clinic to conduct the study.

About PathoQuest

PathoQuest, a spin out of Institut Pasteur, is a life sciences company offering a game changing metagenomics approach to improving pathogen detection in biological samples. PathoQuest’s technology combines a Next-Generation Sequencing (NGS) platform and a proprietary sample preparation process which is applicable to several types of samples with a proprietary pathogen genome sequence database and automated analysis pipeline.

PathoQuest has developed iDTECT Blood Test, the first and only clinical CE IVD metagenomic test in infectious disease. Using a single blood sample, the test provides clinicians and microbiologists with an improved method for detecting and identifying pathogens, particularly for immunocompromised patients with suspected infections. This new molecular diagnostic test is designed with the objective to improve antibiotic stewardship and lead to better patient care through precision medicine.

Based on the company’s technological platform, PathoQuest also offers biopharmaceutical companies a disruptive approach to secure production of biologics like vaccines and recombinant proteins. PathoQuest’s solution is currently being utilized by several major biopharma companies.

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New Rapid Test for Valley Fever Should Help Reduce Diagnosis Delays

Valley fever cases in November saw a 50-percent spike over the previous month, leading experts at the University of Arizona Valley Fever Center for Excellence to predict a significant increase in cases in 2018.

Fortunately, the recent—and timely—approval of a new rapid assay test for Valley fever, developed with assistance from the University of Arizona, should reduce delays in diagnosing the respiratory fungal infections—a frequent problem in treating the disease, which is caused by spores endemic to soils in the U.S. Southwest.

The number of new Valley fever infections reported to the Arizona Department of Health Services has been relatively stable since 2013, but that may be starting to change, said John Galgiani, MD, director of the UA Valley Fever Center for Excellence and head of the Banner – University Medicine Valley Fever Program. For example, in November, more than 900 cases were reported, a 50-percent increase compared to October and the highest monthly total in the past two years. Although Arizona’s total number of cases for 2017 are only slightly more than in 2016, the accelerating monthly case numbers suggest the state may see a sharp increase in cases next year, he said.

“What seems clear is considerably more Valley fever infections are being reported right now,” Dr. Galgiani said. “Arizona clinicians need to be even more alert than usual if their patients develop pneumonia. On average, Valley fever causes one of every three cases of pneumonia in Phoenix, Tucson and surrounding areas. With infections increasing as they are now, pneumonia is even more likely to be due to our local fungal infection.”

Patients who develop persistent symptoms of pneumonia, such as fever, cough, chest pain, or shortness of breath, especially if associated with unusual skin rashes, joint pain or extreme fatigue, should ask their doctor whether they should be tested for Valley fever.

In 2011, more than 16,000 Valley fever infections of Arizonan residents were reported—a record for the state. In fall 2010, signs of that increase already were present, Dr. Galgiani said.

“We don’t know if 2018 will be like what we saw in 2011,” he added. “What we are seeing this fall, however, is very similar to how that epidemic [DM1] started seven years ago.”

Earlier this month, the U.S. Food and Drug Administration gave regulatory clearance for a molecular assay test for rapid detection of coccidioidomycosis (Valley fever, or cocci) using DxNA LLC’s GeneSTAT.MDx Coccidioides test and GeneSTAT System. That test (which reduces the time for results from as long as 21 days to the same day and without need for a Biosafety Level 3 lab to do culture testing) was developed using data licensed from the Translational Genomics Research Institute (TGen) and Northern Arizona University. Among sites that assessed the test were Banner Health and Laboratory Sciences at Banner – University Medical Center Phoenix and the UA BIO5 Institute, under Anne Wertheimer, PhD, associate director, Infectious Disease Research Core, and director, Diagnostic Laboratory Sciences, UA Applied Sciences Graduate Interdisciplinary Program.

“My lab in the UA BIO5 Institute was one of the three external validation and reproducibility testing sites and my team collected prospective, as well as a handful of retrospective, specimens,” Dr. Wertheimer said. “The assay was very robust for use by both entry-level as well as highly skilled technicians and eliminates exposure of lab personnel to a highly infectious culture.”

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BIDMC Researchers Use Artificial Intelligence to Identify Bacteria Quickly and Accurately

Microscopes enhanced with artificial intelligence (AI) could help clinical microbiologists diagnose potentially deadly blood infections and improve patients’ odds of survival, according to microbiologists at Beth Israel Deaconess Medical Center (BIDMC). In a paper published in the Journal of Clinical Microbiology, the scientists demonstrated that an automated AI-enhanced microscope system is “highly adept” at identifying images of bacteria quickly and accurately. The automated system could help alleviate the current lack of highly trained microbiologists, expected to worsen as 20 percent of technologists reach retirement age in the next five years.

“This marks the first demonstration of machine learning in the diagnostic area,” said senior author James Kirby, MD, Director of the Clinical Microbiology Laboratory at BIDMC and Associate Professor of Pathology at Harvard Medical School. “With further development, we believe this technology could form the basis of a future diagnostic platform that augments the capabilities of clinical laboratories, ultimately speeding the delivery of patient care.”

Kirby’s team used an automated microscope designed to collect high-resolution image data from microscopic slides. In this case, blood samples taken from patients with suspected bloodstream infections were incubated to increase bacterial numbers. Then, slides were prepared by placing a drop of blood on a glass slide and stained with dye to make the bacterial cell structures more visible.

Next, they trained a convolutional neural network (CNN) – a class of artificial intelligence modeled on the mammalian visual cortex and used to analyze visual data – to categorize bacteria based on their shape and distribution. These characteristics were selected to represent bacteria that most often cause bloodstream infections; the rod-shaped bacteria including E. coli; the round clusters of Staphylococcus species; and the pairs or chains of Streptococcus species.

“Like a child, the system needed training,” said Kirby. “Learning to recognize bacteria required a lot of practice, making mistakes and learning from those errors.”

To train it, the scientists fed their unschooled neural network more than 25,000 images from blood samples prepared during routine clinical workups. By cropping these images – in which the bacteria had already been identified by human clinical microbiologists – the researchers generated more than 100,000 training images. The machine intelligence learned how to sort the images into the three categories of bacteria (rod-shaped, round clusters, and round chains or pairs), ultimately achieving nearly 95 percent accuracy.

Next, the team challenged the algorithm to sort new images from 189 slides without human intervention. Overall, the algorithm achieved more than 93 percent accuracy in all three categories. With further development and training, Kirby and colleagues suggest the AI-enhanced platform could be used as fully automated classification system in the future.

In the meantime, Kirby suggests automated classification can ameliorate the shortage of human technologists by helping them work more efficiently, “conceivably reducing technologist read time from minutes to seconds,” he said.

While human technologists routinely provide highly accurate diagnoses, demand for these highly skilled workers exceeds supply in the United States. Nine percent of lab technologists remain unfilled, and that number is expected to dramatically increase as technologists of the Baby Boomer generation begin to retire in droves, according to a 2014 survey from the American Society for Clinical Pathology.

What’s more, these images can be sent remotely, bringing the highest level expertise anywhere the internet reaches. That’s critical, as rapid identification and delivery of antibiotic medications is the key to treating bloodstream infections, which can kill up to 40 percent of patients who develop them. Each day a patient goes untreated is linked with an increased risk of mortality.

In addition to its clinical uses, the new tool could also have applications in microbiology training and research, Kirby noted.

“The tool becomes a living data repository as we use it,” he said. “And could be used to train new staff and ensure competency. It can provide unprecedented level of detail as a research tool.”

In addition to Kirby, study authors include co-lead authors, postdoctoral fellow, Kenneth P. Smith, Ph.D., and, medical microbiology fellow, Anthony D. Kang, Ph.D., both members of the Department of Pathology at BIDMC.

This work was supported by the Harvard Clinical and Translational Science Center (National Center for Research Recourses and the National Center for Advancing Translational Science, National Institutes of Health Award UL1 TR001102) and by financial contributions from Harvard University and its affiliated academic healthcare centers. Anthony Kang was supported by the United States Army’s Long Term Health Education and Training program as an American Society for Microbiology Committee on Postgraduate Educational Programs Fellow at BIDMC. Kenneth Smith was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (F32 AI124590).

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