Tag: #diagnostics

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The Quest for Direct-from-Blood Pathogen Detection Technologies

The medical community continues to strive for advancements in diagnostic technologies, particularly those that can detect pathogens directly from blood samples. A recent session at ASM Microbe 2024 in Atlanta chaired by Linoj Samuel delved into the complexities and challenges that have hindered the integration of these technologies into clinical practice. Direct-from-blood pathogen detection technologies are designed to bypass traditional culture methods, which can be time-consuming and sometimes ineffective in identifying fastidious or non-culturable pathogens. By utilizing such tools, healthcare providers can obtain actionable information swiftly, allowing for the narrowing of therapy and de-escalation of antibiotics. This rapid turnaround is crucial in managing sepsis, where every hour counts in the race against mortality and morbidity.

The session highlighted a blend of technical and non-technical challenges, from the intricacies of sample preparation, pathogen detection to the broader implications for clinical decision-making. Dr. Valeria Fabre’s insightful presentation underscored the potential of these technologies to revolutionize patient care, offering a clinician’s perspective on their impact on treatment strategies.

Economically, the implementation of these technologies presents both challenges and opportunities. While initial costs may be higher due to equipment and workforce training, the potential for reducing the length of hospital stays, decreasing the use of broad-spectrum antibiotics, and preventing the spread of resistant pathogens lead to significant savings.

Key takeaways from the discussion emphasized the need for a deeper understanding of the goals behind direct-from-blood pathogen detection. What are the specific outcomes we aim to achieve? How can these technologies influence clinical decisions, patient outcomes, and the economic aspects of healthcare? The current absence of this information hinders assessment of the value such diagnostics bring and thus their adoption. While much of the current efforts are focused on nucleic acid technologies, the development of imaging and spectroscopy-based technologies adds to the diversity of diagnostic approaches, potentially offering complementary benefits to nucleic acid-based methods. These technologies may provide additional layers of information, that may not be available through nucleic acid testing, such as greater confidence in detecting the presence/absence of bacteremia and antimicrobial susceptibility information.

Overall, there is a palpable sense of optimism about the future. The next generation of pathogen detection technologies promises to address current technical limitations more effectively. However, the adoption of these technologies hinges on a much better understanding, and more importantly demonstration, of their value. Failure to take this into account during development and design of validation studies may inhibit their use in clinical settings, which would be a shame.

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Blood Culture Turnaround Times: a pathway for reduction by at least 24 hours

Isolating bacteria directly from blood or positive blood culture present a unique set of problems for clinical microbiologists and researchers. We are happy that multiple recent studies using our Separation Cartridge have performed very well in both applications. This post relates to the positive blood culture application.

One ongoing study at a local hospital has observed that traditional ID results could be obtained within a day (whereas without using the cartridge results have taken 2-5 days) and that the ID results obtained using the cartridge matches that obtained by subculturing. 

The shorter time-to-result using the cartridge was because it eliminated the need for subculturing decreasing the time to ID & AST by at least 24 hours. While it is generally accepted that that direct testing of positive blood culture broths is feasible, results have been variable (for instance better success with Gram-negative rods (GNR) than Gram-positive cocci (GPC)), workflow sub-optimal, or the method too expensive.

Preliminary experiences indicate that the cartridge does not have these limitations. The process takes ≤ 5 minutes, requires no new instrumentation, and uses one buffer that can be easily sourced. Results have been consistent regardless of whether it is GNR / GPC. More studies are taking place at other hospitals and microbiology labs that we will keep you updated on.

If this is an area of interest to you or your organization, please contact us (www.3idx.com). We are interested in setting up demos and additional studies to assess performance in different settings and applications. Thank you.

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Re-visiting the importance of Diagnostics in 2022

The Seventy-fifth World Health Assembly is being held in Geneva, Switzerland, from May 22-28, 2022. It is the first in-person Health Assembly since the start of the COVID-19 pandemic. On the occasion of the start of this assembly, many health-related organizations have released statements on healthcare priorities, inequities, and focus for the future.

Some of these observations relating to diagnostics caught our attention. We list four of them below and see them as further motivation for the work that we are doing at 3i Diagnostics.

  • The capacity to perform basic tests is available in just 1% of primary care clinics in low- and middle-income countries.
  • No diagnostic tests exist for 60% of the pathogens identified by the World Health Organization (WHO) as having the greatest outbreak potential. There are also no appropriate tests for half of the top 20 diseases responsible for the most lives lost.
  • Using COVID tests as an example, high-income countries use COVID tests at 10–100 times the rate of middle- and low-income countries. So, if tests are not inexpensive, testing is likely to be deficient.
  • Early diagnosis has been consistently linked to improved health outcomes and reduced out-of-pocket spending. However, diagnosis is the weakest link in healthcare systems globally.

One of the key learnings from COVID-19 is that investing in diagnostics will be central to rapid response to outbreaks and delivering appropriate care for infections. Deficiencies in testing affect not only people’s lives, but communities and economies, as COVID-19 clearly showed.

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COVID-19 and opportunistic infections: The importance of Diagnostics

There has been a notion among many in the medical community that a significant proportion of the morbidity and mortality associated with COVID-19 are due to secondary bacterial infections. This notion is, in part, attributed to studies from the 2009 H1N1 epidemic (Morris et al. ) , and early reports detailing increased presence of other respiratory pathogens in COVID-19 patients (Gerberding , Zhou et al. , Zhu et al. ). Accordingly treatment of COVID-19 patients have frequently included antibiotics.

As Andrew Jacobs reported in his New York Times article, physicians heavily prescribed antibiotics for treating these patients because of this concern. It now appears that this possibility is not as pervasive or as severe as initially thought (Rawson et al.). 

While the fear of opportunistic infections have not come to pass, the overuse of antimicrobials in treating COVID-19 patients has highlighted concerns about catalyzing a slower-moving crisis namely antimicrobial resistance (AMR). Overuse of antibiotics is one of the factors that induces the development of resistance and its spread, which is precisely what we have done over these past few months. 

What is interesting is that in both situations, COVID-19 and AMR, the immediate challenge has been our inability to identify those patients who need urgent medical attention. The challenges in testing subjects to determine if they are COVID-positive or not are well documented. Less well recognized is the situation in tackling AMR. 

In the case of AMR, while much attention has been devoted to developing new drugs, as they should, the fact is that the fundamental problem is that we do not know which drug to administer to treat the patient efficiently and rapidly. That is, it is at heart a diagnostic problem. As the US Government Accountability Office succinctly explain in their assessment of US efforts to combat AMR “Without information to guide test usage, clinicians may not be able to select appropriate treatments for their patients.”

If you think that waiting for 48-72h to know if you were COVID-positive was unacceptable, why should it be for detecting bacterial infections, which could be just as, if not more, deadly (e.g. Sepsis)? [Today, it takes 1-5 days before the physician can learn if the patient has a bacterial infection or not]  As Dr. Strich of the NIH clinical center is quoted as saying, “being prepared is more cost effective in the long run” and saves lives. “Antimicrobial resistance is a problem we cannot afford to ignore.”

And yet, there is not the same sense of urgency in developing diagnostics that can rapidly determine if a patient has a bacterial or vial infection let alone what the infection-causing pathogen is. Efforts to develop better diagnostics are not sufficiently supported by either the private or the public sectors. 

We should all be asking ourselves why we are not pushing, with a greater sense of urgency, for better diagnostics that will be effective in combating AMR or the next pandemic instead of just hoping that the same approaches that have been tried for 20+ years with limited success will somehow suddenly provide the solution? 

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COVID-19 once again highlights the importance of diagnostics

These are challenging times, and we, at 3iDx, hope that you, your loved ones, friends, and colleagues are well.

The COVID-19 pandemic has impacted the world in ways not seen in modern times. One of these is to bring back the importance of diagnostics and, importantly, the ability to perform tests in a multitude of settings.

It is abundantly clear that controlling the outbreak through social distancing severely impairs a functioning society. Any strategy to “reopen” a country is highly reliant on better testing, which is central to reducing transmission and morbidity and mortality. This not only involves being able to obtain an actionable result but also encompasses producing tests at a scale commensurate with the outbreak and addressing massive challenges in the supply chain.

While DNA-based diagnostic testing offers several reasons to include in our armament of tools. Waiting multiple hours or even days before getting a result for a COVID-19 test does not strike one as an effective strategy especially when battling reagent and buffer shortages.

While high-income countries are facing challenges in meeting the diagnostic needs of their rural and semi-urban populations, these challenges are magnified in low- and middle-income countries. These countries currently have the lowest rates of testing reported to the WHO.

It feels strange to be listing these problems and areas for improvement in yet another global crisis. We had earlier observed how our response to the antimicrobial resistance crisis is being held back because of inadequate diagnostics. The needs in both crises are eerily similar. We need rapid and inexpensive diagnostics that can be scaled easily and used outside a specialized laboratory setting. The options we currently have are not it.

The current COVID-19 crisis will draw down and we will emerge stronger. But if we are to emerge wiser from this experience, we need to invest more (resources, attention, capital) in diagnostic development.

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Infrared-based bacterial identification – a clinically viable alternative to PCR-based bacterial diagnostics

New Year’s greetings and best wishes for 2020 to all!

We had ended last year, coincidentally, pondering why wide spread application of PCR-based tests in bacterial diagnostics has been elusive and identified a couple of key features that limit their use. It seems appropriate to start the new year with a discussion on one technology that can address those limitations – Infrared-based identification (IR).

What, you might be wondering, – that dilapidated instrument I vaguely recall using in undergraduate chemistry lab? Well, not quite that instrument but yes, one that utilizes the same fundamental principles.

The concept of using IR for identifying bacteria is not new. The earliest reference that we have been able to find dates back to 1950s! But, instrumental and computational limitations held back the potential for using this technology for identifying bacteria until the early 1980s. Naumann and colleagues took advantage of computational advances to demonstrate the ability of this technology to identify bacteria rapidly. Since then the use of IR for rapid and reliable identification of microbes to the strain level have been well documented. Reference databases to facilitate rapid identification of microorganisms are already available with some containing as many as 7000 strains.

How does the technology work?
IR, as you may recall, is a widely used vibrational spectroscopy technique that is used to identify compounds, even those present in mixtures. It is routinely used in raw material testing in the pharmaceutical and other industries as well as in testing of milk and milk products. All of the components that make up a bacterium (proteins, lipids, sugars, etc.) contribute to an IR “fingerprint” (see figure below). The nature and concentration of these components differ from one strain to another resulting in unique IR-fingerprints. This bacterial fingerprint has been used to differentiate between multiple bacterial species and strains including differentiating between antibiotic-resistant and -susceptible strains.

Bacterial fingerprint obtained by Infrared spectroscopy. Each species and strain has a different composition and hence a unique fingerprint.

How does it compare to PCR-based identification?
Two key limitations of PCR-based tests that we had discussed previously were clinical sensitivity of the test and cost per test. If a PCR-test yielded a negative result, the clinician would not have any actionable information. On the other hand, with IR-based identification, the profile of a bacteria is very distinctive and its absence clearly indicates the absence of bacteria in the sample. In such a case, the clinician can actively consider whether administering antibiotics will be of any benefit to the patient. In the case of a positive result, the actions are similar to that with a PCR-based test with several important benefits. These are:

  • the result is available in ≤ 10 minutes
  • No custom labels or reagents are needed lowering the cost per test
  • It does not require specialized laboratory for operation
  • The bacteria is intact and viable after the analysis
  • Antibiotic resistance can be determined
  • The number of species and strains that are identified can be easily expanded without requiring new primers or antibiodies. This is done as a software update that consists of the fingerprint of the new bacteria and adjustments to the recognition algorithm, if needed.

You might be wondering at this stage why, if IR has all these benefits, there has not been any IR-based commercial instrument for use in bacterial ID? There are commercial instruments from Bruker, Thermo, and others that are used for bacterial ID in food safety testing. However the methodology used today requires bacteria to be cultured prior to identification (i.e. the same as most PCR-based tests). In addition, the bacteria has to be separated from the matrix components in order to make an accurate ID. Owing to these reasons, the technology has not yet seen widespread adoption for clinical use.

It is this aspect that we have impacted with the development of our separation cartridge. As mentioned previously, our separation cartridge can isolate and concentrate intact bacteria directly from blood with minimal manual intervention. The isolated bacteria can be identified using any technique. Using it upstream of IR however, permits rapid and sensitive identification of bacteria directly from patient sample without using any bacteria-specific labels or reagents. This combination of our separation cartridge and IR-based identification will, we believe, permit rapid, inexpensive, and hypothesis-free detection and identification. We aim to demonstrate this in 2020.

As we have said before, it’s not that IR (or any other ID technique) has to wholly replace PCR-based tests. The problem is large enough that multiple solutions will be needed. But, given the history of limited gains in developing effective PCR-based bacterial ID tests, the more diagnostic options we have, the better we can aid physicians in making the best decisions for treatment while slowing the spread of antimicrobial resistant bacteria. IR-based identification presents a compelling case to be a key diagnostic option.