That, at its simplest, is the approach Mohamed Seleem’s lab at the Center for One Health Research has found may be a key treatment strategy in the battle against Candida auris, a frighteningly deadly fungal pathogen discovered in 2009 that is considered an urgent threat by the Centers for Disease Control and Prevention (CDC).
Candida auris, first discovered in Japan as an ear infection, has a staggering 60 percent mortality rate among those it infects, primarily people with compromised health in hospitals and nursing homes.
Recently, Seleem and Ph.D. students Yehia Elgammal and Ehab A. Salama published a paper in the American Society for Microbiology’s Antimicrobial Agents and Chemotherapy journal detailing the potential use of atazanavir, an HIV protease inhibitor drug, as a new avenue to improving the effectiveness of existing antifungals for those with a Candida auris infection.
A perfect storm of antimicrobial resistance, global warming and the COVID-19 pandemic has resulted in the rapid spread of Candida auris around the world, said Seleem, director of the center, a collaboration between the Virginia-Maryland College of Veterinary Medicine and the Edward Via College of Osteopathic Medicine.
We don’t have lots of drugs to use to treat fungal pathogens. We have only three classes of antifungal drugs. With a fungal pathogen, it’s often resistant to one class, but then we have two other options. What’s scary about Candida auris is it shows resistance to all three classes of the antifungal.
The CDC has a list of urgent threats, but on that list there is just one fungal pathogen, which is Candida auris. Because it’s urgent, we need to deal with it.”
Mohamed Seleem, the Tyler J. and Frances F. Young Chair in Bacteriology at Virginia Tech
Widespread use of fungicides in agriculture, in addition to the three classes of antifungal drugs used widely in medicine, has contributed to fungal pathogens developing more resistance, particularly Candida auris.
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Also, its rise has been linked to rising global temperatures and to easier spread through hospitals filled with COVID-19 patients in recent years during the global pandemic.
Atazanavir, an HIV protease inhibitor drug, has been found by Seleem’s lab to block the ability of Candida auris to excrete antifungals through its efflux pumps.
Think of a boat taking on water and hoses siphoning that water out of the boat to keep it afloat. Atazanavir stops up the hoses.
That allows the azole class of antifungal drugs to not be expelled as easily and perform better against Candida auris, the Seleem lab’s research has found.
The research on atazanavir builds on work three years ago by Seleem’s lab, then at Purdue University, finding potentially similar benefit in lopinavir, another HIV protease inhibitor.
HIV protease drugs are already in wide use among HIV patients, who can also be extra susceptible to Candida auris. Some HIV patients have likely been taking HIV protease drugs and azole-class antifungals in tandem for separate purposes, providing a potential source of already existing data that can be reviewed on whether those patients had Candida auris and what effects the emerging pathogen had on them.
Repurposing drugs already on the market for new uses can allow those treatments to reach widespread clinical use much more rapidly than would happen with the discovery of an entirely new drug, as existing drugs have already been tested and approved by the Food and Drug Administration and have years of further observation of effects in prescriptive use.
In 2022, the Center for One Health Research received a $1.9 million grant from the National Institutes of Health for the Seleem lab’s research on repurposing already approved drugs for treating gonorrhea.
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A new tool which could help reduce the spread of antimicrobial resistance is showing early promise, through exploiting a bacterial immune system as a gene editing tool.
Antimicrobial resistance is a major global threat, with nearly five million deaths annually resulting from antibiotics failing to treat infection, according to the World Health Organisation.
Bacteria often develop resistance when resistant genes are transported between hosts. One way that this occurs is via plasmids – circular strands of DNA, which can spread easily between bacteria, and swiftly replicate. This can occur in our bodies, and in environmental settings, such as waterways.
The Exeter team harnessed the CRISPR-Cas gene editing system, which can target specific sequences of DNA, and cuts through them when they are encountered. The researchers engineered a plasmid which can specifically target the resistance gene for Gentamicin – a commonly used antibiotic.
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In laboratory experiments, the new research, published in Microbiology, found that the plasmid protected its host cell from developing resistance. Furthermore, researchers found that the plasmid effectively targeted antimicrobial-resistant genes in hosts to which it transferred, reversing their resistance.
Antimicrobial resistance threatens to outstrip covid in terms of the number of global deaths. We urgently need new ways to stop resistance spreading between hosts. Our technology is showing early promise to eliminate resistance in a wide range of different bacteria. Our next step is to conduct experiments in more complex microbial communities. We hope one day it could be a way to reduce the spread of antimicrobial resistance in environments such as sewage treatment plants, which we know are breeding grounds for resistance.”
David Walker-Sünderhauf, Lead Author, University of Exeter
The research is supported by GW4, the Medical Research Council, the Lister Institute, and JPI-AMR.
Walker-Sünderhauf, D., et al. (2023) Removal of AMR plasmids using a mobile, broad host-range, CRISPR-Cas9 delivery tool. Microbiology.doi.org/10.1099/mic.0.001334.
Thought LeadersDr. Sandor KasasResearch LeadEcole Polytechnique Fédérale de Lausanne
News Medical speaks with Dr. Sandor Kasas, a lead researcher at Ecole Polytechnique Fédérale de Lausanne in Switzerland. Here we discuss his recent development of a novel and highly efficient method for rapid antibiotic susceptibility testing using optical microscopy.
The new technique, known as Optical Nanomotion Detection (ONMD), is an extremely rapid, label-free, and single-cell sensitive method to test for antibiotic sensitivity. ONMD requires only a traditional optical microscope equipped with a camera or mobile phone. The simplicity and efficiency of the technique could prove to be a game changer in the field of antibiotic resistance.
Please can you introduce yourself, tell us about your career background, and what inspired your career in biology and medicine?
I graduated in medicine but never practiced in hospitals or medical centers. After my studies, I started working as an assistant in histology at the University of Fribourg in Switzerland. My first research projects included image processing, scanning tunneling, and atomic force microscopy.
Later, and for most of the rest of my scientific carrier, I focused primarily on the biological applications of AFM. For the past ten years, my research interest is about nanomotion, i.e., the study of oscillations at a nanometric scale of living organisms.
Image Credit: dominikazara/Shutterstock.com
You started working on biological applications of the atomic force microscope (AFM) in 1992. From your perspective, how has the antibiotic resistance landscape changed over the last two decades? What role has the advancement in technology played in furthering our understanding?
In the early ’90s, the AFM was mainly used for imaging. Later, AFM microscopists noticed that the instrument could also be used to explore the mechanical properties of living organisms. More recently, many “exotic” applications of the AFM have emerged, such as its use to weigh single cells or study their oscillations at the nanometric scale. In the 1990s, antibiotic resistance was not as serious a problem as today, but several teams were already using AFM to assess the effects of antibiotics on bacterial morphology.
The first investigations were limited to structural changes, but later, as the fields of application of AFM expanded, the instrument made it possible to monitor the mechanical properties of the bacterial cell wall upon exposure to antibiotics. In the 2010s, with G. Longo and G. Dietler, we demonstrated that AFM could also track nanoscale oscillations of living organisms. The very first application we had in mind was using the instrument to perform rapid antibiotic susceptibility testing.
We have therefore developed devices based on dedicated AFM technology to perform fast AST (i.e., in 2-4h). AFM-based nanomotion detection instruments are already implemented in medical centers in Switzerland, Spain, and Austria. However, this type of device has some drawbacks, including the need to fix the organism of interest on a cantilever. To overcome this limitation, we have developed with R. Willaert a nanomotion detector based on an optical microscope.
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Your most recent research has led to the development of a novel and highly efficient technique for rapid antibiotic susceptibility testing using optical microscopy. Please could you tell us why the development of rapid, affordable, and efficient testing methods is so important in the world of antimicrobial resistance?
Rapid antibiotic susceptibility testing could reduce the use of broad-spectrum antibiotics. Traditional ASTs based on replication rate require 24 hours (but up to 1 month in the case of tuberculosis) to identify the most effective antibiotic. Doctors prescribe broad-spectrum antibiotics between the patient’s admission to a medical center and the results of the AST.
These drugs quickly improve patients’ conditions but, unfortunately, promote resistance. A rapid AST that could identify the most suitable antibiotic within 2-4 hours would eliminate broad-spectrum antibiotics and increase treatment efficiency and reduce the development of resistant bacterial strains. Since bacterial resistance is a global problem, rapid ASTs should also be implemented in developing countries. Therefore, affordable and simple-to-use tests are needed.
Image Credit: Fahroni/Shutterstock.com
Were there any limitations and obstacles you faced in the research process? If so, how did you overcome them?
Antibiotic sensitivity detection with ONMD is very similar to the AFM-based technique. As long as the bacterium is alive, it oscillates; if the antibiotic is effective, it kills the micro-organism, and its oscillations stop. The first limitation we faced when developing the ONMD was our microscopes’ depth of field of view. To prevent the bacteria from leaving the focal plane of the optical microscope during the measurement, we had to constrain the microbes into microfluidic channels a few micrometers high.
Microfabrication of such devices is relatively straightforward in an academic environment, but we were looking for simpler solutions. One option for constructing such a device is to use 10-micron double-sided rubber tape. It allows you to “build” a microfluidic chamber in 5 minutes with two glass coverslips and a puncher.
Another challenge was nanoscale motion detection. For this purpose, we used freely available cross-correlation algorithms that achieve sub-pixel resolution. (i.e., a few nanometers). We first developed the ONMD for larger organisms, such as yeast cells, and expanded the method to bacteria. This further development took us around two years.
You worked alongside Dr. Ronnie Willaert, a professor of structural biology at Vrije Universiteit Brussel, on developing this new rapid AST technique. How did your areas of expertise and research backgrounds complement each other in developing ONMD?
R. Willaert is an expert in yeast microbiology and microfluidics, while our team in Lausanne is primarily involved in AFM-based nanomotion detection and applying AFM to clinically relevant problems. The two teams were supported by a joint grant from the Swiss National Science Foundation and the Research Foundation Flanders (FWO) which enabled the development of the method.
The field of antimicrobial resistance requires a high level of international collaboration, with everyone working together to achieve a common goal. With antimicrobial resistance rising to dangerously high levels in all parts of the world, how important is collaboration in this field?
Our project required expertise in various fields, such as microbiology, microscopy, microfluidics, programming, and data processing. In the development of rapid AST instruments and many others, only a multidisciplinary approach and close collaboration between teams with complementary expertise is today the only path to success.
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You and Dr. Willaert have said, ‘The simplicity and efficiency of the method make it a game-changer in the field of AST.’ Can you please expand on what makes ONMD a game changer in the AST field and what implications this research could have in clinical and research settings?
As mentioned earlier, bacterial resistance is a global health problem. Rapid AST should also be easily implemented in developing countries to limit the spread of resistant strains. The cheaper and simpler the technique, the more likely it is to be used on a large scale. We are convinced that the ONMD approach can meet these requirements. ONMD could also be used for drug discovery or basic research.
While we recognize the importance of rapid AST, what next steps must be taken before this technique can be used globally in research and clinical landscapes?
For fundamental research, there are no other important developments to be made. Any reasonably equipped research center can implement the technique and use it. Regarding implementing the technique in developing countries or extreme environments, stand-alone devices have to be used, which have yet to be manufactured.
There is a rapidly expanding need for efficient AST globally; however, the need for affordable, accessible, and simple techniques are of grave importance in developing countries disproportionately affected by antibiotic resistance due to existing global health disparities. Could this rapid AST technique be utilized in low-middle-income countries to slow the growing spread of multi-resistant bacteria? What would this mean for global health?
We are confident that ONMD-based AST testing can soon be implemented in research centers in both developed and developing countries. However, accreditation by the health authorities is necessary to use it as a standard diagnostic tool; this process can take several years, depending on the government health policy.
What’s next for you and your research? Are you involved in any exciting upcoming projects?
We want to develop a self-contained device for extreme environments. It would consist of a small microscope equipped with a camera and a data processing unit. The microfluidic part of the device could contain different antibiotics ready to be tested.
The ONMD technique could also monitor contamination levels in enclosed environments such as submarines, spacecraft, and space stations. One of our recent projects is funded by the European Space Agency (ESA) to develop a rapid antifungal susceptibility test that could work in microgravity. Additionally, ONMD could be used for even more exciting projects, such as chemistry-independent life detection in the search for extraterrestrial life.
Where can readers find more information?
Villalba MI, Rossetti E, Bonvallat A, Yvanoff C, Radonicic V, Willaert RG*, Kasas S.*.Simple optical nanomotion method for single-bacterium viability and antibiotic response testing. PNAS 2023, May 2;120(18):e2221284120. doi: 10.1073/pnas.2221284120. Epub 2023 Apr 24. PMID: 37094120. * Contributed equally. https://doi.org/10.1073/pnas.2221284120
Radonicic, V.; Yvanoff, C.; Villalba, M.I.; Devreese, B.; Kasas, S.; Willaert, R.G. Single-Cell Optical Nanomotion of Candida albicans in Microwells for Rapid Antifungal Susceptibility Testing. Fermentation 2023, 9:365. https://doi.org/10.3390/fermentation9040365
Parmar P, Villalba MI, Horii Huber AS, Kalauzi A, Bartolić D, Radotić K, Willaert RG, MacFabe DF and Kasas S. Mitochondrial nanomotion measured by optical microscopy. Front. Microbiol. 2023, 14:1133773. https://doi.org/10.3389/fmicb.2023.1133773
Starodubtseva MN, Irina A. Chelnokova IA, Shkliarava NM, Villalba MI, Tapalski DV, Kasas S, Willaert RG. Modulation of the nanoscale motion rate of Candida albicans by X-rays. Front. Microbiol. 2023, 14:1133027. https://doi.org/10.3389/fmicb.2023.1133027
Radonicic V, Yvanoff C, Villalba MI, Kasas S, Willaert RG. The Dynamics of Single-Cell Nanomotion Behaviour of Saccharomyces cerevisiae in a Microfluidic Chip for Rapid Antifungal Susceptibility Testing. Fermentation. 2022; 8(5):195. https://doi.org/10.3390/fermentation8050195
About Dr. Sandor Kasas
Nanomotion is a fascinating and novel approach to observing living organisms.
Our team focuses almost exclusively on recording the nanomotion of bacterial mitochondria and mammalian cells with optical and AFM-based devices.
Recently, we demonstrated that the technique could be used not only for fast antimicrobial sensitivity testing but also to explore the metabolism of unicellular organisms. We hope our efforts will permit us to expand the application domains of ONMD.
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“The end of modern medicine as we know it.” That’s how the then-director general of the World Health Organization characterized the creeping problem of antimicrobial resistance in 2012. Antimicrobial resistance is the tendency of bacteria, fungus and other disease-causing microbes to evolve strategies to evade the medications humans have discovered and developed to fight them. The evolution of these so-called “super bugs” is an inevitable natural phenomenon, accelerated by misuse of existing drugs and intensified by the lack of new ones in the development pipeline.
Without antibiotics to manage common bacterial infections, small injuries and minor infections become potentially fatal encounters. In 2019, more than 2.8 million antimicrobial-resistant infections occurred in the United States, and more than 35,000 people died as a result, according to the Centers for Disease Control and Prevention (CDC). In the same year, about 1.25 million people died globally. A report from the United Nations issued earlier this year warned that number could rise to ten million global deaths annually if nothing is done to combat antimicrobial resistance.
For nearly 25 years, James Kirby, MD, director of the Clinical Microbiology Laboratory at Beth Israel Deaconess Medical Center (BIDMC), has worked to advance the fight against infectious diseases by finding and developing new, potent antimicrobials, and by better understanding how disease-causing bacteria make us sick. In a recent paper published in PLOS Biology, Kirby and colleagues investigated a naturally occurring antimicrobial agent discovered more than 80 years ago.
Using leading-edge technology, Kirby’s team demonstrated that chemical variants of the antibiotic, called streptothricins, showed potency against several contemporary drug-resistant strains of bacteria. The researchers also revealed the unique mechanism by which streptothricin fights off bacterial infections. What’s more, they showed the antibiotic had a therapeutic effect in an animal model at non-toxic concentrations. Taken together, the findings suggest streptothricin deserves further pre-clinical exploration as a potential therapy for the treatment of multi-drug resistant bacteria.
We asked Dr. Kirby to tell us more about this long-ignored antibiotic and how it could help humans stave off the problems of antimicrobial resistance a little longer.
Q: Why is it important to look for new antimicrobials? Can’t we preserve the drugs we have through more judicious use of antibiotics?
Stewardship is extremely important, but once you’re infected with one of these drug-resistant organisms, you need the tools to address it.
Much of modern medicine is predicated on making patients temporarily — and sometimes for long periods of time — immunosuppressed. When these patients get colonized with these multidrug-resistant organisms, it’s very problematic. We need better antibiotics and more choices to address multidrug resistance.
We have to realize that this is a worldwide problem, and organisms know no borders. So, a management approach for using these therapies may work well in Boston but may not in other areas of the world where the resources aren’t available to do appropriate stewardship.
Q: Your team investigated an antimicrobial discovered more than 80 years ago. Why was so little still known about it?
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The first antibiotic, penicillin, was discovered in 1928 and mass produced for the market by the early 1940s. While a game-changing drug, it worked on only one of the two major classes of bacteria that infect people, what we call gram-positive bacteria. The gram-positive bacteria include staphylococcal infections and streptococcal infections which cause strep throat, skin infections and toxic shock. There still was not an antibiotic for the other half of bacteria that can cause human infections, known as gram-negative organisms.
In 1942, scientists discovered this antibiotic that they isolated from a soil bacterium called streptothricin, possibly addressing gram-negative organisms. A pharmaceutical company immediately licensed the rights to it, but the development program was dropped soon after when some patients developed renal or kidney toxicity. Part of the reason for not pursuing further research was that several additional antibiotics were identified soon thereafter which were also active against gram-negatives. So, streptothricin got shelved.
Q: What prompted you to look at streptothricin specifically now?
It was partly serendipity. My research laboratory is interested in finding new, or old and forgotten, solutions to treat highly drug-resistant gram-negative pathogens like E. coli or Klebsiella or Acinetobacter that we commonly see in hospitalized, immunocompromised patients. The problem is that they’re increasingly resistant to many if not all of the antibiotics that we have available.
Part of our research is to understand how these superbugs cause disease. To do that, we need a way to manipulate the genomes of these organisms. Commonly, the way that’s done is to create a change in the organism linked with the ability to resist a particular antibiotic that’s known as a selection agent. But for these super resistant gram-negative pathogens, there was really nothing we could use. These bugs were already resistant to everything.
We started searching around for drugs that we could use, and it turns out these super resistant bugs were highly susceptible to streptothricin, so we were able to use it as a selection agent to do these experiments.
As I read the literature on streptothricin and its history, I had the realization that it was not sufficiently explored. Here was this antibiotic with outstanding activity against gram-negative bacteria – and we confirmed that by testing it against a lot of different pathogens that we see in hospitals. That raised the question of whether we could get really good antibiotic activity at concentrations that are not going to cause damage to the animal or person in treatment.
Q: But it did cause kidney toxicity in people in 1942. What would be different now?
What scientists were isolating in 1942 was not as pure as what we are working with today. In fact, what was then called streptothricin is actually a mixture of several streptothricin variants. The natural mixture of different types of streptothricins is now referred to as nourseothricin.
In animal models, we tested whether we could kill the harmful microorganism without harming the host using a highly purified single streptothricin variant. We used a very famous strain of Klebsiella pneumoniae called the Nevada strain which was the first pan-drug-resistant, gram-negative organism isolated in the United States, an organism for which there was no treatment. A single dose cleared this organism from an infected animal model while avoiding any toxicity. It was really remarkable. We’re still in the very early stages of development, but I think we’ve validated that this is a compound that’s worth investing in further studies to find even better variants that eventually will meet the properties of a human therapeutic.
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Q. How does nourseothricin work to kill gram-negative bacteria?
That’s another really important part of our study. The mechanism hadn’t been figured out before and we showed that nourseothricin acts in a completely new way compared to any other type of antibiotic.
It works by inhibiting the ability of the organism to produce proteins in a very sneaky way. When a cell makes proteins, they make them off a blueprint or message that tells the cell what amino acids to link together to build the protein. Our studies help explain how this antibiotic confuses the machinery so that the message is read incorrectly, and it starts to put together gibberish. Essentially the cell gets poisoned because it’s producing all this junk.
In the absence of new classes of antibiotics, we’ve been good at taking existing drugs like penicillin for example and modifying them; we’ve been making variations on the same theme. The problem with that is that the resistance mechanisms against penicillin and other drugs already exist. There’s a huge environmental reservoir of resistance out there. Those existing mechanisms of resistance might not work perfectly well against your new variant of penicillin, but they will evolve very quickly to be able to conquer it.
So, there’s recognition that what we really want is new classes of antibiotics that act in a novel way. That’s why streptothricin’s action uncovered by our studies is so exciting. It works in a very unique way not seen with any other antibiotic, and that is very powerful because it means there’s not this huge environmental reservoir of potential resistance.
Q. You emphasize these are early steps in development. What are the next steps?
My lab is working very closely with colleagues at Northeastern University who figured out a way to synthesize streptothricin from scratch in a way that will allow us to cast many different variants. Then we can look for ones that have the ideal properties of high potency and reduced toxicity.
We are also continuing our collaboration with scientists at Case Western Reserve University Medical Center, diving more deeply to understand exactly how this antibiotic works. Then we can use that fundamental knowledge in our designs of future variants and be smarter about how we try to make the best antibiotic.
We have great collaborators that have allowed us to pursue a project that crosses multiple fields. This work is an example of collaborative science really at its best.
Co-authors included first author Christopher E. Morgan and Edward W. Yuof Case Western Reserve; Yoon-Suk Kang,Alex B. Green, Kenneth P. Smith, Lucius Chiaraviglio, Katherine A. Truelson, Katelyn E. Zulauf, Shade Rodriguez, and Anthony D. Kang of BIDMC; Matthew G. Dowgiallo,Brandon C. Miller, and Roman Manetsch of Northeastern University.
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SHENZHEN, China, 10 May 2023 – MGI Tech Co. Ltd. (MGI), a company committed to building core tools and technology to lead life science, today shared that a total of nearly 60,000 samples have been sequenced among 21 institutes and over 10 participating nations throughout Europe, as part of the Million Microbiome of Humans Project (MMHP) that was officially launched in 2019.
Image Credit: MGI
The project was launched as a joint effort by the Karolinska Institute of Sweden, Shanghai National Clinical Research Center for Metabolic Diseases in China, the University of Copenhagen in Denmark, Technical University of Denmark, MetaGenoPolis at the National Research Institute for Agriculture, Food and Environment (INRAE) in France, and the Latvian Biomedical Research and Study Center. Relying on MGI’s core DNBSEQ™ technology, MMHP aims to sequence and analyze microbial DNA from a million human samples to construct a microbiome map of the human body and build the world’s largest human microbiome database.
The rise of microbial metagenomic sequencing
Since the first description of human microbiome was published in 2010, the field of human microbiome has moved fast from sampling hundreds of individuals to thousands. Advances in genome sequencing has enabled researchers to better characterize the composition of the microbiome through identification of unculturable microbes. It has also allowed them the opportunity to study how the microbiome influences the development of some cancers and drug responses.
Metagenomics, coupled with high-throughput sequencing technologies, have revolutionized microbial ecology. Today, metagenomic sequencing has become both a powerful and popular tool for identifying and classifying complex microbial communities. It facilitates accelerated discovery of new markers that translate to virulence or antibiotic resistance, as well as de novo discovery and characterization of novel species and assembly of new genomes. Besides human microbiome, it is highly applicable in agricultural microbiome studies, environmental microbiome studies, pathogen surveillance and identification, and monitoring of antimicrobial resistance genes.
Indeed, the global metagenomic sequencing market was estimated to be worth USD 1.86 billion in revenue in 2022 and is poised to reach USD 4.33 billion by 2027, growing at a CAGR of 18.4% during the forecast period. In particular, Europe and Africa account for approximately 29.7% market share from the globe, ranking second after North America at 45.6%. Thanks to continuous technological innovations in high-throughput sequencing platforms, the metagenomic sequencing market within Europe and Africa is projected to grow from USD 551.7 million in 2022 to 1.29 billion by 2027, presenting huge market opportunities and providing local institutions with the impetus to invest and get involved.
Image Credit: MGI
An optimized workflow with MGI’s cutting-edge technology
Equipped with MGI’s innovative lab systems, the MMHP Consortium guarantees high-throughput processes, extreme precision, and high quality data output. The dedicated, one-stop workflow begins with sample transfer on MGISTP-7000* high-throughput automated sample transfer processing system. It then goes through nucleic acid extraction and library preparation on MGISP-960 high-throughput automated sample preparation system, a flexible and fully automated workstation capable of processing 96 samples per run. MGISP-960’s fully automatic operation design allows DNA extraction of 50,000 samples per year and library preparation of 25,000 samples per year. MGISP-Smart 8, the professional automated pipetting robot, equipped with an independent 8 pipetting channel can be used for the pooling, normalization and DNB making. Lastly, DNBSEQ-T7* ultra-high throughput sequencer and DNBSEQ-G400* versatile benchtop sequencer enables an efficient, productive, and streamlined sequencing experience.
“We are very focused on data quality, cost and time. After contrasting DNBSEQ™ technology by MGI with other sequencing technologies, we are convinced that MGI’s products have met high industry standards and provide a very good user experience,” commented Professor Lars Engstrand, Research Director of Center for Microbial Translational Research (CMTR) at Karolinska Institutet. “MGI’s platforms have enabled our team to upgrade our original microbiological research from 16SrRNA gene amplicon sequencing to shotgun metagenomic sequencing. I look forward to introducing more equipment and super-large projects as human microbiome emerges as a crucial diagnostic and treatment method in precision medicine.”
The next chapter in microbiomics
“Microbiomics will be part of precision medicine in the future, and data from the microbiome biobank that will result from MMHP will be leveraged for therapeutic R&D,” said Professor Stanislav Dusko Ehrlich of University College London, UK. “With 21 public and private institutions and 10+ countries currently involved in MMHP, we are actively looking for more research groups to take part in this landmark international microbiological research partnership and help generate the world’s biggest free-access human microbiome database.”
Since the inception of MMHP, MGI has played an important role in providing the program with state-of-the-art research platforms and technologies. Now entering its second phase towards sequencing and analyzing a final total of one million samples, the project welcomes further exchange and participation from relevant organizations to jointly promote research and applications of cutting-edge translational medicine in the field of microbiome. Those interested can fill the application form on www.mgi-tech.eu/mmhp.
About MGI
MGI Tech Co. Ltd. (MGI), headquartered in Shenzhen, is committed to building core tools and technology to lead life science through intelligent innovation. Based on its proprietary technology, MGI focuses on research & development, production and sales of sequencing instruments, reagents, and related products to support life science research, agriculture, precision medicine and healthcare. MGI is a leading producer of clinical high-throughput gene sequencers*, and its multi-omics platforms include genetic sequencing*, medical imaging, and laboratory automation. MGI’s mission is to develop and promote advanced life science tools for future healthcare. For more information, please visit the MGI website or connect with us on Twitter, LinkedIn or YouTube.
*Unless otherwise informed, StandardMPS and CoolMPS sequencing reagents, and sequencers for use with such reagents are not available in Germany, Spain, UK, Sweden, Italy, Czech Republic, Switzerland and Hong Kong (CoolMPS is available in Hong Kong).
*For Research Use Only. Not for use in diagnostic procedures (except as specifically noted).
One of the scariest things you can be told when at a doctor’s office is “You have an antimicrobial-resistant infection.” That means the bacteria or fungus making you sick can’t be easily killed with common antibiotics or antifungals, making treatment more challenging. You might have to take a combination of drugs for weeks to overcome the infection, which could result in more severe side effects.
The yeast Candida auris has recently emerged as a potentially dangerous fungal infection for hospital patients and nursing home residents. First discovered in the late 2000s, Candida auris has very quickly become a major health challenge due to its ease of spread and ability to resist common antifungal drugs.
How did this fungus become so strong, and what can researchers and physicians do to combat it?
I am a microbiologist researching new ways to kill fungi. Candida auris and other fungi use three common cellular tricks to overcome treatments. Luckily, exciting new research hints at ways we can still fight this fungus.
Fungal cells contain a structure called a cell wall that helps maintain their shape and protects them from the environment. Fungal cell walls are constructed in part from several different types of polysaccharides, which are long strings of sugar molecules linked together.
Two polysaccharides found in almost all fungal cell walls are chitin and beta-glucan. The fungal cell wall is an attractive target for drugs because human cells do not have a cell wall, so drugs that block chitin and beta-glucan production will have fewer side effects.
Some of the most common drugs used to treat fungal infections are called echinocandins. These drugs stop fungal cells from making beta-glucan, which significantly weakens their cell wall. This means the fungal cell can’t maintain its shape well. While the fungus is struggling to grow or is breaking apart, your immune system has a much better chance of fighting off the infection.
Unfortunately, some strains of Candida auris are resistant to echinocandin treatment. But how does the fungus actually do it? For decades, scientists have been studying how fungi overcome drugs designed to weaken or kill them. In the case of echinocandins, Candida auris commonly uses three tricks to beat these treatments: hide, build and change.
The first trick is to hide in a complex mixture of sugars, proteins, DNA and cells called a biofilm. Made with irregular 3D structures, biofilms have lots of places for cells to hide. Drugs aren’t good at penetrating biofilms, so they can’t access and kill cells deep inside. Biofilms are especially problematic when they grow onmedical equipment like ventilators or catheters. Once free of a biofilm, cells that have gained the ability to resist the drugs a patient was taking become more dangerous.
The second trick fungi use to evade treatment is to build cell walls differently. Fungal cells treated with echinocandins can’t make beta-glucan. So instead, they start to make more chitin, another important polysaccharide in the fungal cell wall. Echinocandins are unable to stop chitin production, so the fungus is still able to build a strong cell wall and avoid being killed. While there are some drugs that can stop chitin production, none are currently approved for use in people.
The third trick fungi rely on is to change the shape of thebeta-glucan production enzyme so echinocandins cannot block it. These mutations allow beta-glucan production to continue even in the presence of the drug. It is not surprising that Candida uses this trick to resist antifungal drugs since it is very effective at keeping the cells alive.
What can be done to treat echinocandin-resistant fungal infections? Thankfully, scientists and physicians are researching new ways to kill Candida auris and similar fungi.
The first approach is to find new drugs. For example, there are two drugs in development, rezafungin and ibrexafungerp, that appear to be able to stop beta-glucan production even in fungi resistant to echinocandins.
A complementary approach my research group is exploring is whether a class of enzymes called glycoside hydrolases might also be able to combat drug-resistant fungi. Some of these enzymes actively destroy the fungal cell wall, breaking apart both beta-glucan and chitin at the same time, which could potentially help prevent fungi from surviving on medical equipment or on hospital surfaces.
My lab’s work on discovering enzymes that strongly degrade fungal cell walls is part of a new strategy to combat antifungal resistance that uses a combination of approaches to kill fungi. But the end goal of this research is the same: having a physician tell you, “You’ve got a fungal infection, but we have a good treatment for it now.”
Lecturers of the Faculty of Allied Health Sciences, Chulalongkorn University have developed MTB Strip Test Kit for Tuberculosis (TB) diagnosis that’s accurate and easy to use, guaranteed by the 2023 Invention Award from the National Research Council of Thailand (NRCT) -; Another hope to reduce the spread of tuberculosis in Thailand.
Tuberculosis is one of the most contagious diseases that continues to challenge the public health system today. Although the World Health Organization (WHO) aims for 2035 (the next 12 years) to be the year to end the global tuberculosis crisis, the disease trend is still worrisome.
Thailand is one of the 14 countries with the most severe TB incidence. Fortunately, drug-resistant tuberculosis in Thailand has been removed from the WHO’s list of highest-incidence countries. Only ordinary tuberculosis cases remain.”
Dr. Panan Ratthawongjirakul, Associate Professor, Department of Transfusion Medicine, Faculty of Allied Health Sciences, Chulalongkorn University
Tuberculosis is an airborne disease caused by a bacterium called “Mycobacterium tuberculosis“. It is spread from TB patients to others through small respiratory secretions (AKA droplets) that come from coughing, sneezing, or talking. It is easy to contract and it spreads quickly.
“One of the mechanisms to help end tuberculosis is identifying TB patients as early as possible to control and limit its transmission” said Assoc. Prof. Dr. Panan about the inception of the research project to develop MTB Strip (Mycobacterium tuberculosis Strip) that is easy to use, convenient to read by the naked eye, and with fast and accurate results. More importantly, the cost should not be high to make it accessible to local public health service systems.
“If we can distribute this test to small hospitals everywhere, we will be able to identify TB patients within two hours and screen positive patients quickly into the treatment system. We believe this will help reduce the number of TB cases in our country” said Assoc. Prof. Dr. Panan about the objective of MTB Strip innovation.
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Pros and Cons of the current methods of TB Testing
Assoc. Prof. Dr. Panan mentioned the various advantages and disadvantages of current testing methods for tuberculosis as follows:
Microscopic examination using acid-fast staining is a simple method. It can be done in a small hospital, but the disadvantage is low sensitivity (the minimum bacterial concentration required for a positive signal when examining with a microscopic examination is 5000–10000 cells in 1 ml of sputum.
Sputum culture is the standard method of diagnosing tuberculosis, but it can only be done in well-equipped large hospitals. This method must be done in a room with a high-safety system to prevent it from spreading outside. It takes more than a month to know the results which will result in delayed treatment.
TB Genotyping involves taking the patient’s sputum to extract and amplify the genetic materials which are then tested by a Real-time PCR machine. The disadvantage of this method is that it is costly and requires a lab with specialized personnel, so it can be done only in some hospitals.
Based on the advantages and limitations of various methods used to detect tuberculosis, the research team developed the MTB Strip Test Kit.
Faster and easier TB Screening with MTB Strip
MTB Strip TB Test Kit consists of 2 main parts: 1. Genetic amplification using isothermal amplification with specifically modified and designed primers. 2. Genetic materials detection using developed test strips, which are manufactured from ISO13485-certified industrial plants for medical device manufacturing.
Assoc. Prof. Dr. Panan explained the process of using this test kit “after receiving sputum from the patient, the DNA will be extracted and used as a template. We will put a primer specially designed to amplify the amount of genetic material in the DNA of the pathogen in the patient’s sputum before entering the isothermal amplification process by using a recombinase polymerase amplification technique. It takes only 20 – 40 minutes at 37 degrees Celsius. Then, the developed test strip is dipped into the amplified genetic material. The results will appear on the test strip as positive and negative results like the ATK test that we are familiar with.”
The key feature of the MTB Strip is its sensitivity to tuberculosis. With a small amount of tuberculosis in the sputum, the test can detect it and display the result. In addition, the test process takes less than an hour and does not require any special tools.
“The results are up to 96 percent accurate compared to Realtime PCR and other commonly used acid-resistant dye methods. Importantly, this kit is cheaper than molecular biology tests because it does not require any special tools such as thermocycler” Assoc. Prof. Dr. Panan emphasized.
The MTB Strip kit uses the principle of amplifying genetic material under a single constant temperature in conjunction with a heat box. In a typical laboratory, this type of box is already available. Small hospitals can also use this technique.
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“The MTB Strip TB test kit we have developed will enable many existing small and medium-sized hospitals in Thailand to screen for TB cases so that patients can receive appropriate treatment quickly, thereby reducing the number of TB cases and the spread of TB.”
Fighting tuberculosis with the Distribution of MTB strips to the provinces
The MTB Strip Test prototypes have already been administered at Umphang Hospital, Tak Province in 2019-2020 and the results are good to a certain extent. However, Assoc. Prof. Dr. Panan has not stopped developing methods and innovations to reduce the number of cases of tuberculosis in Thailand.
“Although the MTB Strip kit works satisfactorily, we would still like to develop more sensitivity by making the DNA extraction easier to be used as the kit primer.”
In addition, Assoc. Prof. Dr. Panan also has plans to expand the testing of TB and related diseases by developing an easier-to-use DNA extraction kit and TB test kit that can identify drug-resistant variants of TB right from the outset, so that more specific treatment guidelines can be set.
“We are currently conducting in-depth research on the genetic modification of tuberculosis using a novel technique of genetic modification for a living organism called CRISPR Cas-9 Interference to modify certain TB genes, making the infection less aggressive and more responsive to antituberculosis drugs. CRISPR Cas-9 Interference can be used in conjunction with current antituberculosis drugs.”
If the study is successful, it will be a new TB treatment of the future, which Assoc. Prof. Dr. Panan is sure will help reduce the number of TB cases to reach WHO’s target. Small hospitals interested in the MTBStrip Test kits can contact Assoc. Prof. Dr. Panan Rathwongjirakul, the Research Unit of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University.
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In a recent article published in the Lancet journal, researchers quantified the global bacterial antimicrobial resistance (AMR) burden to present deaths and disability-adjusted life-years (DALYs) attributable to and associated with 23 pathogens, 12 major infectious syndromes, 18 drug categories, and 88 pathogen–drug combinations.
They considered two counterfactual scenarios and used consistent methods to arrive at the study estimates as they had no clue of the extent to which susceptible or no infection would replace drug-resistant infections in a scenario when there was no drug resistance.
Bacterial AMR, an emerging public health threat, is making antibiotic use futile or less effective against many common bacterial diseases affecting animals and humans. A United Kingdom (UK) government-commissioned review of AMR stated that it could claim 10 million lives annually by 2050.
The World Health Organization (WHO) and numerous other researchers have also raised that AMR spread is a pressing issue that needs immediate attention; if left unaddressed, rising AMR will make several bacterial pathogens highly fatal in the near future. The challenge is to gather current data on pathogen–drug combinations contributing to actual bacterial AMR burden for all world regions, even those with minimal surveillance.
According to the authors, studies have only reported AMR-related data for specific regions and a limited number of pathogens and pathogen–drug combinations. For instance, the United States Centers for Disease Control and Prevention (US-CDC) published a report in 2019 on AMR-related deaths for 18 AMR-related threats using surveillance data.
Similarly, Cassini et al. estimated the burden of eight and 16 pathogens and pathogen–drug combinations, respectively, for the European region between 2007 and 2015. Despite the significant contributions made by these studies to the field of AMR, there is a lack of comprehensive global estimates covering all locations, all pathogens, and all pathogen–drug combinations contributing to the rising burden of bacterial AMR.
Key Takeaways
First comprehensive assessment of the global burden of antimicrobial resistance (AMR) for bacterial infections.
Estimated 4.95 million deaths associated with bacterial AMR in 2019, including 1.27 million deaths attributable to bacterial AMR.
Lower respiratory infections accounted for the most deaths associated with resistance in 2019.
Six leading pathogens for deaths associated with resistance.
One pathogen-drug combination, meticillin-resistant S aureus, caused more than 100,000 deaths attributable to AMR in 2019.
Burden of AMR is highest in low-resource settings, particularly in western sub-Saharan Africa.
Serious data gaps in many low-income settings
About the study
In the present study, researchers used predictive statistical modeling to generate global estimates of bacterial AMR burden for all world locations, covering 204 countries for which they used all available data from the Global Burden of Diseases (GBD), Injuries, and Risk Factors study. The GBD study collated age- and gender-specific estimates for 369 injuries and illnesses in 204 nations and territories between 1990 and 2019.
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They retrieved data from published scientific literature, multisite research collaborations, clinical trials, research institutes based in low-income and middle-income countries (LMICs), public and private hospital records, diagnostic testing data, surveillance systems of pharmaceutical companies, global, national, and enhanced surveillance systems, and other relevant sources, encompassing 471 million (MN) patient records or isolates and 7,585 study-location years, which they gathered using varied strategies and used for study estimations.
The researchers modeled deaths and DALYs for 204 countries and territories to present cumulative estimates of AMR burden globally and for 21 GBD regions, including seven GBD super-regions.
For the first counterfactual scenario, where susceptible infections substituted all drug-resistant infections, they estimated only deaths and DALYs directly due to AMR. For the second counterfactual scenario, where no infection substituted all drug-resistant infections, they estimated all deaths and DALYs related to resistant infections. Both estimates had different utilities; however, both could inform the development of intermediation strategies to regulate AMR spread.
The study approach comprised ten estimation steps within five all-encompassing modeling components, each with varied data requirements; consequently, input data for each modeling component also varied.
Study findings
Substituting drug-resistant infections by no infections (first counterfactual scenario) and susceptible infections (second counterfactual scenario) would have saved 4.95MN and 1.27MN deaths, respectively, in 2019, implying that in 2019, the global AMR burden related to drug-resistant infections for 88 pathogen–drug combinations was ~4.95MN deaths (95% UI), of which drug resistance alone caused 1.27MN deaths. Moreover, after ischaemic heart disease and stroke, AMR accounted for most deaths in 2019.
Additionally, the study analysis revealed that AMR-related all-age death rates were highest in some LMICs, as opposed to the common notion that the burden of bacterial AMR would be higher in high-resource settings with higher antibiotic consumption. Indeed, AMR is emerging as a more serious problem for some of the world’s poorest countries. The authors noted the highest AMR-related death rates in sub-Saharan Africa and South Asia as a function of the prevalence of resistance and critical lower respiratory, bloodstream, and intra-abdominal infections, in these regions.
The study also highlighted that in LMICs, there are other drivers of the higher AMR burden, like a scarcity of laboratory infrastructure for microbiological testing needed to narrow antibiotic use or make it more targeted. Among other factors, counterfeit antibiotics, poor sanitation and hygiene, poor regulations on antibiotics use, etc., also drive resistance.
Further, the researchers identified six pathogens, E. coli, K. pneumoniae, S. pneumoniae, A. baumannii, S. aureus, and P. aeruginosa, who contributed most to the burden of AMR in 2019; they accounted for 73.4% (95% uncertainty interval) of deaths attributable to bacterial AMR. WHO has recognized all six as priority pathogens; however, except S. pneumoniae, targeted primarily through pneumococcal vaccination, none is the focus of global health intervention programs.
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Seven pathogen–drug combinations caused more than 50000 deaths, highlighting the need for expanding infection prevention and control (IPC) policies targeting the deadliest combinations, bolstering vaccine and antibiotic development, and improving access to essential second-line antibiotics where needed. Furthermore, resistance to β-lactam antibiotics, e.g., penicillins and cephalosporins, and fluoroquinolones accounted for >70% of deaths attributable to AMR across pathogens. These antibiotics are the first line of empirical treatment for severe infections.
In 2017, the WHO published a priority list to inform research priorities related to new antibiotics for pathogens with multidrug resistance that caused deadly infections. However, this list covered only five of the seven pathogen–drug combinations estimated to have caused the most deaths in 2019; for instance, this list did not feature fluoroquinolone-resistant E. coli and meticillin-resistant S. aureus only as a “high” but not a “critical” priority.
Per study estimates, the magnitude of bacterial AMR as a global public health issue is as much as human immunodeficiency virus (HIV) and malaria, perhaps, much higher. Additionally, the AMR pattern varied with geographical location, pathogens, and pathogen–drug combinations. Thus, the regional estimates made in this study could help tailor local responses as the ‘One Size Fits All’ approach might not be appropriate.
Despite concerted data collection efforts, high-quality data on AMR was sparsely available for many LMICs. Nevertheless, an improved scientific understanding of this rapidly emerging health threat should be the highest priority for global health policymakers.
Conclusions
The present study used major methodological innovations, two varying AMR counterfactual scenarios, and comprehensive data to fetch novel insights into the global AMR burden. Most importantly, it incorporated models tested and iterated over years during GBD study analysis. So, when used collectively, these models provided a complete estimate of AMR burden with robust geographical coverage.
Further, the researchers compared findings with other causes of death, offering much-needed context on the scale of the burden of this rapidly growing public health problem. The study analysis confirmed that bacterial AMR posed the biggest threat to human health in sub-Saharan Africa and South Asia, involved a diverse set of pathogens, and is exceptionally high for multiple essential antibiotic classes, including β-lactams and fluoroquinolones.
Furthermore, efforts to build and enhance laboratory infrastructure and bolster national & global AMR plans of action are essential to addressing the universal AMR burden. Future studies should also evaluate the indirect effects of AMR, such as its effect on the prophylaxis of infections in organ transplant recipients.
In the future, the study estimates could inform treatment guidelines against many predominant bacterial pathogens for a given infectious syndrome, which, along with estimates of pathogen–drug burden, could inform their treatment guidelines customized for a specific location.
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Metagenomic sequencing can provide rapid and actionable antimicrobial resistance predictions to treat bloodstream infections much faster than conventional laboratory tests, and has the potential to save lives and better manage the use of antibiotics, according to new research being presented at this year’s European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) in Copenhagen, Denmark (15-18 April).
The study led by Dr Kumeren Govender from the John Radcliffe Hospital, University of Oxford, UK, indicates that rapid metagenomics can provide accurate results within just 6 hours of knowing bacteria are growing in a blood sample.
Antibiotic-resistant bloodstream infections are a leading killer in hospitals, and rapidly starting the right antibiotic saves lives. Our results suggests that metagenomics is a powerful tool for the rapid and accurate diagnosis of pathogenic organisms and antimicrobial resistance, allowing for effective treatment 18 to 42 hours earlier than would be possible using standard culture techniques.”
Dr Kumeren Govender, John Radcliffe Hospital, University of Oxford, UK
Bloodstream infections can rapidly lead to sepsis, multiple organ failure, and even death. Early and appropriate antibiotic therapy is vital for control of the infection.
Antimicrobial resistance (AMR) is a major challenge when treating bloodstream
Infections, causing around 370,000 deaths and associated with nearly 1.5 million deaths in 2019 [1].
The current method used in clinical settings to identify the pathogen causing the infection is long and laborious, requiring two time-consuming culture and sensitivity tests that take at least 1 to 3 days to complete-;first isolating and identifying the pathogen and then performing antimicrobial susceptibility testing (to expose the bacteria to various antibiotics to see exactly which it will respond to, plus the best route and dose).
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In contrast, clinical metagenomics sequences all the genetic material including infectious pathogens in a sample all at once, so time spent running tests, waiting for results, and running more tests could be reduced.
To find out more, researchers randomly selected 210 positive and 61 negative blood culture specimens for metagenomic sequencing from the Oxford University Hospital’s microbiology laboratory between December 2020 and October 2022.
DNA was sequenced using the Oxford Nanopore GridION platform. Sequences were used to identify the species of pathogen causing infections and also to spot common species that can contaminate blood cultures.
Sequencing was able to identify 99% of infecting pathogens including polymicrobial infections and contaminants, as well as giving negative results in 100% of culture negative samples. In some instances, sequencing detected probable causes of infection missed by routine cultures, and in other instances identified uncultivable species where a result could not be determined.
Sequencing could also be used to detect antibiotic resistance in the ten most common causes of infections. A total of 741 resistant and 4047 sensitive combinations of antibiotics and pathogens were studied. Results of traditional culture-based testing and sequencing agreed 92% of the time. Similar performance could be obtained from raw reads after only two hours of sequencing, overall agreement was 90%.
The average time from sample extraction to sequencing was 4 hours with complete AMR prediction 2 hours later, producing actionable AMR results 18-42 hours before to the conventional laboratory.
David Eyre, Professor of Infectious Diseases at the University of Oxford, who co-led the study, commented, “This is a really exciting breakthrough that means we will be able to diagnose the cause of patients’ infections faster and more completely than has been possible before. We are working hard to continue to overcome some of the remaining barriers to metagenomic sequencing being used more widely, which include its current high cost, further improving accuracy, and creating improved laboratory expertise in these new technologies and simpler workflows for interpreting results.”
The human intestine is an environment inhabited by many bacteria and other microorganisms collectively known as the gut microbiome, gut microbiota or intestinal flora. In most people, it contributes to wellness. A healthy gut indicates a stronger immune system, improved metabolism, and a healthy brain and heart, among other functions.
Escherichia coli is one of the bacteria found in practically everyone’s gut microbiota, where it performs important functions, such as producing certain vitamins.
But there’s a vast amount of genetic diversity in the species. Some of its members are pathogenic and can cause diseases such as urinary tract infections. E. coli is the main agent of this type of infection among both healthy people and hospitalized patients or users of healthcare services.”
Tânia Gomes do Amaral, Head of the Experimental Enterobacterial Pathogenicity Laboratory (LEPE), Federal University of São Paulo’s Medical School (EPM-UNIFESP), Brazil
Amaral is first author of an article published in the journal Pathogens on the virulence of these bacteria and their resistance to antibiotics in hospitalized patients.
“Our study focused on hospitalized patients because patients who stay in hospital for a long period are more likely to undergo various procedures, such as urine catheter insertion or venous access. Although these procedures are performed to assure life support, they may facilitate the entry of bacteria into the organism and cause an infection,” Amaral explained.
She earned a PhD in microbiology from EPM-UNIFESP in 1988, conducting part of her research at New York University Medical School and the Center for Vaccine Development at the University of Maryland, Baltimore (UMB) in the United States.
The article reports the findings of a broader study led by Amaral, with 12 co-authors who are researchers and graduate students, on the virulence and drug resistance of E. coli strains associated with urinary tract infections. The study was supported by FAPESP via three projects (18/17353-7, 19/21685-8 and 17/14821-7).
The main aim of this part of the study, described in the master’s dissertation of José Francisco Santos Neto, was to evaluate the diversity and drug resistance of pathogenic E. coli strains isolated from the gut microbiota of inpatients, and to analyze the frequency of endogenous infection (caused by bacteria from the patient’s own microbiota).
The UNIFESP group first investigated the genetic diversity and drug resistance of E. coli strains isolated from the gut microbiota of hospitalized patients, sequencing these strains as well as others isolated from their urine and comparing the results in order to evaluate dissemination of the bacteria in the hospital environment.
“We also compared the genomes of these strains with those of E. coli strains isolated in different parts of the world in order to see if any globally disseminated pathogenic bacteria were present in the study sample,” said Ana Carolina de Mello Santos, a postdoctoral researcher working on the LEPE team.
Urinary tract infections proved to be endogenous for the vast majority of the patients in the study (more than 70%). The results also showed that the patients’ gut microbiota contained at least two genetically different populations of E. coli and that about 30% were colonized by non-lactose-fermenting E. coli strains, which are less common, with some of the patients studied having only such strains in their gut microbiota.
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“This finding is most interesting because previous research conducted in other countries to analyze the composition of human gut microbiota didn’t investigate non-lactose-fermenting E. coli,” Santos said.
The authors also note the presence of bacteria with all the genetic markers required for classification as pathogenic and the detection of pathogenic bacteria in the gut microbiota of all patients that had not yet developed an infection. “Hospitalized patients are more susceptible to infection because by definition they are already unwell. Colonization by pathogens is the first step in the spread of hospital-acquired infections now so frequent worldwide,” Santos said.
With regard to antibiotics and other antimicrobials, the authors stress that drug resistance is also a growing global problem, and enterobacterial resistance to third-generation cephalosporins as well as colistin is critical. In all patients whose gut microbiota was colonized by drug-resistant bacteria, the same bacteria also caused endogenous urinary tract infections. In other words, the multidrug-resistant bacteria colonized the gut and traveled to the urinary tract, where they caused an infection.
“In light of these findings, early assessment of gut microbiota in hospitalized patients, at least in cases of E. coli infection, can facilitate and guide their treatment, while also identifying patients who risk progressing to extra-intestinal diseases such as urinary tract infections, which were part of the focus for our study,” Amaral said. “We don’t yet know whether the findings also apply to other bacteria found in gut microbiota, such as the genera Klebsiella, Enterobacter, Pseudomonas and others that can cause infections when they travel to extra-intestinal sites.”
These bacterial genera tend to be even more drug-resistant than E. coli, representing a major public health problem in the hospital environment. As the researchers noted, the World Health Organization (WHO) considers E. coli strains resistant to cephalosporin and colistin to be a critical global health threat. “The presence in human gut microbiota of drug-resistant bacteria associated with severe infectious disease is a matter of great concern, not least because they could spread to people outside the hospital environment,” Amaral said.
Another point raised by the study is the importance of finding out when colonization of the patient’s gut by drug-resistant virulent bacteria occurred. The authors of the article were unable to determine whether the bacteria resistant to cephalosporins and colistin colonized the patients before or after they were hospitalized.
By analyzing the genomes of the strains, however, the researchers were able to identify global risk clones that can cause severe disease and are associated with antimicrobial resistance. “One such clone found in the gut microbiota of two patients was identical to others isolated from urinary tract infections in Londrina, Paraná [a state in South Brazil], and in the United States, as well as European and Asian countries. This shows that some strains found in the study are clones generally associated with infections in all regions of the world,” Amaral said.
This type of information is important when patients are hospitalized. Knowledge of bacterial virulence and drug resistance can be used to prevent infection in parts of the organism outside the intestine and stop the bacteria from spreading to other patients in the same hospital.
Santos-Neto, J.F., et al. (2023) Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens.doi.org/10.3390/pathogens11121528.
Microbiome: From Research and Innovation to Market
