Dr. Jesús Mingorance discusses his innovative use of digital PCR to detect HIV-2 and monitor antibiotic-resistant bacteria. From academic research to clinical microbiology, his career reflects both the beauty and complexity of biological science.
HIV, superbugs, and standards—oh my! In this episode of Absolute Gene-ius, we explore the frontier of infectious disease research with Dr. Jesús Mingorance, researcher at Hospital Universitario La Paz in Madrid. His research is translational and uses digital PCR, qPCR, sequencing, and more.
Dr. Mingorance walks us through his application of ultra-sensitive PCR methods to track HIV-2 viral loads—particularly in challenging cases where standard assays fall short. He shares how digital PCR enabled detection in samples where conventional tests failed, and how it's becoming essential for assay calibration and microbial quantification. He also dives into the endemic challenges of carbapenem-resistant Klebsiella pneumoniae in hospitals, revealing the clinical and epidemiological importance of quantifying pathogen load within the microbiome.
In the career corner, Dr. Mingorance recounts his unconventional journey—from humanities student to biologist inspired by a single sentence about DNA. With humor and honesty, he reflects on the patience needed in science, the value of good questions, and the importance of mentoring new scientists. “Biology is beautiful,” he reminds us. We agree.
Visit the Absolute Gene-ius pageto learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.
Jordan Ruggieri 00:00
This one is, seems like an I don't know. This did not fully come from chat GTP this time, so
Christina Bouwens 00:05
this is a good one.
Jordan Ruggieri 00:06
It came from my head this time.
Christina Bouwens 00:08
This is great.
Jordan Ruggieri00:22
Welcome to Absolute Genius, a podcast series from Thermo Fisher Scientific. I'm Jordan Ruggieri, and alongside Christina Bouwens, I'm thrilled to welcome Dr Jesus Mingorance to the show today. Jesus is a scientist in the microbiology department at Hospital Universitario La Paz in Madrid, Spain. In addition to researching genomics and antibiotic-resistant bacteria, he also does a lot of work with evaluating tools, including the ones we love to talk about on our show. It was amazing to hear about his career journey and his current research. And we hope you enjoy. We began by asking Jesus to explain why tools such as ultra-sensitive PCR are so helpful for his work.
Dr. Jesus Mingorance 01:07
Well, there are similar fields where the ultra-sensitive PCR might be useful. In the field of HIV, it's mostly when you are doing some research and you want to measure the virus or the proviral load, no, not only the load of virus, but the provirus. You look for DNA, viral DNA integrated in cells, and another one is in some group that are suppressed with undetectable levels or very low levels of virus. But for some reason, you want to monitor how are these levels going on, and these loads are usually below the quantification level of the standard techniques. qPCR has a quantification level of 20 copies per ml, or in some cases, you want to monitor how it is going around this level between 20 and 10, five and so on.
Jordan Ruggieri02:25
Are there, you know, looking at the, let's say, provirus, or looking at those levels of DNA, and really, maybe smaller amounts of DNA, what are some of the implications of looking at that? Are there, you know, maybe presentations of those amounts that you're looking for, are you looking just to see the presence of that virus and detect that?
Dr. Jesus Mingorance 02:55
Well, that depends on the project. We did, for example, one project was not only to detect but to sequence that, the because we had some group of subjects that were supposed to have resistance mutations, but were not treated, but they were suppressed. So we were curious about what's happened. Why did the virus is not increase long one? So we have to isolate single clones, identify those clones and sequence them to detect whether they had mutations or not. Maybe you are measuring 20 copies per 10 to six PVM cells. But are these 20 copies functional? So in some cases, we found that most of these copies were hyper mutated, so probably nonfunctional.
Jordan Ruggieri04:06
I'm curious to dive into, maybe your recent publication, with your, with your collaborators, and home in a little bit on, you know, looking at ultra-sensitive PCR and digital PCR for that publication in particular, right for, for HIV-2. Can you talk a little bit about the aims of that publication and what you were trying to accomplish?
Dr. Jesus Mingorance 04:35
In this particular case, this was the subject was already diagnosed, so we knew that he had HIV-2, and I think he was not responding correctly to the drugs, but when my colleagues at the microbiology department did, the NASBA assay, they couldn't found find any signal. They couldn't detect the virus. So they send some samples to laboratory in France, and in France, they could detect it, and even they could sequence it. So they were curious what was happening. They thought that maybe this, this virus, was highly mutated and probably was not being detected by the NASBA assay because of this. So they asked us to test something different. At that time, we had the machine, the PCR, Absolute Q machine we were testing for further reasons. So we contactThermo and ask them for a Master Mix for RT, reverse transcription, PCR, and they send us a beta so we tried with a TaqMan assay, HIV to TaqMan assay to detect it. And it was great, because we could detect and quantify the virus. So the our colleagues say, okay, so we have some samples in the freezer. We could try, if we you can detect also with this system, because there was no other system at that time to quantify HIV-2. While we were doing this, this work, Altona commercialized PCR qPCR assay, so that we could test both in parallel the Altona qPCR, the Thermo dPCR, and in parallel with the classical NASBA assay, and those were the results. We were initially trying to identify the viral load in a single subject, but then it became an evaluation.
Christina Bouwens 07:02
I was looking through your publication, and I just wanted to get so this topic of looking through cell free nucleic acids to identify viral load. When you're using something like dPCR, or even qPCR to quantify the viral load. Is it very important to know the exact viral load, or is it more making sure that you have good limit of detection and confidence around that?
Dr. Jesus Mingorance 07:25
Yeah, usually in microbiology is not a precision is not important. You know, you want to know the order of magnitude. You want to know if you have 100, 1,000, but generally speaking, is not a precision is not important.
Christina Bouwens 07:42
Yeah, it does kind of remind me a little bit about, um, you know, to some degree, um, like, you know, on in oncology, are looking for circulating tumor DNA commonly. And that's always a question I love asking is, you know, does that quantity actually matter, or is it the change or variance? And I think your response orders of magnitude makes a lot of sense there. So in oncology, which is where I'm familiar with working a lot, we know like SNPs and rearrangements are like those critically important, important like biomarkers that we're looking for in cell free DNA. When you're looking, you know, at some of the work you're doing, especially for, you know, disease research, what types of targets or markers are most common that you're like, actually designing the assays for? Is it for like, transcript? Is it for specific bacterial sequences? What's the most common?
Dr. Jesus Mingorance 08:27
We basically look for genomes. We look for the presence or absence of pathogen. If it is RNA virus, we look for RNA we'll do our dPCR. Or if it is bacteria or fungi or DNA virus, we look for DNA.
Christina Bouwens 08:45
So do you find yourself doing a lot of custom design of primers for qPCR and dPCR. Or, you know, if something exists in the big menu is that, you know, perfectly reasonable to go ahead and test. I just wonder about, you know, the availability or complexity of designing some of the assays that you're looking at.
Dr. Jesus Mingorance 09:01
Most of the assays that we are doing are for qPCR. We had this opportunity of having the machine for, I think, almost one year. So we did several tests on cytomeval virus, on hepatitis B virus and this HIV business, and we did something on bacteria too. And in any case, it's much more easier to design qPCR assays.
Jordan Ruggieri09:35
I'm even curious, even going back even one more step for our listeners, why would you even need to monitor viral load?
Dr. Jesus Mingorance 09:43
Well, viral load is a marker of disease. All the work that we do is for clinicians. Of course, we have some research projects, and in this case, maybe there is a big role for dPCR and for other more sophisticated techniques. But most of the work of the laboratory is for clinicians. If they find it useful, then we do it. And viral load in HIV is a marker of disease progression and response to antiviral drugs.
Jordan Ruggieri10:21
Makes sense. Do you see some resistance even with viral strains? Maybe mutations that stop certain drugs from working as effectively or evade some of the drugs. Is that something that you often see?
Dr. Jesus Mingorance 10:36
Yeah, that's, this has been a constant in HIV during at least 10 or 20 years. Companies used to commercialize new drugs, to test new drugs, to put new drugs into the market. Subjects take these new drugs. And this work for a while, and the virus developed resistance. So this was the origin of a triple therapy try to to avoid the virus escaping from the drugs, and with the years and with the new drugs, I think now that the level of control is very good, there is almost no resistance.
Christina Bouwens 11:19
You develop methods for clinical research. So what types of tools and technologies do you have on the bench at your disposal when you're working through those you know, researching those new, new tests that could potentially go to clinic.
Dr. Jesus Mingorance 11:35
Well, the main tools are PCR, qPCR and sequencing, which is a massive sequencing, Sanger sequencing, some years ago, now, genomic sequencing, in particular, nanopore sequencing, which is very friendly and quick. But other technologies too, we are now trying to introduce proteomics, but that's difficult, because we have the MALDI -TOF for identification of bacteria. This is very easy. This is not research. This is already established and we are trying to go further. But usually there's one thing that you have to keep in mind when you work for clinicians is that they like the worst we do in a simple way, quickly and cleanly. It's difficult to be better than qPCR. qPCR is very well developed. Now. We have a lot of knowledge tools. It's a robust technique, so it's difficult to go further.
Jordan Ruggieri12:54
As you were looking at digital PCR, we love digital PCR here on Absolute Genius. So we love everything, but I love to talk about digital PCR. Did you find any specific advantages of using that technique, say, over some of the other tools that you have and techniques that you have.
Dr. Jesus Mingorance 13:13
Well, I have to say that I love digital PCR, okay. I'm a biologist. So when you explain the technique, when you see the principle, so, you say, Whoa, that's beautiful. So dPCR is very interesting. When you don't have a standard technique for reference or standard for calibration, then you can do a quick quantification, even if you don't have a calibrator, or you can use it to create your calibrator, and then you can translate this to the PCR to qPCR. So it's a, I mean, maybe this is the more clear advantage.
Jordan Ruggieri14:04
I can imagine, some advantages of either not having to use some type of calibration like a standard curve right or to be able to use it to make sure your standard curve is accurate before you go into maybe more, more well understood qPCR quantification techniques.
Dr. Jesus Mingorance 14:29
Yeah, no, not only you don't depend on the efficiency of the PCR
Christina Bouwens 14:33
if you could pick one thing that you think dPCR would be really great at hands down, it would be the, the best option. What application would you say fits that, though?
Dr. Jesus Mingorance 14:43
Well, in our particular case, we are the we are now part of the European Network of Reference Laboratories, which is a new network which has been created for testing commercial assays and so. And we are going to need standards. We are going to need to calibrate. Item, and dPCR would be an incredible technique for this particular application.
Christina Bouwens 15:14
Yeah, for that, like base standards, calibration, what do you think could help? Because we've talked a little bit about how, you know, qPCR is the gold standard for many, many labs, it's really well accepted, which has been a challenge and, you know, moving dPCR to that next level, what do you think could help propel dPCR to that next level being like the next gold standard of testing?
Dr. Jesus Mingorance 15:37
But for microbiology, we will need to explore the DNA extraction protocols, because there is, this is a strong limit if you if you start with a half milliliter sample, and you want to compare this with a blood culture, for example, that you are studying with 10 milliliters, you are in disadvantage. So we need these some DNA instruction systems that are able to manage larger volumes of samples so that you can put a largest amount of DNA. Because in the case of microbiology, is different from genetics. You know, maybe in genetics, you think, okay, I'm going to put 10 nanograms of DNA. And this is 10 nanograms of human DNA, which is your target. But in microbiology, if you put 10 nanograms of DNA, you don't know how much pathogen DNA is there. If you are looking for in the lower limit. So maybe you have to, you need to increase the volume without increasing the inhibitions development of better systems for extraction, DNA extraction, would be important.
Christina Bouwens 16:51
Yeah, I could see that being super impactful. And then if you have those higher volumes, since dPCR is relatively more tolerant to inhibitors, it can be a really good platform to make sure that you get the sensitivity without losing a ton of the like assay efficiency problems that you could run into.
Dr. Jesus Mingorance 17:06
And then if you could increase a little bit the dynamic range would be great. In many cases, for example, when you do the standard HIV viral load detection quantification, okay, you have subjects on treatment. They are suppressed. They have less than 20 copies per milliliter, so no problem. But when you have some performance objectives, has been just diagnosed, you may have a million copies per milliliter, 500,000 copies per milliliter, and you are over the limit for dPCR, so some increase might be interesting.
Christina Bouwens 17:54
Okay, yeah, so, so you're saying increasing the concentration detection limit actually on the upper side rather than the lower side?
Dr. Jesus Mingorance 18:00
Yes, because it saturates quickly.
Jordan Ruggieri18:02
Makes sense when you, when you are working with an unknown right like, like you had mentioned right here on the microbiology side, you get a you get a sample, you have no idea how much virus might be in it. So it makes sense why.
Dr. Jesus Mingorance 18:17
When you read the saturated sample, then you have to do dilutions to guess which amount is. And in particular, when you are working with bacteria, the amounts used to be larger, so it saturates very easily.
Jordan Ruggieri18:35
Excellent. I have another question that takes us back many, many steps, but I think would be important in the storytelling for the for the podcast episode. You know, we talk a lot about HIV-2. Can you talk a little bit about the differences of HIV-1 versus HIV-2, and any types of implications or considerations when examining these types of viruses.
Dr. Jesus Mingorance 19:04
Well, as I said before, HIV two is mostly limited to West Africa. So for some reason, is not epidemiologically, is not global. Clinically, it's somewhat slower, but the idea is the same as it. And the treatments, I think, are the same, must be the same. The response to the treatments is the same. So that the name in the main difference is epidemiological, geographical.
Christina Bouwens 19:34
In the paper, I know that there was a line that said, there's traditionally a lack of, you know, readily available commercial assays for HIV-2. Is there a specific reason for that, or?,
Dr. Jesus Mingorance 19:44
Well, because we don't have much HIV-2 in Europe or in USA, so companies have not, and probably there is not an international standard.
Jordan Ruggieri19:56
You also mentioned towards the beginning that you work a lot on antibiotic resistance bacteria. Is that anything that relates to any of the techniques we talked about here, or anything that might be similar?
Dr. Jesus Mingorance 20:14
We have doing, we have been doing some research. We have a problem in our hospital , and many other hospitals around the world now, with carbapenemases. We have a bacterium that are resistant to carbapenems, which are antibiotics that are used, usually in hospitals, as a last line, and have most of the cases are Klebsiella pneumonia, which is for some reason, has adapted very well to the hospitals and to the carbapenemases. And when you have a Klebsiella occur in a carbapenemase and enters into the hospital, it explodes and creates an outbreak, so. And there has been a lot of work in the hospital, a lot of effort in trying to contain or to eradicate these carbapenemases. And we couldn't. Has not been possible. We have, indeed, in our hospital, I would say it's endemic Klebsiella pneumonia carrying carbapenemases. So we wonder why this is this so, and we started to measure the bacterial load, the Klebsiella, carbapenemase producing Klebsiella loads in intestinal samples from a colonized subject is not sick, but is sick because it's in the hospital, but it's not the Klebsiella is silent, is part of your gut microbiome. It's silent, does not create any problem, but sometimes it may go out from the gut and create an infection or transmit and create a second which is colonized. No, we try to understand these points and start measuring by qPCR the amounts of Klebsiella, carbapenemase producing Klebsiella, in the guts, in the microbiome of the subject. So we develop some protocols. We wanted to compare the Klebsiella population with a total microbiome population. So we did a qPCR directed to carbapenemase genes, and qPCR direct to 16S rRNA genes, which is a proxy for bacterial population. We found that some of the subjects have only Klebsiella, or mostly Klebsiella, in their guts, so probably they have been receiving some antibiotics that swept away all the microbiome and only the resistance strain could survive, and most of their microbiome is Klebsiella, and that's the reason which is so difficult to stop this from transmitting to other subjects, because any small contamination, any small format, can transmit lots and lots of Klebsiella. So that's a, and we did by qPCR. This, it may be done, could be done by dPCR, maybe, but in this case, the dynamic range is important, because we are working with samples which have high loads of microorganisms.
Christina Bouwens 23:52
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Jordan Ruggieri24:12
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Christina Bouwens 24:36
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Christina Bouwens 25:03
And now back to our conversation.
Jordan Ruggieri25:08
Awesome. Jesus, we are at the career corner portion of our Absolute Genius podcast episode where we talk a little bit about your career, how you got to where you are. Can you give us a little background on your career and maybe, maybe some of the educational and kind of key milestones for you as as you went on your career journey?
Dr. Jesus Mingorance 25:31
Yeah, well, I would say that this has not been a typical career. I studied biology in Barcelona, and then I moved for a while to Japan, to Okayama University, and did a master’s degree in genetic engineering and bacterial genetics there. Then I happened to know a lady there from Madrid, Spain, not from Japan. And so I came back to Madrid, not to Barcelona. And then I did my PhD here. I entered into in a biochemistry laboratory. I had a background in bacterial genetics and genetic engineering, and they wanted to do side directed mutagenesis, some given science. So we cloned and we did a mutagenesis, and that was great, because I learned a lot about proteins and enzymes. But I miss bacteria, so I wanted to go back to microbiologists, so after the PhD I went in laboratory of Professor Miguel Vicente at CSIC here in Madrid. He had a strong background in bacterial cell division, so I carried my knowledge in bacterial genetics and enzymes into bacterial cell division for a while. It was funny, I let a lot of things and we had some projects on antibiotic resistance at that time. It was a kind of paradigm; you have to study antibiotic resistance. But I was not very happy, because I couldn't. Really I did not know the state of the problem. So how important is really antibiotic resistance? I can read some papers, but I wanted to know how important it is. So I move to Hospital La Paz. I thought I would move for a while, just for three, four years, and it's already 18 years, but I am still learning from clinicians, and I think I know something now about antibiotic resistance, and in this time, I tried to bring my knowledge on molecular biology and genetic engineering to the diagnostic field.
Jordan Ruggieri27:55
What a journey.
Dr. Jesus Mingorance 28:00
Yeah, that's been funny.
Jordan Ruggieri28:03
I want to study in Japan. That sounds amazing. You know you mentioned that your career pathway has not been traditional in normal sense here. Are there any key milestones or things that have happened that maybe have changed the trajectory of your career, and what have you learned from some of those?
Dr. Jesus Mingorance 28:32
When try to remember, sometimes I am surprised that, I remember when I decide that I wanted to do biology. And It's a strange because I had at high school when you have to decide between science and humanities, I decided to go to humanities. So I started humanities, and then I stopped there. I didn't enter the university. I went to work around and one day I was reading a book, a science communication book, this I read something about DNA, and I was impressed. I said, okay, I cannot believe that I have studied this at high school. I didn't impress me. I couldn't believe this. I want to study this. I want to go further on this. And then this is when I decided to do to study biology. And this has marked all my career. And one of the tools in my career, the most important tools have been sequencing.
Christina Bouwens 29:49
That's so funny. That's almost exactly what happened to me as well. I was in high school, and I was like, definitely want to be a graphics designer. And then I took, I took an advanced molecular biology class just for credits, and I was like, wow, I cannot believe that I didn't like this. And I have loved it ever since.
Jordan Ruggieri30:08
I think too, it shows that you can always change your mind, right? And that's okay to enjoy things that you maybe didn't before, or didn't think you would until you were exposed to them. And, I mean, I think that's my story as well. Maybe the opposite, right? I always wanted to go into science, and here I am now doing marketing, right. And so it's still science, I would say, but, but maybe a little bit of shift.
Dr. Jesus Mingorance 30:39
But the science, I think science communication is one of the pending matters that we have. There is a lot of good science communication today, but we still need more. We will have to go further and reach more people.
Jordan Ruggieri30:58
Any advice that you would give to say, anybody that's early in their career or just starting along, you know, research or a lab-based pathway?
Dr. Jesus Mingorance 31:10
Well, biology is beautiful. Life is beautiful. Biology is beautiful. Go ahead.
Jordan Ruggieri31:22
I love it. It's a great reminder actually. Another set of questions we ask everybody, what is your proudest moment in your in your career, and what is your most embarrassing moment in your in your career?
Dr. Jesus Mingorance 31:41
Well, I don't remember about embarrassing moments. You always break something and you want to hide it, but you have to assume, okay, it was me. I broke it. So I don't remember much. Also, great moment said that the eureka things usually don't, are not as eureka as many people may think. Sometimes discoveries come slowly. You know, even sometimes, when you have something which is okay, I have found this, you don't believe it the first time. No, let's say, Okay. I have to check probably I did something wrong, and I will repeat it, so the real discovery enters slowly. It's not eureka, I find it.
Jordan Ruggieri32:34
That's great. Is there anything that runs through your mind, like, let's say I don't know, an experiment or some, some research isn't going well? Is there anything you think about, or any mottos that you have that help you stay grounded.
Dr. Jesus Mingorance 32:53
Well, experiments always seem to go wrong, so you have to check everything and trust and repeat and be patient, because results at the end come. Most of the time I'm trying to to increase the the spirit of my students, because they come with the results and they say, okay, everything is wrong. Say, I know, don't worry. Just keep going. Keep going.
Jordan Ruggieri33:27
That's awesome. I say, with my experience, I have more examples of things that didn't work than things that did, so. By far, by far, yeah.
Dr. Jesus Mingorance 33:40
Sometimes you think the perfect experiment. You say, okay, that's great. That's going to work. Never works, never works at the first time or the second time. This is being patient is important.
Jordan Ruggieri33:55
Yeah, I would always ask myself too that, you know, try to ask good questions with some of those failures. Sometimes it's what I like to call user error, where I did something wrong, right, and it was nothing, nothing, but me, that, that you know my hands or I miscalculated something, right. But oftentimes, you know there's, there's something wrong or something that you didn't expect, that it's not the experiment, it's how you approach the question, right.
Dr. Jesus Mingorance 34:22
Even the question, maybe, maybe you are not doing the right question. So, and you have to think that way.
Jordan Ruggieri34:32
That was Dr Jesus Mingorance, researcher at Hospital Universitario La Paz in Madrid, Spain. This episode of Absolute Genius was produced by Sarah Briganti, Matt Ferris and Stock. With more great conversations around the corner in upcoming episodes, stay curious and we'll see you next time.