“In case of resistant lung infection, seek help from the microbiome, not from the petri dish” (Patrick Merel, Portable Genomics)
Surgeons are organ specialists; not microbiologists. Antibiotic resistant infection is something they now little about, but post-op complications killing their patients is something many of them have experienced. This summer, I got the opportunity to train ICU specialists and surgeons about a procedure called pulmonary (or lung) microbiome, with the help of a biologist, and it might have saved a patient’s life.
Wanna disrupt the insurance system? You will have to make sure you have the ancestors of AI, surgeons, on board. Even better: make it look like the whole initiative is coming from surgeons. And make sure nurses, physicians and surgeons get a proper training in that “Precision Medicine” thing. Wait, isn’t that what they call an evangelist? What do you think, Illumina?
Around the 20th of May, my husband and I got a phone call from my dad. We were sitting at the cafeteria in the European Hospital George Pompidou (an oncologist, a friend of mine, works here). In the midst of our conversation about genomic precision medicine, I learn that my “favorite” uncle (a retired surgeon, we have been arguing about “1.0 and 2.0 medicine” for over a decade) was lying in an artificial coma, vital prognosis uncertain. He was being brought to George Pompidou to undergo another surgical procedure; he’s had a hip surgery a couple of days before, but now they suspected… some kind of colon necrosis. His son, living and working in NY, was told by doctors at the ICU that he might want to take the next flight to Paris.
19 days later, my uncle awoke from his coma. But a pulmonary infection seemed to be plaguing him. A resistant lung infection can kill within a few days, especially a frail elderly person waking up from a coma due to postoperative complications — colon and part of the small intestine were removed, my 80-year-old uncle had suffered two strokes in the recent past, and as a consequence, was taking anticoagulant or blood-thinner treatment. So before his coma, he was in a clinic in Paris for that hip surgery. Then the complications happened. Any idea how full colon necrosis can occur after a hip surgery? Highly invasive cardiac surgery can cause lots of internal bleeding, and as the colon is quite fragile, it can sustain damage from some kind of massive bleeding coming from organs nearby. But a hip surgery won’t cause nearly as much bleeding as a cardio-pulmonary surgery for example. So I suspect this kind of complication might be quite unusual. Anyway, the colon was taken away, a colostomy bag is now overtaking the anus and rectum’s functions, and now we were dealing with a lung infection that was causing the vital prognosis to remain uncertain. So I turned to my network on twitter — my own twitter profile says: Bugged humchine, fan of Liu Cixin 三体. MITxBio 7.00x, 7.28.1x-2x, 7.QBWx certified. 7.28.3x student. French microbiologist and geneticist Patrick Merel (university of Bordeaux), who is trying to implement a new business model for healthcare in San Diego, via his start-up, Portable Genomics, answered. “We are developing a patient-centric tool for patients to collect, share & monetize their medical, genomics, lifestyle, IoT data with academics & pharma industry”, says his twitter profile. Merel was informing me about a recent protocol for lung infection, based on genomics, which consists in sending samples to a laboratory in France (Pasteur, Lyon, Rennes, Lille) to analyse the DNA of Bacteria to determine what they are resistant to or sensitive to. I suspected this couldn’t be done by the European Hospital Georges Pompidou because they probably do not have the lab to do it. This examination is called “the pulmonary microbiome” and can reveal which bacteria are present in the lungs, and which genes of resistance, for a better choice of antibiotic. The microbiome test is a DNA or genetics sequencing test of all the bugs that live in our stomach or in our lungs, or genital tract, skin surface, mouth, ears … etc. When we identify bacteria in this way, we can then, in a second “bioinformatic” round, look for the antibiotic resistance genes known in these bacteria. Yes, there are antibiotic resistant bacteria, they adapt. My uncle must have been colonised by some of them. This lung microbiome sequencing, done in a couple of “bioinformatic” rounds, might prove helpful in choosing the antibiotic accordingly to the results. A valuable tool that helps track the “right” antibiotic, in theory. But with this big-data DNA (lots of DNA sequencing data), what can be done? This microbiome test identifies bacteria that are difficult to grow, and that traditional microbiology cannot identify. “In cases of resistant lung infection, seek help from the microbiome, not from the petri dish!” I’m quoting Patrick Merel here. Both of my cousins did a great job liaising with the ICU docs and nurses, inquiring about this microbiome thing. I soon got word via my Parisian cousin (a dentist) that “they performed a DNA/RNA probe (immediate and culture) so this should cover pretty much everything.” This sounded cryptic to me. Then he added: “Jacques is doing better”. That part was less cryptic. And it was great news. My uncle had been discussing his funerals when he awoke from his fairytale sleep, and now he was asking for a book and his glasses.
Again I asked biologist and mHealth evangelist Merel if he could explain what had been done. His answer: “From what I understand, they had to do a molecular test (molecular hybridisation) to detect nonculturable bacteria. Complementary DNA fragments (probes) are used with those of said bacteria. Think of it as a fishing party.
To identify bacteria, one often seeks to identify their RNA16S. In this case of research by molecular hybridisations, RNA probes are used.
Even if it’s less complete than a microbiome sequencing, it’s good enough, when you do not have access to NGS (next generation sequencing).”
Special thanks to Portable Genomics for their expertise. Indeed, translating molecular jargon seems to be a job in demand. Genomics can also make the difference between life and death, even in the form of some kind of microbiome sequencing.
A few days ago, I got in touch again with Dr. Tilly, the digestive surgeon who had removed my uncle’s colon and thought he had a 20% chance to make it. She suggested I should get in touch with AP-HP (public hospital administration in France) and IFSI (nursing schools) to try and budget some kind of training effort. I have worked with Intuitive Surgical Europe (Marketing) and earned myself digital MITx certificates in microbiology, not to forget my university background: post-graduate teacher training. So maybe Dr. Tilly’s suggestion would make sense? People like Portable Genomics’ Merel (or even myself) should rub shoulders with organ specialists like her more often.
Finally, I would like to thank the awesome ICU team at Georges Pompidou hospital in Paris for their great job, as I do not take this high level of professionalism for granted. A few days ago, at the Centre Médical Opéra in Paris — I was forced to make the appointment in March. This physician must be very busy — the doctor did not even examine me but did make a few phone calls to ask for some missing document to be faxed to his secretarial office. “Once I have it, I will scan it for the record.” Then he paused, and still pecking away on the keyboard (using two fingers), asked: “So everything is fine, then, I suppose? That’ll be 25 Euros.” The expensive lack of coordination in health care keeps showing up. A friend of mine lost his leg because of delayed medical treatment. The surgeon he ended up with was left with no choice but to cut his leg. Maybe the fax was out of order that day.
My two cents: if Portable Genomics’ Merel wants to disrupt the insurance system, he will have to make sure he has the ancestors of AI, surgeons, on board. Even better: make it look like the whole initiative is coming from surgeons. And make sure nurses, physicians and surgeons get a proper training in that Precision Medicine thing. Wait, isn’t that what they call an evangelist? What do you think, Illumina?
