Pleuni Pennings
@pleunipennings
Researcher, evolution of drug resistance, modeling, population genetics, coding, no longer at SF State University, instead at the U of Montpellier. Mom, Dutch, now immigrant in France.
Oh wow that is remarkable how similar the data from Michigan are to the data from England. web.archive.org/web/20190720...
peppered moth question! Is this graph based on data? And if so, does anyone know the reference? Or another reference with such a figure including the increase and decrease of dark morphs? www.coursehero.com/tutors-probl... @wtf-r-species.bsky.social
That Bercot 2026 paper shows a cluster of tetracycline resistant strains that has mostly infected people on the doxyPEP part of the clinical trial, suggesting that the treatment helps the resistant strains transmit.
Whittles et al. 2017 showed that resistance to cefixime can spread (Rres > Rsus) when more than 31% of the cases are treated with cefixime. The figure shows that with more treatment (on the x) the resistant type becomes more successful (on the y). journals.plos.org/plosmedicine...
The train ride back to Montpellier from Copenhagen is taking a long time but boredom is good for creativity. #smbe2026 #noflysmbe #flipaclip
"there are traces of eugenics in our data, policy, healthcare" To change things @jazlynmooney.bsky.social teaches eugenics to students.
Lots of people listening to @jazlynmooney.bsky.social talk about eugenics and science - the room is filled to capacity
Impressive talk by Rori Rohlfs without her slides after a rare technical issue here at #smbe2026
If you're at #smbe2026 and you have an interest in drug resistance, pop gen or story telling in science, come check out my poster today! It's upstairs in Arkaden 6.
Poster ready and booklets printed. Come find me if you'd like to have one. Now I just need to pack my bag for #Smbe2026 Catching the train tomorrow #noflysmbe
the poster is too busy and i will probably cut the abba image and lots of text
But resistance to 3rd gen cephalosporins also shows clear plateaus in several countries. This image is from the ECDC surveillance atlas. atlas.ecdc.europa.eu/public/index...
hi @dhelekal.bsky.social thanks for your comments. i enjoyed reading your neisseria papers. I think that in many countries use doesn't change much from year to year because habits don't change. And yes, I agree that fixation is possible in real life. It is also possible in my model.
Last one: this is ST 152 gaining BlaTem1. Also here, resistance (in this case through horizontal gene transfer) is gained in many places in the tree.
But here is the same resistance mutation in another sequence type. It is gained many times but never very successful. It doesn't look like neg-frequency dependence to me.
Here is the case like you describe with a well-defined resistant clone. It is Gyrase 83L in ST 131. Red = resistant.
In HIV the sequencing data are not old enough to show the initial increase, but plateaus exists here too. This graph shows NRTI resistance in sub-saharan Africa, which has been stable at just under 2% of new infections. Data from: hivdb.stanford.edu/project/surv...
I love this type of figure in your paper! And I agree that this level of stable coexistence of sequence types requires some frequency dependent selection. But for resistance I think it is different because resistant strains re-emerge and die out unlike sequence types.
And it is not just resistance to quinolones in E coli that stopped increasing. This graph shows resistance to a different drug (cefotaxime) in a different bacterium (K. pneumonia) in a different country (France) about 5 years later. It also shows an increase and a plateau.
So it turns out that after these six years, there was almost no further increase. One of the big surprises in the world of drug resistance: in many cases resistance levels stop increasing even when we don't change how we use the drugs.
Imagine you had six years of data and every year resistance levels go up ... What would you think will happen in the future? (here showing data from quinolone resistance in E coli in Hungary from the supplement of this paper by @sonjalehtinen.bsky.social et al journals.plos.org/plospathogen...
I love NPR but am annoyed that the newsmakers recently have been all men! @npr.org I have to scroll past 9 men to find a woman ...
Listening to Nancy peloci and AOC on my iPad with zoom meeting with virtual Stand up for science #nokings rally
My colleagues at @sfsu.bsky.social used 3 decades of data to show that students with low undergrad GPA have equal PhD completion rates compared to students with high GPA. @sfstatebio.bsky.social journals.plos.org/plosone/arti...
In 1996 new data came out from clinical trials using three-drug combinations for HIV. I drew a graph based on viral load data from two papers. It shows that 2 is better than 1, but 3 is way better than 2 drugs. Later the 3-drug therapies became even better. But this was huge.
I changed my drawing a bit to fit better to the text. The hard sweep person now is taking 3 drugs (triple drug combination therapy as was introduced for HIV in the mid 1990s). Inside the soft sweep person, there are now 3 particles that acquire resistance.