Within-patient evolution of ciprofloxacin resistance in Pseudomonas aeruginosa across a large-scale clinical trial Matthew J. Shepherd MArch 25 4 PM MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY, BERLIN

📢 Voices in Infection Biology
Join us next week for a talk by Matthew J. Shepherd from @manchester.ac.uk, kindly hosted by @keyfm.bsky.social.

🗓️ March 25
🕓 4 pm
📍 on-site seminar (Berlin)

Event info: www.mpiib-berlin.mpg.de/events/45077...

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...

Our new preprint, led by Martin (@mfenk.bsky.social), is online. We address the microbiome’s role as a source and incubator of acute infections by combining prospective collection of native samples with population-wide, culture-based sequencing. Please check out Martin’s wonderful thread. ⬇️🧵🎉

This work would have not come alive without many bright heads involved (though many not on BlueSky). Special thanks goes out to my supervisor
@keyfm.bsky.social and our clinical collaborator Bastian Pasieka @torbenbjkd.bsky.social; @iatsenkolab.bsky.social, Carey Nadell, and @mpiib-berlin.mpg.de

Bacterial evolution during human infection: Adapt and live or adapt and die Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding of evolutionary dynamics, identify adaptive changes, and answer important questions that impact h...

Our work provides further credence to previously raised concepts of short-lived adapt-and-die bacterial genotypes linked to human infections
@dariavantyne.bsky.social doi.org/10.1371/jour... or
@paulinedscanlan.bsky.social doi.org/10.1073/pnas...

Our results highlight the power of prospective longitudinal investigations of the human microbiome during acute infection leading to yet unknown variants associated with the complex etiology of HAI.

But why was the 𝘧𝘪𝘮𝘡 [F126L] mutant lost shortly after the HAI was cleared? Measuring the antibiotic resistance of isolates over time shows that the replacement was driven by multiple resistance-conferring mutations sweeping across the patient’s body, which were present until the end of the study.

Intrigued by the infection-associated fitness effects, we wondered whether 𝘧𝘪𝘮𝘡 [F126L] is a common marker of infection. Analyzing >400 global 𝘌. 𝘩𝘰𝘳𝘮𝘢𝘦𝘤𝘩𝘦𝘪 genomes from clinical contexts revealed the 𝘧𝘪𝘮 operon evolves under purifying selection and nonsynonyoums mutations in 𝘧𝘪𝘮𝘡 are rare.

Further, utilizing 𝘪𝘯 𝘷𝘪𝘷𝘰 survival assays with immunocompromised Relish 𝘋𝘳𝘰𝘴𝘰𝘱𝘩𝘪𝘭𝘢 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳, we observed an increase in its virulence leading to a more rapid decline in survival rates. This suggests that the 𝘧𝘪𝘮𝘡 [F126L] mutants’ fitness was elevated, potentially beneficial during pneumonia.

Does the 𝘧𝘪𝘮𝘡 [F126L] mutant convey a fitness effect? To answer this, we performed 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 assays and found this genotype translates into a hyperpilated phenotype with increased biofilm formation and adherence to lung epithelia.

During an 𝘌𝘯𝘵𝘦𝘳𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘩𝘰𝘳𝘮𝘢𝘦𝘤𝘩𝘦𝘪 infection, we observe a short-lived, non-synonymous mutation in the fimbriae regulator gene 𝘧𝘪𝘮𝘡 [F126L] that is first observed in the gut, before being associated with HAI but subsequently swiftly replaced by repeated body-wide sweeps of independent genotypes.

The evolutionary trajectory of opportunistic pathogens from asymptomatic carriage to HAI - a critical period for possible pathoadaptation – is rarely studied due to the logistical challenges in prospective sampling. Our population-wide whole-genome sequencing data allowed us to investigate that.

But were those pathogens acquired within the hospital or outside? Inferring the time to the most common recent ancestor reveals, that some lineages arose from a recent bottleneck during the hospital stay, while others have been colonizing the patient already before hospitalization.

While we have not seen one common reservoir microbiome niche for those pathogens, we identified that most pathogen strains are observable within the patient’s microbiome either before or within 6 h of HAI onset – pointing at the importance of the microbiome for HAI.

Of those, 3 patients developed HAIs by 9 different species. We performed culture-based sequencing of each pathogen of ≤10 isolates from the site of infection and ≤20 isolates/microbiome site/timepoint. This uncovered a closely related strain of the pathogens within the microbiome in 73% of cases.

To gain insights into the hidden evolutionary processes before, during and after HAI, we enrolled 13 critically ill patients and prospectively collected every week native nasal, oral, rectal and skin microbiome samples during their hospital stay.

Colonization, translocation, and evolution of opportunistic pathogens during hospital-associated infections Many commensal bacteria that peacefully reside in the human microbiome are also able to cause acute opportunistic infections. Emerging evidence suggests that within-host evolution contributes to infec...

Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...

Finally getting some of my research for my PhD out there! Hopefully soon in a journal near you ;)

Ancient Y. pestis infection from a sheep falls on the LNBA lineage, previously only known from humans! +molecular evolutionary analysis to leverage the ever increasing number of ancient genomes known!