Great discussion with @billhanage.bsky.social and the audience at #ESCMIDGlobal2026 during our session “Pathogens and people: modelling epidemics for preparedness”. Strong focus on how to improve preparedness in collaboration with public health institutes - lots to take forward.
Ian Braga, Lucas Wardil, Ricardo Martinez-Garcia: Fixation probabilities for multi-allele Moran dynamics with weak selection https://arxiv.org/abs/2604.12004 https://arxiv.org/pdf/2604.12004 https://arxiv.org/html/2604.12004
Image of lab scientist with test tubes.
The European Commission will invest $34.7 million in the two public-private partnerships to boost the pipeline for new antibiotics and other AMR medical countermeasures.
Read more: ow.ly/Sap850YFgir
We (with @yanwong.bsky.social) are advertising a 3 year postdoc position for a project on ARG inference and methods! Based at Oxford stats. Closing date noon 7 April, full details at my.corehr.com/pls/uoxrecru...
🚨 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)
We're also happy to see a second paper out today, led by Nicola de Maio, which develops methods to identify and account for mutation rate variation and recurrent errors.
www.nature.com/articles/s41...
Ian Roberts published his first paper "Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model" with me, Jere Koskela and Xavier Didelot. We describe an efficient reversible jump MCMC method for inference for the structured coalescent. journals.plos.org/pl...
Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...
Very happy to have had the opportunity to contribute to this work. Thanks to Robin Thompson for leading, the amazing team of co-authors and the INI for hosting us.
✅ Say: "My manuscript has been metropolised"
❌ Don't say: "My manuscript has been rejected and so I've sent it to MDPI"
Now out in NEJM. Kudos to @dhelekal.bsky.social and @tatumdmortimer.bsky.social : www.nejm.org/doi/10.1056/...
If you are an early career research attending @stihiv2025.org and interested in learning more about data visualization in R, @odileharrison.bsky.social , Sim Dabee, and I are organizing a workshop during the conference (11:30am-1:30pm on Wednesday). Register here: forms.gle/e4UL1NG62PUD...
A fun conversation with Carl this afternoon about his excellent book AIR-BORNE--the recording is available at the HSPH youtube site: www.youtube.com/user/Harvard...
One ceftriaxone-resistant #typhoid case last year set us on a path that is now live on Emerging Infectious Diseases.
47 cases in months, resistance rose from 0 to 5%. We spoke with patients, sequenced samples. 4.3.1.2.B1 lineage+blaCTX-M-15 on pCROB1. #AMR #PublicHealth
wwwnc.cdc.gov/eid/article/...
Looking forward to my visit @ccdd-hsph.bsky.social!
(10/10) Work with @tatumdmortimer.bsky.social & @yhgrad.bsky.social
(9/10) As N. gonorrhoeae strains carrying high-level cephalosporin resistance on a tetM positive background have been emerging globally wwwnc.cdc.gov/eid/article/..., the evident strength of selection for tetM may have created a favorable environment for their expansion in the US.
(8/10) This raises concern for genetic hitchhiking, whereby alleles that may be neutral or deleterious on their own actually increase in frequency due to their presence in lineages that carry another gene or allele that’s beneficial.
(7/10) The number of major N. gonorrhoeae lineages carrying tetM also increased from one before 2020 that accounted for ~40% of all tetM+ isolates to 4 after 2020 that collectively accounted for ~80% of all tetM+ isolates. Two of these lineages carry penA variants that increase cephalosporin MICs.
(6/10) This is consistent with a recent report out of Seattle, showing an increase in resistance in N. gonorrhoeae and an increase in S. aureus tetracycline resistance in those on doxy-PEP: academic.oup.com/cid/advance-... and www.thelancet.com/journals/lan...
(5/10) By May 2024, the estimated proportion of isolates carrying tetM skyrocketed to ~35%, suggesting a large selective pressure for doxycycline resistance. The rise seems most pronounced in HHS regions 9 and 10.
(4/10) To investigate the impact of the increased doxy use, we analyzed a collection of over 14000 N. gonorrhoeae genomes spanning 2018-mid 2024, collected and sequenced through CDC surveillance efforts -- GISP, eGISP, SURRG www.cdc.gov/gonorrhea/hc....
(3/10) This is especially relevant for N. gonorrhoeae. In 2018, an estimated 10% of isolates carried the plasmid-borne gene tetM, which confers high-level tetracycline resistance (MIC ≥ 16 µg/mL) pmc.ncbi.nlm.nih.gov/articles/PMC....
(2/10) Over the past few years, the use of doxycycline to treat bacterial STIs has gone up in the US. Doxy became the recommended treatment for chlamydia (2020), it was used for syphilis treatment during bicillin shortages, and doxy-PEP was rolled out. What’s the impact on resistance?
(1/10) New preprint: Expansion of tetM-carrying Neisseria gonorrhoeae in the US, 2018-2024; Link: www.medrxiv.org/content/10.1...
Work with @tatumdmortimer.bsky.social & @yhgrad.bsky.social
(9/10) As N. gonorrhoeae strains carrying high-level cephalosporin resistance on a tetM positive background have been emerging globally wwwnc.cdc.gov/eid/article/..., the evident strength of selection for tetM may have created a favorable environment for their expansion in the US.
(8/10) This raises concern for genetic hitchhiking, whereby alleles that may be neutral or deleterious on their own actually increase in frequency due to their presence in lineages that carry another gene or allele that’s beneficial.
