New preprint: with increasing resistance to ceftriaxone, the last recommended antibiotic for gonorrhea, we urgently need new drugs. Two--zoliflodacin & gepotdiacin--are up for approval by the FDA in Dec. Here we show a point mutation can result in cross-resistance. www.biorxiv.org/content/10.1...

Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...

Microbiology Postdoctoral Position (Please re-post) A funded postdoctoral position in Chicago will open in 2026 to study aspects of Neisseria gonorrhoeae pathogenesis, antigenic variation, genetics, or physiology. If interested, please get in touch with Hank Seifert [email protected]

Our lab's first paper is out! Led by Jordan Ort, we developed NextClade datasets that enable rapid H5 clade assignment via NextClade. We deployed these during the start of the H5 cattle outbreak, and we finally published the paper in Virus Evolution academic.oup.com/ve/article/1...

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

Our lab is hiring!! We are looking for a research assistant who will be involved with our experimental evolution studies on how stress affects population dynamics in E. coli. Great opportunity for recent grads! E-mail for more info and apply here: ecsr.fa.us2.oraclecloud.com/hcmUI/Candid...

Delighted to see the first version of our new ELife paper. A collaboration with Levi Morran, we show how an intact antibiotic resistance gene (mecA) changes the course of S. aureus evolution on a new host. Kudos to Michelle Su and Kim Hoang for making this happen. elifesciences.org/reviewed-pre...

⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10] www.medrxiv.org/content/10.1...

Using doxycycline after unprotected sex — doxy PEP — is effective at reducing some sexually transmitted infections in some people. But new research suggests is probably also driving development of resistance to tetracycline antibiotics in some bacteria. www.statnews.com/2025/07/09/d...

Now out in NEJM. Kudos to @dhelekal.bsky.social and @tatumdmortimer.bsky.social : www.nejm.org/doi/10.1056/...

The Poultry Diagnostic and Research Center at UGA is looking for an avian microbiologist (open rank, tenure-track position) to lead the bacteriology/mycology diagnostic section! Find out more about the position and apply here: www.ugajobsearch.com/postings/437...

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...

Dr. Yonatan Grad @yhgrad.bsky.social, Professor of immunology and infectious diseases comments on the potential impact of recent decisions related to vaccines made by Health and Human Services Secretary (HHS) Robert F. Kennedy Jr. Read it here at bit.ly/3T2KPqX

I got the opportunity to speak with Science about my individual research fellowship being terminated. I was awarded the NSF GRFP before I chose Harvard for graduate school, but I still got cut. I study how we can improve treatments for a common antibiotic resistant bacteria, so this is sad to see

All of NIH funding to Northwestern University is frozen. This pause includes noncompeting approved funding, new and competing grants with fundable scores. No reimbursements for money already spent have been received since March. This situation is rarely reported so please Please get the word out!

In this preprint, we consider the explanations for the observed drop in gonorrhea incidence in the US and the evidence needed to evaluate them. A critical takeaway: without the CDC data & monitoring, we're unlikely to know. Those huge cuts to the CDC undermine efficient, effective healthcare.

New preprint. After years of increases, gonorrhea diagnosis rates dropped in the US in 2022 and 2023. While the news is promising, understanding WHY is key to sustaining progress. dash.harvard.edu/handle/1/427...

I'm a current Harvard graduate student and I found out today that I had my NSF GRFP terminated without notification. I was awarded this individual research fellowship before even choosing Harvard as my graduate school

Excited to share the newest preprint from the lab for my first post! Driven by @tayellisonwrites.bsky.social and @ianyyen.bsky.social with Lynne Howell we show the protein FimX has diverged in function away from regulating pilus extension to instead regulate pilus localization in A. baylyi

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules

With nearly all of Harvard Chan School’s direct federal grants terminated, we are relying on philanthropy to power our research and support our educational programs. Every gift, regardless of size, advances our vision of health, dignity, and justice for every human. Support our work: hsph.me/whygive

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

Are you able to mentor a summer student and have a good project that can be virtually administered, sign up to be an NSURP mentor today! If you can't, hit that share button please and thank you! #NoLabNoProblem #NSURP uarizona.co1.qualtrics.com/jfe/form/SV_...

Our preprint and much other work was only possible because of data generated by the CDC STD lab, which was shuttered in the HHS layoffs last week. This is a huge blow to efforts to monitor resistance, guide clinical care, & inform policy www.statnews.com/2025/04/05/c... @helenbranswell.bsky.social

(1/10) New preprint: Expansion of tetM-carrying Neisseria gonorrhoeae in the US, 2018-2024; Link: www.medrxiv.org/content/10.1...

Although we are not federally funded for this summer, WE WILL STILL RUN The National Summer Undergraduate Research Project (NSURP) in 2025. We remain committed to the work that needs to be done and will continue to meet people where they are. 1/4 nsurp.org

Some of the most talented people I know have joined, or were about to join, the EIS. This is an immense loss.

Our paper describing the microGWAS pipeline was published yesterday in Microbial Genomics. Lots of fixes and additions to the code/documentation since the preprint, including a hard to reproduce bug that only showed up in a specific HPC 🥵 www.microbiologyresearch.org/content/jour...

How do changes in antibiotic use, various pathways to resistance, multiple drug resistance, and more come together to shape the success and failure of bacterial lineages in a real-world epidemic? #AMR #microsky A preprint: www.biorxiv.org/content/10.1... (1/15)

Call your senators! Do it today! It's better than wallowing

A hitchhiker’s guide to the gonococcal population: biorxiv.org/content/10.1...

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling

Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2 1/n

New preprint: Drug resistant gonorrhea is a big public health problem. Resistance to ceftriaxone, the last approved antibiotic, is spreading globally. When we first detect one of these very resistant isolates, how many undetected cases are there likely to be? www.medrxiv.org/content/10.1...

Pleased to share this preprint on Yaws transmission dynamics following mass azithromycin administration, led by Amber Barton www.medrxiv.org/content/10.1... Following MDA campaign, we sequenced >half of infections, showing recrudescence driven by existing lineages & persistence linked to key SNPs.

Hi BlueSky friends! Postdoc(s) available in my lab! Multiple projects on how bacterial genomic and functional diversity impacts microbial interactions & disease. 🦠🧫 See www.thelewinlab.com/join-us/post... for more information. Please RT & share. #Postdoc #Microbiology #OralMicro #VaginalMicro

New research article in The Lancet Microbe Effects of #doxycycline post-exposure prophylaxis for prevention of sexually transmitted infections on #gonorrhoea prevalence and antimicrobial resistance among men who have sex with men in the USA: a modelling study www.thelancet.com/journals/lan...

Happy that this piece is finally out! Very grateful for all the input and support by Matt Samore, Marc Lipsitch, @yhgrad.bsky.social, Yue Zhang, McKenna Nevers, Haojia Li, and Karim Khader. www.thelancet.com/journals/lan...

New preprint led by Adi Bandekar and w Ethan Garner. What leads to N. gonorrhoeae being diplococci, and how is it that they have sequentially perpendicular division planes? Using beautiful live cell imaging and genetics, Adi showed it’s all about axial asymmetry www.biorxiv.org/content/10.1...

New preprint on doxycycline post-exposure prophylaxis for bacterial STIs: all doxy-PEP guidelines suggest we should monitor for the impact of resistance, but what is the best way to do so in N. gonorrhoeae? www.medrxiv.org/content/10.1...

In response to the H5N1 infections in cows and now a human in Texas, we've just updated our North America specific H5Nx Nextstrain build with the cow and goat sequences, which are viewable under "Species-grouped: Ruminant": nextstrain.org/groups/moncl.... A few notes.

First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) www.biorxiv.org/content/10.1... #microsky

Have you been wondering what's going on with avian influenza in North America? Check out our lab's @nextstrain narrative on phylodynamic analysis of H5Nx evolution and transmission here! nextstrain.org/groups/moncl...

Applications for 2024 are now OPEN! Please share widely amongst your networks! Mentee (undergrad) app: etap.nsf.gov/award/407/op... Mentor (grad student/post doc/faculty) app: uarizona.co1.qualtrics.com/jfe/form/SV_...

10 years on, @bkille.bsky.social @treangen.bsky.social and co. have refreshed Parsnp with a version 2! Build a core genome multi-alignment for 100k SARS genomes or 1k Mtb genomes in under an hour 💨

Happy to see my new paper with @bjesseshapiro.bsky.social published! www.nature.com/articles/s41.... Bonus of this great News and Views article that was a surprise to us both: www.nature.com/articles/s41... Along with our own blog post on the topic where we summarize the work: tinyurl.com/34r87kr9

Check out our new pub on cell wall metabolism in Neisseria gonorrhoeae. Mutation of the gene for the peptidoglycan terminase MltG results in cells that are abnormally large and pour out cell wall fragments. Antibiotic resistant strains become sensitive when mltG is mutated. doi.org/10.1128/jb.0...

. @lokraj.bsky.social and I are hiring a research technician/lab manager for our labs in the Department of Population Health at UGA. Both labs use genomics to inform diagnostics and interventions for microbial pathogens. More information and application here: www.ugajobsearch.com/postings/348...

We have published a manuscript describing a software tool to reduce ambiguity and improve interpretability in microbial GWAS, called panfeed. Here's a quick explainer: www.microbial-pangenomes-lab.org/2023/11/09/M... And here's the link to the paper: www.microbiologyresearch.org/content/jour...

The world desperately needs new antibiotics for gonorrhea. Looks like the first new one in decades may be on the near-term horizon. www.statnews.com/2023/11/01/n...