Mobile integrons encode phage defense systems Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉

Short 🧵
www.science.org/doi/10.1126/...

(1/2) 🌍 Don't miss this groundbreaking study by Guo et al., 2025 and the 10,000 Plant Genomes Project. Profiling over one million nuclei across 20 tissues, the authors have further unraveled the genome of one of the most well studied plant genera: Arabidopsis. #plantgenomics #agriculture

New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky

Genomic surveillance reveals different transmission patterns between third-generation cephalosporin and carbapenem resistance in Klebsiella pneumoniae in the Comunidad Valenciana (Spain), 2018–2020 - ... Background The emergence and spread of third-generation cephalosporins (3GC) and carbapenem-resistant Klebsiella pneumoniae pose a global critical challenge. Understanding the transmission dynamics wi...

Good papers, like good wine, need maturing. I'm proud and thrilled to share our work on genomic epidemiology of K.pneumoniae in Valencia and differential transmission patterns of resistances, part of Neris Garcia's PhD thesis and the NLSAR consortium. go.uv.es/td8iL4c #publichealth #EpiSky 🧬🖥️

Muy buen trabajo! Solo una aclaración: las más de 500 entradas del virus en España corresponden a toda la primera ola, no al mes de febrero. En este mes fueron muchas menos. Identificamos 6 ó 7, pero seguro que es una infraestructura.

Febrero de 2020: el mes en el que España convivió con el coronavirus sin saberlo El patógeno llegó y se propagó masivamente sin ser detectado durante esos días hasta hacer inevitables los confinamientos. Miles de casos de covid fueron confundidos con otras infecciones respiratoria...

Febrero de 2020: el mes en el que España convivió con el coronavirus sin saberlo #publichealth #publichealthsky
elpais.com/sociedad/202...

PopGen Seminar Series Summer Term 2025 04.03.25 – Lutz Becks (Univ. of Konstanz, DE)
The evolutionary dynamics of novel endosymbiosis. 11.03.25 – Ilkka Kronholm (Univ. of Jyväskylä, FI)
How chromatin structure influences genetic and epigenetic variation. 18.03.25 – Katja Hoedjes (Vrije Univ. Amsterdam, NL)
Understanding functional impact of genetic variation on complex traits at a single nucleotide resolution. 25.03.25 – Sophie Armitage (Freie Univ. of Berlin, DE)
Evolutionary ecology of host-pathogen interactions. 01.04.25 – Matthew Rockman (New York Univ., US)
Developmental evolution is a population-genetics problem. 08.04.25 – Wen-Juan Ma (Vrije Univ. Brussels, BE)
The evolution of sex chromosomes and sex determination in frogs. 15.04.25 – Almorò Scarpa (Vetmeduni, AT)
Two centuries of transposable element invasions in Drosophila melanogaster 22.04.25 – Julia Kreiner (Univ. of Chicago, US)
The mode and tempo of genomic adaptation to contemporary agriculture. 29.04.25 – Martin Kaltenpoth (Max Planck Inst. for Chemical Ecology, DE)
Microbial symbionts as sources of evolutionary innovations in beetles. 06.05.25 – Luisa Pallares (Friedrich Miescher Laboratory, DE)
Phenotypic robustness across the genotype-phenotype map, from genes to environment and back. 13.05.25 – Diana Rennison (Univ. of Calif., San Diego, US)
Understanding the predictability of evolutionary trajectories using threespine stickleback.

20.05.25 – Filipa Sousa (Univ. of Vienna, AT)
Bioenergetics Evolution: The link between Earth’s and Life’s history. 27.05.25 – Yun Song (Univ. of California, Berkeley, US)
Learning and applying complex probability distributions over biological sequences. 03.06.25 – April Wei (Cornell Univ., US)
Enabling efficient analysis of biobank-scale data with genotype representation graphs. ALT TEXT OUT OF SPACE, GO TO https://www.popgen-vienna.at/news/seminars/

The PopGen Vienna Seminar series schedule is ready for the next term (Mar-Jun). It's jam-packed with fantastic speakers in #evolution, #genetics, #genomics, #popgen, and more! Details and streaming link signup can be found on our website www.popgen-vienna.at/news/seminars/

The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates dela...

📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint

See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays

doi.org/10.1101/2025...

🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠

bsky.app/profile/flod...

CompBio method developers: software that only runs on your computer and is not available via a repository like CRAN, PyPI, Bioconductor, is not a proper research output —
just like a set of scribbled notes on your desktop is not the same as a preprint or a paper.
Finish the job.

Congratulations!

High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations - Nature Communications Resistance mutations are challenging to characterize because their effects are highly context dependent. Here, authors present a quantitative mutant screening technique that deconstructs how factors l...

Very excited that my 1st first-author paper has just been published!! We present a novel mutant screening technique that can rapidly identify 100s of antibiotic resistance mutations, while evaluating how likely they are in different genetic backgrounds.

www.nature.com/articles/s41...

Figure 1 Mechanisms of action of key antibiotics for the treatment of multidrug-resistant Gram-negative bacterial infections Several classes of antibiotics are available for the treatment of multidrug-resistant Gram-negative bacterial infections. Their mechanisms of action focus on key aspects of bacterial cell function, such as inhibiting cell wall synthesis (ie, β-lactams and fosfomycin) and function (ie, polymyxins), protein synthesis (ie, aminoglycosides and tetracyclines), folic acid synthesis (ie, trimethoprim and sulphonamides), and DNA replication (ie, fluoroquinolones). Because of increasing antimicrobial resistance, novel antibiotics have been developed to overcome some of these mechanisms; for example, by inhibiting antibiotic modification (ie, β-lactamase inhibitors) or by altering entry pathways (ie, cefiderocol, which enters via iron transporters). DHF=dihydrofolic acid. PABA=para-aminobenzoic acid. THF=tetrahydrofolate.

Figure 2 Diagnostic testing of multidrug-resistant Gram-negative bacteria Diagnosis of multidrug-resistant Gram-negative bacterial infections involves both species identification and antibiotic susceptibility testing. Although clinical microbiology laboratories have undergone automation of these processes and have seen the introduction of proteomic methods, such as MALDI-TOF, delays in turnaround time remain and might affect patient outcomes. New biochemical, molecular (eg, PCR), automated microscopy, and hybridisation-based rapid diagnostics now allow faster detection of antimicrobial resistance, including by testing clinical samples directly. Emerging technologies are seeking to improve both the speed of testing and provide more detailed information regarding the underlying mechanisms of antimicrobial resistance. MALDI-TOF=matrix-assisted laser desorption/ionisation time-of-flight.

Figure 3 Summary of new antibiotic agents for the treatment of multidrug-resistant Gram-negative bacterial infections Green=antibiotic is reliably active in vitro and guideline recommended. Yellow=variable activity; antibiotic might be effective if in vitro susceptibility is shown, clinical data might be lacking to support routine use. Red=not recommended, likely absence of in vitro susceptibility. IV=intravenously. *Administered simultaneously via Y-site administration. †Administration was studied in combination with imipenem–cilastatin.

Figure 4 Summary of IDSA and ESCMID guidelines for the treatment of multidrug-resistant Gram-negative bacterial infections 3GCephR-E=third-generation cephalosporin-resistant Enterobacterales. AmpC-E=β-lactamase producing Enterobacterales. CRAB=carbapenem-resistant Acinetobacter baumannii. CRE=carbapenem-resistant Enterobacterales. DTR-P aeruginosa=difficult-to-treat resistant-Pseudomonas aeruginosa. ESBL-E=extended-spectrum β-lactamase-producing Enterobacterales. ESCMID=European Society for Clinical Microbiology and Infectious Diseases. IDSA=Infectious Diseases Society of America. MBL=metallo-β-lactamase. UTI=urinary tract infection.

#IDSky #MedSky required reading:

Multidrug-resistant Gram-negative bacterial infections

Nenad Macesic, Anne-Catrin Uhlemann, Anton Peleg

Review in @thelancet.bsky.social

doi.org/10.1016/S014...

screenshot of the new webpage: [Title] Newly discovered betacoronavirus, Wuhan 2019-2020 A previously unknown betacoronavirus was detected in patients during an outbreak of respiratory illnesses, including atypical pneumonia, that started mid-December 2019 in the city of Wuhan, the capital of Central China's Hubei Province. The newly discovered coronavirus is similar to some of the betacoronaviruses detected in bats, but it is distinct from SARS-CoV and MERS-CoV. The genome of the newly discovered CoV consists of a single, positive-stranded RNA that is approximately 30k nucleotides long. The overall genome organization of the newly discovered CoV is similar to that of other coronaviruses. The newly sequenced virus genome encodes the open reading frames (ORFs) common to all betacoronaviruses, including ORF1 ab that encodes many enzymatic proteins, the spike-surface glycoprotein (S), the small envelope protein (E), the matrix protein (M), and the nucleocapsid protein (N), as well as several nonstructural proteins. [Table] Virus name Accession ID Passage det Collection date Host Originating lab BetaCoV/Wuhan/IVDC-HB-01/2019 EPIISL_402119 Virus Isolate 2019-12-30 Human National Institute for Viral Disease Control and Prevention, China CDC BetaCoV/Wuhan/IVDC-HB-04/2020 EPIISL_402120 Original 2020-01-01 Human National Institute for Viral Disease Control and Prevention, China CDC BetaCoV/Wuhan/IVDC-HB-05/2019 EPI_ISL_402121 Original 2019-12-30 Human National Institute for Viral Disease Control and Prevention, China CDC BetaCoV/Wuhan/IPBCAMS-WH-01/2019 EPI_ISL_402123 Original 2019-12-24 Human Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Pel BetaCoV/Wuhan/WIV04/2019 EPLISL_402124 Original 2019-12-30 Human Wuhan Jinyintan Hospital

Five years ago (Sunday 12 Jan 2020), five sequences of the new coronavirus were officially shared via GISAID, on a dedicated page revealed by a link on the GISAID homepage. ▫️1/

(🖼️: virological.org/t/novel-2019... by @arambaut.bsky.social)

A chart showing wastewater sample stations in California and if H5 bird flu was found there.

H5 bird flu was found in wastewater in Los Angeles, San Francisco, Palo Alto, Paso Robles, Redwood City, Sacramento, San Jose, Santa Rosa, Sunnyvale and Turlock, according to WastewaterSCAN.

screenshot of Eddie Holmes' tweet: @edwardcholmes All, an initial genome sequence of the coronavirus associated with the Wuhan outbreak is now available at Virological.org here: [link to virological]

Five years ago (Saturday 11 Jan 2020), first public announcement and availability of a sequence of the new coronavirus.
It was posted by @eddieholmes.bsky.social at 01:05 UTC on Virological, and announced on Twitter at 01:08 UTC. ▫️1/

web.archive.org/web/20200118...
archive.is/z880d

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social

Suppose a new flu pandemic were to emerge. How quickly could we get going with key epidemiological analysis and modelling?

To find out, I went back through the dozens of reports I was involved in for SPI-M for COVID and estimated where we currently stand: epiverse-trace.github.io/posts/covid-...

🔥 Webinar Series Launch! 🔥
‘#Genomics and Beyond: A Holistic Approach to Tackling #AMR in East Africa’ 🌍
Don't miss Prof. Matthew Holden #StAndMedicine sharing his expertise.
Register Now www.targetamr.org.uk/hdrevents/ja...

🥁 Announcing the Public Domain Image Archive! 🥁

We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive

*** Notification: New class in Evolutionary Cell Biology open to the public during Spring 2025 semester

The class is taught by Dr. Michael Lynch every Tuesday and Thursday, 9:00-10:15 am (MST), starting on 16 January 2025

Join the class on asu.zoom.us/j/86824596554

Details victor.chai@asu.edu

A phylogenetic approach to comparative genomics Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2

We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.

These methods must be considered an essential part of the comparative genomics toolkit.

@lauriebelch.bsky.social @stuwest.bsky.social

Very excited to share our recent publication with Verena Schuenemann and other excellent collaborators, including my former student Marta Pla-Diaz. We have improved the analysis of Treponema pallidum genomes with a Multiple_Reference_Based mapping. Useful for many other bacteria Enjoy rdcu.be/d5GGx

Polymerase mutations underlie adaptation of H5N1 influenza virus to dairy cattle and other mammals. In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds...

Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans.

With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)

American Ingenuity Beat the Polio Outbreak So Why Risk Letting It Return?

History doesn’t lie. Polio—and other disease epidemics—killed, paralyzed, ravaged lives. It’s still here, waiting. 🧪♿️🗃️ #vaccines #polio

brandy-schillace.medium.com/american-ing...

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

⚠️ BREAKING:

H5N1 bird flu virus levels in San Francisco wastewater surged to a record high of 228.8, according to WastewaterSCAN.

This wastewater treatment plant handles 80% of the city's wastewater.

🎁 Early Xmas present from your friends at the MRC-University of Glasgow Centre for Virus Research @cvrinfo.bsky.social

We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠

viro3d.cvr.gla.ac.uk

Department for Environment, Food and Rural Affairs Updated Outbreak Assessment #6 High pathogenicity avian influenza (HPAI) in Great Britain and Europe 18 December 2024 Disease report. Since our previous outbreak assessment on 6 November 2024, there have been ten reports of high pathogenicity avian influenza (HPAI) H5 clade 2.3.4.4b in domestic poultry. All reports have been confirmed as HPAI H5N1, the first confirmation of the subtype in commercial poultry since February 2024. There has also been a further 18 HPAI H5 clade 2.3.4.4b events involving 30 “found-dead” wild birds in Great Britain. Of these, 15 have been confirmed as HPAI H5N1,13 as HPAI H5N5 and 2 as HPAI H5Nx. The wild bird risk level across Great Britain has been raised to very high. The risk level for HPAI H5 incursion in poultry: • With stringent biosecurity is increased to medium with medium uncertainty; and • With non-stringent or suboptimal biosecurity is increased to high with medium uncertainty. HPAI H5 reports continue across Europe, with continued incidences of poultry outbreaks of H5N1 in Germany and France and the first HPAI outbreak in commercial poultry in the Netherlands. Wild bird reports have also increased, with 240 reports between 06 November and 18 December. There have been no further reports of HPAI H5 in mammals in Europe.

1/ Highly pathogenic avian influenza (HPAI) in Great Britain & Europe - DEFRA outbreak assessment for 18 Dec 2024. #IDsky 🧪

🗓️ Report period: 06 Nov – 18 Dec 2024

🔗 to report: assets.publishing.service.gov.uk/media/6765a0...