Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

🎉 Our next monthly webinar!
⚖️ What Do Patients and Publics Consider Ethical? Insights from Deliberative Workshops on Pathogen Genomics
🎙️ With Dr Stephanie Johnson
➕ ECR Presentation on the impact of mass gatherings on antimicrobial resistance
👇 Register now: www.targetamr.org.uk/hdrevents/ta...

We also found that flight duration matters long-haul flights showed higher ARG transcriptional activity. This underscores the need for targeted surveillance at borders.

In our new ES&T paper, we analyzed 130 aircraft sewage samples from flights arriving in Saudi Arabia. We identified distinct AMR profiles compared to local sewage, including 51 unique ARGs (like blaNDM, blaVIM).

Monitoring Cross-Border Dissemination of Antimicrobial Resistance (AMR) via Air Travel to Saudi Arabia: Formulation of Monitoring Strategies to Mitigate AMR Concerns Antimicrobial resistance (AMR) is a global health challenge, and its dissemination can be accelerated by international air travel. Aircraft sewage, aggregating microbial material from global travelers...

New publication! ✈️🦠 How does air travel contribute to the global spread of Antimicrobial Resistance?
#AMR #OneHealth #WastewaterSurveillance

dplyr but make it bussin fr fr no cap `genzplyr` is an alternative syntax for `dplyr` that replaces boring old function names with GenZ slang. Your data wrangling is about to hit different.

A student just shared this with me and it is AWESOME hadley.github.io/genzplyr/

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎

www.pnas.org/doi/10.1073/...

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...

Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...

New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome

Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky

www.biorxiv.org/content/10.1...

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

Competitive metagenomic read recruitment explained A tutorial on the nuts and bolts of competitive read recruitment

I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:

anvio.org/tutorials/co...

I thought I'd try this technical molecular microbiology question here. #MicroSky

Does anyone have experience with cloning 7-10 kbp fragments into a vector for Gram-positives?

We are trying, but the vectors we generally use become quite unstable when we try to clone in a fragment of that size.

Project - Plasmidlab PLAS-FIGHTER Exploiting plasmid-bacteria interactions to fight

Antimicrobial Resistance (AMR) could cause 10 million deaths by 2050. At PLAS-FIGHTER, we are working to change this!
🔎 We study how plasmids spread resistance to open up new avenues for future containment and diagnostic strategies.
Find out more 👇
plasmidlab.es/project/

#AntibioticResistance

Wastewater surveillance tracks spread of antibiotic resistance A study conducted during COVID-19 travel restrictions sheds light on the relationship between mass gatherings and the spread of antibiotic resistance.

Grateful to KAUST BESE for featuring our Nature Water study on wastewater surveillance of AMR. Huge thanks to Prof. Pei-Ying, our collaborators and BESE community for the support. Excited to keep pushing impactful public-health research forward. #KAUST discovery.kaust.edu.sa/en/article/2...

The clinical impact and dissemination of carbapenemase-producing Enterobacter: a genome-based study in China | Microbiology Spectrum Carbapenemase-producing Enterobacter (CPEn) causes difficult-to-treat infections and has emerged globally as a significant antimicrobial resistance threat. Here, we generated genome sequences of 128 CPEn clinical isolates with accompanying clinical data. ...

Latest study with the super-human friend that is Zong. Gen epi of carbapenemase-producing Enterobacter in China. Lots of within and between hospital spread and increasing in incidence

journals.asm.org/doi/10.1128/...

New paper in collaboration with the @asantoslopez.bsky.social lab!

www.biorxiv.org/content/10.1...

This link works: coursesandconferences.wellcomeconnectingscience.org/event/antimi...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

International comparison reveals gender differences in antimicrobial resistance A recent study led by the University of Turku, Finland, analysed the DNA map of more than 14,000 gut metagenomes in a global dataset and found that there are differences in antibiotic resistance be

International comparison reveals gender differences in antimicrobial resistance - an analysis of more than 14,000 open gut metagenomes indicates that in high-income countries women had more antibiotic resistance than men www.utu.fi/en/news/pres... /w @katammp.bsky.social @mahkamehsalehi.bsky.social

Wastewater surveillance unveils the impact of mass gatherings on antimicrobial resistance after the COVID-19 pandemic in Saudi Arabia - Nature Water Mass gatherings can impact the antimicrobial resistance in the environment. Surveillance of wastewater in areas of Saudi Arabia affected by mass gatherings after the lifting of COVID-19 pandemic restr...

My new publication in #NatureWater!
Our study reveals how mass gatherings like Hajj and Umrah contribute to the spread of #AMR in Saudi Arabia, using wastewater-based surveillance during and after COVID-19.
#Metagenomics #WastewaterSurveillance
www.nature.com/articles/s44...

The deadline for the VIB.AI group leader positions is approaching - send in your CV and short research plan before 14th June to start your BioML research lab in Leuven or Ghent

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.

Please see the official job ad here, and spread the word:

jobs.awi.de/Vacancies/20...

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution Antimicrobial resistance is recognized as a major global health threat. Pathogens can rapidly evolve resistance which diminishes the impact of antimicrobial treatments. The presence of other microbes ...

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution.

New paper from the lab, and the third chapter of Lars Zandbergen’s thesis!

www.biorxiv.org/cgi/content/...

Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. #TransposableElements #TEs #Kmer #Phylogenetics #Genomics #Bioinformatics #G3 🧬 🖥️
academic.oup.com/g3journal/ad...

Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that i...

We made three pangenome graphs 🧬 public, one for the Japanese, one for the Saudi population, and a merged graph (JaSaPaGe). Useful for 🖥️ bioinformatics on either population, or to evaluate how pangenome graphs behave when two different populations are included. jasapage.bio2vec.net/view for PanGene

Jumbo phage-mediated transduction of genomic islands Bacteria acquire new genes by horizontal gene transfer (HGT), typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages and certain integrative and conjugative elements (ICE...

@prczhaoyansong.bsky.social posted an update of elegant work on genomic islands. Captured via real-time expts, the GIs define a widespread class of MGE (eg VPI-1 de V. cholerae), encode a diverse cargo of genes & exploit jumbo phages for horizontal transfer 😎👇

www.biorxiv.org/content/10.1...

Plasmid–bacteria associations in the clinical context Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have investigated the ecoevolutionary dynamics between plasmids and their bacterial hosts. However, what drives the epidemiological success of certain plasmid–bacterium associations remains unclear. In this opinion article, we review which factors influence these associations and underline that studying plasmid–host interactions of clinical relevance is critical for understanding the evolution and spread of AMR. We also highlight the increasing importance of integrating experimental research with bioinformatics and machine learning tools to study plasmid–bacteria dynamics. This combined approach will assist researchers to dissect the molecular mechanisms underlying successful plasmid–host associations and to design strategies to prevent and predict future high-risk associations.

Plasmid–bacteria associations in the clinical context

🎓 Officially passed my PhD defense today. :)
After years of wastewater, metagenomes, and a lot of coffee, it's finally done.
Grateful to my advisor, thesis committee, collaborators, and everyone who supported me along the way.

Incidence and prevalence of antimicrobial resistance in outpatients with cancer: a multicentre, retrospective, cohort study AMR proportions and IRRs for most key pathogens were up to three-times higher in isolates from outpatients with cancer than those without cancer, highlighting the need for enhanced surveillance, infec...

This large multi-center study shows cancer patients are infected with #AMR bacteria at 1.2 to 3 times higher rates due to frequent hospital visits and antibiotic use. This highlights the need for better antibiotic #stewardship and surveillance in these patients.

www.thelancet.com/journals/lan...

Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social