Changzhi Wang

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

I love both these stories. They are inspiring, and I am also working heavily on metagenomic diagnostics

But this also shows we have made little to zero progress in a decade in using NGS in clinical microbiology and ID, which is depressing

www.bbc.co.uk/news/article...

www.nejm.org/doi/10.1056/...

Emergence of transferable daptomycin resistance in Gram-positive bacteria - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Emergence of transferable daptomycin resistance in Gram-positive bacteria

This is fascinating, but also terrible news regarding antimicrobial resistance in multidrug-resistant Gram-positives

'Emergence of transferable daptomycin resistance in Gram-positive bacteria'

www.nature.com/articles/s44...

The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling Biological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets feature enormous biological diversity, their utilization as pretraini...

Excited to be at #NeurIPS this week. @ancornman1.bsky.social will give a spotlight talk at the @workshopmlsb.bsky.social on gLM2/OMG! Please reach out if you want to chat about gLM2/OMG/Gaia and our latest projects😇

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

Welcome to my world!

Information storage across a microbial community using universal RNA barcoding - Nature Biotechnology Barcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation.

Fresh in @NatureBiotech! We developed a synthetic biology tool for tracking gene transfer in microbial communities and applied it to study plasmid hosts in a wastewater microbiome. Awesome collab with James Chappell & @joffsilberg.bsky.social and incredible students. www.nature.com/articles/s41...

Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China - Nature Communications The genomic epidemiology of Acinetobacter baumannii, which is rising in virulence and multidrug resistance, was explored. This study examined bloodstream infection isolates from Chinese patients in 20...

Interesting paper

Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China

'A. baumannii is evolving from a low-virulence, multidrug-resistant pathogen to a more virulent one'

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

Study: Over 3 million children died in 2022 due to drug-resistant infections A landmark study presented today at ESCMID Global 2025 has revealed that over 3 million children worldwide lost their lives in 2022 due to antimicrobial resistance (AMR)-related infections.

In 2022, over 3 million children died from #AMR -related #infectiousdisease. Use of last-resort antibiotics rose sharply, prompting urgent calls for global #OneHealth surveillance, national stewardship programs, and stricter antibiotic use guidelines.

www.news-medical.net/news/2025041...

The burden of β-lactam allergy labels in health care: a systematic review and meta-analysis BALs are associated with an array of adverse health outcomes, especially surgical site infection and infection or colonisation with MDROs and C difficile. Although BALs were associated with longer hos...

The burden of β-lactam allergy labels in health care: a systematic review and meta-analysis

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

Tackling the burden of β-lactam allergy labels Physicians frequently encounter patients who report suspected drug allergies. Many physicians adopt a cautious approach by labelling these unverified drug allergies in their medical records, which oft...

Linked comment:

Tackling the burden of β-lactam allergy labels

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

Newest preprint from our lab. Congratulations to all authors!

Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5–55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.

Amazing work from Julie: pubs.acs.org/doi/10.1021/...