Adam Blanchard

Comparative Genomics of Lactococcus spp. From Global Aquaculture Outbreaks Reveals Virulence Determinants, Antibiotic Resistance, and Phage Defence Mechanisms Lactococcus petauri predominated in isolates from outbreaks of lactococcosis, suggesting a shift in disease aetiology. Genomic analysis revealed diverse virulence factors, prophage and resistance gen...

New paper out of the lab this week. Looking at the genomic diversity in isolates from outbreaks of Lactococcosis, and potential virulence mechanisms of the emerging causative pathogen L. pertauri.

doi.org/10.1002/mbo3...

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes. #MAGs #Metagenomics #MetagenomeAssembly #GenomeBiology
genomebiology.biomedcentral.com/articles/10....

Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii | mBio All organisms have the capacity for evolution through mutation. Bacteria with high mutation rates have a survival advantage in some stressful environments because they generate beneficial mutations mo...

Cool result: Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii

"Exposure of a transposon insertion mutant library to extended weak antibiotic selection ... revealed genes that indirectly increased fitness due to elevated general mutation rates"

What determines who a phage can infect?

We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.

👇 A thread!

In vitro determination of essential genes required by Streptococcus uberis to grow in a complex biological media relating to intramammary infection Streptococcus uberis is a leading cause of bovine mastitis, a disease of significant economic impact to the dairy industry. Understanding the genetic factors essential for bacterial survival in milk a...

Another paper from the lab, trying to look at in vitro biological relevant phenotypes in essential genomes www.microbiologyresearch.org/content/jour...

Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy Cattle Ruminant gut microbial communities profoundly influence host health and environmental impacts, yet their viral components remain poorly characterised across developmental transitions. Here, we analyse...

New preprint up on the changes in the bovine virome though different life stages led by @milja001.bsky.social @ryancook94.bsky.social www.biorxiv.org/content/10.1...

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

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace.
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...

Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths - Microbial Ecology Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dom...

New paper where we suggest bacteria in the honeybee stomach may be more interesting to study than generally thought.

doi.org/10.1007/s002...

It’s seems worse now than I remember previously. Had one sent back with an email saying it didn’t have a data statement when it did, then had to waste more time resubmitting it.

Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms - Microbiome Background Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning r...

Interesting paper on novel bacteria isolated from the Phoenix Space Mission
microbiomejournal.biomedcentral.com/articles/10....

Super cool #bioinformatics tool alert: @widdowquinn.bsky.social group releases PyANI-plus, a flexible tool for exploring whole-genome similarity on large AND detailed scales. Walkthrough available below!

Autocycler: long-read consensus assembly for bacterial genomes https://www.biorxiv.org/content/10.1101/2025.05.12.653612v1

GitHub - avantonder/bacQC-ONT: QC pipeline for ONT data QC pipeline for ONT data. Contribute to avantonder/bacQC-ONT development by creating an account on GitHub.

I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback.
github.com/avantonder/b...
github.com/avantonder/b...

We investigated those too. Was told they couldn’t guarantee they would work with cocci.

New awesome Rust bioinformatics tool just dropped!

Progressive evolution of Streptococcus equi from Streptococcus equi subsp.… | Hayley Wilson I'm really excited to share this work with the world! As we know, academic research work will follow you even after you've left. So this is my post-doc project…

I'm really excited to share the postdoc I completed before joining PHG. It combines two great passions - bacteria and horses!!

Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...

A Broad Spectrum Lasso Peptide Antibiotic Targeting the Bacterial Ribosome - PubMed Lasso peptides, biologically active molecules with a distinct structurally constrained knotted fold, are natural products belonging to the class of ribosomally-synthesized and posttranslationally modi...

Worth a read about a new antibiotic: pubmed.ncbi.nlm.nih.gov/39372947/

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii - Nature Communications In this study, authors conduct a genomic analysis of 15,000 Acinetobacter baumannii isolates, revealing a dominant multidrug-resistant super-lineage (accounting for approximately 70% global isolates),...

New work showing that multidrug-resistant 𝘈𝘤𝘪𝘯𝘦𝘵𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘣𝘢𝘶𝘮𝘢𝘯𝘯𝘪𝘪 isn’t a scattered threat—it’s a structured epidemic!

A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange.

Li et al. Nat Commun
#AMR #bacterialgenomics

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

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

This is very important -
shortening antibiotic treatment duration is a good way to reduce consumption

Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island Abstract. In this study, we identify and characterize a novel phage-inducible chromosomal island (PICI) found in commensal Escherichia coli MP1. This novel

An ICE, a PICI, and a phage walk into a cell… and start crosstalking. Interesting read on how MGEs juggle interactions like pros! 🦠

academic.oup.com/ismej/articl...

Understanding the Molecular Interactions Between Influenza A Virus and Streptococcus Proteins in Co-Infection: A Scoping Review Influenza A virus infections are known to predispose infected individuals to bacterial infections of the respiratory tract that result in co-infection with severe disease outcomes. Co-infections invol...

Latest publication with @virologyvet.bsky.social trying to make sense of viral/bacterial interactions in co-infections
www.mdpi.com/2076-0817/14...

PredCMB: Predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data academic.oup.com/bioinformati... #jcampubs

CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes - BMC Bioinformatics Background The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitatin...

CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcentral.com/articles/10.... #jcampubs

I thoroughly enjoyed this read. It put into words my own thought well. Definitely going to take up some of the suggestions.

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...
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DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems https://www.biorxiv.org/content/10.1101/2025.01.08.631726v1

Success of switching to a second antibiotic is contingent on temporally dynamic collateral effects. Top: Twenty replicate populations of E. faecalis V583 were exposed to increasing concentrations of the antibiotic ceftriaxone over the course of 14 days via serial passage. At the end of each day, a sample of the population was isolated and cultured in a range of doxycycline concentrations for 24 h. Middle: Density (OD) after 24 h versus drug (DOX) concentration for all 20 populations (light gray), and the mean over the 20 populations (dark black) at different days of the evolution experiment. Bottom left: Average sensitivity over 20 populations (error bar standard error of the mean) at different time points. Bottom right: Collateral effects; dashed region highlights a transient six-day window where collateral sensitivity is more pronounced.

Evolution of antibiotic resistance #AMR can lead to collateral resistance/sensitivity to other drugs; @jeffmaltas.bsky.social &co show that these effects can fluctuate over time, needing precise timing & stochastic control models to optimize treatment strategies 🧪 @plosbiology.org plos.io/3C2Ao1y

Orthology inference across thousands of genomes within a day‽ that sounds incredible