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Jane Hawkey

@yekwah.bsky.social

Microbial genomics - bacterial evolution, AMR, mobile elements, phylogenetics. Located at Monash University/Alfred Hospital

29 Posts363 Follower167 Folgt
Charlene Rodrigues @cmcrodrigues.bsky.social · 3w ago

Delighted to share our paper-17 years of meningococcal genomic surveillance, looking at changes in diversity, distribution and demographics in Scotland. The positive impact of vaccines and what is now circulating following COVID-19/restrictions period url.uk.m.mimecastprotect.com/s/lJN8CM1Gzc...

Genomic epidemiology of invasive meningococcal disease in Scotland before, during, and after the COVID-19 pandemic: a retrospective observational study

Invasive meningococcal disease (IMD) remains a major global health threat. Despite vaccination, meningococcal genetic diversity means disease, includi…

url.uk.m.mimecastprotect.com

Charles Wei@rositea.bsky.social · 3mo ago

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies - BMC Microbiology

BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...

link.springer.com

Dr Andrew Lonsdale@lonsbio.bsky.social · 5mo ago

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Thiago Carvalho@cyrilpedia.bsky.social · 5mo ago

'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”

Ben Vezina@bananabenana.bsky.social · 7mo ago

Our new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...

Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages

Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

microbiologyresearch.org

Ben Vezina@bananabenana.bsky.social · 8mo ago

(1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪

The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study - Nature Communications

Carbapenemase blaIMP genes between 1996-2023 were analysed across 4,556 genomes, revealing variant-specific epidemiologies and endemicities. Horizontal gene transfer enabled broad inter-species transm...

nature.com

Ben Vezina@bananabenana.bsky.social · 8mo ago

Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation

Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...

journals.plos.org

Alison Mather@alisonmather.bsky.social · 8mo ago

A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample

Aldert Zomer@aldertzomer.bsky.social · 8mo ago

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

Nature Reviews Genetics@natrevgenet.nature.com · 9mo ago

New online! Microbial genomics for antimicrobial resistance ecology and action

Microbial genomics for antimicrobial resistance ecology and action

Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.

nature.com

EMBL-EBI@ebi.embl.org · 10mo ago

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

How to rapidly search the world’s microbial DNA

By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

ebi.ac.uk

Dorottya Nagy@dotnagy.bsky.social · 10mo ago

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Figure 2 from my recently pre-printed manuscript on the completeness and accuracy of Nanopore long-read only bacterial genome assembly for Enterobacterales. a) tile plot of chromosome circularisation, with assembler on the x-axis and sample on the y-axis, shows that the consensus long-read only assembler, Autocycler, circularised more chromosomes at 95% (87/92) than any other long-read or hybrid assembler. b) complex upset plot of plasmid reconstruction, showing that the best plasmid reconstruction was achieved by long-read assemblers incorporating the separate plasmid assembly tool, Plassembler, namely Autocycler and Hybracter, reconstructing >96% of plasmids.
Dorottya Nagy@dotnagy.bsky.social · 11mo ago

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

Christina Faherty@christinafaher1.bsky.social · 11mo ago

A great opportunity to attend the #Shigella meeting April 20-24, 2026! Abstract submissions are open! @shigellameeting.bsky.social #Microsky

Microbiology Society@microbiologysociety.org · 11mo ago

External Event Grant awards of up to £750 are available for eligible members as a contribution towards the costs of registration, travel, and accommodation to attend an event beginning 01 Jan – 30 April 2026. Apply now before the deadline 01 Nov at 23:59: microb.io/ExternalEven...