Last session of the day converting the genomes into phylogenetic trees to understand the evolution and transmission of #AMR @fcic.bsky.social

Day 4 - part 2 AMR of Bacterial Pathogens - Africa course #AMRBactcourse on the sequencing practical with Nanopore led by @effkay88.bsky.social Huge thanks to the team from @nanoporetech.com South Africa @eventswcs.bsky.social @sangerinstitute.bsky.social

The variation and problems encountered demonstrate the importance of QC and QA in AMR testing and that is important to consider when analysing genomics data for AMR. Huge thanks to the team at NICD Charm.

All the data across the different groups is compared. @effkay88.bsky.social @fcic.bsky.social

Day 4 - AMR of Bacterial Pathogens - Africa course #AMRBactcourse. AMR testing results day… Results of disk testing, e-tests, and micro-dilution @eventswcs.bsky.social @sangerinstitute.bsky.social @cam.ac.uk

@eventswcs.bsky.social

@fcic.bsky.social @effkay88.bsky.social @belamalta10.bsky.social

Day 3 of AMR of Bacterial Pathogens - Africa course at NICD Johannesburg. Split day into the lab for AMR disk testing, MICs and broth micro-dilution. On the computers and lectures on online and command line AMR tools, MLST and phylogeny. Busy day! @sangerinstitute.bsky.social @engagewcs.bsky.social

First day covered a lot of the basics including sequencing technology and AMR resistance and evolution

Fantastic second day of Antimicrobial Resistance of Bacterial Pathogens - Africa course at NICD Johannesburg. Packed day - covering the basics of genomics, the command line, QC, genotype-to-phenotype, assembly and alignments. @sangerinstitute.bsky.social @engagewcs.bsky.social @fcic.bsky.social

Lovely work driven by Lizzie Ledger in the group: a new but druggable mechanism by which Staphs produce biofilm using components of human serum. First polysaccharides, then protein, then eDNA, now lipids too!

bsky.app/profile/bior...

Ancestry and somatic profile indicate acral melanoma origin and prognosis - Nature Analysis of the somatic and transcriptomic profile of 123 acral melanoma samples from Mexican patients helps understand tumour origins and prognosis, and highlights the importance of including samples...

We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️

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

Incredible time at #AIR2026 covering breadth of respiratory infection, microbiomes and immunology with some really beautiful biology. Thanks to fellow committee members @resp-micro.bsky.social @drclairesmith.bsky.social @ewanharrison.bsky.social , Alex Kayongo and organisers @eventswcs.bsky.social

Another insightful day of science, discussion and making new friends at #AIR2026

Day 2 Highlights: making sense of big data, spatial transcriptomics and in vitro modelling of respiratory infections @eventswcs.bsky.social @sangerinstitute.bsky.social

Our new preprint which reimplements "the NFDS model" (of Corander et al) to forecast populations after vaccination as a compartmental model, and uses new bioinformatic tools to create and process the pangenome data

We look at which surveillance strategies are best to correctly forecast changes

Brilliant news!

Work on respiratory immunology or microbes? Interested in big data, omics or the latest in vitro models?... Treat your lab to a christmas present of AIR 2026 registration!

Feb 11th-13th, registration closing soon:
coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Other work using the same cohort is in progress looking at the role of human genetics led by @roisinboggan.bsky.social and metagenomics of the nasal microbiome in larger numbers of CARRIAGE study participants by @duncan-ng.bsky.social

We also found some interesting differences in the nasal microbiome between men and women, and between the strains of S. aureus that are present at high abundance. This all now needs evaluation in larger numbers and different human populations.

We found that people less likely to carry S. aureus tended to have more of Dolosigranulum pigrum, Staphylococcus epidermidis and Moraxella catarrhalis. These bacteria may crowd out, kill or compete with S. aureus, but that requires further study.

This confirms previous data and hypothesis that ‘ intermittent carriers’ (people who will sometime be positive for S. aureus and sometimes not) aren’t a distinct biological group - rather they have microbiomes just like persistent or non-carriers.

Combining nasal microbiome data and culture data we show when S. aureus is present, it often dominates. We can group the nasal microbiome into two major patterns:
1. S. aureus dominated with overall low microbial diversity
2. S. aureus is rare, and there is a greater diversity of other bacteria.

This is of important because people who are colonised are at higher risk of S. aureus infection - which is why you get swabbed when you are admitted to hospital.

Over the last 70yrs using nasal swabs and culture it has been established that some people are persistently colonised by Staphylococcus aureus, while others never are - and third group are positive from time to time (intermittent carriers). We investigated the nasal microbiome in these groups

So a few highlights of the study.

Also thanks to the huge contribution and co-leadership of the CARRIAGE study by @julianparkhill.bsky.social John Danesh, Joan Geoghegan, Sharon Peacock and others in the wider CARRIAGE study team at @cam.ac.uk @sangerinstitute.bsky.social and thanks to @wellcometrust.bsky.social for funding

Great to share the latest work from our group and collaborators. First CARRIAGE study paper led by @drdaggarwal.bsky.social and the heroic efforts of Katie Bellis and Beth Blane in the lab plus all the team at @cambridge-ceu.bsky.social Huge thanks goes to the 22,000 participants of the study

High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut

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

Unpacking the spread of pathogens Nature Reviews Microbiology, Published online: 17 November 2025; doi:10.1038/s41579-025-01264-wThis Genome Watch discusses recent advances in genomic epidemiology that enable the reconstruction of transmission events, with greater resolution and across more complex settings at scale.

ICYMI: New online! Unpacking the spread of pathogens

Benchmarking of human read removal strategies for viral and microbial metagenomics Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological a…

Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...