ksbakes.bsky.social
Prof @Cambridge_Uni Genomic epidemiologist. #Shigella and #AMR enthusiast. Views own. http://gen.cam.ac.uk/baker-group also www.pdu.gen.cam.ac.uk also @pducambridge.bsky.social
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her*
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Best inaugural title ever, and congratulations again!
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Is this not also something to do with it being the inverse of the trend in overall scientific publishing volume? (With the qualifier that association is not causation, etc)
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Thank you for writing the package Fiona! There was lots of discussion at ABPHM just now about the need for research software to be better acknowledged/sustainable/celebrated
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This work was led by the incredible @charlotteechong.bsky.social š» š§¬ as part of the @multidefence.bsky.social sLoLa consortium funded by @ukri.org BBSRC and in collaboration with a wonderful set of new (and old!) colleagues 9/n
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This work was intended to discover biologically plausible mechanistic interactions among DSes for downstream studies and comes with (extensive) supplementary info for the community to dig out into on their favourite defence systems 8/n
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This held true even after adjusting for database size and discovery in Pseudomonas with defence and anti-defence systems having a higher proportion of theoretical pairs involved in significant associations or disassociations across the dataset 7/n
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After this we collapsed the accessory genome categories to get a feel for which elements were driving the ongoing accessory genome dynamics of Pseudomonas and found that defence systems contributed the highest number of associations across accessory genome element categories 6/n
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We then expanded this analysis to interactions among DSes and other accessory genome elements including anti-defences, phage, ICEs, plasmids, and AMR, and found convincing evidence of dissociations of multiple DSes with mobilizable blaOXA genes 5/n
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We explored whether these DS interactions arose from genomic co-localisation (as DSes can aggregate in defence islands) and found that associating DSes were only found on the same contig in <1% of cases and often less frequently than DS pairs that were found to dissociate 4/n
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Owing to evidence of mechanistic synergy or antagonism between different defence systems from lab studies, we leveraged natureās experiment here to pull out defence system interactions that were independent of evolutionary relationships (using @whelanfj.bsky.social coinfinder) 3/n
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As part of the @multidefence.bsky.social consortium, we worked with a globally curated dataset of >4,000 P. aeruginosa (from 10.1126/science.adi0908) to reveal differences in the number and composition of defence systems between isolates from (and not from) cystic fibrosis cases 2/n
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As ever, this has been a great collaboration with @clairejenkins2.bsky.social @ukhsa.bsky.social and also with the Robert Koch institute, driven by the magnificent @lewiscemason.bsky.social šØāšš§¬
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If youāre interested in a preview, or to hear more about sexually transmissible shigellosis, come see our work at @bashhuk.bsky.social and/or @stihiv2025.org in Montreal 11/12
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Endemic shigellosis is also moving into other populations (e.g. people experiencing homelessness) in the Americas, and some work to come from us later this year might explain why 10/12
pmc.ncbi.nlm.nih.gov/articles/PMC...
pubmed.ncbi.nlm.nih.gov/36731480/
pubmed.ncbi.nlm.nih.gov/40393962/
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So, although itās not been looking great for sexually transmissible shigellosis, there is hope that the gonnorhea vaccine roll out announced this week may slow for the selection of highly resistant strains 9/n
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We know that since then that AMR acquisition driven by sustained selection pressure for ābystander resistanceā (mostly from gonnorhea treatment) has driven the evolution of XDR strains 8/n
www.nature.com/articles/s41...
pubmed.ncbi.nlm.nih.gov/37031199/
pubmed.ncbi.nlm.nih.gov/36731481/
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This emergence date is co-incident with the emergence of another sexually transmissible lineage, S. flexneri 3a, and we think that increased sexual activity in response to HAART drove the sustained re-emergence of sexually transmissible shigellosis 7/n
www.thelancet.com/journals/lan...
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Temporal dating of the lineage however, showed that it likely emerged in the late 1990s when Highly Active Antiretroviral Therapy was rolled out and HIV became a manageable infection 6/n
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We found the strains came formed an early branch in the Globally disseminated Lineage 3 of S. sonnei but didnāt find any additional/obvious pathogen changes responsible for success 5/n
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We sought out existing Shigella sonnei strains from some of the earliest outbreaks from 2002 ā 2006 and did a genomic epidemiology study to explore if pathogen factors might have influenced this 4/n
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Although we know drug resistance has played a key role in driving outbreaks since the 2010s, we donāt know why shigellosis re-emerged in the first place early in the 21st Century? 3/n
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Although sexual transmission of Shigella was first reported in 1974, there was a lull in outbreaks until the early 2000s when reporting rose and ST shigellosis spread globally 2/n
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I should warn you the songs will get stuck in your head. Potentially for years to come!
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Thanks Heather - Charlotte is amazing and it was nice to stray out of the Enterobacterales. Should be in preprint soon so weāll share more broadly then!
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š #PhDPosition !
š¤° Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social
š
Apply by Monday 14 April
ā”ļø buff.ly/QL3JFtg
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Maybe itās AI gone too far. A couple of TENAs in your shoes might do the trick?