Kate Baker
@ksbakes.bsky.social
Prof @cambridgebiosci.bsky.social Genomic epidemiologist connecting pathogen evolution with public health outcomes. #Shigella and #AMR enthusiast. Views own. http://gen.cam.ac.uk/baker-group also www.pdu.gen.cam.ac.uk also @pducambridge.bsky.social
Are you hungry for some Shigella news? Why not come to the 1st International Shigella meeting www.shigella2026.conferences-pasteur.org/home 20-24 April 2026 Paris
October 29, 2025 at 6:29 PM
Are you hungry for some Shigella news? Why not come to the 1st International Shigella meeting www.shigella2026.conferences-pasteur.org/home 20-24 April 2026 Paris
Output != Productivity, which is a measure of efficiency, and the first Figure in this paper seems to suggest that women actually produce more papers per year than men (albeit from a disadvantaged starting point, x-axis is years in research). Graphical abstract also seems misleading on this.
September 20, 2025 at 6:40 PM
Output != Productivity, which is a measure of efficiency, and the first Figure in this paper seems to suggest that women actually produce more papers per year than men (albeit from a disadvantaged starting point, x-axis is years in research). Graphical abstract also seems misleading on this.
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
September 17, 2025 at 11:58 AM
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
The honour is real ...
August 22, 2025 at 3:41 PM
The honour is real ...
My parents brought the last of my effects over from Oz including my first ever scientific poster (and the only piece of high school work I kept) … maybe I was destined to end up in @geneticscam.bsky.social
August 9, 2025 at 5:32 PM
My parents brought the last of my effects over from Oz including my first ever scientific poster (and the only piece of high school work I kept) … maybe I was destined to end up in @geneticscam.bsky.social
So, welcome to your new genomic understanding of S. Panama and please go ahead and check out the data yourselves on the associated @microreact.bsky.social page! microreact.org/project/span... 9/n
July 27, 2025 at 8:39 AM
So, welcome to your new genomic understanding of S. Panama and please go ahead and check out the data yourselves on the associated @microreact.bsky.social page! microreact.org/project/span... 9/n
As a final analysis we compared the predicted invasiveness of S. Panama with other broad and narrow host range serovars and found it was comparable to other major causes of iNTS (thanks to @nwheeler443.bsky.social for the ML classifier to do so) 8/n
July 27, 2025 at 8:38 AM
As a final analysis we compared the predicted invasiveness of S. Panama with other broad and narrow host range serovars and found it was comparable to other major causes of iNTS (thanks to @nwheeler443.bsky.social for the ML classifier to do so) 8/n
Temporal analysis revealed that the four major clades all emerged in the late 1800s, coincident with European efforts to build the Panama canal (‘Panama Fever’ by @matthewparker70.bsky.social is recommended reading for those with an interest in the history here) 7/n
July 27, 2025 at 8:38 AM
Temporal analysis revealed that the four major clades all emerged in the late 1800s, coincident with European efforts to build the Panama canal (‘Panama Fever’ by @matthewparker70.bsky.social is recommended reading for those with an interest in the history here) 7/n
We also found multidrug resistance cassettes; fluoroquinolone resistance (bumping S. Panama onto the WHO AMR priority pathogens list); and a single extensively drug-resistant isolate 6/n
July 27, 2025 at 8:38 AM
We also found multidrug resistance cassettes; fluoroquinolone resistance (bumping S. Panama onto the WHO AMR priority pathogens list); and a single extensively drug-resistant isolate 6/n
Although antimicrobial resistance (AMR) levels were low overall (14% of isolates), resistant isolates were predominately found in Clade 2 (European-associated) and Clade 4 (associated with Oceania and Asia) 5/n
July 27, 2025 at 8:37 AM
Although antimicrobial resistance (AMR) levels were low overall (14% of isolates), resistant isolates were predominately found in Clade 2 (European-associated) and Clade 4 (associated with Oceania and Asia) 5/n
Population structure analyses revealed the presence of four major Clades that had significant geographic associations 4/n
July 27, 2025 at 8:37 AM
Population structure analyses revealed the presence of four major Clades that had significant geographic associations 4/n
To better characterise S. Panama we sequenced a global collection of isolates (n=731) from public health surveillance datasets from @ukhsa.bsky.social @thedohertyinst.bsky.social, historical collections from @pasteur.fr and publicly available data (n=105) from 1931 to 2019 3/n
July 27, 2025 at 8:37 AM
To better characterise S. Panama we sequenced a global collection of isolates (n=731) from public health surveillance datasets from @ukhsa.bsky.social @thedohertyinst.bsky.social, historical collections from @pasteur.fr and publicly available data (n=105) from 1931 to 2019 3/n
S. Panama causes major disease concerns, including high rates of iNTS in French Guiana, large outbreaks in European pork, AMR in Asia, and outbreaks in American soldiers from where the first (extant) isolate from 1931 came from (More in our 2019 review: 10.1128/IAI.00273-19) 2/n
July 27, 2025 at 8:36 AM
S. Panama causes major disease concerns, including high rates of iNTS in French Guiana, large outbreaks in European pork, AMR in Asia, and outbreaks in American soldiers from where the first (extant) isolate from 1931 came from (More in our 2019 review: 10.1128/IAI.00273-19) 2/n
There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n
July 27, 2025 at 8:35 AM
There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n
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
May 23, 2025 at 6:38 PM
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
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
May 23, 2025 at 6:37 PM
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
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
May 23, 2025 at 6:37 PM
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
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
May 23, 2025 at 6:36 PM
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
Owing to evidence of mechanistic synergy or antagonism between different defence systems from lab studies, we leveraged nature’s experiment here to pull out defence system interactions that were independent of evolutionary relationships (using @whelanfj.bsky.social coinfinder) 3/n
May 23, 2025 at 6:36 PM
Owing to evidence of mechanistic synergy or antagonism between different defence systems from lab studies, we leveraged nature’s experiment here to pull out defence system interactions that were independent of evolutionary relationships (using @whelanfj.bsky.social coinfinder) 3/n
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
May 23, 2025 at 6:34 PM
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
We found the strains came formed an early branch in the Globally disseminated Lineage 3 of S. sonnei but didn’t find any additional/obvious pathogen changes responsible for success 5/n
May 23, 2025 at 12:46 PM
We found the strains came formed an early branch in the Globally disseminated Lineage 3 of S. sonnei but didn’t find any additional/obvious pathogen changes responsible for success 5/n
Although we know drug resistance has played a key role in driving outbreaks since the 2010s, we don’t know why shigellosis re-emerged in the first place early in the 21st Century? 3/n
May 23, 2025 at 12:45 PM
Although we know drug resistance has played a key role in driving outbreaks since the 2010s, we don’t know why shigellosis re-emerged in the first place early in the 21st Century? 3/n
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
May 23, 2025 at 12:45 PM
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
So, that’s a wrap from us - Merry Christmas and a Happy New Year from the Bakery and friends! This was such a genuine team effort both in house and with an amazing set of collaborators (not to mention two babies along the way!) And thanks so much to BBSRC for the funding! 13/n
December 19, 2024 at 8:54 PM
So, that’s a wrap from us - Merry Christmas and a Happy New Year from the Bakery and friends! This was such a genuine team effort both in house and with an amazing set of collaborators (not to mention two babies along the way!) And thanks so much to BBSRC for the funding! 13/n
Single cell physiology studies revealed this was mediated through a combination of persister and short filament former phenotypes that endured antimicrobial insult (50X MIC!) 9/n
December 19, 2024 at 8:52 PM
Single cell physiology studies revealed this was mediated through a combination of persister and short filament former phenotypes that endured antimicrobial insult (50X MIC!) 9/n