Sonja Lehtinen
@sonjalehtinen.bsky.social
Bacterial ecology, evolution and epidemiology | Mathematical and statistical modelling | Genomics | AMR. Assistant professor at the University of Lausanne. https://wp.unil.ch/evolutionaryepidemiology
Pinned
Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae
Competition significantly influences bacterial population dynamics, particularly in how strains interact within and between hosts. This study shows that within-host competition in Streptococcus pneumo...
journals.plos.org
New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...
Reposted by Sonja Lehtinen
🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes
Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...
rdcu.be
November 7, 2025 at 9:15 AM
🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
Reposted by Sonja Lehtinen
Save the date!
𝗦𝘄𝗶𝘀𝘀 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗙𝗼𝗿𝘂𝗺 𝟮𝟬𝟮𝟲
The NCCR Microbiomes presents the third edition of the #Swiss #Microbiomes #Forum
🗓️ Thursday, Feb 5th 2026
🕑 14h00
📍 EPFL Rolex Learning Center, Lausanne
🎟️ Free to attend, but registration is required.
🔗 nccr-microbiomes.ch/tech-transfe...
𝗦𝘄𝗶𝘀𝘀 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗙𝗼𝗿𝘂𝗺 𝟮𝟬𝟮𝟲
The NCCR Microbiomes presents the third edition of the #Swiss #Microbiomes #Forum
🗓️ Thursday, Feb 5th 2026
🕑 14h00
📍 EPFL Rolex Learning Center, Lausanne
🎟️ Free to attend, but registration is required.
🔗 nccr-microbiomes.ch/tech-transfe...
Third edition - 2026 - NCCR
nccr-microbiomes.ch
November 6, 2025 at 9:10 AM
Save the date!
𝗦𝘄𝗶𝘀𝘀 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗙𝗼𝗿𝘂𝗺 𝟮𝟬𝟮𝟲
The NCCR Microbiomes presents the third edition of the #Swiss #Microbiomes #Forum
🗓️ Thursday, Feb 5th 2026
🕑 14h00
📍 EPFL Rolex Learning Center, Lausanne
🎟️ Free to attend, but registration is required.
🔗 nccr-microbiomes.ch/tech-transfe...
𝗦𝘄𝗶𝘀𝘀 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗙𝗼𝗿𝘂𝗺 𝟮𝟬𝟮𝟲
The NCCR Microbiomes presents the third edition of the #Swiss #Microbiomes #Forum
🗓️ Thursday, Feb 5th 2026
🕑 14h00
📍 EPFL Rolex Learning Center, Lausanne
🎟️ Free to attend, but registration is required.
🔗 nccr-microbiomes.ch/tech-transfe...
Reposted by Sonja Lehtinen
The University of Bern seeks a Professor in Plant Population Ecology (Tenure-Track or Open Rank) to develop a research program and teach. Applications due by 23.01.2026. Details: https://www.ips.unibe.ch/questionnaire/ #job
Professor in Plant Population Ecology (80-100%), Tenure-Track Assistant Professor or Open Rank
www.ips.unibe.ch
November 4, 2025 at 12:50 PM
The University of Bern seeks a Professor in Plant Population Ecology (Tenure-Track or Open Rank) to develop a research program and teach. Applications due by 23.01.2026. Details: https://www.ips.unibe.ch/questionnaire/ #job
Love this! I'm so upset this is not available in Switzerland. I'm following it vicariously by listening to Marina Hyde and Richard Osman talk about it on this is entertainment - and now also statistics blogging.
October 31, 2025 at 3:18 PM
Love this! I'm so upset this is not available in Switzerland. I'm following it vicariously by listening to Marina Hyde and Richard Osman talk about it on this is entertainment - and now also statistics blogging.
Very proud of @krishnaaswin77.bsky.social first PhD paper and grateful to all the excellent collaborators!
October 31, 2025 at 3:05 PM
Very proud of @krishnaaswin77.bsky.social first PhD paper and grateful to all the excellent collaborators!
A key motivation for this study was to estimate resistance fitness costs in natura. It’s interesting they remain so elusive. In these data, we can only quantify effects associated with clearance and establishment, not transmission - so one possibility is that we’d see clearer effects there.
October 31, 2025 at 3:05 PM
A key motivation for this study was to estimate resistance fitness costs in natura. It’s interesting they remain so elusive. In these data, we can only quantify effects associated with clearance and establishment, not transmission - so one possibility is that we’d see clearer effects there.
We did find some evidence that resistant strains are worse within-host competitors than sensitive strains, particularly for macrolide resistance. The direction of the overall effect across all analysed antibiotics is consistent with a fitness cost, but with CIs overlapping zero.
October 31, 2025 at 3:05 PM
We did find some evidence that resistant strains are worse within-host competitors than sensitive strains, particularly for macrolide resistance. The direction of the overall effect across all analysed antibiotics is consistent with a fitness cost, but with CIs overlapping zero.
We were also interested in quantifying the fitness cost of resistance. We checked whether there's a cost on clearance rate, but resistant strains are associated with lower clearance. We think this is because resistance is more beneficial on longer carried strains. www.pnas.org/doi/abs/10.1...
www.pnas.org
October 31, 2025 at 3:05 PM
We were also interested in quantifying the fitness cost of resistance. We checked whether there's a cost on clearance rate, but resistant strains are associated with lower clearance. We think this is because resistance is more beneficial on longer carried strains. www.pnas.org/doi/abs/10.1...
We also quantified the fitness effects of antibiotics and antibiotic resistance. Antibiotic exposure is associated with a 71% increase in clearance rate of sensitive strains and, interestingly, a 40% increase in the clearance rate of resistant strains.
October 31, 2025 at 3:05 PM
We also quantified the fitness effects of antibiotics and antibiotic resistance. Antibiotic exposure is associated with a 71% increase in clearance rate of sensitive strains and, interestingly, a 40% increase in the clearance rate of resistant strains.
We find that the presence of another pneumococcal strain (i.e. competitor) in the host is associated with a 33% increase in clearance rate and a 54% reduction in the probability of establishment.
October 31, 2025 at 3:05 PM
We find that the presence of another pneumococcal strain (i.e. competitor) in the host is associated with a 33% increase in clearance rate and a 54% reduction in the probability of establishment.
We used survival analysis to quantify how the presence of a within-host competitor affects the establishment and clearance of serotypes in the Maela pneumococcal carriage study (~1000 infants, sampled monthly over a 2 year period).
October 31, 2025 at 3:05 PM
We used survival analysis to quantify how the presence of a within-host competitor affects the establishment and clearance of serotypes in the Maela pneumococcal carriage study (~1000 infants, sampled monthly over a 2 year period).
New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...
Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae
Competition significantly influences bacterial population dynamics, particularly in how strains interact within and between hosts. This study shows that within-host competition in Streptococcus pneumo...
journals.plos.org
October 31, 2025 at 3:05 PM
New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...
Reposted by Sonja Lehtinen
Please spread the word! 10 days left to apply for this #sciencejobs as Assistant Professor Tenure Track in Quantitative Cell Biology 👩🔬
@izb-unibern.bsky.social @unibe.ch! ohws.prospective.ch/public/v1/jo...
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
@izb-unibern.bsky.social @unibe.ch! ohws.prospective.ch/public/v1/jo...
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
Uni Bern: Assistant Professor with tenure-track for Quantitative Cell Biology
Start date of employment: anticipated for August 2027
ohws.prospective.ch
October 7, 2025 at 11:17 AM
Please spread the word! 10 days left to apply for this #sciencejobs as Assistant Professor Tenure Track in Quantitative Cell Biology 👩🔬
@izb-unibern.bsky.social @unibe.ch! ohws.prospective.ch/public/v1/jo...
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
@izb-unibern.bsky.social @unibe.ch! ohws.prospective.ch/public/v1/jo...
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
Reposted by Sonja Lehtinen
EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
September 30, 2025 at 9:52 AM
EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
This sounds like a super cool project!
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
September 25, 2025 at 2:54 PM
This sounds like a super cool project!
Reposted by Sonja Lehtinen
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 3:49 PM
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
Reposted by Sonja Lehtinen
The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...
Research Informatics - Working with Bacterial Genomes (ONLINE LIVE TRAINING) - Mon 27 Oct 2025
www.training.cam.ac.uk
September 8, 2025 at 2:01 PM
The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...
Reposted by Sonja Lehtinen
Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
Assistant Professor (Research and Education) in Bacterial Genomics at University of Birmingham
Looking for a new job opportunity in academia? Check out this job opening for a Assistant Professor (Research and Education) in Bacterial Genomics on jobs.ac.uk!
www.jobs.ac.uk
September 4, 2025 at 8:22 AM
Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
Reposted by Sonja Lehtinen
A new 4 year PostDoc position in our lab! Modeling + experiments to explore dynamics of carbon fixing hot-spring microbiomes. Part of an exciting multidisciplinary team with Sophie Nixon, @brockhurstlab.bsky.social & others
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Research Associate in Microbiome Ecology:Oxford Road
www.jobs.manchester.ac.uk
August 12, 2025 at 2:59 PM
A new 4 year PostDoc position in our lab! Modeling + experiments to explore dynamics of carbon fixing hot-spring microbiomes. Part of an exciting multidisciplinary team with Sophie Nixon, @brockhurstlab.bsky.social & others
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Reposted by Sonja Lehtinen
Lausanne Comp Bio Symposium 2025 (cbiosymposium.unil.ch)
🗓 Abstract deadline 30 June (𝟑 𝐝𝐚𝐲𝐬 𝐭𝐨 𝐠𝐨!!!)
🎤 Oral presentation notifications: 7 July
✅ Early Bird registration deadline: 11 July
💰 Registration fee for non-PI: 150 CHF
🗓 Abstract deadline 30 June (𝟑 𝐝𝐚𝐲𝐬 𝐭𝐨 𝐠𝐨!!!)
🎤 Oral presentation notifications: 7 July
✅ Early Bird registration deadline: 11 July
💰 Registration fee for non-PI: 150 CHF
June 27, 2025 at 10:00 AM
Lausanne Comp Bio Symposium 2025 (cbiosymposium.unil.ch)
🗓 Abstract deadline 30 June (𝟑 𝐝𝐚𝐲𝐬 𝐭𝐨 𝐠𝐨!!!)
🎤 Oral presentation notifications: 7 July
✅ Early Bird registration deadline: 11 July
💰 Registration fee for non-PI: 150 CHF
🗓 Abstract deadline 30 June (𝟑 𝐝𝐚𝐲𝐬 𝐭𝐨 𝐠𝐨!!!)
🎤 Oral presentation notifications: 7 July
✅ Early Bird registration deadline: 11 July
💰 Registration fee for non-PI: 150 CHF
Reposted by Sonja Lehtinen
Great job opportunity at The Center for Integrative Genomics, Lausanne University, Switzerland unil.ch/cig/en/home....
For a tenure-track Assistant Professor position. More details for how to apply are here nature.com/naturecareer...
For a tenure-track Assistant Professor position. More details for how to apply are here nature.com/naturecareer...
June 16, 2025 at 4:18 PM
Great job opportunity at The Center for Integrative Genomics, Lausanne University, Switzerland unil.ch/cig/en/home....
For a tenure-track Assistant Professor position. More details for how to apply are here nature.com/naturecareer...
For a tenure-track Assistant Professor position. More details for how to apply are here nature.com/naturecareer...
Reposted by Sonja Lehtinen
New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...
research.pasteur.fr/en/job/postd...
Postdoctoral positions in epidemic mathematical/statistical modelling - Research
Job description We are recruiting postdocs to contribute to research projects in the Mathematical Modelling of Infectious Diseases Unit, at Institut Pasteur in Paris. The candidates will be expected t...
research.pasteur.fr
June 5, 2025 at 5:22 AM
New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...
research.pasteur.fr/en/job/postd...
One week left to apply - if you like our papers, we'd love to hear from you!
Come work with us! We're looking of postdoc(s) with experience in bacterial genomics and interest in mathematical modelling to work on bacterial ecology and evolution in the context of public health. tinyurl.com/n34vzszu
Opportunités de carrière : Postdoctoral researcher in bacterial genomics (22209)
tinyurl.com
May 23, 2025 at 1:35 PM
One week left to apply - if you like our papers, we'd love to hear from you!
Reposted by Sonja Lehtinen
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
May 14, 2025 at 2:07 PM
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
Reposted by Sonja Lehtinen
Two Postdocs (Lausanne, Switzerland)
Bacterial genomics in the context of evolutionary epidemiology, with potential projects including antibiotic resistance, HGT and plasmid dynamics.
with @sonjalehtinen.bsky.social
at University of...
More details: http://iddjobs.org/jobs/2309
Bacterial genomics in the context of evolutionary epidemiology, with potential projects including antibiotic resistance, HGT and plasmid dynamics.
with @sonjalehtinen.bsky.social
at University of...
More details: http://iddjobs.org/jobs/2309
May 3, 2025 at 8:47 AM
Two Postdocs (Lausanne, Switzerland)
Bacterial genomics in the context of evolutionary epidemiology, with potential projects including antibiotic resistance, HGT and plasmid dynamics.
with @sonjalehtinen.bsky.social
at University of...
More details: http://iddjobs.org/jobs/2309
Bacterial genomics in the context of evolutionary epidemiology, with potential projects including antibiotic resistance, HGT and plasmid dynamics.
with @sonjalehtinen.bsky.social
at University of...
More details: http://iddjobs.org/jobs/2309