Kyle Gontjes
@kylegontjes.bsky.social
6th year PhD Candidate at the University of Michigan
Microbial genomic epidemiologist in Dr. Evan Snitkin's lab studying the evolutionary dynamics of antibiotic resistance.
MPH from UM-SPH. BSc from Calvin College
Microbial genomic epidemiologist in Dr. Evan Snitkin's lab studying the evolutionary dynamics of antibiotic resistance.
MPH from UM-SPH. BSc from Calvin College
Reposted by Kyle Gontjes
Our new paper out: AI boosted our genomic surveillance investigations by finding 37 missed transmission routes and reaching >90% sensitivity in key scenarios.
AI + WGS can speed outbreak reviews and help IP teams act faster #IDSky
Genomic surveillance is a key must!
📃: doi.org/10.1017/ice....
AI + WGS can speed outbreak reviews and help IP teams act faster #IDSky
Genomic surveillance is a key must!
📃: doi.org/10.1017/ice....
November 14, 2025 at 3:09 PM
Our new paper out: AI boosted our genomic surveillance investigations by finding 37 missed transmission routes and reaching >90% sensitivity in key scenarios.
AI + WGS can speed outbreak reviews and help IP teams act faster #IDSky
Genomic surveillance is a key must!
📃: doi.org/10.1017/ice....
AI + WGS can speed outbreak reviews and help IP teams act faster #IDSky
Genomic surveillance is a key must!
📃: doi.org/10.1017/ice....
Reposted by Kyle Gontjes
Distinct and Shared Impacts of Virulence Plasmids on the Phenotype and Transcriptome in Convergent Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae https://www.biorxiv.org/content/10.1101/2025.11.10.687661v1
November 11, 2025 at 4:17 AM
Distinct and Shared Impacts of Virulence Plasmids on the Phenotype and Transcriptome in Convergent Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae https://www.biorxiv.org/content/10.1101/2025.11.10.687661v1
Reposted by Kyle Gontjes
🆕 New in ICHE: Can we make VRE screening more efficient?
Authors found:
▶️ VRE+ patients had recent high-risk antibiotic exposure
▶️ Using abx-guided screening = avoided 50% of tests
▶️ VRE+ rate = 5.6% w/ targeted vs 2.6% overall
▶️ Maintained 100% NPV
#IDSky
📄: doi.org/10.1017/ice....
Authors found:
▶️ VRE+ patients had recent high-risk antibiotic exposure
▶️ Using abx-guided screening = avoided 50% of tests
▶️ VRE+ rate = 5.6% w/ targeted vs 2.6% overall
▶️ Maintained 100% NPV
#IDSky
📄: doi.org/10.1017/ice....
Antibiotic-exposure guided prevalence screening for vancomycin-resistant Enterococcus: better value for hospitals | Infection Control & Hospital Epidemiology | Cambridge Core
Antibiotic-exposure guided prevalence screening for vancomycin-resistant Enterococcus: better value for hospitals
doi.org
November 10, 2025 at 8:12 PM
🆕 New in ICHE: Can we make VRE screening more efficient?
Authors found:
▶️ VRE+ patients had recent high-risk antibiotic exposure
▶️ Using abx-guided screening = avoided 50% of tests
▶️ VRE+ rate = 5.6% w/ targeted vs 2.6% overall
▶️ Maintained 100% NPV
#IDSky
📄: doi.org/10.1017/ice....
Authors found:
▶️ VRE+ patients had recent high-risk antibiotic exposure
▶️ Using abx-guided screening = avoided 50% of tests
▶️ VRE+ rate = 5.6% w/ targeted vs 2.6% overall
▶️ Maintained 100% NPV
#IDSky
📄: doi.org/10.1017/ice....
Reposted by Kyle Gontjes
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.
www.nature.com
November 3, 2025 at 1:07 PM
New online! Microbial genomics for antimicrobial resistance ecology and action
Reposted by Kyle Gontjes
Some charts for those who don't know the extent of the US public (and private) investment in research (particularly in biomedical research) compared to other countries and institutions. The destruction of the US' scientific institutions has global implications.
November 2, 2025 at 10:52 AM
Some charts for those who don't know the extent of the US public (and private) investment in research (particularly in biomedical research) compared to other countries and institutions. The destruction of the US' scientific institutions has global implications.
Reposted by Kyle Gontjes
It's great to see the kids so excited and R and coding.
October 31, 2025 at 12:14 PM
It's great to see the kids so excited and R and coding.
Reposted by Kyle Gontjes
Delayed discharge of patients considered medically fit for discharge places operational and economic strain on hospitals. This patient population experiences a considerable burden of infection and of hospital acquired pneumonia
📗https://ow.ly/rtrI50XkTHb
📗https://ow.ly/rtrI50XkTHb
October 31, 2025 at 1:05 PM
Delayed discharge of patients considered medically fit for discharge places operational and economic strain on hospitals. This patient population experiences a considerable burden of infection and of hospital acquired pneumonia
📗https://ow.ly/rtrI50XkTHb
📗https://ow.ly/rtrI50XkTHb
Reposted by Kyle Gontjes
New multi-society implementation and practice recs for IPC in nursing homes.
How to balance safety and home-like care. An essential resource for IPC program leaders
with SHEA, APIC, IDSA, PALTmed, PIDS
#IDsky
📄: doi.org/10.1017/ice....
How to balance safety and home-like care. An essential resource for IPC program leaders
with SHEA, APIC, IDSA, PALTmed, PIDS
#IDsky
📄: doi.org/10.1017/ice....
October 28, 2025 at 2:28 PM
New multi-society implementation and practice recs for IPC in nursing homes.
How to balance safety and home-like care. An essential resource for IPC program leaders
with SHEA, APIC, IDSA, PALTmed, PIDS
#IDsky
📄: doi.org/10.1017/ice....
How to balance safety and home-like care. An essential resource for IPC program leaders
with SHEA, APIC, IDSA, PALTmed, PIDS
#IDsky
📄: doi.org/10.1017/ice....
Reposted by Kyle Gontjes
See how much your state benefited economically from NIH in FY2024 here via report from UMR 👀⤵️ @atrupar.com
📄: www.unitedformedicalresearch.org/wp-content/u...
📄: www.unitedformedicalresearch.org/wp-content/u...
July 28, 2025 at 12:21 AM
See how much your state benefited economically from NIH in FY2024 here via report from UMR 👀⤵️ @atrupar.com
📄: www.unitedformedicalresearch.org/wp-content/u...
📄: www.unitedformedicalresearch.org/wp-content/u...
Reposted by Kyle Gontjes
Our paper reporting a highly conserved mechanism by which arginine positively regulates hypervirulent K. pneumoniae mucoid phenotype is now fully online.
rdcu.be/euiWG
Summary picture is below, but details in the 🧵
rdcu.be/euiWG
Summary picture is below, but details in the 🧵
July 1, 2025 at 2:27 PM
Our paper reporting a highly conserved mechanism by which arginine positively regulates hypervirulent K. pneumoniae mucoid phenotype is now fully online.
rdcu.be/euiWG
Summary picture is below, but details in the 🧵
rdcu.be/euiWG
Summary picture is below, but details in the 🧵
Reposted by Kyle Gontjes
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
June 30, 2025 at 12:26 PM
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
Excited to share a preview of our work using phylogenetics to characterize the emergence and spread of antibiotic resistance!
Phylogenetic context of antibiotic resistance provides insights into the dynamics of resistance emergence and spread https://www.medrxiv.org/content/10.1101/2025.06.04.25328982v1
June 9, 2025 at 1:09 PM
Excited to share a preview of our work using phylogenetics to characterize the emergence and spread of antibiotic resistance!
Reposted by Kyle Gontjes
New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
May 8, 2025 at 9:24 PM
New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...
Reposted by Kyle Gontjes
Our paper on how integrons are biobanks of novel minimal defense systems is now out www.science.org/doi/10.1126/... Two main conclusions on this excellent work led by @eloilittner.bsky.social @baptistedarracq.bsky.social 1/n
May 9, 2025 at 1:07 PM
Our paper on how integrons are biobanks of novel minimal defense systems is now out www.science.org/doi/10.1126/... Two main conclusions on this excellent work led by @eloilittner.bsky.social @baptistedarracq.bsky.social 1/n
Reposted by Kyle Gontjes
Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance https://www.biorxiv.org/content/10.1101/2025.05.06.652565v1
May 8, 2025 at 4:17 AM
Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance https://www.biorxiv.org/content/10.1101/2025.05.06.652565v1
Reposted by Kyle Gontjes
An atlas of metabolites driving chemotaxis in prokaryotes
This database compiles the effects (attractant, repellent or neutral) of 926 compounds and the chemotactic behaviour of 394 strains
#ChemicalBiology #Microbiology
This database compiles the effects (attractant, repellent or neutral) of 926 compounds and the chemotactic behaviour of 394 strains
#ChemicalBiology #Microbiology
An atlas of metabolites driving chemotaxis in prokaryotes - Nature Communications
In this meta-analysis, the authors compile results from 60 years of chemotaxis research into a database of prokaryotic chemoeffectors that compares and analyses their effects as attractant, repellent or neutral compounds, as well as the chemotactic behaviour of responding microorganisms.
bit.ly
May 8, 2025 at 12:51 PM
An atlas of metabolites driving chemotaxis in prokaryotes
This database compiles the effects (attractant, repellent or neutral) of 926 compounds and the chemotactic behaviour of 394 strains
#ChemicalBiology #Microbiology
This database compiles the effects (attractant, repellent or neutral) of 926 compounds and the chemotactic behaviour of 394 strains
#ChemicalBiology #Microbiology
Reposted by Kyle Gontjes
A new human study in @nature.com explores the evolution of resistance in gut commensals driven by brief antibiotic exposure.
#MicroSky #AMR 🦠
Read here:
www.nature.com/articles/s41...
#MicroSky #AMR 🦠
Read here:
www.nature.com/articles/s41...
Brief antibiotic use drives human gut bacteria towards low-cost resistance - Nature
Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure a...
www.nature.com
April 30, 2025 at 1:48 PM
A new human study in @nature.com explores the evolution of resistance in gut commensals driven by brief antibiotic exposure.
#MicroSky #AMR 🦠
Read here:
www.nature.com/articles/s41...
#MicroSky #AMR 🦠
Read here:
www.nature.com/articles/s41...
Reposted by Kyle Gontjes
Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact
✅ Just Accepted
⭐ Editor's Choice
✍️ @sundermannaj.bsky.social
#IDSky
✅ Just Accepted
⭐ Editor's Choice
✍️ @sundermannaj.bsky.social
#IDSky
Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact
Current methods are insufficient alone for outbreak detection in hospitals. Real-time genomic surveillance offers the potential to detect otherwise unidentified outbreaks.
doi.org
May 3, 2025 at 6:58 PM
Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact
✅ Just Accepted
⭐ Editor's Choice
✍️ @sundermannaj.bsky.social
#IDSky
✅ Just Accepted
⭐ Editor's Choice
✍️ @sundermannaj.bsky.social
#IDSky
👋 Hi, y'all!
A bit about me:
1️⃣ 5th-year PhD candidate in Microbiology & Immunology at @uofmichigan.bsky.social 🦠
2️⃣ Study drivers of resistance emergence and spread in Dr. Evan Snitkin's lab 💊
3️⃣ Conducted infection prevention research during my MPH with Dr. Lona Mody @uofmcriisplab.bsky.social 😷🧤
A bit about me:
1️⃣ 5th-year PhD candidate in Microbiology & Immunology at @uofmichigan.bsky.social 🦠
2️⃣ Study drivers of resistance emergence and spread in Dr. Evan Snitkin's lab 💊
3️⃣ Conducted infection prevention research during my MPH with Dr. Lona Mody @uofmcriisplab.bsky.social 😷🧤
May 2, 2025 at 5:43 PM
👋 Hi, y'all!
A bit about me:
1️⃣ 5th-year PhD candidate in Microbiology & Immunology at @uofmichigan.bsky.social 🦠
2️⃣ Study drivers of resistance emergence and spread in Dr. Evan Snitkin's lab 💊
3️⃣ Conducted infection prevention research during my MPH with Dr. Lona Mody @uofmcriisplab.bsky.social 😷🧤
A bit about me:
1️⃣ 5th-year PhD candidate in Microbiology & Immunology at @uofmichigan.bsky.social 🦠
2️⃣ Study drivers of resistance emergence and spread in Dr. Evan Snitkin's lab 💊
3️⃣ Conducted infection prevention research during my MPH with Dr. Lona Mody @uofmcriisplab.bsky.social 😷🧤
Reposted by Kyle Gontjes
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
May 1, 2025 at 6:41 PM
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]