Ken Koon Wong
kenkoonwong.bsky.social
Ken Koon Wong
@kenkoonwong.bsky.social
data science enthusiast #rstats. infectious disease provider. lazy gardener. tai chi practitioner. life long learner. views are my own. RT or like != endorsement. https://www.kenkoonwong.com/
Pinned
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they’re just weighted combo of basis functions that make non-linear regression linear. What surprised me is going through Bayesian statistics helped me understand the engine behind the model! #rstats
Understanding Basis Spline (B-spline) By Working Through Cox-deBoor Algorithm | Everyday Is A School Day
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they're just weighted combinations of basis functions that make non-linear regression linear. What ...
www.kenkoonwong.com
Reposted by Ken Koon Wong
Five subphenotypes of Staphylococcus aureus bacteremia (SAB) were identified in diverse cohorts: 40.2% had MRSA. 90-day mortality was highest in subphenotype A. 🦠💔##idsky
Reproducible identification of Staphylococcus aureus bacteremia clinical subphenotypes
Clinical heterogeneity in Staphylococcus aureus bacteremia (SAB) complicates clinical management and research. We have previously identified five clinically distinct subphenotypes of SAB associated with differences in outcomes and response to adjunctive rifampicin. Here, we aimed to identify these subphenotypes in geographically diverse observational cohorts, including a higher prevalence of methicillin-resistant S. aureus (MRSA) bacteremia and the USA300 clone.MethodsWe studied three cohorts of adults with SAB from observational studies: a UK retrospective study (Edinburgh cohort 2, n=463); a Dutch prospective study (IDISA, n=490); and a USA prospective study (SABG-PCS, n=755). Subphenotypes were identified from routinely available clinical data using latent class analysis.ResultsPatients from the SABG-PCS cohort had greater multimorbidity and more MRSA bacteremia (40.2%, 303/755), including infection with the USA300 clone (14.7%, 111/755). Five distinct subphenotypes were identified in each cohort: (A) older age and cardio-metabolic multimorbidity; (B) nosocomial acquisition and intravenous catheter portal of entry; (C) community acquisition and metastatic infection; (D) chronic kidney disease; and (E) younger age, injection drug use, and metastatic infection. Bacterial genotypes varied substantially between the Edinburgh 2 and SABG-PCS cohorts but did not differ between subphenotypes within each cohort. 90-day mortality was highest in subphenotype A, and persistent bacteremia in subphenotypes C and E.ConclusionsWe have reproducibly identified five clinical subphenotypes of SAB in observational cohorts including diverse bacterial genetic lineages and a cohort with a high prevalence of MRSA and USA300 bacteremia. These robustly reproducible clinical subphenotypes provide a framework to rationalize the heterogeneity intrinsic to SAB.
academic.oup.com
November 27, 2025 at 11:30 PM
Reposted by Ken Koon Wong
Study on VGEI in 97 rats showed FDG-PET could differentiate untreated S. aureus infections but not monitor progression. SUVmax declined over time despite constant bacterial load. 📉🦠##idsky
[18F]Fluorodeoxyglucose Positron Emission Tomography for diagnosis and monitoring of acute Staphylococcus aureus vascular graft infection in a rat model
AbstractObjectivesVascular graft or endograft infections (VGEI) pose a detrimental complication when using vascular grafts and are challenging to diagnose and treat. This study examined the progression of infection and the antimicrobial response in VGEI using [18F]Fluorodeoxyglucose (FDG) Positron Emission Tomography (PET), ex vivo bacterial quantification, and histology in a VGEI rat model.MethodsIn this experimental study, 97 male Sprague-Dawley rats had a polytetrafluorethylene graft surgically implanted in the carotid artery. The graft was either pre-inoculated with Staphylococcus aureus, Staphylococcus epidermidis, or saline. Up to 31 days after surgery, rats were FDG-PET-scanned. Subsequently, they were euthanised, and the implants were retrieved for analysis. A subgroup of infected rats received daptomycin and rifampicin from days 20 to 29.ResultsTracer uptake around the implant, measured by maximum standardised uptake value (SUVmax), declined over time in all groups. Between groups, SUVmax was highest in untreated S. aureus-infected rats. When comparing antibiotic-treated and uninfected rats by day 31, there was no difference in SUVmax, although the treated rats were still infected.Histology revealed widespread inflammation by day 10 in S. aureus-infected rats, which decreased by days 20 and 31 with encapsulation of the infection, alongside increased plasma interleukin-10.ConclusionsFDG-PET differentiated untreated S. aureus-infected rats from uninfected ones but failed to monitor infection progression, as SUVmax declined over time despite a constant bacterial load.FDG-PET could not distinguish between uninfected rats and those with suppressed infection, likely due to reduced inflammation and encapsulation of the infection.
academic.oup.com
November 27, 2025 at 1:30 PM
Reposted by Ken Koon Wong
Study of 336 PABSI patients: 30.1% had 90-day mortality. No difference in outcomes based on gallbladder presence. Liver disease linked to higher mortality. Antimicrobial resistance similar in both groups.##idsky
Impact of Remote Cholecystectomy on Clinical Outcomes Following Pseudomonas aeruginosa Bloodstream Infection
Mortality associated with Pseudomonas aeruginosa bloodstream infection (PABSI) remains high despite advances in clinical care and therapeutics. In a recent study using a mouse model of PABSI, the gallbladder was identified as a reservoir for bacterial expansion. Furthermore, bile exposure has been linked to increased antimicrobial resistance. Therefore, we asked whether patients with retained gallbladders might experience more antimicrobial-resistant PABSIs, extended culture positivity, and worsened clinical outcomes.MethodsWe conducted a retrospective cohort study of adults hospitalized over a 5-year period with PABSI. PABSI cases were defined as patients with ≥1 positive P. aeruginosa bacterial culture from the blood. Patients were categorized as those retaining a gallbladder (no cholecystectomy) or not (cholecystectomy). Cholecystectomy was defined as a history of cholecystectomy ≥1 year prior to the index episode of PABSI. Inferential statistics were used to identify associations between remote cholecystectomy and antimicrobial resistance profile, length of blood culture positivity, and in-hospital and 90-day mortality.ResultsThe overall study population included 336 patients: 262 (78%) with a retained gallbladder and 74 (22%) without. Using the entire study population and a matched cohort, we observed no difference in length of culture positivity, 90-day mortality, or in-hospital mortality between groups based on the presence of a gallbladder. Overall, composite 90-day mortality was 30.1%, which was similar to a prior investigation of PABSI outcomes at our institution. While the presence of a gallbladder did not affect the outcome, patients with PABSI and liver disease had significantly higher 90-day mortality than those without liver disease. Furthermore, no robust differences were observed in the antimicrobial resistance profile of P. aeruginosa isolates from the group with or without a gallbladder.ConclusionsIn our study, neither PABSI antimicrobial resistance pattern nor clinical outcomes were affected by remote cholecystectomy. However, we do demonstrate that mortality for patients with PABSI in the modern era remains high despite advances in antipseudomonal therapeutics.
academic.oup.com
November 27, 2025 at 2:30 AM
Reposted by Ken Koon Wong
Febrile neutropenia poses risks for patients with hematological malignancies. The 10th European Conference recommends personalized treatment based on local resistance patterns. Empirical monotherapy is advised in low-resistance settings.##idsky
[Review] Empirical and targeted antimicrobial therapy in patients with febrile neutropenia and haematological malignancy or after haematopoietic cell transplantation: recommendations from the 10th European Conference on Infections in Leukaemia
Febrile neutropenia can lead to life-threatening infections in patients with haematological malignancies or after hematopoietic cell transplantation. Infection management is challenged by rising antibiotic resistance and regional differences in bacterial epidemiology. The 10th European Conference on Infections in Leukaemia panel recommends a personalised approach guided by local resistance patterns and individual risk factors. For patients who are haemodynamically stable without colonisation or infection by resistant Gram-negative bacteria in low-resistance prevalence settings, empirical monotherapy sparing carbapenems or novel β-lactams with or without β-lactamase inhibitors (BLI) is recommended.
www.thelancet.com
November 26, 2025 at 12:00 PM
Reposted by Ken Koon Wong
Kleb4V, a tetravalent vaccine for antibiotic-resistant K. pneumoniae, was tested on 166 adults. It was well tolerated, showing strong immune responses for 3 of 4 serotypes. 💉✨##idsky
Safety and immunogenicity of a Klebsiella pneumoniae tetravalent bioconjugate vaccine (Kleb4V) administered to healthy adults: A first time in human phase I/II randomised and controlled study
Safe and effective vaccines are urgently needed to prevent infections caused by Klebsiella pneumoniae (K. pneumoniae), one of the most common antibiotic-resistant pathogens. We aimed to assess the safety and immunogenicity of a tetravalent bioconjugate vaccine Kleb4V, containing O antigen-polysaccharides of the most predominant K. pneumoniae serotypes (O1v1, O2a, O2afg and O3b).MethodsIn this observer-blind, randomised, placebo-controlled, phase I/II trial [ClinicalTrials.gov (number NCT04959344)], 166 healthy adults (18-40y n=16, 55-70y n=150) were enrolled and randomised to receive two intramuscular injections of Kleb4V (16μg or 64μg of total O-antigen +/- adjuvant AS03) or placebo on days 1 and 57. While the primary outcome was safety, the secondary outcomes included vaccine antigen immunogenicity.ResultsKleb4V was well tolerated, with most solicited and unsolicited AEs of mild to moderate intensity. Kleb4V was immunogenic for all four vaccine-serotypes at both antigen doses. O1v1, O2a and O2afg specific IgG increased two weeks after the 1st vaccination and the immune response persisted at six months after the second vaccination. For three of the four vaccine-serotypes, the AS03-adjuvanted formulations showed a superior immune response. O3b responses were reduced compared to the other vaccine antigens.DiscussionKleb4V is the first K. pneumoniae conjugate vaccine candidate to reach clinical assessment. The Kleb4V bioconjugate was immunogenic, well tolerated and with an acceptable safety profile in the target population of adults aged 55-70 years for all 4 vaccine-serotypes.
academic.oup.com
November 27, 2025 at 12:30 AM
Reposted by Ken Koon Wong
In a phase 2a, randomized trial, oral treatment with high-dose mosnodenvir, a pan–DENV serotype antiviral drug, led to a significantly lower DENV-3 RNA load than placebo after challenge in a controlled human infection model. Full trial results: nej.md/48eUJwJ

#MedSky #IDSky
November 26, 2025 at 10:10 PM
Reposted by Ken Koon Wong
AI-assisted review for CLABSI detection showed 93.2% accuracy vs. 90% AI-alone and 88.2% expert review. It took 14 mins vs. 25 mins for experts. AI was preferred in 52% cases. 🏥💻✨##idsky
Using generative artificial intelligence to identify central line-associated bloodstream infections
Central line-associated blood stream infection (CLABSI) surveillance is mandated and publicly reported in United States hospitals but requires manual chart review. Generative artificial intelligence (AI) may facilitate CLABSI identification.MethodsWe performed a retrospective cohort study of CLABSI surveillance using standardized prompts, clinical data, and Centers for Disease Control and Prevention definitions. In 11 hospitals, 24 infection control (IC) nurses and physicians retrospectively reviewed 220 CLABSI/non CLABSI bacteremias. Three methods of review were compared to original facility expert review: 1) AI-assist review, 2) AI-alone review, and 3) repeat expert review. Disagreement between any method of review was adjudicated by a 2-expert physician referee panel.ResultsAI-assist review had a 93.2% (205/220, 95% CI: 89.0–96.1) overall accuracy (agreement with facility reporting or refereeing panel) vs. AI-alone review, 90.0% (198/220, 95% CI: 85.3–93.6) overall accuracy or repeat expert review, 88.2% (97/110, 95% CI: 80.1–93.6) overall accuracy. Inter-site variability was greater for repeat expert review than AI-assist. AI-assist review required a median of 14 minutes (interquartile range, IQR 6-25.5) vs. 25 minutes (IQR 11-43) for repeat expert (p = 0.0001). AI-assist review was reported as low effort in 52% of cases vs. 21% of repeat expert cases (p < 0.0001). AI-assist review was reported as somewhat or very objective in 72% of cases vs. 61% of repeat expert cases (p=0.092).ConclusionsCLABSI detection by AI methods was at least as accurate as traditional methods, better liked by experts, faster and less variable. AI-assisted review could improve healthcare-associated infection reporting.
academic.oup.com
November 23, 2025 at 2:30 PM
Reposted by Ken Koon Wong
Study of 196 households (623 participants) showed no difference in SSTI incidence after 3 months. Integrated-Approach reduced SSTIs at 6-9 months for those with prior SSTIs. 📉##idsky
Evaluating Personal and Environmental Decolonization Strategies for Children with Skin and Soft Tissue Infection and Their Households – A Randomized Clinical Trial
Staphylococcus aureus colonization predisposes to skin and soft tissue infection (SSTI). Given the waning effectiveness of decolonization, we evaluated periodic personal decolonization and household environmental decontamination to reduce SSTIs among households affected by S. aureus.MethodsHouseholds of children with community-associated S. aureus SSTI participated in an open-label randomized trial. After baseline decolonization, households were randomized 1:1:1 to a 3-month decolonization intervention: 1) Periodic-Personal (twice weekly chlorhexidine bathing and monthly intranasal mupirocin application); 2) Environmental-Hygiene (weekly household surface disinfection and enhanced laundry measures); or 3) Integrated-Approach of both Periodic-Personal and Environmental-Hygiene. Over 9 months, participants and household surfaces were sampled at 5 study visits to detect S. aureus; SSTI incidence was recorded. The primary outcome was household-level cumulative SSTI at 3 months, comparing the Integrated-Approach to the combined Personal-Periodic and Environmental-Hygiene groups.ResultsBetween 2015-2021, 196 index patients and their household contacts (n=623) were enrolled. Cumulative SSTI incidence did not differ between groups during the 3-month intervention. In index patients and household contacts with SSTI in the year prior to enrollment, SSTI incidence was lower among the Integrated-Approach at 6- and 9-months compared to the combined Periodic-Personal and Environmental-Hygiene groups. In multivariable analyses, prior year SSTI was associated with subsequent SSTI; intervention group was not significant. All interventions reduced MRSA, but not MSSA, personal colonization over 9 months.ConclusionsWhile an Integrated-Approach of prolonged personal and environmental decolonization reduced SSTIs among participants with prior year SSTI, prior SSTI strongly predicted SSTI incidence longitudinally. Novel prevention strategies are needed.
academic.oup.com
November 24, 2025 at 12:30 PM
Finally understood TMLE’s “doubly robust” property through simulation. Works well when either outcome OR treatment model is correct. XGBoost + TMLE captured complex relationships without manual specification. It worked on simulated complex data, would it work in real world? 🤔 #rstats #idsky #episky
Bias, Variance, and Doubly Robust Estimation: Testing The Promise of TMLE in Simulated Data | Everyday Is A School Day
Finally understood TMLE's "doubly robust" property through simulation. Works well when either outcome OR treatment model is correct. XGBoost + TMLE captured complex relationships without manual specif...
www.kenkoonwong.com
November 17, 2025 at 1:55 AM
#IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so much from our SoMe community! 📊💙🙏

#idsky
#IDWeek2025 Posts/Tweets Analysis | Everyday Is A School Day
IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so mu...
www.kenkoonwong.com
October 27, 2025 at 1:32 AM
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it

#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
My Attempt To Reproduce Stanford HIVdb Sequence and Mutation Analysis From Scratch | Everyday Is A School Day
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford's HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But th...
www.kenkoonwong.com
October 11, 2025 at 3:51 AM
Learned RNA-seq workflow using C. diff data from a study 🧬. Processed raw reads thru fastp → kallisto → DESeq2 pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.

#idsky #microsky #rstats #deseq2 #bioconductor
Learning And Exploring The Workflow of RNA-Seq Analysis - A Note To Myself | Everyday Is A School Day
Learned RNA-seq workflow using C. difficile data from a published study 🧬. Processed raw reads through fastp → kallisto → DESeq2 pipeline. Results matched the original paper's findings, with clear dif...
www.kenkoonwong.com
September 27, 2025 at 9:00 PM
Hands-on with @nanoporetech.com workflow: pod5 → BAM → assembly -> polish! Processed M. tuberculosis from raw signals to complete genome using #dorado + #samtools + #flye. Fascinating how thousands of contigs became one 4M+ bp sequence.

#idsky #tbsky #microsky #bioinformatics
Exploring The Workflow of The Oxford Nanopore Technologies (ONT) from pod5 to Polished Asembly - A Note To Myself | Everyday Is A School Day
Hands-on with Oxford Nanopore workflow: pod5 → BAM → assembly! Processed M. tuberculosis from raw signals to complete genome using dorado + flye. Fascinating how thousands of contigs became one 4M+ bp...
www.kenkoonwong.com
September 21, 2025 at 4:50 PM
Reposted by Ken Koon Wong
Come join #IDSky at the unofficial @idweek.bsky.social Social Media Meet-Up!

All are welcome.
September 16, 2025 at 1:55 AM
Reposted by Ken Koon Wong
Join us this #IDWeek2025 for a SoMe meet-up! One of the highlights every year of the conference is meeting all of you! #IDSky
Come join #IDSky at the unofficial @idweek.bsky.social Social Media Meet-Up!

All are welcome.
September 16, 2025 at 2:40 AM
We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study www.cdc.gov/mmwr/volumes... using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined!

#idsky #microsky #rstats
Learning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) - A Note To Myself | Everyday Is A School Day
We learnt how to assemble DNA fragments from a recently published *N. meningitidis* outbreak study using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explo...
www.kenkoonwong.com
September 15, 2025 at 11:06 PM
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working thru scoring matrices w simple examples like "CAT" vs "CT" before testing on E. coli sequences. Pretty neat to see the magic! ✨

#microsky #idsky #bioconductor #rstats
Building DNA Sequence Alignment With Needleman-Wunsch Algorithm From Scratch - A Note To My Self | Everyday Is A School Day
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working through scoring matrices by hand with simple examples like "CAT" vs "CT" ...
www.kenkoonwong.com
September 7, 2025 at 8:00 PM
Reposted by Ken Koon Wong
There have been many documented meningococcal meningitis outbreaks.

Here we describe our investigation and response to the first documented meningococcal conjunctivitis outbreak. 🧫

Contributions by 🌟🌟🌟 fellows @sucroselauren.bsky.social @ogallardo.bsky.social
#IDSky

www.cdc.gov/mmwr/volumes...
Outbreak of Neisseria meningitidis Conjunctivitis ...
This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.
www.cdc.gov
September 4, 2025 at 10:05 PM
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with #rstats #bioconductor. Learnt to work with large genomic data. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, barrnap for extraction, rapidNJ for tree building & FigTree for visualization.

#microsky #idsky
Learning The Basics of Phylogenetic Analysis | Everyday Is A School Day
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with R/Bioconductor. Learnt to work with large genomic dataset. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, ...
www.kenkoonwong.com
August 31, 2025 at 3:07 PM
Instead of flashcards, we Rube Goldberg’d this with #Bioconductor ! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gene nomenclature and sequence analysis! 📊🔬

#idsky #microsky #amr #rstats
Learning Antimicrobial Resistance (AMR) genes with Bioconductor | Everyday Is A School Day
Instead of flashcards, we Rube Goldberg'd this with Bioconductor! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gen...
www.kenkoonwong.com
August 15, 2025 at 10:12 PM
Learn how to build a flash-card style question bank using Google Sheets as storage, #rstats Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.

#idsky #medsky #meded
Creating A Question Bank Using Google Sheet, Plumber, and Digital Ocean Droplet | Everyday Is A School Day
Learn how to build a flash-card style question bank using Google Sheets as storage, R’s Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.
www.kenkoonwong.com
June 18, 2025 at 6:24 PM
Reposted by Ken Koon Wong
Our review on hierarchical composite endpoints (HCEs) has just been published in @cidjournal.bsky.social:
doi.org/10.1093/cid/...

We provide a conceptual overview of HCEs, explain the different associated target parameters and analytic methods.

@steventong.bsky.social @gurujosh.bsky.social
Making sense of hierarchical composite endpoints in randomized clinical trials – a primer for infectious disease clinicians and researchers
Hierarchical composite endpoints (HCEs) are increasingly being used in infectious diseases research. In this review aimed at educating the clinical reader,
doi.org
June 16, 2025 at 1:55 AM
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function.

Confusing? Yes! Rewarding? Oh yes!

#rstats
From Math to Code: Building GAM with Penalty Functions From Scratch | Everyday Is A School Day
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function. Confusing? Yes! Rewarding? Oh yes!
www.kenkoonwong.com
June 12, 2025 at 1:52 AM
Wow!!! You can do combo abx too!?!? Amazing!
Congratulations to Matthijs Berends and team for the release of the AMR for R package version 3!

I've been using this package to produce the AGAR Kids reports and can highly recommend.

amr-for-r.org

#Rstats #AMR #IDEpi #MedSky
June 8, 2025 at 12:53 PM
Just listened to this. Awesome insights!
June 4, 2025 at 11:47 AM