Rhys White
@rhystwhite.bsky.social
Scientist | Turning #Genomics into intelligence | Tracking pathogen evolution, diversity, & spread | Welsh expat in New Zealand | Formerly The University of Queensland
If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!
Phage Annotation Server -- phage genome annotation
Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.
phage-annotation.org
Removing coordinate-defined regions from phylogenomic matrices is simple in principle, but editing errors can alter the matrix. NEXCISION provides exact, validated excision from transposed NEXUS matrices 🔗 github.com/RhysWhite/ne... Feedback welcome #Bioinformatics 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
GitHub - RhysWhite/nexcision: Precise region-based excision of coordinate-labelled rows from NEXUS matrices.
Precise region-based excision of coordinate-labelled rows from NEXUS matrices. - RhysWhite/nexcision
github.com
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2mo agoNEXCISION: exact, validated, and scalable excision of genomic regions from phylogenomic NEXUS matrices https://www.biorxiv.org/content/10.64898/2026.07.26.740842v1
We’re using @nanoporetech.com in a frontline lab 157 K. pneumoniae genomes later: No evidence of patient-patient transmission 👉connected genomics👈 Frontline WGS, linked with national public health & bioinformatics expertise www.doi.org/10.1099/mgen... 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics 📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing www.doi.org/10.1099/mgen.0.001644 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem res...
doi.org
It’s 2026. If you submit a #Genomics paper without making the underlying sequence data publicly available, reproducibility is... 👉I M P O S S I B L E👈 #OpenScience data isn’t optional. It’s foundational to #PublicHealth, benchmarking & scientific credibility 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
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media.tenor.com
From a neonatal ICU in Wellington to clinics in Africa & Europe: a new Global Health Now feature shows how onsite @nanoporetech.com sequencing is shaping #InfectionPrevention… helping deliver answers in hours not weeks - turning #Genomic into real-world action 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
Global Health NOW@globalhealthnow.bsky.social · 8mo agoFaster, cheaper technologies that can do onsite genome sequencing are improving pathogen surveillance in lower-income settings.
🧵BIG PROBLEMS can hide in small #Plasmids 📌Integration of blaOXA-48 into a Col156 plasmid drove a carbapenem-resistant Escherichia coli ST131 outbreak in New Zealand: Global genomic evidence for the gene’s multilayered dissemination doi.org/10.1016/j.dr... 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
Redirecting
doi.org
Genomics isn’t just solving #Outbreaks, it’s stopping them before they escalate HOT take from @natrevmicro.nature.com: If you only sequence #MDR outbreaks, you’re already late. Consider susceptible strains & #Plasmids #GenomicSurveillance #InfectionControl 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
Nature Reviews Microbiology@natrevmicro.nature.com · 10mo agoNew online! Genome sequencing for prevention of health-care-associated bacterial infections
⚠️ What is measles (Te mate karawaka)? A HIGHLY contagious virus that spreads through the air. People are infectious before the rash shows Learn more 👉 info.health.nz/conditions-t... 😷💉 #Measles #MMR #VaccinesWork #Aotearoa #PublicHealth
Measles in #NZ Check locations & what to do👉 info.health.nz/conditions-t... Symptoms or exposure? ☎️Call Healthline 0800 611 116 Not immune? Get MMR (2 doses, 1 month apart) Book👉 app.bookmyvaccine.health.nz #Measles #MMR #VaccinesWork #Aotearoa #PublicHealth
info.health.nz
Health New Zealand | Te Whatu Ora@healthnz.govt.nz · 11mo agoIt’s Measles Immunisation Week! 🛡️ 📲 Visit info.health.nz/immunisations/immunisation-clinics for pop up clinics near you where you can get your MMR vaccination. You can also check healthpoint.co.nz. Another option is to book online: info.health.nz/bookavaccine
🚨New paper out! Why does Staphylococcus aureus ST1 dominate in BOTH people🧑⚕️ & cows🐄 in New Zealand… but rarely elsewhere? Our latest comparative genomics study unpacks this mystery👇 📄 doi.org/10.1128/msph... @asm.org #AMR #Genomics #OneHealth 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
Comparative genomics of endemic Staphylococcus aureus ST1 in New Zealand | mSphere
This study presents a comprehensive genomic analysis of S. aureus ST1, a lineage that is unusually dominant in both bovine and human populations in New Zealand. Leveraging New Zealand’s geographical i...
doi.org
🚨Call for abstracts #OneHealth Aotearoa Symposium 2025 📍Wellington + online 🗓️2–3 Dec 2025 Submit an abstract by 30 Sept Themes: #AMR, #Zoonoses, #HealthEquity, #TeAoMāori, #ClimateHealth & more More info👉 onehealth.org.nz/one-health-a... 📩one.health@otago.ac.nz 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
One Health Aotearoa Symposium 2025 - One Health Aotearoa
Our 11th annual symposium will be held on 2-3 December 2025 at the University of Otago, Wellington campus and online. Registrations will open soon! Venue Information Nordmeyer Lecture Theatre – Univer...
onehealth.org.nz
Honoured to present this at #MicroSeq2025💙 This work reflects contributions from MANY colleagues across institutions & I'm grateful for the opportunity to share it Published in @microbiologysociety.org: doi.org/10.1099/mgen... Also in @aunz.theconversation.com: theconversation.com/antibiotic-u...
20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus
Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant public health challenge. In New Zealand, the community-associated MRSA sequence type (ST)5, carrying the staphylococcal cass...
doi.org
MicroSeq2026@microseqasm.bsky.social · last yr.🦠Our first medium talk of #MicroSeq2025 Day 2 is @rhystwhite.bsky.social talking about the #evolution of a methicillin-resistant #Staphylococcus aureus strain, uncovering the genomic and environmental factors contributing to its #emergence and spread. #bacteria #phylogeny
New Zealand’s prescribing habits likely helped create a homegrown #MRSA 🇳🇿🧬💊 Now ‘AK3’ has been detected overseas Our recent study shows how it evolved & how #Genomics can help reduce the impact of the next ‘superbug’ #AMR is an issue for everyone #SciComm 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
The Conversation AUNZ@aunz.theconversation.com · last yr.Over-subscription of a topical antibiotic likely led to the emergence of a superbug which is now the leading cause of resistant infections.
💥How New Zealand's previous 'go-to' #Antibiotic fuelled the rise of a home-grown #MRSA superbug By the 2010s, AK3 took the lead as NZ’s top #MRSA strain, fuelled by years of high fusidic acid use #AntibioticResistance #PublicHealth doi.org/10.1099/mgen... 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus
Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant public health challenge. In New Zealand, the community-associated MRSA sequence type (ST)5, carrying the staphylococcal cass...
doi.org
Peer-reviewed evidence that @nanoporetech.com & #DoradoCorrect (HERRO) can resolve a NICU #MRSA outbreak to SNV precision - no short reads needed (so long as adequate n50 read lengths are met) Fast, decentralised, clinically useful 🔗 doi.org/10.1016/j.jh... #Genomics #PHFScience #InfectionControl
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Absolutely delighted to share the labs latest work. We identify and characterise two pathways for D-ribulose utilisation in pathogenic EHEC and Citrobacter.
Convergent evolution of distinct D-ribulose utilisation pathways in attaching and effacing pathogens - Nature Communications
Cottam et al. identify distinct pathways for D-ribulose utilisation in pathogenic Escherichia coli and Citrobacter rodentium, providing mechanistic details and suggesting convergent evolution towards ...
nature.com
Out & #OpenAccess 📌Community outbreak of OXA-48–producing Escherichia coli linked to food premises, New Zealand, 2018-2022 doi.org/10.3201/eid3... Thanks to folks across NZ who helped investigate & respond #AMR #PublicHealth #Genomics #Epidemiology #Scicomm 🧵 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
Community Outbreak of OXA-48–Producing <em>Escherichia coli</em> Linked to Food Premises, New Zealand, 2018–2022
Outbreak of OXA-48–Producing <em>E. coli</em>, New Zealand
doi.org
One patient, two samples Weeks apart, E. faecium picked up vancomycin resistance By sequencing vancomycin-susceptible strains on-site, we caught this early & avoided unnecessary, disruptive interventions #Genomics Proud to share at #nanoporeconf! @nanoporetech.com 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
Attending #ESCMIDGlobal & curious about community-associated CPE? Craig Thornley is presenting today on a prolonged OXA-48-producing E. coli cluster in New Zealand, with genomic evidence supporting community & hospital transmission. See poster E0434 #ESCMIDGlobal2025 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
Hospital infections are a problem & 'go-to' methods have limits. We trailed @nanoporetech.com in outbreak detection & response 📌Implementing nanopore sequencing in a clinical laboratory: a social systems case study | NZ J Med Lab Sci issuu.com/sharontozer/... 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
NZJMLS V.79 N0. 1 March 2025
New Zealand Journal of Medical Laboratory Science. Volume 79, Number 1, March 2025
issuu.com
📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays doi.org/10.1101/2025... 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory
Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates dela...
doi.org
K. variicola can be misID as K. pneumoniae. Our #OpenAccess paper reports an NICU #Outbreak 📌The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing doi.org/10.1186/s137... @nanoporetech.com 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠
The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing - Antimicrobial Resistance & Infection Control
Background Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as Klebsiella pneumoniae. An increased incidence of K. pneumoni...
doi.org
Amazing work by the NZ MPI team - the full genome from the HPAI H7N6 detection is now available on GISAID. Further information on the impacts and control actions can be found here: bit.ly/4iy3O8n
Situation update H7N6 bird flu detection Otago – 4 December 2024 | NZ Government
Biosecurity New Zealand is taking further action today to stamp out a high pathogenic strain of avian influenza, H7N6, detected on a commercial egg farm in rural Otago. "Work started this morning to h...
bit.ly
Kia ora koutou! 👋 I’ve put together a starter pack of amazing people working in #Genomics across Aotearoa New Zealand. If I’ve missed anyone, please let me know! go.bsky.app/KhMbQxK
NEW Publication!😄 Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more! 🔗: tinyurl.com/yc5ja4xz
Day 6 of @who.int World #AntimicrobialAwarenessWeek: AMR isn't just a global crisis—it has local consequences🌏 It’s not just about humans. #AMR affects animals, the environment & everything in between. To truly understand AMR, we need to see how these 3 are connected #OneHealth #WAAW🧵👇🧪 #WAAW2024
Day 5 of the @who.int World #AntimicrobialAwarenessWeek. We've covered what #AntibioticResistance is & how it spreads. But how do bacteria resist #Antibiotics? From modifying drug targets to producing enzymes that break down antibiotics, here are some common #AMR mechanisms🧵🧪 #WAAW #WAAW2024
Day 4 of the @who.int World #AntimicrobialAwarenessWeek: Composite transposons are another way #AntimicrobialResistance genes spread. These ‘jumping genes’ move resistance genes within & between bacterial DNA, increasing bacterial resistance to #Antibiotics! 🧵👇 #WAAW2024 #AMR 🧪
