Thanks @gringene.org. The Mk1D was the @nanoporetech.com hardware used in this study; the R10.4.1 flow cell chemistry remains current, as stated in the paper.
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
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Reviewers can’t assess data quality, mixtures, coverage, or assembly robustness without access to the sequence data.
Peer review without data isn’t #PeerReview.
Journals should enforce data availability before review, not after.
#OpenScience #Genomics
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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
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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
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Thanks @pursuelearning.net! This is built on the ‘quiet’ everyday work of folks across PHF Science, diagnostic labs & IPC teams in @healthnz.govt.nz
They deliver services, catch patterns & make sure these ‘routine’ samples don’t slip through. We’re fortunate to apply genomics to help tell the story
The uncomfortable question this paper leaves open...
👉 How many other high-risk #AntimicrobialResistance genes are carried on tiny plasmids we’re not even watching for yet?
doi.org/10.1016/j.dr...
#AMR #FutureOfHealth #Surveillance #GlobalHealthThreats
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What didn’t work (at first)
Standard bacterial WGS told us about related cases, but not how the resistance was moving
It took complete genomes to see that this plasmid is global, stable, & quietly successful
#ScientificProcess #Genomics #AMR #LessonsLearned
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What we did👇
We rebuilt bacterial #Genomes end-to-end, including plasmids
Then we compared that tiny col plasmid to hundreds of col plasmids from around the world
Patterns emerged that standard methods miss
#Genomics #Bioinformatics #OpenScience #DataScience
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Why this matters🤔
Small plasmids are 'easy' for bacteria to carry. They don’t slow growth & aren't dropped when antibiotics aren’t used
#AMR genes can sit waiting
When antibiotic use rises, selection pressure flips the switch & AMR bacteria can spread fast
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This is like hiding malware inside a tiny software update, not a giant suspicious download
It installs quietly, runs efficiently, & spreads before anyone notices
#SystemsThinking #InvisibleThreats #CyberSecurity #Biosecurity
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But in these New Zealand cases, the OXA-48 gene wasn’t on a massive #plasmid
It was carried on a tiny plasmid ~8,000 DNA letters long
That’s quite small
#Genetics #DNA #Plasmids #Science #Easyfig
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The gene was OXA-48
It encodes an enzyme that can break carbapenems... which are #Antibiotics we keep for when nothing else works
Typically, this gene spreads on big, obvious DNA mobile elements known as plasmids
#AMRcrisis #InfectiousDiseases #Microbiology
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This project started with a question that genuinely bothered our team...
👉How did a last-line #AntibioticResistance gene show up in the community in New Zealand?
#PublicHealth #Genomics #OneHealth #DrugResistance #HealthSecurity #GlobalHealth #Epidemiology
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🧵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...
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You’re describing diagnostics not surveillance. MALDI/LFIA give ID & phenotype. They don’t produce genomes for cross-site comparison. WGS links cases & supports regional/global surveillance- info used to target isolation, cleaning & screening. Phenotype guides treatment; genotype informs prevention👋
Rapid tests detect. They don’t link cases, map plasmids, or resolve transmission. WGS does & feeds harmonised, shareable genomes into cross-institution & global #PublicHealth surveillance. Lateral-flow assays or MALDI-TOF don’t produce genomic data, so they cannot serve that role
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
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Think you were exposed? Call Healthline 0800 611 116 for advice before visiting care. They’ll advise on what to do & how to protect others ☎️ 😷
Were you at a “location of interest”? Check dates & follow the advice for close or casual contacts here: info.health.nz/conditions-t... 📍
Highest risk: unvaccinated people, babies under 12 months, pregnant people, & those with weakened immunity. Complications can be serious 👶 🤰 🧪
Symptoms to watch: fever (≥38°C), cough, runny nose, sore red eyes, then a rash.
If symptoms start, call your GP or Healthline first.
👉Do not just turn up👈
☎️ 0800 611 116
How can #measles spread?
Breathe the same air as an infectious person & you can catch it. The virus can linger in the air or on surfaces for up to 2 hours 🕒
📍💉 #Measles #HealthNZ #TeWhatuOra #Immunisation #NZ
⚠️ 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
Where else is ST1 hiding?
We need to start thinking about environmental & farm worker sampling to map the spread & persistence of ST1
#AMR #Genomics #OneHealth #Staphylococcus #Biosecurity #NZ
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Timeline analyses show ST1 evolving differently in people & cows
To stay ahead of emerging lineages & resistance, we need a #OneHealth lens linking human, animal, & environmental data 🌍
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We expected human & bovine derived ST1 to be genomically ‘similar’
Instead we found:
🔹 Human derived ST1 = more antibiotic resistance genes #AMR
🔹 Bovine derived ST1 = a unique host-specific prophage (φSabovST1) carrying bovine leukocidins
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Globally, bovine S. aureus usually belong to ST97/ST151
But in NZ 🇳🇿, ST1 dominates in humans & cattle
This unusual overlap raises big questions about possible cross-species #transmission & #evolution
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🚨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
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🚨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
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