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 🧪🧫🦠

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 🧪🧫🦠

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 🧪🧫🦠

🧵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 🧪🧫🦠

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 🧪🧫🦠

⚠️ 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

🚨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 🧪🧫🦠

🚨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... 📩[email protected] 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠

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...

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 🧪🧫🦠

💥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 🧪🧫🦠

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

Absolutely delighted to share the labs latest work. We identify and characterise two pathways for D-ribulose utilisation in pathogenic EHEC and Citrobacter.

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 🧪🧫🦠

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 🧪🧫🦠

📌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 🧪🧫🦠

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 🧪🧫🦠

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

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 🧪

Day 3 of the @who-global.bsky.social World #AntimicrobialAwarenessWeek: Did you know that viruses called phages can also spread #AntimicrobialResistance? A phage can infect bacteria & can sometimes transfer #AMR genes between them. Let’s see how! 🧵👇 🧪 #WAAW2024

It's day 2 of the @who-global.bsky.social World #AntimicrobialAwarenessWeek: How does #AntimicrobialResistance spread between bacteria? Let’s explore how #plasmids, tiny DNA molecules, can transfer resistance genes across bacteria—even different species in some cases! 🧵👇 🧪 #WAAW #AMR

Welcome to Day 1 of the @who-global.bsky.social World #AntimicrobialAwarenessWeek! Today, let’s break down what antimicrobial resistance is & why it’s a threat to New Zealand & the world 🧵👇 #WAAW2024 #WAAW #AMR 🧪

Proactive nanopore WGS in the NICU can detect & help contain bacterial outbreaks early, protecting newborns Genome sequencing developed to trace COVID is now protecting babies in intensive care from infectious diseases theconversation.com/genome-seque... via @theconversation.bsky.social #IDSky

A partial E. coli genome assembly was recovered from a diseased Kākāpō 🤯 ExPEC, ST141, 02/050 O-antigen serogroup

#COVID update for New Zealand - XEC variant (detected 8 Sept) now established, showing 3% daily growth advantage over dominant KP.3.1.1 - Growth rate is slower than JN.1's previous 10% advantage - WHO has designated XEC as Variant Under Monitoring🔍

This is amazing and important work by Glen Carter and colleagues at the University of Melbourne 'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus' www.nature.com/articles/s41...

📌The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing - 48hr turnaround (Nanopore) - Accessible #Genomics for hospitals - Ability to catch subtle outbreaks DOI: doi.org/10.21203/rs.... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

Early bird registration is open #OHA2024 10th #OneHealth Aotearoa Symposium 📅3-4 Dec 2024 📍University of Otago Wellington 💻In-person & online Key speakers & themes on #AntimicrobialResistance, climate change, Te Ao Māori & more Link www.otago.ac.nz/conference/o... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

Bluesky now has over 10 million users, and I was #1,378,954!

🚨 Call for Abstracts! 🚨 One Health Aotearoa invites submissions for the #OneHealth Aotearoa Symposium 2024! 📆 3-4 December 📍University of Otago Submit your 250-word abstract by 31 August 2024 to [email protected] Don't miss out! #Research #Collaboration 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

New short comm out in preprint! 📌Resolving a neonatal intensive care unit outbreak of methicillin-resistant Staphylococcus aureus to the SNV level using Oxford @nanopore simplex reads and HERRO error correction | @biorxivpreprint.bsky.social doi.org/10.1101/2024... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

Exciting news! Our latest #OpenAccess paper is out now 📌Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing doi.org/10.1099/mgen... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

Super proud of our latest #OpenAccess paper: 📌Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance | @ICHEJournal @nanopore doi.org/10.1017/ice.... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

April’s #COVID19 update: - JN.1 & decedents dominate ~98% of sequenced cases - JN.1.11.1 is the fastest growing lineage in New Zealand at present - #Wastewater confirms JN.1 takeover See more👉 www.esr.cri.nz/digital-libr... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

Latest #COVID19 update JN.1 dominates w/ >90% of sequenced cases & virtually all wastewater samples. JN.1.4 & XDK are now monitored; they grow 1% faster daily than other JN.1. Wastewater results show a near-complete shift to JN.1 See: www.esr.cri.nz/digital-libr... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

It’s out! (despite surgeries, pandemic, floods, finishing the #PhD & relocating) 📌Genomic epidemiology reveals geographical clustering of multidrug- resistant Escherichia coli ST131 associated with bacteraemia in Wales | @NatureComms doi.org/10.1038/s414... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

Happy 9th International Day of Women and Girls in Science!🌟 I'd like to take this chance to honour the vital contributions of just a few members of our incredible #science team here at ESR in New Zealand #WomeninSTEM #WomenInScienceDay #AcademicSky #Microsky 🧪🧫🦠

Latest #COVID19 update - featuring a 🟪Purple Reign🟪 🌊 JN.1 now at 68% of recent cases, spreading faster 🏆 First time since winter 2022, a single variant dominates 🚽 #Wastewater analysis confirms a JN.1 takeover See more: www.esr.cri.nz/our-expertis... #AcademicSky 🖥️🧬 #Microsky 🧪🧫🦠

POV: you’ve fractured your wrist & hand, but the grant proposal deadline is looming 👀 #AcademicSky 🖥️🧬 #Microsky 🧪🧫🦠 #AcademicChatter #phdchat #Science

Metabolism of ʟ -arabinose converges with virulence regulation to promote enteric pathogen fitness https://www.biorxiv.org/content/10.1101/2023.12.21.572775v1

Out now: 📌2019 Survey of Extended-spectrum β-lactamase-producing Enterobacterales in New Zealand Latest survey by ESR shows concerning #AntimicrobialResistance rates in Aotearoa, particularly among older community patients #AcademicSky 🖥️🧬 #Microsky 🧪🧫🦠 Full report👉 www.esr.cri.nz/our-research...