iiinova — where your digital self keeps evolving

David Winter @dwinter.bsky.social · 29/04/2026

So sorry to hear this josette, these chronic infections can cause such long lasting impacts

David Winter @dwinter.bsky.social · 29/04/2026

Yes, more common in NZ than in other similar countries. We know pork is a big contributor, but not the whole story: www.phfscience.nz/news-publica...

phfscience.nz

Pork connection to gastric illness strengthened food safety industry engagement

120

David Winter @dwinter.bsky.social · 28/04/2026

Pretty much, when you start doing these programmes at scale, you get a few odd ones that make it through like this.

120

David Winter @dwinter.bsky.social · 28/04/2026

(The weird/new guy will grow in the standard culture conditions which is how it got into or public health surveleince data. Pathogenicity is not entirely clear, though we've seen it in gastro cases hard to know if it's the cause)

010

David Winter @dwinter.bsky.social · 28/04/2026

Sorry to hear that josette! Sadly these tools are only genomic ways to flag our 'interesting" strain from route Y ent. results. No help to those in your situation as we typically need a culture for sequencing

120

David Winter @dwinter.bsky.social · 27/04/2026

eventually we found close relatives in databases, coming from our colleagues in QLD Health. WIth a lot of work we managed to describe our odd ball lineage as a new species, with the name Yersinia fenwicki honours Prof. Stanley Fenwick who did some of the first work on on Yersinia in NZ.

130

David Winter @dwinter.bsky.social · 27/04/2026

Cool slow-burning story I got to be a little part of www.phfscience.nz/news-publica... Way back in 2010 the enteric lab here at PHF Science got a Yersinia isoalte that quite fit with what we expect from Y. enterocolitica. We got a few more of these over time and built some tools to track them

phfscience.nz

Back to the future: discovery of a new bacterial species, decades in the making

154

David Winter @dwinter.bsky.social · 23/12/2025

Really have to be by the sequencers and the samples in porirua for these ones. Our auckland campus is mostly working on forensics

000

David Winter @dwinter.bsky.social · 22/12/2025

You are too kind, but i am very lucky to work with people so dedicated to public health

110

David Winter @dwinter.bsky.social · 22/12/2025

A fixed term scientist position to work with @joannehewittnz.bsky.social and I to help build a more flexible and responsive set of sequencing assays for both wastewater and clinical samples. nzcris.wd3.myworkdayjobs.com/en-US/nzcris... Hit me up if you have questions: david.winter@phfscience.nz

nzcris.wd3.myworkdayjobs.com

Scientist - EEFV

Te tūnga | The role This nine-month fixed-term role focuses on developing and validating PCR and sequencing-based assays to support clinical and wastewater surveillance. The position aims to strengthe...

115

David Winter @dwinter.bsky.social · 22/12/2025

We have three wet lab genomics positions open, all supporting our sequencing for public health Two permanent snr tech roles will be trained for accredited Illumina and ONT workflows (apply for both) nzcris.wd3.myworkdayjobs.com/en-US/nzcris... nzcris.wd3.myworkdayjobs.com/en-US/nzcris... (1/2)

nzcris.wd3.myworkdayjobs.com

Senior Technician

Te tūnga | The role We have a permanent opportunity for a Senior Technician to join the fast-paced Genomics & Bioinformatics group at our Kenepuru Science Centre in Porirua. In this role you will ...

229

David Winter @dwinter.bsky.social · 31/10/2025

Haven't really moved to bluesky,but had to jump on to highlight this cool result from Joanne's team . We have been watching BA.3.2, a highly divergent COVID linage, closely. Wastewater was the first to find it in NZ, with enough resolution to know where it fits among lineages from Australia.

0102

David Winter @dwinter.bsky.social · 21/12/2023

There will be a wee break, partly because we want the ppl at the treatment sites taking the samples to have a clean break. Diagnostic labs are holding samples, so clinical genomics will be able to cover continuously

010

David Winter @dwinter.bsky.social · 21/12/2023

You are too kind, but I hope to do some good!

100

David Winter @dwinter.bsky.social · 21/12/2023

Finally, a little news from me. 2023 is my last year as Technical Lead Pathogen genomcs @ ESR. Next year I'll be back as Science Leader Genomics with less focus on the day-to-day and more on how we can best use genomics to support public health now and in the future.

3160

David Winter @dwinter.bsky.social · 21/12/2023

There are a huge number of dedicated people underneath all those headline statistics, so a massive thanks to everyone collecting samples, growing bugs, running the sequencers and analysing and interpreting the results.

110

David Winter @dwinter.bsky.social · 21/12/2023

This year, we moved Shigella, Vibrio, Yersinia Strep and Legeionlla to genome sequencing. All told we processed 4,361 bacterial genomes gathering information about antimicrobial susceptibility, disease severity, vaccine coverage, outbreak detection, and a lot more.

130

David Winter @dwinter.bsky.social · 21/12/2023

ESR does a lot more than COVID-19. Genomics is increasingly how we support our national reference laboratories to track diseases in the community.

110

David Winter @dwinter.bsky.social · 21/12/2023

`23 was also the year we brought COVID-19 wastewater sequencing in-house. Been great to work with @joannehewittnz.bsky.social 's team and bring results and expertise from the two threads of SARS-Cov-2 surveillance much closer together. Check out poops.co.nz and closer collab in `24

250

David Winter @dwinter.bsky.social · 21/12/2023

In summer 22/23 the "variant soup" meant sequencing was called on to match treatments to genomes, with a tonne of patient-level reports going out for the first time. Later we had XBB sweep through and 'old' lineages like CH.1.1 and XBC stick around locally for a long time. Now our focus is on JN.1

110

David Winter @dwinter.bsky.social · 21/12/2023

Last sequencing run of 2023 about to go on here @ ESR , time for a little review of what we achieved this year before we get stuck into analysing them... First a whole year of COVID genomics:

And epidemological curve of COVID-19 cases in NZ, shaded estimated numbers of cases caused by each variant.

21811

David Winter @dwinter.bsky.social · 11/11/2023

4.5 yo's most endearing trait right now is point blank rejecting any time I say I'm doing a bad job. -do we have any snacks? -no sorry, didn't put them in the swim bag: bad Dadding there -No. You're a good Dad. It's OK!

140

David Winter @dwinter.bsky.social · 11/11/2023

Weekly social media log in.... It's a shield bug, but sure which but not the bad one www.mpi.govt.nz/biosecurity/.... Cute !

110

David Winter @dwinter.bsky.social · 24/10/2023

(also, author limits at the journal means this paper sees the birth of the "ESR Genomics Consortium" to capture the folks that worked on this... possibly the smallest consortium to publish a genomic paper)

000

David Winter @dwinter.bsky.social · 24/10/2023

This paper describes how to fit that workflow into a busy diagnostic lab. Now e have @rhystwhite.bsky.social as our embeded ESR scientist working with Max I expect some really interesting results to come from routine sequencing of common hospital pathogens

110

David Winter @dwinter.bsky.social · 24/10/2023

First little output from a very cool project with Max Bloomfield @ Wellington Hospital. Max is using Nanopore sequencing to help Infection Control teams spot transmission on or between wards. Max does the bulk of the work, and ESR is ready for any tricky bionfo problems: doi.org/10.1016/j.pa...

131

David Winter @dwinter.bsky.social · 24/10/2023

Think you already got there, but looks like a tunnel web. A live one fell out of my jersey the other morning jsut before I put it on... testing my archnophillia to its limit....

230

David Winter @dwinter.bsky.social · 06/10/2023

gotta send a (whatever a tweet is here) about any other topic!

010

David Winter @dwinter.bsky.social · 06/10/2023

still can't edit 'huh. I meant to say ''their advantage is _not very large_' 😑

020

David Winter @dwinter.bsky.social · 06/10/2023

Wastewater surveillance is updated too, till the only way we have found the highly-divergetnt BA.2.86 in NZ: poops.nz

poops.nz

ESR Wastewater Surveillance

060

David Winter @dwinter.bsky.social · 06/10/2023

We try to stay ahead of the variant name game, and look for what might be able to replace our tracked variants in future. HK.3 and FL.2 are contentders, but their advantage is now very larger (1-2% per day)

240

David Winter @dwinter.bsky.social · 06/10/2023

I guess our public covid report is going to be the thing that makes me finally send a message here... www.esr.cri.nz/our-expertis... This month has seen the kākāpō palette really come together as EG.5 became our most common variant. NZ and Aus remain really unusual in having room for XBC...

1194