rhystwhite.bsky.social
Scientist, using #genomics to understand #evolution, diversity, & pathogenesis. Welsh expat living in New Zealand. Formerly The University of Queensland
130 posts
3,387 followers
1,318 following
Regular Contributor
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I was feeling more of a ‘Jedward VÆB’
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Thanks @antobeck.bsky.social!
Traditional methods (culture, MALDI-TOF) give species ID fast but lack strain-level resolution. The ‘go-to’ Illumina WGS requires sending samples to ESR, adding delays. On-site nanopore sequencing can allow for same-day, genomic surveillance for rapid outbreak response
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Huge thanks to the amazing team at Awanui Labs & ESR, especially Suzanne Manning (project lead) & colleagues! We need to keep pushing the boundaries of genomics in clinical settings💪 #Genomics #Microbiology #Nanopore
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But challenges remain—integrating new tech into routine lab workflows takes time & investment. We discuss key enablers & barriers from a social systems perspective
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Early successes include detecting an MRSA outbreak in a NICU before traditional methods would have flagged it. This real-time #genomic surveillance allowed for rapid interventions & better patient outcomes
doi.org/10.1099/mgen...
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This work highlights the power of decentralised whole-genome sequencing combined with centralised #bioinformatics. This model could transform clinical microbiology in New Zealand & beyond 🌏 #scicomm
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What we found:
✅ #Nanopore sequencing enabled faster, more precise tracking of pathogens
✅Close collaboration between Awanui Labs Wellington & ESR was key
✅Barriers included #bioinformatics expertise & data infrastructure challenges
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Democratising genomics: While 'central' #Bioinformatics oversight is key, @solu_bio bridges the expertise gap, bringing on-site & rapid #Genomic #Outbreak analysis to front-line #Hospital labs
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Same-day, high-resolution #Genomic analysis in #Hospital labs is possible. Combined with real-time #Sequencing, it enables agile, data-driven #InfectionControl
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#GameChanging speed: Previous #Outbreak analyses took 4–5 weeks. With @solu_bio, #Phylogenetics gave clear clustering & actionable insights for #InfectionControl—no manual #Bioinformatics expertise needed
MRSA: doi.org/10.1099/mgen...
K. variicola: doi.org/10.1186/s137...
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Using Solu Genomics, a cloud-based platform, we replicated analysis of two real #NICU outbreaks (#MRSA & K. variicola). Results ready in <40 min, matched 'manual' #Bioinformatics in identifying #Outbreak clusters
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Key challenge: Many hospitals can sequence bacterial genomes but lack #Bioinformatics expertise for rapid analysis. This slows #Outbreak detection as samples/#Data is sent to reference labs, delaying #InfectionControl. Faster, decentralised #Genomics solutions are needed
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Could I please be added? Thanks!
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Thanks @josephguhlin.bsky.social!
Added
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Done, done, done, & DONE!
Thanks @natforsdick.bsky.social & @ppgardne.bsky.social!
Please let me know of any others missing!
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#AMR is a web connecting humans, animals, & the environment🕸️
Tackling it requires a #OneHealth approach—thinking beyond just human health to protect the planet too🌍
We are all connected, & the fight against AMR starts with all of us #WAAW2024
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What about the environment?🌊
#Wastewater is a key pathway for #AMR genes. #Antibiotics excreted by humans & animals end up in sewage, & treatment plants may not remove it all.
In NZ, ESBL-producing E. coli have even been found in urban waterways
See: doi.org/10.1128/mra....
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#AMR in humans in New Zealand is a big challenge
We have high #Antibiotic dispensing rates, often for illnesses that don’t need them. This drives #AMR.
While efforts are lowering antibiotic use, NZ’s rates are still higher than many countries
See: doi.org/10.1093/jac/...
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More space=less disease=less need for #Antibiotics
Sounds great right?💡
BUT even with low antibiotic use, #AMR still exists in New Zealand farming—especially in pigs, poultry, & dairy. E.g., vancomycin-resistant Enterococci persist in NZ poultry
See: doi.org/10.1128/AEM....
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Compared to other developed countries, New Zealand has relatively low #AMR levels in animals 🐄🐖🐓
Why? Regulations here prevent #Antibiotics from being used to promote growth in animals, & farming practices are often less intensive than factory farming elsewhere #WAAW2024
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Thanks for putting this together! Just wondering if I could please be added to this? Thanks (from New Zealand) 👋
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Kia ora all the way from NZ 👋
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Efflux Pumps: Efflux pumps remove antibiotics from bacterial cells. This mechanism is common in Pseudomonas aeruginosa and can reduce antibiotic effectiveness #AMR #AntibioticResistance @who.int #WAAW2024 🧪
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Bacteria can acquire an #AMR gene that changes target sites. S. aureus resists penicillin by acquiring an extra copy of PBP2a, a protein that works in the presence of the #Antibiotic. This is how #MRSA (Methicillin-resistant S. aureus) becomes resistant to beta-lactam antibiotics @who.int #WAAW2024
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Bacteria can become resistant by changing the targets #Antibiotics bind to. When bacteria copy DNA, small errors/mutations can occur. If mutations affects the antibiotic's target, the drug may not work, helping the bacteria survive. This happens in Streptococcus pneumoniae with penicillin resistance
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Some bacteria produce enzymes called beta-lactamases which break down #Antibiotics. Staphylococcus aureus can resist penicillin by making a beta-lactamase which destroys a key part of the antibiotic. This resistance is also seen in E. coli & Klebsiella in New Zealand www.esr.cri.nz/digital-libr...
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The fight against #AntimicrobialResistance is a global health priority, as shown by the @who.int. #AMR genes can spread rapidly through plasmids & transposons, fuelling this crisis.
Together, let’s #EducateAdvocateAct to #HandleAntimicrobialsWithCare! #WAAW2024 #scicomm
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Transposons can carry many #AMR genes, allowing bacteria to acquire & share resistance to multiple #Antibiotics in one move! In New Zealand, we found a transposon in Klebsiella variicola that's resistant to multiple drugs. Check out the preprint: doi.org/10.21203/rs.... #WAAW2024
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In New Zealand, we used Oxford Nanopore Technologies & found the same #AMR gene in a hospital bug that's seen in different bacteria from humans, cows, & dogs - dating back to 1988!
These transposons are master travellers between species & across decades! #WAAW2024
See: doi.org/10.1017/ice....
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When bacteria die, they can release DNA into the environment. Other bacteria can then pick up this free-floating DNA - including #AMR genes! This natural process is called transformation & it's another way that #AntimicrobialResistance can spread between bacteria #WAAW2024
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Thanks so much @jlsteenwyk.bsky.social!
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Kia ora all the way from New Zealand! 👋
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Addressing #AMR spread via phages requires careful management across healthcare, agriculture, & natural environments. Collaboration is key to stopping AMR! #AntibioticAwarenessWeek
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Here in New Zealand, we’ve seen this in action! In a 2016 national survey, an E. coli ST648 carrying an #AntimicrobialResistance gene (catA1) was found within a cryptic prophage (called CP4-57) in the bacterial chromosome #WAAW #AMR
ESR 2016 survey here: www.esr.cri.nz/digital-libr...
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When a phage infects a bacterial cell, it can sometimes pick up #AntimicrobialResistance genes from the chromosome or plasmids & move them to other bacteria, a process called transduction. This can spread #AMR between bacteria!
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Controlling plasmid-based #AMR spread requires a #OneHealth approach, addressing #Antibiotic use in humans, animals & the environment
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An example of #AMR carried by plasmids was seen in a recent #MRSA outbreak. Using Oxford Nanopore Technologies long-read sequencing, we uncovered the spread of a #plasmid carrying penicillin resistance genes! Plasmids can amplify #AMR in critical settings #WAAW2024. See: doi.org/10.1099/mgen...