PathoSense

[Nick Vereecke @methenickname]

Fifty shades of Green 🤢. It seems like Halloween 🎃 👻 is around the corner at the @pathosense lab! Any thoughts which green monster is getting tamed here? 👹👽💀

#labfun #halloween #greenmonster @theuns_bas #sequencing #phdlife #october #nucleicacids

[Nick Vereecke @methenickname]

In conclusion:

🐮 @nanopore sequencing as rapid new tool to determine acquired AMR & support evaluation of ECOFF values
🐮 current approach allows shortening of the present sample-to-result workflow (IDx & AST)
🐮 future goal = immediate IDx & AST without pre-enrichment

6/6 🧵

[Nick Vereecke @methenickname]

🟩🟦🟩 Genotypes allowed for re-evaluation of various ECOFF methods 📈

🧐 Existence of single gene mutants (ENRO; n=3) within the Wild-Type population, are overlooked during phenotypic testing. However, the genotype 🧬 provides a higher resolution.

#Antibiotics #wiltype 5/6

[Nick Vereecke @methenickname]

No quick Antimicrobial Susceptibility Tests are available for M. bovis, so quick & accurate sequencing-based approaches are important to
- provide appropriate & rapid antimicrobial treatment in the framework of AMR
- prevent disease from spreading and/or becoming chronic
4/6

[Nick Vereecke @methenickname]

A k-mer-based GWAS analysis allowed to link M. bovis genotypes 🧬 with phenotypes 🧫 based on different ECOFF thresholds. This highlighted potential genetic markers for:
1- macrolides (GAM, TYLT & TIL)
2- fluoroquinolone (ENRO)
3- tetracyclines (OXY & DOXY)
3/6

[Nick Vereecke @methenickname]

📇 The manuscript can be found here:
https://t.co/aQKJ9lFT5l

🛠 100 @nanopore High-Quality & Complete bacterial genomes were generated using an optimized M. bovis 🐮 specific Bonito model (Vereecke et al., 2020 BMC Bioinformatics) 📄 2/6

#Bonito @iiSeymour #genomics @kehoste

[Nick Vereecke @methenickname]

A new week, so a new co-first shared publication from the @pathosense lab 🥳 in @JournalSpectrum

"Genome-Wide Association Study Reveals Genetic Markers for Antimicrobial Resistance in Mycoplasma bovis" 🐮

⏭Read further to learn more in this 🧵 1/6

#sequencing #mycoplasma

[Nick Vereecke @methenickname]

"Evaluation of @nanopore sequencing as a diagnostic tool for the rapid identification of Mycoplasma bovis from individual and pooled respiratory tract samples"

⏩ our latest publication in @JClinMicro
⏩ A nice collaboration between @UGent_VetMed & @pathosense

🔽Check the 🧵

[Mick W@tson ↙️ @BioMickWatson]

This is, sadly, what living in the US does to good people 😥

[Nick Vereecke @methenickname]

New weekend, new #seaofgreen on our MinION. 18h into sequencing and a 10.5 Gbp output so far (still 30h ahead and 83% of @nanopore pores still sequencing).

👉 RT Bacterial IDx ✅
🐷 RT Bacterial (Virulence) Typing ✅
⭕️ RT Bacterial AMR profiling ✅
🧬 Complete HQC genomes ✅

[Nick Vereecke @methenickname]

Ready for this #nanoporeconf 🧬 today & tomorrow! I am very excited to hear about new @nanopore stuff that will be released, but also new applications & research from experts in the field!

Oh, and don't forget to check my Mini Theatre talk 👇 on Mycoplasma bovis 🐄

@pathosense

[Anna Cuscó @anna_cusco]

Finally out! https://t.co/MPzjPvhgPX

See how we have used long-read metagenomics with Nanopore sequencing to profile a canine fecal microbiome sample and retrieve eight single-contig HQ MAGs 🐕💩🦠🧬

@prd_science
@Quinovines
@NormaFabregas
@olga_francino

[Nick Vereecke @methenickname]

Well hello there 💙💚 Let’s finish this Friday with this bacterial 🧬 sequencing run using the @nanopore Rapid Barcoding Kit! Never thought we would reach these N50 values (> 27kbp) & this caption is only after 30 min sequencing! 🤪🥳

@theuns_bas #AMR #Diagnostics

[Oxford Nanopore Events @NanoporeConf]

Check out this talk preview from @methenickname. At #nanoporeconf, he'll demonstrate how nanopore sequencing was used to identify resistance markers & speed up antimicrobial susceptibility analysis in veterinary samples 🐄.

Register to hear in full: https://t.co/smeqHENW0D

[Oxford Nanopore Events @NanoporeConf]

Mycoplasma bovis causes severe respiratory issues & poses a mortality risk to cattle. At #nanoporeconf, @methenickname will demonstrate how nanopore sequencing was used to identify resistance markers & speed up antimicrobial susceptibility analysis.
https://t.co/KTybzeZ67Z

[Nick Vereecke @methenickname]

Delighted to share our #swinedysentery work during the @ECCMID meeting, July 2021 🇦🇹. Together with @pathosense & DGZVlaanderen we sequenced 100 Brachyspira hyodysenteriae genomes 🧬 using @nanopore to unravel #AMR genotypes Vs. phenotypes.

#ECCMID2021 @theuns_bas @UGent_VetMed

[Nick Vereecke @methenickname]

🦠Fresh bacterial release in @Micro_MDPI

Together with @theuns_bas, @pathosense & @UGent_VetMed we showed the presence of BSBL-producing Enterobacteriaceae in 💩 of Zoo mammals with @nanopore sequencing. A potential zoonotic & public health threat? 1/4

https://t.co/RJPxKVn3fl

[Nick Vereecke @methenickname]

#OutbreakAlert 🐎 February-March: Europe's biggest EHV-1 outbreak was reported in Spain (17 dead & >80 infected 🐎). The #Nauwynck lab isolated EHV-1 from 🇧🇪 suspected 🐎 & by the end of the week @pathosense made complete (150kbp) genomes available with @nanopore sequencing 1/6

[Laurens Lambrechts @laulam94]

A quick analysis for Belgium to show how we are doing, and what should be improved. This is all based on public data available on GISAID In panel A you see 98% of the genomes were done by either REGA (@MaesPiet ), Liège (@keithdurkin) and Ghent (@theuns_bas).