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Microbial (meta)genomics researcher @sangerinstitute interested in genomic epidemiology and evolutionary dynamics of STIs/NTDs/AMR. Views my own
The Morges Strategy for Yaws Eradication: the first largescale Total Community Treatment with azithromycin against yaws in the Congo-Basin, using a novel model. https://www.medrxiv.org/content/10.1101/2024.11.07.24316738
The Morges Strategy for Yaws Eradication: the first largescale Total Community Treatment with azithromycin against yaws in the Congo-Basin, using a novel model.

Context and Justification. Yaws is targeted for eradication by 2030. Total Community Treatment with azithromycin (TCT), a major component of the eradication strategy, has witnessed only three pilots since 2012.  We implemented the first large-scale TCT in the Congo-Basin of Central Africa using a novel model. Methodology. We implemented a novel 3-phase TCT model 17 health districts of the Congo-Basin, spanning 3 countries. Two rounds were implemented in Cameroon, and one round each in Central African Republic (CAR) and the Republic of Congo; targeting 1,530,014 people (144,934(9.5%) Pygmies and 1,304,410(90.5%) Bantus). TCT was followed by post-campaign active surveillance, treatment of yaws cases and their contacts. Results. All 17 health districts were confirmed for yaws endemicity. Overall, 1,456,691 (95.21%; 95%CI: 95.17%-95.24%) persons were treated in the first round of TCT, including 552,356/594411 (92.92%; 95%CI: 92.86%-92.99%) in Cameroon, 359,810/373,994 (96.21%; 95%CI: 96.15%-96.27%) in CAR, and 544,526/561,609 (96.96%; 95%CI: 96.91%-97.00%) in Congo. For the second round implemented only in Cameroon, 615,503/642,947 (95.73%; 95%CI: 95.68%-95.78%) were treated. There was a 3-percentage-point increase in therapeutic coverage between the first and second round (P-value<0.001), and from 89.2% to 93.1% (P-value<0.001) among the Pygmies. The prevalence of active yaws decreased from 6.5% to 0.4% (P-value<0.001) overall, and from 6.31% to 0.23% (P-value<0.001, OR=28.67, 95%CI (20.86-40.09) in Cameroon, from 2.4% to 0.8% (P-value=0.002, OR=3.19, 95% CI: 1.45-8.00) in CAR,  and from 10.8% to 3.7% (P-value<0.001, OR=3.18, 95%CI: 2.09 โ€“ 5.01) in Congo. Conclusion. A novel TCT model was successfully implemented at largescale in the Congo-Basin, achieving above recommended threshold of therapeutic coverages. The prevalence of active yaws dropped remarkably following the TCT, however complete interruption of yaws transmission was not achieved. In recommending the novel model of TCT to endemic countries, we suggest that at least three rounds, at six-monthly intervals, are implemented for complete interruption of yaws transmission. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The author(s) received no specific funding for this work. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The intervention was approved by the Cameroon National Ethics Committee for Research in Human Health, and the Ethics Committee for Research in Health Sciences of the Republic of Congo. Administrative authorisations were also obtained from the ministries of health in the three countries involved in the intervention. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All relevant data are within the manuscript and its Supporting Information files.

medRxiv
Research Associate (Fixed Term) - Job Opportunities - University of Cambridge

Research Associate (Fixed Term) in the Department of Medicine at the University of Cambridge.

Types of Microbial Bioinformatics Papers. based on https://xkcd.com/2456/
Types of Scientific Paper

xkcd
Pleased to share this work led by Patrick Musicha. We analysed ~2300 longitudinally collected household-linked carriage strains of E. coli in Malawi and Uganda (DRUM study). We found extensive recent sharing of strains and MGEs between humans, animals and env. https://www.biorxiv.org/content/10.1101/2024.09.18.613694v1

The worst part of receiving almost daily invitations to review is that for every invitation a new account is created on my behalf. Whenever I accept the invitation, I have to start negotiations with the management system to merge accounts, or to modify whatever if I don't want to have 879 accounts to keep track of.

(I also don't review more than one ms at once BTW).

The manipulation game - why certain groups understand online contagion more than others, and what it means for the amplification of extreme views. New post: https://blog.kucharski.io/?the-manipulation-game
Redirecting...

Happy to announce a new preprint from the lab, together with fantastic @richardneher and Liam Shaw! ๐Ÿ“
https://www.biorxiv.org/content/10.1101/2024.07.08.602537v1
We were motivated by the following puzzling observation: microbial genomes can be extremely similar in the core genome, while still differing by large portions of accessory genome.
Therefore we ask the question:
1) how does this diversity accumulate?
2) at what rate do genomes undergo large structural changes?

A thread ๐Ÿงต [1/13]

@typeMAT12 @Psy_Fer_

The good thing with slow5 is only the XYZ -> BLOW5 converter we have to fix everytime ONT does a breaking change to their file formats. Any tools that is written on top slow5 will not require to change. Because of this, we have to fix only the converter only, instead of fixing 100 tools separately :D

@typeMAT12 @hasindu2008 In addition to all of this, there are some issues we have with the design and engineering behind pod5.
It uses a column based system for data that 99% of users will read in a sequential row based manner. Slow5 is row based.
It abuses virtual memory and doesn't play well with HPC, and without it, you lose a lot of its speed
Slow5 is fully open source and will remain that way, there is no such guarantee from ONT (look at dorado licence and closed source libs)
@typeMAT12 @hasindu2008 Slow5 is a much simpler format, with less dependency on other libs ( @hasindu2008 post the dep graph!) It is also super easy to integrate with any tools you might be building, and our version control is more stable than ONTs without breaking backward compatibility.
We have made libraries to make conversion easy, so no matter what you choose, you can always go back to the other format if you want to.
Our conversion tools don't corrupt the data like ONTs have in the past.