Thread by @jay_salsa, 1/12Evolution does not only change virusesHere's the evolutionary trajectory of variants of [...]

1/12

Evolution does not only change viruses

Here's the evolutionary trajectory of variants of Salmonella Typhimurium that cause bloodstream infection in Africa

Published in @NatureMicrobiol
https://www.nature.com/articles/s41564-020-00836-1

@LivUni_IVES @livuninews @1caiseypulford #iNTS #Salmonella

1/12Evolution does not only change virusesHere's the evolutionary trajectory of variants of Salmonella Typhimurium that cause bloodstream infection in AfricaPublished in @NatureMicrobiol https://www.nature.com/articles/s41564-020-00836-1 @LivUni_IVES @livuninews @1caiseypulford #iNTS #Salmonella

2/12

#Salmonella not only causes gastroenteritis, but also bloodstream infection

African epidemic of bloodstream infections began in late 1980s, caused by non-typhoidal Salmonella =iNTS

INTS now endemic across sub-Saharan Africa -killed 500,000 people in the last decade #iNTS

3/12
How did S. Typhimurium ST313 evolve from a gut coloniser to bloodstream infection?

We studied a comprehensive collection of African Salmonella isolates from human blood

Thanks to far-sighted scientists @MlwTrust 1996–2018 & @institutPasteur 1966-2018 who did the collecting

4/12
We generated 680 genomes from S. Typhimurium isolates from 13 African countries

[part of #10KSG consortium, with @EarlhamInst & collaborators worldwide]

90% of Salmonella Typhimurium bloodstream isolates from Malawi were ST313 (1996-2018)

5/12
We put our new S. Typhimurium isolates into context of previously published genomes from @sangerinstitute @UAntwerpen @PHE_uk @institutpasteur & elsewhere

@DrRobKingsley @flashton2003 @implosian @San_VanP

Most of our isolates were ST313 lineage 2…

6/12
We followed step-wise evolution of Salmonella in Africa over 50 years

We saw Lineage 1 disappearing as lineage 2 emerged...

In 2016, new antibiotic-sensitive lineage 3 emerged in Malawi

Lineage 3 is related to UK-ST313 isolates originally identified in England

7/12

S. Typhimurium ST313 Lineages 1, 2 & 3 have distinctive accessory genomes

8/12
The fossil-footprint of African S. Typhimurium

Showing stepwise evolution on a time-line, modelled with BEAST.

Sequential acquisition of #pseudogene mutations, many in gastrointestinal colonisation genes.

9/12
S. Typhimurium ST313 lineage 3 has a higher invasiveness index than other ST313 lineages

[Invasiveness index originally developed by @nwheeler443]

10/12
Remarkable collaboration driven by @1caiseypulford

Involving @MelitaGordon5 @BlancaPerSep @NWenner @knalsal @rodwell_ella @benjkum @zxj931_zhu @joy_hermione @APredeus @josebengoechea @wil_rowe @ksbakes @acdarby @neilhall_uk
FX Weill /Nick Feasey not on twitter
Others

11/12
This couldn’t have been done without funding from @wellcometrust, @GCRF & @BBSRC

@MlwTrust @EarlhamInst @institutpasteur

@LivUni_IVES @LivUni @livuninews

12/12

And finally, @eliza_coli's image puts our work into context…

Showing the stepwise quest of African S. Typhimurium to leave the gastrointestinal tract, and “ascend” to the human bloodstream!

Hope you spot the gut-specialist, ST19 – and ST313 lineages 1, 2 & 3

13/12 (!)

We’re delighted that @NatureMicrobiol agreed to publish our paper #OpenAccess

We hope this will help more scientists from #Africa access our findings

@benjkum @AASciences @AESA_Africa @SooJones @NatureMicrobiol https://www.nature.com/articles/s41564-020-00836-1

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

Stepwise evolution of invasive Salmonella Typhimurium in Africa is defined using genotypic and phenotypic analyses of isolates collected over a 50-yr period.

https://www.nature.com/articles/s41564-020-00836-1

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