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Hi everyone!

After week 12 of MicroTwJC there was a request for a Salmonella paper, having just read the paper below it saved me the bother of thinking for myself! It is a very interesting paper investigating an upsurge in invasive non-typhoidal Salmonella (iNTS) in the context of historical isolates. This allowed them to put a time frame on the emergence of the strain. The authors note that the lineages thought to be responsible for this iNTS surge was emerging around the same time as HIV. Since iNTS is associated with immune suppression the authors raise a suggestive eyebrow at a relationship between these infectious disease events.

I hope there is something there to keep virologists interested. Has anyone done BEAST analysis? Would be great to hear from you in the comments or on the night.

The paper was very kindly made Open Access by the people at Nature Genetics, in fact the editor of the paper is part of the twitterati and is planning on joining us for this weeks session!

Anyway, I hope to have time to knock up a quick blog post summarising the findings, picking out weaknesses and thinking about how this work might apply more broadly. Will post here as and when.

Hope you can join us!

Title: Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

Abstract: A highly invasive form of non-typhoidal Salmonella (iNTS) disease has recently been documented in many countries in sub-Saharan Africa. The most common Salmonella enterica serovar causing this disease is Typhimurium (Salmonella Typhimurium). We applied whole-genome sequence–based phylogenetic methods to define the population structure of sub-Saharan African invasive Salmonella Typhimurium isolates and compared these to global Salmonella Typhimurium populations. Notably, the vast majority of sub-Saharan invasive Salmonella Typhimurium isolates fell within two closely related, highly clustered phylogenetic lineages that we estimate emerged independently ~52 and ~35 years ago in close temporal association with the current HIV pandemic. Clonal replacement of isolates from lineage I by those from lineage II was potentially influenced by the use of chloramphenicol for the treatment of iNTS disease. Our analysis suggests that iNTS disease is in part an epidemic in sub-Saharan Africa caused by highly related Salmonella Typhimurium lineages that may have occupied new niches associated with a compromised human population and antibiotic treatment.