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

Abstract

A highly invasive form of non-typhoidal Salmonella (iNTS) disease has been recently documented in many countries in sub-Saharan Africa. The most common Salmonella enterica serovar causing this disease is Typhimurium. We applied whole-genome sequence-based phylogenetic methods to define the population structure of sub-Saharan African invasive Salmonella Typhimurium and compared these to global Salmonella Typhimurium isolates. Notably, the vast majority of sub-Saharan invasive Salmonella Typhimurium 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 of lineage I by 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.

Using next generation sequencing to tackle non-typhoidal Salmonella infections

“…The genome sequencing of a broad collection of African isolates now shows that S. Typhimurium ST313 is a clonal group of bacteria (sharing common ancestry) which has been circulating for around 50 years and has now split into two lineages that have acquired similar resistance genes on separate occasions [20]. The microevolution of virulence gene expression has been associated with environmental stress [21] and it is possible that in sub-Saharan African countries extreme draught followed by rain storms, and hot days followed by cool nights, could have resulted it the emergence of a successful clone of S. Typhimurium.…”

“…These studies raise the possibility of birds as a source of S. Typhimurium ST313 and the relationship between the S. Typhimurium DT56 isolates from birds and humans remains to be described but is of great interest. The importance of the detailed description of S. Typhimurium ST313 [20] should not be underestimated, but if the opportunities in our post genomic era are to be fully realised then this research must be translated into useful tools to reduce the burden of this dreadful disease [28]. The detailed description of the spread of S. Typhimurium ST313 is a major breakthrough and shows how new nucleic acid sequencing technology can be used for epidemiology of NTS infection but the expansion of S. Typhimurium ST313 only partially explains the emergence of drug resistant, invasive, NTS infection.…”

Genomic Analysis of Bacterial Outbreaks

“…(Snitkin et al, 2012;Espedido et al, 2013;Onori et al, 2015) Legionella pneumophila 3.5 Illumina HiSeq 2x100 bp Illumina MiSeq 2x250 bp, 2x150bp SOLiD 5500XL SE 75bp (Reuter et al, 2013a;Reuter et al, 2013b;Sánchez-Busó et al, 2014;Bartley et al, 2016) Listeria monocytogenes 3 Roche 454 GS-FLX (Gilmour et al, 2010;Schmid et al, 2014;Kwong et al, 2016 (Holt et al, 2008;Lienau et al, 2011;Quick et al, 2015;Allard et al, 2013;Cao et al, 2013;Allard et al, 2012;Taylor et al, 2015;Bekal et al, 2016) Salmonella Typhimurium 4.7 Illumina GA II system (Okoro et al, 2012) Shigella sonnei 5.06 Illumina GAII PE 2x54 bp Illumina MiSeq Illumina HiSeq2000 (Holt et al, 2012;Holt et al, 2013;McDonnell et al, 2013) 32 (Harris et al, 2010;Eyre et al, 2012;McAdam et al, 2012;Young et al, 2012;Köser et al, 2012;Holden et al, 2013;Nübel et al, 2013;Harris et al, 2013;Price et al, 2014;Azarian et al, 2015;Paterson et al, 2015;Senn et al, 2016;Kinnevey et al, 2016;Reuter et al, 2016) Streptococcus pneumoniae 1. Hendriksen et al, 2011;Chin et al, 2011;…”

New genomics studies to understand the link between nontyphoidal Salmonella bacteremia and gastroenteritis in Africa

“…Dear Editor -Nontyphoidal Salmonellae (NTS) are attracting increasing attention as a cause of invasive disease among African children and HIVinfected individuals [1][2][3][4]. However, these invasive (hence iNTS) infections continue to cause confusion, partly because of the contrasting clinical presentations of NTS disease in high-and low-income countries [4].…”

“…Recent whole genome sequencing (WGS) studies demonstrate that invasive African S. Typhimurium is genetically distinct [6], belonging to a new MLST type, ST313. This is characterized by marked genome degradation [7] and has spread throughout the continent [3]. Studies on the genotype/phenotype relationship of ST313, and the genomes of invasive African S. Enteritidis, are awaited.…”