RT Journal
A1 Kingsley, Robert A.
A1 Msefula, Chisomo L.
A1 Thomson, Nicholas R.
A1 Kariuki, Samuel
A1 Holt, Kathryn E.
A1 Gordon, Melita A.
A1 Harris, David
A1 Clarke, Louise
A1 Whitehead, Sally
A1 Sangal, Vartul
A1 Marsh, Kevin
A1 Achtman, Mark
A1 Molyneux, Malcolm E.
A1 Cormican, Martin
A1 Parkhill, Julian
A1 MacLennan, Calman A.
A1 Heyderman, Robert S.
A1 Dougan, Gordon
T1 Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
JF Genome Research 
JO Genome Research 
YR 2009 
FD December 01 
VO 19 
IS 12 
SP 2279 
OP 2287 
DO 10.1101/gr.091017.109 
UL http://genome.cshlp.org/content/19/12/2279.abstract 
AB Whereas most nontyphoidal Salmonella (NTS) are associated with gastroenteritis, there has been a dramatic increase in reports of NTS-associated invasive disease in sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multilocus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, which currently is rarely reported outside of Africa. Whole-genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene formation and chromosomal deletions, when compared with other S. Typhimurium genome sequences. Some of this genome degradation involved genes previously implicated in virulence of S. Typhimurium or genes for which the orthologs in S. Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field.