An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

Sandra Van Puyvelde (), Derek Pickard, Koen Vandelannoote, Eva Heinz, Barbara Barbé, Tessa de Block, Simon Clare, Eve L. Coomber, Katherine Harcourt, Sushmita Sridhar, Emily A. Lees, Nicole E. Wheeler, Elizabeth J. Klemm, Laura Kuijpers, Lisette Mbuyi Kalonji, Marie-France Phoba, Dadi Falay, Dauly Ngbonda, Octavie Lunguya, Jan Jacobs, Gordon Dougan and Stijn Deborggraeve
Additional contact information
Sandra Van Puyvelde: Institute of Tropical Medicine
Derek Pickard: Wellcome Genome Campus, Hinxton
Koen Vandelannoote: Institute of Tropical Medicine
Eva Heinz: Wellcome Genome Campus, Hinxton
Barbara Barbé: Institute of Tropical Medicine
Tessa de Block: Institute of Tropical Medicine
Simon Clare: Wellcome Genome Campus, Hinxton
Eve L. Coomber: Wellcome Genome Campus, Hinxton
Katherine Harcourt: Wellcome Genome Campus, Hinxton
Sushmita Sridhar: Wellcome Genome Campus, Hinxton
Emily A. Lees: Wellcome Genome Campus, Hinxton
Nicole E. Wheeler: Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton
Elizabeth J. Klemm: Wellcome Genome Campus, Hinxton
Laura Kuijpers: Institute of Tropical Medicine
Lisette Mbuyi Kalonji: National Institute for Biomedical Research
Marie-France Phoba: National Institute for Biomedical Research
Dadi Falay: University Hospital of Kisangani
Dauly Ngbonda: University Hospital of Kisangani
Octavie Lunguya: National Institute for Biomedical Research
Jan Jacobs: Institute of Tropical Medicine
Gordon Dougan: Wellcome Genome Campus, Hinxton
Stijn Deborggraeve: Institute of Tropical Medicine

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract Bloodstream infections by Salmonella enterica serovar Typhimurium constitute a major health burden in sub-Saharan Africa (SSA). These invasive non-typhoidal (iNTS) infections are dominated by isolates of the antibiotic resistance-associated sequence type (ST) 313. Here, we report emergence of ST313 sublineage II.1 in the Democratic Republic of the Congo. Sublineage II.1 exhibits extensive drug resistance, involving a combination of multidrug resistance, extended spectrum β-lactamase production and azithromycin resistance. ST313 lineage II.1 isolates harbour an IncHI2 plasmid we name pSTm-ST313-II.1, with one isolate also exhibiting decreased ciprofloxacin susceptibility. Whole genome sequencing reveals that ST313 II.1 isolates have accumulated genetic signatures potentially associated with altered pathogenicity and host adaptation, related to changes observed in biofilm formation and metabolic capacity. Sublineage II.1 emerged at the beginning of the 21st century and is involved in on-going outbreaks. Our data provide evidence of further evolution within the ST313 clade associated with iNTS in SSA.

Date: 2019
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DOI: 10.1038/s41467-019-11844-z

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