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

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Van Puyvelde, Sandra and Pickard, Derek and Vandelannoote, Koen and Heinz, Eva and Barbé, Barbara and de Block, Tessa and Clare, Simon and Coomber, Eve L. and Harcourt, Katherine and Sridhar, Sushmita and Lees, Emily A. and Wheeler, Nicole E. and Klemm, Elizabeth J. and Kuijpers, Laura and Mbuyi Kalonji, Lisette and Phoba, Marie France and Falay, Dadi and Ngbonda, Dauly and Lunguya, Octavie and Jacobs, Jan and Dougan, Gordon and Deborggraeve, Stijn (2019) An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation. Nature Communications, 10 (1). 4280. ISSN 2041-1723 (https://doi.org/10.1038/s41467-019-11844-z)

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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.

ORCID iDs

Van Puyvelde, Sandra, Pickard, Derek, Vandelannoote, Koen, Heinz, Eva ORCID logoORCID: https://orcid.org/0000-0003-4413-3756, Barbé, Barbara, de Block, Tessa, Clare, Simon, Coomber, Eve L., Harcourt, Katherine, Sridhar, Sushmita, Lees, Emily A., Wheeler, Nicole E., Klemm, Elizabeth J., Kuijpers, Laura, Mbuyi Kalonji, Lisette, Phoba, Marie France, Falay, Dadi, Ngbonda, Dauly, Lunguya, Octavie, Jacobs, Jan, Dougan, Gordon and Deborggraeve, Stijn;
CORE (COnnecting REpositories)