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.

Details

Title
An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation
Author
Sandra Van Puyvelde 1   VIAFID ORCID Logo  ; Pickard, Derek 2 ; Vandelannoote, Koen 3 ; Heinz, Eva 4   VIAFID ORCID Logo  ; Barbé, Barbara 5 ; de Block, Tessa 3 ; Simon, Clare 6 ; Coomber, Eve L 6   VIAFID ORCID Logo  ; Harcourt, Katherine 6 ; Sridhar, Sushmita 2 ; Lees, Emily A 2   VIAFID ORCID Logo  ; Wheeler, Nicole E 7   VIAFID ORCID Logo  ; Klemm, Elizabeth J 6   VIAFID ORCID Logo  ; Kuijpers, Laura 8   VIAFID ORCID Logo  ; Kalonji, Lisette Mbuyi 9 ; Marie-France Phoba 9 ; Falay, Dadi 10 ; Dauly Ngbonda 10 ; Lunguya, Octavie 9 ; Jacobs, Jan 8   VIAFID ORCID Logo  ; Dougan, Gordon 2 ; Deborggraeve, Stijn 3   VIAFID ORCID Logo 

1  Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium 
2  Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK 
3  Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium 
4  Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK 
5  Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium 
6  Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK 
7  Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK 
8  Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Microbiology and Immunology, KU Leuven, Herestraat 49—box 1030, Leuven, Belgium 
9  Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo; Department of Microbiology, University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo 
10  Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of the Congo 
Pages
1-12
Publication year
2019
Publication date
Sep 2019
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-019-11844-z
ProQuest document ID
2293852376
Copyright
© 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.