Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo

Pimlapas Leekitcharoenphon; Carsten Friis; Ea Zankari; Christina Aaby Svendsen; Lance B. Price; Maral Rahmani; Ana Herrero-Fresno; Kayode Fashae; Olivier Vandenberg; Frank M. Aarestrup; Rene S. Hendriksen

doi:10.3855/jidc.3328

Authors

Pimlapas Leekitcharoenphon Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute and Center for Biological Sequence Analysis, Department of System Biology Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby,
Carsten Friis Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark
Ea Zankari Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark
Christina Aaby Svendsen Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark
Lance B. Price Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, 3051 W. Shamrell Blvd, Ste 106, Flagstaff AZ 86001,
Maral Rahmani Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark
Ana Herrero-Fresno Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark
Kayode Fashae Department of Microbiology, University of Ibadan, Ibadan,
Olivier Vandenberg Infectious Diseases Epidemiological Unit, Public Health School, Université Libre de Bruxelles, Brussels, Route de Lennik, 808 B 1070, Brussels and Department of Microbiology, Saint-Pierre University Hospital, Rue Haute, Hoogstraat 322, Brussels, 1000
Frank M. Aarestrup Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark
Rene S. Hendriksen Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark

DOI:

https://doi.org/10.3855/jidc.3328

Keywords:

Salmonella serovar Typhimurium ST313, Sub-Saharan Africa, MLST, whole genome sequence typing, SNP analysis, virulence genes

Abstract

Introduction: Salmonella enterica serovar Typhimurium ST313 is an invasive and phylogenetically distinct lineage present in sub-Saharan Africa. We report the presence of S. Typhimurium ST313 from patients in the Democratic Republic of Congo and Nigeria.

Methodology: Eighteen S. Typhimurium ST313 isolates were characterized by antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Additionally, six of the isolates were characterized by whole genome sequence typing (WGST). The presence of a putative virulence determinant was examined in 177 Salmonella isolates belonging to 57 different serovars.

Results: All S. Typhimurium ST313 isolates harbored resistant genes encoded by bla_TEM1b, catA1, strA/B, sul1, and dfrA1. Additionally, aac(6’)1aa gene was detected. Phylogenetic analyses revealed close genetic relationships among Congolese and Nigerian isolates from both blood and stool. Comparative genomic analyses identified a putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and S. Dublin.

Conclusion: We showed in a limited number of isolates that S. Typhimurium ST313 is a prevalent sequence-type causing gastrointestinal diseases and septicemia in patients from Nigeria and DRC. We found three distinct phylogenetic clusters based on the origin of isolation suggesting some spatial evolution. Comparative genomics showed an interesting putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and invasive S. Dublin.