RESEARCH ARTICLE Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo Dadi Falay 1,2,3 , Liselotte Hardy ID 3 *, Jacques Tanzito 4 , Octavie Lunguya 5,6 , Edmonde Bonebe 5 , Marjan Peeters 3 , Wesley Mattheus 7 , Chris Van Geet 8 , Erik Verheyen 9,10 , Dudu Akaibe 4 , Pionus Katuala 4 , Dauly Ngbonda 1 , Franc¸ ois- Xavier Weill 11 , Maria Pardos de la Gandara 11 , Jan Jacobs 2,3 1 Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo, 2 Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium, 3 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium, 4 Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversite´ , CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo, 5 Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo, 6 Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo, 7 Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Brussels, Belgium, 8 Department of Cardiovascular Sciences and Pediatrics, KU Leuven and University Hospital Leuven, Leuven, Belgium, 9 OD Taxonomy & Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium, 10 Evolutionary Ecology, University of Antwerp, Antwerp, Belgium, 11 Institut Pasteur, Universite´ Paris Cite´ , Unite´ des bacte´ ries pathogènes ente´ riques, Paris, France * lhardy@itg.be Abstract Background Invasive non-typhoidal Salmonella (iNTS–mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reser- voir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans. Methodology/Principal findings From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughter- house in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans—obtained from blood cultures at Kisangani University Hospital—was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilo- cus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen PLOS NEGLECTED TROPICAL DISEASES PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0010740 September 6, 2022 1 / 21 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Falay D, Hardy L, Tanzito J, Lunguya O, Bonebe E, Peeters M, et al. (2022) Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo. PLoS Negl Trop Dis 16(9): e0010740. https://doi.org/10.1371/journal. pntd.0010740 Editor: Travis J. Bourret, Creighton University, UNITED STATES Received: May 25, 2022 Accepted: August 13, 2022 Published: September 6, 2022 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pntd.0010740 Copyright: © 2022 Falay et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files. All genomes obtained by WGS