Invasive non-typhoidal Salmonella from stool samples of healthy human carriers are genetically similar to blood culture isolates: a report from the Democratic Republic of the Congo

Lisette Mbuyi-Kalonji; Liselotte Hardy; Jules Mbuyamba; Marie-France Phoba; Gaëlle Nkoji; Wesley Mattheus; Justin Im; Florian Marks; Hyon Jin Jeon; Jan Jacobs; Octavie Lunguya

doi:10.3389/fmicb.2023.1282894

Invasive non-typhoidal Salmonella from stool samples of healthy human carriers are genetically similar to blood culture isolates: a report from the Democratic Republic of the Congo

Front Microbiol. 2023 Nov 24:14:1282894. doi: 10.3389/fmicb.2023.1282894. eCollection 2023.

Authors

Lisette Mbuyi-Kalonji^{1

2

3

4}, Liselotte Hardy³, Jules Mbuyamba^{1

2}, Marie-France Phoba^{1

2}, Gaëlle Nkoji^{1

2}, Wesley Mattheus⁵, Justin Im⁶, Florian Marks^{6

7

8

9}, Hyon Jin Jeon^{6

7

9}, Jan Jacobs^{3

4}, Octavie Lunguya^{1

2}

Affiliations

¹ Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of Congo.
² Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of Congo.
³ Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
⁴ Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.
⁵ Department of Human Bacterial Diseases, Sciensano, Brussels, Belgium.
⁶ International Vaccine Institute, Seoul, Republic of Korea.
⁷ Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.
⁸ Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany.
⁹ Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar.

Abstract

Invasive non-typhoidal Salmonella (iNTS) (serotypes Typhimurium and Enteritidis) are major causes of bloodstream infections in sub-Saharan Africa, but their reservoir is unknown. Aiming to demonstrate human carriers as a reservoir, we assessed an iNTS disease endemic rural community (Kikonka health area, Democratic Republic of the Congo) for intestinal carriage of iNTS. After a census, healthy subjects from randomly selected households provided three successive stool samples for Salmonella culture. We next compared the stool isolates for genetic relatedness with time and health area-matched blood culture isolates obtained from hospitalized patients by multiple locus variable-number tandem repeat analysis (MLVA) and performed whole genome sequencing (WGS) on a subset of stool and blood isolates. Among 2,354 eligible subjects, 2,234 (94.9%) consented and provided at least one stool sample, and 2,219 (94.3%) provided three stool samples. The cumulative proportion of Salmonella carriers after 3 days was 4.4% (n = 98). S. Typhimurium and Enteritidis were found in 26 and 3 carriers, respectively, representing 1.3% (29 out of 2,234) of participants living in 6.0% (26 out of 482) of households. MLVA types of all 26 S. Typhimurium stool isolates matched with the corresponding MLVA types of blood isolates. The MLVA type of one out of three Enteritidis stool isolates matched the single MLVA type of the five Enteritidis blood isolates. WGS analysis of S. Typhimurium (n = 20) and S. Enteritidis (n = 4) isolates revealed Typhimurium multilocus sequence type (ST)313 Lineage 2 and Enteritidis ST11 Central/Eastern African and Outlier clades and confirmed the MLVA clustering. More than three-quarters of Typhimurium isolates showed combined multidrug resistance, ceftriaxone resistance, and fluoroquinolone non-susceptibility. In conclusion, the present study demonstrated iNTS carriage among healthy community members, with stool isolates that were genetically similar to blood culture isolates obtained in patients from the same community. These findings contribute to the evidence of a human reservoir of iNTS.

Keywords: Africa; DR Congo; Salmonella Enteritidis ST11; Salmonella Typhimurium ST313; human carriers; reservoir.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by the Belgian Directorate of Development Cooperation and humanitarian aid (DGD) through the 5th Framework Agreement between the Institute of Tropical Medicine (ITM) in Belgium, Antwerp, Belgium and the National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo (BE-BCE_KBO-0410057701-prg2022-1-CD), as well as by the Bill and Melinda Gates Foundation project OPP1127988 funded to International Vaccine Institute. LM-K holds a PhD scholarship from the Belgian DGD funded to ITM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.