Whole genome sequencing of multidrug-resistant Salmonella enterica serovar Typhimurium isolated from humans and poultry in Burkina Faso

Authors: KAGAMBEGA, ASSETA - Institute Of Environmental And Agricultural Research - Burkina Faso (FORMERLY: UPPER VOLTA); LIENEMANN, TARU - National Institute For Health And Welfare (HELSINKI); Frye, Jonathan; BARRO, NICOLAS - Institute Of Environmental And Agricultural Research - Burkina Faso (FORMERLY: UPPER VOLTA); HAUKKA, KAISA - University Of Helsinki

Submitted to: Tropical Medicine and Health
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2018
Publication Date: 2/12/2018
Citation: Kagambega, A., Lienemann, T., Frye, J.G., Barro, N., Haukka, K. 2018. Whole genome sequencing of multidrug-resistant Salmonella enterica serovar Typhimurium isolated from humans and poultry in Burkina Faso. Tropical Medicine and Health. 46:4. doi: 10.1186/s41182-018-0086-9.
DOI: https://doi.org/10.1186/s41182-018-0086-9

Interpretive Summary: Salmonella is an important food borne infection that can cause gastroenteritis or invasive systemic infections. In Africa it is a major cause of child mortality. Multi drug resistant strains of Salmonella are more difficult to treat during an invasive infection. In this study, we described the whole genome sequencing results of MDR S. Typhimurium strains isolated from feces of humans and poultry in Burkina Faso. The genetic similarity of these isolates suggests their may be transmission from poultry to humans of this Salmonella enterica serovar Typhimurium ST313 strain. This study provides new data to better understand the geographical spread of S. Typhimurium ST313 genotypes and their potential host reservoirs in sub-Saharan Africa. The epidemic caused by S. Typhimurium in sub-Saharan Africa shows that next-generation sequencing facilities should be available also to the scientists in the resource-limited African countries to detect epidemics in their early phase. The present study highlights the need of a good surveillance system of foodborne pathogens to prevent enteric diseases in sub-Saharan Africa.

Technical Abstract: Background. Multidrug-resistant Salmonella is an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistant Salmonella enterica serovar Typhimurium isolates from patients and poultry feces. Methods. Salmonella strains were isolated from poultry and patients using standard bacteriological methods described in previous studies. The strains were serotype according to Kaufmann-White scheme and tested for antibiotic susceptibility to 12 different antimicrobial agents using the disk diffusion method. The whole genome of the S. Typhimurium isolates was analysed using Illumina technology and compared with 20 isolates of S. Typhimurium for which the ST has been deposited in a global MLST database (http://www.mlst.net/) (Fig. 1). The ResFinder Web server was used to find the antibiotic resistance genes from whole genome sequencing (WGS) data. For comparative genomics, publicly available complete and draft genomes of different S. Typhimurium laboratory-adapted strains were downloaded from GenBank. Results. All the tested Salmonella serotype Typhimurium was multiresistant to five commonly used antibiotics (ampicillin, chloramphenicol, streptomycin, sulfonamide and trimethoprim). The Multilocus sequence type ST313 was detected from all the strains. Our sequences were very similar to S. Typhimurium ST313 strain D23580 isolated from a patient with invasive non-typhoid Salmonella (NTS) infection in Malawi, also located in sub-Saharan Africa. The use of ResFinder web server on the whole genome of the strains showed a resistance to aminoglycoside associated with carriage of the following resistances genes: strA, strB and aadA1; resistance to ß-lactams associated with carriage of a blaTEM-1B genes; resistance to phenicol associated with carriage of catA1 gene, resistance to sulfonamide associated with carriage of sul1 and sul2 genes, resistance to tetracycline associated with carriage of tet B gene, and resistance to trimethoprim associated to dfrA1 gene for all the isolates. Conclusion. The poultry and human isolates were genetically similar showing a potential food safety risk for consumers. Our finding of multi-drug resistant S. Typhimurium ST313 in poultry feces calls for further studies to clarify the potential reservoirs of this emerging pathogen.