Preliminary genomic characterisation and antimicrobial resistance of non-typhoidal Salmonella isolates from Burkina Faso within a One Health framework

Purpose Non-typhoidal Salmonella (NTS) is a major foodborne pathogen worldwide, especially in low and middle-income countries. This study used whole-genome sequencing (WGS) to analyze the epidemiological trends, sequence types (STs), antimicrobial resistance (AMR), and genome dynamics, and to assess the phylogenetic relatedness of NTS isolates in Burkina Faso. Methods A total of 34 presumptive Salmonella enterica isolates from animal products ( n  = 20), environmental sources ( n  = 8), and diarrheal stool samples ( n  = 6) were analyzed by Matrix-Assisted Laser Desorption Ionization-Time Of Flight mass spectrometry (MALDI–TOF MS). Isolates confirmed as S. enterica by MALDI–TOF MS were subsequently sequenced, and bioinformatic analysis was performed using the Bactopia pipeline. Results Of the 34 presumptive Salmonella isolates, 21 (61.76%) were confirmed as Salmonella enterica by MALDI–TOF MS. Of the 21 Salmonella enterica detected, 16 were from animal products, 3 were from environmental sources, and 2 were from diarrheal stool samples. The most prevalent serovars were S . Schwarzengrund (ST96) and S . Give (ST516), each accounting for four isolates (19.04%). All isolates carried the resistance genes emrR, pmrE, mdtK, cpxAR, bacA, baeSR, mdtABC, acrA, KdpE, golS, mdsABC, marA, mfd, msbA, sdiA, rob, UhpT and GlpT fosR . One S . Molade or S. Wippra isolate ST544, harbored the AMR genes fosA7-4, sul2, tet(A), dfrA14, qnrB1, and aph(3ʺ)-Ib. In addition, one S. Llandoff isolate carried catA, aac(6ʹ), and fosM . Virulence genes, including invA, avrA, iroB, iroC, and sinH, were observed in all isolates, while 72.73% of the isolates harbored the cdtB gene. Conclusion This is the first extensive study on non-typhoidal Salmonella and their clones in Burkina Faso. Effective AMR-inclusive surveillance strategies and novel control methods are needed to improve the management and treatment of multidrug-resistant (MDR) NTS infections and to mitigate the burden of NTS in the African sub-region.