Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing

Abstract

Background Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 111 strains of Salmonella isolated from poultry feces in Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0. Results Among the 111 Salmonella isolates, serotypes for 17 (15.31%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. Forty-four (44) new SMART codes were developed for common and uncommon serotypes. A total of 105 (94.59%) isolates were serotyped using SeqSero 2.0 for serovar prediction based on WGS data. Conclusion We determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.

Characterization of virulence factors of Salmonella isolated from human stools and street food in urban areas of Burkina Faso

“…This ubiquitous serotype has been closely linked to poultry since 1937 and is now spread in several African countries [ 43 ]. In the current decade in West Africa, the finding of the expansion of Salmonella Kentucky in the poultry sector has also been reported by Igomu et al [ 44 ] and Kagambèga et al [ 45 ].…”

Resistance Genes, Plasmids, Multilocus Sequence Typing (MLST), and Phenotypic Resistance of Non-Typhoidal Salmonella (NTS) Isolated from Slaughtered Chickens in Burkina Faso

“…The present study concurs with previous research that the T57S substitution detected in par C is not always associated with a quinolone resistance phenotype since it has been found in both resistant and susceptible isolates [ 11 , 29 ]. Feng et al [ 30 ] also found similar results in a study of a Salmonella Goldcoast lineage in Northern Taiwan, where a single T57S mutation was not always sufficient to confer clinically significant resistance.…”

“…DNA extraction, library preparation, whole-genome sequencing, assembly, and annotation for the 102 Salmonella strains were completed as previously reported [ 11 ]. Briefly, libraries were prepared using Nextera XT DNA library preparation kits, which were sequenced using either a 300 or 500 cycle Illumina MiSeq version 2 reagent kit.…”

“…Whole-genome sequencing (WGS) allows for the analysis of the Salmonella genome but requires expensive equipment and reagents, which are inaccessible to laboratories in Burkina Faso; therefore, for this study, we collaborated with scientists at the United States Department of Agriculture, Agricultural Research Service (USDA-ARS). Previously, we investigated the genomic characterization of Salmonella isolated from fish in Burkina Faso [ 11 ]. The present study aims to characterize Salmonella strains isolated from slaughtered chickens in Burkina Faso using WGS to better understand their molecular epidemiology.…”

Contamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso

“…As we studied only one Salmonella colony per sample, we were not able to identify cases of sandwich contamination with several different serotypes in this study. Twelve of these 16 serotypes have already been detected in food animals or edible vegetables in Burkina Faso, between 2008 and 2018: Agona (cattle, poultry, fish), Brancaster (cattle, poultry), Bredeney (cattle, poultry, fish, lettuce), Derby (poultry, fish, sheep), Enteritidis (poultry), Hato (cattle, poultry), Kaapstad (poultry, pigs), Kentucky (poultry, fish), Muenster (cattle, poultry, pigs, fish, hedgehogs), Poona (cattle, poultry, fish), Tennessee (cattle), and Tilene (cattle, poultry, fish) [2][3][4][31][32][33]. Eight of these 16 serotypes were also reported in humans in this country (Bredeney, Derby, Enteritidis, Kentucky, Muenster, Poona, Tilene, and Tennessee) [34][35][36].…”