Whole-Genome Analysis of Salmonella Associated with Osteomyelitis in Senegalese Children with Sickle Cell Disease

Objectives Sickle cell disease is one of the most prevalent inherited hemoglobin disorders globally, affecting over 300,000 newborns annually, with the majority born in sub-Saharan Africa. Children with sickle cell disease are particularly vulnerable to severe bacterial infections, which are a major cause of morbidity and mortality. Among these, Salmonella species, especially non-typhoidal Salmonella, are frequently implicated and are notably associated with osteomyelitis, a serious bone infection. In this study, we performed whole genome sequencing and genomic analysis of 12 Salmonella isolates recovered from osteomyelitis cases in children with sickle cell disease in Dakar, Senegal. Methods The isolates’ identity was confirmed using a MALDI-TOF biotyper and antimicrobial susceptibility testing carried out using the disc diffusion method. Whole-genome sequencing was conducted on an Illumina platform and bioinformatic analyses carried out using open-access and custom tools. Results The isolates belonged to seven serovars, with Enteritidis and Typhimurium being the most frequent (three isolates each). Antibiotic susceptibility testing showed that 11 isolates were fully susceptible to all tested drugs, while one was an extensively drug-resistant strain previously linked to a nosocomial outbreak in a neonatal unit. Most of the isolates contained important Salmonella virulence factors including several Salmonella Pathogenicity Islands and plasmid-borne virulence genes. Conclusion These findings highlight the clinical significance of Salmonella infections in children with sickle cell disease in low-income settings and underscore the urgent need for genomic surveillance and targeted public health interventions to protect this high-risk population.