Phylogenetic Characterization of Resistant Salmonella Strains in Typhoid Fever Patients in Nigeria

Abstract

Salmonella species are Enterobacteriaceae associated with typhoid fever. In this study, the distribution of broad-spectrum β-lactamase regulatory genes and genetic relatedness of isolates was determined. Stool samples (400) were collected from patients with fever in Dalhatu Araf Specialist Hospital (DASH), Lafia, Nigeria, between March 2020 and April 2021. Salmonella species were isolated and extended-spectrum β-lactamase distribution was determined among resistant isolates using polymerase chain reaction (PCR). Genetic relatedness of Salmonella species resistant to the 10 first-line antibiotics administered was determined among S typhi isolated. Of the 60 isolates that were confirmed to belong to the genus Salmonella, 12 (20.0%) isolates with bla SHV genes were the most prevalent, blaOXA-1 and blaCTX-M-9 were present in 5 isolates each, while blaCTX-M-4 and blaTEM genes with a prevalence of 1.7% each were the least obtained in the isolates. Two isolates had a multidrug-resistant index (MDRI) of 1, and 2 others were positive with the S typhi staG gene. Sequencing to determine their diversity showed that isolates ST36 and ST138, respectively, had MDRI = 1 and are clustered in a group with a similarity coefficient of 0.00634. The 2 isolates had the highest genetic similarity, which indicates that the genetic diversity between the isolates is low, while Salmonella strain ST313L2 had a high level of genetic distance from the other isolates. The most resistant isolates are closely related which calls for concern.