Sequence type ST313 of Salmonella Typhimurium is a major cause of human bloodstream infections in sub-Sahara Africa. In 2022, an HIV-positive man, who travelled from Kinshasa (Democratic Republic of Congo, DRC) to Liverpool (UK), was hospitalised with a Salmonella Typhimurium bloodstream infection. The pathogen was isolated from both stool and blood samples, and complete genomes were generated using Nanopore, PacBio and Illumina technologies.
Comparative genomics showed that the chromosome of the stool isolate (designated JH4684) was closely related to the ST313 Lineage 2.0 reference strain D23580 with 51 SNP differences. D23580 carries a pBT1 plasmid, which was previously found to carry essential genes for bacterial survival in vitro. However, pBT1 was absent from JH4684. Although the virulence plasmid pSLT was present in both D23580 and JH4684, the pSLTD23580 multidrug resistance (MDR) gene cassette was absent from pSLTJH4684. JH4684 carried an IncHI2 plasmid that encoded resistance to multiple antibiotics, including Ampicillin, Chloramphenicol, Gentamicin, Trimethoprim, Sulphonamide, Ciprofloxacin and Ceftriaxone. The isolate was susceptible to Azithromycin. A similar plasmid, pSTm-ST313-II.1, was reported in ST313 L2.1 strains from DRC and had a similar antibiotic resistance profile with JH4684 (Van Puyvelde et al., 2019 Nature Comms).
A large-scale comparative genomic analysis with identified closely-related IncHI2 MDR plasmids in a variety of sub-lineages of S. Typhimurium ST313 and in different Enterobacteriaceae species (visualisation available in Microreact https://microreact.org/project/beTkG2SptznruioeWJr2P5-plsdbkinshasa).
Overall, we have identified a novel bloodstream-associated S. Typhimurium ST313 L2.0 strain that is closely related to D23580 but has distinct plasmid features. The strain carries an IncHI2 plasmid that was first reported in ST313 L2.1. A variant of the pSTm-ST313-II.1 plasmid has now been acquired by a diverse range of bacterial pathogens in Africa and elsewhere.