Evolutionary History and Spread of Multidrug Resistant IncHI1 Plasmids in Salmonella Typhi

Typhoid fever, infection with Salmonella enterica serovar Typhi (S. Typhi), remains a serious health concern in many parts of the world, particularly where sanitation is poor. While vaccines against S. Typhi are available, coverage in endemic regions is low, leaving antimicrobial therapy central to disease control. Unfortunately, drug resistant S. Typhi emerged in the mid-1970s and multi-drug resistance (MDR) is now a significant problem in many typhoid endemic areas. In the S. Typhi population, MDR is almost exclusively conferred by self-transmissible IncHI1 plasmids carrying a suite of antimicrobial resistance genes. We compared eight IncHI1 plasmid sequences and identified single nucleotide polymorphisms (SNPs) in the plasmid backbone. These were combined with known S. Typhi chromosomal SNPs to simultaneously genotype IncHI1 plasmids and their S. Typhi hosts among a collection of 454 S. Typhi dating back to 1958. Among isolates collected prior to 1995, a variety of IncHI1 plasmid types were observed, present in distinct S. Typhi hosts. Some plasmids were detected among distinct S. Typhi lineages co-circulating in time and space, indicating the spread of MDR via transfer of plasmids among S. Typhi strains. From 1995 onwards, 98% of MDR S. Typhi tested were of the same plasmid-strain combination (IncHI1 plasmid sequence type 6 (PST6) and S. Typhi haplotype H58) suggesting that the recent global spread of MDR typhoid is the result of clonal expansion of a single host-plasmid combination. In competition assays, the ability of PST6-bearing S. Typhi to outcompete S. Typhi bearing a distinct IncHI1 plasmid (PST1) varied depending on the host strain, suggesting plasmid-strain interactions may contribute to the recent success of the PST6 plasmid. Comparison of PST6 and PST1 in a common S. Typhi strain background revealed that PST6 conferred osmotolerance, which we demonstrate is due to the presence of the Tn6062 transposon incorporating betU