Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Abstract

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

Figure 1

Population structure of the 1,832 S. Typhi isolates analyzed in this study. (a) Temporal distribution of the S. Typhi isolates included in the study. (b) Rooted maximum-likelihood tree of S. Typhi inferred from 22,145 SNPs, rooted using an outgroup (S. enterica serovar Paratyphi A, isolate 9953_5_4_Outgroup_ParatyphiA_IndoA270_2010). The colored ring indicates the geographical origin of the isolates. Red arc, H58 lineage; labeled blue dashed lines, public reference genomes reported in Holt et al., including the CT18 (R) reference genome (AL513382); black dashed lines, other publicly available genomes. Branch lengths are indicative of the estimated substitution rate per variable site.

Figure 2

Population structure of the S. Typhi H58 lineage. Rooted maximum-likelihood phylogeny inferred from 1,534 SNPs identified in the 853 H58 isolates, rooted using an S. Typhi isolate from the nearest neighboring cluster of non-H58 isolates as an outgroup (black filled circle; isolate 10060_5_62_ Fij107364_2012). The colored ring indicates the countries of isolation; countries discussed in the text are labeled around the tree. Branch lengths are indicative of the estimated substitution rate per variable site.

Figure 3

Geographical persistence and routes for dissemination of S. Typhi H58. (a) Maximum-likelihood tree for the H58 lineage (I and II), with clades containing isolates from a single country collapsed into nodes (circles), sized to indicate the number of isolates in the clade and colored by country of isolation. Branches are colored to indicate the country of origin of descendant nodes. (b) Years of isolation for each phylogeographical cluster in the tree, indicated by lines spanning the earliest and latest years of isolation for each cluster and colored to indicate the country. Four regions with extensive local clonal expansion are highlighted by shaded boxes, spanning the phylogenetic (y axis) and temporal (x axis) extent of the expansion. Locations from which singleton isolates were clustered within the phylogeographical clusters are shown to the right, indicative of further onward transmission.

Figure 4

Major geographical transfers within the H58 lineage, inferred from the phylogenetic tree. The size of each arrow indicates the relative number of likely transfers between regions or countries.

Figure 5

Insertion site of the 24-kb composite transposon in CT18. A comparative analysis using genoPlotr of CT18 and H58 isolates ERL12960 (ERR343327) and 12148 (ERR343322) showed two integration sites of the transposon in the chromosome. The nucleotide sequence of the composite transposon was identical to that in the IncHI1-PST6 plasmid of H58 isolate 10425_1_48_Viety3-193_1997, which was sequenced for comparison. Tn, transposon; TSD, target site duplication.

Figure 6

Acquired multidrug resistance in the S. Typhi H58 lineage. Maximum-likelihood phylogeny from 1,534 SNPs of 853 H58 isolates rooted using an S. Typhi isolate from the nearest neighboring cluster of non-H58 isolates as an outgroup (isolate 10060_5_62_ Fij107364_2012) and surrounded by five colored rings representing (1) geographical origin in terms of region, (2) number of transposon-encoded resistance genes, (3) presence of resistance plasmids, (4) presence of IS1 insertion near the cyaA gene and (5) the site of chromosomal integration. Black radial dashed lines show the positions of public reference strains. Branch lengths are indicative of the estimated substitution rate per variable site.