Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016

Abstract

Typhoid fever epidemiology was investigated rigorously in Santiago, Chile during the 1980s, when Salmonella enterica serovar Typhi (S. Typhi) caused seasonal, hyperendemic disease. Targeted interventions reduced the annual typhoid incidence rates from 128-220 cases/105 population occurring between 1977-1984 to <8 cases/105 from 1992 onwards. As such, Santiago represents a contemporary example of the epidemiologic transition of an industrialized city from amplified hyperendemic typhoid fever to a period when typhoid is no longer endemic. We used whole genome sequencing (WGS) and phylogenetic analysis to compare the genotypes of S. Typhi cultured from acute cases of typhoid fever occurring in Santiago during the hyperendemic period of the 1980s (n = 74) versus the nonendemic 2010s (n = 80) when typhoid fever was rare. The genotype distribution between "historical" (1980s) isolates and "modern" (2011-2016) isolates was similar, with genotypes 3.5 and 2 comprising the majority of isolations, and 73/80 (91.3%) of modern isolates matching a genotype detected in the 1980s. Additionally, phylogenomically 'ancient' genotypes 1.1 and 1.2.1, uncommon in the global collections, were also detected in both eras, with a notable rise amongst the modern isolates. Thus, genotypes of S. Typhi causing acute illness in the modern nonendemic era match the genotypes circulating during the hyperendemic 1980s. The persistence of historical genotypes may be explained by chronic typhoid carriers originally infected during or before the 1980s.

Fig 1. Genotypes and molecular determinates of AMR and plasmids in the Santiago collection.

SNP based maximum likelihood core genome phylogeny indicating the genotypes of all the Santiago S. Typhi isolates is shown by the branch colour as per the inset legend. A diverse range of 14 genotypes were detected including 1.1, 1.2.1, 2, 2.0.2, 2.2, 2.3.2, 2.3.3, 2.3.4, 3.1, 3.3, 3.5, 4.1, 4.3.1.1, 4.3.1.2. Most of the isolates belonged to genotype 1.1, 2 and 3.5. Year of isolation, SNPs in the QRDR region associated with reduced susceptibility to fluoroquinolones as well as plasmids and detected resistance genes are shown in the columns adjacent to the tree. Bootstrap confidence of 80 or above is indicated with a black circle on the branch.

Fig 2. A global context maximum likelihood core genome phylogeny incorporating publicly available non-H58 and Santiago S. Typhi isolates.

SNP based core genome maximum likelihood tree of 2013 global isolates, branches are coloured by genotype as per the inset legend; the ring indicates country of isolation as per the inset legend; Santiago isolates are highlighted in black and the Colombian isolates in red.

Fig 3. S. Typhi clade 1.1 phylogeny showing sequences carrying ssrA mutation (ssrA-G639E).

Phylogenetic core genome analysis of all S. Typhi isolates of genotype 1.1 identified from the global collection. The majority of these isolates were collected in Santiago (black bar); two isolates belonged to the 1980s collection appearing ancestral to the 2010s collection. The twenty isolates from 2011–2012 showed an interesting cluster with a median SNP distance of 8 SNPs which is unlikely to have evolved among acute cases, where the mutation rate is calculated to be < 1 SNP/genome/year, in one year. Also shown is an alignment of a section of the ssrA gene, showing the conserved SNP at position 1648986 of the S. Typhi CT18 reference genome. * the precise isolation year of one of the 1980s isolates was unclear.

Fig 4. Genetic comparison of cryptic plasmid pHCM2-like sequences.

Global representative collection of pHCM2 aligned to the reference pHCM2 from CT18. (A) Presence and absence of genes located on pHCM2. Red indicates presence of the genes located on the reference pHCM2 sequence from CT18, while blue indicates absence of the genes compared to the reference. Nucleotide BLAST comparison of the 2 Chilean assembled pHCM2-like plasmids (ERR271054, ERR4289185) against the reference pHCM2 plasmid from S. Typhi CT18 (accession no:AL513384) (B). Gene annotations are shown for the reference pHCM2 from CT18, with the shading intensity indicating percent nucleotide homology between the plasmid sequences.