Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

Abstract

Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever, a systemic human infection with a burden exceeding 20 million cases each year that occurs disproportionately among children in low and middle income countries. Antimicrobial therapy is the mainstay for treatment, but resistance to multiple agents is common. Here we report genotypes and antimicrobial resistance (AMR) determinants detected from routine whole-genome sequencing (WGS) of 533 S. Typhi isolates referred to Public Health England between April 2014 and March 2017, 488 (92%) of which had accompanying patient travel information obtained via an enhanced surveillance questionnaire. The majority of cases involved S. Typhi 4.3.1 (H58) linked with travel to South Asia (59%). Travel to East and West Africa were associated with genotypes 4.3.1 and 3.3.1, respectively. Point mutations in the quinolone resistance determining region (QRDR), associated with reduced susceptibility to fluoroquinolones, were very common (85% of all cases) but the frequency varied significantly by region of travel: 95% in South Asia, 43% in East Africa, 27% in West Africa. QRDR triple mutants, resistant to ciprofloxacin, were restricted to 4.3.1 lineage II and associated with travel to India, accounting for 23% of cases reporting travel to the country. Overall 24% of isolates were MDR, however the frequency varied significantly by region and country of travel: 27% in West Africa, 52% in East Africa, 55% in Pakistan, 24% in Bangladesh, 3% in India. MDR determinants were plasmid-borne (IncHI1 PST2 plasmids) in S. Typhi 3.1.1 linked to West Africa, but in all other regions MDR was chromosomally integrated in 4.3.1 lineage I. We propose that routine WGS data from travel-associated cases in industrialised countries could serve as informal sentinel AMR genomic surveillance data for countries where WGS is not available or routinely performed.

Fig 1. Summary of S. Typhi received at Public Health between April 2014 to March 2017.

a) Map highlighting countries that were reported as travel destinations for patients from which S. Typhi cultures were collected. Countries are coloured by major geographical regions. Blank map sourced from https://commons.wikimedia.org/wiki/File:BlankMap-FlatWorld6.svg b) Number of S. Typhi isolates reporting travel to each country over the three-year period of study, stratified by date of receipt at PHE.

Fig 2. Membership of S. Typhi by genotypes and association with AMR.

a) Population framework tree of the S. Typhi genotypes sequenced at PHE. Background shading indicates the primary clades. Tree tips indicate individual genotypes assigned by GenoTyphi; tip sizes and colours indicate number of isolates belonging to each genotype, these values (n) are also printed to the right. b) Frequency of MDR for each genotype (defined based on presence of AMR genes encoding resistance to the first line drugs ampicillin, trimethoprim-sulfamethoxazole, or chloramphenicol). c) Frequency of QRDR mutations by genotype.

Fig 3. Geographic distribution of S. Typhi based on reported country of travel.

S. Typhi isolates with completed travel questionnaires and reporting travel to only one country are shown. The number in each circle indicates the total number of cases reporting travel to that country, circle graphs indicate the genotype composition of the corresponding S. Typhi isolates, stratified by MDR, coloured as per inset legend. Blank map sourced from https://commons.wikimedia.org/wiki/File:BlankMap-FlatWorld6.svg

Fig 4. Minimum inhibitory concentration (MIC) for ciprofloxacin versus number of point mutations in QRDRs in two chromosomal genes.

The number of isolates with different combinations of MIC values and point mutations detected in the QRDRs of two chromosomal genes, gyrA and parC, are shown. The breakpoints of susceptible, reduced susceptibility and resistance are shown by the background gradient of the plot. The triangle indicates an isolate that carries qnrS-1.

Fig 5. Mobilisation of MDR element in S. Typhi.

a) Structure of the MDR composite transposon in S. Typhi strain ERL12960 (4.3.1 lineage I) is shown (accession ERL12960). MDR genes are those encoding resistance to the first line drugs ampicillin, trimethoprim-sulfamethoxazole or chloramphenicol b) Phylogeny showing genetic relationships between the five IncHI1 PST2 S. Typhi isolates identified in this study, based on SNVs identified in the plasmid backbone sequence and rooted using the PST1 plasmid pUI1203_01 (accession ERR340785) as an outgroup. The presence of AMR genes detected in each genome is indicated in the heatmap, with alleles specified for dfrA and bla_TEM genes.