The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study

Abstract

Background: The emergence of increasingly antimicrobial-resistant Salmonella enterica serovar Typhi (S Typhi) threatens to undermine effective treatment and control. Understanding where antimicrobial resistance in S Typhi is emerging and spreading is crucial towards formulating effective control strategies.

Methods: In this genomic epidemiology study, we sequenced the genomes of 3489 S Typhi strains isolated from prospective enteric fever surveillance studies in Nepal, Bangladesh, Pakistan, and India (between 2014 and 2019), and combined these with a global collection of 4169 S Typhi genome sequences isolated between 1905 and 2018 to investigate the temporal and geographical patterns of emergence and spread of antimicrobial-resistant S Typhi. We performed non-parametric phylodynamic analyses to characterise changes in the effective population size of fluoroquinolone-resistant, extensively drug-resistant (XDR), and azithromycin-resistant S Typhi over time. We inferred timed phylogenies for the major S Typhi sublineages and used ancestral state reconstruction methods to estimate the frequency and timing of international and intercontinental transfers.

Findings: Our analysis revealed a declining trend of multidrug resistant typhoid in south Asia, except for Pakistan, where XDR S Typhi emerged in 2016 and rapidly replaced less-resistant strains. Mutations in the quinolone-resistance determining region (QRDR) of S Typhi have independently arisen and propagated on at least 94 occasions, nearly all occurring in south Asia. Strains with multiple QRDR mutations, including triple mutants with high-level fluoroquinolone resistance, have been increasing in frequency and displacing strains with fewer mutations. Strains containing acrB mutations, conferring azithromycin resistance, emerged in Bangladesh around 2013 and effective population size of these strains has been steadily increasing. We found evidence of frequent international (n=138) and intercontinental transfers (n=59) of antimicrobial-resistant S Typhi, followed by local expansion and replacement of drug-susceptible clades.

Interpretation: Independent acquisition of plasmids and homoplastic mutations conferring antimicrobial resistance have occurred repeatedly in multiple lineages of S Typhi, predominantly arising in south Asia before spreading to other regions.

Funding: Bill & Melinda Gates Foundation.

Figure 1

Global phylogeny of Salmonella Typhi (A) Maximum likelihood tree of 7658 S Typhi isolates from the global collection. Branch colours indicate the lineages 2.3.3 (blue), 2.5 (turquoise), 3.2.2 (yellow), 3.3 (green), 4.3.1 (dark red), 4.3.1.1 (red), 4.3.1.1.P1 (orange), 4.3.1.2 (pink), 4.3.1.3 (salmon), and other non-H58 (black). The inner ring indicates the source. The outer ring indicates the region of isolation. The scale bar indicates nucleotide substitutions per site. (B) Temporal distribution of sequenced S Typhi isolates by region.

Figure 2

The effective population size of H58 lineages strains according to antimicrobial resistance genotype in Nepal, Pakistan, and Bangladesh. In Nepal, strains containing 1–2 mutations in the QRDR were compared with those containing three mutations. In Pakistan, XDR strains were compared with non-XDR strains. In Bangladesh, strains containing acrB mutations conferring azithromycin-resistance were compared with those not containing the mutations. Increased values indicate expanding effective population size. Light shading represents the 95% high probability density intervals of the estimates. QRDR=quinolone-resistance determining region. XDR=extensively drug-resistant.

Figure 3

Phylogeography and global expansion of genotype 4.3.1 (H58) Salmonella Typhi isolates Timed phylogenetic tree of genotype 4.3.1 S Typhi isolates. The branch lengths are scaled in years and are coloured according to the location of the most probable ancestor of descendant nodes. The scale bar indicates nucleotide substitutions per site. AZI-R=azithromycin resistant. MDR=multidrug resistant. QRDR=quinolone-resistance determining region. XDR=extensively drug-resistant.

Figure 4

Geographical transfers within lineage 4.3.1 (H58) inferred from ancestral state reconstruction of the timed phylogenetic tree The size of each arrow is scaled to the estimated number of transfers between the countries. Dates indicate the estimated first transfer between each pair of countries.

Figure 5

Major geographical transfers from 1990 onwards within the non-H58 and H58 lineages, inferred from the phylogenetic trees The size of each arrow indicates the relative number of probable transfers between the countries. Arrow colours indicate antimicrobial resistance pattern. FQ-NS=Fluoroquinolone non-susceptible. MDR=multidrug resistant. XDR=extensively drug resistant.