Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam

Abstract

Background: typhoid fever remains a public health problem in Vietnam, with a significant burden in the Mekong River delta region. Typhoid fever is caused by the bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi), which is frequently multidrug resistant with reduced susceptibility to fluoroquinolone-based drugs, the first choice for the treatment of typhoid fever. We used a GoldenGate (Illumina) assay to type 1,500 single nucleotide polymorphisms (SNPs) and analyse the genetic variation of S. Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005.

Principal findings: the population of S. Typhi circulating during the study was highly clonal, with 91% of isolates belonging to a single clonal complex of the S. Typhi H58 haplogroup. The patterns of disease were consistent with the presence of an endemic haplotype H58-C and a localised outbreak of S. Typhi haplotype H58-E2 in 2004. H58-E2-associated typhoid fever cases exhibited evidence of significant geo-spatial clustering along the Sông H u branch of the Mekong River. Multidrug resistance was common in the established clone H58-C but not in the outbreak clone H58-E2, however all H58 S. Typhi were nalidixic acid resistant and carried a Ser83Phe amino acid substitution in the gyrA gene.

Significance: the H58 haplogroup dominates S. Typhi populations in other endemic areas, but the population described here was more homogeneous than previously examined populations, and the dominant clonal complex (H58-C, -E1, -E2) observed in this study has not been detected outside Vietnam. IncHI1 plasmid-bearing S. Typhi H58-C was endemic during the study period whilst H58-E2, which rarely carried the plasmid, was only transient, suggesting a selective advantage for the plasmid. These data add insight into the outbreak dynamics and local molecular epidemiology of S. Typhi in southern Vietnam.

Figure 1. Location of hospitals in the Mekong river delta of Vietnam.

(A) Map showing the 8 Vietnamese regions stretching from the Peoples Republic of China in the north to the Mekong river delta in the south. Highlighted in grey is Mekong river delta (Đ ng B ng Sông C u Long) region, which is the southernmost of the eight regions and covers 40,000 km². The dotted box corresponds to the area magnified in (B). (B) Map showing a ∼22,000 km² of the Mekong river delta; highlighted are An Giang province (green) and Dong Thap province (grey). Also highlighted are the provincial hospitals of An Giang province (x) and Dong Thap (y). The direct distance between the two hospitals is 22.5 km.

Figure 2. Phylogenetic distribution of S. Typhi isolates.

Grey nodes represent control isolates (labelled by isolate code and haplotype group), unfilled grey circle indicates tree root, white nodes correspond to non-H58 S. Typhi isolated in this study (labelled with isolate code), black nodes show H58 isolates. Inset: zoom-in on the H58 haplogroup; grey nodes represent control isolates (labelled by isolate code or haplotype code), unfilled grey circle indicates tree root; coloured circles indicate nodes corresponding to H58 S. Typhi isolated in this study, node labels are as in the text, node colours are as in Figures 3–4, node sizes indicate the number of isolates on the scale as indicated by numbered circles.

Figure 3. Spatial distribution of S. Typhi isolates by haplotype and year.

The spatial distribution of S. Typhi haplotypes surrounding An Giang provincial hospital in (A) 2004 and (B) 2005. Each point corresponds to the residential location of a typhoid fever patient; colour indicates the haplotype of the S. Typhi isolate (with or without plasmid): dark orange  =  H58-E2 with MDR plasmid, light orange  =  H58-E2 without MDR plasmid, dark red  =  H58-C with MDR plasmid, pink, H58-C with MDR plasmid, grey  =  other S. Typhi haplotypes. Locations of the hospitals are indicated by a white cross on a red background; pink circle indicates a radius of 15 km from An Giang Provincial Hospital; arrow indicates the Sông H u branch of the Mekong river.

Figure 4. Monthly incidence of typhoid cases by haplotype.

Bar heights indicate the total number of S. Typhi isolated each month during the study, according to the scale given on the left-hand y-axis; colours indicate the combination of S. Typhi haplotype and presence of IncHI1 ST6 plasmid as given in the legend. Solid black line  =  total rainfall each month recorded in An Giang, dashed line  =  maximum rainfall occurring in a 24 h period during each month in An Giang; rainfall scale is shown on the right-hand y-axis.