Dataset Information

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.

SUBMITTER: Holt KE

PROVIDER: S-EPMC3014949 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The Mekong River Delta is the rice production hub in South-east Asia and has a key role in determining rice prices in the world market. The increasing variability in the local climate due to global climate changes and the increasing severity of the ENSO phenomenon threatens rice production in the region, which has consequences for local and global food security. Though existing mapping efforts delineate the consequences of saline water intrusion during El Niño and flooding events during La Niña in the basin, research to predict future impacts in rice production is rather limited. The current work uses ORYZA, an ecophysiological model, combined with historical climate data, climate change scenarios RCP4.5 and 8.5 and climate-related risk maps to project the aggregate productivity and rice production impacts by the year 2050. Results show that in years of average salinity intrusion and flooding, the winter-spring rice crop in the MRD would experience an average annual decrease of 720,450 tons for 2020-2050 under the RCP4.5 scenario compared to the baseline of 2005-2016 average and another 1.17 million tons under the RCP8.5 scenario. The autumn-winter crop would decrease by 331,480 tons under RCP4.5 and 462,720 tons under RCP8.5. In years of severe salinity intrusion and flooding, the winter-spring rice crop would decrease by 2.13 million tons (10.29% lower than the projection for an average year) under RCP4.5 and 2.5 million tons (13.62%) under RCP8.5. Under severe conditions, the autumn-winter crop would have an average decrease of 1.3 million tons (7.36%) under RCP4.5 and 1.4 million tons (10.88%) for the RCP8.5 scenario. Given that most of the rice produced in this area is exported, a decline in rice supply at this scale would likely have implications on the global market price of rice affecting global food security. Such decline will also have implications for the rural economy and food security of Vietnam. Suggestions for corrective measures to reduce the impacts are briefly discussed.