High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children.
BACKGROUND
Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection.


METHODS
We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu.


RESULTS
Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study.


CONCLUSIONS
Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period.
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK. kholt@unimelb.edu.au
Kathryn E
KE
Holt
Stephen
S
Baker
Sabina
S
Dongol
Buddha
B
Basnyat
Neelam
N
Adhikari
Stephen
S
Thorson
Anoop S
AS
Pulickal
Yajun
Y
Song
Julian
J
Parkhill
Jeremy J
JJ
Farrar
David R
DR
Murdoch
Dominic F
DF
Kelly
Andrew J
AJ
Pollard
Gordon
G
Dougan
D001426:Bacterial Proteins / Q000235:genetics; D015373:Bacterial Typing Techniques; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D027081:DNA Gyrase / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D024881:Drug Resistance, Bacterial; D005260:Female; D005838:Genotype; D006239:Haplotypes; D057166:High-Throughput Screening Assays; D006801:Humans; D007223:Infant; D008297:Male; D017720:Molecular Epidemiology; D009390:Nepal / Q000453:epidemiology; D020641:Polymorphism, Single Nucleotide; D012485:Salmonella typhi / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D014435:Typhoid Fever / Q000453:epidemiology* / Q000382:microbiology*
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D027081:DNA Gyrase