Genomic epidemiology of Salmonella paratyphi A strains isolated in Hangzhou area
Objective 
To understand the genomic epidemiology of Salmonella paratyphi A strains circulating in Hangzhou area in recent years. 
 
 
Methods 
Next generation sequencing (NGS) technology was used to obtain genomes of 60 Salmonella paratyphi A strains isolated in Hangzhou area from 2002 to 2013. Genomes of 391 Salmonella paratyphi A strains were downloaded from the Sequence Read Archive (SRA) and Assembly database. After removing recombinations, the phylogenetic tree of all 451 genomes based on single nucleotide polymorphisms (SNP) was constructed using ATCC9150 as the reference. SRST2 and multilocus sequence typing (MLST) were used to analyze sequence types (ST). The Salmonella In Silico Typing Resource (SISTR) was used for core genome multilocus sequence typing (cgMLST). Resistant genes were screened out with SRST2 and BLASTN. Seven kinds of antibiotics were selected to conduct drug susceptibility test in the 60 strains isolated in Hangzhou. 
 
 
Results 
A total of 19 258 SNP loci were found in 451 genomes. The average distance in the phylogenetic tree between strains was 0.007 0 and the distance less than 0.05 accounted for 96.73%, indicating a little difference in the 451 Salmonella paratyphi A genomes. Fifty-eight Hangzhou strains of ST85 were highly similar in genomic sequences, which suggested that the clonal spread of ST85 strains caused the epidemic of paratyphoid A in Hangzhou area during 2002-2013. Salmonella paratyphi A strains isolated in Hangzhou were distantly related to five domestic strains (average distance: 0.057), but close to 15 Yunnan strains (average distance: 0.003 2) and closest to strains isolated in Cambodia (average distance: 0.001 8), suggesting the possibility of transnational spread of ST85 strains. Among two Hangzhou strains of ST129, HZ333 was closely related to two strains isolated in Jiangsu Province (average distance: 0.009 7), suggesting the possibility of domestic transmission of ST129 strains. Except for two untyped strains, the other 58 strains were divided into nine cgMLST types. Except for 57 untyped strains, the other 334 strains obtained from public databases were classified into 165 cgMLST types. Fifty-six out of the 60 Hangzhou strains carried the resistant gene aac6-Iy and the other four carried aac6-Iaa gene. Thirteen out of the 391 strains obtained from public databases didn′t carry resistant genes, while the other 378 strains carried the resistant gene aac6-Iy. Among the 60 Hangzhou strains, 56 were sensitive to all of the seven kinds of antibiotics; three were resistant to cotrimoxazole and one was resistant to ampicillin and tetracycline. 
 
 
Conclusion 
The epidemic of paratyphoid A fever in Hangzhou from 2002 to 2013 was mainly caused by the clonal spread of ST85 strains that had the possibility of transnational spread. Some Hangzhou strains of ST129 had the possibility of domestic transmission. SNPs analysis had an advantage over pulse field gel electrophoresis (PFGE) technology in resolution and could be used to accurately trace the cause of paratyphoid A fever. Resistant gene aac6-Iy was generally carried. NGS technology had a promising prospect in the control and prevention of infectious diseases. 
 
 
Key words: 
Salmonella paratyphi A; Next generation sequencing; Single nucleotide polymorphisms; Multilocus sequence typing; Core genome multilocus sequence typing; Drug resistant gene