title: Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong.
abstract: BACKGROUND
  Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patterns of virulence determinants among local S. Typhimurium clinical isolates using their genome sequences.
  
  
  RESULTS
  We obtained genome sequences of 20 S. Typhimurium clinical isolates from a local hospital cluster using a 454 GS FLX Titanium sequencing platform. Phylogenetic analysis was performed based on single nucleotide polymorphism positions of the core genome against the reference strain LT2. Antimicrobial susceptibility was determined using minimal inhibitory concentration for five antimicrobial agents and analyses of virulence determinants were performed through referencing to various databases. Through phylogenetic analysis, we revealed two distinct clades of S. Typhimurium isolates and three outliers in Hong Kong, which differ remarkably in antimicrobial susceptibility and presentation and mutations of virulence determinants. The local isolates were not closely related to many of the previously sequenced S. Typhimurium isolates, except LT2. As the isolates in the two clades spanned over 10 years of isolation, they probably represent endemic strains. The outliers are possibly introduced from outside of Hong Kong. The close relatedness of members in one of the clades to LT2 and the Japanese stool isolate T000240 suggests the potential reemergence of LT2 progeny in regions nearby.
  
  
  CONCLUSIONS
  Our study demonstrated the utility of next-generation sequencing coupled to traditional microbiological testing method in a retrospective epidemiological study involving multiple clinical isolates. The evolution of multidrug- and ciprofloxacin-resistant strains among the more virulent clade is also an increasing concern.
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. billyc801@yahoo.com.hk.
authors.forename: Chi Keung
authors.initials: CK
authors.lastname: Cheng
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. mkcheung@cuhk.edu.hk.
authors.forename: Man Kit
authors.initials: MK
authors.lastname: Cheung
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. nongwenyan@cuhk.edu.hk.
authors.forename: Wenyan
authors.initials: W
authors.lastname: Nong
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. patricklaw@cuhk.edu.hk.
authors.forename: Patrick Tik Wan
authors.initials: PT
authors.lastname: Law
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. qin0jing0@hotmail.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Qin
authors.affiliation: Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China. meilunling@cuhk.edu.hk.
authors.forename: Julia Mei-Lun
authors.initials: JM
authors.lastname: Ling
authors.affiliation: Centre for Health Protection, Department of Health, Hong Kong SAR, China. kmkam1@gmail.com.|Current address: Stanley Ho Centre for Emerging Infectious Diseases, JC School of Public Health, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. kmkam1@gmail.com.
authors.forename: Kai Man
authors.initials: KM
authors.lastname: Kam
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. mwcheung@cuhk.edu.hk.
authors.forename: William Man Wai
authors.initials: WM
authors.lastname: Cheung
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. hoishankwan@cuhk.edu.hk.
authors.forename: Hoi Shan
authors.initials: HS
authors.lastname: Kwan
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002648:Child; D002675:Child, Preschool; D024881:Drug Resistance, Bacterial; D005260:Female; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006723:Hong Kong / Q000453:epidemiology; D006801:Humans; D007223:Infant; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012480:Salmonella Infections / Q000453:epidemiology / Q000382:microbiology*; D012486:Salmonella typhimurium / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D014774:Virulence / Q000235:genetics; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents