title: Characterization of Salmonella Typhimurium isolates from domestically acquired infections in Finland by phage typing, antimicrobial susceptibility testing, PFGE and MLVA.
abstract: BACKGROUND
  Salmonella enterica spp. enterica serotype Typhimurium (STM) is the most common agent of domestically acquired salmonellosis in Finland. Subtyping methods which allow the characterization of STM are essential for effective laboratory-based STM surveillance and for recognition of outbreaks. This study describes the diversity of Finnish STM isolates using phage typing, antimicrobial susceptible testing, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA), and compares the discriminatory power and the concordance of these methods.
  
  
  RESULTS
  A total of 375 sporadic STM isolates were analysed. The isolates were divided into 31 definite phage (DT) types, dominated by DT1 (47 % of the isolates), U277 (9 % of the isolates) and DT104 (8 % of the isolates). Of all the isolates, 62 % were susceptible to all the 12 antimicrobials tested and 11 % were multidrug resistant. Subtyping resulted in 83 different XbaI-PFGE profiles and 111 MLVA types. The three most common XbaI-PFGE profiles (STYM1, STYM7 and STYM8) and one MLVA profile with three single locus variants accounted for 56 % and 49 % of the STM isolates, respectively. The studied isolates showed a genetic similarity of more than 70 % by XbaI-PFGE. In MLVA, 71 % of the isolates lacked STTR6 and 77 % missed STTR10p loci. Nevertheless, the calculated Simpson's diversity index for XbaI-PFGE was 0.829 (95 % CI 0.792-0.865) and for MLVA 0.867 (95 % CI 0.835-0.898). However, the discriminatory power of the 5-loci MLVA varied among the phage types. The highest concordance of the results was found between XbaI-PFGE and phage typing (adjusted Wallace coefficient was 0.833 and adjusted Rand coefficient was 0.627).
  
  
  CONCLUSIONS
  In general, the calculated discriminatory power was higher for genotyping methods (MLVA and XbaI-PFGE) than for phenotyping methods (phage typing). Overall, comparable diversity indices were calculated for PFGE and MLVA (both DI > 0.8). However, MLVA was phage type dependent providing better discrimination of the most common phage types. Furthermore, 5-loci MLVA was a less laborious method and easier to interpret than XbaI-PFGE. Thus, the laboratory-based surveillance of the Finnish human STM infections has been conducted with a combination of phage typing, antimicrobial susceptibility testing and 5-loci MLVA since January 2014.
authors.affiliation: Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland. taru.lienemann@thl.fi.
authors.forename: Taru
authors.initials: T
authors.lastname: Lienemann
authors.affiliation: Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland. aino.kyyhkynen@thl.fi.
authors.forename: Aino
authors.initials: A
authors.lastname: Kyyhkynen
authors.affiliation: Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland. jani.halkilahti@thl.fi.
authors.forename: Jani
authors.initials: J
authors.lastname: Halkilahti
authors.affiliation: Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland. kaisa.haukka@helsinki.fi.|Department of Food and Environmental Sciences, Division of Microbiology, University of Helsinki, P.O. BOX 56, 00014, Helsinki, Finland. kaisa.haukka@helsinki.fi.
authors.forename: Kaisa
authors.initials: K
authors.lastname: Haukka
authors.affiliation: Bacterial Infections Unit, National Institute for Health and Welfare, P.O. BOX 30, 00271, Helsinki, Finland. anja.siitonen@thl.fi.
authors.forename: Anja
authors.initials: A
authors.lastname: Siitonen
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D015373:Bacterial Typing Techniques / Q000379:methods*; D001434:Bacteriophage Typing; D004269:DNA, Bacterial / Q000032:analysis*; D005387:Finland; D006801:Humans; D008826:Microbial Sensitivity Tests; D018598:Minisatellite Repeats; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D012480:Salmonella Infections / Q000382:microbiology*; D012486:Salmonella typhimurium / Q000145:classification* / Q000187:drug effects / Q000302:isolation & purification
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial