Characterization of Salmonella Typhimurium isolates from domestically acquired infections in Finland by phage typing, antimicrobial susceptibility testing, PFGE and MLVA

Abstract

BackgroundSalmonella 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.ResultsA 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).ConclusionsIn 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.

Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.

“…Although PFGE is considered as current gold standard for all Salmonella serotypes, it has its limitations moreover, variation between laboratories has been reported when identifying the source of infection and discriminating between the outbreak and non-outbreak isolates (16).…”

“…Other phenotypic tools such as phage typing and antimicrobial resistance profiling have been crucial in the outbreak investigations (16,17). Furthermore, MLVA has been used to distinguish between genetically closely related strains and trace back the sources of disease outbreaks related to food (16,18).…”

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

“…Phage types DT104 and U302, in addition to DT193 and DT12, were clustered within the same genotypic clonal types (Jeoffreys et al, 2001 ; Liebana et al, 2002b ; Lan et al, 2003 ; Lindstedt et al, 2003 ; Ross and Heuzenroeder, 2005 ; Boxrud et al, 2007 ; Prendergast et al, 2011 ). Furthermore, Lienemann et al ( 2015 ) reported that when a particular phage type circulating among animals is well known, phage typing approach still is useful for outbreak detection in humans, especially when the analyzed isolates are considered clones by genotypic technics.…”

Modern Salmonella subtyping methods in outbreak investigations

“…Благодаря высокой разрешающей способности, низкой себестоимости, хорошей воспроизводимости и наличию международного стандартизованного протокола (www.cdc. gov/pulsenet/participants/international), метод PFGE включен в арсенал валидированных методов молекулярной характеристики штаммов большинства серотипов Salmonella в надзоре за сальмонеллезами в США и странах Европы [11][12][13]. В то же время метод имеет ограниченные возможности для субтипирования серотипов c высоко консервативным геномом (S.Enteritidis, S.Typhimurium DT104), генетически отдаленные изоляты которых могут иметь идентичные PFGEсубтипы.…”

“…Число повторов в исследуемом локусе определяют методом капиллярного электрофореза или путем секвенирования продуктов амплификации. MLVA-профили штаммов меняются достаточно быстро, что позволяет идентифицировать клоны и дифференцировать эпидемические штаммы при расследовании вспышек [8,11,13,16,17]. В странах Евросоюза и США метод MLVA широко используется при расследовании вспышек, в том числе международных, вызванных штаммами двух ведущих серотипов (S.Enteritidis, S.Typhimurium), для субтипирования которых разработаны стандартизированные протоколы [18][19][20][21][22][23][24][25].…”