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

MLST based serotype prediction for the accurate identification of non typhoidal Salmonella serovars

Traditional serotyping based on the phenotypic variation of O- and H-antigen remains as the gold-standard for the identification and classification of Salmonella isolates for last 70 years. Although this classification is a globally recognized nomenclature, huge diversity of Salmonella serotypes have made the serovar identification to be very complex. Seven gene multilocus sequence typing (MLST) on the other hand can provide serovar prediction as well as the evolutionary origin between the serovars. In this study non typhoidal Salmonella (NTS) strains (n = 45) isolated from clinical samples (blood, faeces and pus) were identified by traditional phenotypic serotyping and biochemical testing. All the tested Salmonella isolates were designated as serovar Typhimurium based on phenotyping. However, by MLST 60% (27/45) of the isolates were S. Typhimurium, 35.5% (16/45) were S. Agona (ST13), 2.2% (1/45) were S. Kentucky (ST198) and 2.2% (1/45) were S. Saintpaul (ST27). MLST analysis assigned S. Typhimurium isolates as ST36 (18/127), ST19 (7/27) and ST313 (2/27). Mismatches in serovar designation between MLST database and phenotypic serotyping can be due to the misinterpretation of phenotypic serotyping as the antigenic structures of S. Typhimurium, S. Agona differs by a surface antigen. MLST based phylogeny of study isolates showed clustering according to sequence types. Concordance between MLST based sequence type and phenotypic serotype is important to provide insights into genetic population structure of Salmonella.

Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000-2013

Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants). Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59. SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.

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

BACKGROUND

Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation.

METHODS

Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively.

RESULTS

Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak.

CONCLUSIONS

Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.

Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods.

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

Phenotypic Characteristics and Genetic Diversity of Salmonella enterica Serotype Derby Isolated from Human Patients and Foods of Animal Origin

Salmonella enterica serotype Derby is among the three most common serotypes of nontyphoidal Salmonella isolated from patients with diarrhea in China. In this study, 133 Salmonella Derby isolates from human patients (n = 74) and foods of animal origin (n = 59) in Shanghai, China, between September 2013 and December 2014, were selected to study its phenotypic characteristics and genetic diversity. The isolates were subjected to antimicrobial susceptibility testing, plasmid replicon typing, virulence profile determination, and molecular subtyping by pulsed-field gel electrophoresis (PFGE). Isolates were frequently resistant to tetracycline (87.22%), sulfisoxazole (74.44%), and streptomycin (62.41%), and a low frequency of resistance was found toward ofloxacin (3.01%), ceftazidime (2.26%), and cefepime (1.50%); in addition, 93 (69.92%) isolates were multidrug resistant. The most common plasmid incompatibility replicon types were the IncF family (FIA, 51.31%; FIC, 27.82%; and FIB, 21.80%) and IncP types (35.34%): these plasmid types may be associated with the spread of antibiotic resistance and virulence genes. All isolates were positive for the Salmonella pathogenicity island (SPI) gene avrA and the fimbrial gene bcfC from among the 10 virulence genes detected, and most of them carried ssaQ (99.25%), mgtC (97.74%), siiD (98.50%), sopB (97.74%), and sopE (96.99%). PFGE showed 68 patterns in nine main clusters at an 85% similarity threshold. Most of the isolates from different sources possessed the same fingerprints or molecular profiles in each cluster, which strongly suggests the possibility that foods of animal origin, especially pork, serve as an important source for human infection. Moreover, this diversity may suggest strains originating from multiple clones. Therefore, surveillance on this serotype should be strengthened to prevent transmission of Salmonella Derby from foods of animal origin, especially pork, to humans.