DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected Salmonella enterica Serotypes

Abstract

While serotyping and phage typing have been used widely to characterize Salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining Salmonella transmission, ecology, and evolution. A set of 25 Salmonella enterica isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for Salmonella targeting seven housekeeping and virulence genes (panB, fimA, aceK, mdh, icdA, manB, and spaN). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and Salmonella serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since manB, fimA, and mdh allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41 Salmonella isolates representing a larger diversity of serotypes. This "three-gene sequence typing scheme" allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of Salmonella. Three-gene sequence typing also supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages.

Antimicrobial and molecular analysis of Salmonella serovar Livingstone strains isolated from humans in Tunisia and Belgium

“…They deduced that MLST using the combination of housekeeping genes and virulence or flagellin genes was more discriminatory than MLST using only housekeeping genes [21,38,[42][43].…”

Molecular Typing of Isolates ofRickettsia rickettsiiby Use of DNA Sequencing of Variable Intergenic Regions

“…By AluI PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of almost identical nucleotide regions of rompA, Regnery et al (40) (nucleotides 70 to 602) and Eremeeva et al (18) (nucleotides 70 to 701) were able to differentiate Hlp#2 from a combined In the public health setting, molecular typing of infectious agents is important for tracing their origin and spread in outbreak investigations, the detection of disseminated antibioticresistant strains in managed care facilities, the identification of hypervirulent strains, and monitoring failures in live vaccination programs (29). Molecular typing also allows for the study of bacterial population dynamics and may provide an improved understanding of the ecological niches occupied by specific pathogen types in the environment (24,45). Molecular typing schemes based on the sequencing of intergenic regions (IGRs) have been developed for Rickettsia conorii and Rickettsia prowazekii (21,49), and genetic typing of R. rickettsii based on variable-number-tandem-repeat loci was described recently (15, 18a, 48).…”

Molecular Characterization of Antibiotic-Resistant Bacteria in Contaminated Chicken Meat Sold at Supermarkets in Bangkok, Thailand

“…Through data base analysis, the STs of our strains were matched in strains isolated in other countries (Table 5). MLST analysis combined with serotyping could be helpful for further characterization of obtained Salmonella strains (43). The recently published review on new alternative methodologies for S. enterica subsp.…”