Frequent recombination and low level of clonality within Salmonella enterica subspecies I

Octavia, Sophie; Lan, Ruiting

doi:10.1099/mic.0.28486-0

Cited by 38 publications

(30 citation statements)

References 43 publications

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“…The split trees generated for each locus, as well as for the concatenated sequences, showed reticulated structures. The majority of the strains also showed a star phylogeny radiating from the same central point, which suggests frequent recombination (23,37). Furthermore, the phi test for recombination was significant in all loci analyzed (P Ͻ 0.05) (see the supplemental material).…”

Section: Resultsmentioning

confidence: 91%

“…A history of frequent recombination events is further supported by the lack of any observed congruence among the genes analyzed (4). Furthermore, split trees for both concatenated sequences and individual loci resulted in star phylogeny structures radiating from the same central point, which suggest frequent recombination (37). Statistically significant evidence for recombination at each locus was also detected with the phi test (23).…”

Section: Figmentioning

confidence: 86%

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Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

et al. 2008

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Vibrio parahaemolyticus is an important human pathogen whose transmission is associated with the consumption of contaminated seafood. There is a growing public health concern due to the emergence of a pandemic strain causing severe outbreaks worldwide. Many questions remain unanswered regarding the evolution and population structure of V. parahaemolyticus. In this work, we describe a multilocus sequence typing (MLST) scheme for V. parahaemolyticus based on the internal fragment sequences of seven housekeeping genes. This MLST scheme was applied to 100 V. parahaemolyticus strains isolated from geographically diverse clinical (n ‫؍‬ 37) and environmental (n ‫؍‬ 63) sources. The sequences obtained from this work were deposited and are available in a public database (http://pubmlst.org/vparahaemolyticus). Sixty-two unique sequence types were identified, and most (50) were represented by a single isolate, suggesting a high level of genetic diversity. Three major clonal complexes were identified by eBURST analysis. Separate clonal complexes were observed for V. parahaemolyticus isolates originating from the Pacific and Gulf coasts of the United States, while a third clonal complex consisted of strains belonging to the pandemic clonal complex with worldwide distribution. The data reported in this study indicate that V. parahaemolyticus is genetically diverse with a semiclonal population structure and an epidemic structure similar to that of Vibrio cholerae. Genetic diversity in V. parahaemolyticus appears to be driven primarily by frequent recombination rather than mutation, with recombination ratios estimated at 2.5:1 and 8.8:1 by allele and site, respectively. Application of this MLST scheme to more V. parahaemolyticus strains and by different laboratories will facilitate production of a global picture of the epidemiology and evolution of this pathogen.Vibrio parahaemolyticus is a natural inhabitant of coastal waters and is the leading cause of seafood-borne gastroenteritis (34). Since 1996 an increasing number of V. parahaemolyticus infections and outbreaks caused by strains belonging to a pandemic clonal complex have been observed throughout the world (2,8,10,17,18,20,32,33,38,39). The emergence of this clonal complex has elevated public health concerns for pandemic spread previously uncharacteristic of V. parahaemolyticus. Serology, the historic mainstay of V. parahaemolyticus surveillance, has been unreliable in tracking the spread of the epidemic clonal complex because in addition to the original O3:K6 serotype, at least 11 other serovariants have been identified (2, 7, 9). These new serovariants are highly similar to or indistinguishable from the original O3:K6 strains by a variety of molecular fingerprinting techniques, including arbitrarily primed PCR, pulsed-field gel electrophoresis, ribotyping, the intergenic spacer region between the 16S and 23S rRNA genes, and direct genome restriction enzyme analysis (8,18,20,33,38). Accordingly, the molecular subtyping techniques, which usually demonstrate a high degre...

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Section: Resultsmentioning

confidence: 91%

Section: Figmentioning

confidence: 86%

Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

et al. 2008

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“…Incongruence in tree topology is a sign of recombination or hybridization among bacterial species (4,(17)(18)(19)(20)(21). We observed significant incongruence between gapA and ftsZ (p=0.001), and between gapA and topA (p=0.029) using the ILD test.…”

Section: Resultsmentioning

confidence: 99%

Mutation is the Main Driving Force in the Diversification of the Vibrio splendidus Clade

et al. 2009

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The Vibrio splendidus clade is the biggest in Vibrionales composed of 11 described species (25). Diversification of these species may have occurred 260 million years ago. The main driving forces of speciation in this clade have never been studied. Population biological parameters (population base recombination rate (ρ), population base mutation rate (θ), and index of association (Ia)) were determined among 16 strains of 9 defined species in the Splendidus cluster. A comparison of individual gene phylogeny indicated significant incongruence in tree topology, which suggests the occurrence of recombination between species. Homologous recombination between species was detected at four loci. However, the mutation rate θ was higher than the recombination rate ρ, suggesting that mutation is the main driving force in the diversification of V. splendidus-related species.Key words: diversification, population biology, vibrios, Vibrio splendidus, multilocus sequence analysis Vibrio splendidus was originally described by Beijerinck in 1900 as a luminous marine bacterium (1,2,22). The taxonomic status of this species was confirmed through DNA-DNA hybridization by Reichelt et al. (22). V. splendidusrelated strains isolated from marine environments remained in focus due to the psychrophilic nature of these vibrios in the global warming era (27,34,35). A role for V. splendidusrelated strains in the mortality of mollusks and fish was also reported (6, 9, 13). V. splendidus and related species are widespread in marine environments (14,30,32,34,35). Recently, two genetically distinctive populations of V. splendidus-related strains from North Atlantic coastal water have been distinguished. Bacteria of these two populations differed in range of temperature for growth and had less than 1% of the 16S rRNA gene sequence heterogeneity (30,32).Because V. splendidus-related species share niches in the environment, including the gut and tissue of bivalves, it would be reasonable to assume that horizontal gene transfer and recombination are important forces leading to diversification in this group. The multilocus sequence analysis (MLSA) is a reliable tool for both inferring the taxonomic backbone of species groups and estimating the relative contributions of mutation and recombination (31,33,36). Our recent MLSA clearly separated the V. splendidus clade from all other recognized species of vibrios (25). However, V. splendidus-related species are genetically and phenotypically similar (29). Overall, the species have more than 30% reciprocal DNA-DNA similarity, 90.6-96.5% nucleotide sequence similarity of MLSA concatenated genes and 96.5-99.8% average amino acid identity at gene loci, but a rather broad GC content. The high genomic similarity might suggest that these species readily exchange DNA at conserved loci. To test this hypothesis, we analyzed the relative contribution of mutation and recombination to the diversification using an extended set of strains belonging to the Splendidus group by means of MLSA. Materials and Methods Bacteria...

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“…All isolates were subjected to MLVA at the NSW Enteric Reference Laboratory, using a protocol compatible with the European MLVA-5 scheme (8). Genomic DNA was extracted by phenol-chloroform extraction using the method described by Octavia and Lan (9).…”

Section: Methodsmentioning

confidence: 99%

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

et al. 2015

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c Salmonella enterica serovar Typhimurium is an important foodborne human pathogen that often causes self-limiting but severe gastroenteritis. Prolonged excretion of S. Typhimurium after the infection can lead to secondary transmissions. However, little is known about within-host genomic variation in bacteria associated with asymptomatic shedding. Genomes of 35 longitudinal isolates of S. Typhimurium recovered from 11 patients (children and adults) with culture-confirmed gastroenteritis were sequenced. There were three or four isolates obtained from each patient. Single nucleotide polymorphisms (SNPs) were analyzed in these isolates, which were recovered between 1 and 279 days after the initial diagnosis. Limited genomic variation (5 SNPs or fewer) was associated with short-and long-term carriage of S. Typhimurium. None of the isolates was shown to be due to reinfection. SNPs occurred randomly, and the majority of the SNPs were nonsynonymous. Two nonsense mutations were observed. A nonsense mutation in flhC rendered the isolate nonmotile, whereas the significance of a nonsense mutation in yihV is unknown. The estimated mutation rate is 1.49 ؋ 10 ؊6 substitution per site per year. S. Typhimurium isolates excreted in stools following acute gastroenteritis in children and adults demonstrated limited genomic variability over time, regardless of the duration of carriage. These findings have important implications for the detection of possible transmission events suspected by public health genomic surveillance of S. Typhimurium infections. Nontyphoid Salmonella (NTS) infections generally result in a short-term, self-limiting gastroenteritis. However, NTS can be excreted continually and asymptomatically in stools for many weeks, even after the initial diarrheal episode has been resolved. Children are the more common carriers, especially children under the age of 3 years (1, 2). Fecal shedding of NTS after an intestinal infection can last for up to 4 weeks in adults and 7 weeks in children (3). In a very small proportion of cases, carriage can last for a year after the initial onset of the disease (3). Carriers excrete large numbers of bacteria in their feces and can facilitate the transmission of Salmonella to other hosts by contaminating water and food sources. The persistence of fecal shedding in asymptomatic patients can have a duration similar to that for patients with clinical disease (4). Antibiotic treatment of NTS disease is rarely indicated, as it does not assist in clearance of infection but may increase the duration of asymptomatic shedding (4).Salmonella enterica serovar Typhimurium is one of the leading causes of NTS gastroenteritis in humans in Australia and other countries. Salmonellosis is a notifiable disease in all Australian states and territories. In the state of New South Wales (NSW), the notification rate has been around 50 cases per 100,000 population (5). Sequencing of S. Typhimurium genomes or analyses of tandem repeats within the genome have increasingly been employed for tracking community ou...

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Frequent recombination and low level of clonality within Salmonella enterica subspecies I

Cited by 38 publications

References 43 publications

Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

Mutation is the Main Driving Force in the Diversification of the Vibrio splendidus Clade

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

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