Dataset Information

Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions.

ABSTRACT: The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10(-4) mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered.

SUBMITTER: Garcia K

PROVIDER: S-EPMC3265528 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions.

García Katherine K Gavilán Ronnie G RG Höfle Manfred G MG Martínez-Urtaza Jaime J Espejo Romilio T RT

PloS one 20120124 1

The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain ...[more]

PMID: 22292049

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Project description:Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments.IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.

Project description:In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers.We proposed a new dynamic programming based realignment method named STR-realigner that considers repeat patterns in STR regions as prior knowledge. By allowing the size change of repeat patterns with low penalty in STR regions, accurate realignment is expected. For the performance evaluation, publicly available STR variant calling tools were applied to three types of aligned reads: synthetically generated sequencing reads aligned with BWA-MEM, those realigned with STR-realigner, those realigned with ReviSTER, and those realigned with GATK IndelRealigner. From the comparison of root mean squared errors between estimated and true STR region size, the results for the dataset realigned with STR-realigner are better than those for other cases. For real data analysis, we used a real sequencing dataset from Illumina HiSeq 2000 for a parent-offspring trio. RepeatSeq and lobSTR were applied to the sequence reads for these individuals aligned with BWA-MEM, those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner. STR-realigner shows the best performance in terms of consistency of the size of estimated STR regions in Mendelian inheritance. Root mean squared error values were also calculated from the comparison of these estimated results with STR region sizes obtained from high coverage PacBio sequencing data, and the results from the realigned sequencing data with STR-realigner showed the least (the best) root mean squared error value.The effectiveness of the proposed realignment method for STR regions was verified from the comparison with an existing method on both simulation datasets and real whole genome sequencing dataset.

Dataset Information

Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions.

Publications

Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions.

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