Vibrio vulnificus typing based on simple sequence repeats: insights into the biotype 3 group

Vibrio vulnificus mutation rate: an in vitro approach

Vibrio vulnificus is a multi-host pathogenic species currently subdivided into five phylogenetic lineages (L) plus one pathovar with the ability to infect fish due to a transmissible virulence plasmid. This plasmid (or a fragment of it) has been transmitted between lineages within the species, contributing to the evolution of V. vulnificus. This study aimed to provide an experimental approximation to the V. vulnificus mutation rate by determining spontaneous mutation rates from bacterial cultures of representants of the different lineages by whole-genome sequencing. To this purpose, synonymous SNP differences, i.e., spontaneous mutation not subjected to the evolutive forces, between initial and final culture after serial growth were evaluated and used for mutation rate calculation.

Genotypic Diversity and Population Structure of Vibrio vulnificus Strains Isolated in Taiwan and Korea as Determined by Multilocus Sequence Typing

The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23–35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer’s tests) detected significant evidence of recombination. Tajima’s D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus.

Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158

We report the genome sequence of the environmental Vibrio vulnificus biotype 1_cladeA. This draft genome of the CladeA-yb158 strain, isolated in Israel, represents this newly emerged clonal group that contains both clinical and environmental strains.

Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3

Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.

Insight into the evolution of Vibrio vulnificus biotype 3's genome

Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are biochemically classified into three biotypes. The newly emerged biotype 3 appears to be rather clonal and geographically restricted to Israel, where it caused an outbreak of wound infections and bacteremia. To understand the evolution of the bacterium's genome, we sequenced and analyzed the genome of biotype 3 strain VVyb1(BT3), and then conducted a microbial environmental survey of the hypothesized niche from which it probably evolved. The genome of this environmental isolate revealed higher similarity to the published biotype 1 genomes of clinical strains (90%) than to the environmental strains (87%), supporting the virulence of the biotype 3 group. Moreover, 214 of the total 5361 genes were found to be unique to strain VVyb1(BT3), having no sequence similarity to any of the known genomes of V. vulnificus; 35 of them function in DNA mobility and rearrangement, supporting the role of horizontal gene transfer in genome evolution. Interestingly, 29 of the “unique” genes had homologies among Shewanella species. In a survey conducted in aquaculture ponds in Israel, we successfully co-isolated Shewanella and V. vulnificus from the same niche, further supporting the probable contribution of Shewanella to the genome evolution of biotype 3. Indeed, one gene was found in a S. algae isolate. Surprisingly, molecular analysis revealed that some of the considered unique genes are harbored by non-sequenced biotype 1 strains isolated from the same environment. Finally, analyses of the biotype 3 genome together with the environmental survey suggested that its genome originated from a biotype 1 Israeli strain that acquired a rather small number of genes from other bacterial species in the niche, such as Shewanella. Therefore, aquaculture is likely to play a major role as a man-made ecological niche in bacterial evolution, leading the emergence of new pathogenic groups in V. vulnificus.

Molecular characterization and antibiotic susceptibility of Vibrio vulnificus in retail shrimps in Hangzhou, People's Republic of China

Vibrio vulnificus is a gram-negative bacterium that occurs naturally in estuarine and marine water and is associated with wound infections or septicemia related to the consumption of raw shellfish in humans. The molecular characteristics and antibiotic susceptibilities of V. vulnificus strains in shrimps from retail markets in Hangzhou, People's Republic of China, were investigated in this study. Thirty-three samples were positive for V. vulnificus in 78 shrimp samples which were collected from 15 retail markets between July and August 2012; the most-probable-number values ranged from 3 to 1,600 g(-1) in these positive samples, with a median most-probable-number value of 72 g(-1). Twenty-five biotype 1 strains and eight biotype 2 strains were identified by biochemical tests, and all strains could be definitively genotyped. By 16S rRNA genotyping, 21.2% (7 of 33) were classified as genotype A, 63.6% (21 of 33) as genotype B, and 15.2% (5 of 33) as genotype AB, while by virulence-correlated gene (vcg) typing, 21.2% (7 of 33) were characterized as genotype E and 78.8% (26 of 33) were genotype C. More than 50% of those isolates were identified as the potentially virulent type vcg type C-16S rRNA B (CB). The antibiotic susceptibilities of the V. vulnificus strains to 21 antimicrobial agents were tested as well. Some strains showed resistance or intermediate resistance to cefepime (3.03%), tetracycline (6.06%), aztreonam (24.24%), streptomycin (45.45%), gentamicin (93.94%), tobramycin (100%), and cefazolin (100%). Multiple-locus variable-number tandem repeat-based fingerprinting analysis (MLVA) was successfully applied to these 33 isolates and yielded 30 patterns that clustered into two MLVA groups; with a calculated Simpson's index of diversity of 0.994, this revealed that MLVA had great discriminating power for V. vulnificus. To minimize the potential risk of V. vulnificus infections due to the consumption of raw shrimp, it is necessary to monitor the hygiene status of seafood.

Biodiversity of Enterococcus faecalis based on genomic typing

Enterococcus faecalis is a common inhabitant of the gastrointestinal tracts of different animals and is also found in other environments, such as plants, soil, food and water. The diverse nature of E. faecalis, which includes pathogenic, commensal and probiotic strains, calls for the development of tools for accurate discrimination and characterization at the strain level. Here we studied the genetic relationships among 106 E. faecalis strains isolated from diverse origins and possessing different degrees of virulence. Strain typing was conducted using a set of selected simple-sequence repeat (SSR) loci combined with multilocus sequence typing (MLST) analysis, which discriminated among the strains and separated them into three main clusters. While pathogenic and commensal isolates were dispersed along the dendrogram, probiotic and cheese-originated strains were highly associated with one specific cluster (cluster 1). The strain panel was further characterized by testing the occurrence of two virulence determinants (esp gene and β-hemolysis). The two determinants showed low abundance among probiotic and cheese-originated strains within cluster 1 when compared to non-cluster 1 cheese-originated strains, indicating a possible association of cluster 1 with non-virulent strains. Our results further emphasize the importance and challenge of precise characterization of E. faecalis strains from various sources.

Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus Biotype 3

We report the first genome sequence of the pathogenic Vibrio vulnificus biotype 3. This draft genome sequence of the environmental strain VVyb1(BT3), isolated in Israel, provides a representation of this newly emerged clonal group, which reveals higher similarity to the clinical strains of biotype 1 than to the environmental ones.

Genetic diversity of the human pathogen Vibrio vulnificus: a new phylogroup

The biotype 3 group of the human pathogen Vibrio vulnificus emerged in Israel probably as a result of genome hybridization of two bacterial populations. We performed a genomic and phylogenetic study of V. vulnificus strains isolated from the environmental niche from which this group emerged - fish aquaculture in Israel. The genetic relationships and evolutionary aspects of 188 environmental and clinical isolates of the bacterium were studied by genomic typing. Genetic relations were determined based on variation at 12 variable number tandem repeat (VNTR, also termed SSR) loci. Analysis revealed a new cluster, in addition to the main groups of biotype 1& 2 and biotype 3. Similar grouping results were obtained with three different statistical approaches. Isolates forming this new cluster presented unclear biochemical profile nevertheless were not identified as biotype 1 or biotype 3. Further examination of representative strains by multilocus sequence typing (MLST) of 10 housekeeping genes and 5 conserved hypothetical genes supported the identification of this as yet undiscovered phylogroup (phenotypically diverse), termed clade A herein. This new clonal subgroup includes environmental as well as clinical isolates. The results highlight the fish aquaculture environment, and possibly man-made ecological niches as a whole, as a source for the emergence of new pathogenic strains.

Development of a new marker system for identifying the complex members of the low-molecular-weight glutenin subunit gene family in bread wheat (Triticum aestivum L.)

Low-molecular-weight glutenin subunits (LMW-GSs) play an important role in determining the bread-making quality of bread wheat. However, LMW-GSs display high polymorphic protein complexes encoded by multiple genes, and elucidating the complex LMW-GS gene family in bread wheat remains challenging. In the present study, using conventional polymerase chain reaction (PCR) with conserved primers and high-resolution capillary electrophoresis, we developed a new molecular marker system for identifying LMW-GS gene family members. Based on sequence alignment of 13 LMW-GS genes previously identified in the Chinese bread wheat variety Xiaoyan 54 and other genes available in GenBank, PCR primers were developed and assigned to conserved sequences spanning the length polymorphism regions of LMW-GS genes. After PCR amplification, 17 DNA fragments in Xiaoyan 54 were detected using capillary electrophoresis. In total, 13 fragments were identical to previously identified LMW-GS genes, and the other 4 were derived from unique LMW-GS genes by sequencing. This marker system was also used to identify LMW-GS genes in Chinese Spring and its group 1 nulli-tetrasomic lines. Among the 17 detected DNA fragments, 4 were located on chromosome 1A, 5 on 1B, and 8 on 1D. The results suggest that this marker system is useful for large-scale identification of LMW-GS genes in bread wheat varieties, and for the selection of desirable LMW-GS genes to improve the bread-making quality in wheat molecular breeding programmes.

Bacteria associated with wild mud crab (Scylla serrata) from Setiu Wetland, Malaysia with emphasis on antibiotic resistances

A study was carried out to investigate the presence of bacteria flora in wild mud crab (Scylla serrata) from Setiu Wetland as well as their antibiotic resistances. A total of 91 bacterial isolates consisting of 12 bacterial species were successfully isolated from mud crab. Oxolinic acid was found to be effective against all the bacterial isolates whilst the highest percentage of antibiotic resistance was shown by lincomycin (94.5%) followed by ampicillin (90.1%), amoxicillin (86.8%) and oleandomycin (78.0%). The study is very useful to evaluate the safety of mud crab for human consumption based on wild mud crab-associated bacteria as well as their antibiotic resistances.

Environmental monitoring of Vibrio cholerae using chironomids in India

Environmental Vibrio cholerae strains belonging to the non-O1/non-O139 serogroups are natural inhabitants of freshwater including estuarine environments. Recent findings indicated that chironomids (Diptera: Chironomidae), the most widely distributed insects in freshwater, serve as a natural reservoir of these bacteria. Here we study the role of chironomids, particularly exuviae as carriers and as a monitoring tool for the distribution of V. cholerae in the environment. During a survey conducted in India (June 2006), 326 V. cholerae non-O1/non-O139 isolates were isolated from chironomid egg masses, larvae and exuviae. In addition, a heat-stable enterotoxin (nag-st) positive strain was isolated from exuviae during the local cholera outbreak. We identified 62 different strains in a subset of 102 isolates by analysis of variable number of tandem repeats (VNTR), demonstrating a high variation of V. cholerae on hosting chironomids. Our results show that chironomids can both maintain and distribute this overwhelming diversity of environmental V. cholerae strains, including toxigenic ones. Exuviae proved to be an efficient tool for the monitoring of environmental V. cholerae, offering simple, direct and practical access for on-shore collection. Finally, finding toxigenic V. cholerae on chironomids in endemic areas, together with molecular typing, may potentially improve monitoring of cholera in the future.

Epidemiologic study of Vibrio vulnificus infections by using variable number tandem repeats

A 3-year environmental and clinical Vibrio vulnificus survey using simple-sequence repeats typing shows that V. vulnificus biotype 3 constitutes ≈21% of the bacterium population in tested aquaculture ponds as opposed to ≈86% of clinical cases. Simple-sequence repeats proved to be a useful epidemiologic tool, providing information on the environmental source of the pathogen.

Multiple-locus variable-number tandem-repeat analysis for clonal identification of Vibrio parahaemolyticus isolates by using capillary electrophoresis

Epidemics of Vibrio parahaemolyticus in Chile have occurred since 1998. Direct genome restriction enzyme analysis (DGREA) using conventional gel electrophoresis permitted discrimination of different V. parahaemolyticus isolates obtained from these outbreaks and showed that this species consists of a highly diverse population. A multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) approach was developed and applied to 22 clinical and 91 environmental V. parahaemolyticus isolates from Chile to understand their clonal structures. To this end, an advanced molecular technique was developed by applying multiplex PCR, fluorescent primers, and capillary electrophoresis, resulting in a high-resolution and high-throughput (HRHT) genotyping method. The genomic basis of this HRHT method was eight VNTR loci described previously by Kimura et al. (J. Microbiol. Methods 72:313-320, 2008) and two new loci which were identified by a detailed molecular study of 24 potential VNTR loci on both chromosomes. The isolates of V. parahaemolyticus belonging to the same DGREA pattern were distinguishable by the size variations in the indicative 10 VNTRs. This assay showed that these 10 VNTR loci were useful for distinguishing isolates of V. parahaemolyticus that had different DGREA patterns and also isolates that belong to the same group. Isolates that differed in their DGREA patterns showed polymorphism in their VNTR profiles. A total of 81 isolates was associated with 59 MLVA groups, providing fine-scale differentiation, even among very closely related isolates. The developed approach enables rapid and high-resolution analysis of V. parahaemolyticus with pandemic potential and provides a new surveillance tool for food-borne pathogens.

Clinical characteristics and molecular subtyping of Vibrio vulnificus illnesses, Israel

The genetically distinct biotype 3 has penetrated Israeli freshwaters and is causing severe illness in persons who handle tilapia or carp.

During 1996–1997, a new Vibrio vulnificus biotype 3, which caused severe soft tissue infection after fishbone injury, emerged in Israel. We conducted a follow-up study from 1998 through 2005 to assess changing trends, outcomes, and molecular relatedness of the implicated strains. A total of 132 cases (71% confirmed and 29% suspected) of V. vulnificus biotype 3 infection were found. Most infections (95%) were related to percutaneous fish exposure, mainly tilapia (83%) or common carp (13%). Bacteremia, altered immune status, and history of ischemic heart disease were identified as independent risk factors for death, which reached a prevalence of 7.6%. Pulsed-field gel electrophoresis patterns of strains from 1998 through 2005 and from 1996 through 1997 showed a high degree of homogeneity and were distinct from those of V. vulnificus biotype 1. Infections caused by V. vulnificus biotype 3 continue affect the public’s health in Israel.