Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma

Helicobacter pylori is a common pathogen associated with several severe digestive diseases. Although multiple virulence factors have been described, it is still unclear the role of virulence factors on H. pylori pathogenesis and disease progression. Whole genome sequencing could help to find genetic markers of virulence strains. In this work, we analyzed three complete genomes from isolates obtained at the same point in time from a stomach of a patient with adenocarcinoma, using multiple available bioinformatics tools. The genome analysis of the strains B508A-S1, B508A-T2A and B508A-T4 revealed that they were cagA, babA and sabB/hopO negative. The differences among the three genomes were mainly related to outer membrane proteins, methylases, restriction modification systems and flagellar biosynthesis proteins. The strain B508A-T2A was the only one presenting the genotype vacA s1, and had the most distinct genome as it exhibited fewer shared genes, higher number of unique genes, and more polymorphisms were found in this genome. With all the accumulated information, no significant differences were found among the isolates regarding virulence and origin of the isolates. Nevertheless, some B508A-T2A genome characteristics could be linked to the pathogenicity of H. pylori.

Health Benefits of Heat-Killed (Tyndallized) Probiotics: An Overview

Nowadays, the oral use of probiotics is widespread. However, the safety profile with the use of live probiotics is still a matter of debate. Main risks include: Cases of systemic infections due to translocation, particularly in vulnerable patients and pediatric populations; acquisition of antibiotic resistance genes; or interference with gut colonization in neonates. To avoid these risks, there is an increasing interest in non-viable microorganisms or microbial cell extracts to be used as probiotics, mainly heat-killed (including tyndallized) probiotic bacteria (lactic acid bacteria and bifidobacteria). Heat-treated probiotic cells, cell-free supernatants, and purified key components are able to confer beneficial effects, mainly immunomodulatory effects, protection against enteropathogens, and maintenance of intestinal barrier integrity. At the clinical level, products containing tyndallized probiotic strains have had a role in gastrointestinal diseases, including bloating and infantile coli-in combination with mucosal protectors-and diarrhea. Heat-inactivated probiotics could also have a role in the management of dermatological or respiratory allergic diseases. The reviewed data indicate that heat-killed bacteria or their fractions or purified components have key probiotic effects, with advantages versus live probiotics (mainly their safety profile), positioning them as interesting strategies for the management of common prevalent conditions in a wide variety of patients´ characteristics.

Marinobacter maroccanus sp. nov., a moderately halophilic bacterium isolated from a saline soil

During the taxonomic investigation of exopolymer-producing halophilic bacteria, a rod-shaped, motile, Gram-stain-negative, halophilic bacterium, designated strain N4^T, was isolated from a saline soil located in northern Morocco. Optimal growth of the isolate was at 30-37 ºC and at pH 7.0-8.0, in the presence of 5-7 % (w/v) NaCl. Useful characteristics for the phenotypic differentiation of strain N4^T from other Marinobacter species included α-chymotrypsin and α-glucosidase activities and the carbohydrate assimilation profile. The major fatty acids detected in strain N4^T were C16:0 and C18:1ω9c and the predominant respiratory quinone was ubiquinone-9. Sequence analysis of the 16S rRNA gene indicated that strain N4^T belonged to the genus Marinobacter and was closely related to the type strains of Marinobacter adhaerens (99.04 % similarity), Marinobacter salsuginis (98.97 %) and Marinobacter flavimaris (98.36 %). Phylogenetic analysis of the rpoD gene sequence also showed that the nearest neighbours of strain N4^T were M. salsuginis (91.49 % similarity), M. adhaerens and M. flavimaris (90.63 %). Strain N4^T showed 87.98 % average nucleotide identity with M. flavimaris and M. salsuginis, and 87.47 % with M. adhaerens. Regarding in-silico genome-to-genome distance, strain N4^T showed DNA-DNA hybridization values of 33.30 % with M. adhaerens, 34.60 % with M. flavimaris and 34.70 % with M. salsuginis. The DNA G+C content of strain N4^T was 57.3 mol%. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain N4^T represents a novel species of the genus Marinobacter, for which the name Marinobacter maroccanus sp. nov. is proposed. The type strain is N4^T (=CECT 9525^T=LMG 30466^T).

Usefulness of Housekeeping Genes for the Diagnosis of Helicobacter pylori Infection, Strain Discrimination and Detection of Multiple Infection

BACKGROUND

Helicobacter pylori infects human stomachs of over half the world's population, evades the immune response and establishes a chronic infection. Although most people remains asymptomatic, duodenal and gastric ulcers, MALT lymphoma and progression to gastric cancer could be developed. Several virulence factors such as flagella, lipopolysaccharide, adhesins and especially the vacuolating cytotoxin VacA and the oncoprotein CagA have been described for H. pylori. Despite the extensive published data on H. pylori, more research is needed to determine new virulence markers, the exact mode of transmission or the role of multiple infection.

MATERIALS AND METHODS

Amplification and sequencing of six housekeeping genes (amiA, cgt, cpn60, cpn70, dnaJ, and luxS) related to H. pylori pathogenesis have been performed in order to evaluate their usefulness for the specific detection of H. pylori, the genetic discrimination at strain level and the detection of multiple infection. A total of 52 H. pylori clones, isolated from 14 gastric biopsies from 11 patients, were analyzed for this purpose.

RESULTS

All genes were specifically amplified for H. pylori and all clones isolated from different patients were discriminated, with gene distances ranged from 0.9 to 7.8%. Although most clones isolated from the same patient showed identical gene sequences, an event of multiple infection was detected in all the genes and microevolution events were showed for amiA and cpn60 genes.

CONCLUSIONS

These results suggested that housekeeping genes could be useful for H. pylori detection and to elucidate the mode of transmission and the relevance of the multiple infection.

Potential pathogenicity ofAeromonas hydrophilacomplex strains isolated from clinical, food, and environmental sources

Aeromonas are autochthonous inhabitants of aquatic environments, including chlorinated and polluted waters, although they can also be isolated from a wide variety of environmental and clinical sources. They cause infections in vertebrates and invertebrates and are considered to be an emerging pathogen in humans, producing intestinal and extra-intestinal diseases. Most of the clinical isolates correspond to A. hydrophila, A. caviae, and A. veronii bv. Sobria, which are described as the causative agents of wound infections, septicaemia, and meningitis in immunocompromised people, and diarrhoea and dysenteric infections in the elderly and children. The pathogenic factors associated with Aeromonas are multifactorial and involve structural components, siderophores, quorum-sensing mechanisms, secretion systems, extracellular enzymes, and exotoxins. In this study, we analysed a representative number of clinical and environmental strains belonging to the A. hydrophila species complex to evaluate their potential pathogenicity. We thereby detected their enzymatic activities and antibiotic susceptibility pattern and the presence of virulence genes (aer, alt, ast, and ascV). The notably high prevalence of these virulence factors, even in environmental strains, indicated a potential pathogenic capacity. Additionally, we determined the adhesion capacity and cytopathic effects of this group of strains in Caco-2 cells. Most of the strains exhibited adherence and caused complete lysis.

Virulence Factors of Erwinia amylovora: A Review

Erwinia amylovora, a Gram negative bacteria of the Enterobacteriaceae family, is the causal agent of fire blight, a devastating plant disease affecting a wide range of host species within Rosaceae and a major global threat to commercial apple and pear production. Among the limited number of control options currently available, prophylactic application of antibiotics during the bloom period appears the most effective. Pathogen cells enter plants through the nectarthodes of flowers and other natural openings, such as wounds, and are capable of rapid movement within plants and the establishment of systemic infections. Many virulence determinants of E. amylovora have been characterized, including the Type III secretion system (T3SS), the exopolysaccharide (EPS) amylovoran, biofilm formation, and motility. To successfully establish an infection, E. amylovora uses a complex regulatory network to sense the relevant environmental signals and coordinate the expression of early and late stage virulence factors involving two component signal transduction systems, bis-(3'-5')-cyclic di-GMP (c-di-GMP) and quorum sensing. The LPS biosynthetic gene cluster is one of the relatively few genetic differences observed between Rubus- and Spiraeoideae-infecting genotypes of E. amylovora. Other differential factors, such as the presence and composition of an integrative conjugative element associated with the Hrp T3SS (hrp genes encoding the T3SS apparatus), have been recently described. In the present review, we present the recent findings on virulence factors research, focusing on their role in bacterial pathogenesis and indicating other virulence factors that deserve future research to characterize them.

Enhanced polyhydroxyalkanoates accumulation by Halomonas spp. in artificial biofilms of alginate beads

Microbial mats are complex but stable, multi-layered and multi-functional biofilms, which are the most frequent bacterial formations in nature. The functional strategies and physiological versatility of the bacterial populations growing in microbial mats allow bacteria to resist changing conditions within their environment. One of these strategies is the accumulation of carbon- and energy-rich polymers that permit the recovery of metabolic activities when favorable conditions are restored. In the present study, we systematically screened microbial mats for bacteria able to accumulate large amounts of the ester carbon polymers polyhydroxyalkanoates (PHA). Several of these strains were isolated from Ebro Delta microbial mats and their ability to accumulate PHA up to 40-60% of their dry weight was confirmed. According to two identification approaches (16S rRNA and rpoD genes), these strains were identified as Halomonas alkaliphila (MAT-7, -13, -16), H. neptunia (MAT-17), and H. venusta (MAT-28). To determine the mode of growth yielding maximum PHA accumulation, these three different species were cultured in an artificial biofilm in which the cells were immobilized on alginate beads. PHA accumulation by cells that had detached from the biofilm was compared with that of their planktonic counterparts. Experiments in different culture media showed that PHA accumulation, measured as the relative fluorescence intensity after 48 h of incubation at 30 degrees C, was higher in immobilized than in planktonic cells, with the exception of cells growing in 5% NaCl, in which PHA accumulation was drastically lower in both. Therefore, for obtaining high PHA concentrations, the use of immobilized cells may be a good alternative to the PHA accumulation by bacteria growing in the classical, planktonic mode. From the ecological point of view, increased PHA accumulation in detached cells from biofilms would be a natural strategy to improve bacterial dispersion capacity and, consequently, to increase survival in stressed environments.

Reclassification of Aeromonas hydrophila subspecies anaerogenes

Technological advances together with the continuous description of new taxa have led to frequent reclassifications in bacterial taxonomy. In this study, an extensive bibliographic revision, as well as a sequence analysis of nine housekeeping genes (cpn60, dnaJ, dnaX, gyrA, gyrB, mdh, recA, rpoB and rpoD) and a phenotypic identification of Aeromonas hydrophila subspecies anaerogenes were performed. All data obtained from previous physiological, phylogenetic, and DNA-DNA hybridization studies together with those presented in this study suggested that A. hydrophila subspecies anaerogenes belonged to the species Aeromonas caviae rather than A. hydrophila. Therefore, the inclusion of A. hydrophila subsp. anaerogenes in the species A. caviae is proposed.

Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic

During the taxonomic investigation of cold-adapted bacteria from samples collected in the Antarctic area of the South Shetland Islands, one Gram-reaction-negative, psychrotolerant, aerobic bacterium, designated strain M1(T), was isolated from marine sediment collected on Deception Island. The organism was rod-shaped, catalase- and oxidase-positive and motile by means of a polar flagellum. This psychrotolerant strain grew at temperatures ranging from -4 °C to 34 °C. Phylogenetic studies based on 16S rRNA gene sequences confirmed that Antarctic isolate M1(T) was a member of the genus Pseudomonas and was located in the Pseudomonas fragi cluster. 16S rRNA gene sequence similarity values were >98 % between 13 type strains belonging to the Pseudomonas fluorescens lineage. However, phylogenetic analysis of rpoD gene sequences showed that strain M1(T) exhibited high sequence similarity only with respect to Pseudomonas psycrophila (97.42 %) and P. fragi (96.40 %) and DNA-DNA hybridization experiments between the Antarctic isolate M1(T) and the type strains of these two closely related species revealed relatedness values of 58 and 57 %, respectively. Several phenotypic characteristics, together with the results of polar lipid and cellular fatty acid analyses, were used to differentiate strain M1(T) from related pseudomonads. Based on the evidence of this polyphasic taxonomic study, strain M1(T) represents a novel species, for which the name Pseudomonas deceptionensis sp. nov. is proposed. The type strain is M1(T) ( = LMG 25555(T)  = CECT 7677(T)).

Thermophilic bacteria from Mexican thermal environments: isolation and potential applications

Extremophiles are microorganisms that possess application possibilities in several industrial fields, including agricultural, chemical, laundry, pharmaceutical, food, petroleum and bioremediation. This work reports the isolation of 19 thermophilic, alkalitolerant and halotolerant bacterial strains from two thermal sites in Veracruz, México: El Carrizal thermal pool and Los Baños hot spring. These strains belong to the Geobacillus, Anoxybacillus and Aeribacillus genera. The strains produce lipases, proteases, and amylases under thermophilic conditions. They may have good potential for application in microbial enhanced oil recovery, since they are thermophilic and halotolerant, produce exopolymers (up to 11.8 mg/mg) and acids, show emulsifying activity (E24 up to 7.5%), and are able to grow in kerosene as carbon source; these strains may also be used in biodesulphurization since they can grow in dibenzothiophene producing 2-hydroxybiphenyl under thermophilic conditions (up to 2.9 mg/L).

The reference strain Aeromonas hydrophicla CIP 57.50 should be reclassified as Aeromonas salmonicida CIP 57.50

The use of reference strains is a critical element for the quality control of different assays, from the development of molecular methods to the evaluation of antimicrobial activities. Most of the strains used in these assays are not type strains and some of them are cited erroneously because of subsequent reclassifications and descriptions of novel species. In this study, we propose that the reference strain Aeromonas hydrophila CIP 57.50 be reclassified as Aeromonas salmonicida CIP 57.50 based on phenotypic characterization and sequence analyses of the cpn60, dnaJ, gyrB and rpoD genes.

Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen. nov., comb. nov

Although Anoxybacillus and Geobacillus, two genera of thermophilic bacteria close to the genus Bacillus, have only been described recently, the number of species in these genera has increased rapidly. Four thermophilic, lipolytic strains (DR01, DR02, DR03 and DR04) isolated from a hot spring in Veracruz (Mexico), which could not be identified phenotypically, were subjected to 16S rRNA gene sequence analysis. Three strains were identified as belonging to the genus Anoxybacillus, but strain DR03 was identified as Geobacillus pallidus. This result led us to perform a phylogenetic analysis of the genera Anoxybacillus and Geobacillus based on 16S rRNA gene sequences from all the type strains of these genera. Phylogenetic trees showed three major clusters, Anoxybacillus-Geobacillus tepidamans, Geobacillus sensu stricto and Geobacillus pallidus, while the 16S rRNA gene sequences of G. pallidus (DR03 and the type strain) showed low similarity to sequences of Anoxybacillus (92.5-95.1 %) and Geobacillus (92.8-94.5 %) species, as well as to Bacillus subtilis (92.2-92.4 %). In addition, G. pallidus could be differentiated from Anoxybacillus and Geobacillus on the basis of DNA G+C content and fatty acid and polar lipid profiles. From these results, it is proposed that Geobacillus pallidus should be classified in a novel genus, for which we propose the name Aeribacillus, as Aeribacillus pallidus gen. nov., comb. nov. The type strain of Aeribacillus pallidus is H12(T) (=ATCC 51176(T) =DSM 3670(T) =LMG 19006(T)).

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

BACKGROUND

The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.

RESULTS

We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.

CONCLUSION

The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection.

REVIEWERS

This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

Shewanella vesiculosa sp. nov., a psychrotolerant bacterium isolated from an Antarctic coastal area

Two strains of psychrotolerant bacteria, designated M7(T) and M5, isolated from Antarctic coastal marine environments were studied to determine their taxonomic position. The organisms comprised Gram-negative, rod-shaped, facultatively anaerobic cells that were motile by means of single polar flagella. Neither of the bacterial isolates had a requirement for Na(+). These two psychrotolerant strains grew at temperatures ranging from -4 to 30 degrees C. Both strains were capable of producing H(2)S from thiosulfate and were able to use sodium nitrate and trimethylamine N-oxide as terminal electron acceptors during anaerobic growth. 16S rRNA gene sequence analysis placed M7(T) and M5 within the genus Shewanella; the strains showed the highest similarity (99.9 and 99.2 % respectively) with respect to the type strains of Shewanella livingstonensis and Shewanella frigidimarina. However the levels of gyrB sequence similarity between strain M7(T) and the type strains of S. livingstonensis and S. frigidimarina were 87.6 and 87.4 %, respectively. DNA-DNA hybridization experiments performed between the Antarctic isolate M7(T) and S. livingstonensis LMG 19866(T) and S. frigidimarina LMG 19475(T) revealed levels of relatedness of 32 and 35 %, respectively. Strain M5 showed 100 % DNA relatedness with respect to strain M7(T). The DNA G+C content of these bacteria was 42 mol%. Several phenotypic characteristics, the cellular fatty acid compositions and the quinone content of strains M7(T) and M5 served to differentiate them from related shewanellae. On the basis of the data from this polyphasic taxonomic study, M7(T) and M5 constitute a single genospecies. They represent a novel species of the genus Shewanella, for which the name Shewanella vesiculosa sp. nov. is proposed. The type strain is M7(T) (=LMG 24424(T) =CECT 7339(T)).

Aeromonas bivalvium sp. nov., isolated from bivalve molluscs

A polyphasic study was performed to determine the taxonomic position of two Aeromonas strains, 665N and 868E(T), isolated from bivalve molluscs, that could not be identified at the species level in a previous numerical taxonomy study. The DNA G+C content of these isolates was 62.3 and 62.6 mol%, respectively. Sequence analysis of the 16S rRNA gene showed that the two new strains were closely related to members of the genus Aeromonas. Fluorescence amplified fragment length polymorphism fingerprinting revealed that strains 665N and 868E(T) clustered together with a similarity of 78 % but did not cluster with any of the Aeromonas genomospecies. DNA-DNA hybridization experiments revealed a high level of relatedness between the two new isolates (76 %) but low levels of relatedness between these and phylogenetically most closely related Aeromonas genomospecies (30-44 %). Useful tests for the phenotypic differentiation of strains 665N and 868E(T) from other mesophilic Aeromonas species included those for gas from glucose, lysine decarboxylase, Voges-Proskauer reaction, acid from L-arabinose, hydrolysis of aesculin and utilization of L-lactate. On the basis of genotypic and phenotypic evidence, strains 665N and 868E(T) are considered to represent a novel species of the genus Aeromonas, for which the name Aeromonas bivalvium sp. nov. is proposed. The type strain is 868E(T) (=CECT 7113(T)=LMG 23376(T)).

Aeromonas molluscorum sp. nov., isolated from bivalve molluscs

Five Aeromonas strains (848T(T), 93M, 431E, 849T and 869N), which were isolated from bivalve molluscs and were recognized previously by numerical taxonomy as members of an unknown Aeromonas taxon, were subjected to a polyphasic taxonomic study. DNA-DNA hybridization experiments showed that DNA of strain 848T(T) was <70 % similar (27-45 %) to that of the type/reference strains of the current Aeromonas hybridization groups (HGs), but 93 % similar to that of strain 93M. The DNA G+C content of the five strains ranged from 59.0 to 59.4 mol%. 16S rRNA gene sequence analysis confirmed that the strains belonged to the genus Aeromonas and showed high similarity to Aeromonas encheleia. Amplified fragment length polymorphism fingerprinting clustered the novel strains in a homogeneous group with low genotypic relatedness to other Aeromonas species. Useful phenotypic features for differentiating the five isolates from other Aeromonas species include their negative reactions in tests for indole production, lysine decarboxylase, gas from glucose and starch hydrolysis. From the results of this study, the name Aeromonas molluscorum sp. nov. is proposed for these strains, with the type strain 848T(T) (=CECT 5864(T)=LMG 22214(T)).

Genetic diversity and population structure of Aeromonas hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii by multilocus enzyme electrophoresis (MLEE)

Genetic diversity, genetic relationship, identification and population structure of 120 Aeromonas strains (including Aer. hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii) isolated from various sources were studied by analysis of 15 genetic loci by multilocus enzyme electrophoresis (MLEE). All 15 loci were polymorphic, with an average of 9.4 alleles per locus and a mean genetic diversity (H) of 0.64. Cluster analysis defined at H < or = 0.7 differentiated most of the taxa analysed except the Aer. popoffii and Aer. bestiarum strains, which showed a close genetic relationship. Allelic frequencies of five loci (EST1, HEX, IDH, LDH1 and MDH) identified 94% of the strains. The index of association (IA) for the total sample was 2.38 and IA values calculated for the different populations were always significantly different from zero. These results suggest that the population structure of this Aeromonas sample is strongly clonal, confirm the taxonomic status of the analysed species in population genetics terms, and show the usefulness of MLEE for identifying Aeromonas species.

Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain

AIMS

To study the phenotypic characteristics of Aeromonas spp. from environmental and clinical samples in Spain and to cluster these strains by numerical taxonomy.

METHODS AND RESULTS

A collection of 202 Aeromonas strains isolated from bivalve molluscs, water and clinical samples was tested for 64 phenotypic properties; 91% of these isolates were identified at species level. Aeromonas caviae was predominant in bivalve molluscs and Aerom. bestiarum in freshwater samples. Cluster analyses revealed eight different phena: three containing more than one DNA-DNA hybridization group but including strains that belong to the same phenospecies complex (Aerom. hydrophila, Aerom. sobria and Aerom. caviae), Aerom. encheleia, Aerom. trota and three containing unidentified Aeromonas strains isolated from bivalve molluscs.

CONCLUSIONS

Aeromonas spp. are widely distributed in environmental and clinical sources. A selection of 16 of the phenotypical tests chosen allowed the identification of most isolates (91%), although some strains remain unidentified, mainly isolates from bivalve molluscs, suggesting the presence of new Aeromonas species. Numerical taxonomy was not in total concordance with the identification of the studied strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Numerical taxonomy of Aeromonas strains isolated from different sources revealed the presence of potentially pathogenic Aeromonas spp., especially in bivalve molluscs, and phena with unidentified strains that suggest new Aeromonas species.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.