Urease production correlates with possession of the trh gene in Vibrio parahaemolyticus strains isolated in Thailand

Comparison of genome structures of vibrios, bacteria possessing two chromosomes

Vibrios are gram-negative gamma-proteobacteria which are ubiquitous in marine and estuarine environments. Recently, we demonstrated that some, if not all, Vibrio species have two circular chromosomes. The whole genome sequence of Vibrio cholerae N16961 has been reported. In this study, we constructed a physical and genetic map of the genome of Kanagawa phenomenon-positive Vibrio parahaemolyticus strain KX-V237 and compared it with those of V. parahaemolyticus AQ4673 and V. cholerae N16961. The genome of KX-V237 comprised two circular chromosomes (3.3 and 1.9 Mb), similar to the structure of the AQ4673 genome. The relative positions of the genes on the genomes were well conserved in the two strains, but a large inversion on the large chromosomes, probably symmetric around the replication origin, was suggested. Although the sizes of the large chromosomes of KX-V237 and V. cholerae N16961 were similar, the sizes of the small chromosomes were very different. Unlike N16961, the superintegron of KX-V237 was located on the large chromosome. Comparison of the genetic maps of the chromosomes of KX-V237 and V. cholerae N16961 revealed that most of the open reading frames (ORFs) present on the large chromosome of the V. cholerae strain had homologues on the large chromosome of the V. parahaemolyticus strain and that most of the ORFs on the small chromosome of N16961 were present on the small chromosome of KX-V237. The difference in the orders of the ORFs on the chromosomes of N16961 and KX-V237 implies that numerous and frequent genetic exchanges have occurred intrachromosomally rather than interchromosomally.

Prevalence of the pandemic genotype of Vibrio parahaemolyticus in Dhaka, Bangladesh, and significance of its distribution across different serotypes

Sixty-six strains of Vibrio parahaemolyticus belonging to 14 serotypes were isolated from hospitalized patients in Dhaka, Bangladesh, from January 1998 to December 2000. Among these, 48 strains belonging to four serotypes had the pandemic genotype and possessed the tdh gene. A marker (open reading frame ORF8) for a filamentous phage previously thought to correspond to the pandemic genotype was found to have a poor correlation with the pandemic genotype.

Vibrio parahaemolyticus associated with cholera-like diarrhea among patients in North Jakarta, Indonesia

A diarrhea study was conducted in North Jakarta, Indonesia from December 1996 through December 1997. Vibrio parahaemolyticus was isolated from 333 (6.1%) of 5442 rectal swab samples collected from patients with cholera-like diarrhea. Vibrio cholerae O1 was isolated from 545 (10.0%) and V. cholerae non-O1 from 183 samples (3.4%), respectively. Patients positive for V. parahaemolyticus were mostly adults between 20 and 40 years of age, with males constituting 62%. A majority (65%) of these patients demonstrated watery diarrhea with a frequency of fewer than 10 episodes per 24 hour. A large number of the patients had abdominal pain (83%) and vomiting (76%) and were non-febrile (90%). The highest isolation rate (9.6%) of V. parahaemolyticus was found during the dry season (June, July) and the lowest (4.5%) in the rainy season (December, January, February). All of the V. parahaemolyticus isolates were hemolytic on human blood agar (positive Kanagawa) but none was urease positive. Disk diffusion antibiotic susceptibility tests performed on the isolates demonstrated resistance to ampicillin (98%), cephalothin (24%), kanamycin (15%), colistin (97%), neomycin (2%) and ceftriaxone (0.3%). All isolates (100%) were sensitive to chloramphenicol, tetracycline, trimethoprim-sulfamethoxazole, gentamicin, and ciprofloxacin.

Evaluation of nonisotopic DNA hybridization methods for detection of the tdh gene of vibrio parahaemolyticus

Production of the thermostable direct hemolysin (TDH) by Vibrio parahaemolyticus is associated with pathogenicity of the organism and is encoded by the tdh gene. The timely resolution of seafood-associated outbreaks requires rapid and accurate detection of pathogenic V. parahaemolyticus. The specificity of alkaline phosphatase- and digoxigenin-labeled tdh gene probes was evaluated against 61 strains of V. parahaemolyticus (including isolates from recent outbreaks involving oysters from the Pacific Northwest, Texas, and New York), 85 strains of other vibrios, and 7 strains of non-vibrio species from clinical and environmental sources. The probes were specific for detection of the V. parahaemolyticus tdh gene.

A unique and common restriction fragment pattern of the nucleotide sequences homologous to the genome of vf33, a filamentous bacteriophage, in pandemic strains of Vibrio parahaemolyticus O3:K6 O4:K68, and O1:K untypeable

Vf33 is a filamentous bacteriophage isolated from Vibrio parahaemolyticus. We performed Southern blot hybridization analysis to examine the distribution of Vf33-related genetic elements in the pandemic strains (O3:K6 strains isolated between 1995 and 1997, O4:K68 and O1:K untypeable strains isolated between 1997 and 1999) of V. parahaemolyticus. Nucleotide sequences homologous to the Vf33 DNA were detected in all 57 test strains including pandemic and non-pandemic strains. However, the profiles of hybridization, including the restriction fragment length polymorphism, with nine Vf33-derived DNA probes exhibited by the pandemic strains were identical and were different from those by the non-pandemic strains. The results support the hypothesis that the pandemic strains are clonal, and suggest a possibility that they have acquired (a) new gene(s) via a Vf33-like filamentous phage.

Genetic characterization of DNA region containing the trh and ure genes of Vibrio parahaemolyticus

We have demonstrated that possession of the gene for thermostable direct hemolysin-related hemolysin (trh) coincides with the presence of the urease gene among clinical Vibrio parahaemolyticus strains and that the location of the two genes are in close proximity on the chromosome. Here, we cloned and sequenced the 15,754-bp DNA region containing the trh gene and the gene cluster for urease production from the chromosome of clinical V. parahaemolyticus (TH3996). We found 16 open reading frames (ORFs) and a lower G+C content (41%) compared with the total genome of this bacterium (46 to 47%). The ure cluster consisted of eight genes, namely, ureDABCEFG and ureR. ureR was located 5.2 kb upstream of the other seven genes in the opposite direction. The genetic organization and sequences of the ure genes resembled those found in Proteus mirabilis. Between ureR and the other ure genes, there were five ORFs, which are homologous with the nickel transport operon (nik) of Escherichia coli. We disrupted each of the ureR, ureC, and nikD genes in TH3996 by homologous recombination and analyzed the phenotype of the mutants. In the presence of urea these mutant strains had dramatically less urease activity than the strain they were derived from. Disruption of ureR, nikD, or ureC, however, had no effect on TRH production. The DNA region containing the trh, nik, and ure genes was found in only trh-positive strains and not in Kanagawa phenomenon-positive and environmental V. parahaemolyticus strains. At the end of the region, an insertion sequence-like element existed. These results suggest that the DNA region was introduced into V. parahaemolyticus in the past through a mechanism mediated by insertion sequences. This is the first reported case that the genes for an ATP-binding cassette-type nickel transport system, which may play a role in nickel transport through bacterial cytoplasmic membrane, are located adjacent to the ure cluster on the genome of an organism.

Characterization of Vibrio parahaemolyticus isolates obtained from foodborne illness outbreaks during 1992 through 1995 in Taiwan

Vibrio parahaemolyticus is an important foodborne pathogen in Taiwan and many other Asian countries. A total of 371 isolates of V. parahaemolyticus collected from patients involved in foodborne illness outbreaks in Taiwan from 1992 to 1995 were characterized. These isolates had typical biochemical characteristics and only 4% were urease positive. The most frequently isolated serovars were O5:K15 (18.5%), O4:K8 (16.2%), O3:K29 (12.5%), O1:K56 (8.3%), O2:K3 (6.5%), and O4:K12 (6.0%). Most of the isolates were susceptible to nalidixic acid, tetracycline, tobramycin, cephalothin, and gentamicin. About 10% of the isolates were resistant to seven or more antibiotics. Approximately 92.4% of these V. parahaemolyticus showed beta-hemolysis on Wagatsuma blood agar plate and approximately 62.1% of these isolates exhibited detectable amounts of thermostable direct hemolysin. Most of the isolates examined exhibited two copies of tdh genes on the 1.3- and 2.5-kb HindIII-digested chromosome fragments with several variations on other fragments. A pulsed-field gel electrophoresis (PFGE) subspecies typing scheme was used to analyze these domestic isolates and the O3:K6 strains from Japan, Korea, and Taiwan. Fifty seven patterns were differentiated with A, B, C, E, and H being the major domestic types (cumulatively 76% of isolates), while O3:K6 strains (PFGE type I), abruptly occurring since 1996, were genetically distant from the major domestic types.

Isolation of a pandemic O3:K6 clone of a Vibrio parahaemolyticus strain from environmental and clinical sources in Thailand

Application of an immunomagnetic enrichment method selective for Vibrio parahaemolyticus serovar K6 allowed isolation of a strain belonging to the pandemic O3:K6 clone of V. parahaemolyticus from fresh shellfish not implicated in a clinical case in southern Thailand. Arbitrarily primed PCR profiles of this strain, clinical O3:K6 strains isolated from sporadic diarrhea cases in the same area, and a standard pandemic O3:K6 strain were indistinguishable.

Pandemic spread of an O3:K6 clone of Vibrio parahaemolyticus and emergence of related strains evidenced by arbitrarily primed PCR and toxRS sequence analyses

Vibrio parahaemolyticus O3:K6 strains responsible for the increase in the number of cases of diarrhea in Calcutta, India, beginning in February 1996 and those isolated from Southeast Asian travelers beginning in 1995 were shown to belong to a unique clone characterized by possession of the tdh gene but not the trh gene and by unique arbitrarily primed PCR (AP-PCR) profiles (J. Okuda, M. Ishibashi, E. Hayakawa, T. Nishino, Y. Takeda, A. K. Mukhopadhyay, S. Garg, S. K. Bhattacharya, G. B. Nair, and M. Nishibuchi, J. Clin. Microbiol. 35:3150-3155, 1997). Evidence supporting a hypothesis that this clone emerged only recently and is spreading to many countries was obtained in this study. Of 227 strains isolated in a hospital in Bangladesh between 1977 and 1998, only 22 strains isolated between 1996 and 1998 belonged to the new O3:K6 clone (defined by the serovar, the tdh and trh typing, and AP-PCR profiles). The O3:K6 strains isolated from clinical sources in Taiwan, Laos, Japan, Thailand, Korea, and the United States between 1997 and 1998 were also shown to belong to the new O3:K6 clone. The clonality of the new O3:K6 strains was also confirmed by analysis of the toxRS sequence, which has been shown to be useful for phylogenetic analysis of the members of the genus Vibrio. The toxRS sequences of the representative strains of the new O3:K6 clone differed from those of the O3:K6 strains isolated before 1995 at least at 7 base positions within a 1,346-bp region. A new PCR method targeted to 2 of the base positions unique to the new O3:K6 clone was developed. This PCR method could clearly differentiate all 172 strains belonging to the new O3:K6 clone from other O3:K6 strains isolated earlier. One hundred sixty-six strains belonging to 28 serovars other than O3:K6 were also examined by the new PCR method. The tdh-positive and trh-lacking strains that belonged to the O4:K68 and O1:K untypeable serovars and were isolated in three countries and from international travelers beginning in 1997 gave positive results. The AP-PCR profiles of these strains were nearly identical to those of the new O3:K6 clone, and their toxRS sequences were 100% identical to that of the new O3:K6 clone. The results suggest that these strains may have diverged from the new O3:K6 clone by alteration of the O:K antigens. In conclusion, this study presents strong evidence for the first pandemicity in the history of V. parahaemolyticus and reports a novel toxRS-targeted PCR method that will be useful in epidemiological investigation of the cases associated with the current pandemic spread.

Molecular evidence of clonal Vibrio parahaemolyticus pandemic strains

The upsurge in worldwide incidence of Vibrio parahaemolyticus infection in the last 5 years has been attributed to the recent appearance of three serotypes with pandemic potential: O3:K6, O4:K68, and O1:K untypeable (KUT). Thirty-five strains of these serotypes, isolated from different countries over 4 years, were characterized by ribotyping and pulsed-field gel electrophoresis to determine their origin. The ribotypes of the strains of these serotypes were indistinguishable, except for a Japanese tdh- negative O3:K6 strain and a U.S. clinical O3:K6 isolate, which had slightly different profiles. The migration patterns of the NotI-digest of the total DNA of the strains were similar, and only slight variations were observed between the serotypes. By contrast, the O3:K6 and O1:KUT strains isolated before 1995 and strains of other serotypes had markedly different profiles. The O4:K68 and O1:KUT strains most likely originated from the pandemic O3:K6 clone.

Clonal diversity among recently emerged strains of Vibrio parahaemolyticus O3:K6 associated with pandemic spread

The genomes of the O3:K6 strains of Vibrio parahaemolyticus which abruptly emerged in Calcutta, India, in February 1996 and which demonstrated an unusual potential to spread and an enhanced propensity to cause infections were examined by different molecular techniques to determine clonality. No restriction fragment length polymorphism (RFLP) in the gene encoding the thermostable direct hemolysin was observed among the O3:K6 isolates of V. parahaemolyticus. Clonal diversity among the O3:K6 strains became evident by examining the RFLPs of the rrn operons and by the use of pulsed-field gel electrophoresis. Five ribotypes were distinguished among the O3:K6 strains examined, with ribotype R4 constituting the major type. Strains of O3:K6 isolated between June and August 1996 showed different pulsotypes compared to the pulsotypes of strains isolated before and after this period, indicating genetic reassortment among these strains, but those isolated between August 1996 and March 1998 showed identical or nearly similar pulsotypes. It is clear that there is a certain degree of genomic reassortment among the O3:K6 clones but that these strains are predominantly one clone.

Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species

We constructed a physical map of the genomic DNA (5.1 Mb) for Vibrio parahaemolyticus strain AQ4673 by combining 17 adjacent NotI fragments. This map shows two circular replicons of 3.2 and 1.9 Mb. Pulsed-field gel electrophoresis (PFGE) of undigested genomic DNA revealed two bands of corresponding sizes. Analysis both by NotI digestion and by Southern blot of the two isolated bands confirmed the existence of two replicons. The presence of genes for 16S rRNA on both the replicons indicates that the replicons are chromosomes rather than megaplasmids. The two bands were also seen after PFGE of undigested genomic DNA of V. parahaemolyticus strains other than AQ4673, and of strains belonging to other Vibrio species, such as V. vulnificus, V. fluvialis and various serovars and biovars of V. cholerae. It is noteworthy that V. cholerae O1 strain 569B, a classical biovar, was also shown to have two replicons of 2.9 and 1.2 Mb, which does not agree with a physical map proposed in a previous study. Our results suggest that a two-replicon structure is common throughout Vibrio species.

Close proximity of the tdh, trh and ure genes on the chromosome of Vibrio parahaemolyticus

The distribution and location of the virulence-factor genes of Vibrio parahaemolyticus, tdh and trh, and the structural gene of urease, ureC, were examined on the genomic DNAs of 115 clinical isolates of V. parahaemolyticus. The majority of strains (81%) had two copies of tdh on the chromosome, and no copies of trh or ure. Southern hybridization with a tdh probe, after pulsed-field gel electrophoresis of Notl-digested genomic DNA of each strain revealed only single bands, suggesting that the two copies of the exist on single Notl fragments in each strain. Of the 115 strains, 7% had the tdh, trh and ure genes on chromosomal DNA. The three genes were also detected on single Notl fragments in these strains. More detailed analysis revealed that the three genes were localized within 40 kb. By long and accurate polymerase chain reactions (LA-PCR) the distance between trh and ure was shown to be less than 8.5 kb. These results reveal a close proximity of the tdh, trh and ure genes on the chromosome of pathogenic V. parahaemolyticus strains.

Emergence of a unique O3:K6 clone of Vibrio parahaemolyticus in Calcutta, India, and isolation of strains from the same clonal group from Southeast Asian travelers arriving in Japan

Active surveillance of Vibrio parahaemolyticus infection among hospitalized patients in Calcutta, India, was initiated in January 1994. The incidence of cases of V. parahaemolyticus infection suddenly increased in February 1996 and has remained high since then. One hundred thirty-four strains of V. parahaemolyticus isolated from January 1994 to August 1996 were examined for serovar, the presence of the thermostable direct hemolysin gene (tdh) and tdh-related hemolysin genes (trh1 and trh2), production of urease, and antibiogram. Strains of the O3:K6 serovar appeared for the first time in February 1996. The O3:K6 serovar strains accounted for 50 to 80% of the strains isolated during the high-incidence period (February to August 1996). All of the serovar O3:K6 strains carried the tdh gene but not the trh genes and did not produce urease. All of the isolates except two were sensitive to all of the antibiotics tested. These and the results of analysis by an arbitrarily primed PCR method indicated that the O3:K6 serovar strains belong to a unique clone. When the O3:K6 serovar strains, isolated from travelers arriving in Japan from Southeast Asian countries, were compared by the arbitrarily primed PCR method, the strains isolated between 1982 and 1993 were distinct from Calcutta O3:K6 while the strains isolated in 1995 and 1996 were indistinguishable from the Calcutta O3:K6 strains. The results suggest that this unique O3:K6 clone may have become prevalent not only in Calcutta but also in Southeast Asian countries very recently. Not only the O3:K6 strains but also the non-O3:K6, tdh-bearing strains isolated in 1996 produced thermostable direct hemolysin at high levels, and thus the level of hemolysin produced does not appear to have influenced the high incidence of serovar O3:K6 strains.

Analysis of the thermostable direct hemolysin (tdh) gene and the tdh-related hemolysin (trh) genes in urease-positive strains of Vibrio parahaemolyticus isolated on the West Coast of the United States

Urease-positive (Ure+) and urease-negative (Ure-) strains of Vibrio parahaemolyticus isolated from patients on the West Coast of the United States between 1979 and 1995 were analyzed for the thermostable direct hemolysin (tdh) gene and the tdh-related hemolysin (trh) genes (trh1 and trh2). The DNA colony hybridization method with the polynucleotide probes was used to determine the distribution of the genes. Of 60 Ure+ strains, 59 strains (98%) had the trh (either trh1 or trh2) gene and 54 strains (90%) carried the tdh gene. The absence of the trh gene or a related sequence in an exceptional Ure+ strain was confirmed by Southern blot analyses. The stronger correlation with the trh gene than with the tdh gene was mostly attributable to strains possessing only the trh2 gene. Of 25 Ure- strains, 20 strains (80%) had the tdh gene but none had the trh gene. These results indicate a very strong correlation between the Ure+ phenotype and the trh gene and are consistent with those reported for strains isolated in Asia. The Ure+ strains carrying the trh genes were not restricted to a unique group of the strains. The O4:K12 strains carrying the trh1 gene have predominantly been isolated since 1979. However, strains of various non-O4:K12 serovars carrying either the trh1 or the trh2 gene became predominant after 1992. In addition, analysis by the arbitrarily primed PCR method revealed two subgroups within the selected Ure+ O4:K12 strains. Hybridization tests with oligonucleotide probes demonstrated that the trh1 sequences of the West Coast strains differ to some extent from those of Asian strains. Nevertheless, a PCR method previously established to detect both the trh1 and the trh2 genes in Asian strains could detect 98% of those genes in the West Coast strains.

Restriction fragment length polymorphism of the tdh and trh genes in clinical Vibrio parahaemolyticus strains

The restriction fragment length polymorphism of the genes encoding thermostable direct hemolysin (tdh) and thermostable direct hemolysin-related hemolysin (trh) was analyzed for 137 strains of Vibrio parahaemolyticus isolated from specimens from diarrheal patients in Thailand. The HindIII restriction fragment patterns of tdh and trh were grouped into five and four types, respectively. A strong association between the restriction fragment patterns of tdh and trh was observed with V. parahaemolyticus strains.