Complete nucleic acid sequence of Penaeus monodon densovirus (PmDNV) from India

The complete nucleic acid sequence of the Penaeus monodon densovirus (PmDNV) from India was characterized. Analysis of the whole genome, consisting of 6310 bp revealed the presence of three open reading frames (ORFs), comprising 1281 bp, 1734 bp and 2460 bp, respectively. The complete genome and amino acid sequences of three proteins viz., NS1, NS2 and VP were compared with PmDNV from Thailand, PmergDNV from Australia and other partial sequences in GenBank, respectively. Highest nucleotide similarity was observed with the Thai strain (88%), while 33, 32 and 91 amino acid substitutions were observed in the NS2, NS1 and VP, respectively. Phylogenetic analysis of shrimp, insect and vertebrate parvovirus sequences revealed that the Indian PmDNV is more closely related to Thai isolates than all other parvoviruses reported so far.

Quorum sensing negatively regulates chitinase in Vibrio harveyi

Quorum sensing, bacterial cell-to-cell communication, regulates the virulence of Vibrio harveyi towards different hosts. Chitinase can be considered as a virulence factor because it helps pathogenic bacteria to attach to the host and to penetrate its tissues (e.g. in case of shrimp). Here, we show that quorum sensing negatively regulates chitinase in V. harveyi. Chitinolytic activity towards natural chitin from crab shells, the synthetic chitin derivative chitin azure, and fluorogenic chitin oligomers was significantly higher in a mutant in which the quorum-sensing system is completely inactivated when compared with a mutant in which the system is maximally active. Furthermore, the addition of signal molecule containing cell-free culture fluids decreased chitinase activity in a Harveyi Autoinducer 1 and Autoinducer 2-deficient double mutant. Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum-sensing system is maximally active when compared with the mutant in which the system is completely inactivated. [Correction added on 25 September 2009, after first online publication: the preceding sentence was corrected from 'Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum-sensing system is completely inactivated when compared with the mutant in which the system is maximally active.'] We argue that this regulation might help the vibrios to switch between host-associated and free-living life styles.

Recombinant ferritin protein protects Penaeus monodon infected by pathogenic Vibrio harveyi

Hemocytes of shrimp perform an essential role in defense against microbial pathogens, involving both cellular and humoral factors. The gene coding for ferritin in black tiger shrimp Penaeus monodon was cloned, sequenced and expressed using pQE-30-UA vector and SG13009 Escherichia coli host cells. The deduced amino acid sequence of P. monodon ferritin showed 32 to 95% similarity with ferritin proteins of other organisms. The recombinant protein was purified by nickel-nitrilotriacetic acid affinity chromatography. A single thick band of recombinant protein of approximately 21 kDa was observed in 15% sodium dodecyl sulfate polyacrylamide gel electrophoresis. Following mild acid treatment, 2 bands of ca. 14 and 7 kDa were produced; aspartine and proline acid cleavage sites were found at amino acid residues 123-124. The purified recombinant ferritin helped in reducing the mortality in shrimp infected with Vibrio harveyi . However, no direct antimicrobial activity against pathogenic V. harveyi was observed.

Cloning and expression of an outer membrane protein OmpW of Aeromonas hydrophila and study of its distribution in Aeromonas spp

AIMS

The main aims of this study were to clone and express an outer membrane protein (OMP), OmpW, of Aeromonas hydrophila and to study its distribution in Aeromonas spp.

METHODS AND RESULTS

The gene encoding OmpW in A. hydrophila has been cloned and expressed in Escherichia coli. Primers were designed for amplification of full-length ompW gene and used for identification of this gene in different Aeromonas spp. Of the 42 Aeromonas strains tested, all the isolates were positive by polymerase chain reaction (PCR) except one strain of Aeromonas veronii biovar veronii (VTE338). None of the other gram-negative bacteria were positive by PCR with primers specific to ompW gene of A. hydrophila. Polyclonal antibodies were raised in rabbit against the purified recombinant protein and the reaction of these antibodies was confirmed by western blotting using the purified recombinant protein and 42 Aeromonas cultures grown at various salt concentrations.

CONCLUSIONS

The ompW-based PCR method developed in this study was found to be 100% specific and 97% sensitive. Expression of OmpW protein of Aeromonas was found to be salt-dependant. Recombinant OmpW protein was found to be highly immunogenic in fish.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this is the first report on cloning and expression of OmpW protein of A. hydrophila. Full-length ompW gene amplification by PCR can be used for the detection of Aeromonas. Recombinant OmpW protein can be useful for vaccination of fish against Aeromonas spp.

Evaluation of a digoxigenin-labelled probe for detection of Aeromonas spp

An outer membrane protein-based Digoxigenin (DIG)-labelled DNA probe was developed for the specific detection of Aeromonas sp. from food/environmental/clinical samples. Dot blot reaction answered for all the Aeromonas isolates and was negative for Escherichia coli, Pseudomonas sp., Klebsiella sp., Vibrio parahaemolyticus, V. harveyi, V. alginolyticus, V. vulnificus. Edwardsiella tarda and Staphylococcus sp. As this protein is highly conserved in various Aeromonas species, the probe has the potential for use as a rapid and reliable diagnostic tool.

Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR

Two real-time PCR assays targeting the small-subunit (SSU) ribosomal DNA (rDNA) were designed to assess the proportional biomass of diatoms and dinoflagellates in marine coastal water. The reverse primer for the diatom assay was designed to be class specific, and the dinoflagellate-specific reverse primer was obtained from the literature. For both targets, we used universal eukaryotic SSU rDNA forward primers. Specificity was confirmed by using a BLAST search and by amplification of cultures of various phytoplankton taxa. Reaction conditions were optimized for each primer set with linearized plasmids from cloned SSU rDNA fragments. The number of SSU rDNA copies per cell was estimated for six species of diatoms and nine species of dinoflagellates; these were significantly correlated to the biovolumes of the cells. Nineteen field samples were collected along the Swedish west coast and subjected to the two real-time PCR assays. The linear regression of the proportion of SSU rDNA copies of dinoflagellate and diatom origin versus the proportion of dinoflagellate and diatom biovolumes or biomass per liter was significant. For diatoms, linear regression of the number of SSU rDNA copies versus biovolume or biomass per liter was significant, but no such significant correlation was detected in the field samples for dinoflagellates. The method described will be useful for estimating the proportion of dinoflagellate versus diatom biovolume or biomass and the absolute diatom biovolume or biomass in various aquatic disciplines.

Determination of chloramphenicol in shrimp by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS)

A liquid chromatographic method with electrospray ionization tandem mass spectrometric (LC-ESI-MS-MS) detection and identification is described for the determination of chloramphenicol (CAP) in shrimp tissue. Homogenized shrimp samples were extracted by liquid-liquid extraction using ethyl acetate. d5-Chloramphenicol (5D-CAP) was used as the internal standard. Data acquisition was in negative-ion multiple reaction monitoring (NMRM) mode using three transition reactions for CAP (m/z 321 --> 152, m/z 321 --> 257 and m/z 321 --> 194) and two for d5-chloramphenicol (m/z 326 --> 262 and m/z 326 --> 157). Method validation was carried out according to European Commission decision 2002/657/EC. The calibration curve was linear in the range 0.10-2.00 microg l(-1), with typical r2 > 0.99. The decision limit (CC alpha) and detection capability (CC beta) were 0.06 and 0.10 microg kg(-1), respectively. There was no influence of the matrix on the determination of chloramphenicol.

Development and evaluation of a polymerase chain reaction (PCR) assay for the detection of Opisthorchis viverrini in fish

Human opisthorchiais caused by the liver fluke Opisthorchis viverrini is a major fish-borne trematode infection endemic in the Southeast Asian countries. The infection is acquired through consumption of raw fish harboring metacercariae of O. viverrini. Owing to potential risk of transmission of opisthorchiasis through fish trade, rapid and reliable detection methods have gained importance to ensure food safety. In the study described here, we report successful development and evaluation of a polymerase chain reaction (PCR) assay for the detection of O. viverrini, based on the nucleotide sequence derived in this study. The assay is specific with no cross-reaction with other trematodes commonly found in fish including the closely related species, Clonorchis sinensis. The sensitivity of the assay was determined to be 10(-12)ng of O. viverrini DNA while in artificially spiked fish meat, 3 metacercariae could be detected. The results suggest that the PCR method described here is specific to O. viverrini with potential application in fish quarantining.

Microsatellite DNA markers in the giant freshwater prawn, Macrobrachium rosenbergii: a tool for genetic analysis

Eight microsatellite loci were identified and characterized in the commercially important giant freshwater prawn, Macrobrachium rosenbergii. The microsatellite loci were detected by the random screening for dinucleotide repeat units within a partial genomic library developed for the species with biotinylated probes (CA)(15) , (AT)(15) and (GA)(15) . All the eight loci were found to be polymorphic. The number of alleles and observed heterozygosities per locus ranged between three to 16 and 0.22 to 0.71, respectively. These microsatellite markers will be useful for the conservation and management of wild and cultured stocks and population genetic studies of freshwater prawn.

Variable repeat regions in the genome of Vibrio vulnificus and polymorphism in one of the loci in strains isolated from oysters

Vibrio vulnificus an estuarine bacterium is associated with severe wound infections and fatal septicemia related to consumption of raw shellfish. In this study we screened the two whole genome sequences available for V. vulnificus in GenBank for the presence of variable number of tandem repeat (VNTR) regions. Five potential VNTR loci with unit repeat size ranging from 6-7 nucleotides were identified for V. vulnificus genome. One of the loci designated Vv1 was selected to detect the repeat number present in V. vulnificus strains isolated from oyster samples in India. Twenty six of the thirty samples tested were found to be highly polymorphic for the Vv1 locus. Copy numbers for the hexanucleotide motif ranged from 4-55, giving rise to a total of 17 polymorphic groups. Our analysis, shows that different genotypic variants exist in the environment and the VNTR loci studied can be used as a marker for strain discrimination and in epidemiological study of this organism.

Genotyping of white spot syndrome virus prevalent in shrimp farms of India

DNA extracts from white spot syndrome virus (WSSV) that had infected post-larvae and juveniles of cultured shrimp, wild shrimp and crabs, which had been collected from different hatcheries and farms located along both the east and west coasts of India, revealed considerable variation in several previously identified WSSV DNA repeat regions. These include the 54 bp repeat in ORF 94, the 69 bp repeat in ORF 125 and the compound 45 and 57 bp repeat region in ORF 75. In ORF 94, 13 genotypes were observed with the number of repeats ranging from 2 to 16 units. While 7 repeat units were commonly observed (11.3%), no samples with 11 or 15 repeat units were found. In ORF 125, 11 types were found, with repeats ranging from 2 to 14 units. The most prevalent genotype displayed 4 repeat units (47.1%); no samples with 6 or 13 repeats were observed. The compound repeat region of ORF 75 displayed 6 different patterns of repeats. Samples with the same repeat pattern in one ORF did not always show identical repeat patterns in one or both of the other repeat regions. These data suggest that combined analysis of all 3 variable loci could be used to differentiate and characterize specific WSSV strains. For general epidemiological studies, the best marker with maximum variation is ORF 94, followed by ORF 125 and ORF 75. The 3 repeat regions above were used to compare WSSV genotypes from disease outbreaks on 3 sets of farms from different locations in the state of Andhra Pradesh. The genotypes within each farm set were almost identical, but differed between farm sets, suggesting that WSSV transmission occurred directly through virus carriers or water exchange between adjacent farms at each location. These findings show that genotyping can be a useful epidemiological tool for tracing the movement of WSSV within infected populations.

Contamination of community water sources by potentially pathogenic vibrios following sea water inundation

Potentially pathogenic members of the Vibrionaceae family including Vibrio cholerae and Vibrio parahemolyticus were isolated from domestic sources of drinking water in coastal villages following sea water inundation during the tsunami in Southern India. Phenotypic and genotypic studies were done to confirm the identity and detection of toxins. Vibrio-gyr (gyrase B gene) was detected in all sixteen vibrio isolates. Toxin regulating genes i.e.: ctx gene, tdh gene, and trh gene, however were not detected in any of the strains, thereby ruling out presence of toxins which could endanger human life. Other potentially pathogenic bacteria Aeromonas and Plesiomonas were also isolated from hand pumps and wells, in a few localities. There was no immediate danger in the form of an outbreak or sporadic gastroenteritis at the time of the study. Timely chlorination and restoration of potable water supply to the flood affected population by governmental and nongovernmental agencies averted waterborne gastroenteritis. Assessment of quality of water and detection of potential virulent organisms is an important public health activity following natural disasters. This work highlights the importance of screening water sources for potentially pathogenic microorganisms after natural disasters to avert outbreaks of gastroenteritis and other infectious diseases.

Putative virulence genes of Vibrio cholerae from seafoods and the coastal environment of Southwest India

Shrimp, clam and oysters were obtained at two fish markets and at a fish landing dock, and plankton, water and sediment samples were obtained from four river estuaries, in southern India. The samples were analyzed for Vibrio cholerae by conventional isolation techniques and by polymerase chain reaction (PCR) procedures. V. cholerae was isolated from 2 of 5 shrimp, 2 of 5 clam and 5 of 20 water samples. All biochemically confirmed isolates of V. cholerae were positive for toxR. For direct detection of V. cholerae in enrichment broths, PCR was performed using lysates from 0 and 6 h enrichments. All the V. cholerae isolates and enrichment broth lysates were subjected to PCR analysis for the detection of the genes toxR, ctxA, tcpA, ompU, hly, ace, Nag-ST (stn/sto), and ompU. Enrichment broths of all the samples which yielded V. cholerae were positive for toxR, OmpU and hlyA genes, while one of a fresh fish market sample was positive for the ace gene. Choleragenic V. cholerae were absent from all environmental samples and fresh fish from the markets, but one sample of shrimp was positive for V. cholerae O139.

Detection of Laem-Singh virus (LSNV) in cultured Penaeus monodon from India

Viral diseases have become a major constraint on the growth of shrimp aquaculture in India. During a study of new diseases in cultured tiger shrimp Penaeus monodon, diseased samples randomly collected from the southwestern and southeastern coasts of India were analyzed for white spot syndrome virus (WSSV), monodon baculovirus (MBV), and hepatopancreatic parvovirus (HPV) by nested PCR, and for Laem-Singh virus (LSNV) by reverse transcription PCR (RT-PCR). Of the 56 samples analyzed, 3 were positive for LSNV. These samples had signs of loose shell syndrome (LSS). Of the 3 samples that tested positive for LSNV, 2 were also positive for WSSV and MBV, and of these 2 samples, 1 was also positive for HPV. This is the first reported presence of LSNV in cultured shrimp in India.

Evaluation of an alkaline phosphatase-labeled oligonucleotide probe for detection and enumeration of vibrio spp. from shrimp hatchery environment

An alkaline phosphatase (AP)-labeled genus-specific oligonucleotide probe was developed to detect and enumerate vibrios in shrimp larvae and their surrounding environment. The probe was evaluated using 35 laboratory isolates of Vibrio species and 29 isolates of non-vibrio species. The probe was specific for the Vibrio species and no cross reaction was found with the non-vibrios included in the study. The total Vibrio counts obtained by plating on thiosulfate-citrate-bile salts-sucrose agar (TCBS) and using oligonucleotide probe were compared. Total Vibrio counts obtained by probe were comparatively higher than the counts obtained by plating on TCBS agar. The difference between the counts obtained by the probe and by plating on TCBS agar ranged from 2 to 21 times. The study reveals that the use of a non-selective medium such as T1N3 agar followed by detection using a genus-specific probe would help to precisely enumerate the total Vibrio load in the aquaculture environments.

Rapid detection and enumeration of trh-carrying Vibrio parahaemolyticus with the alkaline phosphatase-labelled oligonucleotide probe

An alkaline phosphatase (AP)-labelled oligonucleotide probe was developed to detect and enumerate trh(+)Vibrio parahaemolyticus in seafood. The probe was evaluated using 40 isolates of V. parahaemolyticus, 45 isolates of other vibrios and 55 non-vibrio isolates. The probe reacted specifically with V. parahaemolyticus possessing either the trh1 or trh2 variant of the trh gene and was found to be 100% specific for trh(+)V. parahaemolyticus. Using the trh probe, V. parahaemolyticus carrying trh gene was targeted in 34 seafood samples by direct plating and colony hybridization procedure. The trh(+)V. parahaemolyticus could be detected in five of 34 (14.7%) samples and the levels ranged from 5.0 x 10(2) to 3.4 x 10(3) cfu g(-1). Colonies of trh(+)V.parahaemolyticus were isolated from the five positive samples. Forty seafood samples were analysed for trh(+)V. parahaemolyticus by colony hybridization following enrichment in alkaline peptone water. 16 samples (40%) were positive for trh gene and trh(+)V. parahaemolyticus was isolated from 15 samples (37.5%). To assess the sensitivity of the trh probe, seafood homogenates spiked with known concentrations of trh-positive V. parahaemolyticus were plated and hybridized. Counts obtained using the probe were similar to those of inocula. The results suggest that the AP-labelled trh probe is useful for the detection and enumeration of trh(+)V. parahaemolyticus in seafood.

Detection and characterization of Salmonella associated with tropical seafood

The prevalence of Salmonella in seafood samples collected from the southwest coast of India was studied by conventional culture and by a DNA based molecular technique, polymerase chain reaction (PCR). While conventional culture techniques detected Salmonella in only 20 out of the 100 samples analyzed, direct enrichment lysate PCR detected 52 as positive for Salmonella. A set of three different PCR primers viz., hns, invA and invE were used. It was observed that hns primer detected Salmonella in a significantly higher number of samples. Fourteen out of nineteen isolates belonged to serovar S. enterica Weltevreden. S. Weltevreden isolates were genotyped yielding 4 different patterns both by RAPD and ERIC-PCR but when combined, the overall results discriminated the isolates of S. Weltevreden into 6 different types. This suggests that genetically diverse Salmonella Weltevreden are prevalent in seafood.

Cloning and expression of an outer membrane protein ompTS of Aeromonas hydrophila and study of immunogenicity in fish

The outer membrane proteins of the warm water fish pathogen, Aeromonas hydrophila have a role in the virulence of the organism and are potential candidates for vaccine development. In this study, the gene encoding an outer membrane protein designated ompTS was amplified by PCR excluding the region coding for signal peptide, cloned in pQE 30-UA Vector and expressed using induction with isopropyl thiogalactoside (IPTG). The size of the expressed protein was 37 kDa as estimated by migration in 10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Polyclonal antibodies were raised in mice and rabbit against the purified protein and the reaction of the antibody was confirmed by Western blotting using the purified protein and A. hydrophila cultures. The Indian major carp, Labeo rohita Hamilton was immunized using the purified protein and developed antibodies with mean titers of 1:4000 on day 14 and 1:12,000 on day 28 showing promise that the protein is highly immunogenic in fish.