Molecular characterization of Vibrio harveyi bacteriophages isolated from aquaculture environments along the coast of India

Seven bacteriophages specific to Vibrio harveyi, the causative agent of luminous vibriosis in shrimp, were isolated from coastal aquaculture systems like shrimp farms, hatcheries and tidal creeks along the east and west coast of India. All the seven phages were found to have the typical head and tail morphology with double-stranded DNA as genetic material. Morphologically, six phages were grouped under family Siphoviridae and one under Myoviridae. These phages were further characterized with respect to host range, morphology and structural proteins. Genomic fingerprinting was carried out using restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD). Major capsid proteins of all the phages detected by SDS-PAGE were distinct from one another. All the phages were found to be highly lytic for V. harveyi and had different lytic spectrum for the large number of isolates tested. Six of the seven phages isolated had a broad lytic spectrum and could be potential candidates for biocontrol of V. harveyi in aquaculture systems.

Clonorchis sinensis: development and evaluation of a nested polymerase chain reaction (PCR) assay

Clonorchis sinensis is a fish-borne trematode endemic to East Asia, which infects over 35 million people globally. In the study described here, we developed a nested polymerase chain reaction (PCR) method for the specific and reliable detection of C. sinensis. The primers designed from the nucleotide sequence data derived in this study were evaluated for their specificity and sensitivity for the detection of C. sinensis. The specific amplification products were obtained only with C. sinensis and no amplifications occurred with the DNA of closely related trematodes including Opisthorchis viverrini demonstrating the specificity of the assay. The novel PCR method described here will be useful for the quarantine of fishery products and evaluation of transmission status of clonorchiasis in the endemic areas.

A gyrB-based PCR for the detection of Vibrio vulnificus and its application for direct detection of this pathogen in oyster enrichment broths

A polymerase chain reaction (PCR) method based on the gyrB (encoding gyrase B or topoisomerase II) gene sequence was developed for the detection of Vibrio vulnificus in seafood. The gyrB primers detected all laboratory isolates of V. vulnificus and did not cross react with other Vibiro and non-Vibrio species examined in this study. The sensitivity of detection of V. vulnificus by gyrB PCR was 300 CFU/g in artificially seeded oyster homogenate without enrichment while, 30 CFU/g could be detected following 18 h enrichment in alkaline peptone water (APW). The gyrB-specific PCR was employed for the direct detection of V. vulnificus in oyster enrichment broths. The assay detected V. vulnificus in 75% of natural oyster samples after 18 h enrichment in APW. The gyrB-based PCR described here offers a simple and specific one step PCR method for the detection of V. vulnificus in seafood enrichment broths.

Molecular characterization of thermostable direct haemolysin-related haemolysin (TRH)-positive Vibrio parahaemolyticus from oysters in Mangalore, India

Pathogenic Vibrio parahaemolyticus strains producing either or both of a thermostable direct haemolysin (TDH) and a TDH-related haemolysin (TRH) encoded by tdh and trh genes, respectively, are isolated at a low rate from the environment. However, recently we observed that a considerable percentage of APW (alkaline peptone water) enrichment broths of oysters collected off Mangalore India, were trh(+), rather than tdh(+) by PCR. In order to further investigate the prevalence and genetic diversity of trh bearing V. parahaemolyticus in our coast, we attempted to isolate and characterize trh(+)V. parahaemolyticus from oysters. A total of 27 trh(+) strains were isolated during the period between March 2002 and February 2004, of which nine were also tdh(+). All the trh(+) isolates were positive for urease phenotype. The isolates belonged to diverse phenotypes. In order to explore the possible presence of heterogeneity in the trh gene region among trh(+)V. parahaemolyticus, a 1.5 kb region around trh gene was PCR amplified and restriction digested using selected restriction enzymes. The whole genome comparison of strains was performed by randomly amplified polymorphic DNA PCR (RAPD PCR). The PCR-RFLP results revealed fairly well conserved nature of the trh gene region studied in different serotypes. Though 11 strains were positive by PCR for a genomic fragment that has been reported to be amplified in pandemic strains, all strains were negative by group-specific PCR (GS-PCR), orf8 PCR and showed a different RAPD pattern compared with pandemic strains. The results suggest that genetically diverse V. parahaemolyticus carrying virulence genes are associated with the aquatic environment in this region.

Use of methylation sensitive polymerase chain reaction for detection of fragile X full mutation & carrier state in males

BACKGROUND & OBJECTIVE

Fragile X syndrome is the most common cause of inherited mental retardation. It is characterized by the progressive expansion of polymorphic (CGG) trinucleotide repeats located in the promoter region of the FMRI gene located at Xq27.3. The typical dysmorphic features that help in diagnosis are very often subtle or absent especially in pre-pubertal children. Confirmation is by molecular diagnosis based on repeat size and methylation analysis of the FMR1 gene. The present study was done to evaluate the utility of a methylation sensitive polymerase chain reaction (ms-PCR) method in the molecular diagnosis of fragile X syndrome in a select group of mentally retarded male children.

METHODS

We used a methylation sensitive PCR technique, which initially modified DNA by bisulphite treatment. Two sets of PCR primers one each for methylated and unmethylated DNA sequences, were used. In full mutations, PCR specific for the methylated sequences was designed to amplify the CpG dinucleotide region upstream to the CGG repeats in clinically affected males. In healthy males and carriers, the second set of primers would amplify the unmethylated DNA sequences. The amplified PCR product size would help to differentiate between normal and premutation repeat size.

RESULTS

In all, 25 blood samples collected from mentally retarded male children and five from normal controls were tested. Analysis of cases revealed one full blown mutation and one carrier state. These were further confirmed by southern blotting.

INTERPRETATION & CONCLUSION

Unlike currently used methods, methylation sensitive PCR is a quick and accurate technique which could be used for the rapid screening of fragile X syndrome in mental retardation.

Diagnosis of partially treated culture-negative bacterial meningitis using 16S rRNA universal primers and restriction endonuclease digestion

Cerebrospinal fluid (CSF) obtained from patients with partially treated and culture-negative meningitis was subjected to PCR using 16S rDNA universal primers followed by restriction endonuclease digestion. In all, 43 patients and 7 controls were enrolled in this study. Twenty-one meningitic samples were positive by PCR. Mycobacterium tuberculosis was the causative agent in seven cases followed by Haemophilus influenzae (four), Streptococcus pneumoniae (two), Listeria monocytogenes (one), Escherichia coli (one), Pseudomonas aeruginosa (one) and Staphylococcus aureus (one). Only two meningitic CSF samples were culture-positive. In this study, PCR using bacterial 16S rDNA specific universal primers was found to be superior to conventional methods in the diagnosis of partially treated meningitis.

Seasonal variation in abundance of total and pathogenic Vibrio parahaemolyticus bacteria in oysters along the southwest coast of India

The seasonal abundance of Vibrio parahaemolyticus in oysters from two estuaries along the southwest coast of India was studied by colony hybridization using nonradioactive labeled oligonucleotide probes. The density of total V. parahaemolyticus bacteria was determined using a probe binding to the tlh (thermolabile hemolysin) gene, and the density of pathogenic V. parahaemolyticus bacteria was determined by using a probe binding to the tdh (thermostable direct hemolysin) gene. Furthermore, the prevalence of V. parahaemolyticus was studied by PCR amplification of the toxR, tdh, and trh genes. PCR was performed directly with oyster homogenates and also following enrichment in alkaline peptone water for 6 and 18 h. V. parahaemolyticus was detected in 93.87% of the samples, and the densities ranged from <10 to 10(4) organisms per g. Pathogenic V. parahaemolyticus could be detected in 5 of 49 samples (10.2%) by colony hybridization using the tdh probe and in 3 of 49 samples (6.1%) by PCR. Isolates from one of the samples belonged to the pandemic serotype O3:K6. Twenty-nine of the 49 samples analyzed (59.3%) were positive as determined by PCR for the presence of the trh gene in the enrichment broth media. trh-positive V. parahaemolyticus was frequently found in oysters from India.

The occurrence of Vibrio species in tropical shrimp culture environments; implications for food safety

The occurrence of various Vibrio species in water, sediment and shrimp samples from multiple shrimp farm environments from the east and west coast of India was studied. The relative abundance was higher in west coast farms (ca. 10(4) cfu/ml water) when compared to the east coast (ca. 10(2) cfu/ml water). Vibrio alginolyticus (3-19%), V. parahaemolyticus (2-13%), V. harveyi (1-7%) and V. vulnificus (1-4%) were the predominant Vibrio species identified by standard biochemical testing. In some cases, V. cholerae could be found, but all isolates were negative for the cholera toxin (ctx) gene that is associated with choleragenic strains. The biochemical identification of V. parahaemolyticus, the other human pathogen among the species mentioned above, was confirmed by PCR targeting the toxR gene and a 387 bp chromosomal locus specific for this species. Furthermore, the presence of the virulence-associated tdh (thermostable direct haemolysin) and trh (TDH-related haemolysin) genes in the V. parahaemolyticus isolates was also detected by PCR. Only 2 out of 47 isolates were tdh positive and one contained the trh gene. However, since V. cholerae, V. parahaemolyticus and V. vulnificus species are recognized as a major cause of seafood-borne illness, it is important to pay attention to post-harvest handling and adequate cooking.

Study of the occurrence of Vibrio vulnificus in oysters in India by polymerase chain reaction (PCR) and heterogeneity among V. vulnificus by randomly amplified polymorphic DNA PCR and gyrB sequence analysis

The pathogenic bacterium Vibrio vulnificus is widely distributed in estuarine waters throughout the world. In this study, the presence of V. vulnificus in oysters was studied both by conventional culture and DNA-based molecular technique. Following enrichment in alkaline peptone water (APW), the bacteria were lysed and a nested polymerase chain reaction (PCR) for vvhA gene was performed. The effect of duration of enrichment on the sensitivity of detection by PCR was evaluated. The organism was isolated from 43% of samples after 18 h enrichment in APW by conventional culture method. Nested PCR amplifying a fragment of vvhA gene detected the organism in 11%, 60% and 81% of samples following 0, 6 and 18 h of enrichment. All the biochemically identified V. vulnificus strains possessed vvhA gene and belonged to biotype 1. The genetic relatedness among the strains was studied by randomly amplified polymorphic DNA (RAPD) PCR and gyrB sequence analysis. The results suggest the presence of two distinct clonal groups of V. vulnificus in oysters in India. The study demonstrates, for the first time that gyrB sequence analysis could be used to study the genetic diversity of V. vulnificus.

Detection of hepatopancreatic parvovirus (HPV) in wild shrimp from India by nested polymerase chain reaction (PCR)

The prevalence of hepatopancreatic parvovirus (HPV) in wild penaeid shrimp samples from India was studied by nested polymerase chain reaction (PCR) using primers designed in our laboratory. The virus could be detected in 9 out of 119 samples by non-nested PCR. However, by nested PCR 69 out of 119 samples were positive. The PCR results were confirmed by hybridization with digoxigenin-labelled DNA probe. Shrimp species positive by non-nested PCR included Penaeus monodon, Penaeus indicus and Penaeus semisulcatus and by nested PCR Parapenaeopsis stylifera, Penaeus japonicus, Metapenaeus monoceros, M. affinis, M. elegans, M. dobsoni, M. ensis and Solenocera choprai. This is the first report on the prevalence of HPV in captured wild shrimp from India.

Detection and enumeration of Vibrio vulnificus in oysters from two estuaries along the southwest coast of India, using molecular methods

This study was conducted to understand the seasonal distribution of Vibrio vulnificus in oysters from two estuaries and the effect of environmental factors on the abundance of V. vulnificus in tropical waters. V. vulnificus was detected in 56.6% of the samples tested by colony hybridization with an alkaline phosphatase-labeled oligonucleotide probe (VV-AP), and the counts ranged from <10/g during the summer months to 10(3)/g in the monsoon season at both sites. The density of V. vulnificus appeared to be controlled more by salinity than by temperature. A nested PCR used in this study detected V. vulnificus in 85% of the samples following 18 h of enrichment in alkaline peptone water.

Characterisation of Shiga toxin-producingEscherichia coli(STEC) isolated from seafood and beef

Shiga toxin-producing Escherichia coli (STEC) strains isolated in Mangalore, India, were characterised by bead-enzyme-linked immunosorbent assay (bead-ELISA), Vero cell cytotoxicity assay, PCR and colony hybridisation for the detection of stx1 and stx2 genes. Four strains from seafood, six from beef and one from a clinical case of bloody diarrhoea were positive for Shiga toxins Stx1 and Stx2 and also for stx1and stx2 genes. The seafood isolates produced either Stx2 alone or both Stx1 and Stx2, while the beef isolates produced Stx1 alone. The stx1 gene of all the beef STEC was found to be of recently reported stx1c type. All STEC strains and one non-STEC strain isolated from clam harboured EHEC-hlyA. Interestingly, though all STEC strains were negative for eae gene, two STEC strains isolated from seafood and one from a patient with bloody diarrhoea possessed STEC autoagglutinating adhesion (saa) gene, recently identified as a gene encoding a novel autoagglutinating adhesion.

Detection by PCR of hepatopancreatic parvovirus (HPV) and other viruses in hatchery-reared Penaeus monodon postlarvae

The prevalence of hepatopancreatic parvovirus (HPV), monodon baculovirus (MBV) and white spot syndrome virus (WSSV) in samples of Penaeus monodon postlarvae (PL10 to PL20, 10 to 20 d old postlarvae) in India was studied by PCR. Samples collected from different hatcheries, and also samples submitted by farmers from different coastal states, were analyzed. HPV was detected in 34%) of the hatchery samples and 31% of the samples submitted by farmers, using a primer set designed for detection of HPV from P. monodon in Thailand. However, none of these samples were positive using primers designed for detection of HPV from P. chinensis in Korea. This indicated that HPV from India was more closely related to HPV from P. monodon in Thailand. MBV was detected in 64% of the samples submitted by the farmers and 71% of the hatchery samples. A total of 84 % of the samples submitted by farmers, and 91% of the hatchery samples, were found positive for WSSV. Prevalence of concurrent infections by HPV, MBV and WSSV was 27% in hatchery samples and 29%, in samples submitted by farmers. Only 8% of the hatchery samples and 16% of the samples submitted by farmers were negative for all 3 viruses. This is the first report on the prevalence of HPV in P. monodon postlarvae from India.

Detection of Salmonella spp. in tropical seafood by polymerase chain reaction

The incidence of Salmonella spp. in tropical seafood was studied using standard microbiological techniques and polymerase chain reaction (PCR). Six of 20 finfish (30%), 4 of 20 clams (20%) and 1 of 20 shrimp (5%) were positive by culture techniques and by PCR. In a comparative study of different selective enrichment broths and selective plating media, more than one enrichment broth and selective agar were found to be necessary for efficient detection of Salmonella from seafood. Selenite cystine broth (SCB) was found to be more efficient compared to tetrathionate broth (TTB) while both bismuth sulfite agar (BSA) and hektoen enteric agar (HEA) were equally effective as selective plating media for fish. In the case of clams, HEA was found to be more effective. The presence of Salmonella spp. could be detected by PCR amplification of DNA extracted directly from the enrichment broths. In two cases, enrichment broths that were positive by PCR did not yield Salmonella by conventional methods.

ompU genes in non-toxigenic Vibrio cholerae associated with aquaculture

AIMS

The study was undertaken with the objective of understanding the virulence-associated genes of the CTX and TCP gene clusters in environmental isolates of Vibrio cholerae, an important human pathogen, isolated from the aquaculture environment. The involvement of the ompU gene in conferring bile resistance in these isolates was also evaluated.

METHODS AND RESULTS

The V. cholerae isolates were tested by PCR and fluorescent antibody test for O1 (Ogawa and Inaba) and O139 serotypes. All isolates were found to be non-toxigenic V. cholerae confirmed by their positive PCR reaction for toxR but negative for ctx, zot and tcp gene. The hlyA gene was detected in 85% of the strains and ompU in 77%. The results on the bactericidal effect of bile salts suggest that ompU may play a role in conferring bile resistance in non-O1/non-O139 strains.

CONCLUSION

The results of the study indicate that most environmental strains lacked the CTX and TCP gene clusters. However, most isolates had the hlyA gene indicating the potential of these environmental strains to cause mild gastroenteritis. It was also observed that strains lacking ompU showed less tolerance to bile salts.

SIGNIFICANCE AND IMPACT OF THE STUDY

Information on virulence factors of V. cholerae associated with aquaculture environment and products would be of value in risk assessment for human health.

Application of polymerase chain reaction for detection of Vibrio parahaemolyticus associated with tropical seafoods and coastal environment

AIMS

To study the incidence of Vibrio parahaemolyticus in seafoods, water and sediment by molecular techniques vs conventional microbiological methods.

METHODS AND RESULTS

Of 86 samples analysed, 28 recorded positive for V. parahaemolyticus by conventional microbiological method, while 53 were positive by the toxR-targeted PCR, performed directly on enrichment broth lysates. While one sample of molluscan shellfish was positive for tdh gene, trh gene was detected in three enrichment broths of molluscan shellfish.

CONCLUSIONS

Direct application of PCR to enrichment broths will be useful for the rapid and sensitive detection of potentially pathogenic strains of V. parahemolyticus in seafoods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Vibrio parahaemolyticus is an important human pathogen responsible for food-borne gastroenteritis world-wide. As, both pathogenic and non-pathogenic strains of V. parahaemolyticus exist in the seafood, application of PCR specific for the virulence genes (tdh & trh) will help in detection of pathogenic strains of V. parahaemolyticus and consequently reduce the risk of food-borne illness.

Typing of Listeria monocytogenes isolates by random amplification of polymorphic DNA

BACKGROUND & OBJECTIVES

Listeria monocytogenes is an important food-borne pathogen causing meningitis and septicaemia in newborns and immunocompromised persons, abortion and preterm labour in pregnant women. Though various methods are available for typing L. monocytogenes, RAPD analysis has been used for epidemiological purposes in developed countries due to its greater discriminating ability. However, as there are no published reports from India on the typing of L. monocytogenes by RAPD technique the present study was undertaken to type isolates of L. monocytogenes from clinical, food and veterinary samples.

METHODS

Isolates of L. monocytogenes were subjected to RAPD using four decamer random primers R1, R2, R3 and R4. Amplified products were analysed by agarose gel electrophoresis.

RESULTS

Eight strains of L. monocytogenes on RAPD analysis generated 4 distinct profiles each with R1 and R4 primers and 3 different profiles with R2 and R3 primers. The isolates from fish, clinical and veterinary samples showed different profiles with respect to each other. Isolate from flat fish (serovar 4) showed a different profile from that of clams (serovar 1). Two isolates from placenta (serovar 1) showed similar profiles and all the isolates from veterinary samples generated similar profiles.

INTERPRETATION & CONCLUSION

RAPD analysis in the present study allowed discrimination of isolates among the same serotype but from different sources. Since RAPD is a rapid technique and offers greater discrimination of strains, this method may be used for typing L. monocytogenes in India.

Multiple viral infection in Penaeus monodon shrimp postlarvae in an Indian hatchery

Moribund Penaeus monodon postlarvae (PL8-PL10) in a hatchery in India were found to be simultaneously infected by 3 different viruses. They were highly infected with monodon baculovirus (MBV) and hepatopancreatic parvovirus (HPV) by histology and with white spot syndrome virus (WSSV) by non-nested polymerase chain reaction (PCR). Apparently healthy postlarvae tested from the same hatchery were positive for MBV and WSSV by nested PCR only. Tissue sections of such postlarvae did not show any histopathological changes. The simultaneous occurrence of these 3 viruses in hatchery-reared postlarval P. monodon is being reported for the first time.

Detection of Shiga-toxigenic Escherichia coli (STEC) in fresh seafood and meat marketed in Mangalore, India by PCR

AIMS

To study the incidence of Shiga-toxigenic Escherichia coli (STEC) in seafoods from India.

METHODS AND RESULTS

Escherichia coli isolated from various seafoods such as fresh fish, clams and water were screened for the presence of stx, hlyA and rfbO157 genes by PCR; 5% of clams and 3% of fresh fish samples were positive for non-O157 STEC.

CONCLUSIONS

STEC is prevalent in seafoods in India, and non-O157 serotype is more common.

SIGNIFICANCE AND IMPACT OF THE STUDY

Seafood could be a vehicle for transmission of STEC even in tropical countries.

Biofilm formation by salmonella spp. on food contact surfaces and their sensitivity to sanitizers

Biofilm formation by two poultry isolates of Salmonella on three commonly used food contact surfaces viz plastic, cement and stainless steel were studied. Biofilm formation of both the isolates showed a similar trend with the highest density being on plastic followed by cement and steel. Salmonella weltevreden formed biofilm with a cell density of 3.4 x 10(7), 1.57 x 10(6) and 3 x 10(5) cfu/cm2 on plastic, cement and steel respectively while Salmonella FCM 40 biofilm on plastic, cement and steel were of the order of 1.2 x 10(7), 4.96 x 10(6) and 2.23 x 10(5) cfu/cm2 respectively. The sensitivity of the biofilm cells grown on these surfaces to different levels of two sanitizers namely hypochlorite and iodophor for varying exposure times was studied. Biofilm cells offered greater resistance when compared to their planktonic counterparts. Such biofilm cells in a food processing unit are not usually removed by the normal cleaning procedure and therefore could be a source of contamination of foods coming in contact with such surfaces.

Polymerase chain reaction in detection of Gymnodinium mikimotoi and Alexandrium minutum in field samples from southwest India

Polymerase chain reaction (PCR) primers were constructed for the detection of two toxic dinoflagellate species, Gymnodinium mikimotoi and Alexandrium minutum. The primers amplified a product of expected size from cultured cells of G. mikimotoi and A. minutum. The species-specific primers targeting G. mikimotoi did not yield any product with a wide range of other cultured algae used as negative controls. Primers designed for A. minutum were species-group-specific since it PCR yielded a product from the closely related species A. ostenfeldii and A. andersonii, but not from other species of this genus tested. The confirmation of PCR products was performed by digestion of the products with restriction enzymes. Sensitivity analyses of the primers on DNA template from cultured cells was positive by PCR at a DNA template concentration of 1.5 x 10(-4) ng/microl (0.3 cells/L) for A. minutum, and at a DNA concentration of 2.5 x 10(-2) ng/microl (697 cells/L) for G. mikimotoi. The PCR method for detection of G. mikimotoi and A. minutum was applied on field samples collected with a plankton net. Gymnodinium mikimotoi could be detected in 11 field samples by microscopy, and all these field samples were positive by PCR. The cell counts of G. mikimotoi in simultaneously collected water samples ranged from 306 to 2077/L. Alexandrium minutum could be detected by microscopy in 3 different field samples. The cell counts in water samples collected at the same time as the net samples ranged from 115 to 1115 cells/L. Alexandrium minutum was detected by PCR in these field samples, with the exception of the sample displaying the lowest cell count (115 cells/L). Plankton samples that were negative by microscopy for any of the two target species were also negative by PCR. All the PCR products from field samples were confirmed by restriction enzyme digestion. The application of PCR-based detection of harmful algal bloom species for aquaculture and monitoring purposes in natural field samples is discussed.

Listeria in tropical fish and fishery products

Listeria monocytogenes is considered to be a ubiquitous organism occurring in both terrestrial and aquatic habitats. This organism has been isolated from fish and fishery products from different parts of the world and interestingly the incidence rate reported from tropical fish is rather low. Varying methodologies have been used by different investigators to study the incidence of L. monocytogenes in fish. Data on virulence of seafood-associated strains are lacking. For quality assurance in the fish processing industry, rapid and sensitive methods for the detection of L. monocytogenes are required.

Complementation of Listeria seeligeri with the plcA-prfA genes from L. monocytogenes activates transcription of seeligerolysin and leads to bacterial escape from the phagosome of infected mammalian cells

Infection experiments have shown that the avirulent species Listeria seeligeri invaded the enterocyte-like cell line Caco-2 with low efficiency but was unable to escape from the phagosome. Introduction of the listeriolysin gene (hly) from L. monocytogenes into L. seeligeri via a recombinant plasmid did not change these characteristics. No measurable transcription of this gene or of the structurally intact chromosomal seeligerolysin gene (lso) was detected. Transformation with a plasmid carrying the bicistronically transcribed plcA-prfA genes from L. monocytogenes resulted in the efficient expression of the plasmid-encoded transcription activator PrfA, a readily detectable synthesis of seeligerolysin and the escape of the bacteria from the phagosome of infected mammalian cells, followed by intracytoplasmic multiplication.