Quadruplex PCR for simultaneous detection of serotype, biotype, toxigenic potential, and central regulating factor of Vibrio cholerae

Prevalence and molecular characterization of Vibrio cholerae from fruits and salad vegetables sold in Jakarta, Indonesia, using most probable number and PCR

OBJECTIVE

Cholera is an intestinal infection caused by Vibrio cholerae, it is usually occurs in developing countries that lack of sanitation. In developing country including Indonesia, awareness importance of sanitation is still low. Unfortunately, research related to the detection of V. cholerae from fruit and vegetables in Indonesia is still rare. In this study, MPN method was used to determine the prevalence of V. cholerae followed by single and multiplex PCR to detect virulence genes, including toxR, ctxA, tcpA, hlyA, ace, ompU, and zot.

RESULTS

We found 3 fruits and 2 vegetables positive for toxR gene. Fruit samples which were showed toxR positive found from East Jakarta while for vegetables, it was recovered from West Jakarta and Central Jakarta. Twenty-three isolates were recovered from toxR positive samples. The result of antibiotic resistance analysis showed that 4.35% of the isolates resistant to gentamicin, streptomycin (17.39%), trimethoprim (52.17%), ciprofloxacin (30.43%), ampicillin (13.04%), nalidixic acid (82.61%), and polymyxin B (91.30%). None of these isolates were resistant to kanamycin. Combination of MPN and Multiplex PCR method can be used to detect the prevalence and characterize the virulence properties of V. cholerae.

Incidence of Bacterial Enteropathogens among Diarrhea Patients from Tribal Areas of Odisha

Infectious diarrheal diseases remain a leading cause of morbidity and mortality in developing and underdeveloped countries. The present study documented the etiology of bacterial enteropathogens in three tribal districts of Odisha from July 2010 to September 2013. A total of 1427 rectal swabs were collected and bacteriologically analyzed by following standard procedure. Among the 930 (65.2%) culture positive samples, Escherichia coli (E. coli) constituted 636 (44.6%); Vibrio cholerae (V. cholerae) O1, 146 (10.2%); Salmonella species (spp.), 10 (0.7%); Shigella spp., 79 (5.5%); and Aeromonas spp., 59 (4.1%). Of the 729 environmental water samples taken from river, open well, Nala (a small stream), and Chua (a shallow pit on a river bed), 14 (1.9%) contained non-O1/non-O139 V. cholerae and 13 (1.8%) had V. cholerae O1 strains. An analysis of the demographics showed that people in the 14 to 40-year age group were highly susceptible to diarrhea caused by V. cholerae which occurred mainly during the rainy and post-rainy seasons. All enteropathogens were multidrug-resistant and found throughout the study period. The V. cholerae strains isolated were El Tor variants carrying the classical, El Tor, and Haitian cholera toxin subunit B (ctxB) genes. The classical ctxB was the dominant allele, and the prevalence of the Haitian ctxB allele increased during the test period. These findings indicate that active surveillance is needed to monitor the changing antibiotic resistance patterns of V. cholerae serogroups and biotypes present in this region.

Simultaneous Identification of Ten Bacterial Pathogens Using the Multiplex Ligation Reaction Based on the Probe Melting Curve Analysis

Pathogenic Vibrio spp., Aeromonas spp. and Plesiomonas shigelloides are associated with human gastroenteritis and wound infections, as well as fish diseases. The comprehensive and accurate identification of these pathogens is crucial for the current public health. The present study describes the development of a multiplex assay for the simultaneous identification of ten bacterial pathogens in a single reaction by using a multiplex ligation reaction based on probe melting curve analysis (MLMA). The specificity for target genes was 100%, as assessed with a panel of 67 bacterial pathogens, which indicated no cross-reactions. The detection limit of this assay ranged from 0.8 × 10⁷ CFU/mL to 1.5 × 10⁸ CFU/mL at the pure bacterial culture level and from 0.1 ng to 1.0 ng at the DNA level. The MLMA assay was used to detect ten species of pathogens in 269 clinical and seafood samples, and for further validation, the results were compared with the conventional culture method. The results indicated greater than 90% sensitivity and 100% specificity for each bacterial pathogen tested, and the kappa correlation for all the pathogens ranged from 0.95 to 1.00. Overall, this assay is well suited for public health laboratories for its high throughput, accuracy, and low cost.

Unique Clones of Vibrio cholerae O1 El Tor with Haitian Type ctxB Allele Implicated in the Recent Cholera Epidemics from Nigeria, Africa

Background and Objectives

The antimicrobial susceptibility patterns and genetic characteristics of Vibrio cholerae O1, which is responsible for several cholera epidemics in Nigeria, are not reported in detail since 2007. In this study, we screened V. cholerae O1 El Tor biotype isolates from cholera cases and water samples from different states to investigate their phenotypic and genetic attributes with special reference to their clonality.

Results

All the V. cholerae O1 biotype El Tor isolates isolated during 2007–2013 were susceptible to fluoroquinolones and tetracycline, the drugs currently used in the treatment of cholera cases in Nigeria. Emergence of CT genotype 7 (Haitian type of ctxB allele) was predominantly seen among Ogawa serotype and the CT genotype 1 (classical ctxB allele) was mostly found in Inaba serotype. Overall, V. cholerae O1 from clinical and water samples were found to be closely related as determined by the pulsed-field gel electrophoresis. V. cholerae isolates from Abia, Kano and Bauchi were found to be genetically distinct from the other states of Nigeria.

Conclusion

Fecal contamination of the water sources may be the possible source of the cholera infection. Combined prevalence of Haitian and classical ctxB alleles were detected in Ogawa and Inaba serotypes, respectively. This study further demonstrated that V. cholerae O1 with the ctxB has been emerged similar to the isolates reported in Haiti. Our findings suggest that the use of fluoroquinolones or tetracycline/doxycycline may help in the effective management of acute cholera in the affected Nigerian states. In addition, strengthening the existing surveillance in the hospitals of all the states and supply of clean drinking water may control cholera outbreaks in the future.

Large outbreak of cholera caused by El Tor variant Vibrio cholerae O1 in the eastern coast of Odisha, India during 2009

A large outbreak of cholera reported during April-July 2009 in the Kendrapada district of Odisha, India was investigated. Forty-one rectal swabs and 41 water samples, collected from diarrhoeal patients and from different villages were bacteriologically analysed for the isolation of bacterial enteriopathogens, antibiogram profile and detection of various toxic genes. The bacteriological analysis of rectal swabs and environmental water samples revealed the presence of V. cholerae O1 Ogawa biotype El Tor. The V. cholerae strains were resistant to ciprofloxacin, co-trimoxazole, chloramphenicol, streptomycin, ampicillin, furazolidone and nalidixic acid. The multiplex polymerase chain reaction (PCR) assay on V. cholerae strains revealed the presence of ctxA and tcpA genes. The mismatch amplification of mutation assay (MAMA) PCR on clinical and environmental isolates of V. cholerae revealed that the strains were El Tor biotype, which harboured the ctxB gene of the classical strain. The random amplified polymorphic DNA PCR analysis and pulsed-field gel electrophoresis results indicated that the V. cholerae isolates belonged to the same clone. This investigation gives a warning that the El Tor variant of V. cholerae has spread to the coastal district causing a large outbreak that requires close monitoring and surveillance on diarrhoeal outbreaks in Odisha.

Design of a multiplex PCR method for detection of toxigenic-pathogenic in Vibrio cholerae

OBJECTIVE

To study virulence and regulatory genes (hlyA, ctxB, tcpI) in clinical strains of Vibrio cholerae (V. cholerae), simultaneously.

METHODS

Three important genes, tcpI, hlyA and ctxB were used for detection of toxigenic and pathogenic V. cholera by chain reaction assay method.

RESULTS

According to the results of the PCR, the incidence of hlyA, tcpI, and ctxB genes in clinical isolates was obtained as 94.7% (72 sample), 90.8% (69 sample), and 92.1% (70 sample), respectively. Five strains possessed all genes except ctxB, six strains possessed all genes except tcpI, four strains possessed all genes except hlyA, one strain possessed only hlyA and 60 strains contained a combination of three genes, Including hlyA, ctxB and tcpI.

CONCLUSIONS

Result show that this method could be reliable to detect toxigenic-pathogenic strains of V. cholerae in Iran.

Triplex PCR assay for the rapid identification of 3 major Vibrio species, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio fluvialis

A triplex PCR assay was developed for the identification of 3 major Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio fluvialis by targeting their haemolysin, haem-utilizing, and central regulatory genes, respectively. This simple, rapid, sensitive, and specific assay using cell lysates from 227 samples established its usefulness in research and epidemiology.

Rapid spread of Vibrio cholerae O1 El Tor variant in Odisha, Eastern India, in 2008 and 2009

The emergence and spread of Vibrio cholerae O1 El Tor variant strains causing severe diarrhea has been witnessed worldwide in recent years. In the state of Odisha, India, the spread of the V. cholerae O1 El Tor variant strains was studied during outbreaks in 2008 and 2009. Analysis of 194 V. cholerae O1 Ogawa strains revealed that V. cholerae O1 El Tor variant strains are spreading gradually throughout the state, causing outbreaks replacing typical V. cholerae O1 El Tor biotype strains.

Prevalence and molecular characterization of Vibrio cholerae from ice and beverages sold in Jakarta, Indonesia, using most probable number and multiplex PCR

Vibrio cholerae is well recognized as the causative agent of cholera, an acute intestinal infection characterized by watery diarrhea that may lead to dehydration and death in some cases. V. cholerae is a natural inhabitant of the aquatic environment in the tropical regions. Jakarta has the highest percentage of individuals affected by sporadic diarrheal illness compared with other areas in Indonesia. Inadequate safety measures for drinking water supplies, improper sanitation, and poor hygiene can increase the risk of cholera outbreaks. Few studies have been conducted on the prevalence of these bacteria in ice and beverages that are popularly sold and consumed in Jakarta. In this study, we detected and quantified V. cholerae from ice and beverages collected from several areas in five regions of Jakarta. Levels of V. cholerae in both ice and beverages were determined with the three-tube most-probable-number (MPN) method and ranged from < 0.3 to > 110 MPN/ml. The presence of regulatory and virulence gene sequences was determined by using uniplex and multiplex PCR assays. Of 110 samples tested, 33 (30%) were positive for V. cholerae; 21 (64%) were ice samples and the remaining 12 (36%) were beverages. A total of 88 V. cholerae strains were isolated, based on the presence of the toxR gene sequence identified by PCR. Other genetic markers, such as hlyA (59%), ompU (16%), and ctxA (19%), also were found during the search for potential pathogenic strains. The detection and isolation of potentially harmful V. cholerae from ice and beverages in Jakarta indicate that these products pose a health risk from choleragenic vibrios, particularly because of the emergence of classical biotypes of V. cholerae O1 and potentially harmful non-O1 serovars of this species.

Identification of virulence factors in Vibrio cholerae isolated from Iraq during the 2007–2009 outbreak

Thousands of people were infected with Vibrio cholerae during the outbreak in Iraq in 2007–2009. Vibrio cholerae was shown to be variable in its content of virulence determinants and in its antibiotic sensitivity. This study was designed to isolate and characterize clinical and environmental V. cholerae isolates and to determine antibiotic sensitivity, enzyme and toxin production, and the presence of virulence genes. Eighty clinical and five environmental bacterial isolates were collected and diagnosed by subjecting them to microscopic, biochemical, serological, and molecular analysis. The results revealed that 55% of clinical isolates belonged to the Inaba serotype, 32.5% to the Ogawa serotypes, and 12.5% to the Non-O1 serotype. All environmental V. cholerae isolates belonged to the Non-O1 serotype. All environmental isolates were sensitive to all examined antimicrobial agents, while all clinical isolates showed a high sensitivity (100%) to ampicillin, gentamicin, cephalothin, tetracycline, erythromycin, and ciprofloxacin, and a high resistance (97.5%) to co-trimoxazole, nalidixic acid, and chloramphenicol. It was found that all V. cholerae (O1) isolates were resistant to the Vibrio static O129 and all Non-O1 V. cholerae isolates were sensitive to the Vibrio static O129. All clinical and environmental isolates produced hemolysin (100%) and lecithinase (100%), while they showed various production rates of protease (90% of clinical and 60% of environmental) and lipase (50% of clinical and 20% of environmental). The ompW gene was amplified in all the clinical and environmental V. cholerae isolates, but not in other related and nonrelated bacteria. Multiplex PCR analysis showed that the toxR gene was amplified in all clinical and environmental isolates, while ctxA, ctxB, tcpA genes were amplified only in clinical (O1) isolates. This study indicates the differences in the production of some enzymes and toxins and in the content of virulence genes between clinical and environmental isolates in Iraq during the outbreak (2007–2009).

Detection of ctx gene positive non-O1/non-O139 V. cholerae in shrimp aquaculture environments

Water and post-larvae samples from black tiger (Penaeus monodon) shrimp hatcheries; pond water, pond sediment and shrimp from aquaculture farms were screened for the presence of V. cholerae. A V. cholerae-duplex PCR method was developed by utilizing V. cholerae species specific sodB primers and ctxAB genes specific primers. Incidence of V. cholerae was not observed in shrimp hatchery samples but was noticed in aquaculture samples. The incidence of V. cholerae was higher in pond water (7.6%) than in pond sediment (5.2%). Shrimp head (3.6%) portion had relatively higher incidence than shrimp muscle (1.6%). All the V. cholerae isolates (n = 42) belonged to non-O1/non-O139 serogroup, of which 7% of the V. cholerae isolates were potentially cholera-toxigenic (ctx positive). All the ctx positive V. cholerae (n = 3) were isolated from the pond water. Since, cholera toxin (CT) is the major contributing factor for cholera gravis, it is proposed that the mere presence of non-O1/non-O139 V. cholerae need not be the biohazard criterion in cultured black tiger shrimp but only the presence of ctx carrying non-O1/non-O139 V. cholerae may be considered as potential public health risk.

Comparison between a TaqMan polymerase chain reaction assay and a culture method for ctx-positive Vibrio cholerae detection

The main objective of the present work was to evaluate a real-time polymerase chain reaction (PCR) method to detect toxigenic Vibrio cholerae in Pangasius hypophthalmus, a freshwater fish cultured mainly in South East Asia. A FDA traditional culture method and a real-time PCR method of the ctx gene were used for detection of V. cholerae in spiked samples of pangasius fish. After an overnight enrichment of samples at 37 degrees C in alkaline peptone water, 2 cfu/25 g of fish was detected with both methods. Although both methods were very sensitive, obtaining results with culture methods may take several days, while real-time PCR takes only a few hours. Furthermore, with traditional methods, complementary techniques such as serotyping, although not available for all serogroups, are needed to identify toxigenic V. cholerae. However, with real-time PCR, toxigenic serogroups are detected in only one step after overnight enrichment.

Quadruplex real-time PCR assay for detection and identification of Vibrio cholerae O1 and O139 strains and determination of their toxigenic potential

Vibrio cholerae is a natural inhabitant of the aquatic environment. However, its toxigenic strains can cause potentially life-threatening diarrhea. A quadruplex real-time PCR assay targeting four genes, the cholera toxin gene (ctxA), the hemolysin gene (hlyA), O1-specific rfb, and O139-specific rfb, was developed for detection and differentiation of O1, O139, and non-O1, non-O139 strains and for prediction of their toxigenic potential. The specificity of the assay was 100% when tested against 70 strains of V. cholerae and 31 strains of non-V. cholerae organisms. The analytical sensitivity for detection of toxigenic V. cholerae O1 and O139 was 2 CFU per reaction with cells from pure culture. When the assay was tested with inoculated water from bullfrog feeding ponds, 10 CFU/ml could reliably be detected after culture for 3 h. The assay was more sensitive than the immunochromatographic assay and culture method when tested against 89 bullfrog samples and 68 water samples from bullfrog feeding ponds. The applicability of this assay was confirmed in a case study involving 15 bullfrog samples, from which two mixtures of nontoxigenic O1 and toxigenic non-O1/non-O139 strains were detected and differentiated. These data indicate that the quadruplex real-time PCR assay can both rapidly and accurately detect/identify V. cholerae and reliably predict the toxigenic potential of strains detected.

RNA colony blot hybridization method for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria

A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.