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

Characterization of a Nonagglutinating Toxigenic Vibrio cholerae Isolate

Toxigenic Vibrio cholerae serogroup O1 is the etiologic agent of the disease cholera, and strains of this serogroup are responsible for pandemics. A few other serogroups have been found to carry cholera toxin genes-most notably, O139, O75, and O141-and public health surveillance in the United States is focused on these four serogroups. A toxigenic isolate was recovered from a case of vibriosis from Texas in 2008. This isolate did not agglutinate with any of the four different serogroups' antisera (O1, O139, O75, or O141) routinely used in phenotypic testing and did not display a rough phenotype. We investigated several hypotheses that might explain the recovery of this potential nonagglutinating (NAG) strain using whole-genome sequencing analysis and phylogenetic methods. The NAG strain formed a monophyletic cluster with O141 strains in a whole-genome phylogeny. Furthermore, a phylogeny of ctxAB and tcpA sequences revealed that the sequences from the NAG strain also formed a monophyletic cluster with toxigenic U.S. Gulf Coast (USGC) strains (O1, O75, and O141) that were recovered from vibriosis cases associated with exposures to Gulf Coast waters. A comparison of the NAG whole-genome sequence showed that the O-antigen-determining region of the NAG strain was closely related to those of O141 strains, and specific mutations were likely responsible for the inability to agglutinate. This work shows the utility of whole-genome sequence analysis tools for characterization of an atypical clinical isolate of V. cholerae originating from a USGC state. IMPORTANCE Clinical cases of vibriosis are on the rise due to climate events and ocean warming (1, 2), and increased surveillance of toxigenic Vibrio cholerae strains is now more crucial than ever. While traditional phenotyping using antisera against O1 and O139 is useful for monitoring currently circulating strains with pandemic or epidemic potential, reagents are limited for non-O1/non-O139 strains. With the increased use of next-generation sequencing technologies, analysis of less well-characterized strains and O-antigen regions is possible. The framework for advanced molecular analysis of O-antigen-determining regions presented herein will be useful in the absence of reagents for serotyping. Furthermore, molecular analyses based on whole-genome sequence data and using phylogenetic methods will help characterize both historical and novel strains of clinical importance. Closely monitoring emerging mutations and trends will improve our understanding of the epidemic potential of Vibrio cholerae to anticipate and rapidly respond to future public health emergencies.

Absolute quantification of viable Vibrio cholerae in seawater samples using multiplex droplet digital PCR combined with propidium monoazide

Introduction

Toxigenic Vibrio cholerae serogroup O1 and O139 are the pathogens responsible for the global cholera epidemic. V. cholerae can settle in the water and spread via the fecal-oral route. Rapid and accurate monitoring of live V. cholerae in environmental water has become an important strategy to prevent and control cholera transmission. Conventional plate counting is widely used to detect viable bacteria but requires time and effort.

Methods

This study aims to develop a new assay that combines triplex droplet digital PCR (ddPCR) with propidium monoazide (PMA) treatment for quantitatively detecting live V. cholerae O1/O139 and cholera enterotoxin. Specific primers and probes were designed according to the conserved regions of gene rfb O1, rfb O139, and ctxA. The amplification procedures and PMA treatment conditions were optimized. The specificity, sensitivity, and ability of PMA-ddPCR to detect viable bacteria-derived DNA were evaluated in simulated seawater samples.

Results and Discussion

The results revealed that the optimal primer concentrations of rfb O1, rfb O139, and ctxA were 1 μM, while the concentrations of the three probes were 0.25, 0.25, and 0.4 μM, respectively. The best annealing temperature was 58°C to obtain the most accurate results. The optimal strategy for distinguishing dead and live bacteria from PMA treatment was incubation at the concentration of 20 μM for 15 min, followed by exposure to a 650-W halogen lamp for 20 min. In pure culture solutions, the limit of detection (LODs) of V. cholerae O1 and O139, and ctxA were 127.91, 120.23 CFU/mL, and 1.5 copies/reaction in PMA-triplex ddPCR, respectively, while the LODs of the three targets were 150.66, 147.57 CFU/mL, and 2 copies/reaction in seawater samples. The PMA-ddPCR sensitivity was about 10 times higher than that of PMA-qPCR. When detecting spiked seawater samples with live bacterial concentrations of 1.53 × 10² and 1.53 × 10⁵ CFU/mL, the assay presented a higher sensitivity (100%, 16/16) than qPCR (50.00%, 8/16) and a perfect specificity (100%, 9/9). These results indicate that the developed PMA-triplex ddPCR is superior to the qPCR regarding sensitivity and specificity and can be used to rapidly detect viable toxigenic V. cholerae O1 and O139 in suspicious seawater samples.

Emerging bioanalytical sensors for rapid and close-to-real-time detection of priority abiotic and biotic stressors in aquaculture and culture-based fisheries

Abiotic stresses of various chemical contamination of physical, inorganic, organic and biotoxin origin and biotic stresses of bacterial, viral, parasitic and fungal origins are the significant constraints in achieving higher aquaculture production. Testing and rapid detection of these chemical and microbial contaminants are crucial in identifying and mitigating abiotic and biotic stresses, which has become one of the most challenging aspects in aquaculture and culture-based fisheries. The classical analytical techniques, including titrimetric methods, spectrophotometric, mass spectrometric, spectroscopic, and chromatographic techniques, are tedious and sometimes inaccessible when required. The development of novel and improved bioanalytical methods for rapid, selective and sensitive detection is a wide and dynamic field of research. Biosensors offer precise detection of biotic and abiotic stressors in aquaculture and culture-based fisheries within no time. This review article allows filling the knowledge gap for detection and monitoring of chemical and microbial contaminants of abiotic and biotic origin in aquaculture and culture-based fisheries using nano(bio-) analytical technologies, including nano(bio-)molecular and nano(bio-)sensing techniques.

Assay for Evaluating the Abundance of Vibrio cholerae and Its O1 Serogroup Subpopulation from Water without DNA Extraction

Cholera is a severe diarrheal disease caused by Vibrio cholerae, a natural inhabitant of brackish water. Effective control of cholera outbreaks depends on prompt detection of the pathogen from clinical specimens and tracking its source in the environment. Although the epidemiology of cholera is well studied, rapid detection of V. cholerae remains a challenge, and data on its abundance in environmental sources are limited. Here, we describe a sensitive molecular quantification assay by qPCR, which can be used on-site in low-resource settings on water without the need for DNA extraction. This newly optimized method exhibited 100% specificity for total V. cholerae as well as V. cholerae O1 and allowed detection of as few as three target CFU per reaction. The limit of detection is as low as 5 × 10³ CFU/L of water after concentrating biomass from the sample. The ability to perform qPCR on water samples without DNA extraction, portable features of the equipment, stability of the reagents at 4 °C and user-friendly online software facilitate fast quantitative analysis of V. cholerae. These characteristics make this assay extremely useful for field research in resource-poor settings and could support continuous monitoring in cholera-endemic areas.

Development and Application of a Multiplex Fluorescent PCR for Shigella Detection and Species Identification

This study was to develop a multiplex fluorescent PCR for Shigella detection and species identification. Five primer pairs for Shigella detection and species identification were designed by Primer Premier 5.0. The multiplex fluorescent PCR was optimized by varying single parameter while other parameters were maintained. The multiplex fluorescent PCR assay could correctly detect Shigella and identify four Shigella species with a detection limits of 10 pg genomic DNA per reaction. Testing different strains and clinical samples confirmed the sensitivity and specificity of the multiplex fluorescent PCR. The newly developed multiplex fluorescent PCR assay is simple, sensitive and specific for Shigella detection and species identification. It has a potential to be used in routine Shigella detection and species identification in clinical laboratories.

A method for correcting underestimation of enteric pathogen genome quantities in environmental samples

Exposure to enteric pathogens in the environment poses a serious risk for infection and disease. The accurate detection and quantification of enteric pathogens in environmental samples is critical for understanding pathogen transport and fate and developing risk assessment models. In this study, we successfully applied TaqMan real-time PCR assays to quantitatively detect five human-specific pathogens (Shigella/EIEC, Salmonella Typhi, Vibrio cholera, Norovirus, and Giardia) in samples from open drains, canals, floodwater, septic tanks, and anaerobic baffled reactors (ABR) collected in Mirpur, Dhaka, Bangladesh from April to October 2019. Overall, the grab and sediment samples showed low inhibition but the ultrafiltration samples collected from open drain had significantly higher (P = 0.0049) degree of PCR inhibition (median Ct = 31.06) compared to the extraction controls (Ct = 28.54). We developed a two-step method to adjust underestimation of pathogen quantities due to PCR inhibition and non-optimum PCR efficiency. Compared to other sample types, ultrafiltration samples demonstrated a wide range of concentration increase (1.0%-182.5%) by pathogens after adjusting for PCR inhibition and non-optimum efficiencies. These quantitative qPCR assays are successful in quantifying multiple enteric pathogens in environmental samples, and the adjustment method would be useful for correcting underestimates of pathogen quantities due to partial PCR inhibition and non-optimum efficiency.

A multiplex PCR assay for the detection of five human pathogenic Vibrio species and Plesiomonas

A multiplex PCR (mPCR) assay was established to detect five pathogenic Vibrio species and Plesiomonas shigelloides. Twelve genes were included: ompW, ctxA, rfbN, and wbfR from V. cholerae; tl, tdh, and trh from V. parahaemolyticus; toxR and vmhA from V. mimicus; toxR from V. fluvialis; vvhA from V. vulnificus; and the 23S rRNA gene from P. shigelloides. The specificity of the mPCR assay was 100% for the detection of 136 strains and the limits of detection (LoD) were 12.5-50 pg/reaction. The assay exhibited higher sensitivity than cultivation methods in the detection of APW cultures of 113 diarrhea samples. In the analysis of 369 suspected Vibrio populations from estuarine water samples, the specificity of the mPCR for V. cholerae and V. parahaemolyticus was 100% for both, while the sensitivities were 100% and 96.1%, respectively. The assay can be applied to screen enrichment cultures and suspected colonies from environmental and clinical samples.

Pathogen flows from on-site sanitation systems in low-income urban neighborhoods, Dhaka: A quantitative environmental assessment

BACKGROUND

Despite wide usage of on-site sanitation, there is limited field-based evidence on the removal or release of pathogens from septic tanks and other primary treatment systems, such as anaerobic baffled reactors (ABR). In two low-income areas in Dhaka, we conducted a cross-sectional study to explore pathogen loads discharged from commonly used on-site sanitation-systems and their transport in nearby drains and waterways.

METHODS

We collected samples of drain water, drain sediment, canal water, and floodwater from April-October 2019. Sludge, supernatant, and effluent samples were also collected from septic tanks and ABRs. We investigated the presence and concentration of selected enteric pathogens (Shigella, Vibrio cholerae (V. cholerae), Salmonella Typhi (S. Typhi), Norovirus Genogroup-II (NoV-GII), and Giardia) and presence of Cryptosporidium in these samples using quantitative polymerase chain reaction (qPCR).The equivalent genome copies (EGC) of individual pathogens were estimated in each sample by interpolation of the mean Ct value to the corresponding standard curve and the dilution factor for each sample type. Absolute quantification was expressed as log₁₀ EGC per 100 mL for the water samples and log₁₀ EGC per gram for the sediment samples.

RESULTS

Among all samples tested (N = 151), 89% were contaminated with Shigella, 68% with V. cholerae and NoV-GII, 32% with Giardia, 17% with S. Typhi and 6% with Cryptosporidium. A wide range of concentration of pathogens [range: mean log₁₀ concentration of Giardia = 0.74 EGC/100 mL in drain ultrafiltration samples to mean log₁₀ concentration of NoV-GII and Giardia = 7.11 EGC/100 mL in ABR sludge] was found in all environmental samples. The highest pathogen concentrations were detected in open drains [range: mean log₁₀ concentration = 2.50-4.94 EGC/100 mL], septic tank effluent [range: mean log₁₀ concentration = 3.32-4.65 EGC/100 mL], and ABR effluent [range: mean log₁₀ concentration = 2.72-5.13 EGC/100 mL].

CONCLUSIONS

High concentrations of pathogens (particularly NoV-GII, V.cholerae and Shigella) were frequently detected in environmental samples from two low-income urban neighbourhoods of Dhaka city. The numerous environmental exposure pathways for children and adults make these findings of public health concern. These results should prompt rethinking of how to achieve safe sanitation solutions that protect public health in dense low-income areas. In particular, improved management and maintenance regimes, further treatment of liquid effluent from primary treatment processes, and appropriate application of onsite, decentralised and offsite sanitation systems given the local context.

Cholera

Cholera is an acute, watery diarrhoeal disease caused by Vibrio cholerae of the O1 or O139 serogroups. In the past two centuries, cholera has emerged and spread from the Ganges Delta six times and from Indonesia once to cause global pandemics. Rational approaches to the case management of cholera with oral and intravenous rehydration therapy have reduced the case fatality of cholera from more than 50% to much less than 1%. Despite improvements in water quality, sanitation, and hygiene, as well as in the clinical treatment of cholera, the disease is still estimated to cause about 100 000 deaths every year. Most deaths occur in cholera-endemic settings, and virtually all deaths occur in developing countries. Contemporary understanding of immune protection against cholera, which results from local intestinal immunity, has yielded safe and protective orally administered cholera vaccines that are now globally stockpiled for use in the control of both epidemic and endemic cholera.

Development and Validation of a Novel Real-time Assay for the Detection and Quantification of Vibrio cholerae

Vibrio cholerae O1 and O139 has been known for its ability to cause epidemics. These strains produce cholera toxin which is the main cause of secretory diarrhea. V. cholerae non-O1 and non-O139 strains are also capable of causing gastroenteritis as well as septicemia and peritonitis. It has been proven that virulence factors such as T6SS, hapA, rtxA, and hlyA are present in almost all V. cholerae strains. It is imperative that viable but non-culturable cells of V. cholerae are also detected since they are also known to cause diarrhea. Thus, the aim of this study was to develop an assay that detects all V. cholerae regardless of their serotype, culturable state, and virulence genes present, by targeting the species specific conserved ompW sequence. The developed assay meets these goals with 100% specificity and is capable of detecting as low as 5.46 copy number of V. cholerae. Detection is rapid since neither lengthy incubation period nor electrophoresis is required. The assay had excellent repeatability (CV%: 0.24-1.32) and remarkable reproducibility (CV%: 1.08-3.7). Amplification efficiencies in the 89-100% range were observed. The assay is more economical than Taqman-based multiplex real-time PCR assays. Compared to other real-time assays, the ompW assay is specific and sensitive, has better repeatability and reproducibility, and is more economical.

Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water

The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks.

Multiplex real-time PCR assay for detection of pathogenic Vibrio parahaemolyticus strains

Foodborne disease caused by pathogenic Vibrio parahaemolyticus has become a serious public health problem in many countries. Rapid diagnosis and the identification of pathogenic V. parahaemolyticus are very important in the context of public health. In this study, an EvaGreen-based multiplex real-time PCR assay was established for the detection of pathogenic V. parahaemolyticus. This assay targeted three genetic markers of V. parahaemolyticus (species-specific gene toxR and virulence genes tdh and trh). The assay could unambiguously identify pathogenic V. parahaemolyticus with a minimum detection limit of 1.4 pg genomic DNA per reaction (concentration giving a positive multiplex real-time PCR result in 95% of samples). The specificity of the assay was evaluated using 72 strains of V. parahaemolyticus and other bacteria. A validation of the assay with clinical samples confirmed its sensitivity and specificity. Our data suggest the newly established multiplex real-time PCR assay is practical, cost-effective, specific, sensitive and capable of high-throughput detection of pathogenic V. parahaemolyticus.

Diagnosis of Vibrio cholerae O1 infection in Africa

Isolation of Vibrio cholerae O1 is necessary for cholera outbreak confirmation. Rapid diagnostic testing of fecal specimens, based on lipopolysaccharide detection of V. cholerae O1 or O139, may assist in early outbreak detection and surveillance. Cary-Blair transport medium is recommended for specimen transport. Filter paper, although used in epidemics, needs evaluation against rectal swab specimens. Fecal specimens are subcultured onto selective and nonselective media, including 5% blood agar and TCBS agar, for detection of V. cholerae O1 or O139. Suspicious, oxidase-positive isolates are serotyped in monovalent antisera. Antimicrobial-susceptibility testing is performed to detect resistance. Molecular characterization supports phenotypic identification and outbreak investigations. The presence of genes encoding cholera toxin, lipopolysaccharide, and El Tor biotype traits can be confirmed. Standardized pulsed-field gel electrophoresis analysis facilitates strain comparison. Quality management ensures reliability of results through validation and verification of functional laboratory equipment; quality control of testing procedures, laboratory reagents, and consumables; and participation in proficiency-testing schemes.

Quantitative detection of Vibrio cholera toxin by real-time and dynamic cytotoxicity monitoring

We report here the quantitative detection of Vibrio cholerae toxin (CT) in isolates and stool specimens by dynamic monitoring of the full course of CT-mediated cytotoxicity in a real-time cell analysis (RTCA) system. Four cell lines, including Y-1 mouse adrenal tumor cells, Chinese hamster ovary (CHO) cells, small intestine epithelial (FHs74Int) cells, and mouse adrenal gland (PC12-Adh) cells, were evaluated for their suitability for CT-induced cytotoxicity testing. Among them, the Y-1 line was demonstrated to be the most sensitive for CT-mediated cytotoxicity, with limits of detection of 7.0 pg/ml for purified CT and 0.11 ng/ml for spiked CT in pooled negative stool specimens. No CT-mediated cytotoxicity was observed for nontoxigenic V. cholerae, non-V. cholerae species, or non-V. cholerae enterotoxins. The CT-RTCA assay was further validated with 100 stool specimens consecutively collected from patients with diarrhea and 200 V. cholerae isolates recovered from patients and the environment, in comparison to a reference using three detection methods. The CT-RTCA assay had sensitivities and specificities of 97.5% and 100.0%, respectively, for V. cholerae isolates and 90.0% and 97.2% for stool specimens. For stool specimens spiked with CT concentrations ranging from 3.5 pg/ml to 1.8 ng/ml, the inoculation-to-detection time was 1.12 ± 0.38 h, and the values were inversely correlated with CT concentrations (ρ = -1; P = 0.01). The results indicate that the CT-RTCA assay with the Y-1 cell line provides a rapid and sensitive tool for the quantitative detection of CT activities in clinical specimens.

Rapid oligonucleotide suspension array-based multiplex detection of bacterial pathogens

A gene-specific microsphere suspension array coupled with 15-plex polymerase chain reaction (PCR) was developed to screen bacterial samples rapidly for 10 strains of bacteria: Shigella spp. (S. flexneri, S. dysenteriae, and S. sonnei), Staphylococcus aureus, Vibrio cholerae (serology O1 and O139), Legionella pneumophila, and Clostridium botulinum (types A, B, and E). Fifteen sets of highly validated primers were chosen to amplify target genes simultaneously. Corresponding oligonucleotide probes directly conjugated with microsphere sets were used to specifically identify PCR amplicons. Sensitivity tests revealed that the array coupled with single PCR was able to detect purified genomic DNA at concentrations as low as 10 copies/μL, while the multiplex detection limit was 10-10⁴ copies/μL. The assay was validated using water samples artificially spiked with S. aureus and S. dysenteriae, as well as water specimens from swimming pools previously identified to contain S. aureus.

Quadruplex real-time polymerase chain reaction assay for molecular diagnosis of Y-chromosomal microdeletions

OBJECTIVE

To develop a rapid and reliable method for molecular diagnosis of Y-chromosomal microdeletions.

DESIGN

Study of diagnostic accuracy.

SETTING

Molecular diagnostics laboratories in three hospitals.

PATIENT(S)

A total of 701 men with nonobstructive azoospermia or oligozoospermia from three hospitals.

INTERVENTION(S)

We developed a quadruplex real-time polymerase chain reaction (PCR) assay and evaluated its performance in molecular diagnosis of Y-chromosomal microdeletions.

MAIN OUTCOME MEASURE(S)

Analytic sensitivity, analytic specificity, clinical sensitivity, and clinical specificity.

RESULT(S)

The limit of detection of quadruplex real-time PCR assay was 100 pg genomic DNA. The method attained 100% analytic specificity, 100% clinical sensitivity, and 100% clinical specificity.

CONCLUSION(S)

We have successfully upgraded the diagnostic method published by the European Academy of Andrology and the European Molecular Genetics Quality Network. Our method was validated to be fast, simple, contamination free, of high analytic sensitivity and specificity. Therefore, it is strongly suggested that such quadruplex real-time PCR assay can be readily applied as clinical routine in the near future.

Molecular detection of pathogens in water--the pros and cons of molecular techniques

Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed.