Accuracy of six commercially available systems for identification of members of the family vibrionaceae

Vibrio pathogenicity island and phage CTX genes in Vibrio alginolyticus isolated from different aquatic environments

In the present study, we investigated the presence of four Vibrio cholerae virulence genes (ctxA, VPI, Zot and ace) in 36 Vibrio alginolyticus isolates obtained from different seawater, sediments and aquatic organisms. We tested the virulence of 13 V. alginolyticus strains against juveniles of Sparus aurata and this virulence was correlated with the presence of V. cholerae virulence genes. A positive amplification for the virulence pathogenicity island was produced by five V. alginolyticus strains and four for cholerae toxin. Some of the V. alginolyticus strains are pathogenic to aquatic animals and might have derived their virulence genes from V. cholerae. V. alginolyticus strains can be considered as a possible reservoir of V. cholerae virulence genes.

Prevalence, Antibiotics Resistance and Plasmid Profiling of Vibrio spp. Isolated from Cultured Shrimp in Peninsular Malaysia

Vibrio is the most common bacterium associated with diseases in crustaceans. Outbreaks of vibriosis pose a serious threat to shrimp production. Therefore, antibiotics are commonly used as preventative and therapeutic measures. Unfortunately, improper use of antibiotics leads to antibiotic resistance. Nevertheless, information on the occurrence of Vibrio spp. and antibiotic use in shrimp, particularly in Malaysia, is minimal. This study aimed to provide information on the occurrence of Vibrio spp., its status of antibiotic resistance and the plasmid profiles of Vibrio spp. isolated from cultured shrimp in Peninsular Malaysia. Shrimp were sampled from seven farms that were located in different geographical regions of Peninsular Malaysia. According to the observations, 85% of the shrimp were healthy, whereas 15% were unhealthy. Subsequently, 225 presumptive Vibrio isolates were subjected to biochemical tests and molecular detection using the pyrH gene. The isolates were also tested for antibiotic susceptibility against 16 antibiotics and were subjected to plasmid profiling. Eventually, 13 different Vibrio spp. were successfully isolated and characterized using the pyrH gene. They were the following: V. parahaemolyticus (55%), V. communis (9%), V. campbellii (8%), V. owensii (7%), V. rotiferianus (5%), Vibrio spp. (4%), V. alginolyticus (3%), V. brasiliensis (2%), V. natriegens (2%), V. xuii (1%), V. harveyi (1%), V. hepatarius (0.4%) and P. damselae (3%). Antibiotic susceptibility profiles revealed that all isolates were resistant to penicillin G (100%), but susceptible to norfloxacin (96%). Furthermore, 16% of the isolates revealed MAR of less than 0.2, while 84% were greater than 0.2. A total of 125 isolates harbored plasmids with molecular weights between 1.0 and above 10 kb, detected among the resistant isolates. The resistant isolates were mediated by both chromosomal and plasmid factors. These findings support the use of surveillance data on the emerging patterns of antimicrobial-resistance and plasmid profiles of Vibrio spp. in shrimp farms. The findings from this study can be used to develop a better disease management strategy for shrimp farming.

Rapid and Sensitive Detection of Vibrio vulnificus Using CRISPR/Cas12a Combined With a Recombinase-Aided Amplification Assay

Vibrio vulnificus is an important zoonotic and aquatic pathogen and can cause vibriosis in humans and aquatic animals (especially farmed fish and shrimp species). Rapid and sensitive detection methods for V. vulnificus are still required to diagnose human vibriosis early and reduce aquaculture losses. Herein, we developed a rapid and sensitive diagnostic method comprising a recombinase-aided amplification (RAA) assay and the CRISPR/Cas12a system (named RAA-CRISPR/Cas12a) to detect V. vulnificus. The RAA-CRISPR/Cas12a method allows rapid and sensitive detection of V. vulnificus in 40 min without a sophisticated instrument, and the limit of detection is two copies of V. vulnificus genomic DNA per reaction. Meanwhile, the method shows satisfactory specificity toward non-target bacteria and high accuracy in the spiked blood, stool, and shrimp samples. Therefore, our proposed rapid and sensitive V. vulnificus detection method, RAA-CRISPR/Cas12a, has great potential for early diagnosis of human vibriosis and on-site V. vulnificus detection in aquaculture and food safety control.

Sensitively and quickly detecting Vibrio vulnificus by real time recombinase polymerase amplification targeted to vvhA gene

Vibrio vulnificus (V. vulnificus) is a Gram-negative bacterium living in warm and salty water. This marine bacterium could produce hemolysin (VVH), which often causes serious gastroenteritis or septicemia when people contact to seawater or seafood containing V. vulnificus. Timely diagnosis is regard as essential to disease surveillance. In this paper, we aimed at developing a quick and sensitive method for the detection of Vibrio vulnificus using real time recombinase polymerase amplification (real time RPA). Specific primers and an exo probe were designed on the basis of the vvhA gene sequence available in GenBank. Target DNA could be amplified and labeled with specific fluorophore within 20 min at 38 °C. The method exhibited a high specificity, only detecting Vibrio vulnificus and not showing cross-reaction with other bacteria. The sensitivity of this method was 2 pg per reaction (20 μL) for DNA, or 200 copies per reaction (20 μL) for standard plasmid. The detection limit (LOD) stated as the target level that would be detected 95% of the time and estimated was 1.58 × 10² copies by fit of the probit to the results of 8 replicates in different concentration. For quantitative analysis of the real time RPA, the second order polynomial regression was adopted in our study. The results showed the correlation coefficients were raised above 0.98, which suggested this model might be a better choice for the quantitative analysis of real time RPA compared to the routine linear regression model. For artificially contaminated plasma samples, Vibrio vulnificus could be detected within 16 min by real time RPA at concentration as low as 1.2 × 10² CFU/mL or 2.4 CFU per reaction (20 μL). Thus, the real time RPA method established in this study shows great potential for detecting Vibrio vulnificus in the research laboratory and disease diagnosis.

Biochemical and Virulence Characterization of Vibrio vulnificus Isolates From Clinical and Environmental Sources

Vibrio vulnificus is a deadly human pathogen for which infections occur via seafood consumption (foodborne) or direct contact with wounds. Virulence is not fully characterized for this organism; however, there is evidence of biochemical and genotypic correlations with virulence potential. In this study, biochemical profiles and virulence genotype, based on 16S rRNA gene (rrn) and virulence correlated gene (vcg) types, were determined for 30 clinical and 39 oyster isolates. Oyster isolates were more biochemically diverse than the clinical isolates, with four of the 20 tests producing variable (defined as 20–80% of isolates) results. Whereas, for clinical isolates only mannitol fermentation, which has previously been associated with virulence potential, varied among the isolates. Nearly half (43%) of clinical isolates were the more virulent genotype (rrnB/vcgC); this trend was consistent when only looking at clinical isolates from blood. The majority (64%) of oyster isolates were the less virulent genotype (rrnA or AB/vcgE). These data were used to select a sub-set of 27 isolates for virulence testing with a subcutaneously inoculated, iron-dextran treated mouse model. Based on the mouse model data, 11 isolates were non-lethal, whereas 16 isolates were lethal, indicating a potential for human infection. Within the non-lethal group there were eight oyster and three clinical isolates. Six of the non-lethal isolates were the less virulent genotype (rrnA/vcgE or rrnAB/vcgE) and two were rrnB/vcgC with the remaining two of mixed genotype (rrnAB/vcgC and rrnB/vcgE). Of the lethal isolates, five were oysters and 11 were clinical. Eight of the lethal isolates were the less virulent genotype and seven the more virulent genotype, with the remaining isolate a mixed genotype (rrnA/vcgC). A discordance between virulence genotype and individual mouse virulence parameters (liver infection, skin infection, skin lesion score, and body temperature) was observed; the variable most strongly associated with mouse virulence parameters was season (warm or cold conditions at time of strain isolation), with more virulent strains isolated from cold conditions. These results indicate that biochemical profiles and genotype are not significantly associated with virulence potential, as determined by a mouse model. However, a relationship with virulence potential and seasonality was observed.

A Real-Time Recombinase Polymerase Amplification Method for Rapid Detection of Vibrio vulnificus in Seafood

As an important foodborne pathogen, Vibrio vulnificus gives a significant threat to food safety and public health. Rapid and accurate detection methods for V. vulnificus are required to control its spread. The conventional detection methods are time-consuming and labor-intensive, while the polymerase chain reaction (PCR)- and quantitative PCR (qPCR)-based methods are limited because of their dependence on laboratory equipment. Nucleic acid isothermal amplification technologies have been applied to develop simpler assays. In this study, a rapid detection method based on real-time recombinase polymerase amplification (RPA) targeting the extracellular metalloprotease (empV) gene of V. vulnificus has been established. The method finished the detection in 2–14 min at 39°C with good specificity. The limit of detection was 17 gene copies or 1 colony-forming unit (CFU) per reaction, or 1 CFU/10 g of spiked food with enrichment. In a clinical sample detection test, the results of real-time RPA were 100% consistent with bioassay and qPCR. Moreover, the method could resist the effect of food matrix and could tolerate crude templates. The real-time RPA method established in this study is rapid and simple and has the potential to be widely applied for V. vulnificus detection in food safety control.

An isothermal recombinase polymerase amplification and lateral flow strip combined method for rapid on-site detection of Vibrio vulnificus in raw seafood

Vibrio vulnificus is an important foodborne pathogenic bacterium that mainly contaminates seafood. Rapid and accurate technologies that suitable for on-site detection are critical for effective control of its spreading. Conventional detection methods and polymerase chain reaction (PCR)-based and qPCR-based approaches have application limitations in on-site scenarios. Application of loop-mediated isothermal amplification (LAMP) technology was a good step towards the on-site detection. In this study, a recombinase polymerase amplification (RPA)-based detection method for V. vulnificus was developed combining with lateral flow strip (LFS) for visualized signal. The method targeted the conservative empV gene encoding the extracellular metalloproteinase, and finished detection in 35 min at a conveniently low temperature of 37 °C. It showed good specificity and an excellent sensitivity of 2 copies of the genome or 10^-1 colony forming unit (CFU) per reaction, or 1 CFU/10 g in spiked food samples with enrichment. The method tolerated unpurified templates directly from sample boiling, which added the convenience of the overall procedure. Application of the RPA-LFS method for clinical samples showed accurate and consistent detection results compared to bioassay and quantitative PCR. This RPA-LFS combined method is well suited for on-site detection of V. vulnificus.

Vibrios from the Norwegian marine environment: Characterization of associated antibiotic resistance and virulence genes

A total of 116 Vibrio isolates comprising V. alginolyticus (n = 53), V. metschnikovii (n = 38), V. anguillarum (n = 21), V. antiquarius (n = 2), and V. fujianensis (n = 2) were obtained from seawater, fish, or bivalve molluscs from temperate Oceanic and Polar Oceanic area around Norway. Antibiotic sensitivity testing revealed resistance or reduced susceptibility to ampicillin (74%), oxolinic acid (33%), imipenem (21%), aztreonam (19%), and tobramycin (17%). Whole-genome sequence analysis of eighteen drug-resistant isolates revealed the presence of genes like β-lactamases, chloramphenicol-acetyltransferases, and genes conferring tetracycline and quinolone resistance. The strains also carried virulence genes like hlyA, tlh, rtxA to D and aceA, E and F. The genes for cholerae toxin (ctx), thermostable direct hemolysin (tdh), or zonula occludens toxin (zot) were not detected in any of the isolates. The present study shows low prevalence of multidrug resistance and absence of virulence genes of high global concern among environmental vibrios in Norway. However, in the light of climate change, and projected rising sea surface temperatures, even in the cold temperate areas, there is a need for frequent monitoring of resistance and virulence in vibrios to be prepared for future public health challenges.

A real-time recombinase polymerase amplification assay for the rapid detection of Vibrio harveyi

Vibrio harveyi is a pathogen that infects fish and shellfish worldwide, causing severe economic losses for the aquaculture industry. As the early diagnosis of V. harveyi infection is crucial to disease surveillance and prevention in cultured marine animals, a fast and accurate method to detect V. harveyi is required. Here, we performed recombinase polymerase amplification (RPA) using novel primers specifically designed to recognize the V. harveyi toxR gene, which encodes a transmembrane protein, and then hybridized this gene with a carboxy fluorescein (FAM)-labeled probe. The optimal conditions for the real-time RPA assay were a probe concentration of 90 nM and a 20 min incubation at 37 °C. The sensitivity of our real-time RPA assay was 50 copies of the standard plasmid, while that of real-time PCR was 500 copies. In V. harveyi-spiked Pseudosciaena crocea samples, the sensitivity of our real-time RPA was 60 CFUs per reaction, while that of PCR was 600 CFUs per reaction. SPSS probit regression analysis indicated that the limit of detection (LOD) of our RPA assay, with 95% probability, was 18 copies. The LOD was reached within 20 min and was highly reproducible across eight independent assays. Our novel RPA method successfully differentiated V. harveyi from all other tested Vibrio species, including some that were closely related. Our real-time RPA assay, in combination with a rapid DNA extraction protocol, is a fast and accurate tool for the detection of V. harveyi and for monitoring disease outbreaks. This tool will be valuable for the aquaculture industry.

Nanoparticle-based lateral flow biosensor combined with multiple cross displacement amplification for rapid, visual and sensitive detection of Vibrio cholerae

Vibrio cholerae is an important human pathogen that is responsible for cholera, a severe acute watery diarrhea. In the current study, a multiple cross displacement amplification (MCDA) coupled with amplicon detection by chromatographic lateral flow biosensor (LFB) method (MCDA-LFB) was successfully established and evaluated for the identification of V. cholerae. A set of 10 primers was designed specifically to recognize 10 different regions of the V. cholerae-specific gene ompW. The optimized time and temperature conditions for the MCDA were 30 min and 63°C, respectively. The MCDA-LFB assay correctly identified 31 strains of V. cholerae but did not detect 13 non-cholerae Vibrio strains and 30 non-Vibrio strains. The sensitivity of MCDA-LFB for target pathogen detection in pure culture was 10 fg per reaction. In the case of spiked shrimp samples without enrichment, the limit of detection was 4.1 CFUs per reaction or equivalent to 4.1 × 102 CFU g-1. The whole process, including shrimp homogenates processing (30 min), MCDA reaction (30 min) and results reporting (2 min), could be finished within 65 min. These results show that this assay is suitable for the rapid, sensitive and specific detection of V. cholerae in food, environmental and clinical samples.

Development of a rapid PCR protocol to detect Vibrio parahaemolyticus in clams

Vibrio parahaemolyticus is part of the natural microflora of estuarine and coastal marine waters and can be also present in seafood, especially shellfish and bivalve molluscs. In this study we compared the reference cultural method ISO 6887-3 with two molecular methods, multiplex PCR and real-time PCR, for the detection of two distinct genetic markers (tlh species-specific gene and tdh virulence gene) of V. parahaemolyticus in bivalve mollusc. The analyses were performed on clams inoculated with V. parahaemolyticus ATCC 43996 at T0 and after a 3 and 6 h of pre-enrichment in alkaline saline peptone water. Counts on agar plates were largely inaccurate, probably due to other Vibrio species grown on the TCBS selective agar. Multiplex PCR assays, performed using primers pairs for tdh and tlh genes, showed a detection limit of 10⁴ CFU/g of shell stock within 6 h of pre-enrichment, respecting however the action level indicated by the National Seafood Sanitation Program guideline. Detection by tdh gene in real-time PCR reached the definitely highest sensitivity in shorter times, 10¹ CFU/g after 3 h of pre-enrichment, while the sensitivity for the tlh gene was not promising, detecting between 10⁵ and 10⁶ CFU/g after 6 h of pre-enrichment. Our findings provide a rapid routine method of detection of V. parahaemolyticus based on tdh gene by real-time PCR for commercial seafood analysis to identify the risk of gastrointestinal diseases.

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.

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.

Antimicrobial susceptibility of Vibrio alginolyticus isolated from oyster in Korea

Pathogenic Vibrio alginolyticus, a cause of severe infection in shellfish, as well as in humans, has been found at high frequency around all coastal areas of Korea. The aim of this study was to determine the occurrence of V. alginolyticus, to identify the strains isolated from oysters in West Sea, and to investigate their antimicrobial resistance profiles. Biochemical analyses of the 90 initially recovered presumptive V. alginolyticus colonies indicated that 16 isolates were V. alginolyticus. PCR analysis to detect the presence of the gyrB gene confirmed that 15 (93.8 %) of the 16 isolates were V. alginolyticus. These 15 isolates had the following profiles of resistance against 16 antibiotics: all isolates were resistant to ampicillin and vancomycin, and 26.7 % of the isolates exhibited resistance to cephalothin. A large number of isolates showed intermediate resistance to erythromycin (100 %) and rifampin (73.3 %). Five (33.3 %) of the V. alginolyticus isolates demonstrated multiple resistance to at least three antimicrobials.

Hybridoma as a specific, sensitive, and ready to use sensing element: a rapid fluorescence assay for detection of Vibrio cholerae O1

Over the last decade, isolation and purification of monoclonal antibodies, for diagnostic analysis, have been carried out using the hybridoma expression system. The present study describes a novel example of a detection system using hybridoma cells containing antibody against O1 antigen directly for V. cholerae diagnosis, which is a major health problem in many parts of the world, especially in developing countries. This method has advantages such as simplicity, ease of process, and it does not require manipulation of hybridoma cell. For this approach, an efficient amount of fluorescence calcium indicator, fura 2-AM, was utilized, which emitted light when the intracellular calcium concentration increased as result of antigen binding to specific antibody. More reliable results are obtained via this method and it is considerably faster than other methods, which has the response time of less than 45 s for detection of V. Cholerae O1. Also, the limit of detection was computed to be 50 CFU/mL (<13 CFU per assay). In addition, no significant responses were observed in the presence of other bacteria with specific hybridoma or other cell lines exposed to V. cholerae O1. Furthermore, this method was successfully applied to V. cholerae O1 detection in spiked environmental samples, including water and stool samples without any pretreatment. All results reveal that hybridoma cells can provide a valuable, simple, and ready to use tool for rapid detection of other pathogenic bacteria, toxins, and analytes.

Use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant

The study of bacterial communities throughout a drinking water treatment plant could provide a basic understanding of the effects of water processing that could then be used to improve the management of such plants. However, it is necessary to develop new analytical techniques that are sufficiently efficient, robust and fast for their effective and useful application in routine analysis. The aim of this study is therefore to assess the performance of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), as compared to the PhenePlate™ system, for routine analysis in a drinking water treatment plant. To this end we studied a total of 277 colonies isolated in different seasons and from different points throughout the water treatment process, including: raw water, sand filtration, ultrafiltration, reverse osmosis and chlorination. The colonies were analysed using MALDI-TOF MS by direct deposition of the cells on the plate. The colonies were also biochemically fingerprinted using the PhenePlate™ system, clustered according to their similarity and a representative strain was selected for 16S rRNA gene sequencing and API^® gallery-based identification. The use of MALDI-TOF MS was reliable compared to the PhenePlate™ system and has the advantage of being faster and relatively cheap. Bacteria typing by MALDI-TOF MS is therefore a promising method to replace conventional routine phenotypic methods for the identification of bacteria in drinking water laboratories, thanks to its robustness. The major limiting factor for MALDI-TOF MS is the lack of a suitable mass spectra database; although each laboratory can develop its own library. This methodology will provide a tracking tool for companies to use in risk management and the detection of possible failures in both the water treatment processes and the distribution network, as well as offering characterization of the intrinsic microbial populations.

A luminescent hybridoma-based biosensor for rapid detection of V. cholerae upon induction of calcium signaling pathway

In this study, a hybridoma based biosensor was developed for rapid, sensitive and selective detection of Vibrio cholerae O1 which converts the antibody-antigen binding to bioluminescence light. After investigation on hybridoma performance, the biosensor was constructed by transfecting specific hybridoma cells with aequorin reporter gene and the bioluminescence activities of stable biosensor were measured. The sensitivity of biosensor was as few as 50 CFU/ml and it showed no responses to other entric bacteria. Moreover, the response time of biosensor was estimated in 7th second which means this method is considerably faster than many available detection assays. In addition, this biosensor was successfully applied to V. cholerae detection in environmental samples with no significant loss in sensitivity, demonstrating our proposed biosensor provides a sensitive and reliable method for detection of V. cholerae in natural samples. The application of whole hybridoma cell directly as a sensing element in biosensor construction which mentioned for the first time in present study suggests that hybridoma cells could provide a valuable tool for future studies in both basic and diagnostic sciences and could be considered as a fast and specific sensing element for detection of other pathogens in different applications.

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

Bacterial gastroenteritis is a disease that is pervasive in both the developing and developed worlds. While for the most part bacterial gastroenteritis is self-limiting, identification of an etiological agent by bacterial stool culture is required for the management of patients with severe or prolonged diarrhea, symptoms consistent with invasive disease, or a history that may predict a complicated course of disease. Importantly, characterization of bacterial enteropathogens from stool cultures in clinical laboratories is one of the primary means by which public health officials identify and track outbreaks of bacterial gastroenteritis. This article provides guidance for clinical microbiology laboratories that perform stool cultures. The general characteristics, epidemiology, and clinical manifestations of key bacterial enteropathogens are summarized. Information regarding optimal specimen collection, transport, and processing and current diagnostic tests and testing algorithms is provided. This article is an update of Cumitech 12A (P. H. Gilligan, J. M. Janda, M. A. Karmali, and J. M. Miller, Cumitech 12A, Laboratory diagnosis of bacterial diarrhea, 1992).

Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Vibrio species

Among 56 blood isolates of Vibrio species identified by sequencing analysis of 16S rRNA and rpoB genes, the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system correctly identified all isolates of Vibrio vulnificus (n = 20), V. parahaemolyticus (n = 2), and V. fluvialis (n = 1) but none of the isolates of serogroup non-O1/O139 (non-serogroup O1, non-O139) V. cholerae (n = 33) to the species level. All of these serogroup non-O1/O139 V. cholerae isolates were correctly identified using the newly created MALDI-TOF MS database.

Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Vibrio cholerae

We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MS) for the identification of Vibrio cholerae. MS identified all 42 isolates of V. cholerae O1 and O139 and 7 of 9 non-O1/O139 isolates. MS correctly discriminated between all Aeromonas and V. cholerae isolates. Overall, MS performed as well as or better than biochemical methods.

VibrioBase: A MALDI-TOF MS database for fast identification of Vibrio spp. that are potentially pathogenic in humans

Mesophilic marine bacteria of the family Vibrionaceae, specifically V. cholerae, V. parahaemolyticus and V. vulnificus, are considered to cause severe illness in humans. Due to climate-change-driven temperature increases, higher Vibrio abundances and infections are predicted for Northern Europe, which in turn necessitates environmental surveillance programs to evaluate this risk. We propose that whole-cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling is a promising tool for the fast and reliable species classification of environmental isolates. Because the reference database does not contain sufficient Vibrio spectra we generated the VibrioBase database in this study. Mass spectrometric data were generated from 997 largely environmental strains and filed in this new database. MALDI-TOF MS clusters were assigned based on the species classification obtained by analysis of partial rpoB (RNA polymerase beta-subunit) sequences. The affiliation of strains to species-specific clusters was consistent in 97% of all cases using both approaches, and the extended VibrioBase generated more specific species identifications with higher matching scores compared to the commercially available database. Therefore, we have made the VibrioBase database freely accessible, which paves the way for detailed risk assessment studies of potentially pathogenic Vibrio spp. from marine environments.

Vibrio fluvialis: an emerging human pathogen

Vibrio fluvialis is a pathogen commonly found in coastal environs. Considering recent increase in numbers of diarrheal outbreaks and sporadic extraintestinal cases, V. fluvialis has been considered as an emerging pathogen. Though this pathogen can be easily isolated by existing culture methods, its identification is still a challenging problem due to close phenotypic resemblance either with Vibrio cholerae or Aeromonas spp. However, using molecular tools, it is easy to identify V. fluvialis from clinical and different environmental samples. Many putative virulence factors have been reported, but its mechanisms of pathogenesis and survival fitness in the environment are yet to be explored. This chapter covers some of the major discoveries that have been made to understand the importance of V. fluvialis.

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.

Severe Wound Infection with Photobacterium damselae ssp. damselae and Vibrio harveyi, following a Laceration Injury in Marine Environment: A Case Report and Review of the Literature

Marine microorganisms are uncommon etiologies of skin and skin structure infections, that is, wound infections. We report a case of severe wound infection, caused by the marine Photobacterium damselae (Vibrionaceae), in a 64-year-old male patient, returning from Australia. The isolate tested positive for pPHDD1, a plasmid conferring high-level virulence. Furthermore, the wound was coinfected with Vibrio harveyi, a halophile bacterium, which has never been reported from human infections before. Identification was achieved by use of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry (MALDI-TOF) and confirmed by 16S rDNA sequencing. Data retrieval from bibliography was complicated since P. damselae has been renamed often with a number of synonyms present in the literature: Photobacterium damsela, Vibrio damselae, Vibrio damsela, Pasteurella damselae, and Listonella damsela. With all synonyms used as query terms, a literature search provided less than 20 cases published worldwide. A majority of those cases presenting as severe wound infection are even fatal following progression into necrotizing fasciitis. Management with daily wound dressing and antibiotic therapy (ofloxacin empirically, followed by doxycycline after availability of microbiology) led in the reported case to a favorable outcome, which seems to be, however, the exception based on a review of the available literature.

Multiplex Real-time Polymerase Chain Reaction Assays for Simultaneous Detection of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus

Objectives

A multiplex real-time polymerase chain reaction (RT-PCR) method was developed for the identification of three Vibrio species: Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus.

Methods

Specific primers and probes targeting the hlyA, tlh, and vvhA genes were selected and used for multiplex real-time PCR to confirm the identification of V. cholerae, V. parahaemolyticus, and V. vulnificus, respectively. This method was applied to screen Vibrio species from environmental samples and combining it with a culture-based method, its effectiveness was evaluated in comparison with culture-based methods alone.

Results

Specific PCR fragments were obtained from isolates belonging to the target species, indicating a high specificity of this multiplex real-time PCR. No cross-reactivity with the assay was observed between the tested bacteria. The sensitivity of the multiplex real-time PCR was found to have a lower limit of 10⁴ colony-forming units/reaction for all three Vibrio species. The combination strategy raised the isolation ratio of all three Vibrio species 1.26- to 2.75-fold.

Conclusion

This assay provides a rapid, sensitive, and specific technique to detect these three Vibrio species in the environment.

Rapid identification of Vibrio parahaemolyticus isolated from shellfish, sea water and sediments of the Khnifiss lagoon, Morocco, by MALDI-TOF mass spectrometry

We establish the presence of Vibrio parahaemolyticus and deepen the comparison of isolates using MALDI-TOF MS for the typing of isolates originating from the Khnifiss lagoon (Morocco). Amongst 48 samples from sea water, sediment and shellfish isolated from different sites of Khnifiss lagoon, Morocco, we obtained 22 isolates of V. parahaemolyticus identified by Vitek 2™ System (bioMérieux) and MALDI Biotyper™ (Bruker Daltonics). All isolates were highly resistant to ampicillin and ticarcillin, moderately resistant to cefalotin, but sensitive to 16 other antimicrobials tested. MALDI-TOF MS was used to discriminate between closely related environmental strains of V. parahaemolyticus. A clustering and distribution based on MALDI-TOF spectra were generated using the BioTyper 1.1™ software. Despite low diversity in regard to the biochemical characteristics and antimicrobial resistance, the isolates evoke a larger biodiversity when analysed through mass spectra of abundant proteins. Different evaluations of a cut-off value showed that, when placed at a 10% threshold of the whole diversity, isolates differed by at least three mass peaks.

Discrepancies in identification of Vibrio cholerae strains as members of Aeromonadaceae and Enterobacteriaceae by automated microbial identification system

AIMS

Incidental observation of a discrepancy in identification of Vibrio cholerae prompted a study to understand the ability of an automated microbial identification system to identify this important pathogen.

METHODS AND RESULTS

Twenty clinical isolates of V. cholerae showing difference in genetic profiles by random amplified polymorphic DNA (RAPD) fingerprinting, serologically confirmed as O1, and showing presence of ctxA and tcpA genes in PCR were subjected to analysis by Vitek 2 Compact automated identification system for identification. Vitek 2 Compact detected 10 of 20 isolates correctly, whereas the remaining 10 were identified as various members of Aeromonadaceae and Enterobacteriaceae.

CONCLUSIONS

Our results indicate that Vitek 2 Compact automated microbial system does not always identify V. cholerae strains correctly.

SIGNIFICANCE AND IMPACT OF STUDY

These observations should create awareness among end users about possible misidentifications by automated systems and encourage simultaneous use of serology and/or PCR for correct identification at least for V. cholerae, which is one of the most important enteric pathogens.

Rapid and sensitive detection of Vibrio vulnificus by loop-mediated isothermal amplification combined with lateral flow dipstick targeted to rpoS gene

A novel loop-mediated isothermal amplification (LAMP) combined with amplicon detection by chromatographic lateral flow dipstick (LFD) assay was developed and evaluated for the detection of Vibrio vulnificus. Biotinylated LAMP amplicons were produced by a set of six designed primers that recognized the V. vulnificus RNA polymerase subunit sigma factor S (rpoS) gene followed by hybridization with an FITC-labeled probe and LFD detection. The optimized time and temperature conditions for the LAMP assay were 90 min at 65 °C. The LAMP-LFD method accurately identified 14 isolates of V. vulnificus but did not detect 25 non-vulnificus Vibrio isolates and 37 non-Vibrio isolates. The sensitivity of LAMP-LFD for V. vulnificus detection in pure culture was 1.5 × 10(3) CFU ml(-1) or equivalent to 2.8 CFU per reaction. In the case of spiked oyster samples without enrichment, the detection limit for V. vulnificus was 1.2 × 10(4) CFU g(-1) or equivalent to 11 CFU per reaction. The results show that this method appears to be accurate, precise and valuable tool for identification of V. vulnificus and can be used efficiently for detection of V. vulnificus in contaminated food sample.

Sensitive and rapid detection of Vibrio corallilyticus by loop-mediated isothermal amplification targeted to the alpha subunit gene of RNA polymerase

AIMS

A diagnostic protocol was developed for rapid detection of Vibrio corallilyticus by method of loop-mediated isothermal amplification (LAMP).

METHODS AND RESULTS

For cloning and sequencing of rpo A gene of V. corallilyticus, a set of four LAMP primers were designed by targeting the rpoA gene. With Bst DNA polymerase, the reaction time and temperature were optimized for 70 min at 65 degrees C, respectively. The amplification products were detected by electrophoresis. The detection limit of V. corallilyticus by LAMP was 3.6 x 10(3) CFU ml(-1) (8 CFU per reaction), but PCR could detect up to 3.6 x 10(4) CFU ml(-1) (72 CFU per reaction). The LAMP method was ninefold more sensitive than conventional PCR. The results also indicated that the LAMP reaction was highly specific to V. corallilyticus.

CONCLUSIONS

The LAMP assay was a sensitive, specific and cost-effective method for the rapid detection of V. corallilyticus.

SIGNIFICANCE AND IMPACT OF THE STUDY

This LAMP method provides an important diagnostic tool for the detection of V. corallilyticus infection. It can replace laborious biochemical tests for the identification of V. corallilyticus.

Detection of pathogenic Vibrio parahaemolyticus through biochemical and molecular-based methodologies in coastal waters of the Gulf of Trieste (North Adriatic Sea)

Culturable vibrios were isolated from seawater collected during an annual sampling study performed along the Gulf of Trieste coast (Northern Adriatic Sea), and conventional culturing and identification methods were used to investigate the presence of Vibrio parahaemolyticus. Biochemically selected Vibrio strains were subjected to phenotypical identification performed using Alsina's scheme, API 20E and API 20NE. PCR and sequence analysis of the 16S rRNA gene and detection of the species-specific toxR and tlh genes were carried out on strains presumptively identified as V. parahaemolyticus and on a set of unidentified strains to confirm biochemical characterizations. In addition, PCR assays targeting the virulence genes, tdh and trh, were carried out to detect pathogenic strains. PCR results were compared with phenotypic characterizations to evaluate the accuracy of the biochemical methods applied. False-negative identifications were obtained by all phenotypic-based procedures, while API 20E yielded only one false positive. Because the amplification of the 16S rRNA gene produced uncertain results, toxR and tlh gene detections were necessary to confirm the biochemical identifications. Finally, molecular characterization demonstrated the presence of V. parahaemolyticus trh-positive strains and underlined the difficulty in the recognition of the pathogenic environmental organism using conventional methods.

Evaluation of genotypic and phenotypic methods to distinguish clinical from environmental Vibrio vulnificus strains

Vibrio vulnificus is a heterogeneous bacterial species that comprises virulent and avirulent strains from environmental and clinical sources that have been grouped into three biotypes. To validate the typing methods proposed to distinguish clinical from environmental isolates, we performed phenotypic (API 20E, API 20NE, and BIOLOG tests) and genetic (ribotyping and DNA polymorphism at several loci) studies with a large strain collection representing different biotypes, origins, and host ranges. No phenotypic method was useful for biotyping or grouping strains with regard to the origin of an isolate, and only the BIOLOG system was reliable for identifying the strains at the species level. DNA polymorphisms divided the population into three major profiles. Profile 1 strains were vcg type C, 16S rRNA type B, and vvh type 1 and included most of the biotype 1 human septicemic isolates; profile 2 strains were vcg type E, 16S rRNA type A, and vvh type 2 and included all biotype 2 isolates together with biotype 1 isolates from fish and water and some human isolates; and profile 3 strains were vcg type E, 16S rRNA type AB, and vvh type 2 and included biotype 3 strains. Ribotyping divided the species into two groups: one group that included profile 1 biotype 1 isolates and one group that included isolates of all three biotypes with the three profiles described above. In conclusion, no genotyping system was able to distinguish either clinical strains from environmental strains or biogroups within the species V. vulnificus, which suggests that new typing methodologies useful for public health have to be developed for this species.

Performance of microbiological control by a point-of-use filter system for drinking water purification

Purification capacity of a faucet mounted type water filter for home use was evaluated, particularly with regard to microbiological performance under different running conditions. Biofilms were formed inside the filter, affecting the bacterial quality of the effluent water. Low flow rate, long stagnation period and high filter temperature were found favorable for bacterial growth inside. By commercial analytical profile index (API) kits, ten different bacterial species were identified in drinking water, four of which were probably contributed to the biofilm formation since they were also present in the biofilm. Fluorescence in situ hybridization (FISH) was used to confirm the API identification results, and direct viable count (DVC) method was employed to improve the sensitivity of FISH for the isolated Acinetobacter spp. and Pseudomonas putida as models. Relationship between the filter operating condition and the bacterial community alteration was partly revealed, which could provide the basic knowledge for the filter design and its practical use.

Grimontia hollisae, a potential agent of gastroenteritis and bacteraemia in the Mediterranean area

Vibrio hollisae was first described in 1982 as an agent of diarrhoea and was reclassified in 2003 into a novel genus as Grimontia hollisae. We report the first case of G. hollisae bacteraemia in the Mediterranean area, in an 81-year-old man with a severe gastroenteritis and hepatitis following the consumption of raw oysters. The incidence of this micro-organism as an agent of gastroenteritis may be underestimated because it may not be detected using routine culture conditions.

Acute infectious peritonitis caused by Vibrio fluvialis

Vibrio fluvialis is a Gram-negative, oxidase-producing, halophilic bacterium that, as a pathogen, has been implicated mainly as a cause of gastroenteritis. We describe a case of V. fluvialis peritonitis after a traffic accident that is, to our knowledge, the 1st report of non-continuous ambulatory peritoneal dialysis-related acute peritonitis caused by this organism.

Comparison of biochemical and molecular methods for the identification of bacterial isolates associated with failed loggerhead sea turtle eggs

AIMS

Comparison of biochemical vs molecular methods for identification of microbial populations associated with failed loggerhead turtle eggs.

METHODS AND RESULTS

Two biochemical (API and Microgen) and one molecular methods (16s rRNA analysis) were compared in the areas of cost, identification, corroboration of data with other methods, ease of use, resources and software. The molecular method was costly and identified only 66% of the isolates tested compared with 74% for API. A 74% discrepancy in identifications occurred between API and 16s rRNA analysis. The two biochemical methods were comparable in cost, but Microgen was easier to use and yielded the lowest discrepancy among identifications (29%) when compared with both API 20 enteric (API 20E) and API 20 nonenteric (API 20NE) combined. A comparison of API 20E and API 20NE indicated an 83% discrepancy between the two methods.

CONCLUSIONS

The Microgen identification system appears to be better suited than API or 16s rRNA analysis for identification of environmental isolates associated with failed loggerhead eggs.

SIGNIFICANCE AND IMPACT OF THE STUDY

Most identification methods are not intended for use with environmental isolates. A comparison of identification systems would provide better options for identifying environmental bacteria for ecological studies.

Vibrio cholerae in the environment: a simple method for reliable identification of the species

A simple screening and identification protocol was assessed for the efficient distinction of colonies of Vibrio cholerae species from others obtained on thiosulphate citrate bile salts sucrose agar after isolation from different environmental specimens. It was demonstrated here that the yellow colonies (sucrose-fermenting), which are able to grow on nutrient agar without added NaCl and which present a positive oxidase reaction, can be confidently considered as presumptive V. cholerae. Confirmation of the identification was carried out using the API 20E microtest and by species-specific ompW-based polymerase chain reaction: 809 of 925 isolates obtained by this screening procedure were identified as V. cholerae by API 20E and confirmed by PCR. The results showed that the direct use of the PCR-based method for the definite identification of the screened colonies gave better results than the API 20E method: of a selection of 100 isolates presumptively identified as V. cholerae according to the proposed screening procedure, all gave a positive result with PCR but only 94 were confirmed by API 20E. This protocol provides reliable identification of V. cholerae species and is adapted to the capabilities of routine clinical, food-testing and environmental microbiology laboratories.