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Electronic Journal of Biotechnology

On-line version ISSN 0717-3458

Electron. J. Biotechnol. vol.18 no.6 Valparaíso Nov. 2015

http://dx.doi.org/10.1016/j.ejbt.2015.09.007 

RESEARCH ARTICLE

Amplification of tlh gene in other Vibrionaceae specie by specie-specific multiplex PCR of Vibrio parahaemolyticus

 

Romina Yáñeza, Roberto Bastíasa, Gastón Higuerab, Oscar Salgadoc, Pantelis Kathariosd, Jaime Romerob, Romilio Espejob, Katherine Garcíac, *

a Laboratorio de Microbiología, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330, Curauma, Valparaíso, Chile
b Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Santiago, Chile
c Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Av. El Llano Subercaseaux 2801, San Miguel, Santiago, Chile
d Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Crete, Greece


ABSTRACT

Background

The surveillance of Vibrio parahaemolyticus in the Chilean coast has been mainly performed by multiplex PCR amplification of three different hemolysin genes, which are specie-specific virulence factors. These genes are also employed in the determination of V. parahaemolyticus pathogenic load in seafood and for characterization of pathogenic strains associated to diarrhea cases in human. During environmental surveillance that we performed every summer, we occasionally observed a thermolabile hemolysin (tlh) PCR product of a slightly smaller size than expected, which was coincident with low loads of V. parahaemolyticus in the environment. In order to understand this observation, we probed the specificity of tlh primers for the detection of V. parahaemolyticus at different bacterial loads and DNA concentrations.

Results

Primers used for the detection of V. parahaemolyticus specific tlh amplified a slightly smaller tlh gene, which is found in Vibrio alginolyticus and other related strains. These amplicons were observed when V. parahaemolyticus was absent or in undetectable loads in the environment.

Conclusions

Surveillance of V. parahaemolyticus using tlh primers can be imprecise because amplification of a V. parahaemolyticus specific marker in V. alginolyticus and other related strains occurs. This situation complicates potentially the estimation of bacterial load in seafood, because do not ensure the correct identification of V. parahaemolyticus when his load is low. Additionally, it could complicate the tracking of outbreaks of V. parahaemolyticus infections, considering the genetic markers used would not be specie-specific.

Keywords: Hemolysin; Multiplex PCR; Pathogen surveillance; Virulence factor; Vibrio parahaemolyticus


 

1. Introduction

Vibrio parahaemolyticus is a halophilic gram negative bacterium widely distributed in marine environments and is recognized as the world's leading cause of gastroenteritis in humans due to raw or undercooked seafood [1]. Some strains are capable of causing disease and most of them are related to the pandemic serotype O3:K6 [2]. This serotype comprises a clonal complex originally observed in Southeast Asia that reached Antofagasta, northern Chile, in 1998 [3], and reached and remained in Region de Los Lagos, southern Chile since 2004. During this period, seafood consumption-related diarrhea increased drastically in Chile, because approximately 69% of the country's shellfish are produced in this region [4]. Filter-feeding bivalve, such as mussels, can concentrate pathogenic strains of V. parahaemolyticus resulting in bacterial loads capable of producing infection to the people that ingest them [5]. Consequently, virulent V. parahaemolyticus strains are clearly a concern for seafood safety, and hence, their reliable detection in mussels is crucial.

In Chile, surveillance of V. parahaemolyticus in seafood has been performed mainly by multiplex PCR (mPCR) [6] including amplification of thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh) and tdh-related hemolysin (trh) genes [7]. The tlh gene encodes a phospholipase A2 [8], while its contribution to V. parahaemolyticus pathogenicity is not clear, the expression of tlh is upregulated under conditions mimicking the human intestine [9]. This gene is considered a specie-specific marker for V. parahaemolyticus and is frequently employed to identify this specie [10]. On the other hand, most of pathogenic strains additionally possess tdh and/or trh hemolysin genes, which are considered important markers of clinical strains [1] and [11].

Using mPCR, Fuenzalida et al. [2] observed tlh amplicons slightly smaller than expected (450 bp) derived from shellfish extracted in Antofagasta. Authors sequenced tlh amplicon and observed 91% similarity with tlh gene found in Vibrio alginolyticus [12] and 82% similarity with V. parahaemolyticus tlh gene. Smaller tlh amplicons were later observed in Puerto Montt, coinciding with lower loads of V. parahaemolyticus (geometric average < 0.3 to 2 g-1) than observed in previous years (geometric average < 2 to 110 g-1). To understand these observations and the potentially critical consequences for V. parahaemolyticus surveillance, we performed sampling to quantify the bacterial load in mussels using mPCR, including tlh primers. Additionally, we studied the specie-specificity of these primers for isolates obtained from Chile and we performed PCR at different loads of V. parahaemolyticus and V. alginolyticus, simultaneously.

2. Materials and methods

2.1. Sampling and load estimation

Mussel samples obtained in Quillaipe, Puerto Montt, were analyzed by mPCR as described previously [13]. Briefly, samples of shellfish soft tissue were enriched for V. parahaemolyticus in three-tube serial dilutions in alkaline peptone water for the assessment of bacterial load by the most probable number (MPN) method; tubes with bacterial growth were tested for tlh, tdh and trh by multiplex PCR [6]. PCR was performed using approximately 10 ng of total bacterial DNA per reaction tube. The tlh amplicons were visualized in 8% polyacrylamide gels and stained with silver nitrate. Total and pandemic V. parahaemolyticus loads were calculated according to the number of tubes positive for tlh and for tdh and trh, respectively.

2.2. Phenotypic characterization

According to the mPCR results, tlh positive enrichment tubes were plated on TCBS agar (Difco) and chromogenic agar CHROMagar Vibrio (CHROMagar Microbiology, Paris, France). Furthermore, purified colonies were characterized with Api20E kit for enteric bacteria (Biomerieux, Halzelwood, MO) and referred as A1 to A7. V. alginolyticus strains R4 and VA1 were isolated from Crete, Greece and were identified by BIOLOG GENIII and molecular methods (16s RNA sequence and PCR using collagenase gene primers) [14].

2.3. tlh amplification

PCR using tlh primers (Forward 5'-AAA GCG GAT TAT GCA GAA GCA CTG-3', Reverse 5'-GCT ACT TTC TAG CAT TTT CTC TGC-3') [6] was performed using V. alginolyticus strains R4, and VA1. As positive controls, reference V. parahaemolyticus, Vp222, RIMD 2210633 (VpKX) and Vp7 strains were used. All of these strains were previously confirmed by growth in CHROMagar Vibrio. Same conditions of mPCR amplification were used [6] and PCR products were visualized in 1% agarose gels and stained with ethidium bromide.

2.4. tlh restriction assay

To determine the sequence similarity of tlh PCR products, in silico restriction analysis was performed with Webcutter 2.0 (http://rna.lundberg.gu.se/cutter2/) using tlh sequence of V. alginolyticus (JF718655.1) and V. parahaemolyticus (JX262976.1). Of the tested enzymes, HhaI and MboI were selected because they showed clear differences between species. Experimental restriction analysis of tlh was performed using HhaI (Fermentas) and MboI (Fermentas) for V. alginolyticus and V. parahaemolyticus amplicons according to the manufacturer's instructions, and PCR products were visualized in 1% agarose gels and stained with ethidium bromide.

2.5. Sequencing and phylogenetic analysis

PCR product of tlh gene from colonies obtained from sampling (A1 to A7) along with V. alginolyticus R4 and ANw1 (Antofagasta's strain referred as X in [2]) were sequenced in Macrogen (Korea) and results were compared with tlh sequences obtained from Genbank [15] using BLAST [16]. Phylogenetic tree was constructed using MEGA5 software v5.2 [17] based on UPGMA method.

2.6. tlh PCR assay specificity

The strains V. alginolyticus R4 and V. parahaemolyticus Vp222 were selected to determine tlh primer specificity at different DNA concentrations and bacterial load of both species. For PCR with different concentrations of DNA, the genome was extracted with Wizard Genomic DNA purification kit (Promega). The PCR was performed using DNA concentrations from 0.0001 ng to 30 ng of each bacterial strain and templates were mixed using proportional inverse concentration of genomic DNA. For PCR with different bacterial loads, cells were counted under microscope and serial dilutions were prepared from 100 to 105 total cells for each species. Six mixtures of R4 and Vp222 were performed using proportional inverse bacterial load. PCR was performed according amplification conditions mentioned in [6]. The tlh amplicons were visualized in 8% polyacrylamide gels and stained with silver nitrate or gel red as appropriate.

3. Results

3.1. Vibrio parahaemolyticus load estimation and isolates characterization

Of 28 samples analyzed, tlh was detected in 89% and all samples were negatives for tdh and trh genes. Vibrio parahaemolyticus load was estimated between 0.7 g-1 and 110 g-1, with a geometric mean of 2.1 g-1. tlh amplicons obtained from some of these samples (A1 to A5; size 440 bp) were slightly smaller than that obtained with bona fide V. parahaemolyticus (A6, A7; size 450 bp), as was reported previously in Antofagasta [2]. To confirm this observation, PCR with tlh primers was repeated for isolates A1, A2, A4, A6 and A7, using VpKX and ANw1 as positive control (Fig. 1). All the isolates with a smaller tlh amplicon showed phenotypic characteristics of V. alginolyticus: they were yellow and white colonies in TCBS and CHROMagar Vibrio, respectively, and Voges Proskauer positive and ara negative according Api20E. While isolates with expected tlh amplicon showed phenotypic characteristic from V. parahaemolyticus.

Fig. 1. tlh amplification. 8% polyacrylamide gel shows that in samples A1, A2 and A4 PCR amplification rendered a tlh amplicon slightly smaller than obtained with bona fide V. parahaemolyticus (A6 and A7). VpKX and ANw1 were used as positive control. Molecular weight, in the first line, corresponds to ladder 100 bp.

 

3.2. Analysis of tlh in V. alginolyticus strains

To corroborate that tlh amplicons were effectively amplified from V. alginolyticus or related isolates, tlh primers were used to perform PCR using strains R4 and VA1 isolated in Crete, Greece and V. parahaemolyticus Vp7, Vp222, and VpKX. Slightly size differences of approximately 10 bp were observed between V. alginolyticus and V. parahaemolyticus amplicons (Fig. 2), as was observed in isolates obtained during sampling (Fig. 1).

Fig. 2. tlh amplification in reference strains. 1% agarose gel shows amplicons of tlh in all strains. Two strains of V. alginolyticus (R4 and VA1, lanes 2 and 3, respectively) and three strains of V. parahaemolyticus (Vp222, Vp7 and VpKX, lanes 4, 5 and 6, respectively) were used. Molecular weight, in the first line, corresponds to ladder 100 bp.

 

Additionally, restriction pattern analysis of tlh amplicon showed difference between V. alginolyticus R4 and VA1 strains and V. parahaemolyticus strains. This distinctiveness was observed using HhaI (Fig. 3A) or MboI (Fig. 3B) restriction enzymes, suggesting that tlh sequence were not equal in both species.

Fig. 3. Restriction pattern of tlh amplicons from V. alginolyticus and V. parahaemolyticus strains. Amplicons were cut with MhaI (a) or MboI (b).
Molecular weight, in the first line, corresponds to ladder 100 bp.

 

3.3. Sequencing and phylogenetic analysis of tlh gene from isolates obtained during sampling

According to the suggested differences between tlh sequences of the reference strains (Fig. 3), tlh of isolates from sampling (A1 to A7) was sequenced, including R4 and ANw1 strains as control. Additionally, other tlh sequences reported for other Vibrio were obtained from GenBank and considered for analysis. Phylogenetic tree showed that isolates with smaller tlh amplicons (A1 to A5) do not clustered with V. parahaemolyticus (Fig. 4). Of this smaller tlh amplicons, isolates A1, A2, and A3 were clustered with V. alginolyticus strains, including reference strain R4. Isolates A4 and A5 grouped with Vibrio diabolicus strains and formed a cluster with ANw1 strain, previously isolated in Antofagasta [2] (Fig. 4).

Fig. 4. Phylogenetic tree of tlh sequences constructed with the UPGMA method. Sequences from smaller tlh (isolates A1-A3 and R4) grouped with those tlh previously reported in V. alginolyticus or V. diabolicus (A4, A5 and ANw1). By contrast, sequences from tlh of expected size (isolates A6 and A7) grouped with those tlh previously reported in V. parahaemolyticus. Bootstrap values based on 1000 replications are shown at the nodes. The bottom scale denotes the degree of dissimilarity.
Genbank accession number is showed in brackets. DQ663485.1 (Listonella anguillarum) is a GenBank synonym of Vibrio anguillarum.

 

3.4. Specificity of tlh primers

As we mentioned before, our previous observations suggest that tlh primers could amplify a tlh gene from other Vibrio when loads of V. parahaemolyticus are lower. To prove this observation, we performed a simultaneously tlh amplification with different concentrations of DNA (Fig. 5, upper panel) or bacterial load (Fig. 5, bottom panel) from V. alginolyticus R4 and V. parahaemolyticus Vp222. The results show that at lower concentration of V. parahaemolyticus DNA (30 ng R4/0.0001 ng Vp222), the tlh from V. alginolyticus is amplified. A decrease in the DNA of V. alginolyticus and increased in the DNA of V. parahaemolyticus will lead to the amplification of both amplicons (Fig. 5, upper panel, lane 2) until the tlh from V. alginolyticus is no longer amplified (Fig. 5, upper panel, lanes 3-8). Similar results were observed when the template DNA was determined by different loads of cells. Polyacrylamide electrophoresis show that a lower V. parahaemolyticus load determine tlh amplification corresponding to V. alginolyticus (105 R4/100 Vp222) which is characterized by smaller size. Again, it is observed that when V. parahaemolyticus load is low, smaller tlh amplicon take place. Inversely, when V. parahaemolyticus load increased is observed bona fide tlh amplification (Fig. 5, bottom panel).

Fig. 5. 8% polyacrylamide gel. Upper panel: tlh amplification using different concentrations of DNA from V. alginolyticus R4 and V. parahaemolyticus Vp222. Proportions of DNA template start from 30 ng of R4 and 0.0001 ng of Vp222 in lane 1 to 0.0001 ng of R4 and 30 ng of Vp222 in lane 8. A 10 fold dilution of PCR product was loaded in lanes 4-8 due to oversaturation of gel images. Bottom panel: tlh amplification using different bacterial loads of R4 and Vp222. Cells load start from 105 of R4 and 100 of Vp222 in lane 1 to 100 of R4 and 105 of Vp222 in lane 6. Lane 7: DNA positive control for R4. Lane 8: DNA positive control for Vp222. Ladder 100 bp.

 

4. Discussion

Since V. parahaemolyticus reached Chile in 1998, the mPCR proposed by Bej and collaborators [6] has provided a high-throughput and convenient means to determine total and pathogenic V. parahaemolyticus numbers in shellfish. However, these last years, we observed that during surveillance when V. parahaemolyticus loads were lower in Chilean coasts, mPCR was clearly a subject to false positives because thermolabile hemolysin gene was amplified from other Vibrio species (V. alginolyticus and V. diabolicus).

The presence of tlh in other species of Vibrio is not novel and had already been previously reported. Wang et al. [18], showed that tlh is widespread in vibrios [18], including V. alginolyticus, Vibrio harveyi, Vibrio fischeri, Vibrio mimicus, Vibrio natriegens, V. parahaemolyticus, Vibrio proteolyticus, Vibrio anguillarum, and Vibrio vulnificus among others. In other study, Xie et al. [12] showed that tlh sequence data was recovered from non-V. parahaemolyticus strains, indicating that tlh gene sequences in V. diabolicus, Vibrio tubiashii-like, and Photobacterium damselae are highly similar to those in V. parahaemolyticus. Worryingly, Xie also reported that V. alginolyticus strains often possess homologues of the V. parahaemolyticus and V. cholerae virulence genes such as toxR, and VPI [12], which suggests that V. alginolyticus maybe contain other known virulence genes of V. parahaemolyticus, besides tlh, potentially complicates the analysis employed during surveillance of V. parahaemolyticus, including pathogenic strains. Additionally, Klein and their coworkers [19] reported that virulence-related genes occurred at high frequencies in non-V. parahaemolyticus-Vibrionaceae species. In this study, V. diabolicus was of particular interest, as several strains were recovered, and the large majority (> 83%) contained virulence-related genes [19].

Similarity sequence between different Vibrio tlh genes makes the specie distinction imprecise. Consequently, the use of tlh as marker for V. parahaemolyticus loads may lead to overestimation by including other Vibrio species carrying tlh. The level of overestimation may be variable among different systems and sample types. Considering that tlh detection is formally recommended to the detection of V. parahaemolyticus [20] and [21], the results of this study are critical for surveillance in coasts. It is essential to find additional specie-specific probes and perform supporting analysis, to find reliable markers for V. parahaemolyticus quantitative detection, and to avoid overestimation of loads and erroneous identification of this specie in the environment.

Conflict of interest

The authors declare that they have no conflicts of interest in the research.

Financial support

This research was supported by Fondecyt11140257, Fondecyt11140412, and Scientific Information Program/Fund for Scientific Journals Publishing, Year 2014, ID FP140010.

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*Corresponding author: E-mail address: katherine.garcia@uautonoma.cl (K. García).

Received 30 July 2015, Accepted 23 September 2015, Available online 28 October 2015

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