Multiplex SYBR Green and duplex TaqMan real-time PCR assays for the detection of Photorhabdus Insect-Related (Pir) toxin genes pirA and pirB.

Acute hepatopancreatic necrosis disease (AHPND), also known as Early mortality syndrome (EMS), is a recently emerged lethal disease that has caused major economic losses in shrimp aquaculture. The etiologic agents are Vibrio spp. that carry Photorhabdus Insect-Related (Pir) toxin genes pirA and pirB. A multiplex SYBR Green real-time PCR was developed that detects pirA, pirB, and two internal control genes, the shrimp 18S rRNA and the bacterial 16S rRNA genes in a single reaction. The pirB primers amplify the 3'-end of the pirB gene allowing the detection of Vibrio spp. mutants that contain a complete deletion of pirA and the partial deletion of pirB. The assay also detects mutants that contain the entire pirA gene and the deletion of the pirB gene. Since both toxin genes are needed for disease development, this assays can distinguish between pathogenic strains of Vibrio spp. that cause AHPND in shrimp and mutants that do not cause disease. The amplicons for pirA, pirB, 18S rRNA and 16S rRNA showed easily distinguishable melting temperatures of 78.21 ± 0.18, 75.20 ± 0.20, 82.28 ± 0.34 and 85.41 ± 0.21 °C respectively. Additionally, a duplex real-time PCR assay was carried out by designing TaqMan probes for the pirA and pirB primers. The diagnostic sensitivity and specificity was compared between the SYBR Green and TaqMan assays. Both assays showed similar sensitivity with a limit of detection being 10 copies for pirA and pirB, and neither assays showed any cross reaction with other known bacterial and viral pathogens in shrimp. The high sensitivity of both assays make them suitable for the detection of low copies of the pirA and pirB genes in AHPND causing Vibrio spp. as well as for detecting non-pathogenic mutants.

Introduction

Acute hepatopancreatic necrosis disease (AHPND, initially referenced to as early mortality syndrome, EMS) is a deadly shrimp disease caused by particular Vibrio spp. [[1], [2], [3]]. The disease first emerged in China in 2009 and has rapidly spread throughout Southeast Asia to Vietnam, Malaysia, Thailand and reached Mexico in Latin America in 2013 [1,4]. The impact of AHPND in shrimp farming at a global scale has been catastrophic with an estimated global loss of $1 billion per year [5].

The etiologic agent of AHPND was shown to be a specific strain of Vibrio parahaemolyticus that carries the pirA and pirB genes homologous to the Pir (Photorhabdus insect-related) binary toxin of entomopathogenic bacteria [1,3]. Since the initial report, several other Vibrio species including V. owensii [6], V. campbelli [7], V. harveyi [8] and Vibrio punensis [9] have been reported that cause AHPND. More recently, a non-Vibrio bacterium, Microccocus luteus, has been found that contains the pirA and pirB genes [10].

The pathogenic Vibrio spp. harbor a large plasmid that ranges from 69 to 74 kb, on average of 33 copies per cell, and contains Photorhabdus Insect-Related (Pir) toxin genes pirA and pirB [3,11,12]. The binary toxin pirAB has been confirmed to be the etiological agent for AHPND [11]. To date, two conventional PCR based methods have been reported to detect both toxins genes pirA and pirB, a duplex conventional PCR reported by Han et al. [3] and a two-tube nested AP4 PCR developed by Dangtip et al. [13]. However, the two-tube nested AP4 PCR cannot detect deletion mutants that have only one gene pirA or pirB. A qPCR assay that detects pirA but does not detect mutants with the deletion of pirB has been reported [14]. The detection of both types of mutants is fundamental for the study of plasmid transmission dynamics and for recording the presence of the virulence plasmid since a recent study [2] suggests that the pirA and pirB genes may be lost or acquired by horizontal gene transfer via transposition or homologous recombination. In fact, the genome of a mutant strain of V. parahaemolyticus has been published that lacks the entire pirA gene and has a partial deletion of the 5′-end of the pirB gene [15]. In this study, we report a multiplex SYBR Green real-time PCR that detects the pirA and pirB toxin genes, and two internal control genes, the shrimp 18S rRNA and the bacterial 16S rRNA. Furthermore, we report a duplex TaqMan PCR that also detects pirA and pirB simultaneously. These assays will greatly aid in the detection and monitoring of low quantities of AHPND causing Vibrio spp. and mutant strains containing either pirA or pirB.

Methods

Primer design

Three different primer pairs were designed with Geneious R11 [16] to detect the pirA and pirB toxin genes (Table 1 ). The primers for the pirB were designed to amplify the 3’-end of the pirB gene allowing the detection of Vibrio spp. that have a partial deletion of this gene (Fig. 1 ). The genes used as internal controls for shrimp and bacteria were β-Actin, Elongation factor1-alpha, Glyceroldehyde-3 phosphate dehydrogenase, 18S rRNA, and 16S rRNA (Table 2 ).

Table 1

A list of primers that were used for the amplification of pirA and pirB toxin genes. For each primer, the nucleotide sequence, the Tm, the amplicon size and the location on the virulence plasmid in the reference strain V. parahaemolyticus A3 (GenBank accession: KM067908.1) are shown.

Primer Set	Primer pair	Primer sequence (5′ to 3′)	Primer Tm	Product size (bp)	Location in the virulence plasmid of reference strain Vibrio parahaemolyticus A3
Set 1	pirA F1	TGAAACTGACTATTCTCACGATTG	57	80	17,218 -> 17,241
	pirA R1	TGATAGGTGTATGTTTGCTGTC	56.2	80	17,297 -> 17,276
	pirB F1	TCACGGCTTTGAACATATGC	56.8	149	18,268 -> 18,287
	pirB R1	CATCTTCCGTACCTGTAGCA	56.8	149	18,416 -> 18,397
Set 2	pirA F2	AACTGACTATTCTCACGATTGGACT	59.8	101	17,221 -> 17,245
	pirA R2	CTACACTACGACCGACTTCCG	59.9	101	17,321 -> 17,301
	pirB F2	TTGGGGAACGTCGAAATCGT	60	216	18,447 -> 18,466
	pirB R2	TTGCTTCAGGTCCATTGGCA	60.2	216	18,662 -> 18,643
Set 3	pirA F3	ACTGTCGAACCAAACGGAGG	60.3	165	17,243 -> 17,262
	pirA R3	TTTAGCCACTTTCCAGCCGC	61.2	165	17,407 -> 17,388
	pirB F3	TTGCCAATGGACCTGAAGCA	60.2	94	18,642 -> 18,661
	pirB R3	ACACTTGGCTTGCCTGAGTT	60.1	94	18,735 -> 18,716

Fig. 1

The pirA and pirB primer locations on the virulence plasmid in the reference strain Vibrio parahaemolyticus A3. The primers pirA F1, pirA R1, pirB F1 and pirB R1 for dual detection of the pirA and pirB genes are shown in blue. The primers pirA F2, pirA R2, pirB F2 and pirB R2 for dual detection of the pirA and pirB genes are shown in green. The primers pirA F3, pirA R3, pirB F3 and pirB R3 for dual detection of the pirA and pirB genes are shown in red. The pirB primers are located near the 3′ end of the pirB gene allowing the detection of mutants with a partial deletion of pirB.

Table 2

A list of the internal control primers used in the SYBR Green assay for the amplification of Photorhabdus Insect-related (Pir) toxin genes pirA and pirB. For each primer, the nucleotide sequence, the Tm, the product size and the reference is shown. The genes used as internal controls were: β-Actin, Elongation factor1-alpha (EF1-α), Glyceroldehyde-3 phosphate dehydrogenase (GAPDH), 18S rRNA, and 16S rRNA.

Gene	Primer pair	Primer sequence (5′ to 3′)	Primer Tm	Product size (bp)	Reference
β-Actin	178F	GGTCGGTATGGGTCAGAAGGA	56	51	[17]
	228R	TTGCTTTGGGCCTCATCAC	59
EF1-α	123F	TCGCCGAACTGCTGACCAAGA	51	55	[17]
	123R	CCGGCTTCCAGTTCCTTACC	51
GAPDH	72F	CGTTGGACACCACCTTCA	59	55	[17]
	126R	GTGTGCGGTGTCAACATGGA	55
18S rRNA	185F	ACCTGAGGCATCACAAGGGTTAT	48	61	[17]
	185R	GCTTGGTGTGCAATGTATTAACCTA	40
16S rRNA	16S-rRNAF	TCCTACGGGAGGCAGCAGT	59.4	466	[18]
	16S-rRNAR	GGACTACCAGGGTATCTAATCCTGTT	58.1
18S rRNA Set1	18S rRNAF1	GAGAGGGAGCCTGAGAAACG	59.8	72	This study
	18S rRNA R1	GTGCCGGGAGTGGGTAATTT	60.3
18S rRNA Set 2	18S rRNA F1	TTTGAGTTCCGGGGGAAGTA	58.1	72	This study
	18S rRNA R1	ACTCCTGGTGGTGCCCTTC	61.5

Multiplex SYBR Green real-time PCR

Multiplex SYBR Green real-time PCR was performed using a StepOnePlus PCR system (Applied Biosystems ™). Each assay was carried out in a total volume of 20 μl containing 1 μl of template DNA, 10 μl of PowerUp™ SYBR™ Green Master Mix (2X), 125 nM of pirA primers (Set 1, Set 2 and Set3), 150 nM of pirB primers (Set 1, Set 2 and Set2), 75 nM of shrimp internal control primers (β-Actin, EF1-α, G3PD and 18S rRNA) and 350 nM of 16S rRNA bacterial internal control primers. The primer concentration was determined by testing each primer set with concentrations that ranged from 50 nM to 500 nM. Each primer set listed in Table 1 was tested with one shrimp internal control primer pair and the bacterial 16S rRNA internal control primers. The real-time PCR conditions consisted of a UDG activation at 50 °C for 2 min, denature and Dual-Lock ™ DNA polymerase activation at 95 °C for 2 min, followed by 40 cycles at 95 °C for 3s and 59 °C for 30s. Following amplification, the melt curve analysis was performed. The reaction temperature was increased to 95 °C for 15s, then decreased to 60 °C for 1 min, and increased to 95 °C at a rate 0.1 °C per second with a continuous fluorescence monitoring. The melt curves were used to determine if the primers were compatible and primer combinations that showed four clear specific amplification peaks were considered adequate for the multiplex real-time PCR.

TaqMan probe design and duplex real-time PCR

TaqMan probes were designed for primer pair pirA F1/R1 and pirB F1/R1 using Geneious R11 [16]. The TaqMan probe for pirA F1/R1 (5′- GAACCAAACGGAGGCGTCA-3′) was synthesized and labeled with 6-Carboxy-4′,5′-Dichloro-2′, 7′-Dimethoxyfluorescein, Succinimidyl Ester (JOE) on the 5′ end and N, N, N′, N′-Tetramethyl-6-carboxyrhodamine (TAMARA) on the 3′ end. The TaqMan probe for pirB F1/R1 (5′- TCACCTGCTGTTGGTTTTCCT-3′) was synthesized and labeled with 6-carboxyfluorescein (FAM) on the 5′ end and TAMARA on the 3′-end. For the assay, TaqMan™ Fast Virus 1-Step Master Mix (Applied Biosystems ™) was used, the final concentration for each primer was 0.2 μM and 0.07 μM for the TaqMan probe at a final volume of 10 μl. The real-time PCR profile was 20 s at 95 °C followed by 40 cycles of 1 s at 95 °C and 20 s at 59 °C. The amplification, detection and the analysis of the data for the real-time PCR assay was carried out with a StepOnePlus PCR system (Applied Biosystems ™).

Detection of the pirA and pirB genes in Vibrio spp.

Three natural known mutant strains of V. parahaemolyticus (pirA and partial pirB deletion), three strains of AHPND causing V. campbelli, one strain of V. shiloi (pirA positive and pirB negative) and ten strains of AHPND causing V. parahaemolyticus were obtained from the Aquaculture Pathology Laboratory bacterial collection. These bacteria were originally isolated from either the gastrointestinal tract of diseased shrimp, water or sediments from AHPND-affected farms in Asia or Latin America during 2013–2018. As negative controls three strains of V. parahaemolyticus without the pirA and pirB genes were used. These Vibrio spp. isolates were used to test the pirA, pirB and internal control primers (18S rRNA and 16S rRNA) for the SYBR Green and the TaqMan real-time PCR assays. All the tested strains were run by triplicate and the mean Ct values and melting temperatures were calculated. The DNA from the bacteria was extracted using the NORGEN Biotek Bacterial Genomic DNA isolation kit following the manufacturer's instructions.

Experimental challenge of Penaeus vannamei with AHPND causing Vibrio parahaemolyticus

Specific Pathogen Free (SPF) Penaeus vannamei shrimp (average weight 1.0 g) were experimentally challenged via immersion following a previously published protocol [14]. Briefly, V. parahaemolyticus (Strain 13–028A/3) was grown in Tryptic Soy Broth containing 2% NaCl (TSB+) and incubated for 18 h before using for an immersion challenge (CFU 106/ml). The hepatopancreas was dissected out from the moribund animals and recently deceased animals, and it was used for detecting the pathogen via real-time PCR assays. The DNA from the hepatopancreas was extracted using Maxwell-16® Cell LEV DNA purification kit (Promega).

Specificity test

To verify there was no cross reactivity with other shrimp pathogens, the multiplex SYBR Green and the duplex TaqMan assays were tested using genomic DNA isolated from P. vannamei known to be infected with white spot syndrome virus (WSSV), Enterocytozoon hepatopenaei (EHP), infectious hypodermal and hematopoietic necrosis virus (IHHNV), necrotizing hepatopancreatic bacteria (NHPB), hepatopancreatic parvovirus (HPV), monodon baculovirus (MBV) and baculovirus penaei (BP).

Cloning of pirA and pirB amplicons

The DNA fragments for the pirA (80 bp) and pirB (149 bp) were amplified from V. parahaemolyticus 18–408 and cloned into the pDrive Cloning Vector (QIAGEN®). The plasmids were designated as VppirA80 and VppirB149. The plasmids were purified using QIAprep® Spin Miniprep Kit. The sequence of the pirA and pirB fragments was verified by sequencing at the sequencing facility of The University of Arizona, Tucson, AZ.

Sensitivity

The sensitivity of the SYBR Green and TaqMan real-time PCR assays were determined using 6-fold serial dilutions of purified VppirA80 and VppirB149 plasmids. The concentrations of plasmid DNA that were utilized ranged from 106 to 101 copies/μl for all the plasmids. Additionally, ten-fold serial dilutions of 20 ng/μl of total genomic DNA extracted from shrimp hepatopancreas (infected with reference strain A3) were used to determine the detection limit of both the SYBR Green and TaqMan PCR assays. All samples were tested in triplicates.

Results

Three sets of primers listed in Table 1 were tested for compatibility against the internal control primers listed in Table 2. Only primer set 1 and the internal controls 18S rRNA set 1 and 16S rRNA showed 4 distinguishable melt peaks corresponding to each amplified fragment (Fig. 2 A). The amplicons for pirA, pirB, 18S rRNA and 16S rRNA from AHPND-infected shrimp showed easily distinguishable melting temperatures of 78.21 ± 0.18, 75.20 ± 0.20, 82.28 ± 0.34 and 85.41 ± 0.21 °C, respectively (Fig. 2).

Fig. 2

Melt curve analysis of PCR amplicons derived from AHPND-infected shrimp tissue and Vibrio spp. (A) Melt curve analysis of infected shrimp tissue for pirA, pirB, 18S rRNA and 16S rRNA, the amplicons presented melting temperatures of 78.21 ± 0.18, 75.20 ± 0.20, 82.28 ± 0.34 and 85.41 ± 0.21 °C, respectively. (B) Melt curve analysis of V. parahaemolyticus pirA negative strain. The melting temperatures of pirB and 16S rRNA are 75.20 ± 0.20 and 85.41 ± 0.21 °C respectively. Each amplicon shows a clearly defined peak. (C) Melt curve pattern of V. shiloi pirB negative strain. The melting temperatures of pirA and 16S rRNA are 78.21 ± 0.18 and 85.41 ± 0.21 °C respectively. In (D) we can observe the melt curve analysis of AHPND-causing strains of Vibrio spp. The melting temperatures of pirA, pirB and 16S rRNA are 78.21 ± 0.18, 75.20 ± 0.20 and 85.41 ± 0.21 °C respectively. In A, B, C and D each amplicon shows a clearly defined peak.

Detecting the pirA and pirB genes in deletion mutants of Vibrio spp.

The real-time PCR results for different strains of bacteria are summarized in Table 3 . The mean Ct and mean melting temperature are shown in Table 4 . When a Vibrio sp. contained both the pirA and pirB genes or one of the two genes, a unique melting curve with unique peak(s) was produced. The pirA negative V. parahaemolyticus strains showed two amplicons, pirB and 16S rRNA, with melting temperatures of 75.20 ± 0.20 and 85.41 ± 0.21 °C, respectively (Fig. 2B). Similarly, the pirB negative strain showed two amplicons, pirA and 16S rRNA, with melting temperatures of 78.21 ± 0.18 and 85.41 ± 0.21 °C, respectively (Fig. 2C). The AHPND causing strains showed three amplicons, pirA, pirB and 16S rRNA, with melting temperatures of 78.21 ± 0.18, 75.20 ± 0.20 and 85.41 ± 0.21 °C, respectively (Fig. 2D).

Table 3

A summary of the results for the detection of the pirA, pirB, 18S rRNA and 16S rRNA genes by the multiplex SYBR Green real-time PCR and the duplex TaqMan |real-time PCR.

Strain	Species	pirA		PirB		18S rRNA	16S rRNA
		SYBR	TaqMan	SYBR	TaqMan
DA 16-250-8	V. parahaemolyticus pirA negative	Neg	Neg	Pos	Pos	Neg	Pos
D 16-250-9	V. parahaemolyticus pirA negative	Neg	Neg	Pos	Pos	Neg	Pos
DB 16-250	V. parahaemolyticus pirA negative	Neg	Neg	Pos	Pos	Neg	Pos
	V. shiloi	Pos	Pos	Neg	Neg	Neg	Pos
D 16-192	V. campbelli AHPND	Pos	Pos	Pos	Pos	Neg	Pos
D3 16-137	V. campbelli AHPND	Pos	Pos	Pos	Pos	Neg	Pos
D 52 B	V. campbelli AHPND	Pos	Pos	Pos	Pos	Neg	Pos
	V. parahaemolyticus AHPND (N = 9)	Pos	Pos	Pos	Pos	Neg	Pos
13–028 A3	AHPND Reference strain	Pos	Pos	Pos	Pos	Neg	Pos
B24-38	V. parahaemolyticus AHPND negative	Neg	Neg	Neg	Neg	Neg	Pos
B29-43	V. parahaemolyticus AHPND negative	Neg	Neg	Neg	Neg	Neg	Pos
C24-78	V. parahaemolyticus AHPND negative	Neg	Neg	Neg	Neg	Neg	Pos
Hepatopancreas tissue from Penaeus vannamei shrimp (N = 30)	Laboratory challenge test	Pos	Pos	Pos	Pos	Pos	Pos

Table 4

Mean Ct and melt temperatures of the different strains of Vibrio spp. and five samples of infected tissue. The table shows the mean and standard deviation of the Ct for the different strains of Vibrio spp. and five samples of infected tissue using the SYBR Green and TaqMan assays. For the TaqMan assay the Ct of the pirA and pirB amplicons is shown. Additionally, the mean and standard deviation of the melt temperatures (Tm) of the pirA, pirB, 18S rRNA and 16S rRNA amplicons is shown for all the Vibrio spp. and five samples of infected tissue.

Strain	Species	Mean Ct SYBR Green	Mean Ct TaqMan pirA	Mean Ct TaqMan pirB	Mean Tm pirA	Mean Tm pirB	Mean Tm 18S rRNA	Mean Tm 16S rRNA
DA 16-250-8	V. parahaemolyticus pirA negative	11.24 ± 0.63	-	12.97 ± 0.06		75.66 ± 0.17		85.74 ± 0.10
D 16-250-9	V. parahaemolyticus pirA negative	11.64 ± 0.33		12.26 ± 0.26		75.08 ± 0.05		85.56 ± 0.22
DB 16-250	V. parahaemolyticus pirA negative	14.69 ± 0.16		15.28 ± 0.01		75.27 ± 0.10		85.54 ± 0.086
	V. shiloi pirB negative	11.21 ± .59	12.42 ± 0.23		78.59 ± 0.38			85.62 ± 0.11
D 16-192	V. campbelli AHPND	12.48 ± 0.53	10.11 ± 0.04	9.81 ± 0.25	78.20 ± 20	75.21 ± 0.08		85.49 ± 0.08
D3 16-137	V. campbelli AHPND	10.52 ± 0.49	8.20 ± 0.11	8.25 ± 0.09	78.25 ± 0.22	75.29 ± 0.22		85.45 ± 0.25
D 52 B	V. campbelli AHPND	11.02 ± 0.39	16.19 ± 0.38	13.39 ± 0.11	78.21 ± 0.15	75.41 ± 0.07		85.57 ± 0.14
	V. parahaemolyticus AHPND	12.±0.19	11.81 ± 22	10.25 ± 0.05	78.20 ± 0.11	75.11 ± 0.01		85.44 ± 0.17
13–028 A3	AHPND Reference strain	15.05 ± 0.57	10.83 ± 0.07	10.92 ± 0.12	78.06 ± 0.6	75.10 ± 0.04		85.44 ± 0.84
B24-38	V. parahaemolyticus AHPND negative	9.75 ± 0.12						85.42 ± 0.02
B29-43	V. parahaemolyticus AHPND negative	10.75 ± 0.19						85.39 ± 0.10
C24-78	V. parahaemolyticus AHPND negative	9.33 ± 0.10						85.37 ± 0.07
1-Hepatopancreas from infected P. vannamei	Laboratory challenge test	23.14 ± 0.45	19.72 ± 0.22	20.03 ± 0.26	78.11 ± 0.28	75.10 ± 0.24	82.02 ± 0.06	85.40 ± 0.29
2- Hepatopancreas from infected P. vannamei	Laboratory challenge test	20.53 ± 0.42	17.30 ± 0.23	17.03 ± 0.15	78.18 ± 0.26	75.12 ± 0.27	82.00 ± 0.06	85.53 ± 0.23
3- Hepatopancreas from infected P. vannamei	Laboratory challenge test	19.36 ± 0.88	16.84 ± 0.21	16.69 ± 0.33	78.09 ± 0.25	75.11 ± 0.23	82.01 ± 0.06	85.42 ± 0.23
4- Hepatopancreas from infected P. vannamei	Laboratory challenge test	22.03 ± 0.58	18.07 ± 0.05	18.41 ± 0.03	78.09 ± 0.23	75.15 ± 0.20	82.32 ± 0.12	85.38 ± 0.48
5- Hepatopancreas from infected P. vannamei	Laboratory challenge test	28.26 ± 0.17	24.35 ± 0.07	25.86 ± 0.03	78.13 ± 0.09	75.12 ± 0.04	82.05 ± 0.10	85.35 ± 0.47

The duplex TaqMan assay was also able to detect and differentiate when Vibrio spp. contained either pirA or pirB or both pirA and pirB. When Vibrio spp. contained both genes unique amplification curves were detected simultaneously in filter 1 (FAM/pirB) and filter 2 (JOE/pirA) (Fig. 3 ). In contrast, strains that contained only one gene showed a single amplification curve in filter 1 (FAM/pirB) or filter 2 (JOE/pirA) (Fig. 3). The results for the TaqMan assay for the different strains of bacteria are shown in Table 3. The SYBR Green assay and the TaqMan assay showed 100% agreement in the results for the detection of the pirA and pirB genes in the axenic Vibrio cultures and the hepatopancreas samples derived from AHPND-infected shrimp (N = 30). Both SYBR Green and TaqMan assays detected pirA and pirB genes in all the samples tested (Table 3). In Supplementary Fig. 1-3. the melt curves for each Vibrio spp. is presented.

Fig. 3

Simultaneous amplification of the pirA and pirB genes by the duplex TaqMan assay. The amplification curves of pirA and pirB are indicated.

The lower limit of detection of the SYBR Green assay and the TaqMan assay for the pirA and pirB amplicons was 10 and 10 copies of recombinant plasmid containing these gene fragments (Fig. 4 ). Furthermore, the limit of detection for the pirA and pirB genes in infected shrimp hepatopancreas tissue for both assays was 200 fg of total DNA (Fig. 5 ). In Supplementary Fig 4. the melt curves of the serial dilution of DNA from infected tissue is shown. In Supplementary Fig 5. the detection limit (20 pg) of the conventional duplex PCR reported by Han et al. [11], is shown.

Fig. 4

Standard curve for the pirA and pirB genes. The VppirA80 and VppirB149 plasmids were serially diluted from 106 to 101 copies/μl and were used as a template for PCR. The Ct values are plotted against the logarithm of their respective copy number. (A) A standard curve for the pirA gene generated using the SYBR Green assay with a log linear dynamic range of 6 orders of magnitude with an R2 value of 0.998, slope of −3.34 and amplification efficiency of 99.12%. (B) A standard curve for the pirB gene generated using the SYBR Green assay with a log linear dynamic range of 6 orders of magnitude with an R2 value of 0.999, slope of −3.381 and amplification efficiency of 97.59%. (C) A standard curve for the pirA gene generated using the TaqMan assay with a log linear dynamic range of 6 orders of magnitude with an R2 value of 0.998, slope of −3.549 and amplification efficiency of 91.32%. (D) A standard curve for the pirB gene generated using the TaqMan assay with a log linear dynamic range of 6 orders of magnitude with an R2 value of 0.980, slope of −3.101 and amplification efficiency of 110.14%.

Fig. 5

Detection sensitivity of the SYBR Green and TaqMan assays using AHPND-infected Penaeus vannamei from the experimental challenge test. (A) The SYBR Green assay was able to detect the pirA, pirB, 18S rRNA and 16S rRNA down to 200 fg of total DNA. (B) The TaqMan assay showed a similar sensitivity also detecting both genes down to 200 fg of total DNA. The red amplification plot represents 20 ng of total DNA, pirA (Ct = 19.39 ± 0.44), pirB (Ct = 17.11 ± 0.23). The yellow amplification plot represents 2 ng of total DNA pirA (Ct = 22.80 ± 0.41), pirB (Ct = 20.53 ± 0.24). The green amplification plot represents 200 pg of total DNA pirA (Ct = 26.49 ± 0.15), pirB (Ct = 23 ± 0.27). The turquoise amplification plot represents 20 pg of total DNA pirA (Ct = 29.34 ± 0.26), PirB (Ct = 27.19 ± 0.33). The light blue amplification plot represents 2 pg of total DNA pirA (Ct = 32.18 ± 12), pirB (Ct = 30.55 ± 0.27). The navy blue amplification plot represents 200 fg of total DNA pirA (Ct = 35.03 ± 0.32), pirB (Ct = 32.55 ± 0.30).

Specificity assay

In order to determine the specificity of SYBR Green and TaqMan assays described here, the methods were tested using DNA isolated from P. vannamei shrimp infected with several known viral (WSSV, IHHNV, HPV, MBV, BP), bacterial (NHPB) and fungal (EHP) pathogens. No amplification was obtained in the SYBR Green and TaqMan assays when DNA from other shrimp pathogens were used as a template indicating both assays are specific to Vibrio spp. that contain the pirA and pirB genes.

Discussion

Acute hepatopancreatic necrosis disease is caused by the Vibrio spp. that harbor a large plasmid with Photorhabdus Insect-Related (Pir) toxin genes pirA and pirB [11]. Both of these genes are necessary for virulence of the bacterium which can be highly lethal to cultured shrimp species of commercial importance. In this study, we developed a multiplex SYBR Green real-time PCR assay and a duplex TaqMan real-time PCR assay for the specific detection of the toxin genes pirA and pirB. The main advantage of both assays is the simultaneous detection and differentiation of the pirA and pirB genes, by utilizing the melt curve analysis for the SYBR Green assay and by using different reporter dyes for the TaqMan assay. To date, these are the only two real-time PCR assays published that can detect and simultaneously differentiate both genes in Vibrio spp.

Recently, Han et al. [3] and Kanrar & Dhar [15] reported the presence of mutant strains of Vibrio spp. that contained either the pirA or pirB gene. In AHPND-causing Vibrio spp., the binary toxin genes are flanked by transposes [11]. It has been proposed that due to a unique genome organization of the V. parahaemolyticus virulence plasmid, it may be lost or acquired by horizontal gene transfer via transposition or homologous recombination [2]. Further evidence of the transfer of these genes between bacteria is reported by Duran-Avelar et al. [10]. These authors detected the first non-Vibrio bacterium, M. luteus, that contains the pirA and pirB genes. It has not been reported if M. luteus is capable of causing AHPND. The discovery of several species of Vibrio and non-Vibrio bacteria carrying the binary toxin genes and causing AHPND suggest that there is an active transmission of the pirA and pirB genes between different bacteria and that these bacteria could acquire or lose pathogenicity. Therefore, the assays reported in this manuscript are fundamental tools for the study of plasmid transmission dynamics and for the detection of mutant strains that contain either pirA or pirB.

Multiplex SYBR Green real-time PCR using melt curve analysis has been previously used for the simultaneous detection of human pathogens (metapheumovirus, rhinovirus, enterovirus and coronavirus), plant pathogens (Plum pox virus), avian pathogens (avian influenza viruses) and bovine pathogens (Clostridium botulinum) [[19], [20], [21], [22], [23]]. The SYBR Green real-time PCR has been used for the detection and quantification of several shrimp pathogens including IHHNV, WSSV, TSV and YHV [24,25]. Considering the sensitivity and specificity of the SYBR Green assay when compared with the TaqMan assay and the low cost of the SYBR Green dyes, the method described here is a suitable tool for the detection of Vibrio spp. that cause AHPND and mutants strains that contain either the pirA or pirB gene. Furthermore, the SYBR Green assay described here has two internal controls (the shrimp 18S rRNA and the bacterial 16S rRNA) to avoid false negatives due to the poor DNA quality or the inhibition during amplification. Based on the need, the assay can be performed in a single or duplex format for the detection of either one or both toxin genes. Duplex TaqMan real-time PCR has also been extensively used for the simultaneous detection of avian pathogens (avian reovirus and Myoplasma synoviae), human pathogens (Eschrichia coli O157), amphibian pathogens (Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans) and shrimp pathogens (WSSV, Taura Syndrome Virus and PstDNV1) [[26], [27], [28], [29], [30]]. The sensitivity and specificity of the TaqMan assay was equal to the SYBR Green assay and it can also be used in a single format to detect just one of the two toxin genes. An added advantage of the TaqMan assay is it requires much less time for completion (27 min) since no melt curve analysis is needed making this a valuable tool in detecting Vibrio spp. that causes AHPND as well as mutant strains. However, TaqMan assay is costlier than the SYBR Green assay due to the higher cost of the reagents and the probes.

To summarize, we have developed a multiplex SYBR Green and a duplex TaqMan real-time PCR for the simultaneous detection of the binary toxin genes, pirA and pirB, that are the virulence factors in causing AHPND in shrimp. The current OIE-recommended methods for AHPND detection is based on a one-step conventional PCR [3] and a nested PCR [13]. Therefore, the real-time PCR assays described here represent a valuable tool for detecting AHPND-causing Vibrio spp. The sensitivity and specificity of the assays will reduce time significantly compared to the current OIE-recommended methods.

Declaration of interest

None.

Authors' contributions

Roberto Cruz-Flores, Hung Nam Mai, Arun K. Dhar designed the experiments. Roberto Cruz-Flores wrote the manuscript, designed the primers and optimized the conditions of the multiplex SYBR Green real-time PCR and the duplex TaqMan real-time PCR. Roberto Cruz-Flores and Hung Nam Mai prepared the DNA samples. Hung Nam Mai prepared, maintained and extracted DNA from the axenic cultures of the different Vibrio spp. All authors reviewed and approved the final version of the manuscript.