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Evaluation of a Loop-Mediated Isothermal Amplification Method For Journal of Microbiological Methods 63 (2005) 36–44 www.elsevier.com/locate/jmicmeth Evaluation of a loop-mediated isothermal amplification method for rapid detection of channel catfish Ictalurus punctatus important bacterial pathogen Edwardsiella ictaluri Hung-Yueh YehT, Craig A. Shoemaker, Phillip H. Klesius United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Post Office Box 952, Auburn, AL 36831-0952, USA Received 23 November 2004; received in revised form 17 February 2005; accepted 17 February 2005 Available online 31 March 2005 Abstract Channel catfish Ictalurus punctatus infected with Edwardsiella ictaluri results in $40–50 million annual losses in profits to catfish producers. Early detection of this pathogen is necessary for disease control and reduction of economic loss. In this communication, the loop-mediated isothermal amplification method (LAMP) that amplifies DNA with high specificity and rapidity at an isothermal condition was evaluated for rapid detection of E. ictaluri. A set of four primers, two outer and two inner, was designed specifically to recognize the eip18 gene of this pathogen. The LAMP reaction mix was optimized. Reaction temperature and time of the LAMP assay for the eip18 gene were also optimized at 65 8C for 60 min, respectively. Our results show that the ladder-like pattern of bands sizes from 234 bp specifically to the E. ictaluri gene was amplified. The detection limit of this LAMP assay was about 20 colony forming units. In addition, this optimized LAMP assay was used to detect the E. ictaluri eip18 gene in brains of experimentally challenged channel catfish. Thus, we concluded that the LAMP assay can potentially be used for rapid diagnosis in hatcheries and ponds. D 2005 Elsevier B.V. All rights reserved. Keywords: Edwardsiella ictaluri; Ictalurus punctatus; LAMP 1. Introduction lose about one billion dollars annually to various diseases (USDA, 2003a). Among them, enteric Diseases have been a very critical limiting factor in septicemia of catfish (ESC) caused by Edwardsiella aquaculture. It is estimated that U.S. aquatic industries ictaluri (Hawke et al., 1981) is the leading disease that hinders the catfish production industry in the south- eastern U.S. (Wagner et al., 2002; USDA, 2003b). E. T Corresponding author. Tel.: +1 334 887 3741; fax: +1 334 887 ictaluri, a member of the Enterobacteriaceae family, is 2983. a facultative anaerobic, rod-shaped, Gram-negative, E-mail address: [email protected] (H.-Y. Yeh). oxidase-negative, glucose-positive and nitrate-nega- 0167-7012/$ - see front matter D 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.mimet.2005.02.015 H.-Y. Yeh et al. / Journal of Microbiological Methods 63 (2005) 36–44 37 tive microorganism (Hawke et al., 1981; Waltman et (Enosawa et al., 2003; Iwamoto et al., 2003; al., 1986). The factors associated with its pathogenesis Maruyama et al., 2003; Savan et al., 2004), protozoa are not well defined. Recent studies have showed (Kuboki et al., 2003) and fungus (Endo et al., 2004). several potential virulence factors, including extrac- In this communication, we applied this recently ellular capsular polysaccharide (Stanley et al., 1994; developed loop mediated isothermal amplification Williams et al., 2003), lipopolysaccharide (Arias et al., method (Notomi et al., 2000) to detect the channel 2003; Klesius and Shoemaker, 1997, 1999; Lawrence catfish important pathogen—E. ictaluri. Initially, we et al., 2001, 2003), outer membrane proteins (Baldwin designed the primers and optimized the LAMP assay et al., 1997; Skirpstunas and Baldwin, 2003) and for detection of E. ictaluri. Second, the specificity and chondroitinase (Cooper et al., 1996). sensitivity of the primers in the LAMP assay for To prevent these diseases effectively, good man- detection of E. ictaluri were determined. Finally, the agement practices such as rapid early and accurate specific and sensitive LAMP assay for detection of the detection of the pathogen are necessary for disease pathogen from experimentally challenged channel control and reduction of economic loss (Bader et al., catfish was tested. 2003). Traditionally, isolation and biochemical speci- ation are the primary tools for detection and identi- fication of this microorganism. These procedures take 2. Materials and methods at least 48 h by which time the diseases may have already spread throughout the fish population (Bilo- 2.1. Bacterial strains and DNA preparation deau et al., 2003; Klesius, 1994). Recently, powerful nucleic acid-based real-time PCR for rapid detection Bacteria and their sources used in this study are of E. ictaluri was developed (Bilodeau et al., 2003) listed in Table 1. These bacteria were cultured and its application for rapid diagnosis seems to be according to a standard protocol (Arias et al., 2003; promising. However, PCR inherits its intrinsic dis- Bader et al., 2003). Bacterial genomic DNA was advantages, such as (1) Taq DNA polymerase is often prepared by lysis of the bacterial pellet in 100 Alof inactivated by inhibitors present in biological samples lysis buffer (20 mM Tris–HCl, pH 8.0, 2 mM EDTA, (e.g. Abu Al-Soud and Ra˚dstro¨m, 2000; Abu Al-Soud pH 8.0 and 1.2% Triton X-100) that was boiled for 10 et al., 2000; de Franchis et al., 1988; Lantz et al., min (Iwamoto et al., 2003). 2000), (2) high-cost, sophisticated instruments for amplification and detection of the amplified products 2.2. Design of LAMP DNA oligonucleotide primers are required, and (3) minimal 1 h are needed for the procedure. Thus, a rapid, simple cost-effective assay To design the species-specific LAMP DNA oligo- is needed to complement the current methods. nucleotide primers, we first searched the nucleic acid We evaluated the loop-mediated isothermal ampli- sequences of E. ictaluri deposited in the GenBank fication method (LAMP) that is also nucleic acid- database, and used the BLAST program (Altschul et based amplification and was developed by Notomi et al., 1997) to choose the species-specific gene sequen- al. (2000). The principle of LAMP is based on ces. The accession number of the sequence was autocycling strand displacement DNA synthesis in AF037441. The sequence was further analyzed by the presence of exonuclease-negative Bst DNA the PrimerExplorer V1 software program (http:// polymerase under isothermal condition within 1 h venus.netlaboratory.com/partner/lamp/pevl.html)to (Notomi et al., 2000). Because four specific primers have the LAMP primers: F3 (Forward outer primer), that recognize six different sequences on the DNA B3 (Backward outer primer), FIP (Forward inner target are used, LAMP amplifies DNA in high primer) and BIP (Backward inner primer) (Table 2, specificity. Since it was published in 2000, the LAMP See Ref. Notomi et al., 2000 for nomenclature of method has been tested in diagnosis of viruses primers). In addition, each internal primer that (Fukuta et al., 2003a,b; Hong et al., 2004; Ihira et recognizes both sense and anti-sense strands of the al., 2004; Kono et al., 2004; Parida et al., 2004; Poon target DNA was connected by a TTTT spacer (Notomi et al., 2004; Yoshikawa et al., 2004), bacteria et al., 2000). The LAMP primers were synthesized 38 H.-Y. Yeh et al. / Journal of Microbiological Methods 63 (2005) 36–44 Table 1 Bacterial strains used in this study Bacterial species Medium Growth temperature Edwardsiella ictaluri ATCC 33202 Brain heart infusion broth 28 8C Edwardsiella ictaluri AL93-58 Brain heart infusion broth 28 8C Edwardsiella ictaluri AL93-75 Brain heart infusion broth 28 8C Edwardsiella ictaluri S94-1034 Brain heart infusion broth 28 8C Edwardsiella ictaluri S94-1051 Brain heart infusion broth 28 8C Edwardsiella tarda AU98-24 Brain heart infusion broth 37 8C Flavobacterium columnare ATCC 23463 Shieh medium 28 8C Flavobacterium columnare ARS-1 Shieh medium 28 8C Flavobacterium columnare ALG-522 Shieh medium 28 8C Flavobacterium aquatile ATCC 11947 Shieh medium 28 8C Flavobacterium johnsoniae ATCC 17061 Shieh medium 28 8C Tenacibaculum maritimum ATCC 43398 Shieh medium+1.5% NaCl 28 8C Salmonella choleraesuis Brain heart infusion broth 37 8C Vibrio vulnificus CECT 61 Brain heart infusion broth 28 8C Escherichia coli ATCC 25922 Brain heart infusion broth 37 8C Pseudomonas aeruginosa ATCC 27853 Brain heart infusion broth 37 8C Enterococcus faecalis Brain heart infusion broth 37 8C Streptococcus iniae ARS 58B Brain heart infusion broth 28 8C commercially by Sigma-Genosys (The Woodlands, well) were analyzed by 2% agarose gel electro- TX) or MWG Biotech (High Point, NC). phoresis and stained with ethidium bromide. 2.3. LAMP reaction 2.4. Detection of E. ictaluri in experimentally challenged catfish by LAMP assay The LAMP reaction was carried out in a 25-Al reaction mixture containing the following reagents E. ictaluri infected channel catfish were prepared with final concentrations: 1Â reaction mix with 6 mM by intraperitoneal injection (Bilodeau et al., 2003)of MgSO4 (New England Biolabs, Beverly, MA), 0.8 M the AL93-75 isolate. Uninfected fish were inoculated betaine (USB Corporation, Cleveland, OH), 1.0 mM with brain heart infusion broth. After 24 h post dNTP (USB Corporation, Cleveland, OH), 0.2 AM infection, brains (3 mmÂ3mmÂ3 mm) were each of F3 and B3 primers, 1.6 AM each of FIP and aseptically excised from both uninfected and infected BIP, 0.32 U/Al Bst DNA polymerase (New England fish. The DNA templates were prepared by using a Biolabs, Beverly, MA) and appropriate amount of DNeasy tissue kit (Qiagen,
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