DISEASES OF AQUATIC ORGANISMS Vol. 7: 203-210, 1989 Published December 7 Dis. aquat. Org.

A specific DNA hybridization probe for detection of Pasteurella piscicida

Jiang Zhao, Takashi Aoki*

Department of Fisheries. Faculty of Agriculture, Miyazaki University, Miyazaki 889-21, Japan

ABSTRACT: A 692 (bp) DNA fragment from the bacterial fish pathogen Pasteurella piscicida was cloned into pUC9 and used as a hybridization probe for the identification of P, piscicida. The radiolabeled probe hybridized with itself, but did not hybridize in colony hybridization with other fish pathogens (including Aeromonas hpdrophila,A. salmonicida,Edwardsiella tarda,Pseudomonas angul- liseptica, Vibrio anguillarum and Yersinia ruckeri), or with other related organisms (Haen~ophilus influenzae, Pasteurella haemolytica, and P. multocida). Photobiotin-labeled probe hybridization detected P. piscicida chromosomal DNA by Southern and dot hybridizations. The radiolabeled probe directly detected P. piscicida on nitrocellulose filters smeared with infected kidney and spleen tissue of yellowtail Seriola quinqueradiata.The 3"P-labeled DNA probe was capable of detect~ng3.9 ng of purified DNA and lo5cells of P. piscicida. The cloned specific DNA probe can be used for rapid detection and identification of P. piscicida.

INTRODUCTION MATERIALS AND METHODS

Pasteurella piscicida is the causative agent of Bacterial strains and plasmid. The bacterial strains pseudotuberculosis in yellowtail Serjola quin- used are listed in Table 1. Twenty-nine strains of Pas- queradiata (Kimura & Kitao 1971), one of the most teurella piscicida were collected from diseased yellow- important causes of mortality in cultured yellowtail. tail in various areas of Japan and 1 strain from white The identification of P. pisciada has been based on its perch, Morone anlericana, in the USA(Janssen & Sur- morphological and biochemical characteristics. How- galla 1968). One P, piscicida strain (KG8601), isolated ever, classification using these features is cumbersome in 1986 from Kagoshima in Japan, was used for the and time-consuming. The different illorphological and cloning of its chromosomal DNA. Other fish pathogens biochemical characteristics of the species of (4 strains of Aeromonas hydrophila, 4 of A. sal- are prescribed by their genes. Recently, randomly monicida, 4 of Edwardsiella tarda, 2 of Pseudomonas cloned chromosomal DNA fragments and cloned genes anguilliseptica, 4 of Vibl-io anguillarum, and 2 of Yer- encoding species-specific characteristics have been sinia ruckeri), were used in testing the specificity of used as specific hybridization probes for rapid identifi- the probe, as were 1 strain each of Haemophilus cation of organisms (Salyers et al. 1983, N~shibuchiet influenzae, Pasteurella haemolytica and Pasteurella al. 1985, Carter et al. 1987, Mifflin et al. 1987). By using molutocida. Escherichia coli Strain JM103 (Maniatis et a species-specific DNA probe to a specific al. 1982) was used as the host for propagating the sequence of chromosomal DNA from Vibrio anguil- plasmid. The plasmid, pUC9 (Maniatis et al. 1982), larun~,we easily and rapidly identified V. anguillarunl was used for the cloning of P. piscicida chromosomal using colony hybridization (Aoki et al. 1989). DNA. In the present study, we describe a species-specific Media and growth conditions. Pasteurella pisclcida DNA fragment of chromosomal DNA from Pasteurella strains were cultured at 25 "C in nutrient (N) broth piscicida which, by direct hybridization, specifically (beef extract: 15 g; polypeptone: 10 g; NaC1: 5 g; distil- detects the causative agent in diseased marine fish. led water: 1 1; pH: 7.2) supplemented with 0.3 % yeast extract and 1.5 % NaC1. The other Pasteurella species and Haemophilus influenzae were grown at 37 "C in

Addressee for correspondence heart infusion broth (HI, Nissui Co. Ltd.) containing 5 O/o

Inter-Research/Printed in F. R. Germany 204 Dis. aquat. Org. 7: 203-210, 1989

Table l. Bacterial strains used in this study

Bacterid Slrdin Hvst Source

Aeromonas h ydrophila ATCC15467 Schubert (19741 Wakabayashi et al. (1981) 1;; ] Eel Nomura & Aoki (1985) A-54 Nomura & Aoki (1985) Aeron~onassalmonicida ATCC14 174 Brooktrout ltao et al. (1985) N8004 OB8101 Amago HR8101 l Edwardslella tarda SA83 18 Thls study Flounder NG8407 t M2840 1 Eel E-l 1-2 l Haemophilus influenzae NCTC8143 Kilian & Blberste~n(1984) Fasteul-ella haen~olytica rJCTC338G Carter (1984) Pasteurella multocida NCTC10322 Carter (1984) Pasteurella pisac~da El-18218 KG8206 KG8232 MEP8215 EH8306 EH8310 M28303 M28309 NG8304 EH8405 EH84 11 EHP84133 EHP84 135 SA8406 SA8407 Yellowtail This study KG84305 EHP85468 EHP85477 WKY8575 NZ8574 MZ8575 SA8514 SA85 16 KG8601 EH860 1 EH8606 EH86 10 NG8609 M286 15 Snieszko Whlte perch Janssen & Surgalla (1968) Pseudornonas angullliseptica NCMB1949 Nakajima et al. (1983) Eel ET-2 l Nakajima et al. (1983) Vibrio anguillarun~ ATCC 19264 Baumann et al. (1984) PT834 1 Aoki et al. (1989) PT-24 } AYU Kitao et al. (1983) ET- l Eel htao et al. (1983) Yersinla rucker) 114 I Stave et al. (1987) Rainbow trout 11-29 I Stave et al. (1987)

fildes extract (Oxoid Ltd.). Vibrio anyr~illarumstrains ruckeri were cultured at 25 "C in N broth. Escherichia were cultured at 25 "C in HI broth containing l '?LNaC1, col; was grown at 37 "C in Luria-Bertani broth (LB) Pseudomonas anguilliseptjca and Aeromonas salmon- (polypeptone: 10 g; yeast extract: 5 g; NaCI. 5 g; distil- icida were cultured at 20 'C in HI and N broth, respec- led water: l l; pH 7.0) (Maniatis et al. 1982). Each tively. A. hydrophila, Edwardsiella tarda, and Yersinja medium also contained 1.5 O/O agar to isolate organisms. Zhao & Aoki: A DNA probe for PasteureUa pksacida 205

Isolation of DNA. The chromosomal DNA of Pas- 7.8, and 3.9 ng of DNA were blotted on nitrocellulose teurella piscjcida, Strain KG8601, and the fish-patho- filters. gens Aeromonas hydrophila A-10, A. saln~onicjda Hybridization with 32P labeled DNA probe was car- HTCC14174, and Vibrio anguillarum PT8341 were iso- ried out on filters at 65 "C for 36 h in 4 x SSC containing lated by previously reported methods (Silhavy 1984). 10 X Denhardt's solution (l '10 Ficoll, 1 % polyvinylpyr- Plasmid DNA was prepared by the alkaline lysis rolidone, 1 % bovine serum albumin), 0.5 % sodium method of Birnboim & Doly (1979). Both isolated dodecyl sulfate (SDS), and 1.5 mg ml-' heat-denatured chromosomal DNA and plasmid DNA were purified by salmon-sperm DNA. Filters were washed with 2 X SSC centrifugation to equilibrium in cesium chloride- + 0.1 % SDS, dried, and subjected to autoradiography. ethidium bromide gradients. Hybridization with the photobiotin-labeled probe was of DNA probe. The chromosomal carried out at 42 "C for 12 to 18 h in a hybridization DNA of Pasteurella piscicida was digested with Hind solution containing 45 % formamide, 5 X SSC, l x 111. The vector plasmid, pUC9, was also digested with Denhardt's solution, 25 mM sodium phosphate (pH 6.5), the same enzyme and then dephosphorylated with 5 YO dextran sulfate, and 0.2 mg ml-' heat-denatured bacterial phosphatase (Takara Shuzo Co. Ltd, Kyoto, salmon-sperm. After hybridization, the probe-target Japan). The digested DNA was mixed together and DNA hybrid was detected with conjugate dyes of the ligated with T4 ligase (Nippon Gene Co. Ltd, Osaka, B1.u GENE (Bethesda Research Laboratories) strep- Japan). The recombinant plasmids were transformed to ta.uidin-alkaline phosphatase. Escherichia coli JM103, and transformants selected on Colony hybridization. The organisms were inocu- L-agar (Maniatis et al. 1982) supplemented with 50 yg lated onto autoclaved, gridded nitrocellulose filters ml- ' ampicillin and X-gal (5-bromo-4-chloro-3-indolyl- (Toyo Roshi Co. Ltd, Japan) overlayed on an agar plate. P-D-galactopyranoside). After incubation, the filter was removed from the plate Labeling of DNA probe. A cloned DNA fragment and treated with NaOH, neutralized, baked, and hy- with a molecular weight of about 0.7 kilobase (kb) was bridized with probe DNA. Hybridization reactions selected, at random, for use as the probe, and was were carried out by the method of Grunstein & Hog- isotopically labeled with (CV-~*P)~CTP(New England ness (1975). Nuclear Corp., Boston, USA) by nick translation (Rigby The minimum number of Pasteurella piscicida (Strain et al. 1977). KG8601) cells detected was determined by hybridi.za- The DNA probe was labeled with photobiotin tion with the same probe. Bacterial cells diluted 10-fold (Biotechnology Research Enterprises S.A. Pty Ltd), and from 10"o 10' were spotted on a nitrocellulose filter. the Blu GENE nonradioactive DNA detection system DNA hybridization was thcn performed as described (Bethesda Research Laboratories, USA) was used. by Grunstein & Hogness (1975). Probe DNA was mixed with equal volumes of photo- Detection of Pasteurella piscicida in fish. Nineteen biotin acetate in an Eppendorf tube, irradiated for 20 diseased and 3 healthy Seriola quinqueradiata were min with a 400W lamp from a distance of 10 cm, and obtained from an experimental fishery station. These diluted to 100 p1 with TE buffer (10 mM Tris HCl, 1mM fish were dissected and examined to determine EDTA, pH 8.0) followed by 100 111 2-butanol. The mix- whether nodules of kidney and spleen, characteristic of ture was centrifuged and the 2-butanol phase dis- the pseudotuberculosis, were present in the kidney and carded. Photobiotin-labeled DNA was purified by 3 spleen of fish. Kidney and spleen tissue from each fish successive ethanol precipitations, and finally resus- was sampled using a platinum loop and smeared onto pended in TE buffer and stored at -20 'C. nitrocellulose filters. Hybridization was then carried Southern and dot blot hybridization. For Southern out with the same probe and by the same method as blot hybridization, chromosomal of Pasteurella used in the colony hybridization procedure. At the pjscicida, Aeromonas hydrophila, A, salmonicida, and same time, the causative agent was isolated on agar Vibrio anguillarum were cleaved by Hind 111, and elec- media and identified. trophoresed in 0.8 '10 agarose gel at 80 mA for ca 3 h. Restriction sites and nucleotide sequence of the Electrophoresed gels containing digested DNAs were probe. A cloned DNA fragment of Pasteurella pis- transferred to nitrocellulose filters (0.45 pm, Schleicher cicida, which was chosen at random and used as the & Schuell Inc., FRG) using a transfer pyramid for probe, was digested by various endonucleases: AvaII, Southern blotting (Southern 1975). BamHI, EcoRI, HapII, HincII, HindIII, HinfI, HpaI, RsaI, For dot blot hybridization, chromosomal DNA from San, Sau3A1, SmaI, TaqI, and Xhol (Takara Shuzo Co. Pasteurella piscicida was denatured by heating at 90 "C Ltd, Nippon Gene Co. Ltd, Japan). Nucleotide for 5 min and diluted from 125 pg to 1.95 pg ml-' with sequences of this cloned DNA fragment were deter- 2 X SSC (1 X SSC = 0.15 M NaCl + 0.015 M sodium mined using pUC9 by the dideoxy method of Hattori et citrate, pH 7.0). Samples of 250, 125, 62.5, 31.3, 15.7, al. (1985). 206 Dis, aquai. &g. 7: 203-210. 1989

Panel 1 Panel 2 ABCDE CDE

Fig.1. hybridization of "'P- Iabeled cloned DNA fragment from Pas- teurella pisciada with chromosomal DNAs of various fish pathogens. Panel 1: agarose gel electropherogram ol chromo- somal DNAs d~gestedby HindlII. Panel 2. autoracfiogtam of a n~trocellulose filter blotted with DNA from Panel 1 and prob- ed wlth 'IP labeled cloned DNA of P p~snada.Lane A. standard molecular size of X DNA digested by HmdIII, Lane B chromosomal DNA of P. p~scicida:Lane C; chromosomal DNA of Vibno angulllarum; Lane D. chromosomal DNA of Aeromonas salmonicida; Lane E: chromosomal DNA of A. hydrophild

RESULTS Further colony hybridization experiments were car- ried out to determine the speciflcity of the 0.7 kb frag- Screening of DNA probe ment. Four colonies of different strains of Pasteurella piscicida and l of Escherichia coli (carrying the recom- The molecular weights of the cloned DNA fragment binant plasmid contained the 0.7 kb fragment from P. obtained from 14 recombinant plasmids ranged from piscicida) hybridized with the 32P-labeled probe (Fig. 2). 0.4 to 4.0 kb. A cloned DNA fragment with a molecular Others, i.e., Aeromonas hydrophila, A. saln~onicida, size of about 0.7 kb was chosen as the probe for experi- Edwardsiella tarda, Pseudornonas anguilliseptica, Wb- ments. rio anguillarum, and Yersinia rrlckeri did not hybridize (Fig.2). No cross hybridization was seen between the probe and closely related Haemophilus influenzae,Pas- Specificity of DNA probe teurella haemolytica, and P. nlultocida (Fig.3). Fig. 4 shows that the probe hybridized, not only with The specificity of the 0.7 kb fragment was verified by 29 strains of Pasteurella piscicida isolated from Seriola Southern blot hybridization with chromosome DNAs of quinqueradiatil cultured in various districts of Japan, various fish pathogens. The radio- and photobiotin- but also with the 1 strain of P. piscicida isolated from labeled probes of the 0.7 kb fragment only hybridized white perch, A.lorone americana, in the USA.(Janssen with themselves. Probe DNA did not hybridize with & Surgalla 1968).Photobiotin-labeled probe DNA used chromosomal DNA from other fish pathogens tested for colony hybridization was unsuccessful due to the (Fig 1). high background it produced. Zhao & .\oki A DNA probe for Pasteurrll~rp~scir~da 207

Fig.2. Colony hybridization of "P-labeled cloned DNA fragment from Pasl~[lrrlld ~x.sr.icidawith chron~osomdlDNA of varl- ou5 fish pathogens. DYA sanipl~\of t~ac- 123456 7 8 9 trr~alstralns located above numbers. 1 to

3. \'ihno anguillerun~:5 to $3:..'I~rornonas l~!.droph~l~j:9 to 12: ,,l. si11nionic.ida; 13 to m a 16: Erlni~rd.siello tilrda; 17 to 20. P&s- 10 11 12 13 14 15 16 17 78 te~1rc8llapiscicida; 21 to 22 Y'ersinia ruck- eri; 23 to 24: Pseudononils anguillisept~ca; 44 25: Escherichia coli Jh1103; 2G: E coli 19 20 2 1 2 2 23 24 2 5 2 JM103 carrying recombinant pLlCA-0.7 kb a fragment from P. piscicida

Quantitation of DNA and bacteria containing probe The sensitivity of the probe technique was deter- mined by dot blot hybridization with radio- and photo- biotin-labeled probe DNA. The 32Plabeled DN.4 probe detected 3.9 to 250 ng of purified DNlZ in Pasteurella piscicida.The same amounts of DNA were detected by photobiotin-labeled probe DNA. Again, there was no hybridization with chromosomal DN.4s of the other fish pathogens, Aerornonas hydr-ophila, A.salnionicida and Vibrio anguillal-un~(Fig. 5). nulnber of P~~~~~~~~I~plscicida cells detectable Fig. 3. Colony hybridization of '-'P-lilbclcd cloned DNA frag- Inenl Irrjm P,isteumlla piscicitiii with closcly related patho- by the probe determl"ed by hybridi7.a- gcns. 1: Pai!r~#rrrIlc,~nr~ltocid~i NCTC:10322, 2. 1'. haenlolytlrd tion 'using radiolabeled probe DNA and was from 10'' to NCTC9380; 3: Ffdenrophilus influrnzi~eNCTC8143; 4: Pas- 10"ells (Fig. 6). teurc!ld pisrldda KG8601; 5: P. piqcic.~ciaSnleszko

Fig. 4. Colony hybridization 01 '"P-labeled cloned DNA fragment from Pastetirelld piscicida with d~fferentstrains of P. piscicida isolated from various areas. 1 to 30 (except 23): different strains of P.pjscicida isolated from diseased Sei-iola ql~inqr~eradiatafrom various locat~onsIn Japan: 24: straln of P.p~sclcida isolated from while perch, A?orone aniericana, In the [:SA; 31: Eschenchia col1 JM103; 32: L: coli 3x1103 casrvlng rrcombinant pLlC9-0.7 kb fragnicnt from I? pisclrrda 208 Dis. aquat. Org 7: 203-210, 1989

Panel 1 Panel 2

250 125 625 31.3 15.7 250 125 82.5 31.3 15.7 7.8 3.9

(ng DNA) (ng DNA) Fig.5. Dot blot hybndizatiofl of radio- and photobiom-labeled probe wth chromosomal DNAs of varlous fish pathogens,Panel 1: hybridization of 3aP-labeleddoned fragment DNA fmm Pasteurella p~scicida Panel 2: hybridization of pho-tobiotin-lakled fragment DNA born P,piscfcida. kule A: chromosod DNAcf Lfi/:br:oanguiIIanun, Lane B: chinosofftal DNA of P.plsciuda, Lane C: chromosomal DNA of Aerornonas hydrophila;Lane D: chromosornaI DNA of A. s&nonMde

Fig. R. Minimum number of of Pasteurella plscicida cells detectable using 3'P- 102 labeled DNA fragment

Analysis of DNA Probe base pairs (bp) and the guanine + cytosine (G +C) content was 39.2%. Fig. 7 illustrates the endonuclease restriction sites and the nucleotide sequences of cloned DNA frag- ment of Pasteurella piscicida, (i.e., the probe). The Detection of Pasteurella piscicida cloned DNA fragment had single HapII, HindIII, and in clinical specimens Tag1 sites, and double sites for RsaI; there were no restriction sites for the other endonucleases, i. e., All filters from diseased yellowtail proved positive, AvaII. BamHI, EcoRI, HincII, HinfI, HpaI, PstI, San, both by radiolabeled probe and by culture for Pas- SauSAI, SmaI, and XhoI. The fragment contained 692 teurella piscicida. Some hybridizations results are

KGCTTGTAGCTCTTGTGGAGTAATGCTGACAGAAGAAC~Hind m

TATCTCAACCTGAAATAGAAAACTGCGGCCTAGAGCTCACTTTTAGCCCCTCATGCTCGCTAA

TTTAGCGGGCAATTTTTATTTTATATCACTACAATACATATTGTATTGGCCATATCTATGAGT Ha rf AAAcAcAGcTAGAAAAAAGAAGAAGAAAccAcAAAGAAATGGcGTc~TTcAGcTTcAGTGc

TTTTGATAGCTATGAGCAATATGAACACATGATATGTCATCAGTGTTAAATGCCAATTGATAC

TGCACCACCAAAGATCACGATGAAGAAATAACACCAATTTATCAATATCTTATGATAAGTTTG

GTGACACAEACTACTGCATTCAAATTACATGAAGTATTAATCTCGCTTGCTCATTAGCAGA GCGAGATGG~CATGACATACTAACAGTGATATGCATGTGT~~TAGAG~~A~~AAA~T~AT~TRsaI

Fia. 7. Restriction sites and nucleotide TTAATAAAGATGAGCTTGGAAAAATATCTCACGCACTGTGGCGATAACATCACCACCAATCAA - RsaI sequence in the 692 base pair fragment ATAGAGTGTATAGAAAAAATGCTTCGCTTGCGGTACCAGCAAAGTGGGCAGTAAGCAmACGA of DNA from Pasteurella piscicida (the HindIII probe) ATGTGAAAACCCTTATTGTGAGCACCGCAAAGTCATCTATAACTCTTGTAAGAGTA~CTT Zhao & Aoki: A DNA probe for Pasteurella piscjcida 209

Fig 8 Autoradiogram of "P-labeled cloned DNA fragmeht from Pasteurella p~sactdahybndized on ruttocellulose 111- ter with smeared krdney and spleen tis- sues from diseased [i.e.. 1 to 6) and heal- thy (7 to 9) Serida quinquexadiata. For each yellowtail Smears 1 to 5 represent kidney twe, Smear 6 to 9 spleen tissue shown in Fig. 8. The hybridization signal strength All smears from diseased yellowtail yieled positive appeared to be a function of pathogen concentration in reactions, the strength of reaction apparently being tissues. Healthy fish proved negative both by the probe related to the number of P. piscicjda cells in the smear. and culture techniques. We did not determine the detecting limit of the filter hybridization procedure for the pathogen, but we think that it is lower than the 10%ells per sample detected by DISCUSSION the dlrect hybridization method in this study. This method allowed us to rapidly detect and identify P. A 692 bp fragment of chromosomal DNA from Pas- piscicjda in infected tissues and to rapidly identify teurella piscicida was cloned in the pUC9 plasmid and colonies of the pathogen on culture plates. used as a probe for detecting P. piscicida. The probe The photobiotin-labeled probe used in these experi- only hybndized with itself. There was no hybridization ment was successful in detecting the chromosomal DNA with any other tested fish pathogens or with closely of Pasteurella piscicida by dot blot hybridization. How- related organisms. The 692 bp nucleotide sequence ever, the photobiotin-labeled probe could not be used to differed from any of the sequences in the nucleotide detect P. piscicida by colony hybridization. In colony sequence library of GENAS (Kuhara et al. 1984). hybridization, some component of the bacterial cells on The probe was successfully used to detect Pas- the nitrocellulose filter appeared to bind, non-specifi- teurella piscjcida on filters smeared with kidney and cally, with the coloring reagents of the detection system, spleen tissues from diseased Seriola quinqueradiata. thus resulting in unacceptably high background signals. 210 Dis. aquat. Org. 7. 203-210, 1989

The colony hybridization technique is more easily Mizuno, Y. (1983). Serotyping of Vibrio anguiflarum isolated and quickly applied than the dot blot hybridization from diseased freshwater f~shin Japan. J. Fish Dis. 6: method. However, radiolabeled probes are generally 175-181 Itao, T., Yoshida, T., Aoki, T., and Fukudon~e,M. (1985). unacceptable for routine clinical use and further Characterization of an atypical Aerornorlas salrnonicida development of detection procedures based on non- strain causing epizootic ulcer disease in cultured eel. Fish lsotope labellng is, therefore, still required. Pathol. 20: 107-1 14 Kuhara, S.. Matsuo. F., Futamura, S., Fujita, A., Shinohara, T.. Takagi, T., Sakaki, Y (1984). GENAS: a database system Acknowledgements. This research was supported in part by a for sequence analysis. Nucleic Acids Res. 12: Grant-in-Aid from the Ministry of Education. Science and 89-99 Culture (625660199) of Japan. We thank Professor Tadatoshi Maniatis, T., Fritsch, E. 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Responsible Subject Editor Dr T Evelyn, Nanaimo, B.C. Manuscript first received: November 4. 1988 Canada Revised version accepted: September 27, 1989