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Applied and Environmental Microbiology, January 2004, p. 527-534, Vol. 70, No. 1
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.1.527-534.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Department of Bioengineering, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
Received 16 April 2003/ Accepted 22 September 2003
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Rapid and sensitive detection of E. coli O157:H7 is essential for minimizing the outbreak of infection, for surveillance, and for sanitary supervision. Three methods, culturing, PCR analysis, and immunoassay, are available for the detection of E. coli O157:H7. These culture methods are laborious and expensive and require a minimum of 3 days to perform (4). PCR analysis of E. coli O157:H7 has often been aimed at detecting the genes for Stx1 and Stx2 (6). Although these assays may be useful for the examination of human or animal fecal samples, their usefulness for the examination of environmental samples is limited due to the widespread presence of these genes in nonpathogenic bacteria. Enzyme immunoassays have also been used for detecting E. coli O157 in enrichment cultures of food and environmental samples (2). Although sensitive, these assays are laborious and expensive and tend to yield positive results that cannot be confirmed by culturing (2).
E. coli O157:H7 enters a viable but nonculturable (VBNC) state after a lengthy exposure to oligotrophic fresh- and seawater at an ambient temperature. Although the role of VBNC cells in food or water safety is not fully known, VBNC E. coli O157:H7 was shown to occur widely in a natural freshwater environment in Tokyo, Japan (12). Direct viable cell counts of E. coli O157:H7, determined by acridine orange staining, remained essentially the same for 12 weeks at 25°C, whereas viable cell counts on tryptic soy agar plates decreased to undetectable levels within 12 weeks (7). Direct viable cell counts, however, can be applied only to axenic cultures and not to E. coli in natural environments, where mixed bacterial populations exist. Conventional culture methods also fail to detect VBNC E. coli O157:H7 in the natural environment.
A virulent phage (PP01), previously isolated from swine stool samples, was found to infect E. coli O157:H7 strains with a high specificity (15). In phages of the T2 family, the gene 38 product (Gp38), which is present at the tip of long tail fibers, is the determinant of host range (19). Analysis of deduced amino acid alignments of the tail fiber proteins revealed that the PP01 phage is related to the T2 phage. Moreover, the specific recognition of the E. coli O157:H7 OmpC protein by Gp38 determines PP01's host range (14). In this study, PP01 was used for the detection of E. coli O157:H7 in viable and VBNC states. One of the outer capsid proteins, named small outer capsid (SOC) protein, was fused with green fluorescent protein (GFP). Labeled recombinant PP01 phage provided a rapid and sensitive method for E. coli O157:H7 detection.
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In batch cultures, E. coli O157:H7 ATCC 43888 was cultured overnight in 2 ml of Luria-Bertani (LB) broth at 37°C with shaking (120 rpm). The optical density of the medium at 600 nm (OD600) was measured with a Klett spectrophotometer (Hitachi High-Technologies Corp.) to estimate the cell concentration. Bacteriophage PP01 infection at a multiplicity of infection (MOI) of 2 was performed at an OD600 of 0.1. For dilution and preservation of the phage, SM buffer (10 mM MgSO4, 100 mM NaCl, 0.01% gelatin, and 50 mM Tris-HCl [pH 7.5]) was used. Phosphate-buffered saline (PBS) was used for the phage binding assay.
Sequencing of phage DNA.
The plasmids used in this study are listed in Table 1. PP01 phage DNA was extracted with phenol-chloroform-isoamyl alcohol (25:24:1) and precipitated with ethanol. PP01 phage DNA was diluted with distilled water and used as a template for PCR. The oligonucleotide primers used for PCR and sequencing are listed in Table 2. The DNA fragment encoding PP01 SOC protein was amplified by use of the primer set of g56+ and mrh-. The primer set was designed based on the DNA sequence of T2 phage genome DNA. The PCR fragment was digested with PstI and XbaI and inserted into the PstI and XbaI sites of pUC118 to obtain pUC-SOC, which encodes the PP01 soc gene and its surrounding region. Sequencing of the cloned DNA was performed by using a Thermo Sequenase fluorescence-labeled primer cycle sequencing kit and a 7-deaza-dGTP kit (Amersham Pharmacia Biotech). The sequencer used was DSQ-2000L (Shimadzu, Kyoto, Japan).
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TABLE 1. Phages, E. coli strains, and plasmids used in this study
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TABLE 2. Oligonucleotide primers used for PCR
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The DNA fragments encoding PP01 soc, its upstream region (about 200 bp), and its downstream region (about 100 bp) were amplified by use of the primer sets g56+-socC- and socC+-mrh-, respectively, with the PP01 phage genome as the template. The two PCR fragments were digested with XbaI-KpnI and KpnI-PstI, and the two fragments were inserted into the XbaI and PstI sites of pUC118 to produce pUC-SOC/KpnI. Then the gfp gene digested with KpnI from pQB2 was inserted into the KpnI site of pUC-SOC/KpnI to produce pUC-SOC/GFP.
Homologous recombination.
The protocol used to integrate gfp into the phage genome is outlined in Fig. 1. E. coli O157:H7 (ATCC 43888) was transformed with two plasmids, pUC-GFP/SOC and pUC-SOC/GFP, by electroporation. The transformant E. coli cells were incubated in LB medium supplemented with 50 mg of ampicillin per liter. When the OD600 reached 0.1, the PP01 phage was added at an MOI of 0.01. After 5 h of incubation, chloroform was added to lyse the cells and the culture was centrifuged to remove cell debris. The cell lysate was diluted with SM buffer to obtain a phage concentration of 104 PFU/ml. The diluted phage lysate was mixed with E. coli O157:H7 in 0.7% agar and overlaid on an LB plate. The recombinant phage was detected by plaque hybridization with a digoxigenin (DIG)-labeled probe. The plaques were transferred to a nylon membrane (Roche Diagnostics) and immersed in denaturing solution (0.5 M NaOH, 1.5 M NaCl) for 5 min, in neutralizing buffer (1.0 mM Tris-HCl, 1.5 M NaCl, pH 7.5) for 15 min, and in 2x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7.0) for 10 min. Phage DNA was cross-linked on the membrane by UV radiation (1,200 J/cm2) and incubated in 2 mg of proteinase K solution per liter for 1 h at 37°C. The membrane was rinsed with distilled water and prehybridized in DIG-Easy-Hyb buffer (Roche Diagnostic) for 1 h at 55°C. The membrane was hybridized with the DIG-labeled gfp probe overnight at 55°C. The probe DNA was amplified by use of a PCR DIG-Probe-Synthesis kit (Roche Diagnostic), using pQB2 as the template and gfp+(KpnI) and gfp- as the primer set. The hybridized membrane was washed twice with 2x SSC containing 0.1% sodium dodecyl sulfate for 5 min at room temperature and once with 0.1x SSC containing 0.1% sodium dodecyl sulfate for 15 min at 68°C. Then the hybridized spot was detected by use of a DIG-Luminescent-Detection kit (Roche Diagnostic).
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FIG. 1. Outline of the homologous recombination process leading to insertion of gfp upstream (A) or downstream (B) of the major capsid protein gene soc. The multiplication signs indicate the recombination events (double crossover) between phage DNA (top) present in infected cells and pUC-GFP/SOC (A) or pUC-SOC/GFP (B).
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Phage adsorption assay.
E. coli O157:H7 cells in the logarithmic growth phase (107 CFU/ml) were preserved on ice until use. The cell culture (400 µl) was prewarmed at 25°C for 10 min and mixed with the same amount of phage solution (105 PFU/ml) in SM buffer. The mixture was incubated at 25°C. After infection, 110 µl of the mixture was sampled periodically, and the samples were centrifuged (174,000 x g, 1 min, 4°C). The phage titer of the supernatant was determined by plaque assay using E. coli O157:H7 (ATCC 43888), and the phage titer at time zero was defined as 100%.
Phage stability under alkaline conditions.
Phage solution (107 PFU/ml; 10 µl) was mixed with 990 µl of alkaline SM buffer (pH 10.6) and incubated at 37°C. The mixture was sampled periodically and diluted 1:100 with SM buffer (pH 7.5). The stability was estimated by comparing the phage titer in alkaline SM buffer with that in neutral SM buffer (pH 7.5).
Detection of E. coli O157:H7 by using GFP-labeled PP01 phage.
E. coli O157:H7 cell culture (107 CFU/ml) in the logarithmic growth phase was allowed to stand on ice until use. The cell culture was prewarmed at 25°C for 10 min and then mixed with the same amount of phage solution (5 x 109 PFU/ml). The mixture was allowed to stand at 25°C for 10 min, followed by centrifugation (17,400 x g for 1 min at 4°C), washing with PBS, and resuspension in PBS. Luminescent E. coli O157:H7, due to adsorbed GFP-labeled PP01 phage, was observed under an epifluorescence microscope (BX60; Olympus, Tokyo, Japan) equipped with a filter (U-MWIBA/GFP; Olympus). Photographs were taken with a digital still camera, with an exposure setting of 1/5 s for phase-contrast microscopy and 2 s for fluorescence microscopy.
Establishment of VBNC state.
An E. coli O157:H7 cell culture (107 CFU/ml; 30 ml) in the logarithmic growth phase was centrifuged (12,000 x g for 3 min at 4°C) and resuspended in the same amount of PBS. After 1 week of incubation at 4°C, cell viability was estimated by counting of colonies on LB plates.
Nucleotide sequence accession number.
The nucleotide sequence data reported in this paper for soc will appear in the DDJB/EMBL/GenBank nucleotide sequence databases under accession number AY247798.
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FIG. 2. Nucleotide sequences of upstream and downstream soc regions from phages PP01, RB15, T4, and T2. Dashes indicate nucleotides that are deleted. Completely conserved nucleotides are shown in dark gray, and partially conserved regions are shown in light gray.
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To introduce gfp adjacent to soc, homologous recombination between the plasmid and the phage genome was conducted. The frequencies of recombination were approximately 0.3% for PP01-GFP/SOC and 0.5% for PP01-SOC/GFP. Several positive plaques, which emitted green fluorescence, were isolated from the agar plate and purified. Integration of gfp into the phage genome was confirmed by plaque hybridization and sequencing of the PCR-amplified DNA region around the soc-gfp and gfp-soc junctions (data not shown).
Characterization of GFP-labeled PP01.
The turbidity and fluorescence changes of the E. coli O157:H7 culture after phage infection were measured (Fig. 3). Three phages, PP01-wt, PP01-GFP/SOC, and PP01-SOC/GFP, were added to the medium at time zero at an MOI of 0.1. Incubation was performed at 28°C to increase the fluorescence intensity. After a 1.5-h incubation of E. coli O157:H7 with one of the phages, a decrease in OD600 was observed. Since the LB medium contains self-luminous compounds, the initial fluorescence intensity of the culture was 125 (no dimension). The PP01-wt infection did not influence the fluorescence intensity of the culture. On the other hand, PP01-GFP/SOC and PP01-SOC/GFP infections increased the fluorescence intensity of the culture. Fluorescence intensity of the culture reached 220 (no dimension) 3 h after infection of PP01-GFP/SOC and remained almost constant. The maximum fluorescence intensity of the PP01-GFP/SOC culture was higher than that of PP01-SOC/GFP culture.
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FIG. 3. (A) E. coli O157:H7 lysis by PP01-wt (squares), PP01-GFP/SOC (circles), and PP01-SOC/GFP (triangles). (B) Phage-induced fluorescence of the culture. A 200-µl E. coli O157:H7 overnight culture was inoculated into 20 ml of LB medium at time zero and incubated at 28°C. When the OD600 of the culture reached 0.2, 200 µl of phage containing PBS was added at an MOI of 0.04.
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TABLE 3. Host range of GFP-labeled PP01 phage
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The ka value (milliliters per CFU per minute) is an adsorption rate constant. Under low-MOI (<0.01) conditions, Bfree can be assumed to be constant, that is B0, until lysis of the host cells. Therefore, integration of equation 2 is as follows.
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According to equation 3, the time course of the free phage concentration (Pfree) in the culture provided ka(B0) and ka, which represents phage adsorption affinity on the host cell. An E. coli O157:H7 cell culture (107 CFU/ml) in the early logarithmic growth phase was mixed with the same amount of one of the three phage solutions (105 PFU/ml) at 25°C. Pfree in the mixture was analyzed and plotted against the incubation time to estimate the ka(B0) and ka values (Table 4). The ka value of PP01-wt was smaller than those of PP01-GFP/SOC and PP01-SOC/GFP, indicating that the GFP fusion to SOC enhanced the phage binding affinity for the host cells.
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TABLE 4. Phage adsorption assay results
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FIG. 4. Phage stability in alkaline solution. Three phages, PP01-wt (squares), PP01-GFP/SOC (circles), and PP01-SOC/GFP (triangles), were incubated in SM buffer (pH 10.6) at 37°C, without shaking. Survival ratios were estimated by comparing phage titers in the alkaline SM buffer with those in neutral SM buffer (pH 7.5).
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FIG. 5. Optical microscope images (upper panels) and fluorescence microscope images (lower panels) of E. coli O157:H7 (A, B, D, and E) and E. coli K-12 (W3119) (C). The bacteria (107 CFU/ml) were incubated at 25°C for 10 min with PP01-SOC/GFP (A, C, D, and E) or PP01-GFP/SOC (B) (1010 PFU/ml). The E. coli cell states were logarithmic growth phase (A to C), VBNC (D), and dead (E). Scale bar, 2.5 µm.
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FIG. 6. Correlation of E. coli O157:H7 percentage in cell mixture. A mixture of E. coli O157:H7 and E. coli K-12 (W3110) cells was incubated with PP01-GFP/SOC for 10 min at 25°C. The observed percentages were based on microscope counts and were plotted against calculated percentages from the initial concentrations of E. coli O157:H7 and K-12 cells.
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The PP01 phage used in this study was isolated from a swine stool sample. The finding that PP01 phage is a member of the T-even phage family enables us to apply genetic information on T-even phages to gene manipulation of PP01. T4 SOC is used as the platform for T4 phage display (10, 18). Since the high amino acid homology between PP01 SOC and T4 SOC was identified, PP01 SOC was also assumed to be available for PP01 phage display. Since the binding site of the SOC protein for the phage capsid protein is not located in the N or C terminus of SOC, foreign protein fusion to SOC does not disrupt the interaction between SOC and the phage capsid (10, 18). Gene alignments around soc for T-even phages are as follows: for T4, g56-g69-soc; for T2, g56-soc.2-soc.1-soc; and for RB15, g56-soc (17). The similarity of gene alignment around soc in PP01 and T2 also supported the finding that PP01 is a member of the T2 family. Even though PP01 is closely related to T2, the host cell specificities of these two phages are discriminative. The host range of PP01 is limited to E. coli serotype O157:H7 (16). Since the phage capsid is not involved in host cell recognition, modification of SOC did not change the host range of PP01. The adsorption rate constants, or ka values, of the recombinant phages, PP01-SOC/GFP and PP01-GFP/SOC, were larger than that of wild-type PP01. The number of SOC molecules present on the capsid was estimated to be 840 (9). Fusion of GFP to SOC enlarged the surface area of the capsid and may increase the collision probability for the recombinant phage and its host. A precise investigation of phage stabilities under various conditions, such as different temperatures and ionic strengths, was necessary for the preservation of the phage.
Infection of culturable E. coli O157:H7 cells by GFP-labeled phages increased the fluorescence intensity of the culture. The initial fluorescence was derived from the added phage and from auto-fluorescence of E. coli O157:H7 and the LB medium. Following a 1-h incubation with the recombinant phage, the fluorescence intensity of the culture increased gradually and reached a plateau at 3 h of incubation. The increase in fluorescence intensity reflected replication of recombinant progeny phage in cells. On the other hand, when the recombinant phages were added to VBNC or pasteurized E. coli O157:H7, no increase in fluorescence intensity was observed (data not shown). It is obvious that the host cell function is indispensable for phage replication in cells. Recombinant phages recognized both VBNC and pasteurized E. coli O157:H7 cells (Fig. 5). Based on these observations, discrimination of culturable cells from VBNC or dead cells may be possible by monitoring the change in the culture fluorescence intensity or by modifying the MOI. Under low-MOI conditions, the fluorescence intensity of phage-infected cells may be low. However, a 1-h incubation enables phage replication in the culturable cells, which are countable under a fluorescence microscope. On the other hand, the fluorescence intensity of VBNC or pasteurized E. coli O157:H7 cells infected by recombinant phages may remain constant. For the detection of both culturable and VBNC E. coli O157:H7 cells, a high MOI is desirable to enable strong visualization of the cells. Lysis from without (LO) is peculiar to the T4 phage (20). LO is lysis due to adsorption of a large number of T4 particles on the cell wall and occurs at MOIs of >20. However, LO of PP01 was not observed up to an MOI of 1,000.
Attempts to detect bacteria by use of specific phages have been reported previously (3, 5, 13, 23). However, the basic principles of these trials were based on the expression of fluorescence marker proteins, such as GFP and luciferase, in the host cells by integration of genes encoding the marker protein into the phage genome. Since the production of a marker protein depends on host cell activities, these methods fail to detect bacteria in the VBNC state, which is the most common state for bacteria in natural environments. GFP-labeled PP01 phage enables us to detect E. coli O157:H7 in both culturable and VBNC states. For the detection of both culturable and VBNC cells, a high MOI and a short incubation were used. On the other hand, for the detection of culturable cells alone, a low MOI and a long incubation time were needed. By changing the experimental conditions, we could distinguish culturable and VBNC cells.
The utilization of flow cytometry or image analysis might enhance the reliability of the method and shorten the detection time. For the application of this method for food enrichment or water samples, further studies, such as the assignment of a positive versus negative cutoff point, will be necessary.
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