We thank M. Channey, E. Chau, and K. Tomas for their assistance on the project. Project supplies were partially funded by California Polytechnic State University.

1. Media and Culturing of Microbial Strains
NOTE: Use aseptic techniques in all experiments. Use sterile materials. Sterilize all containers, tools and reagent prior to use. Autoclave all waste materials prior to disposal because they are considered biohazardous. Autoclave temperature and time combination is &#8805;121 &#176;C x &#8805;15 min for all of the following procedures.
<ol>
	<li>To make ~1-L tryptic soy agar (TSA), first add 1 L deionized water in a 2-L Erlenmeyer flask containing a magnetic stir bar. Use a flask that is at least two times larger than the final volume. Add 30 g of tryptic soy broth powder and 20 g agar granules into the flask. 
	NOTE: Use 2% agar instead of 1.5% to limit swarming of some Vibrio spp.
	<ol>
		<li>Mix thoroughly by turning on the stirrer. While stirring, turn on the heat to boil the mixture. Remove the flask from the heater as soon as the mixture begins to boil. Loosely cover the flask with a tin foil. Tape the foil to secure it to the flask before autoclave.</li>
		<li>To make tryptic soy broth (TSB), omit the agar from the recipe in step 1.1. 
		NOTE: May use bottles instead of Erlenmeyer flask.</li>
		<li>To make tryptic soy agar supplemented with 2% sodium chloride or NaCl (TSAS), add 20 g of NaCl in the mixture prior to stirring and heating. To make tryptic soy broth supplemented with 2% NaCl (TSBS), omit the agar, add 20 g of NaCl in the mixture prior to stirring and heating.</li>
	</ol>
	</li>
	<li>To make brain heart infusion (BHI) agar, suspend 37 g of BHI powder and 15 g agar granules in 1 L of purified water. Heat with frequent agitation to dissolve the powder. Autoclave. Omit the agar to make BHI broth.</li>
	<li>To make TCBS agar, suspend 89 g of the TCBS powder in 1 L of purified water. Heat with frequent agitation and boil for 1 min to completely dissolve the powder. Do not autoclave.</li>
	<li>For all agar media, cool the hot agar to 45-50 &#176;C in a water bath. Arrange empty Petri plates in stacks of five to six plates. Starting from the bottom of the stack, pour the molten agar into each Petri plate to reach about half full. Close the Petri plate lid after pouring. Allow the agar to solidify by letting the plates sit at room temperature.
	<ol>
		<li>Use the agar plates the next day or after 12 hr. Store unused plates in a refrigerator for up to two weeks. Before use, remove plates from the refrigerator and equilibrate them at room temperature for at least 15 min. 
		NOTE: One-liter agar makes ~45 agar plates. Allow the agar plates to dry sufficiently on the day of preparation, and equilibrate them to room temperature after cold storage to effectively reduce the spreading of the colonies.</li>
	</ol>
	</li>
	<li>Obtain chocolate and chromogenic agar plates and equilibrate them at room temperature before each experiment.</li>
	<li>Subculture all 54 microbial strains shown in Table 1 every few days.
	<ol>
		<li>Use a sterile inoculating loop to transfer cultures from a frozen stock or a previous batch to nonselective media such as BHI, TSB/TSA or chocolate agar. Grow halophilic Vibrio spp. on TSBS/TSAS.</li>
		<li>To check the purity of the culture, streak all strains in a pattern that would allow for observation of isolated colonies. For example, use a three-phase streaking pattern to dilute a large amount of bacteria to smaller amount, eventually yielding isolated colonies.</li>
	</ol>
	</li>
	<li>Incubate the plates upside-down at 35-37 &#176;C for up to 48 hr. For Campylobacter spp., incubate tubes or plates in a closed-lid jar containing a gas pouch to produce a microaerophilic environment. Observe colony morphology after incubation. Pure cultures should yield colonies that exhibit similar colony morphology. 
	NOTE: Incubate all plates upside-down to prevent condensed water droplets formed on the underside of the lid from falling on the colonies.</li>
</ol>
2. Species Determination by PCR
<ol>
	<li>Conduct tlh-PCR to confirm the identity of V. parahaemolyticus strains. Use primers tlh-F (5&#39; AAA GCG GAT TAT GCA GAA GCA CTG 3&#39;) and tlh-R (5&#39; GCT ACT TTC TAG CAT TTT CTC TGC 3&#39;) to amplify a 450-bp fragment of the thermolabile hemolysin gene20.
	<ol>
		<li>Use a sterile inoculating loop to transfer a few isolated colonies of each V. parahaemolyticus strain from TSAS to 5 ml of TSBS. Incubate at 35-37 &#176;C for 16-24 hr.</li>
		<li>Centrifuge cultures at 14,000 x g for 1 min. Remove supernatant and wash the pellet twice with phosphate buffered saline (PBS). Boil the suspension for 3 min to yield cell lysate. 
		NOTE: V. parahaemolyticus is easy to be lysed. Therefore lysis reagent is not required. It is also possible to use a bit of colony directly as the template.</li>
		<li>Perform PCR in a 25-&#181;l reaction volume. Prepare a reaction mixture containing a final concentration of 1x PCR buffer, 1.5 mM MgCl2, 100 &#181;M of each dNTP, 1 &#181;M of each primer, 1 U Taq Polymerase and 1 &#181;l of cell lysate. After preincubation at 94 &#176;C for 5 min, run 35 amplification cycles of 94 &#176;C for 30 sec, 58 &#176;C for 30 sec, and 72 &#176;C for 60 sec21.</li>
		<li>Load aliquots of 5-&#181;l amplicon in 1.5% agarose gels. Turn on power supply to start electrophoresis. Visualize the presence or absence of amplicons under UV illumination after ethidium bromide staining.</li>
	</ol>
	</li>
</ol>
3. Growth on Selective and Differential Media
<ol>
	<li>Two to four days before the experiment, streak all microbial strains shown in Table 1 on nonselective medium (TSAS, BHI or chocolate agar) for colony isolation. Incubate plates at 35-37 &#176;C for 48 hr. Check the purity of the cultures by observing colony morphology after incubation. Pure cultures should yield colonies that exhibit similar colony morphology.</li>
	<li>Transfer a few isolated colonies from Step 3.1 into 5 ml of broth. Incubate tubes at 35-37 &#176;C for 16-24 hr. 
	NOTE: Use young colonies, which are less than four days old, to prepare overnight cultures in all experiments.</li>
	<li>Streak a loopful of overnight cultures on selective and differential media (TCBS and chromogenic agar) for colony isolation. Incubate plates at 35-37 &#176;C for up to 96 hr.</li>
	<li>Record the overall growth of all strains by examining both the culture density on the plate and the size of isolated colonies. Record the color of colonies under ambient and/or UV light. Note other characteristics of isolated colony such as the elevation, margin and form.</li>
</ol>
4. Recovery Assay
<ol>
	<li>Select a representative subset of V. parahaemolyticus strains (n=14) that encompass different serotypes and origins of isolation22. Inoculate young cultures from the plates into 5 ml of TSBS. Incubate the tubes at 35-37 &#176;C for 16-24 hr.</li>
	<li>Conduct a Standard Plate Count method of the overnight cultures as described below.
	<ol>
		<li>Vortex to mix the overnight cultures well. Make a 10-fold or 10-1 dilution by transferring 100 &#181;l of the overnight culture into a tube containing 900 &#181;l PBS. Vortex to mix well.</li>
		<li>Use a new pipet tip to transfer 100 &#181;l from the 10-1 dilution tube to another tube containing 900 &#181;l PBS. Vortex to mix well. This constitutes 10-2 dilution. Repeat the process sequentially to obtain 10-7 dilution.</li>
		<li>Using the 10-4 to 10-7 dilution tubes, plate 100 &#181;l each on the chromogenic, TCBS and TSAS agar plates. 
		NOTE: The dilution factor (df) on the plate becomes 10-5 to 10-8, respectively.</li>
		<li>Spread the aliquots evenly on the agar surface. 
		NOTE: It is fine to use the same spreader per strain on the same medium, as long as the most diluted aliquot is spread first (i.e., from 10-8 to 10-5). Do not use the same spreader for different media.</li>
		<li>Incubate plates at 35-37 &#176;C for up to 96 hr. Count colonies on the plates. Ignore plates bearing colonies that are too numerous to count (tntc) or less than 25. Calculate CFU/ml according to the following: 
		<img alt="Equation 1" src="/files/ftp_upload/54493/54493eq1.jpg" /> 
		Where 
		N = the number of cells in the undiluted tube, expressed as CFU/ml or CFU/g 
		C = the total number of colonies counted on plates that bear 25-300 colonies 
		n1 = the number of plate(s) where counted colonies are from the lower df 
		n2 = the number of plate(s) where counted colonies are from the subsequent 10-fold dilution 
		df = the lower dilution factor (i.e., more concentrated dilution)</li>
	</ol>
	</li>
	<li>Compare CFU/ml among different media. Use CFU/ml on TSAS as 100%, calculate the % recovery of V. parahaemolyticus grown on the chromogenic and TCBS agar.</li>
</ol>
5. Competition Assay
<ol>
	<li>Choose a subset of strains that exhibit different colony morphologies on the chromogenic and TCBS agar. 
	NOTE: This way, it will be possible to count colonies originated from V. parahaemolyticus only, despite the presence of other species in the inoculum.
	<ol>
		<li>Choose a V. parahaemolyticus strain that yields the expected turquoise and cyan colonies on TCBS and the chromogenic agar, respectively.</li>
		<li>Choose a non-V. parahaemolyticus and a non-Vibrio species that do not grow on either of these media, or exhibit different colony color. 
		NOTE: For example, V. metschnikovii grows very weakly on TCBS and did not grow on the chromogenic agar. Shigella sonnei does not grow on TCBS but yields magenta colonies on the chromogenic agar.</li>
	</ol>
	</li>
	<li>After selection of the strains above, prepare overnight broth cultures using isolated colonies grown on nonselective media.
	<ol>
		<li>Make overnight cultures of V. parahaemolyticus and V. metschnikovii by transferring a few isolated colonies from TSAS to 5 ml of TSBS. Incubate at 35-37 &#176;C for 16-24 hr.</li>
		<li>Make overnight cultures of Shigella sonnei by transferring a few isolated colonies from BHI agar to 5 ml of BHI broth. Incubate at 35-37 &#176;C for 16-24 hr.</li>
	</ol>
	</li>
	<li>For each strain, perform a dilution series similar to Steps 4.2.1 and 4.2.2. Plate appropriate dilutions on TSAS or BHI to determine CFU/ml of the overnight culture, using the equation shown in Step 4.2.5. 
	NOTE: Typically, 100 &#181;l from the 10-5 to 10-7 dilution tubes works for most cultures. Use the CFU/ml values to back calculate the exact amount of cells used in next step. The calculated CFU/ml values are obtained after incubation, although the following steps are performed on the same date as Step 5.3.</li>
	<li>Using the overnight cultures and dilution tubes in Steps 5.2 and 5.3, mix different amounts of a V. parahaemolyticus strain and a non-V. parahaemolyticus species. For example, mix 500 &#181;l of the 10-5 dilution tube of V. parahaemolyticus with 500 &#181;l of the overnight cultures of V. metschnikovii. 
	NOTE: This mixture simulates high microflora background. To simulate a low microflora background, mix 500 &#181;l each of the 10-5 dilution tube from both species. </li>
	<li>Spread 100 &#181;l of the mixture each on the chromogenic, TCBS and TSAS agar plates.</li>
	<li>After incubation at 35-37 &#176;C for up to 96 hr, count colonies of V. parahaemolyticus and the non-V. parahaemolyticus species based on their difference in growth and colony morphology on the chromogenic and TCBS agar. 
	NOTE: For example, if the non-V. parahaemolyticus species does not grow on the chromogenic and TCBS agar, all colonies will be of V. parahaemolyticus. If the non-V. parahaemolyticus species grows on both media, only the turquoise colonies on TCBS and cyan colonies on chromogenic agar will be of V. parahaemolyticus. The non-V. parahaemolyticus species may or may not exhibit similar colony morphology to V. parahaemolyticus on TSAS.
	<ol>
		<li>If the non-V. parahaemolyticus species grows similarly to V. parahaemolyticus on this nonselective medium, divide the colony count by two to obtain numbers for V. parahaemolyticus only. Compare the actual colony count with the expected count derived from Step 5.3.</li>
	</ol>
	</li>
</ol>
6. Effects of Oyster Homogenates
<ol>
	<li>Weigh &#8805;50 g oyster meat from &#8805;12 molluscan shellfish including meat and liquor.
	<ol>
		<li>Add equal amount of PBS to the oyster meat and liquor. Blend the mixture at high speed for 90 sec. This constitutes 2-1 diluted oyster homogenate.</li>
		<li>Add 100 g of 2-1 diluted oyster homogenate to 400 g of PBS. Use a scale to measure the weight, not volume. Blend the mixture at high speed for 1 min. Autoclave the oyster homogenate. 
		NOTE: This will be the oyster homogenate used for spiking.</li>
	</ol>
	</li>
	<li>Repeat the Recovery assay (Step 4) in the presence of oyster homogenate.
	<ol>
		<li>After the 500 g oyster homogenate cools down, add 100 &#181;l of V. parahaemolyticus overnight cultures grown in TSBS to it. Determine the actual amount of V. parahaemolyticus cells in the inoculum by conducting the Standard Plate Count procedures described in Step 4.2.</li>
	</ol>
	</li>
	<li>Repeat the Competition assay (Step 5) in the presence of oyster homogenate.
	<ol>
		<li>After the 500 g oyster homogenate cools down, add 100 &#181;l each of overnight cultures of V. parahaemolyticus and non-V. parahaemolyticus to it. Determine the actual amount of bacterial cells in the inoculum by conducting the Standard Plate Count procedures described in Step 4.2</li>
	</ol>
	</li>
	<li>Mix the bacterial cells with oyster homogenate well by using a homogenizer. 
	NOTE: After mixing, the oyster homogenate containing the intentionally added cells is called spiked oyster homogenate.</li>
	<li>Make dilutions of the spiked oyster homogenate to obtain 10-1 to 10-3 dilution tubes according to the procedures described in Step 4.2.2. Spread 100 &#181;l of each dilution onto the chromogenic, TCBS and TSAS agar. Incubate plates at 35-37 &#176;C for up to 96 hr.</li>
	<li>Compare the actual colony count on chromogenic and TCBS agar with the expected colony count deduced from Steps 6.2.1 and 6.3.1. 
	NOTE: For example, if a tube of V. parahaemolyticus overnight culture contains 108 CFU/ml, an inoculum of 100 &#956;l means that 107 cells are added to the 500-g of oyster homogenate, yielding 5 x 104 cells/g. After dilution and plating, the plate having df = 10-2 should yield 500 colonies; while that having df = 10-3 should yield 50 colonies. These are the expected colony counts.</li>
</ol>

<ol>
	<li>Yeung, P. S., Boor, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epidemiology,+pathogenesis,+and+prevention+of+foodborne+Vibrio+parahaemolyticus+infections.">Epidemiology, pathogenesis, and prevention of foodborne Vibrio parahaemolyticus infections.</a> Foodborne Pathog. Dis. 1 (2), 74-88 (2004).</li><li>Yeung, P. S. M., Boor, K. J., Faruque, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epidemiology,+molecular+biology,+and+detection+of+foodborne+Vibrio+parahaemolyticus+infections.">Epidemiology, molecular biology, and detection of foodborne Vibrio parahaemolyticus infections.</a> Foodborne and Waterborne Bacterial pathogens: Epidemiology, Evolution and Molecular Biology. , 153-184 (2012).</li><li>Centers for Disease Control and Prevention. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vital+Signs:+Incidence+and+Trends+of+Infection+with+Pathogens+Transmitted+Commonly+Through+Food+-+Foodborne+Diseases+Active+Surveillance+Network,+10+U.S.+Sites,+1996-2010.">Vital Signs: Incidence and Trends of Infection with Pathogens Transmitted Commonly Through Food - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 1996-2010.</a> Morbidity and Mortality Weekly Report. 10, 1996-2010 (2011).</li><li>. Summary of human Vibrio cases reported to CDC, 2008 Available from: <a target="_blank" href="https://stacks.cdc.gov/view/cdc/21591">https://stacks.cdc.gov/view/cdc/21591</a> (2008)</li><li>Scallan, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Foodborne+illness+acquired+in+the+United+States+-+major+pathogens.">Foodborne illness acquired in the United States - major pathogens.</a> Emerg. Infect. Dis. 17 (1), 7-15 (2011).</li><li>Baross, J., Liston, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Occurrence+of+Vibrio+parahaemolyticus+and+related+hemolytic+vibrios+in+marine+environments+of+Washington+State.">Occurrence of Vibrio parahaemolyticus and related hemolytic vibrios in marine environments of Washington State.</a> Appl. Microbiol. 20 (2), 179-186 (1970).</li><li>Baross, J., Liston, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+Vibrio+parahaemolyticus+from+the+Northwest+Pacific.">Isolation of Vibrio parahaemolyticus from the Northwest Pacific.</a> Nature. 217 (5135), 1263-1264 (1968).</li><li>Kueh, C. S., Chan, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacteria+in+bivalve+shellfish+with+special+reference+to+the+oyster.">Bacteria in bivalve shellfish with special reference to the oyster.</a> J. Appl. Bacteriol. 59 (1), 41-47 (1985).</li><li>Food and Drug Administration. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Bad Bug Book, Foodborne Pathogenic Microorganisms and Natural Toxins. , (2012).</li><li>Qadri, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adaptive+and+inflammatory+immune+responses+in+patients+infected+with+strains+of+Vibrio+parahaemolyticus.">Adaptive and inflammatory immune responses in patients infected with strains of Vibrio parahaemolyticus.</a> J. Infect. Dis. 187 (7), 1085-1096 (2003).</li><li>MacFaddin, J. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Media for isolation-cultivation-identification-maintenance of medical bacteria. 1, (1985).</li><li>Bottone, E. J., Robin, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vibrio+parahaemolyticus:+suspicion+of+presence+based+on+aberrant+biochemical+and+morphological+features.">Vibrio parahaemolyticus: suspicion of presence based on aberrant biochemical and morphological features.</a> J. Clin. Microbiol. 8 (6), 760-763 (1978).</li><li>Lotz, M. J., Tamplin, M. L., Rodrick, G. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thiosulfate-citrate-bile+salts-sucrose+agar+and+its+selectivity+for+clinical+and+marine+vibrio+organisms.">Thiosulfate-citrate-bile salts-sucrose agar and its selectivity for clinical and marine vibrio organisms.</a> Ann. Clin. Lab. Sci. 13 (1), 45-48 (1983).</li><li>Hara-Kudo, Y., Nishina, T., Nakagawa, H., Konuma, H., Hasegawa, J., Kumagai, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+method+for+detection+of+Vibrio+parahaemolyticus+in+seafood.">Improved method for detection of Vibrio parahaemolyticus in seafood.</a> Appl. Environ. Microbiol. 67 (12), 5819-5823 (2001).</li><li>Eddabra, R., Piemont, Y., Scheftel, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+a+new+chromogenic+medium,+chromID+Vibrio,+for+the+isolation+and+presumptive+identification+of+Vibrio+choleare+and+Vibrio+parahaemolyticus+from+human+clinical+specimens.">Evaluation of a new chromogenic medium, chromID Vibrio, for the isolation and presumptive identification of Vibrio choleare and Vibrio parahaemolyticus from human clinical specimens.</a> Eur. J. Clin. Microbiol. Infect. Dis. 30 (6), 733-737 (2011).</li><li>Kodaka, H., Teramura, H., Mizuochi, S., Saito, M., Matsuoka, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+the+Compact+Dry+VP+method+for+screening+raw+seafood+for+total+Vibrio+parahaemolyticus.">Evaluation of the Compact Dry VP method for screening raw seafood for total Vibrio parahaemolyticus.</a> J. Food. Prot. 72 (1), 169-173 (2009).</li><li>Su, Y. C., Duan, J., Wu, W. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selectivity+and+specificity+of+a+chromogenic+medium+for+detecting+Vibrio+parahaemolyticus.">Selectivity and specificity of a chromogenic medium for detecting Vibrio parahaemolyticus.</a> J. Food Prot. 68 (7), 1454-1456 (2005).</li><li>Bej, A. K., Patterson, D. P., Brasher, C. W., Vickery, M. C., Jones, D. D., Kaysner, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+total+and+hemolysin-producing+Vibrio+parahaemolyticus+in+shellfish+using+multiplex+PCR+amplification+of+tl,+tdh+and+trh.">Detection of total and hemolysin-producing Vibrio parahaemolyticus in shellfish using multiplex PCR amplification of tl, tdh and trh.</a> J. Microbiol. Methods. 36 (3), 215-225 (1999).</li><li>Yeung, P. S. M., DePaola, A., Kaysner, C. A., Boor, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+PCR+assay+for+specific+detection+of+the+pandemic+Vibrio+parahaemolyticus+O3:K6+clone+from+shellfish.">A PCR assay for specific detection of the pandemic Vibrio parahaemolyticus O3:K6 clone from shellfish.</a> J. Food Sci. 68 (4), 1459-1466 (2003).</li><li>Yeung, P. S. M., Hayes, M. C., DePaola, A., Kaysner, C. A., Kornstein, L., Boor, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+phenotypic,+molecular,+and+virulence+characterization+of+Vibrio+parahaemolyticus+O3:K6+isolates.">Comparative phenotypic, molecular, and virulence characterization of Vibrio parahaemolyticus O3:K6 isolates.</a> Appl. Environ. Microbiol. 68 (6), 2901-2909 (2002).</li><li>Duan, J., Su, Y. -. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+a+chromogenic+medium+with+thiosulfate-citrate-bile+salts-sucrose+agar+for+detecting+Vibrio+parahaemolyticus.">Comparison of a chromogenic medium with thiosulfate-citrate-bile salts-sucrose agar for detecting Vibrio parahaemolyticus.</a> J. Food Sci. 70, M125-M128 (2005).</li><li>Pinto, A. D., Terio, V., Novello, L., Tantillo, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+between+thiosulphate-citrate-bile+salt+sucrose+(TCBS)+agar+and+CHROMagar+Vibrio+for+isolating+Vibrio+parahaemolyticus.">Comparison between thiosulphate-citrate-bile salt sucrose (TCBS) agar and CHROMagar Vibrio for isolating Vibrio parahaemolyticus.</a> Food Control. 22 (1), 124-127 (2011).</li><li>Canizalez-Roman, A., Flores-Villase&#241;or, H., Zazueta-Beltran, J., Muro-Amador, S., Le&#242;n-Sicairos, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+evaluation+of+a+chromogenic+agar+medium-PCR+protocol+with+a+conventional+method+for+isolation+of+Vibrio+parahaemolyticus+strains+from+environmental+and+clinical+samples.">Comparative evaluation of a chromogenic agar medium-PCR protocol with a conventional method for isolation of Vibrio parahaemolyticus strains from environmental and clinical samples.</a> Can J Microbiol. 57 (2), 136-142 (2011).</li><li>Kriem, M. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prevalence+of+Vibrio+spp.+in+raw+shrimps+(Parapenaeus+longirostris)+and+performance+of+a+chromogenic+medium+for+the+isolation+of+Vibrio+strains.">Prevalence of Vibrio spp. in raw shrimps (Parapenaeus longirostris) and performance of a chromogenic medium for the isolation of Vibrio strains.</a> Lett Appl Microbiol. 61 (3), 224-230 (2015).</li><li>Food Drug Administration. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+guidance+on+reporting+results+from+studies+evaluating+diagnostic+tests.">Statistical guidance on reporting results from studies evaluating diagnostic tests.</a> http://www.fda.gov/RegulatoryInformation/Guidances/ucm071148.htm. , (2007).</li><li>Burd, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Validation+of+laboratory-developed+molecular+assays+for+infectious+diseases.">Validation of laboratory-developed molecular assays for infectious diseases.</a> Clin Microbiol Rev. 23 (3), 550-576 (2010).</li></ol>

Some media were generously provided by Hardy Diagnostics, Santa Maria, CA. Thorsen conducted this study while a student at California Polytechnic State University. He is currently an employee of Hardy Diagnostics.

This study focuses on culture media development and evaluation. Conventionally, TCBS is the selective and differential medium used for isolating and detecting V. parahaemolyticus, V. cholerae and V. vulnificus12. However, limitations have been reported for this medium, such as the inability to differentiate V. cholerae from other Vibrio species. Sucrose and pH indicator are the differentiation agents of TCBS. Thus, acid production by sucrose fermenter causes color change of ...

As a member of the Vibrio genus, V. parahaemolyticus is a Gram-negative, non-spore-forming, curved, rod-shaped bacterium. It exhibits high motility in both liquid and semi-solid environments. Most V. parahaemolyticus strains are non-pathogenic to humans, yet the pathogenic subtypes have caused epidemics and pandemics, hence this species is considered to be an important foodborne pathogen in many countries1,2. The incidence of Vibrio infection in the US has shown an upward trend since 20003. Among Vibrio spp., V. parahaemolyticus is the most frequently reported species causing illnesses in the US4,5. Other clinically relevant species include V. alginolyticus, V. vulnificus, V. cholerae, etc. A small percentage of the illnesses is caused by multiple species simultaneously.
V. parahaemolyticus is a natural inhabitant of marine water and therefore widely distributed in marine waters throughout the world including the estuaries. The species was discovered in 1950 following an outbreak of food poisoning in Japan. In the US, the species was first isolated in seawater, sediments, and shellfish in the Puget Sound region6,7. Filter feeders in marine habitats, such as bivalve shellfish, can harbor V. parahaemolyticus as part of their natural flora8. As such, V. parahaemolyticus infections in human are often linked to the consumption of contaminated seafood, especially raw or undercooked shellfish. A less common route of entry occurs when open wound is exposed to seawater, leading to skin infection. Most V. parahaemolyticus strains do not cause human disease, yet certain subtypes harboring virulence factors such as thermostable direct hemolysin (TDH) are pathogenic. The most prevalent symptoms of foodborne V. parahaemolyticus infection are diarrhea and abdominal pain, followed by nausea, vomiting, and fever. Headache and chills are also reported. The median incubation period is 15 hr, but can be up to 96 hr after consumption of sufficient amount of pathogenic strains9. The illness lasts from two to three days. The gastroenteritis symptoms caused by V. parahaemolyticus are largely self-limiting and therefore special treatment is not necessary. Mild cases of gastroenteritis can be effectively treated by oral rehydration. More severe illnesses can be treated by antibiotics such as tetracycline or ciprofloxacin10. Mortality rate is about 2% for gastroenteritis cases, but may be as high as 29% for those who develop bloodstream infection or septicemia. Any person who consumes seafood or has open wound exposed to seawater is at risk of V. parahaemolyticus infection. The more severe form of illnesses, life-threatening septicemia, is more common in a subpopulation with underlying medical conditions11, which include alcoholism, liver disease, diabetes, renal disease, malignancy, and other conditions leading to a weakened immune response. Notably, this group of individuals is also at a higher risk for contracting severe illnesses caused by V. vulnificus, which can be found in natural habitats similar to V. parahaemolyticus.
V. parahaemolyticus is routinely isolated using thiosulfate-citrate-bile salts-sucrose (TCBS) agar as a selective and differential medium. Enrichment in alkaline peptone water may precede isolation on TCBS agar. Presumptive colonies on TCBS are then further tested in an array of biochemical tests and/or molecular assays targeting the presence of species-specific genes. PCR-based methods are often used to confirm the identities of V. parahaemolyticus by amplifying the thermolabile hemolysin gene, tlh12. 
Regardless of the choice of confirmation methods, it is important to have an effective medium to isolate and differentiate V. parahaemolyticus from other marine vibrios in the first place. TCBS has routinely been used to differentiate species within the Vibrio genus according to their abilities to ferment sucrose12. Positive fermentation reaction is accompanied by a color change of the pH indicator Bromothymol blue. V. parahaemolyticus colonies are fairly distinctive on TCBS, exhibiting blue to green color. However, this medium cannot easily differentiate V. alginolyticus and V. cholerae. Sucrose-fermenting Proteus species may produce yellow colonies resembling V. cholerae or V. alginolyticus13. On initial isolation on TCBS, V. parahaemolyticus may also be misidentified as Aeromonas hydrophila, Plesiomonas shigelloides, and Pseudomonas spp14. Strains with delayed sucrose fermentation may be confused with other sucrose nonfermenting Vibrio13, which include V. parahaemolyticus. TCBS was found to be not sensitive against Escherichia coli, Pseudomonas putrefaciens, among others. Several other species yield green to gray colonies which are potentially confused with V. parahaemolyticus or V. vulnificus15. As a result, it is desirable to develop alternative culture media with better sensitivity and specificity toward detecting and isolating V. parahaemolyticus and other closely related species.
Several media alternatives have been recently developed. In addition to the inclusion of selective agents, most incorporate chromogenic substrates to differentiate species based on their differential enzymatic activities. For example, indoxyl-&#946;-glucoside and indoxyl-&#946;-galactoside have been used as the chromogenic substrates to differentiate V. parahaemolyticus colonies (which appear bluish-green) from those of V. cholerae (purple) due to their differential abilities to produce &#946;-glucosidase and &#946;-galactosidase16. Different formulations of chromogenic agar developed by several groups have been evaluated and were reported to perform comparably to or better than TCBS17,18,19. An advantage of using a chromogenic medium is that the coloring of the surrounding medium is minimal thereby facilitating the isolation of particular colonies. In this study, we evaluated the ability of a newly formulated chromogenic medium to detect and isolate V. cholerae, V. parahaemolyticus, and V. vulnificus; with a special focus on its ability to differentiate V. parahaemolyticus from other species.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >Reagent/Equipment</td>
			<td ></td>
			<td ></td>
			<td ></td>
		</tr>
		<tr >
			<td >Agar</td>
			<td>Fisher Scientific</td>
			<td>DF0140-15-4</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Autoclave</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >BHI powder</td>
			<td>Fisher Scientific</td>
			<td>DF0418-17-7</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Blender</td>
			<td>Any</td>
			<td></td>
			<td>to blend oyster meat</td>
		</tr>
		<tr >
			<td >CampyGen gas generator</td>
			<td>Hardy Diagnostics</td>
			<td>CN035A</td>
			<td>to provide a microaerophilic atmosphere; may use other brands</td>
		</tr>
		<tr >
			<td >Chocolate agar plates</td>
			<td>Hardy Diagnostics</td>
			<td>E14</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Common PCR reagents (dNTPs, MgCl2, Taq Polymerase)</td>
			<td>Any</td>
			<td></td>
			<td>or use PCR beads (Fisher Sci 46-001-014)</td>
		</tr>
		<tr >
			<td >Culture tubes</td>
			<td>Fisher Scientific</td>
			<td>S50712</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Eppendorf tubes</td>
			<td>Fisher Scientific</td>
			<td>S348903</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Gel doc</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >HardyChrom Vibrio agar plates</td>
			<td>Hardy Diagnostics</td>
			<td>G319</td>
			<td>This study evaluates this medium</td>
		</tr>
		<tr >
			<td >Incubator</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Inoculating loops</td>
			<td>Fisher Scientific</td>
			<td>22-363-606</td>
			<td>10 microliter-size was used in this study</td>
		</tr>
		<tr >
			<td >NaCl</td>
			<td>Fisher Scientific</td>
			<td>BP358-212</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Oysters</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >PBS</td>
			<td>Fisher Scientific</td>
			<td>R23701</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Petri dish</td>
			<td>Fisher Scientific</td>
			<td>FB0875713</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >Pipette and tips</td>
			<td>Any</td>
			<td></td>
			<td>Sterilized tips</td>
		</tr>
		<tr >
			<td >Primers for tlh</td>
			<td>IDT DNA</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Scale</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Spreader</td>
			<td>Fisher Scientific</td>
			<td>08-100-11</td>
			<td>Beads may be used instead</td>
		</tr>
		<tr >
			<td >Stomacher blender</td>
			<td>Stomacher</td>
			<td >400</td>
			<td>Samples were homogenized at 200 rpm for 30 sec.&#160; Other homogenizer can be used.</td>
		</tr>
		<tr >
			<td >Sterile filter bags for blenders</td>
			<td>Fisher Scientific</td>
			<td>01-812-5</td>
			<td></td>
		</tr>
		<tr >
			<td >TCBS powder</td>
			<td>Hardy Diagnostics</td>
			<td >265020</td>
			<td>This study evaluates this medium</td>
		</tr>
		<tr >
			<td >Thermocycler</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >TSB powder</td>
			<td>Fisher Scientific</td>
			<td>DF0370-07-5</td>
			<td>may use other brands</td>
		</tr>
		<tr >
			<td >UV viewing cabinet</td>
			<td>Any</td>
			<td></td>
			<td>Emit long-wave UV light</td>
		</tr>
		<tr >
			<td >Water bath</td>
			<td>Any</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Name</td>
			<td>Sources</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr >
			<td >Bacterial species and strains</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Aeromonas hydrophila</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Candida albicans</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Campylobacter jejuni</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Escherichia coli</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Proteus mirabilis</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Pseudomonas aeruginosa</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Staphylococcus aureus</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Salmonella Choleraesuis</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Shigella boydii</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Shigella flexneri</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Shigella sonnei</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >Vibrio alginolyticus</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. cholerae (serotypes include O139, O1, non O1, El Tor biovars)</td>
			<td >FDA, ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. damsela</td>
			<td >FDA</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. fisherii</td>
			<td >Environment</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. fluvialis</td>
			<td >CDC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. furnissii</td>
			<td >CDC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. hollisae</td>
			<td >FDA</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. metschnikovii</td>
			<td >ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. mimicus</td>
			<td >FDA</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. parahaemolyticus(serotypes include O3:K6, O1:K56, O4:K8, O5:K15, O8, etc)</td>
			<td >ATCC, FDA, CDC, Environment</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. proteolyticus</td>
			<td >FDA</td>
			<td></td>
			<td></td>
		</tr>
		<tr >
			<td >V. vulnificus</td>
			<td >FDA</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

development of a more sensitive and specific chromogenic agar medium for the detection of vibrio parahaemolyticus and other vibrio species

Foodborne infections in the US caused by Vibrio species have shown an upward trend. In the genus Vibrio, V. parahaemolyticus is responsible for the majority of Vibrio-associated infections. Thus, accurate differentiation among Vibrio spp. and detection of V. parahaemolyticus is critically important to ensure the safety of our food supply. Although molecular techniques are increasingly common, culture-depending methods are still routinely done and they are considered standard methods in certain circumstances. Hence, a novel chromogenic agar medium was tested with the goal of providing a better method for isolation and differentiation of clinically relevant Vibrio spp. The protocol compared the sensitivity, specificity and detection limit for the detection of V. parahaemolyticus between the new chromogenic medium and a conventional medium. Various V. parahaemolyticus strains (n=22) representing diverse serotypes and source of origins were used. They were previously identified by Food and Drug Administration (FDA) and Centers for Disease Control and Prevention (CDC), and further verified in our laboratory by tlh-PCR. In at least four separate trials, these strains were inoculated on the chromogenic agar and thiosulfate-citrate-bile salts-sucrose (TCBS) agar, which is the recommended medium for culturing this species, followed by incubation at 35-37 &#176;C for 24-96 hr. Three V. parahaemolyticus strains (13.6%) did not grow optimally on TCBS, nonetheless exhibited green colonies if there was growth. Two strains (9.1%) did not yield the expected cyan colonies on the chromogenic agar. Non-V. parahaemolyticus strains (n=32) were also tested to determine the specificity of the chromogenic agar. Among these strains, 31 did not grow or exhibited other colony morphologies. The mean recovery of V. parahaemolyticus on the chromogenic agar was ~96.4% relative to tryptic soy agar supplemented with 2% NaCl. In conclusion, the new chromogenic agar is an effective medium to detect V. parahaemolyticus and to differentiate it from other vibrios.

In this study, 54 microbial strains were assembled, which included 22 strains within the V. parahaemolyticus species, 19 other Vibrio species, and 13 non-Vibrio species (Table 1). Most V. parahaemolyticus strains were either received from FDA, CDC or other state health departments. They represent diverse serotypes and isolation sources. These strains were previously identified by the regulatory agencies. We further confirmed the identit...

Watch this Scientific Journal Video about Development of a More Sensitive and Specific Chromogenic Agar Medium for the Detection of Vibrio parahaemolyticus and Other Vibrio Species at JoVE.com

Development of a More Sensitive and Specific Chromogenic Agar Medium for the Detection of Vibrio parahaemolyticus and Other Vibrio Species

Detection and isolation of clinically relevant Vibrio species require selective and differential culture media. This study evaluated the ability of a new chromogenic medium to detect and identify V. parahaemolyticus and other related species. The new medium was found to have better sensitivity and specificity than the conventional medium.

Development of a More Sensitive and Specific Chromogenic Agar Medium for the Detection of Vibrio parahaemolyticus and Other Vibrio Species

Foodborne infections in the US caused by Vibrio species have shown an upward trend. In the genus Vibrio, V. parahaemolyticus is responsible for the ...

development-more-sensitive-specific-chromogenic-agar-medium-for

Universidad de Cartagena UDEC

Research

JoVE Journal

Immunology and Infection

14.4K Views.  California Polytechnic State University. Detection and isolation of clinically relevant Vibrio species require selective and differential culture media. This study evaluated the ability of a new chromogenic medium to detect and identify V. parahaemolyticus and other related species. The new medium was found to have better sensitivity and specificity than the conventional medium. 

Video: Development of a More Sensitive and Specific Chromogenic Agar Medium for the Detection of Vibrio parahaemolyticus and Other Vibrio Species

Colonization of Euprymna scolopes Squid by Vibrio fischeri

Specific bacteria are found in association with animal tissue1-5. Such host-bacterial associations (symbioses) can be detrimental (pathogenic), have no fitness consequence (commensal), or be beneficial (mutualistic). While much attention has been given to pathogenic interactions, little is known about the processes that dictate the reproducible acquisition of beneficial/commensal bacteria from the environment. The light-organ mutualism between the marine Gram-negative bacterium V. fischeri and the Hawaiian bobtail squid, E. scolopes, represents a highly specific interaction in which one host (E. scolopes) establishes a symbiotic relationship with only one bacterial species (V. fischeri) throughout the course of its lifetime6,7. Bioluminescence produced by V. fischeri during this interaction provides an anti-predatory benefit to E. scolopes during nocturnal activities8,9, while the nutrient-rich host tissue provides V. fischeri with a protected niche10. During each host generation, this relationship is recapitulated, thus representing a predictable process that can be assessed in detail at various stages of symbiotic development. In the laboratory, the juvenile squid hatch aposymbiotically (uncolonized), and, if collected within the first 30-60 minutes and transferred to symbiont-free water, cannot be colonized except by the experimental inoculum6. This interaction thus provides a useful model system in which to assess the individual steps that lead to specific acquisition of a symbiotic microbe from the environment11,12.
Here we describe a method to assess the degree of colonization that occurs when newly hatched aposymbiotic E. scolopes are exposed to (artificial) seawater containing V. fischeri. This simple assay describes inoculation, natural infection, and recovery of the bacterial symbiont from the nascent light organ of E. scolopes. Care is taken to provide a consistent environment for the animals during symbiotic development, especially with regard to water quality and light cues. Methods to characterize the symbiotic population described include (1) measurement of bacterially-derived bioluminescence, and (2) direct colony counting of recovered symbionts.

Colonization of Euprymna scolopes Squid by Vibrio fischeri

The method outlines the procedure by which the Hawaiian bobtail squid, Euprymna scolopes and its bacterial symbiont, Vibrio fischeri, are raised separately and then introduced to allow for specific colonization of the squid light organ by the bacteria. Colonization detection by bacterially-derived luminescence and by direct colony counting are described.

Specific bacteria are found in association with animal tissue1-5. Such host-bacterial associations (symbioses) can be detrimental (pathogenic), have no ...

TransFLP &#x2014; A Method to Genetically Modify Vibrio cholerae Based on Natural Transformation and FLP-recombination

Several methods are available to manipulate bacterial chromosomes1-3. Most of these protocols rely on the insertion of conditionally replicative plasmids (e.g. harboring pir-dependent or temperature-sensitive replicons1,2). These plasmids are integrated into bacterial chromosomes based on homology-mediated recombination. Such insertional mutants are often directly used in experimental settings. Alternatively, selection for plasmid excision followed by its loss can be performed, which for Gram-negative bacteria often relies on the counter-selectable levan sucrase enzyme encoded by the sacB gene4. The excision can either restore the pre-insertion genotype or result in an exchange between the chromosome and the plasmid-encoded copy of the modified gene. A disadvantage of this technique is that it is time-consuming. The plasmid has to be cloned first; it requires horizontal transfer into V. cholerae (most notably by mating with an E. coli donor strain) or artificial transformation of the latter; and the excision of the plasmid is random and can either restore the initial genotype or create the desired modification if no positive selection is exerted. Here, we present a method for rapid manipulation of the V. cholerae chromosome(s)5 (Figure 1). This TransFLP method is based on the recently discovered chitin-mediated induction of natural competence in this organism6 and other representative of the genus Vibrio such as V. fischeri7. Natural competence allows the uptake of free DNA including PCR-generated DNA fragments. Once taken up, the DNA recombines with the chromosome given the presence of a minimum of 250-500 bp of flanking homologous region8. Including a selection marker in-between these flanking regions allows easy detection of frequently occurring transformants.
This method can be used for different genetic manipulations of V. cholerae and potentially also other naturally competent bacteria. We provide three novel examples on what can be accomplished by this method in addition to our previously published study on single gene deletions and the addition of affinity-tag sequences5. Several optimization steps concerning the initial protocol of chitin-induced natural transformation6 are incorporated in this TransFLP protocol. These include among others the replacement of crab shell fragments by commercially available chitin flakes8, the donation of PCR-derived DNA as transforming material9, and the addition of FLP-recombination target sites (FRT)5. FRT sites allow site-directed excision of the selection marker mediated by the Flp recombinase10.

A quick method to modify the genome of V. cholerae is described. These modifications include the deletion of single genes, gene clusters and genomic islands as well as the integration of short sequences (e.g. promoter elements or affinity-tag sequences). The method is based on the natural transformation and FLP-recombination.

Several methods are available to manipulate bacterial chromosomes1-3. Most of these protocols rely on the insertion of conditionally replicative plasmids ...

Use of Artificial Sputum Medium to Test Antibiotic Efficacy Against Pseudomonas aeruginosa in Conditions More Relevant to the Cystic Fibrosis Lung

There is growing concern about the relevance of in vitro antimicrobial susceptibility tests when applied to isolates of P. aeruginosa from cystic fibrosis (CF) patients. Existing methods rely on single or a few isolates grown aerobically and planktonically. Predetermined cut-offs are used to define whether the bacteria are sensitive or resistant to any given antibiotic1. However, during chronic lung infections in CF, P. aeruginosa populations exist in biofilms and there is evidence that the environment is largely microaerophilic2. The stark difference in conditions between bacteria in the lung and those during diagnostic testing has called into question the reliability and even relevance of these tests3.
 Artificial sputum medium (ASM) is a culture medium containing the components of CF patient sputum, including amino acids, mucin and free DNA. P. aeruginosa growth in ASM mimics growth during CF infections, with the formation of self-aggregating biofilm structures and population divergence4,5,6. The aim of this study was to develop a microtitre-plate assay to study antimicrobial susceptibility of P. aeruginosa based on growth in ASM, which is applicable to both microaerophilic and aerobic conditions.
 An ASM assay was developed in a microtitre plate format. P. aeruginosa biofilms were allowed to develop for 3 days prior to incubation with antimicrobial agents at different concentrations for 24 hours. After biofilm disruption, cell viability was measured by staining with resazurin. This assay was used to ascertain the sessile cell minimum inhibitory concentration (SMIC) of tobramycin for 15 different P. aeruginosa isolates under aerobic and microaerophilic conditions and SMIC values were compared to those obtained with standard broth growth. Whilst there was some evidence for increased MIC values for isolates grown in ASM when compared to their planktonic counterparts, the biggest differences were found with bacteria tested in microaerophilic conditions, which showed a much increased resistance up to a &gt;128 fold, towards tobramycin in the ASM system when compared to assays carried out in aerobic conditions.
 The lack of association between current susceptibility testing methods and clinical outcome has questioned the validity of current methods3. Several in vitro models have been used previously to study P. aeruginosa biofilms7, 8. However, these methods rely on surface attached biofilms, whereas the ASM biofilms resemble those observed in the CF lung9 . In addition, reduced oxygen concentration in the mucus has been shown to alter the behavior of P. aeruginosa2 and affect antibiotic susceptibility10. Therefore using ASM under microaerophilic conditions may provide a more realistic environment in which to study antimicrobial susceptibility.

Use of Artificial Sputum Medium to Test Antibiotic Efficacy Against Pseudomonas aeruginosa in Conditions More Relevant to the Cystic Fibrosis Lung

Current diagnostic antimicrobial susceptibility testing relies on the planktonic growth of isolates in nutrient rich, aerobic conditions. Here, we employ an alternative artificial sputum medium to study antimicrobial susceptibility of Pseudomonas aeruginosa biofilms under both aerobic and microaerophilic conditions more representative of the cystic fibrosis lung.

There  is growing concern about the relevance of in vitro antimicrobial  susceptibility tests when applied to isolates of P. aeruginosa from  cystic ...

Loop-mediated Isothermal Amplification (LAMP) Assays for the Species-specific Detection of Eimeria that Infect Chickens

Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the absence of effective control clinical coccidiosis can be devastating. Resistance to the chemoprophylactics frequently used to control Eimeria is common and sub-clinical infection is widespread, influencing feed conversion ratios and susceptibility to other pathogens such as Clostridium perfringens. Despite the availability of polymerase chain reaction (PCR)-based tools, diagnosis of Eimeria infection still relies almost entirely on traditional approaches such as lesion scoring and oocyst morphology, but neither is straightforward. Limitations of the existing molecular tools include the requirement for specialist equipment and difficulties accessing DNA as template. In response a simple field DNA preparation protocol and a panel of species-specific loop-mediated isothermal amplification (LAMP) assays have been developed for the seven Eimeria recognised to infect the chicken. We now provide a detailed protocol describing the preparation of genomic DNA from intestinal tissue collected post-mortem, followed by setup and readout of the LAMP assays. Eimeria species-specific LAMP can be used to monitor parasite occurrence, assessing the efficacy of a farm&#8217;s anticoccidial strategy, and to diagnose sub-clinical infection or clinical disease with particular value when expert surveillance is unavailable.

Loop-mediated Isothermal Amplification LAMP Assays for the Species-specific Detection of Eimeria that Infect Chickens

Diagnosis of Eimeria infection in chickens remains demanding. Parasite morphology- and host pathology-led approaches are commonly inconclusive, while molecular approaches based on PCR have proven demanding in cost and expertise. The aim of this protocol is to establish loop-mediated isothermal amplification (LAMP) as a straightforward molecular diagnostic for eimerian infection.

Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the ...

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. burnetii DNA in cell cultures and clinical samples. PCR requires specialized equipment and extensive end user training, and therefore, it is not suitable for routine work especially in a resource-constrained area. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of C. burnetii in patient samples. This method is performed at a single temperature around 60 &#176;C in a water bath or heating block. The sensitivity of this LAMP assay is very similar to PCR with a detection limit of about 25 copies per reaction. This report describes the preparation of the reaction using lyophilized reagents and visualization of results using hydroxynaphthol blue (HNB) or a UV lamp with fluorescent intercalating dye in the reaction. The LAMP reagents were lyophilized and stored at room temperature (RT) for one month without loss of detection sensitivity. This LAMP assay is particularly robust because the reaction mixture preparation does not involve complex steps. This method is ideal for use in resource-limited settings where Q fever is endemic.

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

We described here a simple loop-mediated isothermal amplification (LAMP) method using lyophilized reagents for the detection of C. burnetii in patient samples.

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. ...

Visualization of the Charcoal Agar Resazurin Assay for Semi-quantitative, Medium-throughput Enumeration of Mycobacteria

There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the etiological agent of TB, is refractory to rapid and lasting chemotherapy due to the presence of bacilli exhibiting phenotypic drug resistance. The charcoal agar resazurin assay (CARA) was developed as a tool to characterize active molecules discovered by high-throughput screening campaigns against replicating and non-replicating M. tuberculosis. Inclusion of activated charcoal in bacteriologic agar medium helps mitigate the impact of compound carry-over, and eliminates the requirement to pre-dilute cells prior to spotting on CARA microplates. After a 7-10 day incubation period at 37 &#176;C, the reduction of resazurin by mycobacterial microcolonies growing on the surface of CARA microplate wells permits semi-quantitative assessment of bacterial numbers via fluorometry. The CARA detects approximately a 2-3 log10 difference in bacterial numbers and predicts a minimal bactericidal concentration leading to &#8805;99% bacterial kill (MBC&#8805;99). The CARA helps determine whether a molecule is active on bacilli that are replicating, non-replicating, or both. Pilot experiments using the CARA facilitate the identification of which concentration of test agent and time of compound exposure require further evaluation by colony forming unit (CFU) assays. In addition, the CARA can predict if replicating actives are bactericidal or bacteriostatic.

The charcoal agar resazurin assay (CARA) is a semi-quantitative, medium-throughput method to assess activity of test agents against mycobacteria that are replicating, non-replicating, or both. The CARA permits rapid evaluation of time- and concentration-dependent activity and identifies parameters to pursue by colony forming unit (CFU) assays.

There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the ...

Development of Stem Cell-derived Antigen-specific Regulatory T Cells Against Autoimmunity

Autoimmune diseases arise due to the loss of immunological self-tolerance. Regulatory T cells (Tregs) are important mediators of immunologic self-tolerance. Tregs represent about 5 - 10% of the mature CD4+ T cell subpopulation in mice and humans, with about 1 - 2% of those Tregs circulating in the peripheral blood. Induced pluripotent stem cells (iPSCs) can be differentiated into functional Tregs, which have a potential to be used for cell-based therapies of autoimmune diseases. Here, we present a method to develop antigen (Ag)-specific Tregs from iPSCs (i.e., iPSC-Tregs). The method is based on incorporating the transcription factor FoxP3 and an Ag-specific T cell receptor (TCR) into iPSCs and then differentiating on OP9 stromal cells expressing Notch ligands delta-like (DL) 1 and DL4. Following in vitro differentiation, the iPSC-Tregs express CD4, CD8, CD3, CD25, FoxP3, and Ag-specific TCR and are able to respond to Ag stimulation. This method has been successfully applied to cell-based therapy of autoimmune arthritis in a murine model. Adoptive transfer of these Ag-specific iPSC-Tregs into Ag-induced arthritis (AIA)-bearing mice has the ability to reduce joint inflammation and swelling and to prevent bone loss.

We present here a method to develop functional antigen (Ag)-specific regulatory T cells (Tregs) from induced pluripotent stem cells (iPSCs) for immunotherapy of autoimmune arthritis in a murine model.

Autoimmune diseases arise due to the loss of immunological self-tolerance. Regulatory T cells (Tregs) are important mediators of immunologic ...

Use of the Soft-agar Overlay Technique to Screen for Bacterially Produced Inhibitory Compounds

The soft-agar overlay technique was originally developed over 70 years ago and has been widely used in several areas of microbiological research, including work with bacteriophages and bacteriocins, proteinaceous antibacterial agents. This approach is relatively inexpensive, with minimal resource requirements. This technique consists of spotting supernatant from a donor strain (potentially harboring a toxic compound(s)) onto a solidified soft agar overlay that is seeded with a bacterial test strain (potentially sensitive to the toxic compound(s)). We utilized this technique to screen a library of Pseudomonas syringae strains for intraspecific killing. By combining this approach with a precipitation step and targeted gene deletions, multiple toxic compounds produced by the same strain can be differentiated. The two antagonistic agents commonly recovered using this technique are bacteriophages and bacteriocins. These two agents can be differentiated using two simple additional tests. Performing a serial dilution on a supernatant containing bacteriophage will result in individual plaques becoming less in number with greater dilution, whereas serial dilution of a supernatant containing bacteriocin will result a clearing zone that becomes uniformly more turbid with greater dilution. Additionally, a bacteriophage will produce a clearing zone when spotted onto a fresh soft agar overlay seeded with the same strain, whereas a bacteriocin will not produce a clearing zone when transferred to a fresh soft agar lawn, owing to the dilution of the bacteriocin.

We describe a simple method for screening bacterial cultures for the production of compounds inhibitory towards other bacteria.

The soft-agar overlay technique was originally developed over 70 years ago and has been widely used in several areas of microbiological research, ...

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

B cells reactive with a specific antigen usually occur at a frequency of &lt;0.05% of lymphocytes. For decades researchers have sought methods to isolate and enrich these rare cells for studies of their phenotype and biology. Approaches are inevitably based on the principle that B cells recognize native antigen by virtue of cell surface receptors that are representative in specificity of antibodies that will eventually be secreted by their differentiated daughters. Perhaps the most obvious approach to the problem involves use of fluorochrome-conjugated antigens in conjunction with fluorescence-activated cell sorting (FACS). However, the utility of these methods is limited by cell frequency and the achievable rate of analysis and isolation by electronic sorting. A novel method to enrich rare antigen-specific B cells using magnetic nanoparticles that results in high yield enrichment of antigen-reactive B cells from large starting cell populations is described. This method enables improved monitoring of the phenotype and biology of antigen reactive cells before and following in vivo antigen encounter, such as after immunization or during development of autoimmunity.

A simple yet effective method that employs magnetic nanoparticles to detect and enrich antigen-reactive B cells for functional and phenotypic analysis is described.

B cells reactive with a specific antigen usually occur at a frequency of &lt;0.05% of lymphocytes. For decades researchers have sought methods to isolate ...

Laboratory Techniques Used to Maintain and Differentiate Biotypes of Vibrio cholerae Clinical and Environmental Isolates

The aquatic Gram-negative bacterium Vibrio cholerae is the etiological agent of the infectious gastrointestinal disease cholera. Due to the global prevalence and severity of this disease, V. cholerae has been extensively studied in both environmental and laboratory settings, requiring proper maintenance and culturing techniques. Classical and El Tor are two main biotypes that compose the V. cholerae O1 serogroup, each displaying unique genotypic and phenotypic characteristics that provide reliable mechanisms for biotype characterization, and require distinct virulence inducing culturing conditions. Regardless of the biotype of the causative strain for any given infection or outbreak, the standard treatment for the disease involves rehydration therapy supplemented with a regimen of antibiotics. However, biotype classification may be necessary for laboratory studies and may have broader impacts in the biomedical field. In the early 2000&#39;s clinical isolates were identified which exhibit genotypic and phenotypic traits from both classical and El Tor biotypes. The newly identified hybrids, termed El Tor variants, have caused clinical and environmental isolate biotype identification to become more complex than previous traditional single assay identification protocols. In addition to describing V. cholerae general maintenance and culturing techniques, this manuscript describes a series of gene specific (ctxB and tcpA) PCR-based genetic screens and phenotypic assays (polymyxin B resistance, citrate metabolism, proteolytic activity, hemolytic activity, motility, and glucose metabolism via Voges-Proskauer assay) collectively used to characterize and/or distinguish between classical and El Tor biotypes. Together, these assays provide an efficient systematic approach to be used as an alternative, or in addition, to costly, labor-intensive experiments in the characterization of V. cholerae clinical (and environmental) isolates.

Laboratory Techniques Used to Maintain and Differentiate Biotypes of Vibrio cholerae Clinical and Environmental Isolates

This manuscript describes proper Vibrio cholerae maintenance techniques in addition to a series of biochemical assays, collectively utilized for quick and reliable differentiation between clinical and environmental V. cholerae biotypes in a laboratory setting.

Development of a More Sensitive and Specific Chromogenic Agar Medium for the Detection of Vibrio parahaemolyticus and Other Vibrio Species

Summary

Explore More Videos

Chapters in this video

Colonization of Euprymna scolopes Squid by Vibrio fischeri

TransFLP — A Method to Genetically Modify Vibrio cholerae Based on Natural Transformation and FLP-recombination

Use of Artificial Sputum Medium to Test Antibiotic Efficacy Against Pseudomonas aeruginosa in Conditions More Relevant to the Cystic Fibrosis Lung

Loop-mediated Isothermal Amplification (LAMP) Assays for the Species-specific Detection of Eimeria that Infect Chickens

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

Visualization of the Charcoal Agar Resazurin Assay for Semi-quantitative, Medium-throughput Enumeration of Mycobacteria

Development of Stem Cell-derived Antigen-specific Regulatory T Cells Against Autoimmunity

Use of the Soft-agar Overlay Technique to Screen for Bacterially Produced Inhibitory Compounds

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

Laboratory Techniques Used to Maintain and Differentiate Biotypes of Vibrio cholerae Clinical and Environmental Isolates