This work was supported by the National Institutes of Health (NIH) grants R44GM113545 and P20GM103434.

Before beginning animal experiments, the protocol to be used must be approved by the Institutional Animal Care and Use Committee (IACUC). Approval for the protocol described was obtained through the IACUC at Marshall University (Huntington, WV, USA).
1. Plasmid Design
<ol>
	<li>To generate a genetic deletion using the pEX100T-NotI plasmid, clone the regions of DNA flanking the desired deletion sequence and insert into the NotI restriction site of the plasmid. The plasmid insert should contai...

<ol>
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T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+improved+system+for+gene+replacement+and+xylE+fusion+analysis+in+Pseudomonas+aeruginosa.">An improved system for gene replacement and xylE fusion analysis in Pseudomonas aeruginosa.</a> Gene. 158 (1), 15-22 (1995).</li><li>Damron, F. H., Qiu, D., Yu, H. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Pseudomonas+aeruginosa+sensor+kinase+KinB+negatively+controls+alginate+production+through+AlgW-dependent+MucA+proteolysis.">The Pseudomonas aeruginosa sensor kinase KinB negatively controls alginate production through AlgW-dependent MucA proteolysis.</a> Journal of Bacteriology. 191 (7), 2285-2295 (2009).</li><li>Yu, H., Boucher, J. C., Hibler, N. 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L., Vazquez, E., Villaverde, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+factories+for+recombinant+pharmaceuticals.">Microbial factories for recombinant pharmaceuticals.</a> Microbial Cell Factories. 8, 17 (2009).</li><li>Horton, R. M., Cai, Z. L., Ho, S. N., Pease, L. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+splicing+by+overlap+extension:+tailor-made+genes+using+the+polymerase+chain+reaction.">Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction.</a> Biotechniques. 8 (5), 528-535 (1990).</li><li>Horton, R. M., Hunt, H. D., Ho, S. N., Pullen, J. K., Pease, L. 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The pEX100T-Not1 plasmid is an efficient mediator of sequential genomic deletions that are marker-free and in-frame. When engineering bacterial strains for attenuated virulence, deletion of entire gene sequences rather than generating point mutations decreases the likelihood of reversion to a virulent phenotype. Additionally, each pathogenicity gene deletion attenuates the pathogen further, reinforcing the stability of the attenuation.
This method can also be used to generate genomic modificat...

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that can cause life-threatening diseases in humans, especially in the immunocompromised. The pathogenicity of P. aeruginosa is due to the expression of many virulence factors, including proteases and lipopolysaccharide, as well as its ability to form a protective biofilm1. Because of its ability to produce virulence factors and cause disease in humans, using P. aeruginosa to make commercial products presents safety concerns. Nonpathogenic strains of E. coli have traditionally been used to bioengineer medical and commercial products for human use. However, some products are difficult for E. coli to make, and many are packaged in inclusion bodies, making extraction laborious. Engineered bacterial strains with the ability to make and secrete specific products is highly desirable, as secretion would likely increase yield and ease purification processes. Thus, nonpathogenic strains of other species of bacteria (e.g., species that utilize more secretion pathways) may provide useful alternatives to E. coli. We recently reported the development of a strain of P. aeruginosa, PGN5, in which the pathogenicity and toxicity of the organism is highly attenuated2. Importantly, this strain still produces large quantities of the polysaccharide alginate, a commercially interesting component of the P. aeruginosa biofilm.
The PGN5 strain was generated using a two-step allelic exchange procedure with the pEX100T-NotI plasmid to sequentially delete five genes (toxA, plcH, phzM, wapR, aroA) known to contribute to the pathogenicity of the organism. pEX100T-NotI was generated by changing the SmaI to a NotI restriction enzyme recognition site within the multiple cloning site of the plasmid pEX100T, which was developed in Herbert Schweizer&#39;s lab3,4. The recognition site for the restriction enzyme NotI is a rarer DNA sequence compared to SmaI and less likely to be present in sequences being cloned, thus it is more convenient for cloning purposes. The plasmid carries genes that allow for selection, including the bla gene, which encodes &#223;-lactamase and confers resistance to carbenicillin, and the B. subtilissacB gene, which confers sensitivity to sucrose (Figure 1A). The plasmid also carries an origin of replication (ori) compatible with E. coli, and an origin of transfer (oriT) that allows for plasmid transfer from E. coli to Pseudomonas species via conjugation. However, the plasmid lacks an origin of replication compatible with Pseudomonas, and thus cannot replicate within Pseudomonas species (i.e., it is a Pseudomonas suicide vector). These characteristics make pEX100T-NotI ideal for targeting genetic deletions from the Pseudomonas chromosome. Plasmid cloning steps are carried out using E. coli and the resultant plasmid is transferred to Pseudomonas by transformation or conjugation. Then, through homologous recombination events and selective steps, the targeted in-frame deletion is generated, marker-free. This method of sequentially deleting genomic regions from the chromosome of P. aeruginosa could be used to generate highly attenuated Pseudomonas strains, like PGN5, or to design strains for other specific uses (e.g., strains deficient in endonucleases for plasmid propagation or strains deficient in proteases for production of proteins of interest).
The overall virulence of strains of bacteria is affected by growth conditions and phases, during which mutations occur frequently. Therefore, measuring the safety of genetically-engineered strains can be challenging. To evaluate bacterial isolates for systemic virulence, we adapted a previously published protocol of infection by intraperitoneal injection of C57BL/6 mice5. We modified this procedure to use frozen bacterial stocks for injection, which allowed for precise dosing and easy validation of the strains used. In this model, the E. coli strain BL21, which has been FDA-approved for production of biopharmaceuticals, was used as a control safety standard for determining the relative pathogenesis of the strain6,7,8. The main advantage to using this method is that it is reproducible and minimizes sources of variation, as infecting strains are validated for bacterial cell number, phenotype, and genetic markers both before and after infection. With these controlled steps, the number of animals required is reduced. In this model, P. aeruginosa strains that result in C57BL/6 murine mortality rates equal to or less than E. coli BL21 when injected intraperitoneally may be considered attenuated. This simple mouse model of infection may also be used to assess the attenuated pathogenicity of genetically engineered strains from other species using the FDA-approved E. coli strain as the reference. Steps 1-7 detail the generation of sequential genomic deletions in P. aeruginosa (Figure 1) and steps 8-12 detail the use of a mouse model to test the pathogenicity of P. aeruginosa strains.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.2 mL tubes with flat caps</td>
			<td>ThermoScientific</td>
			<td>AB-0620</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>1 mL Syringe</td>
			<td>BD</td>
			<td>22-253-260</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>1.5 mL disposable polystyrene cuvette</td>
			<td>Fisher Scientific</td>
			<td>14955127</td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 mL Microcentrifuge Tubes</td>
			<td>Fisher Scientific</td>
			<td>05-408-129</td>
			<td></td>
		</tr>
		<tr>
			<td>2.0 mL Cryogenic Vials</td>
			<td>Corning</td>
			<td>430659</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>27G needle</td>
			<td>BD</td>
			<td>14-821-13B</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>50 mL tubes</td>
			<td>Fisher Scientific</td>
			<td>05-539-13</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Accu block Digital Dry Bath</td>
			<td>Labnet</td>
			<td>NC0205808</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Benchtop Centrifuge 5804R</td>
			<td>Eppendorf</td>
			<td>04-987-372</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Benchtop Microcentrifuge</td>
			<td>Sorvall</td>
			<td>75-003-287</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Cabinet Incubator</td>
			<td>VWR</td>
			<td>1540</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbenicillin disodium salt</td>
			<td>Fisher Scientific</td>
			<td>BP2648250</td>
			<td></td>
		</tr>
		<tr>
			<td>Culture Test Tube, Polystyrene</td>
			<td>Fisher Scientific</td>
			<td>14-956-6D</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Diposable Inoculation Loops</td>
			<td>Fisher Scientific</td>
			<td>22-363-597</td>
			<td></td>
		</tr>
		<tr>
			<td>Dneasy UltraClean Microbial Kit (50)</td>
			<td>Qiagen</td>
			<td>12224-50</td>
			<td>or preferred method/vendor</td>
		</tr>
		<tr>
			<td>E.Z.N.A. Cycle Pure Kit (50)</td>
			<td>Omega bio-tek</td>
			<td>D6493-01</td>
			<td>or preferred method/vendor</td>
		</tr>
		<tr>
			<td>EcoRI-HF, restriction endonuclease</td>
			<td>New England BioLabs</td>
			<td>R3101L</td>
			<td></td>
		</tr>
		<tr>
			<td>Electroporation Cuvettes</td>
			<td>Bulldog Bio</td>
			<td>NC0492929</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>FastLink II DNA Ligation Kit</td>
			<td>Epicentre Technologies</td>
			<td>LK6201H</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Gentamycin Sulfate</td>
			<td>Fisher Scientific</td>
			<td>BP918-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Fisher Scientific</td>
			<td>BP229-4</td>
			<td></td>
		</tr>
		<tr>
			<td>GoTaq G2 Colorless Master Mix</td>
			<td>Promega</td>
			<td>M7833</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Isothesia Isoflurane</td>
			<td>Henry Schein Animal Health</td>
			<td>29405</td>
			<td></td>
		</tr>
		<tr>
			<td>IVIS Lumina XRMS Series III In Vivo Imaging System</td>
			<td>Perkins and Elmer</td>
			<td>CLS136340</td>
			<td></td>
		</tr>
		<tr>
			<td>Kanamycin monosulfate</td>
			<td>Fisher Scientific</td>
			<td>BP906-5</td>
			<td></td>
		</tr>
		<tr>
			<td>LE agarose</td>
			<td>Genemate</td>
			<td>3120-500</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Luria Broth</td>
			<td>Difco</td>
			<td>240230</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>MicroPulser Electroporator</td>
			<td>BioRad</td>
			<td>1652100</td>
			<td></td>
		</tr>
		<tr>
			<td>Noble agar, ultrapure</td>
			<td>Affymetris/USB</td>
			<td>AAJ10907A1</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>NotI-HF, restriction endonuclease</td>
			<td>New England BioLabs</td>
			<td>R3189</td>
			<td></td>
		</tr>
		<tr>
			<td>One Shot TOP10 Electrocomp E. coli</td>
			<td>Invitrogen</td>
			<td>C404052</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Phosphate buffered saline powder</td>
			<td>Sigma</td>
			<td>P3813-10PAK</td>
			<td>Sigma-Aldrich</td>
		</tr>
		<tr>
			<td>Prism 7</td>
			<td>GraphPad</td>
			<td></td>
			<td><a href="https://www.graphpad.com/scientific-software/prism/" target="_blank">https://www.graphpad.com/scientific-software/prism/</a></td>
		</tr>
		<tr>
			<td>Pseudomonas isolation agar</td>
			<td>Difco</td>
			<td>292710</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Pseudomonas isolation broth</td>
			<td>Alpha Biosciences</td>
			<td>P16-115</td>
			<td>Custom made batch</td>
		</tr>
		<tr>
			<td>QIAprep Spin Miniprep Kit (250)</td>
			<td>Qiagen</td>
			<td>27106</td>
			<td>or preferred method/vendor</td>
		</tr>
		<tr>
			<td>Shaking Incubator</td>
			<td>New Brunswick Scientific</td>
			<td>Innova 4080</td>
			<td>shake at 200 rpm</td>
		</tr>
		<tr>
			<td>SimpliAmp Thermal Cycler</td>
			<td>Applied Biosystems</td>
			<td>A24811</td>
			<td></td>
		</tr>
		<tr>
			<td>Skim Milk</td>
			<td>Difco</td>
			<td>DF0032-17-3</td>
			<td>via Fisher Scientific</td>
		</tr>
		<tr>
			<td>Small Plates (100 O.D. x 10 mm)</td>
			<td>Fisher Scientific</td>
			<td>FB0875713</td>
			<td></td>
		</tr>
		<tr>
			<td>SmartSpec Plus Spectrophotometer</td>
			<td>Bio-Rad</td>
			<td>170-2525</td>
			<td>or preferred method/vendor</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Fisher Scientific</td>
			<td>S5-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Toothpicks, round</td>
			<td>Diamond</td>
			<td></td>
			<td>Any brand of toothpicks, autoclaved</td>
		</tr>
		<tr>
			<td>TOPO TA Cloning Kit, for seqeuncing</td>
			<td>Invitrogen</td>
			<td>45-0030</td>
			<td></td>
		</tr>
		<tr>
			<td>XAF-8 Anesthesia System Filters</td>
			<td>Perkins and Elmer</td>
			<td>118999</td>
			<td></td>
		</tr>
		<tr>
			<td>XGI 8 Gas Anesthesia System</td>
			<td>Caliper Life Sciences/Xenogen</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

generation of in-frame gene deletion mutants in pseudomonas aeruginosa and testing for virulence attenuation in a simple mouse model of infection

Microorganisms are genetically versatile and diverse and have become a major source of many commercial products and biopharmaceuticals. Though some of these products are naturally produced by the organisms, other products require genetic engineering of the organism to increase the yields of production. Avirulent strains of Escherichia coli have traditionally been the preferred bacterial species for producing biopharmaceuticals; however, some products are difficult for E. coli to produce. Thus, avirulent strains of other bacterial species could provide useful alternatives for production of some commercial products. Pseudomonas aeruginosa is a common and well-studied Gram-negative bacterium that could provide a suitable alternative to E. coli. However, P. aeruginosa is an opportunistic human pathogen. Here, we detail a procedure that can be used to generate nonpathogenic strains of P. aeruginosa through sequential genomic deletions using the pEX100T-NotI plasmid. The main advantage of this method is to produce a marker-free strain. This method may be used to generate highly attenuated P. aeruginosa strains for the production of commercial products, or to design strains for other specific uses. We also describe a simple and reproducible mouse model of bacterial systemic infection via intraperitoneal injection of validated test strains to test the attenuation of the genetically engineered strain in comparison to the FDA-approved BL21 strain of E. coli.

As shown in Figure 2, the targeted genomic deletion can be confirmed using colony PCR with specific primers that amplify the region of interest. Colonies that carry a genomic deletion will yield a shorter PCR band size in comparison to wild-type colonies. A PCR-screen of 10-12 colonies is usually sufficient to detect at least one colony that carries the targeted deletion. If no deletions are detected after multiple rounds of screens, repeat the procedure begi...

Watch this Scientific Journal Video about Generation of In-Frame Gene Deletion Mutants in Pseudomonas aeruginosa and Testing for Virulence Attenuation in a Simple Mouse Model of Infection at JoVE.com

Generation of In-Frame Gene Deletion Mutants in Pseudomonas aeruginosa and Testing for Virulence Attenuation in a Simple Mouse Model of Infection

Here, we describe a simple and reproducible protocol of mouse model of infection to evaluate the attenuation of the genetically modified strains of Pseudomonas aeruginosa in comparison to the United States Food and Drug Administration (FDA)-approved Escherichia coli for commercial applications.

Generation of In-Frame Gene Deletion Mutants in Pseudomonas aeruginosa and Testing for Virulence Attenuation in a Simple Mouse Model of Infection

Microorganisms are genetically versatile and diverse and have become a major source of many commercial products and biopharmaceuticals. Though some of ...

This protocol is significant for creating and determining mind-body desired mutations in the genome of Pseudomonas aeruginosa, as well as the testing the effect of mutations on virulence reduction in a reproducible mouse model. The key advantage of this technique is a chrome validation and a reproducibility of mouse infection model. Bacteria are constantly working, continually changing.To slow down this process, we use a frozen stops, bag them, hang them on multiple rungs on modification before testing them in the mouse model. Someone unfamiliar with these methods will most likely struggle with the development and selection of possible crossover recombinant to test. Furthermore, the handling of the mice for infection will be difficult for someone unfamiliar with animal work.This method can be applied to testing other pathogens and their mutants, as well as virulence infect in mice. Compared to current models, procedures with reproducibility plus clone validation before and after infection can benefit other investigators in the field. Visual demonstration of this protocol provides insight to extensive procedures that may be difficult to understand or comprehend through reading alone.Start by growing single crossover, recombinant colonies in Pseudomonas Isolation Broth, or PIB. Inoculate and streak 10 microliters of each culture onto pre-warmed PIA plates, supplemented with 10%sucrose. Then incubate the plates overnight at 37 degrees Celsius.On the next day, remove the plates from the incubator and inspect them for growth. The sucrose resistant colony should be double crossover recombinants. Use sterile toothpicks to patch at least 20 colonies onto pre-warmed plates of PIA, PIA supplemented with 10%sucrose, and PIA supplemented with carbenicillin.Incubate the plates overnight and examine them for growth on the next day. True double crossover recombinants will be carbenicillin-sensitive and sucrose-resistant. Screen 10 to 20 colonies for deletion, using colony PCR.Pick up the growth of a suspected double crossover recombinant with a sterile toothpick and suspend it in 50 microliters of PBS. Boil the suspension at 100 degrees Celsius for 10 minutes. Centrifuge it for three minutes at 13, 000 times G and place it on ice.Then, perform PCR according to manuscript directions. Once PCR is finished, perform Agarose gel electrophoresis on the products. Smaller amplification products indicate colonies in which the region of interest has been deleted.On the morning of injections, thaw the cryovials of bacterial cells at four degrees Celsius for three to four hours. Keep the vials on ice after thawing and inject the mice within two hours. Transfer the contents of each cryovial to a new two milliliter tube and centrifuge it at 4, 500 times G for 10 minutes.Discard the supernatant and re-suspend the cell pellet in one milliliter of PBS. Repeat the centrifugation and re-suspend the cells in PBS to a final concentration of 2.5 times 10 to the ninth colony forming units per milliliter. Take three samples from the final suspension of each strain to validate concentration, genotype, and phenotype.For each strain, aliquot 1.5 milliliters of the cell suspension into a two milliliter tube and prepare the PBS for control injections. Gather the mice and materials needed for injections in a sterile animal surgical room and wipe all surfaces with sanitizing wipes prior to starting. Wear two pairs of latex gloves to limit the risk of puncture, if bitten, as well as a lab coat, safety glasses, and face mask.Remove the mouse from the cage and weigh it, marking the tail with permanent marker for post-injection tracking. Open a new one milliliter syringe with a 27 gauge needle and draw up 200 microliters of sterile PBS. Grab the mouse behind its ears, using the thumb and forefinger, and pinch to create a skin fold at the nape of the neck.Then, secure the tail into the palm using the pinky to hold the mouse flat and immobile. Insert the needle at a 30 degree angle into the peritoneal cavity to the left or right of the midline. Slightly lift the needle to ensure that it was not inserted into organs.Then, slowly inject the PBS and withdraw the needle. A bolus at the injection site is typical. Place the needle in the designated sharps disposal container and move the mouse to a separate cage.Repeat the procedure with the next mouse and after all mice from one cage are injected, move them back to their original cage. After injecting the control group, inject the test groups using the same procedure. Once all injections are complete, return the mice to the housing room and clean the work area with sanitizing wipes.To image the animals, prepare the imaging system by setting the camera parameters and heating the stage. Set the oxygen flow to 1.5 liters per minute and isoflurane to 3.5%and move the mouse to the anesthetic chamber, then to the temperature stabilized stage, following anesthesia. Position the mouse on its back with arms outstretched and fit a nose cone for administration of 2.5%isoflurane during imaging.Close the door and take bioluminescent images and x-rays of the mouse. When imaging is complete, return the mouse to its cage and monitor it. It should regain consciousness within three to five minutes.The targeted genomic deletions were confirmed by colony PCR with specific primers that amplified the region of interest. Colonies with the genomic deletion yield a shorter PCR band compared to wild type colonies. Intraperitoneal injection of the attenuated strain of P aeruginosa, PGN five, resulted in 0%mortality, equivalent to mortality observed with E.coli BL 21.Injection of the parent strain, however, was fatal to 80%of the mice. Infection progression was tracked using bioluminescence-marked parent and attenuated strains. The attenuated strain remained localized at the injection site until bioluminescence faded, which likely coincided with clearance of infection.The method presented only examined the mortality produced by the strain. More in depth immunological and toxicological aspects could be utilized to determine the dynamics of infection and the end effect the infection has that does not result in death. The most important thing in the procedure is the extensive validation done, between various steps from initial identification to animal testing.Missing certain validation steps could potentially lead to wrong result, as the strains tested may undergo mutation and selection, or become contaminated. With the development of these two techniques, we think this will allow our researchers in the field of infection immunology to more effectively investigate how powerful package interaction leads to the extreme phenotype, sepsis, and mortality. Different nutrients'impact on variants can be compared through size dosing of bacteria.

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Research

JoVE Journal

Immunology and Infection

6.5K vistas.  Progenesis Technologies, LLC. Este protocolo es significativo para crear y determinar mutaciones deseadas mente-cuerpo en el genoma de Pseudomonas aeruginosa, así como para probar el efecto de mutaciones en la reducción de la virulencia en un modelo de ratón reproducible. La principal ventaja de esta técnica es la validación de cromo y la reproducibilidad del modelo de infección del ratón. Las bacterias están trabajando constantemente, cambiando continuamente.Para ralentizar este proceso, usamos una parada ...

Video: Generation of In-Frame Gene Deletion Mutants in Pseudomonas aeruginosa and Testing for Virulence Attenuation in a Simple Mouse Model of Infection