Name: a reference broth microdilution method for dalbavancin in vitro susceptibility testing of bacteria that grow aerobically
Uploaded: 2015-09-09T14:00:00
Duration: 11 min 28 s
Description: Watch this Scientific Journal Video about A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically at JoVE.com

Prior work with regard to susceptibility testing of dalbavancin has been valuable in development of a standardized methods and acknowledgement for this work is given to JMI Laboratories, Robert Rennie and Beth Goldstein.

Note: Refer to CLSI documents M7-A10 and M100-S25 and/or ISO/FDIS 20776-1 for full details of the reference broth microdilution method for antimicrobial susceptibility2, 3, 4. The reference methods allow for options in some of the procedures specific to inoculum preparation and MIC panel production to achieve the same end result. The method detailed here relates to one antimicrobial agent, dalbavancin, and some of the steps represent one of potentially several ways the reference procedure can be done. Appropriate safety precautions (consistent with biosafety level 2) should be utilized10. The MIC panel format used for the purpose of this video publication is shown in Table 1.
1. Store Dalbavancin Powder
<ol>
	<li>Upon receipt of diagnostic grade dalbavancin powder, store at -20 oC in a desiccated environment in a non-defrosting freezer. Prior to use, the powder should equilibrate to reach RT before opening.</li>
</ol>
2. Prepare MIC Panel Dilutions
<ol>
	<li>Prepare a stock solution no higher than 1,600 &#181;g/ml of dalbavancin in neat (pure) DMSO in sterile glass or plastic tubes, and use on the same day of preparation or store at -20 to -60 oC or below for future use in a non-defrosting freezer. Take into consideration the potency of dalbavancin as provided on the documentation received with the powder, when weighing the powder (see Equation 1 for example 800 &#181;g/ml stock preparation).</li>
	<li>Dilute the stock dilution similar to the scheme as is shown in column 1 (&#8220;Source Concentration&#8221;) in Table 2 with neat DMSO in sterile glass or plastic tubes. Use one pipet for measuring diluent and another pipet for adding the initial dalbavancin stock to the first tube. For each subsequent dalbavancin stock concentration use a new pipet.</li>
	<li>Prepare 100X final MIC panel concentration dilutions (intermediate concentrations) with neat DMSO. As is shown in columns 2-4 of Table 2, combine appropriate volumes of source and DMSO to achieve desired intermediate concentration (volumes to be used will depend on number of MIC panels to be made).</li>
	<li>Prepare 0.004% P80: Prepare a fresh working stock solution of 2% P80 by adding 0.1 ml P80 to 4.9 ml dH2O. Sterilize by passing through a 0.22 micron filter and use solution on the same day of preparation. Prepare 0.004% P80 diluent by making a 1:500 dilution of 2% P80 (e.g., 0.3 ml of 2% P80 to 149.7 ml of CAMHB).</li>
	<li>Further dilute the intermediate concentrations prepared in Step 2.2 1:100 in cation adjusted Mueller Hinton broth (CAMHB) supplemented with 0.004% (v/v) polysorbate-80 (P-80) P-80 and/or LHB (for streptococci) added at double the final concentration because addition of inoculum (step 4.3) will result in a 1:2 dilution. See columns 6 and 7 in Table 2.</li>
</ol>
3. Prepare MIC Panels
<ol>
	<li>Dispense 50 &#181;l of each dalbavancin solution prepared in step 2.3 into appropriate wells of the MIC panel and include media only in one well (growth control well). A multi-channel pipet with sterile tips can be used for this step.</li>
	<li>Use panels immediately or seal with plastic film, place in plastic bags and immediately place in a non-defrosting freezer at &#8804;-20 oC (preferably at &#8804;-60 oC) until needed. If frozen panels are used, remove seals and place individual panels on lab bench for 15-30 min&#160;(until well contents are thawed) before proceeding to panel inoculation.</li>
</ol>
4. Inoculate MIC Panels, Perform Purity and Setup Colony Count
<ol>
	<li>Select several well-isolated colonies from an 18-24 hr blood agar or other non-selective agar plate. Touch the top of each colony with a sterile loop or swab and transfer to 1-5 ml CAMHB or saline until turbidity is equivalent to a 0.5 McFarland standard. Assess turbidity by visual comparison to the 0.5 McFarland or with a photometric device.</li>
	<li>Within 15-30 min&#160;of preparation, dilute the inoculum 1:100 in CAMHB (100 &#181;l into 10 ml CAMHB). For most bacteria tested against dalbavancin, with the exception of S. pneumoniae, this dilution will provide a final well concentration of 5 x 105 CFU/ml (acceptable range is 2-8 x 105 CFU/ml). For S. pneumoniae, bacterial concentration based on comparison of turbidity to a 0.5 McFarland is typically considerably less, therefore, dilute the inoculum 1:25 (400 &#181;l into 10 ml CAMHB+10% +LHB).</li>
	<li>Within 15 min after inoculum preparation, transfer 50 &#181;l of the final inoculum to each well (with exception of the sterility control well) of the MIC panel prepared in step 3. A multi-channel pipet using sterile tips can be used for this step.</li>
	<li>Perform a purity check by transferring and spreading a 1-10 &#181;l aliquot from the positive growth control well using a sterile loop to a nonselective agar (e.g., trypticase soy agar with 5% sheep blood).</li>
	<li>Setup colony count by removing 10 &#181;l from the growth control well with a single channel pipet and sterile tip and transfer to 10 ml of saline (1:1,000 dilution). Mix and transfer 100 &#181;l with a single channel pipet and sterile tip to a suitable, nonselective agar medium (e.g., trypticase soy agar with 5% sheep blood) and spread over the entire agar surface with a sterile loop, repeating two times in different directions to assure even distribution of the inoculum (1:10 dilution).</li>
</ol>
5. Incubate MIC Panels, Colony Count and Purity Plates
<ol>
	<li>Seal each MIC panel or stack of no more than 4 panels in a plastic bag, with plastic tape or with a tight-fitting plastic cover before incubating. Alternatively, place empty MIC panel on the top of stack of no more than 4 MIC panels, place a damp paper towel in a plastic container, place MIC panels in the plastic container and close container securely with lid.</li>
	<li>Incubate MIC panels in an ambient air incubator at 35 &#176;C &#177; 2 &#176;C for 16-20 hr (staphylococci and enterococci) and 20-24 hr (streptococci) within 30 min&#160;of inoculation. Incubate the colony count and purity plates under same conditions except incubate streptococci in a 5% CO2 incubator.</li>
</ol>
6. Read the MIC and Colony Count Plates; Check Purity Plate
<ol>
	<li>Read the MIC as the lowest concentration that completely inhibits bacterial growth in the wells as detected by the unaided eye.</li>
	<li>Count colonies on the colony count plate. Multiply each colony by dilution factor (1:10,000) (e.g., 50 colonies is equivalent to 5 x 105 CFU/ml). An acceptable range is 20-80 colonies (2-8 x 105 CFU/ml) and is used as an approximate guideline.</li>
	<li>Check purity plate. If all colonies are similar to the colonies used in step 4.1, then the inoculum can be considered pure. If there are any other colonies present, then there is potential for a contaminant to be present in the MIC panel and the test should be repeated.</li>
</ol>
7. Check Quality Control Results.
<ol>
	<li>Refer to Table 3 for expected ranges of CLSI quality control strains. Only report results of test isolates if dalbavancin MIC results for quality control organism(s) are within the expected range.</li>
	<li>If an MIC of &#8805;0.25 &#181;g/ml is obtained for any clinical S. aureus isolate, repeat the dalbavancin MIC testing and/or send to a reference laboratory for verification.</li>
</ol>

<ol>
	<li>Boucher, H. W., 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=Once-weekly+dalbavancin+versus+daily+conventional+therapy+for+skin+infection.">Once-weekly dalbavancin versus daily conventional therapy for skin infection.</a> The New England journal of medicine. 370, 2169-2179 (2014).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> M07-A10. Methods for Dilution Antimicrobial Tests for Bacteria that Grow Aerobically.: Approved Standard. , (2015).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> M100-S25. Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fifth Informational Supplement. , (2015).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+laboratory+testing+and+in+vitro+diagnostic+test+systems+--+Susceptibility+testing+of+infectious+agents+and+evaluation+of+performance+of+antimicrobial+susceptibility+test+devices+--+Part+1:+Reference+method+for+testing+the+in+vitro+activity+of+antimicrobial+agents+against+rapidly+growing+aerobic+bacteria+involved+in+infectious+diseases.">Clinical laboratory testing and in vitro diagnostic test systems -- Susceptibility testing of infectious agents and evaluation of performance of antimicrobial susceptibility test devices -- Part 1: Reference method for testing the in vitro activity of antimicrobial agents against rapidly growing aerobic bacteria involved in infectious diseases.</a> ISO/FDIS. 20776-1, (2006).</li><li>Jones, R. N., Farrell, D. J., Flamm, R. K., Sader, H. S., Dunne, M. W., Mendes, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surrogate+analysis+of+vancomycin+to+predict+susceptible+categorization+of+dalbavancin.">Surrogate analysis of vancomycin to predict susceptible categorization of dalbavancin.</a> Diagn Microbiol Infect Dis. , (2015).</li><li>Turnidge, J., Paterson, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Setting+and+revising+antibacterial+susceptibility+breakpoints.">Setting and revising antibacterial susceptibility breakpoints.</a> Clinical microbiology reviews. 20, 391-408 (2007).</li><li>Rennie, R. P., 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=Factors+influencing+broth+microdilution+antimicrobial+susceptibility+test+results+for+dalbavancin,+a+new+glycopeptide+agent.">Factors influencing broth microdilution antimicrobial susceptibility test results for dalbavancin, a new glycopeptide agent.</a> Journal of clinical microbiology. 45, 3151-3154 (2007).</li><li>Arhin, F. 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=Effect+of+polysorbate+80+on+oritavancin+binding+to+plastic+surfaces:+implications+for+susceptibility+testing.">Effect of polysorbate 80 on oritavancin binding to plastic surfaces: implications for susceptibility testing.</a> Antimicrobial agents and chemotherapy. 52, 1597-1603 (2008).</li><li>Farrell, D. J., Mendes, R. E., Rhomberg, P. R., Jones, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Revised+reference+broth+microdilution+method+for+testing+telavancin:+effect+on+MIC+results+and+correlation+with+other+testing+methodologies.">Revised reference broth microdilution method for testing telavancin: effect on MIC results and correlation with other testing methodologies.</a> Antimicrobial agents and chemotherapy. 58, 5547-5551 (2014).</li><li>Ribbon Panel, B. l. u. e. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Guidelines+for+Safe+Work+Practices+in+Human+and+Animal+Medical+Diagnostic+Laboratories.">Guidelines for Safe Work Practices in Human and Animal Medical Diagnostic Laboratories.</a> MMWR Supplements. 61 (01), 1-101 (2012).</li><li>Anderegg, T. R., Biedenbach, D. J., Jones, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Initial+quality+control+evaluations+for+susceptibility+testing+of+Dalbavancin+(BI397),+an+investigational+glycopeptide+with+potent+gram-positive+activity.">Initial quality control evaluations for susceptibility testing of Dalbavancin (BI397), an investigational glycopeptide with potent gram-positive activity.</a> Journal of clinical microbiology. 41, 2795-2796 (2003).</li><li>Koeth, L. M., Windau, A. R., Goldstein, B. P. <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+Broth+Microdilution+and+Agar+Dilution+Dalbavancin+and+Vancomycin+MIC+Results+for+42+Aerobic+Gram-positive+Bacteria.+Poster+132.">Comparison of Broth Microdilution and Agar Dilution Dalbavancin and Vancomycin MIC Results for 42 Aerobic Gram-positive Bacteria. Poster 132.</a> ASM. , (2012).</li><li>Fritsche, T. R., Rennie, R. P., Goldstein, B. P., Jones, R. N. <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+dalbavancin+MIC+values+determined+by+Etest+(AB+BIODISK)+and+reference+dilution+methods+using+gram-positive+organisms.">Comparison of dalbavancin MIC values determined by Etest (AB BIODISK) and reference dilution methods using gram-positive organisms.</a> Journal of clinical microbiology. 44, 2988-2990 (2006).</li><li>Mushtaq, S., Warner, M., Johnson, A. P., Livermore, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity+of+dalbavancin+against+staphylococci+and+streptococci,+assessed+by+BSAC+and+NCCLS+agar+dilution+methods.">Activity of dalbavancin against staphylococci and streptococci, assessed by BSAC and NCCLS agar dilution methods.</a> The Journal of antimicrobial chemotherapy. 54, 617-620 (2004).</li><li>Jones, R. N., Flamm, R. K., Sader, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surveillance+of+dalbavancin+potency+and+spectrum+in+the+United+States+(2012).">Surveillance of dalbavancin potency and spectrum in the United States (2012).</a> Diagnostic microbiology and infectious disease. 76, 122-123 (2013).</li></ol>

Sandra McCurdy is an employee of Durata Therapeutics; Laboratory Specialists, Inc., employer of Laura Koeth and Jeanna Fisher, was contracted by Durata Therapeutics to prepare the manuscript. Publication fees for this article were paid by Laboratory Specialists, Inc.

The following method details are presented for additional considerations when preparing for dalbavancin MIC testing. The design of the MIC panel will depend on the number of antimicrobial agents to be tested (i.e., dalbavancin alone or multiple agents) and the species of bacteria to be tested. The dalbavancin concentrations should encompass the interpretive breakpoints for all bacterial species to be tested and the entire range of dilutions expected for at least one QC strain. The antimicrobial dilution series can be organized either in rows or columns depending on the number of antimicrobial agents and/or isolates/plate and method of inoculation. The volume of dalbavancin powder and broth should be calculated to assure that optimal amounts are produced and waste is minimal. For the example used in this publication, volumes are based on preparation of two MIC panels. Cation adjusted Mueller Hinton broth should be prepared and autoclaved according to manufacturer&#8217;s instructions and sterility of the media verified. MIC panels can be made and used on same day of preparation or they can be tested with appropriate quality control organisms and the validated panels stored frozen for future use. It is important to use sterile techniques throughout the procedure.
There is no strict criteria for verification of inoculum concentration with colony counts. Colony counts may be checked initially for each species tested and/or periodically to validate the dilution step performed in step 4.2. It is important that the validity of the 0.5 McFarland standard is also checked routinely with E. coli ATCC 25922 using a procedure similar to step 4.5. If results are not equivalent to 1-2 x 108 CFU/ml, a new 0.5 McFarland standard should be obtained. If the colony counts from MIC wells are outside of the acceptable range (2-8 x 105 CFU/ml and MIC results for the clinical isolate(s) vary from the expected normal distribution (eg. 0.03-0.12 ug/ml for S. aureus) and/or MIC results for quality control isolate(s) are outside of expected ranges, validation testing is necessary and method modification may be warranted. It is suggested that a validated 0.5 McFarland standard is used to repeat the colony count(s) and if results are again outside of expected results, the inoculum dilution as performed in step 4.2 should be adjusted accordingly and the MIC repeated. Note that a purity check is necessary even if a colony count is performed because the colony count procedure uses a diluted volume that may not necessarily detect lower concentrations of contaminating organisms.
For a MIC test to be considered valid, acceptable growth must occur in the growth control well. For most bacteria that will be tested against dalbavancin (i.e., staphylococci, streptococci and enterococci, growth will be seen as a button (typically &#62;2 mm) and less frequently, growth may appear as turbidity in the well. Unlike some antimicrobial agents that may exhibit trailing effect as concentrations increase, dalbavancin endpoints are typically well defined. There are various viewing devices intended to facilitate reading microdilution tests, which may be used to read dalbavancin containing plates as long as there is no compromise in the ability to discern growth in the wells.
The critical steps within the protocol are related to the parts of the procedure that are related to the solubility of dalbavancin and addition of P80. It is important that the maximum concentration of dalbavancin used is no greater than 1,600 &#181;g/ml, that DMSO is used as a solvent and that intermediate concentrations are prepared in DMSO prior to making the broth dilutions so that the final concentration of DMSO in the MIC panel wells is no greater than 1%. DMSO is hygroscopic and therefore, the use of older bottles of DMSO was a consideration with regard to dalbavancin solubility. However, while a small BMD study with quality control strains has shown this not to be an important variable (see results section), it is good practice to use new or recently opened bottles of DMSO. It is also important that P80 is added to the broth in the final step of drug dilution preparation and is at a final concentration of 0.002% in the MIC well.
The BMD procedure included here utilizes preparation of MIC panels using 50 &#181;l/well at dalbavancin and P-80 concentrations two times the final concentration and addition of inoculum with 50 &#181;l/well so that final volume/well is 100 &#181;l. This method allows for one MIC panel format to be produced for the testing of both S. aureus and S. pneumoniae because the lysed horse blood can be added to the inoculum. Alternative methods for preparation of MIC panels using 100 &#181;l/well with addition of up to 10 &#181;l/well are described in the CLSI and ISO procedures.
The dalbavancin susceptible breakpoint for S. aureus is &#8804;0.12 &#181;g/ml (FDA package insert). As is shown in recent surveillance, the majority of isolates are inhibited by dalbavancin at levels of 0.06 &#181;g/ml15. With a susceptible breakpoint close to the modal MIC, any variation in MIC as a result of method differences can affect susceptibility rates. Because the BMD procedure for dalbavancin includes some unique steps (specifically, the use of DMSO in preparation of stock and intermediate drug dilutions and 0.002% P80 in the MIC well, it is imperative that the method is followed exactly. The S. aureus QC organism (ATCC 29213) with a very clear dalbavancin modal MIC of 0.06 &#181;g/ml, has been a good indicator of method variation and should be used routinely to validate the BMD method. If MIC results are with the expected range of 0.03-0.12 &#181;g/ml, but are trending to either the low or high side of this range, further validation of the method is warranted.
The addition of 0.002% P80 is recommended for all relevant Gram-positive organisms (staphylococcci, enterococci, and streptococci.) However, it is noteworthy that it has been shown that lysed horse blood acts similar to P-80 relative to its anti-binding capability and that the addition of P-80 to CAMHB+LHB has no additional effect on dalbavancin streptococci MIC results.
There is currently no disk diffusion method for testing dalbavancin and because of the poor correlation of BMD and AD results, susceptibility testing of dalbavancin using the AD method is not recommended12, 14. The BMD method should be used for the future assessment of dalbavancin susceptibility and as a gold standard for the development of commercial antimicrobial susceptibility tests.

Dalbavancin is a semi-synthetic lipoglycopeptide that was approved by the FDA in May 2014 for the treatment of acute bacterial skin and skin structure infections caused by Gram-positive organisms1. The primary goal of detailing this method in a video format is to provide clear guidance to the clinical laboratory and research scientists for testing and reporting of accurate and reproducible dalbavancin susceptibility results.
The determination of an antimicrobial agent MIC by commercial methods is routinely performed in clinical laboratories for assessment of an agent&#8217;s in vitro activity against pathogenic bacteria. The method described here is the broth microdilution method as recommended by CLSI and ISO 2,3,4. Since dalbavancin commercial susceptibility methods are not currently available (at the time of this publication) and disk diffusion and agar dilution methods are not currently recommended for dalbavancin, reference broth dilution methods are the current options available 12,14. As this reference method is not a commercial and FDA cleared in vitro diagnostic method, clinical laboratories in the USA that use this procedure for patient testing must abide by regulatory requirements for a laboratory developed test (LDT). It is anticipated that as the dalbavancin use increases, more laboratories will have a need to test this compound. Vancomycin testing as a surrogate for determination of dalbavancin susceptibility of S. aureus has been validated5. However, dalbavancin may be active against vancomycin intermediate S. aureus (VISA) and therefore, clinicians may request dalbavancin MIC results. In addition, MIC results for other bacterial species may be requested.
The FDA susceptible breakpoint for dalbavancin against S. aureus has been established at &#8804;0.12 &#181;g/ml. FDA assigned only a susceptible category because of the lack of data on resistant isolates. The normal MIC distribution among wild type S. aureus isolates is between 0.03-0.12 &#181;g/ml, with a clear modal MIC of 0.06 &#181;g/ml. A slight variation in MIC results due to method difference, in addition to the inherent BMD variation of &#177; one dilution, could potentially have a significant impact on the susceptibility rates.6 Similar to other lipoglycopeptide agents, dalbavancin susceptibility testing can be challenging as a result of solubility and the relatively large size of the molecule and its binding properties7,8,9. The reference BMD method described here includes two specific steps that are unique to insoluble agents and/or lipoglycopeptide agents: (1) the use of DMSO for preparation of stock solutions and (2) addition of 0.002% P-80 in the final MIC panel dilutions. The objective of this video publication is to provide clarity to the dalbavancin BMD method and to specifically focus on these key steps, to assure accurate and reproducible MIC results.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Dalbavancin</td>
			<td>Metrics, Inc.</td>
			<td>Greenville, NC</td>
			<td>BI-397</td>
		</tr>
		<tr>
			<td>Vancomycin</td>
			<td>Sigma-Aldrich</td>
			<td>St. Louis, MO</td>
			<td>C5793</td>
		</tr>
		<tr>
			<td>Cation Adjusted Mueller Hinton Broth</td>
			<td>Becton Dickinson</td>
			<td>Sparks, MD</td>
			<td>212322</td>
		</tr>
		<tr>
			<td>Lysed horse blood</td>
			<td>Cleveland Scientific</td>
			<td>Bath, OH</td>
			<td></td>
		</tr>
		<tr>
			<td>Dose-it peristaltic pump</td>
			<td>Integra Biosciences</td>
			<td>Hudson, NH</td>
			<td></td>
		</tr>
		<tr>
			<td>Multi-channel pipet (Viaflo II)</td>
			<td>Integra</td>
			<td>Hudson, NH</td>
			<td>4164</td>
		</tr>
		<tr>
			<td>12 channel pipet (Matrix)</td>
			<td>ThermoFisher Scientific</td>
			<td>Waltham, MA</td>
			<td></td>
		</tr>
		<tr>
			<td>Single channelpPipets (Ovation 10 &#181;L - 100 &#181;L)</td>
			<td>VistaLab</td>
			<td>Brewster, NY</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well microplate</td>
			<td>Greiner Bio-one</td>
			<td>Monroe, NC</td>
			<td>650161</td>
		</tr>
		<tr>
			<td>50 mL flat cap conical bottom centrifuge tubes</td>
			<td>ThermoFisher Scientific</td>
			<td>Waltham, MA</td>
			<td></td>
		</tr>
		<tr>
			<td>16x125mm disposable glass tubes</td>
			<td>ThermoFisher Scientific</td>
			<td>Waltham, MA</td>
			<td></td>
		</tr>
		<tr>
			<td>12x17mm snap cap, polystyrene tubes</td>
			<td>ThermoFisher Scientific</td>
			<td>Waltham, MA</td>
			<td></td>
		</tr>
		<tr>
			<td>16 mL centrifuge tubes</td>
			<td>BioExpress</td>
			<td>Kaysville, UT</td>
			<td>C-3394-2</td>
		</tr>
		<tr>
			<td>Reagent reservoirs</td>
			<td>Integra Biosciences</td>
			<td>Hudson, NH</td>
			<td>4312</td>
		</tr>
		<tr>
			<td>Disposable sterilelLoops (1 uL &#38; 10 uL)</td>
			<td>Biologix</td>
			<td>Lenexa, KA</td>
			<td>65-0001,65-0010</td>
		</tr>
		<tr>
			<td>Tryptic soy agar + 5% sheep blood</td>
			<td>Becton Dickinson</td>
			<td>Sparks, MD</td>
			<td></td>
		</tr>
		<tr>
			<td>Incubator (ambient)</td>
			<td>Sanyo</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Incubator (5% CO2)</td>
			<td>Sanyo</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Analytical balance&#160;</td>
			<td>ThermoFisher Scientific</td>
			<td>Waltham, MA</td>
			<td></td>
		</tr>
		<tr>
			<td>Gloves</td>
			<td>Kimberly-Clark</td>
			<td></td>
			<td>52817</td>
		</tr>
		<tr>
			<td>Lab coats</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

a reference broth microdilution method for dalbavancin in vitro susceptibility testing of bacteria that grow aerobically

Antimicrobial susceptibility testing (AST) is performed to assess the in vitro activity of antimicrobial agents against various bacteria. The AST results, which are expressed as minimum inhibitory concentrations (MICs) are used in research for antimicrobial development and monitoring of resistance development and in the clinical setting for antimicrobial therapy guidance. Dalbavancin is a semi-synthetic lipoglycopeptide antimicrobial agent that was approved in May 2014 by the Food and Drug Administration (FDA) for the treatment of acute bacterial skin and skin structure infections caused by Gram-positive organisms. The advantage of dalbavancin over current anti-staphylococcal therapies is its long half-life, which allows for once-weekly dosing. Dalbavancin has activity against Staphylococcus aureus (including both methicillin-susceptible S. aureus [MSSA] and methicillin-resistant S. aureus [MRSA]), coagulase-negative staphylococci, Streptococcus pneumoniae, Streptococcus anginosus group, &#946;-hemolytic streptococci and vancomycin susceptible enterococci. Similar to other recent lipoglycopeptide agents, optimization of CLSI and ISO broth susceptibility test methods includes the use of dimethyl sulfoxide (DMSO) as a solvent when preparing stock solutions and polysorbate 80 (P80) to alleviate adherence of the agent to plastic. Prior to the clinical studies and during the initial development of dalbavancin, susceptibility studies were not performed with the use of P-80 and MIC results tended to be 2-4 fold higher and similarly higher MIC results were obtained with the agar dilution susceptibility method. Dalbavancin was first included in CLSI broth microdilution methodology tables in 2005 and amended in 2006 to clarify use of DMSO and P-80. The broth microdilution (BMD) procedure shown here is specific to dalbavancin and is in accordance with the CLSI and ISO methods, with step-by-step detail and focus on the critical steps added for clarity.

Watch this Scientific Journal Video about A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically at JoVE.com

A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically

Here, we present a protocol for determination of dalbavancin susceptibility of clinically relevant Gram-positive bacteria using a broth microdilution reference methodology.

A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically

Antimicrobial susceptibility testing (AST) is performed to assess the in vitro activity of antimicrobial agents against various bacteria. The AST results, ...

a-reference-broth-microdilution-method-for-dalbavancin-vitro

Research

JoVE Journal

Immunology and Infection

A 96 Well Microtiter Plate-based Method for Monitoring Formation and Antifungal Susceptibility Testing of Candida albicans Biofilms

Candida albicans remains the most frequent cause of fungal infections in an expanding population of compromised patients and candidiasis is now the third most common infection in US hospitals. Different manifestations of candidiasis are associated with biofilm formation, both on host tissues and/or medical devices (i.e. catheters). Biofilm formation carries negative clinical implications, as cells within the biofilms are protected from host immune responses and from the action of antifungals. We have developed a simple, fast and robust in vitro model for the formation of C. albicans biofilms using 96 well microtiter-plates, which can also be used for biofilm antifungal susceptibility testing. The readout of this assay is colorimetric, based on the reduction of XTT (a tetrazolium salt) by metabolically active fungal biofilm cells. A typical experiment takes approximately 24 h for biofilm formation, with an additional 24 h for antifungal susceptibility testing. Because of its simplicity and the use of commonly available laboratory materials and equipment, this technique democratizes biofilm research and represents an important step towards the standardization of antifungal susceptibility testing of fungal biofilms.

A 96 Well Microtiter Plate-based Method for Monitoring Formation and Antifungal Susceptibility Testing of Candida albicans Biofilms

We describe a simple, rapid and robust method for the formation of Candida albicans biofilms using 96 well microtiter plates and its utility in antifungal susceptibility testing of cells within biofilms.

Candida albicans remains the most frequent cause of fungal infections in an expanding population of compromised patients and candidiasis is now the third ...

In vitro Biofilm Formation in an 8-well Chamber Slide

The chronic nature of many diseases is attributed to the formation of bacterial biofilms which are recalcitrant to traditional antibiotic therapy. Biofilms are community-associated bacteria attached to a surface and encased in a matrix. The role of the extracellular matrix is multifaceted, including facilitating nutrient acquisition, and offers significant protection against environmental stresses (e.g. host immune responses). In an effort to acquire a better understanding as to how the bacteria within a biofilm respond to environmental stresses we have used a protocol wherein we visualize bacterial biofilms which have formed in an 8-well chamber slide. The biofilms were stained with the BacLight Live/Dead stain and examined using a confocal microscope to characterize the relative biofilm size, and structure under varying incubation conditions. Z-stack images were collected via confocal microscopy and analyzed by COMSTAT. This protocol can be used to help elucidate the mechanism and kinetics by which biofilms form, as well as identify components that are important to biofilm structure and stability.

In vitro Biofilm Formation in an 8-well Chamber Slide

This article describes the procedure for the formation and visualization of a bacterial biofilm grown within an 8-well chamber slide

The chronic nature of many diseases is attributed to the formation of bacterial biofilms which are recalcitrant to traditional antibiotic therapy. ...

Antimicrobial Susceptibility Testing of Mycobacterium Tuberculosis Complex for First and Second Line Drugs by Broth Dilution in a Microtiter Plate Format

The rapid detection of antimicrobial resistance is important in the effort to control the increase in resistant Mycobacterium 
tuberculosis (Mtb). Antimicrobial susceptibility testing (AST) of Mtb has traditionally been performed by the agar method of proportion or by 
macrobroth testing on an instrument such as the BACTEC (Becton Dickinson, Sparks, MD), VersaTREK (TREK Diagnostics, Cleveland, OH) or BacT/ALERT (bioM&eacute;rieux, Hazelwood, MO). The agar proportion method, while considered the &#x201C;gold&#x201D; standard of AST, is labor intensive and requires calculation of resistance by performing colony counts on drug-containing agar as compared to drug-free agar. If there is &ge;1% growth on the drug-containing medium as compared to drug-free medium, the organism is considered resistant to that drug. The macrobroth methods require instrumentation and test break point ("critical") drug concentrations for the first line drugs (isoniazid, ethambutol, rifampin, and pyrazinamide). The method described here is commercially available in a 96 well microtiter plate format [MYCOTB (TREK Diagnostics)] and contains increasing concentrations of 12 antimicrobials used for treatment of tuberculosis including both first (isoniazid, rifampin, ethambutol) and second line drugs (amikacin, cycloserine, ethionamide, kanamycin, moxifloxacin, ofloxacin, para-aminosalicylic acid, rifabutin, and streptomycin). Pyrazinamide, a first line drug, is not included in the microtiter plate due to its need for acidic test conditions. Advantages of the microtiter system include both ease of set up and faster turn around time (14 days) compared with traditional agar proportion (21 days). In addition, the plate can be set up from inoculum prepared using either broth or solid medium. Since the microtiter plate format is new and since Mtb presents unique safety challenges in the laboratory, this protocol will describe how to safely setup, incubate and read the microtiter plate.

Antimicrobial susceptibility testing of Mycobacterium tuberculosis is challenging but critical for patient care. This microtiter plate format offers testing of 12 antimycobacterial drugs and provides minimum inhibitory concentration (MIC) values, which will aid in appropriate treatment.

The rapid detection of antimicrobial resistance is important in the effort to control the increase in resistant Mycobacterium 
tuberculosis (Mtb). ...

A Method for Labeling Vasculature in Embryonic Mice

The establishment of a functional blood vessel network is an essential part of organogenesis, and is required for optimal organ function. For example, in the thymus proper vasculature formation and patterning is essential for thymocyte entry into the organ and mature T-cell exit to the periphery. The spatial arrangement of blood vessels in the thymus is dependent upon signals from the local microenvironment, namely thymic epithelial cells (TEC). Several recent reports suggest that disruption of these signals results in thymus blood vessel defects 1,2. Previous studies have described techniques used to label the neonatal and adult thymus vasculature 1,2. We demonstrate here a technique for labeling blood vessels in the embryonic thymus. This method combines the use of FITC-dextran or Griffonia (Bandeiraea) Simplicifolia Lectin I (GSL 1 - isolectin B4) facial vein injections and CD31 antibody staining to identify thymus vascular structures and PDGFR-&beta; to label thymic perivascular mesenchyme 3-5. The option of using cryosections or vibratome sections is also provided. This protocol can be used to identify thymus vascular defects, which is critical for defining the roles of TEC-derived molecules in thymus blood vessel formation. As the method labels the entire vasculature, it can also be used to analyze the vascular networks in multiple organs and tissues throughout the embryo including skin and heart 6-10.

This article describes a method for labeling embryonic skin and thymus blood vessels.

The establishment of a functional blood vessel network is an essential part of organogenesis, and is required for optimal organ function. For example, in ...

Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional identification requires the sub-culture of signaled blood culture broth with identification available only after colonies on solid agar have matured. MALDI-TOF MS is a reliable, rapid method for identification of the majority of clinically relevant bacteria when applied to colonies on solid media. The application of MALDI-TOF MS directly to blood culture broth is an attractive approach as it has potential to accelerate species identification of bacteria and improve clinical management. However, an important problem to overcome is the pre-analysis removal of interfering resins, proteins and hemoglobin&#160;contained in blood culture specimens which, if not removed, interfere with the MS spectra and can result in insufficient or low discrimination identification scores. In addition it is necessary to concentrate bacteria to develop spectra of sufficient quality. The presented method describes the concentration, purification, and extraction of Gram negative bacteria allowing for the early identification of bacteria from a signaled blood culture broth.

The application of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) directly to blood culture broth expedites the identification of bacteria. The presented method is a rapid and reliable method for identification of Gram negative bacteria directly from blood culture broth.

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional ...

Preparation of a Blood Culture Pellet for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections.

A rapid bacterial pellet preparation from a positive blood culture can be used as a sample for applications such as identification by MALDI-TOF, Gram staining, antibiotic susceptibility testing and PCR-based test. The results can be rapidly communicated to clinicians to improve the outcome of patients suffering from bloodstream infections.

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a ...

In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation

Acid-triggered molecular processes closely control cell entry of many viruses that enter through the endocytic system. In the case of influenza A virus (IAV), virus fusion with the endosomal membrane as well as the subsequent disassembly of the viral capsid, called uncoating, is governed by the ionic conditions inside endocytic vesicles. The early steps in the virus life cycle are hard to study because endosomes cannot be directly accessed experimentally, creating the need for an in vitro approach. Here, we describe a method based on velocity gradient centrifugation of purified virions through a two-layer glycerol gradient, which enables analysis of the IAV core and its stability. The gradient contains a non-ionic detergent (NP-40) in its lower layer to remove the viral membrane by solubilization as the virus sediments toward the bottom. At neutral pH, viral cores are pelleted as stable structures. The major core components, matrix protein (M1) and the viral ribonucleoproteins (vRNPs), can be clearly identified in the pellet fraction by SDS-PAGE. Decreasing the pH to 6.0 or lower in the bottom layer selectively removes M1 from the pellet followed by release of vRNPs at more acidic conditions. Viral protein bands on Coomassie-stained gels can be subjected to densitometric quantification to monitor intermediate states of IAV disassembly. Besides pH, other factors that influence viral core stability can be assessed, such as salt concentration and putative viral uncoating factors, simply by modifying the detergent-containing glycerol layer accordingly. Taken together, the presented technique allows highly reproducible and quantitative analysis of viral uncoating in vitro. It can be applied to other enveloped viruses that undergo complex uncoating processes.

In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation

Disassembly of influenza A virus cores during virus entry into host cells is a multistep process. We describe an in vitro method to analyze the early stages of viral uncoating. In this approach, velocity gradient centrifugation is used to biochemically dissect the steps that initiate uncoating under defined conditions.

Acid-triggered molecular processes closely control cell entry of many viruses that enter through the endocytic system. In the case of influenza A virus ...

Establishment of a High-throughput Setup for Screening Small Molecules That Modulate c-di-GMP Signaling in Pseudomonas aeruginosa

Bacterial resistance to traditional antibiotics has driven research attempts to identify new drug targets in recently discovered regulatory pathways. Regulatory systems that utilize intracellular cyclic di-GMP (c-di-GMP) as a second messenger are one such class of target. c-di-GMP is a signaling molecule found in almost all bacteria that acts to regulate an extensive range of processes including antibiotic resistance, biofilm formation and virulence. The understanding of how c-di-GMP signaling controls aspects of antibiotic resistant biofilm development has suggested approaches whereby alteration of the cellular concentrations of the nucleotide or disruption of these signaling pathways may lead to reduced biofilm formation or increased susceptibility of the biofilms to antibiotics. We describe a simple high-throughput bioreporter protocol, based on green fluorescent protein (GFP), whose expression is under the control of the c-di-GMP responsive promoter cdrA, to rapidly screen for small molecules with the potential to modulate c-di-GMP cellular levels in Pseudomonas aeruginosa (P. aeruginosa). This simple protocol can screen upwards of 3,500 compounds within 48 hours and has the ability to be adapted to multiple microorganisms.

Establishment of a High-throughput Setup for Screening Small Molecules That Modulate c-di-GMP Signaling in Pseudomonas aeruginosa

This article describes the high-throughput assay that has been successfully established to screen large libraries of small molecules for their potential ability to manipulate cellular levels of cyclic di-GMP in Pseudomonas aeruginosa, providing a new powerful tool for antibacterial drug discovery and compound testing.

Bacterial resistance to traditional antibiotics has driven research attempts to identify new drug targets in recently discovered regulatory pathways. ...

An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

The eradication of tuberculosis disease requires drug regimens that can penetrate the multiple layers of complex pulmonary lesions. Drug distribution in the caseous cores of cavities and lesions is especially crucial because they harbor subpopulations of drug-tolerant bacteria also commonly referred to as persisters. Existing methods for the measurement of drug penetration in tuberculosis lesions involve costly and time-consuming in vivo pharmacokinetic studies coupled to bioanalytical or imaging techniques. The in vitro measurement of drug binding to caseum macromolecules was proposed as an alternative to such techniques since this binding hinders the passive diffusion of drug molecules through caseum. Rapid equilibrium dialysis is a fast and reliable system for performing plasma protein and tissue binding studies. In this protocol, we used a rapid equilibrium dialysis (RED) device to measure drug binding to homogenates of caseum that is excised from the lesions and cavities of tuberculosis-infected rabbits. The protocol also describes how to generate a surrogate matrix from lipid loaded THP-1 macrophages to use in place of caseum. This caseum/surrogate binding assay is an important tool in tuberculosis drug discovery and can be adapted to help study drug distribution in lesions or abscesses caused by other diseases.

An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

Here we describe a rapid equilibrium dialysis (RED) method to measure drug binding to caseum from pulmonary tuberculosis lesions and cavities. The protocol is also used with a foamy macrophage-derived matrix that is an effective surrogate to caseum.

The eradication of tuberculosis disease requires drug regimens that can penetrate the multiple layers of complex pulmonary lesions. Drug distribution in ...

Fluorescence-based Neuraminidase Inhibition Assay to Assess the Susceptibility of Influenza Viruses to The Neuraminidase Inhibitor Class of Antivirals

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against currently circulating strains. In addition to their use in treating seasonal influenza, the NA inhibitors have been stockpiled by a number of countries for use in the event of a pandemic. It is therefore important to monitor the susceptibility of circulating influenza viruses to this class of antivirals. There are different types of assays that can be used to assess the susceptibility of influenza viruses to the NA inhibitors, but the enzyme inhibition assays using either a fluorescent substrate or a chemiluminescent substrate are the most widely used and recommended. This protocol describes the use of a fluorescence-based assay to assess influenza virus susceptibility to NA inhibitors. The assay is based on the NA enzyme cleaving the 2&#8242;-(4-Methylumbelliferyl)-&#945;-D-N-acetylneuraminic acid (MUNANA) substrate to release the fluorescent product 4-methylumbelliferone (4-MU). Therefore, the inhibitory effect of an NA inhibitor on the influenza virus NA is determined based on the concentration of the NA inhibitor that is required to reduce 50% of the NA activity, given as an IC50 value.

We describe the use of a phenotypic fluorescence-based neuraminidase inhibition assay to assess the susceptibility of influenza A and B viruses to the neuraminidase inhibitor class of antivirals.

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against ...