MicroScan LabPro Information Manager Antibiogram Export Tool Instructions Single Institution Format 2016 For use with LabPro version v4.42
Creating an Antibiogram from LabPro Data CLSI M39-A4 recommends annual preparation of a cumulative antibiogram report to assist physicians in empiric therapy decisions. The MicroScan LabPro System generates antibiogram reports according to the CLSI M39-A4 recommendations. The goal of this document and the associated template is to use the LabPro Export function in conjunction with Microsoft Excel, to create an antibiogram for a single institution. This antibiogram can then be formatted to suit the user s needs, and printed if desired. The following procedure will guide you through creating a query to gather your data in LabPro, creating an export format to export your gathered data to a removable media, and importing that data into an Excel template for analysis and printing of the antibiogram. Please note: This template is capable of handling 30,000 rows of data in the Raw and Working Data sheets. The formulas in this template are password protected, and are not visible to or changeable by the user. The organisms listed for creating your export from LabPro with identifications obtained from Beckman Coulter and/or Bruker Maldi Biotyperare the CLSI M39 A4 recommended organisms. The LabPro screen shots in these instructions may look slightly different than yours, depending on your software version. This will not impact your ability to create your antibiogram. The screen shots in these instructions represent Microsoft Windows 7 and Microsoft Excel 2010. Microsoft Excel 2013 may also be used. It is important that only those software versions that have been validated and are supported be used when creating your antibiogram. The Single Site Antibiogram template has been validated and verified with these instructions as written. Do not deviate from the instructions, as this may result in inaccurate results. If you have any questions or need assistance with this process, call the MicroScan Customer Technical Solutions at 1-800-677-7226. 2
BEFORE YOU BEGIN- PLEASE READ THIS SECTION You will be exporting your data from your LabPro computer, and importing it onto another computer that is running Microsoft Windows and Excel. Microsoft Excel SHOULD NOT be loaded on your LabPro computer. On the Computer running Microsoft Windows and Excel, check the software versions and settings. 1. Use of the Antibiogram Export Tool requires Microsoft Excel 2010 or Microsoft Excel 2013 and Microsoft Windows 7. No other versions are supported. To verify you have these versions, you may contact your IT department, or follow the steps below. 2. Check your Windows version by right clicking the Computer icon on your desktop. 3. Click Properties. Figure 1 Figure 2 4. Check your Windows version. Microsoft Windows 7 as shown above is the only supported version. NOTE: If the Computer icon is NOT on your desktop, click Start, right click Computer, and then click Properties to see your Windows version. 5. If your screen looks different than Figure 2, you may have a different version of Windows. Please contact your IT department to confirm your Windows version. 6. To check your Excel version, open Excel, click the File tab, and then click Help. 7. Check your Excel version. 3
Excel 2010 is shown below. Figure 3 8. If your screen does not indicate Microsoft Excel 2010 or Microsoft Excel 2013 or if you cannot determine which version of Microsoft Excel is installed on your computer, please contact your IT department. On Your LabPro computer: 9. In Utilities>Customization>Reports>Formatting- verify that your Epidemiology Duplicate Isolate Time limit is set to 365 days and Any Source. 4
See Figures 4 and 5. Figure 4 Figure 5 10. Note that isolates from specimens that have a status of preliminary in LabPro will not be exported or included in your LabPro printed antibiogram. It is advisable to query your data for preliminary specimens prior to exporting, and either delete or complete them. 11. If you have processed Proficiency Survey samples, ensure that those isolates have been flagged to be excluded from epidemiology. 12. From the Patient Order Entry screen create and run a query to find Proficiency Survey isolates not excluded from epidemiology. 13. Open Patient Order Entry from the LabPro Command Center, and if the Work List is not already open, click on Show/Hide Work List to open it. 5
Figure 6 14. Click the radio button by Query, and then click the look up button. 15. Click + to create a new query. Figure 7 Figure 8 16. Click, drag, and drop Specimen # parameter into the first cell that states To begin: drag a desired parameter to this cell. 6
Figure 9 17. Using the look up button in the Specimen # From lookup box, and based on how survey samples are entered into your system, scroll to each survey sample, double click it, and then hit enter. This builds a list of the survey samples in the Selected Specimen # List. Figure 10 18. When all survey samples have been listed, click and drag Test Group Status/Date, dropping it so that it is in a separate box from Specimen #. Click the calendar look ups to select appropriate From and To dates for your antibiogram, and hit enter. 7
Figure 11 19. Enter a Code and Description, and save. Figure 12 20. Double click the new query from the Patient Query Rules box. Figure 13 21. The work list will now list the survey samples. Double click each specimen, enter the isolate number and click enter. Check the Exclude from Epi check box for each isolate, click on Accept Isolate, and Save. 8
Figure 14 22. Check for User-defined organisms customized in your LabPro system. Go to Utilities>Customization>Codes>Organisms. 23. Point to the right side of the User Defined column header, and click the black down arrow that will appear. Figure 15 24. If YES is available, check it, and all User-defined organisms will then be listed. If YES is not available, there are no User Defined Organisms. Figure 16 25. If you do not have User-defined organisms, proceed to the Exporting Your Data Section of these instructions. If you do have User-defined organisms continue to step 26. 26. Determine if your User-defined organisms have been in use during the time frame being used for this Antibiogram. If they have not, proceed to the Exporting Your Data Section of these instructions. Otherwise continue to step 27. 9
27. Compare the User-defined organisms in use in your lab to the list of organisms in Figure 17 below. Acinetobacter baumannii Citrobacter freundii Coagulase Negative Staphylococcus Enterobacter aerogenes Enterobacter cloacae Enterococcus faecalis Enterococcus faecium Enterococcus spp, not faecalis or faecium Escherichia coli Klebsiella oxytoca Klebsiella pneumoniae Methicillin Resistant Staphylococcus aureus Methicillin Susceptible Staphylococcus aureus Morganella morganii Proteus mirabilis Providencia species Pseudomonas aeruginosa Salmonella species Serratia marcescens Shigella species Stenotrophomonas maltophilia Streptococcus pneumoniae Figure 17 28. If any of the User-defined organisms in use in your lab are equivalent to an organism on this list, print the User-defined Organism list. Click Data, then click Print. You will need to include these organisms in your LabPro query along with the other organisms listed on pages 16-19. 29. Also, these same User-defined organisms need to be added to the appropriate Epidemiology Organism Groups you will create on page 13, beginning at step 9. 10
Exporting Your Data 11
At the end of this entire process, it is recommended that you print the LabPro Antimicrobic % Interpretive Report and compare it to your exported antibiogram, verifying that the values on the two reports match each other. Steps 1-19 detail LabPro customization required to make this verification easier. The Antibiogram Export Tool automatically groups organisms as recommended in the CLSI M39-A4, Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data. Customization of LabPro Epidemiology Organism Groups will be used to group the organisms on your LabPro Antimicrobic % Interpretive Report print out into these same groups. In this way, when the two reports are checked to ensure that they match each other, it will be much easier. This customization will be a two-step process, consisting of deleting any Epidemiology Organism Groups you currently have in your LabPro system, and then creating new ones. Your existing Epidemiology Organism Groups will first be printed, so that if desired, they can be recreated after the export process is complete. 1. On your LabPro computer, start at the desktop with the LabPro Command Center open. 2. From the LabPro Command Center, click on Utilities. Figure 18 3. Click the + sign next to Customization. 4. Click the + sign next to Code Groups and then double click Epidemiology Organisms. 5. Click Data, and then Print. Save this printout for reference to recreate your existing Epidemiology Organism Groups. As you follow the steps below to create Epidemiology Organism groups, be sure to include in the appropriate Epidemiology Organism Group any User-defined organism names in use at your facility. Refer to the list you made on page 10 step 28. 6. Click the first Epidemiology Organism Group listed, and then click the Delete icon. 12
Figure 19 7. Repeat for each existing Epidemiology Organism Group. 8. When all have been deleted, you are now ready to create the Epidemiology Organism Groups used for this process. 9. Click on the Blue +. The Epidemiology Organism Groups Add dialogue box appears. 10. Enter the Code EXSALM for the group, and enter Salmonella spp. for the description. 11. In the Organism Set look up box, double click Gram Negative. 12. Open the Members List look up box, highlight the Salmonella spp. indicated below, and click the green check mark. Figure 20 13. Click Save. Your Salmonella spp. group is now created. 14. Also make a group for all of the coagulase negative staphylococci. Use code EXCNS and the description Staph (coag.neg.). Choose Gram Positive as the Organism Set. Be sure to include number 109, Coagulase-negative Staphylococcus spp., number 3109, Coagulase-negative Staphylococcus species MRS, and numbers 177 Staphylococcus lugdunensis, and 3177 Staphylococcus lugdunensis MRS. 15. The remaining required groups to be created are listed in the table below. 13
Code Description Special Notes EXACIN Acinetobacter baumannii EXEC Escherichia coli Include E. coli, ESBL, E. coli (Inactive), and E. coli O157:H7 EXEFCM E. faecium EXEFLS E. faecalis EXENTSPP Enterococcus spp. Include only species not E. faecium or E. faecalis EXKOX Klebsiella oxytoca Include K. oxytoca, ESBL EXKP Klebsiella pneumoniae Include K. pneumoniae, ESBL EXPMIR Proteus mirabilis Include P. mirabilis, ESBL EXPROV Providencia spp. EXSAUR Total S. aureus Include MRSA, S. aureus EXSHIG Shigella spp. EXSTPN S. pneumoniae (if tested on the MICroSTREP plus panel) This group is not needed if you do not test S. pneumoniae on the MICroSTREP plus panel. Figure 21 NOTE: Refer to the organism list in Appendix A of this document, beginning on page 44, for a list of the organisms to be used in the groups, along with their corresponding organism numbers. Also review your User-defined Organism List, printed on page 10 step 28, and add those organisms to the appropriate group(s). 16. There should be a total of 13 Epidemiology Organism Groups created, or 14 if you are using the MICroSTREP plus panel to test S. pneumoniae. 17. When the last group has been added, close the Epidemiology Organism Groups- Add window, close the Epidemiology Organism Groups window, and exit Utilities. You are now ready to begin the export process. 18. Click the Print Reports icon. Figure 22 19. On the Print Reports screen click the Epidemiology tab. 14
Figure 23 20. On the Epidemiology tab, click the radio button next to Export To File. 21. Ensure that the checkbox next to Exclude Duplicate Isolates is checked. 22. Click the lookup button in the Stored Queries box. Figure 24 Figure 25 23. The Patient Query Rules dialog box opens and displays your existing list of Queries, if any. Click on the + sign. The Patient Query Rules-Add box opens. 24. Click and drag the Organism parameter into the cell containing the words To begin: drag a desired parameter to this cell. Your screen should look like Figure 26. 15
Figure 26 25. In the Organism text box on the right, type the Organism Numbers listed in Appendix A at the end of this document beginning on page 44 one at a time, pressing the enter key between each number. The organisms in the list are the organisms recommended by the CLSI M39 document for reporting on your antibiogram, and is based on MicroScan LabPro 4.42 software. In addition to the organisms on the list, be sure to include in your Query any appropriate User-defined organisms from the list created on page 10, step 28. 26. Entering each number builds a list of organisms in the Selected Organism List as in Figure 27 below. Continue until all numbers have been entered. Also enter the numbers of the User-defined organisms you listed in step 28, page 10. Figure 27 16
27. Click and drag the parameter Excluded from Epidemiology to the bottom left of the screen, under the organism cell. Release it, making sure that it is in a different cell than the Organism cell, and that the word AND appears between the cells. 28. On the right side of the screen, click the radio button next to Isolates not excluded. Figure 28 29. Click and drag the parameter Test Group to the bottom left of the screen under the Excluded from Epidemiology cell. Release it, making sure that it is a different cell than the Excluded from Epidemiology cell, and that the word AND appears between the cells. See Figure 28. 30. On the right side of the screen, click the look up button in the Test Group look up box. 31. Holding down the shift key, click on each MIC only and Combo panel that you used for your clinical isolates during the time frame for this antibiogram. 32. Release the control key and click the green check mark. Figure 29 17
33. Click and drag the parameter Test Group Status/Date to the bottom left of the screen, under your Test Group cell. Release it, making sure that it is in a different cell than the Test Group cell, and that the word AND appears between the cells. Figure 30 34. On the right, put a check in the Complete box. See Figure 31. 35. Below that, click on the calendar in the From box. Click PY for previous year, and press Enter. See Figure 31. Or, enter the starting date you want in the From box, press tab, and enter the ending date you want in the To box. Then press Enter. Figure 31 Instructions for changing the dates for future use of this query are at the end of this section. Note this query pulls ALL sources. If you want separate antibiograms for URINE sources 18
and SYSTEMIC sources, create two different queries. Add SOURCE as another parameter on each. For one query choose all URINE sources, for the other choose all NON URINE sources. Perform your export with each query, using a separate copy of the Epidemiology Template for each. Figure 32 36. At the top of the window- type the Code and Description as shown above. 37. Click Save in the top left of the window. The Patient Query Rules Add box clears but remains open. Close the Patient Query Rules-Add window. 38. Double click the Query you just created- Epidemiology for Export. Figure 33 39. Your screen will return to the Print Reports, Epidemiology tab, with your new query in the Stored Queries box. 40. Click the Export Configuration look up button. See Figure 34. Figure 34 19
Figure 35 41. The Export Configurations box will open as in Figure 35. It will display any Export Configurations you have previously defined, if any. Click the +. The Export Configurations-Add box will open. 42. Click the + next to Isolate Data. Figure 36 43. A list of parameters appears. Click Organism, and then click Add. Figure 37 20
44. Organism is now listed in the Selected Data box. Figure 38 45. Click Isolate Data again to close the Isolate Data drop down. 46. Click the + next to Antimicrobial Data. 47. Click the + next to Formulary, and click the + next to Non Formulary. The antibiotic order is critical! If you have customized the formulary in LabPro, you will have to choose from both the Formulary and Non-Formulary lists. Figure 39 48. Click the + next to Interpretation under Formulary and under Non-Formulary, a list of antibiotic interpretations appears under each. 21
Figure 40 49. Click Amikacin Interpretation. 50. Click Add. Figure 41 Amikacin Interpretation is now listed in the Selected Data box. Figure 42 22
51. Click Amox/K Clav Interpretation. 52. Click Add. Amox/K Clav Interpretation is now listed in the Selected Data box. Figure 43 53. Continue adding antibiotics in the order listed in Figure 44, next page. If you make an error, highlight the antibiotic and choose Remove, Move Up or Move Down, as appropriate. The antibiotic order is critical! 54. If you do not find one of the antibiotics on the list under Formulary, scroll down and look under Non Formulary. Make sure this antibiotic gets placed in the correct order. We have included all antibiotics available on current panels in this export to accommodate all customer needs. It is important that you export all of these antibiotics, even if you don t want them on your final antibiogram, so that the template performs properly. You will be able to customize the final antibiogram prior to printing by deleting unwanted antibiotics. Figure 45 shows the correct order of antibiotics for adding both the interpretations and MICs when building the export configuration. Please note: This template is designed to work only with the system defined antibiotics currently in LabPro. However, user-defined antibiotic tests resulted in LabPro that represent any of these antibiotics may be exported in lieu of the system defined antibiotics. Ensure that they are exported in the proper order, and that each antibiotic is listed only once in this export configuration. 23
1. Amikacin 19. Cephalothin 37. Ofloxacin 2. Amox K/Clav 20. Chloramphenicol 38. Oxacillin 3. Amp/Sulbactam 21. Ciprofloxacin 39. Penicillin 4. Ampicillin 22. Clarithromycin 40. Penicillin-E 5. Ampicillin-E 23. Clindamycin 41. Penicillin- S 6. Ampicillin- S 24. Daptomycin 42. Pip/Tazo 7. Azithromycin 25. Doripenem 43. Piperacillin 8. Aztreonam 26. Ertapenem 44. Rifampin 9. Cefaclor 27. Erythromycin 45. Strep. Synergy Screen 10. Cefazolin 28. Gent. Synergy Screen 46. Synercid 11. Cefepime 29. Gentamicin 47. Tetracycline 12. Cefotaxime 30. Imipenem 48. Ticar/ K Clavulanate 13. Cefotetan 31. Levofloxacin 49. Ticarcillin 14. Cefoxitin 32. Linezolid 50. Tigecycline 15. Cefpodoxime 33. Meropenem 51. Tobramycin 16. Ceftazidime 34. Moxifloxacin 52. Trimeth/Sulfa 17. Ceftriaxone 35. Nitrofurantoin 53. Trimethoprim 18. Cefuroxime 36. Norfloxacin 54. Vancomycin Figure 44 55. Click the - sign by Formulary Interpretation and Non Formulary Interpretation to close the lists. 56. Click the + sign by MIC under Formulary and Non Formulary. A list of Antibiotic MICs appears. 57. Click Amikacin MIC and choose Add. 58. Amikacin MIC then moves to the Selected Data box. Continue adding MICs in the same order that you added interpretations. See figure 45. When you have added all Antibiotic Interpretations and MICs, the number of columns selected should be 109. 59. Click the - sign by Antimicrobial Data to close the list. 24
Figure 45 60. Click the + next to Specimen Data. A list of parameters will appear. Figure 46 Figure 47 61. Click Specimen. 62. Click Add. 63. After adding all of the parameters, check the Columns selected. This number should be 110. If it is not, recheck your list and make corrections as needed. 25
Figure 48 64. Under LabPro Data Format at the bottom, click Description. Under Delimiter, click Tab. Figure 49 65. Complete the Code and Description boxes as shown above. 66. Click on Save, click on Close. This is the only Export Configuration you need to make for use with the Antibiogram Export Tool. 67. The Export Configuration box appears with the export you just created listed. Double click on Epidemiology for Export. The Print Reports screen appears. Figure 50 26
68. Epidemiology for Export should be in the Stored Queries box. 69. Epidemiology for Export should be in the Export Configuration box. 70. Insert the removable media you will be using to transfer your data to another computer- Place a CD in the CD drive or attach a flash drive to a USB port. 71. Click Export. See Figure 51. Figure 51 72. The Save As window appears. See Figure 52. 73. Click on your removable media on the left. 74. Click in the File Name box and press backspace to erase the existing file name. Type an appropriate name for your export in this box. In this example LabPro Export is used. 75. Click Save to begin the process of gathering and transferring your data. Figure 52 76. Depending on the volume of data, this transfer could take 30 minutes or more. Your screen may remain partially unpainted during the export process. 27
77. Be sure to wait for the message below that indicates your transfer is complete. Figure 53 78. Click OK. 79. The Print Reports window is displayed. 80. To safely remove a flash drive, click on the icon indicated in Figure 54. If this icon is not visible, click the arrow at the end of the tool tray. Figure 54 81. Each export you perform should have a corresponding antibiogram printed from LabPro using the same query used to export the data. It is recommended that you compare the values on the printed report to those on your exported antbiogram to rule out errors in the export process. Follow the steps below. 82. Click the radio button for Epidemiology Reports. Check the box for Antimicrobic % Interpretive Report, and check boxes to include % Sensitive, % Intermediate, and % Resistant, as in Figure 55. Figure 55 83. Ensure that Exclude Duplicate Isolates and Use Epidemiology Organism Groups are checked. Do not check Exclude Non Formulary Drugs. 84. In the Report Name box at the bottom type a name for the report. 28
85. Click Print Please note that there may be minor differences with the same set of data between the LabPro Antimicrobic % Interpretive Report and the exported antibiogram derived from this template. The percent S, I and R may vary +/- 1 percentage points. Sources of variation may include: The same organism ID is stored multiple times on the same specimen. The same organism is tested for the same patient multiple times on different specimens on the same day. Now that you have created your query and export format, the only steps you will have to take to create your next antibiogram, is to change the date range on the query and export. If you used the PY option for Previous Year, you do not have to edit this from year to year. To change the date range on your query for use in subsequent years: 1. Click the Print Reports icon from the LabPro Command Center. Figure 1 2. Click the Epidemiology tab. 3. Click the look up button in the Stored Queries box. See Figure 2. Figure 2 4. From the Patient Query Rules box click on the Epidemiology for Export query. 5. Click the Edit icon. 29
Figure 3 6. In the bottom left portion of the screen, click on the Test Group Status/Date cell. 7. The date range selection window appears on the right. 8. Right click the existing date range and choose Delete. Click OK to confirm the deletion. 9. Click Complete in the status box, and then enter the new starting and ending dates. 10. Press Enter. 11. Click the Save icon in the upper left corner of the Query Configuration box. 12. Double click the query from the list to use it for an export. 30
Import Instructions 31
This section provides instructions for taking the data that you have exported from LabPro and importing it into the MicroScan Antibiogram Export Tool 4.42 (2016) for analysis and printing of your antibiogram. Notes: * Save functions may take an extended amount of time depending on the amount of data and the speed of your computer. * It is recommended that each time you are creating your antibiogram, you download the template from the website to ensure you have the most updated version. * Before beginning the export process, make a copy of the Epidemiology Template that you downloaded from the website, and use the copy for this process. If you make a mistake, and have to begin again, make another copy of the original to use. * This template will be referred to as the Antibiogram Export Tool 4.42 (2016). * These instructions will detail creating a raw data sheet containing your export, as well as copying this data into another sheet for processing and analysis. 1. Download the Antibiogram Export Tool 4.42 (2016) from the Beckman Coulter MicroScan website, and save it to the hard drive of the computer in your lab that has Microsoft Excel. DO NOT load the template on to the LabPro computer. 2. Insert the media containing your LabPro export into this same computer. For help regarding To Enable a USB Flash Drive on a computer running Windows 7, please see TSB203b. 3. Open the Antibiogram Export Tool 4.42 (2016). If you obtain a Security Warning, chose the option to Enable Content. See Figure 1. Macros automate frequently used tasks to save time, keystrokes, and mouse actions. While the macros in this tool were created to automate steps that are necessary for the functionality of the tool, some macros may be perceived as being unsafe. If you have questions or concerns about enabling the macros in this tool, please contact your local IT department. We have also scanned these instructions and our Antibiogram Export Tool 4.42 (2016) for viruses to ensure they are virus free. 32
Figure 1 4. Ensure only one copy of the template is open at a time, as having multiple copies open will prevent the macros from running. 5. Open the Raw Data sheet of the template by clicking on the tab labeled Raw Data. 6. Click the first cell of column A. Figure 2 Figure 3 33
7. To bring your LabPro data into the template, click Data, and then click From Text. If a security warning appears on the screen, click OK. Figure 4 8. The Import Text File window appears. Click on your removable media on the left and click on your export file in the center. Figure 5 9. Your export file will now show in the File name box. 10. Click Import. 11. The Text Import Wizard Step 1 of 3 window appears. 34
Figure 6 12. Confirm that the radio button by Delimited is checked. 13. Click Next. 14. The Text Import Wizard- Step 2 of 3 window appears. Under Delimiters confirm Tab is checked, and note your data should be in readable columns. Figure 7 15. Click Next. 16. The Text Import Wizard- Step 3 of 3 window appears. 35
Figure 8 17. Highlight the first column by clicking it with the mouse. Hold down the shift key and pull the scroll bar at the bottom of the grid to the right, until you get to the last column, Specimen #. Click the last column while still holding down the shift key. All the columns will appear selected or highlighted, and will be black. 18. Click the radio button by Text. 19. Click the Finish button. Figure 9 36
Figure 10 20. The system will display the Import Data dialog box allowing the user to specify the location for the imported data. The choices are Existing worksheet or New worksheet. 21. Choose Existing worksheet and click OK. The data will import to the template beginning in the cell you clicked in the Raw Data sheet in step 5. 22. A header row will import with your data - check to see that the imported header matches the header already in the template. This will ensure that antibiotics have been exported and imported in the correct order. 23. In Figure 11 below, the imported header row does not match the header row of the template. If this happens, exit your template without saving. Return to LabPro and edit your export configuration so that the antibiotics are in the correct order. Refer to the Export section of this document beginning at page 25. Figure 11 24. When the imported header row (row 2) matches the header row in the template, delete the imported header row (row 2) by clicking on the left end of the imported header row to highlight it. Right click and select Delete. See Figure 12. 37
Before delete Template Header Row Imported header row Figure 12 After delete. Template header row only. Figure 13 25. Save the file. 26. To copy your data to the Working Data sheet, all cells must be selected. To do this, click in the first cell, containing the Organism header, of the Raw Data sheet. Figure 14 38
27. HOLDING DOWN THE SHIFT KEY, position your mouse over the bottom border of this cell until your mouse pointer has a symbol with four arrows. Then double click. Figure 15 28. This highlights all rows in this column that contain data. Your curser will be at the last cell of this column. Figure 16 29. Still HOLDING DOWN THE SHIFT KEY, press the right arrow on your keyboard until your specimen number column is highlighted. Figure 17 39
30. Release the shift key. Right click in the highlighted area and choose Copy. 31. Click on the Working Sheet, and position your cursor in the first empty cell of the sheet. Figure 18 32. Right click on your mouse and choose Paste. 33. You will again have two header rows- Check once more that the header row that you have imported matches the header row of the sheet. This is a final check to verify that your imported antibiotics are in the correct order. Return to step 23 if these two header rows do not match. 34. If the header rows match, delete the second header row as in step 24. 35. A macro must be run to prepare your data for calculation. This macro will group the organism names in your export to the organism groups on the final M39 Gram Pos and M39 Gram Neg tabs, change IB interpretations to S, ESBL interpretations to R, etc. To run this macro, click View, and then click Macros. Figure 19 36. The Macro window below appears. Click the first macro listed, ANTIBIOGRAM. See Figure 20. 40
Figure 20 37. Click Run. It has completed when the hour glass goes away. The length of time will depend on how much data you have. Usually not more than a couple of seconds. The Macro window will close. This is the only macro you need to run. Do not click on the other items in the list, and do not attempt to run this macro more than once! 38. If you included User-defined Organisms in your Query in LabPro, you must now find these organisms on the Working Data sheet, and change their names to one of the organisms in Figure 21 below. 39. Your data is currently sorted by organism name. Locate your User-defined organisms and rename. Spelling and spacing is critical. Methicillin Susceptible Staphylococcus aureus Methicillin Resistant Staphylococcus aureus Coagulase Negative Staphylococcus Streptococcus pneumoniae Enterococcus faecalis Enterococcus faecium Enterococcus spp. Escherichia coli Klebsiella pneumoniae Klebsiella oxytoca Proteus mirabilis Stenotrophomonas maltophilia Enterobacter aerogenes Enterobacter cloacae Serratia marcescens Pseudomonas aeruginosa Acinetobacter baumannii Citrobacter freundii Morganella morganii Providencia species Salmonella species Shigella species Figure 21 40. Save the file. This initiates the calculations for the M39 tabs. This may take some time depending on the amount of data in your workbook. You can monitor the progress at the bottom right of your computer screen. 41. When the calculations are complete, check your final out put on the M39 tabs. 41
42. Use the printed Antimicrobic % Interpretative Report to verify your results. 43. Review your final results. Check the following: The % susceptible for Methicillin Resistant Staphylococcus aureus, Methicillin Susceptible Staphylococcus aureus, and Total Staphylococcus aureus versus Linezolid and Daptomycin. Resistance for these drug/bug combinations is uncommon The % susceptible for Enterococcus faecalis, Enterococcus faecium, and Enterococcus species versus daptomycin. The % susceptible for staphylococci and Streptococcus pneumoniae vs. vancomycin. The % susceptible for gram negative isolates versus tigecycline. Resistance for these drug bug combinations is uncommon. If your % susceptible for any of these combinations is less than 100%, and this is unexpected at your institution, you may want to investigate the validity of these results. When there is no I or R breakpoints defined, i.e. non susceptible, results have been calculated as resistant. Refer to the Working Data sheet. Use the specimen number in the last column as a reference for your investigation. You may delete these isolates from your Working Data sheet to not include them in the calculations, or modify the interpretation as appropriate. 44. The data on the M39-A4 Gram Pos and M39-A4 Gram Neg sheets can now be copied and pasted into another sheet in the workbook, where you can edit the formatting prior to printing. For example, you may want to remove antibiotics not used at your institution, add color or shading, etc. 45. To copy the data, highlight the entire spreadsheet by clicking in the upper left corner of the data area. See Figure 22. 46. Right click. Click Copy. Figure 22 42
47. Open the sheet or workbook where you want your printable data to be. 48. Right click. Click Paste. 49. The data should look like the M39 sheet you copied from. Repeat steps 45 to 48 for the other M39 sheet. 50. You can now reformat as desired; add Hospital name header, change fonts, add color, delete columns etc. 51. When you are ready to print, highlight the entire sheet, and click File and Print. 52. Choose the desired settings. For example Landscape Orientation and Fit All Columns on One Page. Click Print to print your antibiogram. If you need assistance, please call the MicroScan Customer Technical Solutions at 1-800-677-7226. MicroScan and LabPro and all associated marks are trademarks of Beckman Coulter. All other trademarks and brands are the property of their respective owners. Beckman Coulter, the stylized logo, and the Beckman Coulter product and service marks mentioned herein are trademarks or registered trademarks of Beckman Coulter, Inc. in the United States and other countries. All other trademarks are the property of their respective owners. 43
Appendix A Organism List = NEWLY ADDED IN LABPRO 4.42, NEED TO BE ADDED TO EXISTING EXPORT QUERIES. ** = FOR BRUKER USERS ONLY Organism Number Organism 1 Escherichia coli 2 Shigella dysenteriae 3 Shigella flexneri 4 Shigella boydii 5 Shigella sonnei 7 Salmonella enterica 8 Salmonella enterica serotype Typhi 9 Salmonella enterica serotype Choleraesuis 10 Salmonella enterica serotype Paratyphi A 11 Salmonella enterica subspecies arizonae 12 Citrobacter freundii complex 15 Klebsiella pneumoniae 16 Klebsiella oxytoca 19 Enterobacter aerogenes 20 Enterobacter cloacae 25 Serratia marcescens 30 Proteus mirabilis 31 Morganella morganii 32 Providencia rettgeri 33 Providencia stuartii 34 Providencia stuartii 51 Escherichia coli 52 Shigella species 55 Pseudomonas aeruginosa 59 Stenotrophomonas maltophilia 71 Acinetobacter baumannii complex 96 Providencia heimbachae 103 Enterococcus species 109 Coagulase-negative Staphylococcus species 122 Enterococcus avium 124 Enterococcus durans 125 Enterococcus faecalis 126 Enterococcus faecium 127 Streptococcus pneumoniae 142 Methicillin Resistant Staphylococcus aureus 148 Staphylococcus hominis subsp. novobiosepticus 149 Staphylococcus species 44
Organism Number Organism 150 Staphylococcus aureus 151 Staphylococcus epidermidis 152 Staphylococcus saprophyticus 153 Staphylococcus xylosus 154 Staphylococcus cohnii 155 Staphylococcus haemolyticus 156 Staphylococcus hominis 157 Staphylococcus simulans 158 Staphylococcus capitis 159 Staphylococcus warneri 167 Staphylococcus sciuri 168 Staphylococcus lentus 169 Staphylococcus hyicus/chromogenes 170 Staphylococcus hyicus 171 Staphylococcus chromogenes 172 Staphylococcus intermedius 174 Staphylococcus chromogenes 175 Staphylococcus hominis subsp. hominis 176 Staphylococcus carnosus 177 Staphylococcus lugdunensis 178 Staphylococcus schleiferi 179 Staphylococcus caprae 182 Staphylococcus kloosii 183 Staphylococcus gallinarum 184 Staphylococcus auricularis 185 Staphylococcus equorum 186 Staphylococcus arlettae 188 Staphylococcus capitis subsp. capitis 193 Staphylococcus cohnii subsp. cohnii 194 Staphylococcus schleiferi subspecies coagulans 195 Staphylococcus schleiferi subspecies schleiferi 283 Enterococcus casseliflavus 284 Enterococcus gallinarum 285 Enterococcus hirae 286 Enterococcus raffinosus 287 Enterococcus mundtii 318 Enterococcus durans/hirae 319 Staphylococcus capitis subsp. urealyticus 320 Staphylococcus cohnii subsp. urealyticus 523 Providencia species 574 Citrobacter freundii 586 Escherichia coli O157:H7 589 Shigella boydii/dysenteriae/flexneri 704 Acinetobacter baumannii complex /haemolyticus 45
Organism Number Organism 733 Salmonella species 758 Acinetobacter baumannii complex/haemolyticus 832 Providencia alcalifaciens 833 Providencia rustigianii 851 Escherichia coli 958 Providencia alcalifaciens/rustigianii 2001 Escherichia coli ESBL 2015 Klebsiella pneumoniae ESBL 2016 Klebsiella oxytoca ESBL 2030 Proteus mirabilis ESBL 2125 Enterococcus faecalis VIE 2126 Enterococcus faecium VIE 2127 Streptococcus pneumoniae PRSP 3109 Coagulase-negative Staphylococcus species MRS 3125 Enterococcus faecalis VRE 3126 Enterococcus faecium VRE 3127 Streptococcus pneumoniae PISP 3148 Staph hominis subsp. novobiosepticus MRS 3149 Staphylococcus species MRS 3151 Staphylococcus epidermidis MRS 3152 Staphylococcus saprophyticus MRS 3153 Staphylococcus xylosus MRS 3154 Staphylococcus cohnii MRS 3155 Staphylococcus haemolyticus MRS 3156 Staphylococcus hominis MRS 3157 Staphylococcus simulans MRS 3158 Staphylococcus capitis MRS 3159 Staphylococcus warneri MRS 3167 Staphylococcus sciuri MRS 3168 Staphylococcus lentus MRS 3169 Staphylococcus hyicus/chromogenes MRS 3170 Staphylococcus hyicus MRS 3171 Staphylococcus chromogenes MRS 3172 Staphylococcus intermedius MRS 3174 Staphylococcus chromogenes MRS 3175 Staphylococcus hominis ssp hominis MRS 3176 Staphylococcus carnosus MRS 3177 Staphylococcus lugdunensis MRS 3178 Staphylococcus schleiferi MRS 3179 Staphylococcus caprae MRS 3182 Staphylococcus kloosii MRS 3183 Staphylococcus gallinarum MRS 3184 Staphylococcus auricularis MRS 3185 Staphylococcus equorum MRS 46
Organism Number Organism 3186 Staphylococcus arlettae MRS 3188 Staphylococcus capitis ssp capitis MRS 3193 Staphylococcus cohnii ssp cohnii MRS 3319 Staphylococcus capitis ssp ureolyticus MRS 3320 Staphylococcus cohnii ssp ureolyticus MRS 5460 ** Staphylococcus pasteuri 5461 ** Staphylococcis pettenkoferi 5463 ** Staphylococcus pseudintermedius 5885 ** Klebsiella pneumoniae ssp ozaenae 5886 ** Klebsiella pneumoniae ssp pneumoniae 5887 ** Klebsiella pneumoniae ssp rhinoscleromatis 5894 ** Morganella morganii ssp morganii 5895 ** Morganella morganii ssp sibonii 5910 ** Serratia marcescens ssp sakuensis 5916 ** Enterobacter cloacae ssp cloacae 5917 ** Enterobacter cloacae ssp dissolvens 5922 ** Serratia marcescens ssp marcescens 5923 ** Staphylococcus aureus ssp anaerobius 5924 ** Staphylococcus aureus ssp aureus 5925 ** Staphylococcus carnosus ssp carnosus 5926 ** Staphylococcus carnosus ssp utilis 5927 ** Staphylococcus equorum ssp equorum 5928 ** Staphylococcus saprophyticus ssp bovis 5929 ** Staphylococcus saprophyticus ssp saprophyticus 5967 ** Salmonella sp. (bongori) 5968 ** Salmonella sp. (choleraesuis) 5970 ** Salmonella sp. (enterica st Arizonae) 5971 ** Salmonella sp. (enterica st Diarizonae) 5973 ** Salmonella sp. (enterica st Enterica) 5976 ** Salmonella sp. (enterica st Houtenae) 5977 ** Salmonella sp. (enterica st Indica) 5978 ** Salmonella sp. (enterica st Salamae) 5998** Escherichia coli (Inactive) 6375 ** Enterobacter cloacae complex 6419 ** Staphylococcus equorum ssp linens 6529 ** Enterococcus avium group 47
For Customers Storing RUO Identifications from Bruker, also add these organisms to the export query. Organism Number R1 ** R15 ** R16 ** R20 ** R30 ** R31 ** R32 ** R33 ** R55 ** R96 ** R124 ** R125 ** R126 ** R283 ** R284 ** R285 ** R286 ** R287 ** R574 ** R758 ** R832 ** R833 ** R4644 ** R4645 ** R4650 ** R4651 ** R4654 ** R4655 ** R4657 ** R4659 ** R5246 ** R5453 ** Organism RUO Escherichia coli RUO Klebsiella oxytoca RUO Klebsiella pneumoniae RUO Enterobacter cloacae RUO Proteus mirabilis RUO Morganella morganii RUO Providencia rettgeri RUO Providencia stuartii RUO Pseudomonas aeruginosa RUO Providencia heimbachae RUO Enterococcus durans RUO Enterococcus faecalis RUO Enterococcus faecium RUO Enterococcus casseliflavus RUO Enterococcus gallinarum RUO Enterococcus hirae RUO Enterococcus raffinosus RUO Enterococcus mundtii RUO Citrobacter fruendii RUO Acinetobacter baumannii complex/haemolyticus RUO Providencia alcalifaciens RUO Providencia rustigianii RUO Enterococcus caccae RUO Enterococcus canintestini RUO Enterococcus dispar RUO Enterococcus gilvus RUO Enterococcus italicus RUO Enterococcus malodoratus RUO Enterococcus pallens RUO Enterococcus pseudoavium RUO Providencia vermicola RUO Staphylococcus condiment 48
Organism Number R5456 ** R5457 ** R5458 ** R5459 ** R5460 ** R5461 ** R5462 ** R5463 ** R5464 ** R5465 ** R5885 ** R5886 ** R5887 ** R5894 ** R5895 ** R5910 ** R5916 ** R5917 ** R5922 ** R5923 ** R5924 ** R5925 ** R5926 ** R5927 ** R5928 ** R5929 ** R5930 ** R5931 ** R5932 ** R5933 ** R5967 ** R5968 ** R5969 ** R5970 ** R5971 ** Organism RUO Staphylococcus fleurettii RUO Staphylococcus lutrae RUO Staphylococcus muscae RUO Staphylococcus nepalensis RUO Staphylococcus pasteuri RUO Staphylococcus pettenkoferi RUO Staphylococcus piscifermentans RUO Staphylococcus pseudintermedius RUO Staphylococcus simiae RUO Staphylococcus succinus ssp casei RUO Klebsiella pneumoniae ssp. ozaenae RUO Klebsiella pneumoniae ssp pneumoniae RUO Klebsiella pneumoniae ssp rhinoscleromatis RUO Morganella morganii ssp morganii RUO Morganella morganii ssp sibonii RUO Serratia marcescens ssp sakuensis RUO Enterobacter cloacae ssp cloacae RUO Enterobacter clocae ssp dissolvens RUO Serratia marcescens ssp marcescens RUO Staphylococcus aureus ssp anaerobius RUO Staphylococcus aureus ssp aureus RUO Staphylococcus carnosus ssp carnosus RUO Staphylococcus carnosus ssp utilis RUO Staphylococcus equorum ssp equorum RUO Staphylococcus saprophyticus ssp bovis RUO Staphylococcus saprophyticus ssp saprophyticus RUO Staphylococcus sciuri ssp carnaticus RUO Staphylococcus sciuri ssp rodentium RUO Staphylococcus sciuri ssp sciuri RUO Staphylococcus succinus ssp succinus RUO Salmonella sp. (bongori) RUO Salmonella sp. (choleraesuis) RUO Salmonella sp. (enterica st Anatum) RUO Salmonella sp. (enterica st Arizonae) RUO Salmonella sp. (enterica st Diarizonae) 49
Organism Number R5972 ** R5973 ** R5974 ** R5975 ** R5976 ** R5977 ** R5978 ** R5979 ** R5980 ** R5981 ** R5998 ** R6234 ** R6375 ** R6419 ** Organism RUO Salmonella sp. (enterica st Dublin) RUO Salmonella sp. (enterica st Enterica) RUO Salmonella sp. (enterica st Gallinarum) RUO Salmonella sp. (enterica st Hadar) RUO Salmonella sp. (enterica st Houtenae) RUO Salmonella sp. (enterica st Indica) RUO Salmonella sp. (enterica st Salamae) RUO Salmonella sp. (enterica st Stanley) RUO Salmonella sp. (enteritidis) RUO Salmonella sp. (typhimurium) RUO Escherichia coli ( Inactive) RUO Acinetobacter baumannii RUO Enterobacter cloacae complex RUO Staphylococcus equorum ssp linens 50