Antibiogram Export Instructions V4.11

9020-6886

Antibiogram Export Tool Instructions Final May 2015 July 2015

MicroScan®

LabPro Information Manager

Antibiogram Export Tool Instructions Single Institution Format

2015

9020-6886 2 Antibiogram Export Tool Instructions Final May 2015 July 2015

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

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 are the CLSI M39

A4 recommended organisms.

The LabPro screen shots in these instructions represent LabPro 4.11 and may

look slightly different if you have a different 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, and these versions are required.

If you have any questions or need assistance with this process, call the

MicroScan Customer Technical Solutions at 1-800-677-7226.


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 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.

Figure 1

3. Click Properties.

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.


Excel 2010 as shown below is the only supported version.

Figure 3

8. If your screen looks different than figure 3, you may have a different

version of Excel. Please contact your IT department to confirm your Excel

version.


On Your LabPro computer:

9. In Utilities>Customization>Report> Formatting- verify that your

Epidemiology Duplicate Isolate criteria is set to 365 days and Any Source. 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.

Figure 6

14. Click the radio button by Query, and then click the look up button.

Figure 7

15. Click + to create a new query.

Figure 8


16. Click, drag, and drop Specimen # into the first cell that states To begin: drag

a desired parameter to this cell.

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.


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.

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.

27. Compare the User-defined organisms in use in your lab to the list of

organisms in Figure 17 below.

Methicillin Susceptible Staphylococcus aureus Enterobacter aerogenes Methicillin Resistant Staphylococcus aureus Enterobacter cloacae Coagulase Negative Staphylococcus Serratia marcescens Streptococcus pneumoniae Pseudomonas aeruginosa Enterococcus faecalis Acinetobacter baumannii Enterococcus faecium Citrobacter freundii complex Escherichia coli Morganella morganii Klebsiella pneumoniae Providencia species Klebsiella oxytoca Salmonella species Proteus mirabilis Shigella species

Stenotrophomonas (X.) maltophilia

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.


Exporting Your Data


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 M39A-4, 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, then click the Delete icon.


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, and highlight all of the Salmonella spp. 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. 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. Use code EXCNS and the description Staph

(coag.neg.)

15. The remaining required groups to be created are listed in the table below.

Refer to the organism list in this document, figure 27 on pages 16-19, 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 one of these groups, if applicable.


Code Description Notes

EXSAUR Total S. aureus

EXEFLS E. faecalis

EXEFCM E. faecium

EXEC Escherichia coli Include E. coli, ESBL

EXKP Klebsiella pneumoniae Include K. pneumoniae, ESBL

EXKOX Klebsiella oxytoca Include K. oxytoca, ESBL

EXPMIR Proteus mirabilis Include P. mirabilis, ESBL

EXPROV Providencia spp

EXSHIG Shigella spp

EXENTSPP Enterococcus spp. Include only species not E. faecium or E.

faecalis

EXACIN Acinetobacter 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

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.

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.


Figure 26

25. In the Organism text box on the right, type the Organism Numbers listed below

one at a time, pressing the enter key between each number. Continue through

page 19. The organisms in this list are the organisms recommended by the CLSI M39

document for reporting on your antibiogram, and is based on MicroScan LabPro 4.11

software. In addition to the organisms on this list, be sure to include in your Query

any appropriate User-defined organisms from the list created on page 10, step 28.

Organism Number Organism

1 Escherichia coli

2 Shigella dysenteriae

3 Shigella flexneri

4 Shigella boydii

5 Shigella sonnei

7 Salmonella species

8 Salmonella typhi

9 Salmonella cholerasuis

10 Salmonella paratyphi A

11 Salmonella/Arizona

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 (X.) maltophilia

71 Acinetobacter baumannii

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

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

589 Shigella boydii/dysenteriae/flexneri

704 Acinetobacter baumannii/haemolyticus

832 Providencia alcalifaciens 1-2

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

3109 Coagulase-negative Staphylococcus species MRS

3125 Enterococcus faecalis VRE

3126 Enterococcus faecium VRE

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 subsp. 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

3186 Staphylococcus arlettae MRS

3188 Staphylococcus capitis subsp. capitis MRS

3193 Staphylococcus cohnii subsp. cohnii MRS

3319 Staphylococcus capitis subsp. ureolyticus MRS

3320 Staphylococcus cohnii subsp. ureolyticus MRS Figure 27

26. Entering each number builds a list of organisms in the Selected Organism

List as in Figure 28 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 28

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 29

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 30.

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 use.

32. Release the control key and click the green check mark.

Figure 30

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 31

34. On the right, put a check in the Complete box. See Figure 32.

35. Below that, click on the calendar in the From box. Click PY for previous year, and

press Enter. See Figure 36. 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 32

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


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 33

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 34


Figure 35

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 35.

Figure 36

41. The Export Configurations box will open as in Figure 36. 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 37

43. A list of parameters appears. Click Organism, and then click Add.

Figure 38

44. Organism is now listed in the Selected Data box.


Figure 39

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 order

of antibiotics is crucial! If you have customized the formulary in LabPro, you will

have to choose from both the Formulary and Non-Formulary lists.

Figure 40

48. Click the + next to Interpretation under Formulary and under Non-Formulary, a list

of antibiotic interpretations appears under each.


Figure 41

49. Click Amikacin Interpretation.

50. Click Add.

Figure 42

Amikacin Interpretation is now listed in the Selected Data box.


Figure 43

51. Click Amox/K Clav Interpretation.

52. Click Add. Amox/K Clav Interpretation is now listed in the Selected Data box.

Figure 44

53. Continue adding antibiotics in the order listed in Figure 45, next page. If you make

a mistake, highlight the antibiotic and choose Remove, Move Up or Move Down, as

appropriate. The order of the antibiotics 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.

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 45

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.


Figure 46

60. Click the + next to Specimen Data. A list of parameters will appear.

Figure 47


Figure 48

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.

Figure 49

64. Under LabPro Data Format at the bottom, click Description. Under Delimiter,

click Tab.


Figure 50

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.

Figure 51

The Print Reports screen appears.

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.


Figure 52

72. The Save As window appears. See Figure 53.

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 53


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.

77. Be sure to wait for the message below that indicates your transfer is complete.

Figure 54

78. Click OK.

79. The Print Reports window is displayed. 80. To safely remove a flash drive, click on the icon indicated in Figure 55. If this

icon is not visible, click the arrow at the end of the tool tray.

Figure 55

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 56.


Figure 56

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.

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.

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.


Import Instructions


This section provides instructions for taking the data that you have exported

from LabPro and importing it into the MicroScan Antibiogram Export Tool

(2015) 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 (2015).

* 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 (2015) from the 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.

3. Open the Antibiogram Export Tool (2015). 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 (2015) for viruses to ensure they are virus free.


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.

Figure 2

6. Click the first cell of column A.

Figure 3


7. To bring your LabPro data into the template, click Data, 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.


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.


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.

Figure 9

19. Click the Finish button.


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 10 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 your imported header row matches the header row in the template,

delete the imported header row by clicking on the left end of the imported header

row to highlight it. Right click and select Delete. See Figure 12.


Before delete

Template Header Row

Figure 12

Imported header row

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


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

key board until your specimen number column is highlighted.

Figure 17


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 24

if these two header rows do not match.

34. If the header rows match, delete the second header row as in step 23.

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.


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 Enterobacter aerogenes

Methicillin Resistant Staphylococcus aureus Enterobacter cloacae

Coagulase Negative Staphylococcus Serratia marcescens

Streptococcus pneumoniae Pseudomonas aeruginosa

Enterococcus faecalis Acinetobacter baumannii

Enterococcus faecium Citrobacter freundii complex

Escherichia coli Morganella morganii

Klebsiella pneumoniae Providencia species

Klebsiella oxytoca Salmonella species

Proteus mirabilis Shigella species

Stenotrophomonas (X.) maltophilia

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.

42. Use the printed % Susceptible 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

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 have any problems with this process or 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.

Documents

Antibiogram Export Instructions V4.11