Antibiogram Export Instructions V4.11
Transcript of 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.
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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.
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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.
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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.
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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
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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.
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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
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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
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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.
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Exporting Your Data
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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.
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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.
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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.
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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.
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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
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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
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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
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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.
9020-6886 20 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 21 Antibiogram Export Tool Instructions Final May 2015 July 2015
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
9020-6886 22 Antibiogram Export Tool Instructions Final May 2015 July 2015
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
9020-6886 23 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
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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.
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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.
9020-6886 26 Antibiogram Export Tool Instructions Final May 2015 July 2015
Figure 41
49. Click Amikacin Interpretation.
50. Click Add.
Figure 42
Amikacin Interpretation is now listed in the Selected Data box.
9020-6886 27 Antibiogram Export Tool Instructions Final May 2015 July 2015
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
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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.
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Figure 46
60. Click the + next to Specimen Data. A list of parameters will appear.
Figure 47
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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.
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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.
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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
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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.
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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.
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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.
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Import Instructions
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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.
9020-6886 38 Antibiogram Export Tool Instructions Final May 2015 July 2015
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
9020-6886 39 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 40 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 41 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 42 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 43 Antibiogram Export Tool Instructions Final May 2015 July 2015
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
9020-6886 44 Antibiogram Export Tool Instructions Final May 2015 July 2015
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
9020-6886 45 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 46 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 47 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
9020-6886 48 Antibiogram Export Tool Instructions Final May 2015 July 2015
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.
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