Page 1 of 16
Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Prepared by: Poolak Akhavan
Original Date: November 13, 2009
Issued by: Laboratory Manager
Revision Date: July 14, 2010
Approved by: Dr Susan Poutanen
Annual Review Date: May 31, 2013
I.
Introduction:
This document describes the method for preparing a cumulative antimicrobial
susceptibility report (antibiogram).
II.
Materials:
SOFT Laboratory Information System (LIS) system
Excel program
Antibiogram Working Template and Antibiogram Report Template (Appendix H)
III.
Procedure:
A. LIS search:
1)
2)
3)
4)
5)
6)
7)
8)
Open the LIS software.
Login: mic.
Enter your username and password.
Go to “6-Epidemiology”.
Click on Epidemiology report.
Choose” 0-Logbook”.
Using the arrow key (↑) to highlight the “Run name”.
Press F2 to see the list of stored searches. All antibiogram saved searches start
with XX. The criteria used in stored search queries are shown in Appendix G.
9) Find the relevant file and press enter.
10) All settings in the stored search should be confirmed with a Laboratory
Information System specialist every year for any possible changes. The wards
and specimen types, which change frequently, are of particular importance to
review.
11) Enter the search date; update the wards and codes if needed.
If a new search is required, please refer to the appendices A-F and press F5 to
change the options to reflect those in the appendices.
12) Press F12 to run the search.
13) Confirm printing(Y).
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Page 2 of 16
Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
14) Save to file or ASCII, transfer the file to a folder (“User id: print”, “Password:
shuttle”).
B. Transfer of data to an excel file:
1)
2)
3)
4)
5)
Open the ASCII file in excel.
Choose: “Delimited “and click on “Next”.
Choose “Comma” and click on “Next”.
Click on “Finish”.
Save this file as “Microsoft excel 97; excel 2003 &5.0/95 workbook” type.
C. Selection of antibiotics and arrangement of the isolates in the excel file:

Cleaning the data:
Open the “Antibiogram working template” file.
Copy and paste the saved excel sheet into in the “complete work sheet” tab.
Copy it again into the other blank tab to make the necessary changes.
Separate the entire Gram-Negative followed by the Gram-Positive isolates and
sort them from high to low sequence (descending).
5) Delete the two rows between the “#isolates” and “antibiotics”.
6) Insert a column at the beginning of the table in order to accommodate
antibiotic numbers in step 8.
7) Copy and paste this worksheet into new tab.
8) Copy and paste the list of antibiotics and their numbers under these data from
the Gram Neg & Pos Template tab.
9) Sort the antibiotic names from A to Z.
10) Move the order numbers one cell up in order to have them align with the
antibiotics that have the same name.
11) Highlight the antibiotic data (excluding the organism names and isolate
numbers) and sort the antibiotic numbers in an ascending order.
12) Delete the drugs that do not have a matching antibiotic number.
13) Copy only the rows and columns with data.
14) Special Paste (ONLY THE VALUE) in the Gram Neg & Pos Template tab, the
data will be transferred to the bottom table of the sheet.
15) Copy and Special Paste the bottom table to the FINAL DATA for Report
Template tab and delete the antibiotic columns that have no data as necessary.
16) Save this file.
17) Add and delete to the saved file as follows if applicable:
A) Streptococcus pneumoniae:
1)
2)
3)
4)
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
a) Ceftriaxone susceptibility results for Streptococcus pneumoniae has
to be entered as “meningitis breakpoints/non-meningitis
breakpoints”.e.g. 100/100. Report out ceftriaxone with both nonmeningitis and -meningitis interpretations for Streptococcus
pneumoniae for bloods and respiratory sources where data are
provided.
b) Penicillin susceptibility results for Streptococcus pneumoniae has to
be entered as penicillin IV- meningitis / IV non – meningitis
breakpoints e.g:100/100. Report out penicillin with all IV nonmeningitis and IV- meningitis interpretations for Streptococcus
pneumoniae for blood and respiratory sources where data are
provided.
 Do not report out PO penicillin results for Streptococcus
pneumoniae.
 Penicillin IV- meningitis, IV non – meningitis results were
implemented in the last quarter of 2009.
B) Staphylococcus aureus
Enterococcus faecium
Viridans group streptococci
Streptococcus anginosus group
Combining the data within a genus is done for the following gram positive
isolates:
a) Staphylococcus aureus
All Staphylococcus aureus reported from the LIS are methicillinsusceptible. Calculate the isolate number and susceptibilities for
“Staphyloccocus aureus, all isolates” as per the following example.
Example:
Organism
# of isolates tested
Cloxacillin
Susceptibility
Staphyloccocus aureus, all isolates
206
76%
- methicillin-susceptible
158
99%
- methicillin-resistant (MRSA)
48
0%
Calculation method:
 # of isolates: 158 + 48= 206
 susceptibilities [(48 x 0%) + (158 x 99%)]/ (158+48) =76%
b) Enterococcus faecium
All Enterococcus faecium reported from the LIS are vancomycinsusceptible. Calculate the isolate number and susceptibilities for
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
“Enterococcus faecium, all isolates” using the same calculation method
as for Staphylococcus aureus.
c) Viridans group streptococci and Streptococcus anginosus group
There may be more than one entry for these isolates. Only report out the
combined isolate number and susceptibilities as shown in the following
example.
Example:
Organism
# of isolates tested
Penicillin
Susceptibility
Combined Viridans Group
Streptococci
364
76%
“Viridans group streptococci”
206
76%
“Streptococcus viridans group”
158
75%
Calculation method:
 # of isolates: 158 + 206= 364
 susceptibilities [(206 x .76) + (158 x .75)]/ (158+206) =76
C) Haemophilus influenzae:
Make a separate search using Logbook for respiratory (Appendix B) and
blood sites (Appendix C) for each hospital. Calculate the percentage of betalactamase positive isolates and enter this percent under the ampicillin results
in the final report.
Calculation is done based on the following example:
ORDER
DH8190608
eH8190608
l H7280646
eH7280646
t H7152859
eH7152859
H6131751
LAST
FIRST
MRN
CDATE
AREA
CurLoc
OrdLoc
SRC
TEST
08.10.19
TH
ES10T
10CMS
BAL
GM
08.10.19
TH
ES10T
10CMS
BAL
C&S
08.09.28
TH
ES13
10CMS
SPT
GM
08.09.28
TH
ES13
10CMS
SPT
SPT
08.09.15
TH
5CB
10CMS
SPT
GM
08.09.15
TH
5CB
10CMS
SPT
SPT
08.08.13
TH
ES9
10CMS
SPT
GM
ORG
betalac
haeinf
Neg
haeinf
Neg
haeinf
Neg
08.08.13
TH
ES9
10CMS
SPT
SPT
haeinf
Pos
aH6131751
H4171048
08.06.17
TH
GIP
10CMS
ETT
GM
l
08.06.17
TH
GIP
10CMS
ETT
C&S
haeinf
Neg
l H4171048
The repeats and unrelated tests first. Then count the total number of H.
influenzae and also the number of beta-lactamase positive. In this example
we have one beta-lactamase positive isolate out of 5 H. influenzae i.e. % 20
ampicillin susceptible.
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Note: As of 2008, ampicillin and beta-lactamase for Moraxella catarrhalis
were not tested and only beta-lactamase for H. influenzae is reported out.
Prior to 2008, the combination of both ampicillin and beta-lactamase for H.
influenzae and M. catarrhalis was reported.
D) Moraxella catarrhalis:
Report the total number of isolates only for respiratory site using Logbook
results (Appendix B).
18) Delete all organisms along with their antibiotic data that have < 5 isolates.
Exceptions:
 If the total number of bacteria in Gram-positive/Gram-negative group is
less than 5 then report the first 5 isolates with highest prevalence.
 For S. aureus, E. faecium, viridans group streptococci, and S. anginosus
group for which data are combined (e.g. MRSA and S. aureus), consider
the total combined number as the total number of isolates.
D. Transferring the data into a final antibiogram report:
1) Open the “Antibiogram Report Template” file.
2) Fill all the required information using drop down list data.
3) Copy the two columns of organisms from the FINAL DATA for Report
Template tab to the first two columns of the Antibiogram Report Template.
4) Order the organisms in the template by cutting the organisms along with their
row of highlighted antibiotics and insert the cut cells to match the order from
the FINAL Data for Report Template.
5) Delete the unused organisms.
6) Copy and paste all rows excluding the header (ONLY THE VALUE) from the
FINAL DATA for Report Template tab of the Working Template into this
“Final Antibiogram Report Template”.
7) Make sure to keep the gram negative and positive isolates separate.
8) The most common bacteria are listed in the template. Find all the unlisted
bacteria names in hidden sheet named “Bacteria master list”.
 To open a hidden sheet: Click on “Format” on toolbar. Go to “sheet” and
click on “unhide”. Click on the sheet needed. Make sure to hide back all
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
the hidden sheets before saving the file so that the hidden sheets are not
printed out with the final antibiogram report.
 If an organism has to be added from the Bacteria master list, please
contact a medical microbiologist regarding which drugs should be
reported out for that organism.
9) Delete the drugs that are not highlighted.
10) Adjust the page break to have each tab in one page.
11) Save the file.
12) The final antibiogram report should be reviewed by a medical microbiologist
prior to being released.
VI.
Reporting:
1) Prepare report annually or at intervals as requested by hospitals.
2) Report percent susceptible (%S) only and do not include the intermediate (I) or
resistant (R) percentages.
3) Include only the results from the first isolates of a given species; “one isolate per
patient”.
4) Exclude surveillance isolates.
5) Report results for all drugs tested that are appropriate for the species, and do not
report supplemental drugs that are selectively tested on resistant isolates only.
These drugs are highlighted in the report template for the most common bacteria.
6) Provide the antibiogram report for 14 selected hospitals (Appendix D).
7) The antibiogram report is provided for inpatients only with the exception of PMH
where both in- and out-patient data are included
IV.
Quality Control:
Validation of calculations: Line listing of data should be used as a quality
assurance check to ensure that the analytical software is calculating data
accurately. The results from the computer generated reports using the “Drug
Susceptibility Short format” can be compared to the manual calculation from the
“Logbook” report. This should be done only the first time the program is used
(completed in 2008) and subsequently if any changes are made to the analytical
software.
V.
Reference:
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Recommendation in CLSI document M39-A2 is used for preparation of a
cumulative antimicrobial susceptibility test data report. [M39-A2, Vol25, No.28;
Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data;
Approved Guideline-Second Edition]
VI.
Appendices:
Appendix A. Generic Antibiogram Search Criteria (Drug Susceptibility
Short Format)


Add the relevant hospital name, source code(s), ward codes(s), and patient
type code according to Appendices D-F, and add the appropriate date
range in the following template.
Note: All settings should be confirmed with a Laboratory Information
System specialist every year for any possible changes. The wards and
specimen types, which change frequently, are of particular importance to
review.
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
NOTE: This is a CONTROLLED document for internal use only. Any documents appearing in paper form are not controlled and
should be checked against the document (titled as above) on the server prior to use.
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
NOTE: This is a CONTROLLED document for internal use only. Any documents appearing in paper form are not controlled and
should be checked against the document (titled as above) on the server prior to use.
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Page 9 of 16
Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
NOTE: This is a CONTROLLED document for internal use only. Any documents appearing in paper form are not controlled and
should be checked against the document (titled as above) on the server prior to use.
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Appendix B. Generic Search Criteria for Haemophilus influenzae and
Moraxella catarrhalis, Respiratory Source (Logbook)



Add the relevant hospital name, source code(s), ward codes(s), and patient
type code according to Appendices D-F, and add the appropriate date
range in the following template.
Note: All settings should be confirmed with a Laboratory Information
System specialist every year for any possible changes. The wards and
specimen types, which change frequently, are of particular importance to
review.
Note: only the first page of Logbook is shown. The second page is
identical to that shown in Appendix A.
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Appendix C. Generic Search Criteria for Haemophilus influenzae and
Moraxella catarrhalis, Blood Source (Logbook)



Add the relevant hospital name, source code(s), ward codes(s), and patient
type code according to Appendices D-F, and add the appropriate date
range in the following template.
Note: All settings should be confirmed with a Laboratory Information
System specialist every year for any possible changes. The wards and
specimen types, which change frequently, are of particular importance to
review.
Note: only the first page of Logbook is shown. The second page is
identical to that shown in Appendix A.
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Appendix D. Hospital Name Codes used in the Laboratory lnformation
System
Mount Sinai Hospital
Toronto Western Hospital
Toronto General Hospital
Princess Margaret Hospital
Centenary Health Care
Ajax Pickering Hospital
Baycrest Hospital
Bridgepoint Health Center
Lyndhurst Center
Hillcrest Center
Queen Elizabeth University Avenue site
Queen Elizabeth Dunn Avenue site
Toronto Grace Hospital
Center for Addiction and Mental Health
MSH
TWH
TH
PMH
CHC
APG
BCH
BPH
TLC
THC
QEU
QED
GRC
CAMH
Appendix E. Source Codes Used in the Laboratory Information System
Source
ONLY for Spec. Proc.: UCULT, UCULR, SUPU
Urine
For MSH, BCH, BPH, QED, QEU, GRC, THC, TLC:
NOT for Tests :MRSA, MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
For TW, PMH,TH, APG, CHC,CAMH:
NOT for Tests: MRSA, MRS, VRE, VRES, VREP, PSEUX, ESBLM, STAA, SERMS
Blood
ONLY for Tests: BC
Resp.
Misc.
ONLY for Spec. Proc: FLD2, LUN, BALMS,BALCF,BALM,SPUT
ONLY for Sources: ABS, ABSS,ORSB,SUR,WND,WNDD,SKNB
Appendix F. Ward and Patient Type Codes used in the Laboratory
Information System
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Hospital
Ward
PMH
All
Med/Surg ICU
MSH
TH
TW
Codes
Patient Type
Comments
Only for Ward: ICU(Sue wants to exclude the 7L3 and ICC
Patient type: IA
TICU is inactive
Patient type: E
includes all the Ers
ER
nonER/nonICUinpatients
Not for Ward: ICU
ICU
Only for Ward:10CMS, CCU,SURS,CVC2,CVC1
ER
Only for Ward:GEMG,GEP,GER0,GER1,GER2,GER3,MDUER
Transplant
Only for Ward: 7NCSB,10WA
nonER/ nonICU/
nonTransplant-inpatients
Not for Ward:10CMS, CCU,SURS,CVC2,CVC1,7NCSB,10WA
ICU
Only for Ward: MSNI,2FICU,9BICU
ER
Only for Ward:EMER,EMEW,PESER,WEP,WER,WERM
nonICU/nonERinpatients
Not for Ward:MSNI,2FICU,9BICU
Patient type: IA
MSIC is inactive
Patient type: I
WCV,WMSU,WNSUE
are inactive Wards
Patient type: I
CHC
All inpatients
Patient type: I
APG
All inpatients
Patient type: I
BCH
All inpatients
BPH
All inpatients
CAMH
All inpatients
QED
All inpatients
QEU
All inpatients
GRC
All inpatients
THC
All inpatients
TLC
All inpatients
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Not for the Ward: CKMB
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Not for the Ward: RHICE, RHCS, RHDC, RHCC, RHOHC
Not for Test: MRSA, MRS, VRE, VRES, VREP, PSEUX, ESBLM,
STAA, SERMS
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Not for the Ward: CTSCI,HETRI
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Not for Test: MRSA,
MRS,VRE,VRES,ESBLM,SERM,STA,ESBL,PSEUD
Patient type: H
Patient type: H
Patient type: H
Patient type: H
Patient type: H
Patient type: H
Patient type: H
Patient type: H
Appendix G. Saved Search Queries in the Laboratory Information System
Site
TGH
(Inpatient)
Ward
Source
Drug Susceptibility
Short Format
Blood
√
Misc
√
ER
Logbook Search
for haeinf
Logbook Search
for morcat
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Resp
√
Urine
√
Blood
√
Misc
√
Resp
√
Urine
√
Blood
√
Misc
√
Resp
√
Urine
√
Blood
√
Misc
√
Resp
√
Urine
√
ICU
Transplant
NonICU/ nonER/ nonTrans
Blood
√
Misc
√
Resp
√
Urine
√
Blood
√
Misc
√
Resp
√
Urine
√
Blood
√
Misc
√
Resp
√
Urine
√
ER
ICU
NonICU/ nonER
PMH
(In and Out
Patient)
All Urines
√
All But-Urines
√
Ward
√
√
√
√
√
√
√
√
√
√
√
√
Logbook Search
for haeinf
Logbook Search
for morcat
√
√
√
All But-Urines
Site
√
√
All Urines
MSH
TW
(Inpatient)
√
Source
Drug Susceptibility
Short Format
All Blood
√
All Misc
√
All Resp
√
All Urine
√
All But-Urines
√
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
APG
CHC
BPH
BCH
CAMH
QED
QEU
GRC
THC
TLC
(Inpatients)
All Urines
√
All But-Urines
√
√
√
Appendix H. Templates and Files
1) Templates:
Antibiogram Working TEMPLATE QPCMI14003b
Antibiogram Report TEMPLATE QPCMI14003a
2) Manual
Cumulative Antimicrobial Susceptibility Report (Antibiogram) QPCMI14003
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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Policy QPCMI14003.09
Department of Microbiology
Laboratory Policy & Procedure Manual
Section: Quality Manual – Process Control
Subject Title: Preparing a Cumulative
Antimicrobial Susceptibility
Report (Antibiogram)
Record of Edited Revisions
Manual Section Name: Preparing a Cumulative Antimicrobial Susceptibility
Report (Antibiogram)
Page Number / Item
Revised
Annual Review
Annual Review
Date of Revision
July 14, 2010
May 31, 2011
May 31, 2013
Signature of
Approval
Dr. T. Mazzulli
Dr. T. Mazzulli
Dr. T. Mazzulli
LABORATORY MANUAL
UNIVERSITY HEALTH NETWORK /MOUNT SINAI HOSPITAL, DEPARTMENT OF MICROBIOLOGY
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