Professional Documents
Culture Documents
Combined Database
The system uses the following documents and computer files
1. Request and reporting form for culture examination of sputumV2, MS WORD
2. TB culture and DST laboratory performance report, Cult&DSTreportform.xls. It
also exists in a version that can call upon an automatic analysis program
CU&DSTreport_with_update_function.xls
3. Primary culture register, part of CultReg&DSTReg.xls. It also exists as a version in
which the left page can be filled automatically with information looked up in the
database, CultReg_with_automatic _fill.xls
4. Drug susceptibility testing (DST) and identification register, part of CultReg
&DSTReg.xls
5. Reference Laboratory analysis workbooks: CUanalysisbook.xls and
DSTanalysisbook.xls. They also exist as versions that can call upon automatic
analysis programs CUanalysisBook_with_automatic_fill.xls and
DSTanalysisBook_with_automatic_fill.xls.
6. Reference Laboratory database file, Reflab.rec: it must be installed together with its
associated files (.chk, .qes, .eix) in the same subdirectory. In case the name of this file
is changed when customizing the database and associated files for a specific country,
all the names of the files and references to these files in the automatic analysis
programmes under 7. here below (DSTrep.pgm and CUrep.pgm), will have to be
changed accordingly.
7. Reference Laboratory database analysis files: DSTrep.pgm with assisting files
DSTrep1.rpt, DSTrep2.rpt and DSTrep.txt for DST results analysis; and CUrep.pgm
with assisting files CUrep.rpt and CUrep.txt for culture results analysis. The name of
the laboratory-specific record file must be indicated in each of the .pgm files on the
first line. For instance READ c:\epidata\reflab\REFLAB.REC could be changed to
READ c:\epidata\reflab\UGREFLAB.REC in case UG has been added as the first
characters to the name of the database, for example for the country Uganda.
For automatic analysis including writing to the report forms above, the .rec, .pgm, .rpt, .txt
files above must be in the same subdirectory called c:\epidata\reflab\. This subdirectory
must also contain the Epi-Info 6.0 analysis.exe software (supplied with this set). The
correct name and path to the correct subdirectory must be specified in the .pgm files, if
placed elsewhere.
The output reports CU&DSTreport_with_update_function.xls, CUanalysisBook_with_
automatic_fill.xls and DSTanalysisBook_with_automatic_fill.xls can be anywhere.
The link to a .dbf version of the culture&DST database needed for the CultReg_with_
automatic _fill.xls will have to be adjusted to the subdirectory containing this Dbaseexported version, but they can be placed anywhere.
Description of the system and requirements
The forms and registers are recommended formats that can simply be printed and used
manually. More efficiently, they would be used partly manually, partly as computerized
databases with some associated computer-facilitated analyses, for internal monitoring of
culture performance, reporting of cultures and DST, redaction of working lists etc.. However,
these functions require basic knowledge of EXCEL and Epidata for initial customization and
proper usage. Knowledge of Epidata Analysis or Epi Info is not required to maintain the
1
database or to run these simple analyses, but Epi Info 6 Analysis must be installed to run
automatically in the background. For special manipulations using Epi Info may also be easier,
as explained under point 4 below.
For each specimen, a request form (1 above) has to be filled out by the person requesting
the culture and/or DST, and sent to the lab together with the specimen. The lower part of the
form can be used by the lab to return the results; this can be done in different steps (first
smear, later on culture and still later DST result), as shown on the form.
At the reference laboratory, a clerk enters the information from the request form in the
computer database (6). This database is the main document for all analyses, retrieval of strains
from the freezer collection, linking to patient data etc..., and for this reason it contains a large
variety of information. While entering the information from the request form, the clerk gives a
unique reference lab identification number to the specimen, enters it in the file and writes it on
the form together with the date of receipt at the lab, before the form is filed.
In contrast, the paper registers (3 and 4) are meant for bench work only, and for this reason
they only contain a small part of the same information that can be useful for the technicians at
the bench. Since many specimens do not require DST (not requested, or culture negative..)
and while the benches may be separated as well, there are two separate registers. The
specimen is preferably identified in both registers with the same unique ref. lab identification
number; if not, the DST register must contain a reference to the number of the specimen in the
culture register. These registers have several columns for registration of repeated and
quantified readings, results of identification tests . This will not be entered in the database,
but it is useful information to check when searching for the cause of a problem and should
thus be filled completely. Only the final result of all the different culture, identification or
DST tests performed on the same sample is recorded in the database.
The columns should be adapted to individual needs, depending on standard procedures:
o a reference column to the culture ID number in the DST register is not needed if one
and the same ID is used for all tests done on a sample
o the columns for drugs and their concentrations should be adapted to local practice, i.e.
types of drugs tested, one or more concentrations per drug, one or more bacilli
suspension strengths per drug, control suspension strengths. Also the identification
tests used should be individualized
The lines in the columns at the right of the register have been subdivided, to accommodate for
different media used for the same specimen (culture register) or for readings at different times
(DST register). These can of course also be adjusted to local needs.
The TB culture and DST laboratory performance report (2) is a quarterly report meant for the
NTP or any other authority which needs to be informed. It gives a summary report of both
culture and DST results batch-wise, i.e. for all tests set up during a certain quarter (or year).
In the automatic version, the figures needed for this report can be obtained from the database
by running the two analysis programmes (7), one for the culture part, and the other for the
DST part, by clicking on the knobs besides the tables and specifying the year and quarter or
month when asked to do so.
The two EXCEL analysis books (5) will compile the annual data from quarterly input, with
automatic calculation of some percentages. The cultures workbook will also turn the
percentages for internal monitoring into a graph (based on either quarterly, either monthly
counts). This graphical representation will make it easier to check for deviations from the
norm. In the automatic versions, the counts and filling is done automatically after clicking the
knob and specifying the month or quarter and/or year found besides the various tables in these
books. A monthly run is recommended for the cultures analysis, since this will provide the
figures needed for internal monitoring of culture quality.
Automatic filling of the left-hand pages of the culture register from the database can be done
only after exporting the .rec-file to an EXCEL or DBase file format under the same
subdirectory (export function of Epidata). At first installation, the link of the EXCEL sheet
formulas to the database will have to be re-directed. If the .rec-file was customized with added
or deleted fields, the formulas in the EXCEL register page cells may have to be adapted to the
changed sequence number of the columns. Filling the unique reference lab identification
number in the left column of the culture register, written (or better copied as a value)
exactly as it is in the EXCEL database-version will cause the other fields to be updated with
the appropriate information for the same specimen. This can be done for 1 page at a time, and
this L-hand page could then be printed to the verso of sheets with the R-hand page on the
recto side. From these the paper register can then be constituted, i.e. in a ring binder. From
these the paper register can then be constituted, i.e. in a ring binder. An example is included in
this set, REFLABTE.dbf and CultReg_with_automatic _fill.xls.
In a similar way, reports on individual sample test results can be made after customisation of
the database and of the reporting form format, using the EXCEL VLOOKUP function to add
the appropriate information to the form format for a specified unique identifier. In view of
individual preferences as well as database customization, no such automatic report form has
been included.
Daily working lists can be made directly from an EXCEL-exported extract of the database,
specifying the record numbers and fields wanted. It is not possible to select dates when
exporting a file. If desired, the output can also be adapted to include new columns to record
for instance the reference laboratory microscopy result, culture or direct DST inoculation
date, new identification numbers etc. After processing the samples and recording this
information on the lists, a clerk can then add these data to the database.
Other lists, for instance of pending results, can be made in the same way, using EXCEL to sort
the records in a way that will regroup those wanted. It is not possible to make such selections
in Epidata before exporting the file. However, this is relatively simple to do in Epidata or Epi
Info analysis, with writing of the file or list of fields wanted to a new .rec file, that can
eventually be exported to EXCEL for printing.
Since these are simple to make and in view of individual preferences as well as database
customization, no pre-determined format for such lists has been included.
All these automatic entries can be changed manually, if needed. They will also be updated
after entering certain results:
- entering for both liquid and solid culture results OTHER THAN TBC will set the
culture request to completed, the DST request fields to impossible, and the DST1
and DST2 profile fields to UUUUU. Other entries in both the solid and liquid
culture results fields will set the culture request field to completed.
- after going through all fields for the DST results (various series), at the bottom of the
series a profile will appear. In this profile, U stands for unknown (not done,
contaminated..), - for susceptible, and the symbol of the drug for resistant, in the
following sequence: INH (H)-RMP (R)-EMB (E)-SM (S)-PZA (Z) -for first-line- or
Cm (C), Km (K), Ofl (O), PAS (P), Eto (E) -for the second-line drugs.
So, for instance the first-line drug profile HR--U means resistant to INH and RMP,
susceptible to EMB and SM, and PZA not done.
- with any entry in the 4 main first-line drug fields (INH, RMP, EMB and SM), the
DST1 request field will be set automatically to CPT or completed, except if this
DST1 field already contains IMP orNOT; the same happens for the request field
for 2nd line DST after entering the individual drug results (or U for unknown). Should
this CPT not be correct, the value can be changed back manually to RQU
(requested), allowing results to be added later on.
Adding results using a filter thus depends on consistent use of the test request fields, so that
the correct records will be retrieved. This is done by placing the cursor in the request field
concerned, selecting from the menu Filter, then Define filter, and entering in the box
RQU to show those with a requested test only. Only records with RQU in this field will
then be shown using F7 (previous) or F8 (next record), entering the new results and saving
while passing to the next record. After entering the results, the request field will be changed
automatically as described above. For culture or DST on first or second-line drug results, the
same system can be used defining a filter PND (pending) on the respective fields, provided
that the inoculation / setting-up dates were filled previously. If not, dates and results may be
added at the same time using a requested filter as above. After entering results, make sure
the profiles appear correctly, and the RQU in the request fields is changed to CPT. After
entering all new data, the filter must be deactivated (menu Filter, then Deactivate).
The same fields can be used to select complete results that need to be reported, setting the
filter to CPT. The value is automatically changed to RPT after entering the date of
reporting.
4. Other
Some operations can be better done in Epi Info
- revising the file structure after modifying the questionnaire file. To keep the
questionnaire and field names as they are, such a revision should be done using
Enter,Revise of Epi Info. If done in Epidata, curled brackets will appear in the
questionnaire screen around the parts of the field names.
sorting the file and re-writing it, for instance to facilitate entering large series of new
results. The REFLABTE file could then first be rewritten sorted on the specimen
identification, culture or DST number, as is easiest from the paper records that will be
used. Open the file in Epi Info Analysis, use the sort command and field name for the
sort, then rewrite the file under a new name (for instance, route
c\.....\REFLABT2.rec, then write recfile). Check if OK after opening the new
REFLABT2, then close and rename to the old name after erasing the original
REFLABTE.