Laboratory EPI Technical and User Guide Home
Laboratory
Emerging Pathogens Initiative (EPI)
Version 5.2
Technical and User Guide
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September 2015
Department of Veterans Affairs (VA)
Office of Information and Technology (OI&T)
Product Development (PD)
Revision History
|Date |Version |Description |Author |
|9/2015 |LR*5.2*442 |Updates for LR*5.2*442, ICD-10 Patient Treatment File |T.B., PM |
| | |(PTF) Modifications: |K.R., Technical Writer |
| | |Updated title page and footers, updated Preface (p.vi), | |
| | |updated Pre-installation Instructions (p.9), added DBIA | |
| | |#6130 (p.11), reformatted and updated Routine List | |
| | |(p.11), updated Patches Required (p.14), updated | |
| | |Installation Instructions (p.23), updated Post | |
| | |Installation Instructions (p.30). | |
|07/2014 |LR*5.2*421 |Added Revision History. |K.K., VA PM; |
| | |Added summary of features for patch LR*5.2*421 |D.G., ICD-10 PM; |
| |pp. v-vi | |E.P., Technical Writer |
| | |Updated TOC. | |
| |p. vii | | |
| | |Updated VDL URL. | |
| |p. 8 |Added note on pre-installation. | |
| |p. 9 | | |
| | |Added routines for patch LR*5.2*421. | |
| |p. 11 | | |
| | |Updated File #69.5 fields for Help Text and generic | |
| |pp. 18-19 |change from ICDM-9 to ICD. | |
| | | | |
| | |Added Data Dictionary changes. | |
| |p. 21 | | |
| | |Added note on installation. | |
| |p. 23 | | |
| | |Added note on post installation. | |
| |p. 31 | | |
| | |Updated DG1 Segment of HL7 message to utilize ~ rather | |
| |pp. 36, 38 |than ^. | |
| | | | |
| | |Added ICD-10 to definitions table. | |
| |p. 47 | | |
| | |Updated Primary Menu and examples for addition of Code | |
| |pp. 49, 53, 55-56, 58-59, |System prompt. | |
| |61-62, 65, 68-69, 71-72, | | |
| |74-75, 77-78, 80-81, 83-84, | | |
| |86-87, 90 | | |
| | | | |
| |pp. 38, 114 |Removed Personally Identifiable Information (PII). | |
| | | | |
| | |Updated all references from ICDM-9 to ICD. | |
| |Multiple pages | | |
| | |Changed AAC to Austin Information Technology Center | |
| | |(AITC) throughout manual | |
| |Multiple pages | | |
|02/1997 |LR*5.2*132 |Initial release. |VA OI&T |
Preface
The Veterans Health Information Systems and Architecture (VISTA) formerly Decentralized Hospital Computer Program (DHCP) Laboratory Emerging Pathogens Initiative (EPI) Patch LR*5.2*132 Technical and User Guide provides the Department of Veterans Affairs Medical Center (DVAMC) Information Resource Management (IRM) and other medical center users with a straightforward means for installing and implementing the EPI software package.
NOTE: It is highly recommended that the Laboratory Information Manager (LIM), and a representative from the Microbiology section (director, supervisor, or technologist) jointly participate in reviewing the 14 Emerging Pathogen parameters descriptions and entering of data for the EPI software package. The individual(s) will be responsible for initially defining the EPI parameters and a yearly review of the 14 Emerging Pathogens.
It is also suggested that a Total Quality Improvement/Quality Improvement/ Quality Assurance (TQI/QI/QA) staff (or person at the site with similar function) be involved in the EPI process. The individual(s) will assist in initially defining the EPI parameters, a yearly review of the 14 Emerging Pathogens, and a periodic review of the ICD codes to assure they are current. Also, this function will help coordinate the overall implementation at each site.
The International Classification of Diseases, Tenth Revision (ICD-10) Remediation patch LR* 5.2*421 makes the following changes to the EPI application:
• The following fields and screens have been updated to refer to “ICD” rather than “ICD9”:
o Laboratory Search/Extract Parameters Input screens
o Enter/Edit Local Pathogens screens
o Detailed Verification Report
o Help text
• Within the Enter/Edit Local Pathogens and Laboratory Search/Extract Parameters Input screens, users are prompted to specify a code set on which to search prior to entering an ICD code. Based on this input, the system will only allow ICD-9 entry or ICD-10 entry.
• The Pathogen Inquiry option has been modified to list both ICD-9 and ICD-10 codes.
• The Generate Local Report/Spreadsheet option has been modified to include both the Diagnosis Code Set Designation and the Diagnosis Code.
• Health Level 7 (HL7) Reports that are sent to Austin Information Technical Center (AITC) have been modified to include ICD-10 Codes and Descriptions, which are included in the DG1 HL7 Segments.
The ICD-10 PTF Modifications patch LR*5.2*442 made changes to accommodate the expanded number of ICD-10 codes that can now be entered in a patient record.
EPI Technical and User Guide focuses on easy-to-follow, step-by-step instructions. This guide includes the following four sections:
Pre-Installation: This section covers the requirements that must be performed prior to installing the software.
Installation Instructions: This section includes a detailed example of the actual EPI Patch LR*5.2*132 installation process.
Post Installation Instructions: This section provides all the necessary information required for the IRM personnel to implement the EPI software package after the installation process is completed.
User Guide: This section provides all necessary information required for the user to implement and maintain the EPI software.
Table of Contents
Preface iv
Introduction 1
Major functions: 1
Objectives: 1
How The Software Accomplishes The Objective: 1
VISTA Process 2
Local Reports 2
Austin Automation Center: 3
EPI Technical and User Guide Notations 7
Screen Displays 7
Computer Dialogue 7
User Response 7
Return Symbol 7
Tab Symbol 7
References 8
EPI Technical and User Guide Distributions 8
Electronic Distributions 8
Hyper Text Markup Language (HTML) 8
Portable Document Format (PDF) 8
Hard Copy 8
Pre-installation Instructions 9
Hardware and Operating System Requirements 9
Performance/Capacity Impact 9
Backup Routines 9
EPI Test Sites 10
Test Account 10
Installation Time 10
Kernel Installation and Distribution System (KIDS) 11
Health Level Seven (HL7) 11
Database Integration Agreements (DBIA) 11
EPI Routines 11
Staffing Requirement 13
IRM Staff 13
Laboratory Staff 13
Total Quality Improvement/Quality Improvement/Quality Assurance (TQI/QI/QA) Staff 13
VISTA\DHCP Software Requirements 14
Patches Required 14
EPI Files 14
EPI Namespace 14
EPI Menu and Options 15
Emerging Pathogens Nightly Task Option 15
New Q-EPI.MED. Domain 16
Protocols 16
EPI-Mail Groups 16
Data Dictionaries 17
Installation Instructions 23
Installation Time 23
Installation Process 24
Post Installation Instructions 30
DSM/Alpha Sites 30
MSM Sites 30
IRM Staff 30
Health Level Seven (HL7) Protocol 34
Laboratory EPI Patch LR*5.2*132 User Guide 44
Emerging Pathogens 44
Emerging Pathogen Primary Menu 45
Emerging Pathogens Descriptions and Screen Displays 47
Candida (Reference #8) 47
Clostridium difficile (Reference #4) 51
Creutzfeldt-Jakob Disease (CJD) (Reference #13) 54
Cryptosporidium (Reference #9) 57
Dengue (Reference #12) 60
E. coli O157:H7 (Reference #10) 63
Hepatitis C Antibody Positive (Reference #2) 67
Legionella (Reference #7) 70
Leishmaniasis (Reference #14) 73
Malaria (Reference #11) 76
Penicillin- Resistant Pneumococcus (Reference #3) 79
Streptococcus-Group A (Reference #6 82
Tuberculosis (Reference #5) 85
Vancomycin-Resistant Enterococcus (VRE) (Reference #1) 88
Conclusion 92
Appendix 96
Validation Of Data Capture 96
Emerging Pathogens Verification Report 98
Table of Reject and Warning Codes 100
Editing TOPOGRAPHY file (#61) 103
How to Link Antimicrobial Entries to Workload Codes Entries 104
Request Form 105
Helpful Hints: 107
Screens Enter/Edits 107
How to delete a entry. 107
How to add a entry 108
Clostridium difficile 109
EPI Mail Groups Assignments 111
Office of the Director (00) 111
Transmitting a Message to Austin 113
EPI Processing Report 114
Introduction
Under the auspices of the Program Office for Infectious Diseases VAHQ the Laboratory Emerging Pathogens Initiative (EPI) software package is to allow the Department of Veterans Affairs (DVA) to track Emerging Pathogens on the national level without the necessity for additional local data entry. Using this objective information, plans can be formulated on the national level for intervention strategies and resource needs. Results of aggregate data can also be shared with appropriate public health authorities for planning on the national level for the non-VA and private health care sectors.
Major functions:
The Laboratory EPI program is designed to automatically provide data on emerging pathogens to Veterans Affairs Headquarters (VAHQ) without additional individual data entry at the site level. The data will be sent to Austin Information Technology Center (AITC) for initial processing and coupling with denominator data related to workload. VAHQ data retrieval and analysis can then be accomplished.
Objectives:
Identify Emerging Pathogens.
Extract specific data associated with the Emerging Pathogen.
Transmit data to AITC.
Create national Statistical Analysis System (SAS) data sets for Infectious Diseases Program Office access.
How The Software Accomplishes The Objective:
Emerging Pathogens (as defined by VAHQ) act as triggers for data acquisition for the automated program. The system then retrieves relevant, predetermined, patient-specific information for transmission to the central data repository. Once at that location, the data will be analyzed using a SAS based statistical package. VAHQ Reports can then be generated for appropriate use and distribution.
VISTA Process
The Department of Veterans Affairs provides a unique opportunity to assist public health surveillance activities for new, antibiotic-resistant, or otherwise problematic pathogens. The Laboratory EPI software interface will obtain data from the VistA database and report the data to a registry that will assist the Emerging Pathogens Initiative of the VAHQ Infectious Disease Program Office to produce predictive trends in health care events.
The EPI software consists of two new files, 10 new routines, two mail groups, one menu consisting of three options, and one Emerging Pathogens Nightly Task option. After installation minimal file setup will be required. Two mail groups are created and will require populating with the appropriate members. Some of the Emerging Pathogens data will have to be added using the Emerging Pathogens Parameter update option if the installation process cannot make the match. IRM personnel will assign the Emerging Pathogens Primary Menu to a specified user (TQI/QI/QA staff, Laboratory Information Manager (LIM), and Microbiology personnel are highly recommended).
The Search/Extract process runs once a month. This process uses the criteria defined in the EMERGING PATHOGEN file (#69.5) to search the verified Lab results in the LAB DATA file (#63) and PTF file (#45) for any of the defined Emerging Pathogens. If an Emerging Pathogen is identified the Search/Extract process builds an entry into the ^TMP global along with the appropriate inpatient or outpatient information. An inpatient associated PTF number is placed into the EMERGING PATHOGEN file (#69.5) for the appropriate Emerging Pathogen until the inpatient is discharged. During the sequential months the inpatient associated PTF record is monitored until discharged. The additional discharge information is sent to Austin as a “patient update.”
Local Reports
On a monthly basis the EPI data is transmitted to the AITC. Before the EPI data is transmitted, an Emerging Pathogens Verification Report is available for the sites to review, verify, and make corrections if needed. After the EPI data is transmitted to AITC, it is then added to the National Database.
The purpose of the Emerging Pathogen Verification Report is to determine that the information being sent to ACC is accurate (i.e. complete social security numbers, valid Date of Births, and the Period of Services are present). The purpose of verification is not to determine that the total reported for actual laboratory or ICD collected data are valid (i.e. that there were X numbers of cases of positive tests for Hepatitis C or that there were X positive culture results for Streptococcus, Group A). The validation of laboratory and ICD capture should be done with the initial setup of the patch and at intermittent periodic review as determined by site (e.g. see Appendix section).
Austin Automation Center:
The Austin Automation Center creates two file structures, both in Statistical Analysis System (SAS) file format, which are used primarily as a source of data for the Infectious Diseases Program Office. The data will be available to the Infectious Diseases Program Office to be manipulated and used for analysis and reporting.
The two file structures are referred to as the “Numerators” and the “Denominators” because of their planned utilization.
Numerator:
This file is an accumulation of the EPI data sent from all medical centers. It will contain twelve individual months worth of data and will be updated monthly. Each month the oldest month will be dropped from the file and the latest month’s data will be added. Upon receipt of the monthly input, the AITC will return acknowledgments to the facility, and will identify any “problem” transmissions. These “problem” transmissions are records that, because of field format or the actual field value, either Austin is rejecting as invalid records or is just warning the facility that the record has some discrepancy, but it is not being rejected. Both the “problem” transmissions and the accepted records are documented on a Processing Report that will be transmitted from Austin to the facility. This Processing Report will itemize all of the transmissions received by Austin and will document the records status as either being accepted or rejected (with the reason code identified) but with a warning that there is something unusual about the value of one or more fields (warning reason code identified). An example of the “Tables of Reject and Warning codes” are located in the Appendix section of this guide. The Numerator information will be specific to unique patients with a VAHQ designated Emerging Pathogen which has been flagged through the VistA process. Numerator data will be collected and transmitted to Austin monthly.
Denominator:
This file will provide to the Infectious Diseases Program Office, data elements for each facility. The source of these data elements will be the corporate medical data base residing in Austin. The individual files that these data elements will be extracted from are the National Patient Care (NPC), Inpatient Treatment File (PTF), Automated Management Information System (AMIS) and Cost Distribution Report (CDR) systems.
The data elements are:
Unique SSN served (inpatient and outpatient together)
Total # of discharges
Total unique SSN discharges
Inpatient hospital days
Inpatient ICU days
Unique SSN encounters for both inpatient and outpatient
A “running 12 month” accumulation is required (i.e., there will always be one year’s worth of monthly counts) with the oldest month dropped off each cycle and a new one added.
NOTE: The need to track individual station data and to consolidate by parent station has not been specified. At this time we are only gathering by individual station number.
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EPI Technical and User Guide Notations
This section addresses the symbols and computer dialogue that are displayed in this guide.
Screen Displays
The EPI Primary menu options are using VA FileMan-ScreenMan forms for editing and displaying data. For detailed instructions using ScreenMan forms please refer to the VA FileMan V. 21.0 User Manual, Section 6 - ScreenMan.
Computer Dialogue
The computer dialogue appears in Courier font, no larger than 10 points.
Example: Courier font 10 points
User Response
User entry response appears in boldface type Courier font, no larger than 10 points.
Example: Boldface type
Return Symbol
User response to computer dialogue is followed by the symbol which appears in Courier font, no larger than 10 points, and bolded.
Example:
Tab Symbol
User response to computer dialogue is followed by the symbol which appears in Courier font, no larger than 10 points, and bolded.
Example:
References
Kernel V. 8.0 Systems Manual
HL7 V. 1.6 Manuals
PIMS V. 5.3 Manuals
VA FileMan V. 21.0 User Manual, Section 6 - ScreenMan.
EPI Technical and User Guide Distributions
The EPI Technical and User Guide is distributed in hard copy and electronic formats. Listed below are the ways the EPI guide may be obtained.
Electronic Distributions
Hyper Text Markup Language (HTML)
The EPI Technical and User Guide is available on the Intranet at the following address
Portable Document Format (PDF)
The EPI Technical and User Guide is available on the ANONYMOUS.SOFTWARE accounts at the Albany, Hines, and Salt Lake City Information Resources Management Field Offices (IRMFOs) in the Portable Document Format (PDF).
IRMFO FTP Address
Albany 152.127.1.5 - anonymous.software
Hines 152.129.1.110 - anonymous.software
Salt Lake City 152.131.2.1 - anonymous.software
NOTE: This guide is also available in PDF on the Intranet at the following address
Hard Copy
The EPI Technical and User Guide hard copies are distributed to all VA Medical Centers by the National Center for Documentation (NCD).
Pre-installation Instructions
NOTE: For patch LR*5.2*442 pre-installation instructions, please refer to the ICD-10 PTF Modifications Installation Guide:
NOTE: For patch LR*5.2*421 pre-installation instructions, please refer to the ICD-10 Release Notes for LR*5.2*421.
This Pre-Installation Instructions section provides the necessary information and requirements for installing EPI Patch LR*5.2*132.
Hardware and Operating System Requirements
VISTA software operates on two hardware platforms. The hardware platforms are mini-computer category, providing multi-tasking and multi-user capabilities.
The hardware systems are:
υ Digital Equipment Corporation (DEC) Alpha series using DEC Open Virtual Memory System (VMS), Version 6.1 or greater, operating system. This platform uses DEC System Mumps (DSM), version 6.3 or greater, of American National Standards Institutes (ANSI) of Massachusetts General Hospital Utility Multi-Programming System (MUMPS) also known as ‘M’ language. MUMPS is a Federal Information Processing Standard (FIPS) language.
Personal Computer (PC) System with 486 or Pentium computer processor chip using Microsoft Disk Operating System (MS-DOS). This platform uses Micronetics Standard Mumps (MSM), Version 3.0.14 or greater, of American National Standards Institutes (ANSI) of Massachusetts General Hospital Utility Multi-Programming System (MUMPS) also known as 'M' language. MUMPS is a Federal Information Processing Standard (FIPS) language.
Performance/Capacity Impact
There are no changes in the performance of the system once the installation process is complete.
Backup Routines
It is highly recommended that a backup of the transport global is performed.
EPI Test Sites
This chart displays the sites that assisted in testing the EPI Patch LR*5.2*132 prior to the release date.
| | | |Hardware Platform |
|Test Site |Type of Test Site |Date Installed |/Operating System |
| | |11/4/96 test and production | |
| | |accounts | |
|Cincinnati VAMC |Alpha | |DEC Alpha/DSM |
| | |1/9/97 test and production | |
| | |accounts | |
|Miami VAMC |Beta | |DEC Alpha/DSM |
| | |1/27/97 test and production | |
| | |accounts | |
|Muskogee VAMC |Beta | |MSM |
| | |1/28/97 test and production | |
|North Hampton VAMC | |accounts | |
| |Beta | |MSM |
Test Account
It is highly recommended that the EPI Patch LR*5.2*132 is installed into a test account before installing into a live Production Account. The Test and Production Accounts must include all required software versions and patches to assure a successful installation of this patch.
Installation Time
The actual installation time for this patch should take no more than 10 minutes. Although users may remain on the system, it is recommended that you install this patch during non-peak hours.
Kernel Installation and Distribution System (KIDS)
The Kernel Installation and Distribution System(KIDS) is a new method of installing DHCP software and a new module in Kernel Version 8.0. The Emerging Pathogens Initiative LR*5.2*132 patch is distributed using KIDS. For further instructions on using KIDS please refer to the Kernel Version 8.0 Systems Manual.
Health Level Seven (HL7)
The Emerging Pathogen Initiative Patch LR*5.2*132 is using the DHCP HL7 software to transport the EPI health care data onto the AITC, formerly AAC system. These health care data are extracted from the Laboratory, PIMS, Social Work, and EPI data bases. The health care data are used to assist public health surveillance activities for new antibiotic - resistant or otherwise problematic pathogens. The EPI health care data reside on the AITC system.
Database Integration Agreements (DBIA)
The following new DBIA was approved for VistA Laboratory ICD-10 PTF Modifications patch LR*5.2*442:
• DBIA#6130
There are three DBIAs (#418, #1372, and #1881) that were approved for the EPI Patch LR*5.2*132.
EPI Routines
NOTE: The below routine list includes three routines (LRAPQAT1, LREPI3 and LREPI5) that have been modified for patch LR*5.2*442.
NOTE: The below routine list includes three routines (LR421P, LREPICD, and LRESPIXDG) that have been added for Patch LR*5.2*421.
• LR132
• LR132P
• LR175
• LR175P
• LR421P
• LRAPQAT1
• LREPI
• LREPI1A
• LREPI2
• LREPI3
• LREPI4
• LREPI5
• LREPIAK
• LREPICD
• LREPICY
• LREPILK
• LREPIPH
• LREPIPI
• LREPIRM
• LREPIRN
• LREPIRP
• LREPIRP3
• LREPIRP5
• LREPIRP7
• LREPIRS1
• LREPIRS3
• LRESPIXDG
Staffing Requirement
IRM Staff
IRM staff is required for installing EPI Patch LR*5.2*132, setting up the EPI-Domain, EPI-Lab mail groups and menu assignments.
Laboratory Staff
It is highly recommended that the Laboratory Information Manager (LIM), and a representative from the Microbiology section (director, supervisor, or technologist) jointly participate in reviewing the 14 Emerging Pathogen descriptions and entering of data for the EPI software package. The individual(s) will assist in the initially setting of the EPI parameters and doing periodic reviews of the parameters to assure they are current.
Total Quality Improvement/Quality Improvement/Quality Assurance (TQI/QI/QA) Staff
It is highly recommended that a Total Quality Improvement/Quality Improvement/ Quality Assurance (TQI/QI/QA) staff (or persons at site with similar function) be involved in the EPI process due to the multi-disciplinary nature of the information to be retrieved by the EPI program (both patient-specific for pathogens and site-specific for denominators). This will facilitate coordination of subsequent site interactions once the actual patch has been installed (i.e. to be responsible for reviewing verification reports, transmitting data once it is determined to be correct, review the data error messages and make corrections as needed, periodic validation of verification reports, to assist with coordinating the yearly update of parameters, and the intermittent specific update of parameters requests from Veterans Affairs Headquarters).
VISTA\DHCP Software Requirements
Packages Versions (or Greater)
VA FileMan 21 (with patches installed)
Kernel 8.0 (with patches installed)
Laboratory 5.2 (with patches installed)
MAS/PIMS 5.3 (with patches installed)
HL7 1.6 (with patches installed)
Social Work 3.0 (with patches installed)
MailMan 7.1 (with patches installed)
Patches Required
NOTE: For patches required for LR*5.2*442, please refer to the ICD-10 PTF Modifications Installation Guide:
Prior to the installation of LR*5.2*132, the following patches MUST be installed:
Packages Patches
Kernel V. 8.0 XU*8*44
MailMan V.7.1 XM*DBA*103 (EPI-Lab Domain)
Health Level Seven V. 1.6 HL*1.6*17
Laboratory V. 5.2 LR*5.2*128
Social Work V. 3.0 SOW*3*42 (install after LR*5.2*128)
EPI Files
EMERGING PATH PROTOCOL file (#69.4): This file contains additional parameters that are not specific to entries in EMERGING PATHOGENS file (#69.5), but are specific to the protocol used.
EMERGING PATHOGENS file (#69.5): This file contains search criteria along with additional information associated with the Emerging Pathogen Initiative (EPI) software. This file should only be edited using the ScreenMan ‘Emerging Pathogens Parameter update’ option which is provided by the EPI Software.
EPI Namespace
The EPI Patch LR*5.2*132 is using Laboratory’s LR namespace.
EPI Menu and Options
The Laboratory EPI software has one stand-alone menu. There are no locks or security keys created for this menu. The Emerging Pathogen Primary Menu consists of the following three options:
Antimicrobial Link Update: This option will allows the user to link the ANTIMICROBIAL SUSCEPIBILTY' file (#62.06) with WKLD CODE file (#64).
NOTE: Please see the Appendix section of this guide on “How to Link Antimicrobial Entries to Workload Codes Entries” using this option.
Emerging Pathogen Manual Run: This option allows the user to select any month to run the Search/Extract process manually. The first and last day of the month will be determined automatically.
Emerging Pathogens Parameter update: This option is used to define the search criteria along with additional information associated with the Emerging Pathogen Initiative.
NOTE: The Emerging Pathogen Primary Menu options are using VA FileMan screens displays, referred to as ScreenMan. For detailed instructions on how to use the screens displays please review the VA FileMan V. 21.0 User Manual, Section 6 ScreenMan.
Emerging Pathogens Nightly Task Option
The Emerging Pathogens Nightly Task option must be scheduled to run each night by TaskMan. This option will build the Emerging Pathogen HL7 Message for Austin. The HL7 message is built after the 15th day of each month for the previous month search data.
New Q-EPI.MED. Domain
The new Q-EPI.MED. domain implementation instructions are released by MailMan XM*DBA*103 informational patch.
Protocols
LREP: This event driver protocol defines the associated parameters needed to build the HL7 Message used to send the EPI data to Austin.
LREPI CLIENT: This subscriber protocol defines the parameter needed by the HL7 package to determine where to send the HL7 formatted message containing the EPI information.
EPI-Mail Groups
The EPI Patch LR*5.2*132 creates two mail groups during the installation process.
EPI: This mail group is used for the transmission of HL7 messages derived from the parameters defined in the EMERGING PATHOGEN file (#69.5) to the Austin Automation Center. This mail group will also receive Confirmation and Processing Report Messages from Austin.
EPI-REPORT: This mail group is used to deliver a formatted report taken from the HL7 message that is created to assist in the verification of data.
NOTE: The Office of the Director (00) will be the initial individual/function to whom the EPI mail and EPI-Report mail groups will be directed. The Office of the Director at each site will then determine responsible individual(s)/function(s) for the mail groups. For further information regarding the EPI mail groups please see the Appendix section page 122.
NOTE: To transmit a mail message please reference the example in the Appendix section of this guide.
Data Dictionaries
EMERGING PATH PROTOCOL file (#69.4)
STANDARD DATA DICTIONARY #69.4 -- EMERGING PATH PROTOCOL FILE 01/30/97 PAGE 1
STORED IN ^LAB(69.4, (1 ENTRY) SITE: DALLAS ISC-DEVELOPMENT
DATA NAME GLOBAL DATA
ELEMENT TITLE LOCATION TYPE
-------------------------------------------------------------------------------
This file contains additional parameters that are not specific to entries in file (#69.5), but are specific to the protocol used.
POINTED TO BY: PROTOCOL field (#12) of the EMERGING PATHOGENS File (#69.5)
CROSS REFERENCED BY: PROTOCOL(B)
CREATED ON: NOV 8,1996
69.4,.01 PROTOCOL 0;1 POINTER TO PROTOCOL FILE (#101)
(Required)
INPUT TRANSFORM: S DINUM=X
LAST EDITED: NOV 08, 1996
DESCRIPTION: Select the protocol from the Protocol file
(#101) that will be used to build the HL7
Message. This allows additional parameters to
be associated with the protocol.
NOTES: XXXX--CAN'T BE ALTERED EXCEPT BY PROGRAMMER
CROSS-REFERENCE: 69.4^B
1)= S ^LAB(69.4,"B",$E(X,1,30),DA)=""
2)= K ^LAB(69.4,"B",$E(X,1,30),DA)
69.4,1 Report Mail Group 0;2 POINTER TO MAIL GROUP FILE (#3.8)
LAST EDITED: NOV 08, 1996
HELP-PROMPT: Select what mail group to send the verification
report.
DESCRIPTION: This defines what mail group to send the
verification report.
69.4,2 Message Size 0;3 NUMBER
INPUT TRANSFORM: K:+X'=X!(X>999999)!(X50!($L(X)99)!
(^LAB(69.5,"C",X)) X
LAST EDITED: NOV 29, 1996
HELP-PROMPT: Type a Number between 100 and 999. Numbers from
1 to 99 are reserved for future use.
UNEDITABLE
NOTES: XXXX--CAN'T BE ALTERED EXCEPT BY PROGRAMMER
DESCRIPTION: This is a unique number used to identify this
entry.
CROSS-REFERENCE: 69.5^C
1)= S ^LAB(69.5,"C",$E(X,1,30),DA)=""
2)= K ^LAB(69.5,"C",$E(X,1,30),DA)
69.5,1 ACTIVE 0;2 SET
'0' FOR YES;
'1' FOR NO;
LAST EDITED: AUG 29, 1996
HELP-PROMPT: Indicates if the entry is active or inactive.
DESCRIPTION: This defines if this entry is active or not.
69.5,2 LAB TEST 1;0 POINTER Multiple #69.52
DESCRIPTION: This is the test that is searched for.
69.52,.01 LAB TEST 0;1 POINTER TO LABORATORY TEST FILE (#60)
(Multiply asked)
INPUT TRANSFORM: I $P($G(^(0)),U,4)="CH" D ^DIC K DIC S DIC=DIE
,X=+Y K:Y15!($L(X) LR*5.2*132
This Distribution was loaded on Jan 23, 1997@07:36:06 with header of
LR*5.2*132
It consisted of the following Install(s):
LR*5.2*132
LR*5.2*132
Will first run the Environment Check Routine, LR132
Environment Check is Ok ---
Install Questions for LR*5.2*132
62.06 ANTIMICROBIAL SUSCEPTIBILITY (Partial Definition)
Note: You already have the 'ANTIMICROBIAL SUSCEPTIBILITY' File.
69.4 EMERGING PATH PROTOCOL
69.5 EMERGING PATHOGENS (including data)
Want to DISABLE Scheduled Options, Menu Options, and Protocols? YES// NO
Enter the Device you want to print the Install messages.
You can queue the install by enter a 'Q' at the device prompt.
Enter a '^' to abort the install.
DEVICE: HOME//
Phase 3: KIDS installation of the patch.
Install Started for LR*5.2*132 :
Jan 23, 1997@07:59:07
Installing Routines:
Jan 23, 1997@07:59:08
Installing Data Dictionaries:
Jan 23, 1997@07:59:12
Installing Data:
Jan 23, 1997@07:59:13
Installing PACKAGE COMPONENTS:
Installing HELP FRAME
Installing FORM
Installing MAIL GROUP
Installing HL LOWER LEVEL PROTOCOL PARAMETER
Installing HL LOGICAL LINK
Installing HL7 APPLICATION PARAMETER
Installing PROTOCOL
Installing OPTION
Jan 23, 1997@07:59:24
Running Post-Install Routine: ^LR132P
Adding Protocol 'LREPI' to the Emerging Pathogen File (69.5)
********
**Updating Emerging Pathogen File (69.5) with ICD9 Codes**
Adding 085.0 VISCERAL LEISHMANIASIS into LEISHMANAISIS
Adding 085.1 CUTAN LEISHMANIAS URBAN into LEISHMANAISIS
Adding 085.2 CUTAN LEISHMANIAS ASIAN into LEISHMANAISIS
Adding 085.3 CUTAN LEISHMANIAS ETHIOP into LEISHMANAISIS
Adding 085.4 CUTAN LEISHMANIAS AMER into LEISHMANAISIS
Adding 085.5 MUCOCUTAN LEISHMANIASIS into LEISHMANAISIS
Adding 085.9 LEISHMANIASIS NOS into LEISHMANAISIS
Adding 084.0 FALCIPARUM MALARIA into MALARIA
Adding 084.1 VIVAX MALARIA into MALARIA
Adding 084.2 QUARTAN MALARIA into MALARIA
Adding 084.3 OVALE MALARIA into MALARIA
Adding 084.4 MALARIA NEC into MALARIA
Adding 084.5 MIXED MALARIA into MALARIA
Adding 084.6 MALARIA NOS into MALARIA
Adding 084.7 INDUCED MALARIA into MALARIA
Adding 084.8 BLACKWATER FEVER into MALARIA
Adding 084.9 MALARIA COMPLICATED NEC into MALARIA
Adding 007.8 PROTOZOAL INTEST DIS NEC into CRYPTOSPORIDIUM
Adding 046.1 JAKOB-CREUTZFELDT DIS into CREUTZFELDT-JAKOB DISEASE
Adding 061. DENGUE into DENGUE
Adding 065.4 MOSQUITO-BORNE HEM FEVER into DENGUE
Adding 482.80 LEGIONNAIRE'S DISEASE into LEGIONELLA
********
**Updating Emerging Pathogen File (69.5) with Etiology**
Adding CANDIDA ALBICANS into CANDIDA
Adding CANDIDA GUILLIERMONDII into CANDIDA
Adding CANDIDA KRUSEI into CANDIDA
Adding CANDIDA PARAPSILOSIS into CANDIDA
Adding CANDIDA PSEUDOTROPICALIS into CANDIDA
Adding CANDIDA SKIN TEST ANTIGEN into CANDIDA
Adding CANDIDA STELLATOIDEA into CANDIDA
Adding CANDIDA TROPICALIS into CANDIDA
Adding CANDIDA, NOS into CANDIDA
Adding ENTEROCOCCUS (STREPT. FAECALI into VANC-RES ENTEROCOCCUS
Adding LEGIONELLA BOZEMANII into LEGIONELLA
Adding LEGIONELLA DUMOFFII into LEGIONELLA
Adding LEGIONELLA MICDADEI into LEGIONELLA
Adding LEGIONELLA PNEUMOPHILIA into LEGIONELLA
Adding LEGIONELLA SP into LEGIONELLA
I will auto link file '62.06 ANTIMICROBIAL SUSCEPTIBILITY' to file '64 WKLD CODE.
AMIKACN Amikacin
AMPICLN Ampicillin
CLINDAM Clindamycin
CARBCLN Carbenicillin
CEFMAND Cefamandole
CEFOPERAZONE Cefoperazone
CEFOTAXIME Cefotaxime
CEFOXITIN Cefoxitin
CEFAZOLIN Cefazolin
CHLORAM Chloramphenicol
ERYTHROMYCIN Erythromycin
KANAMCN Kanamycin
METHCLN Methicillin
MEZLOCILLIN Mezlocillin
NEOMYCN Neomycin
NETILMICIN Netilmicin
NITROFURANTOIN Nitrofurantoin
NOVOBIOCIN Novobiocin
OXACILLIN Oxacillin
PENICLN Penicillin
PIPERACILLIN Piperacillin
POLYMYXIN B No Match Found
RIFAMPIN Rifampin
TETRCLN No Match Found
TOBRMCN Tobramycin
TRMSULF No Match Found
VANCMCN Vancomycin
MOXALACTAM Moxalactam
GENTMCN Gentamicin
SULFISOXAZOLE No Match Found
BACTRCN Bacitracin
NAFCILLIN Nafcillin
NALIDIXIC ACID Nalidixic Acid
COLISTIN Colistin
CEPHALOTHIN Cephalothin
METRONIDAZOLE Metronidazole
Updating Routine file
Updating KIDS files
LR*5.2*132 Installed.
Jan 23, 1997@07:59:35.
Install Message sent #13957
Install Completed
Post Installation Instructions
NOTE: There are no post installation instructions for LR*5.2*442.
NOTE: For patch LR*5.2*421 post installation instructions, please refer to the ICD-10 Release Notes for LR*5.2*421.
The post installation instructions for the EPI Patch LR*5.2*132 should be followed as recommended. This will assure a successful implementation of the EPI software.
DSM/Alpha Sites
If you have disabled journaling, you may now re-enable it.
MSM Sites
It is recommended that MSM sites move the routines to the other servers. Using a mapped system, rebuild your map set.
IRM Staff
1. Assure that the Q-EPI- Domain is set-up as instructed by MailMan Patch XM*DBA*103.
2. Set-up the EPI-Lab and EPI-Report Lab mail groups. Recipients of these mail groups are designated by the EPI coordinator.
3. Using VA FileMan V. 21.0 edit the facility name field in the HL7 APPLICATION PARAMETER file (#771) for the EPI-LAB entry.
Example:
Select OPTION: ENTER OR EDIT FILE ENTRIES
INPUT TO WHAT FILE: HL7 APPLICATION PARAMETER
(7 entries)
EDIT WHICH FIELD: ALL// FACILITY NAME
THEN EDIT FIELD:
Select HL7 APPLICATION PARAMETER NAME: EPI-LAB ACTIVE
FACILITY NAME: 170 ( Enter your facility number
Select HL7 APPLICATION PARAMETER NAME:
4. Start the Lower Level Protocol of the HL7 V. 1.6 background job for EPI.
Select Systems Manager Menu Option: HL7 Main Menu
1 V1.5 OPTIONS ...
2 V1.6 OPTIONS ...
3 Activate/Inactivate Application
4 Print/Display Menu ...
5 Purge Message Text File Entries
Select HL7 Main Menu Option: 2 V1.6 OPTIONS
1 Communications Server ...
2 Interface Workbench
3 Message Requeuer
Select V1.6 OPTIONS Option: 1 Communications Server
1 Edit Communication Server parameters
2 Manage incoming & outgoing filers ...
3 Monitor incoming & outgoing filers
4 Start LLP
5 Stop LLP
6 Systems Link Monitor
7 Logical Link Queue Management ...
8 Report
Select Communications Server Option: 4 Start LLP
This option is used to launch the lower level protocol for the
appropriate device. Please select the node with which you want
to communicate
Select HL LOGICAL LINK NODE: EPI-LAB
The LLP was last shutdown on JAN 30, 1997 12:06:19.
Select one of the following:
F FOREGROUND
B BACKGROUND
Q QUIT
Method for running the receiver: B// ACKGROUND
Job was queued as 131225.
5. Assign the Emerging Pathogen Primary Menu to specified users.
NOTE: It is highly recommended that the Laboratory Information Manager (LIM), TQI/QA/QI, and a representative from the Microbiology section (director, supervisor, or technologist) are assigned the Emerging Pathogen Primary Menu. This will be the individual(s) responsible for initially setting the parameters and doing periodic reviews of parameters to assure they are current.
6. Schedule the Emerging Pathogen Nightly Task option to run each night.
Health Level Seven (HL7) Protocol
The Emerging Pathogen Initiative Patch LR*5.2*132 is using the VISTA HL7 software to transport the EPI health care data onto the ACC system. This health care data is extracted from the Laboratory, PIMS, and EPI data bases. The health care data is used to assist public health surveillance activities for new antibiotic - resistant or otherwise problematic pathogens. The EPI health care data is transmitted to ACC system monthly where it will be processed.
3. General Specifications
3.1 Communication Protocol
The VISTA MailMan electronic mail system will be used as the communications protocol for sending HL7 messages between D VISTA and EPI.
3.2 Application Processing Rules
The HL7 protocol itself describes the basic rules for application processing by the sending and receiving systems. The HL7 Version 2.2 protocol will be used. The ORU message will be sent using the HL7 batch protocol.
3.3 Messages
The following HL7 messages will be used to support the exchange of EPI data.
ORU Observational Results Unsolicited
3.4 Segments
The following HL7 segments will be used to support the exchange of EPI data.
DG1 Diagnosis OBR Observation Request
MSH Message Header PID Patient Identification
NTE Notes and Comments PV1 Patient Visit
3.5 Fields: The following HL7 fields will be used to support the exchange of EPI data for each of the segments listed in the 3.4 Segments.
| |FIELD | | |
| |SEQUENCE | |USER/HL7 |
|SEGMENT |NUMBER |FIELD ELEMENT NAME |DEFINED |
|DG1 |1 |Set ID-Diagnosis (Sequence #) |HL7 |
| |3 |Diagnosis Code (Code(id) ~Text (St.) ~ Name of coding system (st) |HL7 |
|MSH |1 |Field Separator |HL7 |
| |2 |Encoding Characters |HL7 |
| |3 |Sending Application |HL7 |
| |4 |Sending Facility |HL7 |
| |5 |Receiving Application |HL7 |
| |6 |Receiving Facility |HL7 |
| |7 |Date/Time of Message |HL7 |
| |8 |Security |HL7 |
| |9 |Message Type |HL7 |
| |10 |Message Control ID |HL7 |
| |11 |Processing ID |HL7 |
| |12 |Version ID |HL7 |
|OBR |1 |Set ID-Observation Request (Seq #) |HL7 |
| | |Universal Service ID (identifier^ text ^ name of coding system ^ alt id ^ alt text ^ alt| |
| |4 |coding system) |HL7 |
| |7 |Observation Date/Time |HL7 |
| |15 |Specimen Source (Specimen source code (CE) ^^ text (TX) ) |HL7 (Table 0070) |
| |26 |Parent Results (OBX observation id of parent ^OBX sub ID |HL7 |
|NTE |1 |Set ID Notes and Comments (Seq #) |HL7 |
| |3 |Comment |HL7 |
|OBX |1 |Set Id-Observational Simple (seq. #) |HL7 |
| |2 |Value Type |HL7 |
| | |Observation Identifier (identifier ^ text ^ name of coding system ^ alt id ^ alt text ^ | |
| |3 |alt coding system) |HL7 |
| |4 |Sub Id |HL7 |
| |5 |Observation Value (Result) |HL7 |
| |6 |Units (Units) |HL7 |
| | | |HL7 (Table 0078) |
| |8 |Abnormal Flags | |
| |15 |Date/Time of the Observation (Verified Date/Time) |HL7 |
|PID |2 |Patient ID (External ID) |HL7 |
| |3 |Patient ID (Internal ID) |HL7 |
| |5 |Patient Name |HL7 |
| |7 |Date of Birth |HL7 |
| |8 |Sex |HL7 (Table 0001) |
| | | |HL7 (Table VA07) |
| |10 |Race | |
| |11 |Address (Homeless) |HL7 |
| |19 |SSN |HL7 |
| |27 |Veteran’s Military Status |HL7 (Table Va011) |
|PV1 |1 |Set ID - Patient Visit |HL7 |
| |2 |Patient Class |HL7 |
| |36 |Discharge Disposition |HL7 |
| |44 |Admit Date/Time (Event Date/Time) |HL7 |
| |45 |Discharge Date/Time |HL7 |
4.0 Transaction Specifications
4.1 General
The VistA system will send the ORU observation result type HL7 message whenever one or more of the defined pathogens have been identified.
4.2 Specific Transaction
A. Identified Encounter
When the Emerging Pathogens have been identified an ORU message is sent from the VistA system to the EPI database. These ORU messages will consist of the following segments.
Example:
ORU OBSERVATIONAL RESULT UNSOLICITED
MSH Message Header
NTE Notes and Comments
PID Patient Identification
PV1 Patient Visit
NTE Notes and Comments
DG1 Diagnosis
OBR Observation Report
OBX Results
Example: Message
MSH|~|\&|EPI-LAB|170|EPI-LAB|170|19961018113521||ORU~R01|107|P|2.2|||||USA
NTE||REPORTING DATE FROM 19850101 TO 19961018
PID|1|000-16-7946~0~M10|5~5~M10||LABPATIENT, EIGHT||000000008|M||7|||||||||000167946
PV1|1|O||||||||||||||||||||||||||||||||||||||||||19950315151907
NTE|1|1^Vanc-Res Enterococcus
DG1|1| |451.19~DEEP PHLEBITIS-LEG NEC~I9
DG1|2| |511.9~PLEURAL EFFUSION NOS!I9
DG1|3| |670.02~MAJOR PUERP INF-DEL P/P~I9
DG1|4| |331.0~ALZHEIMER'S DISEASE~I9
DG1|5| |500.~COAL WORKERS' PNEUMOCON~I9
OBR|1|||^CHEMISTRY TEST^VANLT|||19950315151907||||||||SER^^SERUM
OBX|1|ST|84330.0000^Glucose Quant^VANLT^175^GLUCOSE1^VA60||25|mg/dL|70-125|L*
NTE|2|2^Hepatitis C antibody
OBR|2|||^CHEMISTRY TEST^VANLT|||19950315151907||||||||SER^^SERUM
OBX|1|ST|84330.0000^Glucose Quant^VANLT^175^GLUCOSE1^VA60||25|mg/dL|70-125|L*
PID|2|000-45-6666~8~M10|7~7~M10||LABPATIENT, NINE||000000009|F||7|||||||||000456666
PV1|1|O||||||||||||||||||||||||||||||||||||||||||19950315152721
NTE|1|1^Vanc-Res Enterococcus
OBR|1|||87999.0000^MICRO CULTURE^VANLT|||198612100835||||||||^^BLOOD
OBX|1|CE|87993.0000^BACTERIOLOGY CULTURE^VANLT|1|^ESCHERICHIA COLI
OBR|2||^ANTIBIOTIC MIC^VANLT||||198612100835||||||||^^BLOOD|||||||||||87993.0000^1
OBX|1|ST|81812.0000^Neomycin^VANLT^18^NEOMYCN^VA62.06|||||R
OBX|2|ST|^^^35^BACTRCN^VA62.06|||||R
OBX|3|ST|81852.0000^Penicillin^VANLT^23^PENICLN^VA62.06|||||R
OBX|4|ST|81676.0000^Clindamycin^VANLT^3^CLINDAM^VA62.06|||||S
OBX|5|ST|81307.0000^Gentamicin^VANLT^33^GENTMCN^VA62.06|||||R
OBX|6|ST|81656.0000^Chloramphenicol^VANLT^10^CHLORAM^VA62.06|||||R
OBX|7|ST|81946.0000^Tetracycline NOS^VANLT^27^TETRCLN^VA62.06|||||R
OBX|8|ST|81532.0000^Ampicillin^VANLT^2^AMPICLN^VA62.06|||||R
OBX|9|ST|81475.0000^Tobramycin^VANLT^28^TOBRMCN^VA62.06|||||R
OBX|10|ST|^^^29^TRMSULF^VA62.06|||||R
OBX|11|ST|81098.0000^Amikacin^VANLT^1^AMIKACN^VA62.06|||||R
OBX|12|ST|81604.0000^Cefamandole^VANLT^5^CEFMAND^VA62.06|||||R
OBX|13|ST|81886.0000^Piperacillin^VANLT^24^PIPERACILLIN^VA62.06|||||R
OBX|14|ST|81616.0000^Cefoperazone^VANLT^6^CEFOPERAZONE^VA62.06|||||R
OBX|15|ST|81794.0000^Mezlocillin^VANLT^16^MEZLOCILLIN^VA62.06|||||R
Table VA011 - Period of Service
|Value |Description |
|0 |KOREAN |
|1 |WORLD WAR I |
|2 |WORLD WAR II |
|3 |SPANISH AMERICAN |
|4 |PRE-KOREAN |
|5 |POST-KOREAN |
|6 |OPERATION DESERT SHIELD |
|7 |VIETNAM ERA |
|8 |POST-VIETNAM |
|9 |OTHER OR NONE |
|A |ARMY--ACTIVE DUTY |
|B |NAVY, MARINE--ACTIVE DUTY |
|C |AIR FORCE--ACTIVE DUTY |
|D |COAST GUARD--ACTIVE DUTY |
|E |RETIRED, UNIFORMED FORCES |
|F |MEDICAL REMEDIAL ENLIST |
|G |MERCHANT SEAMEN--USPHS |
|H |OTHER USPHS BENEFICIARIES |
|I |OBSERVATION/EXAMINATION |
|J |OFFICE OF WORKERS COMP. |
|K |JOB CORPS/PEACE CORPS |
|L |RAILROAD RETIREMENT |
|M |BENEFICIARIES-FOREIGN GOV |
|N |HUMANITARIAN (NON-VET) |
|O |CHAMPUS RESTORE |
|P |OTHER REIMBURS. (NON-VET) |
|Q |OTHER FEDERAL - DEPENDENT |
|R |DONORS (NON-VET) |
|S |SPECIAL STUDIES (NON-VET) |
|T |OTHER NON-VETERANS |
|U |CHAMPVA--SPOUSE, CHILD |
|V |CHAMPUS |
|W |CZECHOSLOVAKIA/POLAND SVC |
|X |PERSIAN GULF WAR |
|Y |CAV/NPS |
|Z |MERCHANT MARINE |
Table 0070 - Specimen Source Codes
|Abbreviations |Descriptions |Abbreviations |Descriptions |Abbreviations |Descriptions |
|ABS |Abscess |FLU |Body fluid, unsp |SER |Serum |
|AMN |Amniotic fluid |GAS |Gas |SKN |Skin |
|ASP |Aspirate |GAST |Gastric fluid/contents |SKM |Skeletal muscle |
|BPH |Basophils |GEN |Genital |SPRM |Spermatozoa |
|BIFL |Bile fluid |GENC |Genital cervix |SPT |Sputum |
|BBL |Blood bag |GENV |Genital vaginal |SPTT |Sputum tracheal |
| | | | | |aspirate |
|BLDC |Blood capillary |HAR |Hair |STON |Stone (use CALC) |
|BPU |Blood product unit |IHG |Inhaled Gas |STL |Stool = Fecal |
|BLDV |Blood venous |IT |Intubation tube |SWT |Sweat |
|BON |Bone |ISLT |Isolate |SNV |Synovial fluid |
| | | | | |(Joint fluid) |
|BRTH |Breath |LAM |Lamella |TEAR |Tears |
| |(use EXHLD) | | | | |
|BRO |Bronchial |WBC |Leukocytes |THRT |Throat |
|BRN |Burn |LN |Line |THRB |Thrombocyte |
| | | | | |(platelet) |
|CALC |Calculus (=Stone) |LNA |Line arterial |TISS |Tissue |
|CDM |Cardiac muscle |LNV |Line venous |TISG |Tissue gall bladder |
|CNL |Cannula |LIQ |Liquid NOS |TLGI |Tissue large |
| | | | | |intestine |
|CTP |Catheter tip |LYM |Lymphocytes |TLNG |Tissue lung |
|CSF |Cerebral spinal fluid |MAC |Macrophages |TISPL |Tissue placenta |
|CVM |Cervical mucus |MAR |Marrow |TSMI |Tissue small |
| | | | | |intestine |
|CVX |Cervix |MEC |Meconium |TISU |Tissue ulcer |
|COL |Colostrum |MBLD |Menstrual blood |TUB |Tube NOS |
|CBLD |Cord blood |MLK |Milk |ULC |Ulcer |
|CNJT |Conjunctiva |MILK |Breast milk |UMB |Umbilical blood |
|CUR |Curettage |NAIL |Nail |UMED |Unknown medicine |
|CYST |Cyst |NOS |Nose (nasal passage) |URTH |Urethra |
|DIAF |Dialysis fluid |ORH |Other |UR |Urine |
|DOSE |Dose med or |PAFL |Pancreatic fluid |URC |Urine clean catch |
| |substance | | | | |
|DRN |Drain |PAT |Patient |URT |Urine catheter |
|DUFL |Duodenal fluid |PRT |Peritoneal fluid ascites |URNS |Urine sediment |
|EAR |Ear |PLC |Placenta |USUB |Unknown |
| | | | | |substance |
|EARW |Ear wax (cerumen) |PLAS |Plasma |VOM |Vomitus |
|ELT |Electrode |PLB |Plasma bag |BLD |Whole blood |
| | | |Pleural fluid | | |
|ENDC |Endocardium |PLR |(thoracentesis fld) |BDY |Whole body |
| | | |Polymorphonuclear | | |
|ENDM |Endometrium |PMN |neutrophils |WAT |Water |
|EOS |Eosinophils |PPP |Platelet poor plasma |WICK |Wick |
|RBC |Erythrocytes |PRP |Platelet rich plasma |WND |Wound |
|EYE |Eye |PUS |Pus |WNDA |Wound abscess |
|EXHLD |Exhaled gas (breath) |RT |Route of medicine |WNDE |Wound exudate |
|FIB |Fibroblasts |SAL |Saliva |WNDD |Wound drainage |
| | | | | |To be specified in |
|FLT |Filter |SEM |Seminal fluid |XXX |another part of the |
| | | | | |message |
|FIST |Fistula | | | | |
Table VA07 - Race
|Value |Description |
|1 |HISPANIC, WHITE |
|2 |HISPANIC, BLACK |
|3 |AMERICAN INDIAN OR ALASKA NATIVE |
|4 |BLACK, NOT OF HISPANIC ORIGIN |
|5 |ASIAN OR PACIFIC ISLANDER |
|6 |WHITE NOT OF HISPANIC ORIGIN |
|7 |UNKNOWN |
Table 0001 - Sex
|Value |Description |
|F |FEMALE |
|M |MALE |
|O |OTHER |
|U |UNKNOWN |
Table 0078 - Abnormal flags
|Value |Description |
|L |Below low normal |
|H |Above high normal |
|LL |Below lower panic limits |
|HH |Above upper panic limits |
|For microbiology sensitivities only | |
|S |Sensitive |
|R |Resistant |
|I |Intermediate |
|MS |Moderately sensitive |
|VS |Very sensitive |
LABORATORY EPI PATCH LR*5.2*132 USER GUIDE
Laboratory EPI Patch LR*5.2*132 User Guide
The Laboratory EPI Patch LR*5.2*132 User Guide section provides all the necessary information, instructions, illustrations, and examples required for the EPI coordinators, Laboratory personnel, and other users to implement and maintain the EPI software package. This information should be adhered to as recommended to assure a successful implementation of the EPI software.
NOTE: It is highly recommended that the Laboratory Information Manager (LIM), TQI/QA/QI, and a representative from the Microbiology section (director, supervisor, or technologist) jointly participate in reviewing the 14 Emerging Pathogen descriptions and entering of data for the EPI software package. The individual(s) will be responsible for initially setting the EPI parameters, doing periodic reviews of ICD codes and parameters to assure they are current.
Emerging Pathogens
Listed below are the 14 Emerging Pathogens that the EPI software package has been defined to track:
Candida Legionella
Clostridium difficile Leishmanaisis
Creutzfeldt-Jakob Disease Malaria
Cryptosporidium Pen- Res Pneumococcus
Dengue Streptococcus-Group A
E. coli O157:H7 Tuberculosis
Hepatitis C Antibody Pos Vanc-Res Enterococcus
NOTE: Descriptions for each of the 14 Emerging Pathogens are located in the “Emerging Pathogens Descriptions and Screen Displays” section of this User Guide.
Emerging Pathogen Primary Menu
The Laboratory EPI software has one stand-alone menu. There are no locks or security keys created for this menu. The Emerging Pathogen Primary Menu consists of the following three options:
Antimicrobial Link Update: This option will allows the user to link the ANTIMICROBIAL SUSCEPIBILTY' file (#62.06) with WKLD CODE file (#64).
NOTE: Please see the Appendix section of this guide on “How to Link Antimicrobial Entries to Workload Codes Entries” using this option.
Emerging Pathogen Manual Run: This option allows the user to select any month to run the Search/Extract process manually. The first and last day of the month will be determined automatically.
Emerging Pathogens Parameter update: This option is used to define the search criteria along with additional information associated with the Emerging Pathogen Initiative.
NOTE: The Emerging Pathogen Primary Menu options are using VA FileMan screens displays, referred to as ScreenMan. For detailed instructions on how to use the screens displays please review the VA FileMan V. 21.0 User Manual, Section 6 ScreenMan.
Emerging Pathogens Parameter update option screen and help prompts definitions:
|Emerging Pathogen update option Parameters |Emerging Pathogen Parameter update option |
|Screens Prompts |Screens Help Prompts |
|Serology Lab Test (s) |Consider this synonymous with, chemistry, serology, hematology “blood/serum” tests. Results |
| |anticipated to be found here will have had a test done, under chemistry/hematology accession |
| |areas, even if physically performed in microbiology other areas. Select from the LABORATORY TEST|
| |file (#60) |
|Indicator |Select the code that will determine how to match lab results. |
| |‘1’ FOR Use Reference Ranges |
| |‘2’ FOR Contains |
| |‘3’ FOR Greater Than |
| |‘4’ FOR Less Than |
| |‘5’ FOR Equal To |
|Value |Positive, etc. Answer must be 1-15 characters in length. This is a Free Text field. |
|ICD-9 |ICD-9 standardized code used nationwide in federal and non-federal/private health care |
| |facilities. Select from the ICDM-9 DIAGNOSIS file (#80). |
|ICD Description |Title of ICD diagnosis |
|ICD-10 |ICD-10 standardized code used nationwide in federal and non-federal/private health care |
| |facilities. Select from the ICD DIAGNOSIS file (#80). |
|Selected Etiology |Consider synonymous with organism, final microbial diagnosis/isolate. Select from the ETIOLOGY |
| |FIELD file (61.2). |
|Antimicrobial Susceptibility |Enter the Antimicrobial that will be used in screening out sensitive Etiologies (e.g., |
| |“Vancomycin” for Vancomycin Resistant Enterococcus). Select from the ANTIMICROBIAL |
| |SUSCEPTIBILITY file (#62.6). |
|NLT Code: |Displays the associated NLT code if linked. If no NLT Code is displayed use the Antimicrobial |
| |Link Update option. |
|NLT Description |Displays the Description of the linked NLT code. |
|Topography Selection | |
|Include |Selection of a Topography screens all others out except the ones selected. For "ALL" leave |
| |blank. Not to be used in conjunction with the exclude Topography selection. Select from the |
| |TOPOGRAPHY file (#61). |
|Exclude |Select the Topography to screen out. Not to be used in conjunction with the Include Topography |
| |selection. Select from the TOPOGRAPHY file (#61). |
|Follow PTF: |Indicates if the PTF record will be followed until a discharge has been entered. |
| |Choose: ‘1’ FOR YES |
| |‘0’ FOR NO |
|Run Date: |Date that the last Auto Search/Extract processed. |
|Run Cycle: |This field is currently not used. For future use. |
|First Encounter: |Limits the output to the first encounter for the patient. Otherwise list all encounters. |
| |Choose: ‘1’ FOR YES |
| |‘0’ FOR NO |
|Protocol: |Defines the protocol used to define the output messages. Select from the EMERGING PATH PROTOCOL |
| |file (#69.4). |
|General Description: |To review or edit the General Description use the key instead of the key. |
Emerging Pathogens Descriptions and Screen Displays
This section includes the 14 Emerging Pathogens descriptions and screen displays. The screen displays contains examples of the pre-populated fields. The ETIOLOGY FIELD file (#61.2) site specific data is used to partially pre-populate the fields in the EMERGING PATHOGENS file (#69.5). However, further entries will be required for site specific data. Additional entries may be added or deleted to meet your site specific needs. These examples will assist in the initial Emerging Pathogens parameter updates.
Candida (Reference #8)
Fungal infections are rising in significance especially in severely ill patients. The same is true for bloodstream infections acquired in the hospital, especially those associated with intravenous lines. Fungal bloodstream infections are increasing in prevalence.
As a marker of bloodstream infections we have chosen the fungus Candida (and Torulopsis) as an initial indicator organism. This may not be a prevalent or significant entity at your site, but its presence is more likely to be indicative of serious or true infection than other organisms which may commonly be isolated from the blood in association with IV lines. Additionally this yeast is more likely to be associated with nosocomial acquisition than other organisms such as Staphylococcus aureus and coagulase negative Staphylococcus, which can cause a number of community acquired syndromes not at all related to IV lines.
We wish to capture all episodes of Candida (Torulopsis, yeast) isolation from blood or a blood source (central line, IV catheter tip, etc.). For Candida a partial pre-populated list of (etiologies/organisms) to choose from has been included. These should be entered, in addition to any site specific (etiologies organisms) which also fit the description.
NOTE: The Emerging Pathogen Primary Menu options are using VA FileMan screens displays, referred to as ScreenMan. For detailed instructions on how to use the screens displays please review the VA FileMan V. 21.0 User Manual, Section 6 ScreenMan.
Emerging Pathogen Primary Menu
ENH Lab Search/Extract Manual Run (Enhanced)
VR Print Detailed Verification Report
LO Local Pathogen Menu ...
PI Pathogen Inquiry
UP Lab EPI Parameter Setup
Lab EPI Protocol Edit
LK Antimicrobial Link Update
Select Emerging Pathogens (EPI) Primary menu Option: UP Emerging Pathogens Parameter update
Select EMERGING PATHOGENS NAME: ?
Answer with EMERGING PATHOGENS NAME, or REFERENCE NUMBER
Do you want the entire 14-Entry EMERGING PATHOGENS List? Y (Yes)
Choose from:
CANDIDA
CLOSTRIDIUM DIFFICILE
CREUTZFELDT-JAKOB DISEASE
CRYPTOSPORIDIUM
DENGUE
E. COLI 0157:H7
HEPATITIS C ANTIBODY POS
LEGIONELLA
LEISHMANIASIS
MALARIA
PEN-RES PNEUMOCOCCUS
STREPTOCOCCUS-GROUP A
TUBERCULOSIS
VANC-RES ENTEROCOCCUS
Select EMERGING PATHOGENS NAME:CANDIDA
NOTE: Please be consistent with site specific data spelling or alternate spelling to assure accurate EPI data capture.
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 1 of 4
NAME: Candida ACTIVE: YES
____________________________________________________________________________
Serology Lab Test(s) Indicator Value
ICD Coding System [ICD-9 or ICD-10]? (9/10):
ICD Code Cd Set ICD Description
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 2 of 4
NAME: CANDIDA ACTIVE: YES
____________________________________________________________________________
Selected Etiology
Examples:CANDIDA
CANDIDA GUILLIERMONDII
CANDIDA KRUSEI
CANDIDA PARAPSILOSIS
CANDIDA PSEUDOTROPICALIS
CANDIDA SKIN TEST ANTIGEN
CANDIDA STELLATOIDEA
CANDIDA TROPICALIS
CANDIDA, NOS
Note: During the post Init, the ETIOLOGY FIELD file (#61.2) was searched to pre-populate the Etiology field (#3) in the EMERGING PATHOGENS file (#69.5). Listed above are examples of etiology entries which may have been populated from your site’s file. Additional etiologies may be added or deleted at the Selected Etiology prompt to meet your site specific needs.
Note: If spelling differences occur within your ETIOLOGY FIELD file (#61.2), be consistent with your local file and spell the results here, as it is spelled in your file (even if it is spelled differently in the example). We are concerned more importantly with data recovery.
Antimicrobial Susceptibility NLT Code NLT Description
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 3 of 4
NAME: Candida ACTIVE: YES
____________________________________________________________________________
Topography Selection
Include Exclude
Blood
Bloodstream
Catheter Tip
Note: These are only suggestions. Please add accordingly to your site definition.
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 4 of 4
NAME: Candida ACTIVE: YES
___________________________________________________________________________
Follow PTF: YES Run Date:
Run Cycle: MONTHLY First Encounter:
Protocol: LREPI General Description:
Note: To review or
edit the General
Description use the
key instead of
the key.
____________________________________________________________________________
Exit Save Refresh
COMMAND: E Press H for help Insert
Save changes before leaving form (Y/N)?Y
Clostridium difficile (Reference #4)
Disease associated with the presence of Clostridium difficile enterotoxin A can cause significant morbidity, as well as mortality. It is of importance as its predominant acquisition seems to occur nosocomially. Presence of Clostridial toxin (either enterotoxin A or cytotoxin L) by assay (whether it be EIA, latex agglutination, cytotoxicity of cell culture + neutralization, or culture of organism with subsequent colony testing) is the best indicator that an inflammatory diarrheal disease is due to presence of Clostridium difficile. Laboratory services are quite varied as to how they identify the presence of Clostridium difficile. Some labs are set up to identify C. difficile as the final microbiological (bacterial) etiology of a culture, even if a culture method was not used. Other labs use a final etiology of “see comment” and then enter the results in a free text format. Still others enter the text under a hematology or chemistry format where a reference range and “positive” and “negative” result values can be entered. Wherever the facility lab places the results which are used to demonstrate the presence of toxin-producing C. difficile, we need to be able to track them (that means it must occur as a retrievable “positive” or “negative” result, or as a “bacterial etiology”). Any results contained in a “Comments” or “Free-text” sections are not acceptable.
There are a number of different ways that sites have chosen to enter Clostridium difficile toxin assay results into the VistA system. As long as the toxin assay results are in a retrievable format (straight from the VistA system without additional manual input needed), how it is entered is not of significance to the EPI package.
NOTE: However, there are two preferred methods that makes it easy to capture the EPI data. Please reference the Appendix section of this guide for the two methods.
Emerging Pathogen Primary Menu
ENH Lab Search/Extract Manual Run (Enhanced)
VR Print Detailed Verification Report
LO Local Pathogen Menu ...
PI Pathogen Inquiry
UP Lab EPI Parameter Setup
Lab EPI Protocol Edit
LK Antimicrobial Link Update
Select Emerging Pathogens (EPI) Primary menu Option: UP Emerging Pathogens Parameter update
Select EMERGING PATHOGENS NAME: ?
Answer with EMERGING PATHOGENS NAME, or REFERENCE NUMBER
Do you want the entire 14-Entry EMERGING PATHOGENS List? Y (Yes)
Choose from:
CANDIDA
CLOSTRIDIUM DIFFICILE
CREUTZFELDT-JAKOB DISEASE
CRYPTOSPORIDIUM
DENGUE
E. COLI 0157:H7
HEPATITIS C ANTIBODY POS
LEGIONELLA
LEISHMANIASIS
MALARIA
PEN-RES PNEUMOCOCCUS
STREPTOCOCCUS GROUP A
TUBERCULOSIS
VANC-RES ENTEROCOCCUS
Select EMERGING PATHOGENS NAME: CLOSTRIDIUM DIFFICILE
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 1 of 4
NAME: CLOSTRIDIUM DIFFICILE ACTIVE: YES
____________________________________________________________________________
Serology Lab Test(s) Indicator Value
Clostridium difficile toxin Contains Pos
Note: This is only a suggestion. Please add accordingly to your site definition.
ICD Coding System [ICD-9 or ICD-10]? (9/10):
ICD Code Cd Set ICD Description
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 2 of 4
NAME: CLOSTRIDIUM DIFFICILE ACTIVE: YES
____________________________________________________________________________
Selected Etiology
Clostridium difficile toxin positive
Note: This is only a suggestion. Please add accordingly to your site definition.
Antimicrobial Susceptibility NLT Code NLT Description
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 3 of 4
NAME: CLOSTRIDIUM DIFFICILE ACTIVE: YES ____________________________________________________________________________
Topography Selection
Include Exclude
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 4 of 4
NAME: CLOSTRIDIUM DIFFICILE ACTIVE: YES
____________________________________________________________________________
Follow PTF: YES Run Date:
Run Cycle: MONTHLY First Encounter:
Protocol: LREPI General Description:
Note: To review or
edit the General
Description use the
key instead of
the key.
____________________________________________________________________________
Exit Save Refresh
COMMAND: E Press H for help
Creutzfeldt-Jakob Disease (CJD) (Reference #13)
Creutzfeldt-Jakob Disease (CJD) disease is a rare illness associated with prions. The VA has chosen to follow this entity because of historic problems with certain blood products in use in both the private and public health care sectors. The EPI data will be one of a number of ways used to identify changes in trends of incidence of this illness. This task is remarkably complex because of the long incubation period of CJD. There are no specific tests for diagnosis other than central nervous system histology combined with clinical presentation. As such, we will follow this entity through ICD coding.
Emerging Pathogen Primary Menu
ENH Lab Search/Extract Manual Run (Enhanced)
VR Print Detailed Verification Report
LO Local Pathogen Menu ...
PI Pathogen Inquiry
UP Lab EPI Parameter Setup
Lab EPI Protocol Edit
LK Antimicrobial Link Update
Select Emerging Pathogens (EPI) Primary menu Option: UP Emerging Pathogens Parameter update
Select EMERGING PATHOGENS NAME: ?
Answer with EMERGING PATHOGENS NAME, or REFERENCE NUMBER
Do you want the entire 14-Entry EMERGING PATHOGENS List? Y (Yes)
Choose from:
CANDIDA
CLOSTRIDIUM DIFFICILE
CREUTZFELDT-JAKOB DISEASE
CRYPTOSPORIDIUM
DENGUE
E. COLI 0157:H7
HEPATITIS C ANTIBODY POS
LEGIONELLA
LEISHMANIASIS
MALARIA
PEN-RES PNEUMOCOCCUS
STREPTOCOCCUS GROUP A
TUBERCULOSIS
VANC-RES ENTEROCOCCUS
Select EMERGING PATHOGENS NAME: CREUTZFELDT-JAKOB DISEASE
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 1 of 4
NAME: CREUTZFELDT-JAKOB DISEASE ACTIVE: YES
____________________________________________________________________________
Serology Lab Test(s) Indicator Value
ICD Coding System [ICD-9 or ICD-10]? (9/10):
ICD Code Cd Set ICD Description
046.1 ICD-9 JAKOB-CREUTZFELDT DIS
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 2 of 4
NAME: CREUTZFELDT-JAKOB DISEASE ACTIVE: YES
____________________________________________________________________________
Selected Etiology
Antimicrobial Susceptibility NLT Code NLT Description
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 3 of 4
NAME: CREUTZFELDT-JAKOB DISEASE ACTIVE: YES
____________________________________________________________________________
Topography Selection
Include Exclude
____________________________________________________________________________
Exit Save Next Page Refresh
COMMAND: N Press H for help Insert
EMERGING PATHOGEN SITE PARAMETERS INPUT SCREEN Page 4 of 4
NAME: CREUTZFELDT-JAKOB DISEASE ACTIVE: YES
____________________________________________________________________________
Follow PTF: YES Run Date:
Run Cycle: MONTHLY First Encounter:
Protocol: LREPI General Description:
Note: To review or
edit the General
Description use the
key instead of
the key.
____________________________________________________________________________
Exit Save Refresh
COMMAND: E Press H for help Insert
Cryptosporidium (Reference #9)
The parasite Cryptosporidium parvum is a cause of water-borne diarrheal disease. It has gained recent prominence after evaluation of the outbreak in the greater Milwaukee area in 1993 which is estimated to have affected ................
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