Laboratory EPI Technical and User Guide



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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