Tuberculosis Information

TB cases increased in U.S. for the first time in 23 years 2-4

Rate per 100,000 among selected population
Public Health Information
Awareness
Earlier Diagnosis
Prevention
How was it discovered?

• Healthcare provider collects a specimen from a patient

• The specimen is transported to a public health laboratory and tested
• The results are reported back to the healthcare provider to enable diagnosis and treatment of the patient
• The results are also reported to the jurisdiction's health department, CDC, and other stakeholders

Information Flow?
Who plays a role?
What data are needed?
What data are provided?
Hare data relationships formed?
Data Quality and Data Standards?
HL7 Messaging?
Information Systems Used?

What is Informatics?
❖ Informatics is a broad field encompassing information science, information technology, algorithms, and
social science.
❖ There are two types of informatics that we will cover:
Laboratory Informatics Public Health Informatics
Laboratory informatics is the specialized application Public health informatics is the systematic application
of information technology aimed at applying of information and computer science and
process, information, and data relationships to technology to support public health practice,
enable and optimize the scientific process and research, and learning driven by the optimization of
delivery of information as a product of the public health goals.
laboratory.

Why is Laboratory Informatics Important for Public Health?

❖ Informatics is a growing field with multiple disciplines. This evolution has proven to be a crucial component
in helping meet public health objectives.
Laboratory Informatics
• Allows data to be collected, interpreted, stored,
and shared for immediate use and future
research
• Creates interoperability between multiple data
sets
• Maximizes the efficiency of laboratory operations
Public Health Informatics
• Enables effective monitoring, detection and
investigation of diseases and environmental
hazards
• Key to local, regional, and national health
surveillance efforts, outbreak investigations, and
many other public health functions
• Supports improved decision- making, guiding
public policy, and improving population health

Who is Involved in Laboratory Informatics?

1. Laboratory Informaticians
• Formal or informal subject matter experts in laboratory informatics who ensure quality data and efficient
processes within the information flow support laboratory functions.
• Laboratory informaticians bridge the gaps between the performance of laboratory science and the
delivery of business functions, using computing technology and technology services.
 • They conduct and manage the steps of laboratory testing and Laboratory Information Management
System, or LIMS, processing. This includes the tracking of physical specimen through the laboratory,
laboratory test scheduling, and the electronic exchange of laboratory data with data partners.
2. Managers/Directors/ Administrators
• Policy, decision makers, and implementers who oversee or support laboratory operations to ensure
sustainability and functionality of information systems
• Laboratory Managers, Directors, and Administrators are also responsible for building competencies of
their staff around the management, procurement, and successful implementation of computing
technology and services that support the business requirements of their laboratories.

3. IT/IS Personnel
• Maintain physical and virtual functionality of hardware and software of information systems
• Laboratory Managers, Directors, and Administrators are also responsible for building competencies of
their staff around the management, procurement, and successful implementation of computing
technology and services that support the business requirements of their laboratories.

4. Other Laboratory Professionals

• Users of information systems
• Generators of data
• The majority of testing personnel and other laboratory staff fall into this category.
• At a minimum, all laboratory staff need to understand the "relevance" of informatics and data in the
laboratory. They should, therefore, have a solid understand of how informatics is an important enabler
of the services and products of the laboratory and that everyone can impact the quality of the
information produced by the laboratory.

Key Concepts Overview

Tuberculosis Example
Life of a Specimen
This case study will give a
This flow will be a high-
plausible real- life
level overview, showing
scenario of how
how a specimen moves
informatics plays a role in
through the laboratory
dianosing and
with respect to public
managing the potential
health informatics
spread of diseases like
processes.
TB.

DATA RELATIONSHIPS
DATA QUALITY
DATA STANDARDS
LABORATORY
INFORMATION
MANAGEMENT SYSTEMS
(LIMS) AND OTHER
SYSTEMS
Data Quality
• Laboratories play a crucial role in supporting the public's health
• Accurate and effective patient care and public health practice rely on the laboratory's ability to produce
quality data
• Areas where data quality can be compromised are:
•Was the information collected properly, following all
Data Collection
Standard Operating Procedures (SOPs) and best practices?

•Did the information enter the system correctly at each

Data Entry
stage?

•Was the integrity of the information maintained during the

Data Processing
processing through the system?

•Are the information and data analyzed in a manner

Data Analysis
appropriate to the situation/request?

•Is the stored information maintained to keep its integrity,

Data Storage
persistence, and availability?

NOTE: Data Quality is the single most important factor that drives informatics.

Data Standards
❖ Data standards provide a method to convey information in valid, meaningful, and actionable ways. There
are many types of data standards; however, we will focus on data representation and data exchange
standards. They include:
1. ICD Standards 5
• The U.S. health system's health adaption of International Classification of Diseases (ICD) list of six-character
codes to describe patient diagnoses.
• The International Classification of Diseases, Clinical Modification (ICD-CM) is a system used by physicians
and other healthcare providers to classify and code all diagnoses, symptoms and procedures recorded
in conjunction with clinical care in the United States. ICD Standards offer great detail and significant ability
to accommodate new technologies and procedures. These codes have the potential to provide
accurate data for evaluating and improving the quality of patient care. The current version of standards
in use in the United States is ICD-10.
2. SNOMED CT 6
• A coding ontology used primarily to code the test results, such as identification of an organism.
• Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT®) is a standardized, multilingual
vocabulary of clinical terminology that is used in clinical documentation and reporting. SNOMED
CT® helps facilitate the interoperable health information exchange between electronic health records,
or EHRs.
3. LOINC 7
• A coding system defined by six specific attributes that identify exactly what test was performed on a
specimen.
• The Logical Observation Identifiers Names and Codes (LOINC ®) were developed to provide a definitive
standard for identifying clinical information in electronic reports. The LOINC® database provides a set of
universal names and ID codes for identifying laboratory and clinical tests executed. LOINC ® fosters the
development and use of suitable standardized diagnostic test and procedure terminologies to support
the safe, accurate, and effective exchange of health information.
4. HL7 8
• Standards that govern the electronic structure rules used to build a message coming from the laboratory
so that the receiver can understand how to interpret the message.
• Health Level 7® (HL7®) is set of international standards for transfer of clinical and administrative data
between software applications used by various healthcare providers. This allows a protocol for the
exchange of patient demographic, financial and clinical data among compatible programs or systems.
NOTE: Data standards are a key component that enables interoperability and promotes data quality.
What is a LIMS?
❖ A Laboratory Information Management System (LIMS) is one or more pieces of software for the collection,
management, reporting, and analysis of laboratory data. The LIMS may also interface with other equipment
or systems.
Capabilities Benefits Limitations
• Logs/tracks specimens • Faster, more accurate, and • Data may not be shareable
• Automates workflow reliable results across unique systems
• Interfaces with instruments • Easier storage, tracking, and • Requires significant
• Tracks results/calculations assessment of data over time communication between
• Performs data analysis and across test runs laboratory and IT personnel
• Electronically reports results • Provides strong audit trail and • Limited staff available to run
• Interfaces with other information security data reports
laboratory sysemts • Allows operational efficiency
evaluation/improvement

Life of a Specimen Flow Overview

1. Collection, Labeling, and Communication
• Collect specimen
• Label specimen
• Communicate test requisition information
2. Transportation
• Package and transport specimen to laboratory
3. Testing and Recording Results
• Perform testing prep
• Complete tests
• . Analyze results
• . Record results
4. Communicating Results
• Communicate results to submitter and other stakeholders
5. Storage/ Disposal
• Store or dispose specimen
PRE-ANALYTIC PHASE: Collection, Labeling, and Communication
1a. Collect specimen 1b. Label specimen 1c. Communicate test requisition information
• Identify the concern • Patient Name or • Select the communication channel to
• Decide what tests are needed unique identifier send the test requisition information.
• Collect type of specimen • Other patient data
needed (e.g., age, sex
• Capture the data required to • Specimen metadata
meet regulatory requirements

NOTE: Check the label for errors. Errors will follow the specimen and have an effect on the results.
Error - Collecting the Specimen
Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Incorrect specimen type
• Insufficient quantity of specimen collected to run the requested tests
• Contamination of the specimen
• Incorrect method of specimen collection
• Incorrect specimen storage

Data and Relationships - Collecting the Specimen

The data connected to the specimen up to this step includes:
• Patient name and Patient Identifier(s)
• Patient metadata (e.g., age, date of birth, and gender)
• Specimen identifier
• Tests requested
• Specimen type (e.g., sputum)
• Date and time of specimen collection
• Clinical provider/submitter information
PRE-ANALYTIC PHASE: Labeling the Specimen
TB EXAMPLE
Specimen Label
Specimen labels include the following:
• Patient name
• Date of birth
• Patient identifier
• Date of collection

Laboratory Test Requisition Information

Specimens must be accompanied by a paper test requisition form unless the order was transmitted
electronically.
Error - Labeling
Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Missing specimen label
• Incorrect or missing specimen information (including specimen ID and specimen type)
• Incorrect or missing patient information (including patient ID)
• Wrong test(s) requested
• Incorrect submitter information

Data Information/Relationships - Labeling

The data connected to the specimen up to this step include:
• Patient name and Patient Identifier(s)
• Patient metadata (e.g., age, date of birth, and gender)
• Specimen identifier
• Test(s) requested
• Specimen type (e.g., sputum)
• Date and time of specimen collection
• Specimen information/specimen metadata
• Clinical provider/submitter information
• Specimen storage and transportation information
• Information about the testing laboratory/specimen recipient laboratory
PRE-ANALYTIC PHASE: Communicating Specimen Information with the Laboratory
TB EXAMPLE
Select the Communication Channel
• Paper requisition (accompanies specimen)
• Phone
• Email or Fax
• Electronic Data Sharing
o Electronic Test Order and Result (ETOR)
o Computerized Physician Order Entry (CPOE)
o Web Portal

Inform the Laboratory

NOTE: Sending data begins the audit process for the specimen flow.
Error - Communicating Specimen Information
Within this phase, there are many ways where data quality can be compromised. There are common pitfalls of
each communication method:
• Regular Mail/Paper
A hard copy may not include all required specimen and patient information. This may also have printed
or handwritten text that is illegible.
• Phone
Information can get lost in translation or incomplete information can be exchanged and may not meet
compliance requirements.
• Fax
The fax may not be properly connected, may run out of paper, or incomplete information can be sent.
• Email
Emails can get lost in a participant's inbox, in their junk mail, or incomplete information can be sent.
There can also be confidentiality issues when sending information over email. DIRECT® is one example
of an email-based messaging system that is used in some laboratories.
• Electronic Data Sharing Systems
Some systems, such as web portals, may not be able to exchange information seamlessly since the
sender and recipient software/technology may not be compatible.
PRE-ANALYTIC PHASE: Transportation
2. Package and transport specimen to the lab
• Package the specimen following standards and regulations for each type of specimen
• Follow the transportation guidelines for shipping biological specimens
NOTE: Integrity of the specimen is imperative for high quality, reliable, and accurate results

PRE-ANALYTIC PHASE: Transportation

TB EXAMPLE
Packaging and Storing Specimen Transporting Specimen
Package and store the specimen following standards Because of time sensitivity with our Tuberculosis
and regulations for a sputum specimen. testing, we can use couriers to ensure the sample is
delivered safely and quickly.
Error - Transportation
Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Improper packaging and labeling
• Specimen leakage
• Damaged package
• Faulty handling of the specimen
• Faulty storage, and/or transportation of the specimen (e.g., specimen held or transported at incorrect
temperature)
• Unreadable label information after transport
• Extended time period for transportation or in storage
PRE-ANALYTIC PHASE: Receiving and Evaluating Quality
3a. Receiving and Accessioning Specimen 3b. Evaluate Quality
• Receive, sort, and triage specimen per SOP • Check specimen integrity
• Assign specimen laboratory-specific identifiers or • Check specimen labeling
bar codes and label as needed • Review testing requests
• Accession specimen data into the LIMS
• Pre-process/prepare specimens as necessary
NOTE Any breakdown of data quality or application of data standards will produce unreliable test results.

PRE-ANALYTIC PHASE: Receiving and Accessioning the Specimen

TB EXAMPLE
• The TB specimens are received by the laboratory and all data are entered into the LIMS. TB specimens are
often accessioned within a designated TB laboratory for safety purposes.
• The laboratory is requested to perform a combination of smear microscopy, molecular testing, and culture.
Error - Receiving and Accessioning
Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Barcode or label does not match test requisition form
• Test request form doesn't match sample / patient ID
• Specimen is unsuitable for test(s) requested
• Incomplete information on:
o Specimen type
o Specimen and patient metadata
• Specimen is received, triaged, or accessioned to the wrong laboratory department or section
• Transcription and scanning errors
• Specimen processing errors
PRE-ANALYTIC PHASE: Checking Quality
TB EXAMPLE
Quality of the specimen (s) collected and delivered to the laboratory directly impacts test results and, thus, the
downstream uses of those results (e.g., patient diagnosis and treatment, public health surveillance and
outbreak detection).
Some possible criteria for specimen rejection include the following:
Possible Rejection Criteria
• Specimen labeling does not match requisition form or incorrect labeling
• Inappropriate specimen type for test requested
• Incorrect collection method
• Broken or leaking specimen container
• Excessive delay between specimen collection and receipt in the lab
• Insufficient specimen volume
NOTE The suboptimal quality of specimens and unreliable test results ultimately affect patient care, treatment,
and interventions from public health surveillance.
Error - Checking Quality
Within this phase, there is one way that data quality can be compromised. The potential source of error is:
• The specimen does not pass specimen acceptance criteria

ANALYTIC PHASE: Testing and Recording Results

4a. Perform Testing Prep 4b. Complete and Analyze Tests 4c. Record Results
• Complete preparations prior to testing: • Complete testing • Record individual
o Preparation of reagents and • Analyze individual tests laboratory tests
supplies separately • Record final analysis of all
o Preparation of the specimen (e.g., • Review all test results tests
extraction of DNA) together for final analysis
ANALYTIC PHASE: Preparation, Testing, and Analysis
TB EXAMPLE
• Laboratory staff will prep TB specimens for some or all of the following tests:
o Acid Fast Bacilli Smear
o Culture
o Molecular Test
• Individual tests will be performed
• Laboratory staff and the section supervisor review the results of all tests performed before releasing reports
NOTE Testing results and analysis will be covered in more detail in the Life of a Result course.

Error - Preparation, Testing, and Analysis

Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Laboratory instruments are not adequately performing
• Incorrect treatment or processing of specimen before testing
• Laboratory equipment malfunction
• Test specimen mix-up/contamination
• Missing/incorrect quality control materials (internal and external)
• Undetected failure in quality control
• Incorrect SOP or SOP not followed
• Incorrect specimen for testing
• Incorrect use of test reagents
• Incorrect use of instrument software
Data Information/Relationships - Preparation, Testing, and Analysis
The data connected to the specimen up to this step includes:
• Patient name and Patient Identifier(s)
• Patient metadata (e.g., age, date of birth, and gender)
• Specimen identifier
• Tests requested
• Specimen type (e.g., sputum)
• Date and time of specimen collection
• Specimen information/specimen metadata
• Clinical provider/submitter information
• Specimen storage and transportation information
• Information about the testing laboratory/specimen recipient lab
• Date and time of specimen accessioning into the laboratory
• Identifier for the person that received or accessioned the specimen
• Laboratory test result(s)
• Analytical device performance data
• Quality control material data (internal and external QC materials)
ANALYTIC PHASE: Recording Results
TB EXAMPLE
• Results can be recorded both manually and through automation into the LIMS.
• It is important that a quality check be completed during this process so that errors in recording test
results are not made.
• After each additional test is completed, the specimen record in the LIMS must be updated to reflect
additional information. This updated information in the LIMS can help with diagnosis and final analysis.
NOTE: Ensuring accurate results in the LIMS is critical for accurate analysis, patient diagnosis, and public health
use of the data
Error - Recording Results
Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Results incorrectly entered into the LIMS
• Patient or specimen identifier(s) in results do not match those identifiers in the LIMS
• Results in LIMS are not updated or connected to additional testing
• QC information missing or incorrect
• Results are not validated
Data Information/Relationships - Recording Results
The data connected to the specimen up to this step include:
• Patient name and Patient Identifier(s)
• Patient metadata (e.g., age, date of birth, and gender)
• Specimen identifier
• Tests requested
• Specimen type (e.g., sputum)
• Date and time of specimen collection
• Specimen information/specimen metadata
• Clinical provider/submitter information
• Specimen storage and transportation information
• Information about the testing laboratory/specimen recipient lab
• Date and time of specimen accessioning into the laboratory
• Identifier for the person who received or accessioned the specimen
• Laboratory test result(s)
• Analytical device performance data
• Quality control material data (internal and external QC materials)
POST-ANALYTIC PHASE: Communicating Results & Storage / Disposal
5. Communicating Results
• Report preparation in the LIMS
• Communicate results to appropriate stakeholders
6. Sample Storage / Disposal
• Store the specimen or dispose of the specimen

POST-ANALYTIC PHASE: Communicating Results & Storage / Disposal

TB EXAMPLE
Communicating Results
• The laboratory director's office sends approved results and analysis to the approved stakeholders
o Results can be sent through HL7 messaging, by fax, or with a PDF or document through email
Storage Disposal
• Specimens are stored for a specific period of time prior to disposal
• The specimen results and all associated information live on within the LIMS once the testing is complete
• Laboratory specimen safety, storage and disposal guidelines must be followed
NOTE: Timely and accurate results to Dr. Lee are imperative to quickly treating John and informing public health
surveillance and outbreak efforts.
Error - Communicating Results
Within this phase, there are many ways that data quality can be compromised. These potential sources of error
include:
• Results are not validated
• Wrong transcription from results to reports, resulting in inaccurate reports
• Results are not communicated to stakeholders using the most efficient medium
• Mismatch of technology (if transmitted electronically) or differing use of data standards
• Stakeholders do not receive results in a timely fashion
Data Information/Relationships - Communicating Results
The data connected to the specimen up to this step include:
• Patient name and Patient Identifier(s)
• Patient metadata (e.g., age, date of birth, and gender)
• Specimen identifier
• Tests requested
• Specimen type (e.g., sputum)
• Date and time of specimen collection
• Specimen information/specimen metadata
• Clinical provider/submitter information
• Specimen storage and transportation information
• Information about the testing laboratory/specimen recipient lab
• Date and time of specimen accessioning into the laboratory
• Identifier for the person who received or accessioned the specimen
• Laboratory test result(s)
• Analytical device performance data
• Quality control material data (internal and external QC materials)
• Specimen storage and disposal guidelines
Conclusion
You should now be able to:
• Recognize what laboratory informatics is and how it directly supports patient care and public health
goals
• Identify who plays a role in laboratory informatics and explain the purpose of each role
• Identify the sequence of data and information flow within the laboratory from specimen collection and
receipt to specimen storage and disposal
• Recognize the importance of data quality and the factors that impact data quality
• Identify the different types of data standards and the importance of using those standards
• Define what a Laboratory Information Management System (LIMS) and Laboratory Information System
(LIS) are, their capabilities, and how they differ from other systems used in the laboratory
NOTE: You have completed the Life of a Specimen course. You are ready for the Life of a Result course.