Towards Unified Data Exchange Formats for Reporting Molecular Drug Susceptibility Testing.

Data Exchange Formats Electronic Laboratory Reporting Health Information Exchange Health Level Seven LOINC Public Health Surveillance

Journal

Online journal of public health informatics
ISSN: 1947-2579
Titre abrégé: Online J Public Health Inform
Pays: Canada
ID NLM: 101536954

Informations de publication

Date de publication:
2020
Historique:
entrez: 31 12 2020
pubmed: 1 1 2021
medline: 1 1 2021
Statut: epublish

Résumé

With the rapid development of new advanced molecular detection methods, identification of new genetic mutations conferring pathogen resistance to an ever-growing variety of antimicrobial substances will generate massive genomic datasets for public health and clinical laboratories. Keeping up with specialized standard coding for these immense datasets will be extremely challenging. This challenge prompted our effort to create a common molecular resistance Logical Observation Identifiers Names and Codes (LOINC) panel that can be used to report any identified antimicrobial resistance pattern. To develop and utilize a common molecular resistance LOINC panel for molecular drug susceptibility testing (DST) data exchange in the U.S. National Tuberculosis Surveillance System using California Department of Public Health (CDPH) and New York State Department of Health as pilot sites. We developed an interface and mapped incoming molecular DST data to the common molecular resistance LOINC panel using Health Level Seven (HL7) v2.5.1 Electronic Laboratory Reporting (ELR) message specifications through the Orion Health™ Rhapsody Integration Engine v6.3.1. Both pilot sites were able to process and upload/import the standardized HL7 v2.5.1 ELR messages into their respective systems; albeit CDPH identified areas for system improvements and has focused efforts to streamline the message importation process. Specifically, CDPH is enhancing their system to better capture parent-child elements and ensure that the data collected can be accessed seamlessly by the U.S. Centers for Disease Control and Prevention. The common molecular resistance LOINC panel is designed to be generalizable across other resistance genes and ideally also applicable to other disease domains. The study demonstrates that it is possible to exchange molecular DST data across the continuum of disparate healthcare information systems in integrated public health environments using the common molecular resistance LOINC panel.

Sections du résumé

BACKGROUND BACKGROUND
With the rapid development of new advanced molecular detection methods, identification of new genetic mutations conferring pathogen resistance to an ever-growing variety of antimicrobial substances will generate massive genomic datasets for public health and clinical laboratories. Keeping up with specialized standard coding for these immense datasets will be extremely challenging. This challenge prompted our effort to create a common molecular resistance Logical Observation Identifiers Names and Codes (LOINC) panel that can be used to report any identified antimicrobial resistance pattern.
OBJECTIVE OBJECTIVE
To develop and utilize a common molecular resistance LOINC panel for molecular drug susceptibility testing (DST) data exchange in the U.S. National Tuberculosis Surveillance System using California Department of Public Health (CDPH) and New York State Department of Health as pilot sites.
METHODS METHODS
We developed an interface and mapped incoming molecular DST data to the common molecular resistance LOINC panel using Health Level Seven (HL7) v2.5.1 Electronic Laboratory Reporting (ELR) message specifications through the Orion Health™ Rhapsody Integration Engine v6.3.1.
RESULTS RESULTS
Both pilot sites were able to process and upload/import the standardized HL7 v2.5.1 ELR messages into their respective systems; albeit CDPH identified areas for system improvements and has focused efforts to streamline the message importation process. Specifically, CDPH is enhancing their system to better capture parent-child elements and ensure that the data collected can be accessed seamlessly by the U.S. Centers for Disease Control and Prevention.
DISCUSSION CONCLUSIONS
The common molecular resistance LOINC panel is designed to be generalizable across other resistance genes and ideally also applicable to other disease domains.
CONCLUSION CONCLUSIONS
The study demonstrates that it is possible to exchange molecular DST data across the continuum of disparate healthcare information systems in integrated public health environments using the common molecular resistance LOINC panel.

Identifiants

DOI: 10.5210/ojphi.v12i2.10644 PMID: 33381280 PMC: PMC7758061
pubmed: 33381280
doi: 10.5210/ojphi.v12i2.10644
pii: ojphi-12-e14
pmc: PMC7758061
doi:

Types de publication

Journal Article

Langues

eng

Pagination

e14

Informations de copyright

This is an Open Access article. Authors own copyright of their articles appearing in the Journal of Public Health Informatics. Readers may copy articles without permission of the copyright owner(s), as long as the author and OJPHI are acknowledged in the copy and the copy is used for educational, not-for-profit purposes.

Déclaration de conflit d'intérêts

Competing Interests: No competing interests.

Références

Fed Regist. 2010 Jul 28;75(144):44589-654
pubmed: 20677416
AMIA Jt Summits Transl Sci Proc. 2019 May 06;2019:686-695
pubmed: 31259025
Yearb Med Inform. 2018 Aug;27(1):129-139
pubmed: 30157516
Clin Lab Med. 2014 Jun;34(2):297-314
pubmed: 24856529
Clin Infect Dis. 2019 Oct 15;69(9):1631-1633
pubmed: 30883637
Hum Mutat. 2016 Jun;37(6):564-9
pubmed: 26931183

Auteurs

Wilfred Bonney (W)

Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Public Health Informatics Fellowship Program, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Sandy F Price (SF)

Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Public Health Informatics Fellowship Program, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, USA.
LOINC and Health Data Standards, Regenstrief Institute, Inc., Indianapolis, IN, USA.
Association of Public Health Laboratories, Silver Spring, MD, USA.
California Department of Public Health, Richmond, CA, USA.
Wadsworth Center, New York State Department of Health, Albany, NY, USA.
New York State Office of Information Technology Services, Albany, NY, USA.

Swapna Abhyankar (S)

LOINC and Health Data Standards, Regenstrief Institute, Inc., Indianapolis, IN, USA.

Riki Merrick (R)

Association of Public Health Laboratories, Silver Spring, MD, USA.

Varsha Hampole (V)

California Department of Public Health, Richmond, CA, USA.

Tanya A Halse (TA)

Wadsworth Center, New York State Department of Health, Albany, NY, USA.

Charles DiDonato (C)

New York State Office of Information Technology Services, Albany, NY, USA.

Tracy Dalton (T)

Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Beverly Metchock (B)

Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Angela M Starks (AM)

Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Roque Miramontes (R)

Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Classifications MeSH