View source for Journal:Development of an electronic information system for the management of laboratory data of tuberculosis and atypical mycobacteria at the Pasteur Institute in Côte d’Ivoire

{{Infobox journal article
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|image        = 
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|caption      = 
|title_full   = Development of an electronic information system for the management of laboratory data of tuberculosis and atypical mycobacteria at the Pasteur Institute in Côte d’Ivoire
|journal      = ''Journal of Health Management and Informatics''
|authors      = Koné, Constant J.; Touré, Assata; N’Dri, Mathias K.; Nguessan, Raymond; Soumahoro, Man-Koumba
|affiliations = Pasteur Institute of Côte d’Ivoire
|contact      = Email: koneconstant at pasteur dot ci
|editors      = 
|pub_year     = 2019
|vol_iss      = '''6'''(1)
|pages        = 1–6
|doi          = None
|issn         = 2423-5857
|license      = [http://creativecommons.org/licenses/by/3.0/ Creative Commons Attribution 3.0 Unported]
|website      = [http://jhmi.sums.ac.ir/index.php/JHMI/article/view/513/160 http://jhmi.sums.ac.ir/index.php/JHMI/article/view/513/160]
|download     = [http://jhmi.sums.ac.ir/index.php/JHMI/article/download/513/160 http://jhmi.sums.ac.ir/index.php/JHMI/article/download/513/160] (PDF)
}}
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==Abstract==
'''Introduction''': Tuberculosis remains a public health problem despite all the efforts made to eradicate it. To strengthen the surveillance system for this condition, it is necessary to have a good data management system. Indeed, the use of electronic information systems in [[Information management|data management]] can improve the quality of data. The objective of this project was to set up a laboratory-specific electronic information system for mycobacteria and atypical tuberculosis.

'''Methods''': The design of this [[laboratory information system]] required a general understanding of the workflow and the implementation processes in order to generate a realistic model. For the implementation of the system, Java technology was used to develop a web application compatible with the intranet of the company. The impact and the acceptability of the use of the system on the running of the [[laboratory]] were evaluated using the Likert scale.

'''Results''': The system in place has been in operation for about 12 months, in conjunction with the paper registers. Since then, 4811 requests for examinations concerning 6083 samples have been registered. The results of analysis of 3892 patients were printed from the laboratory information system. In order to produce tuberculosis drug resistance reports and laboratory performance reports, dashboards have been developed.

'''Conclusion''': The system has been adopted by the staff because of the time and efficiency gained in managing laboratory data. However, obtaining an optimized tool will only be done in a cycle of sustained improvement.

'''Keywords''': clinical laboratory information systems, public health, tuberculosis

==Introduction==
Tuberculosis remains a public health problem despite all efforts to eradicate it. According to the World Health Organization (WHO), the number of tuberculosis cases in the world was estimated 9.6 million in 2014.<ref name="WHOWorld16">{{cite book |title=Global Tuberculosis Report 2016 |author=Wourld Health organization |publisher=World Health Organization |pages=214 |year=2016 |isbn=9789241565394 |url=http://apps.who.int/medicinedocs/en/d/Js23098en/ |accessdate=04 October 2017}}</ref> To strengthen the surveillance system for this disease, we need to have a good data management system. 

The use of electronic information systems can improve the quality of clinical data<ref name="CastelnuovoImp12">{{cite journal |title=Implementation of provider-based electronic medical records and improvement of the quality of data in a large HIV program in Sub-Saharan Africa |journal=PLoS One |author=Castelnuovo, B.; Kiragga, A.; Afayo, V. et al. |volume=7 |issue=12 |pages=e51631 |year=2012 |doi=10.1371/journal.pone.0051631 |pmid=23284728 |pmc=PMC3524185}}</ref> and thus the management of patients. Studies have shown that the implementation of computer tools is a performance factor for laboratory activities.<ref name="RhoadsClin14">{{cite journal |title=Clinical microbiology informatics |journal=Clinical Microbiology Reviews |author=Rhoads, D.D.; Sintchenko, V.; Rauch, C.A. et al. |volume=27 |issue=4 |pages=1025-47 |year=2014 |doi=10.1128/CMR.00049-14 |pmid=25278581 |pmc=PMC4187636}}</ref> The results of laboratory analyses provide important data for clinical decision-making and treatment. Effective management of this data is essential for strengthening the health care system as a whole. 

Laboratory information systems have been developed and used for about half a century.<ref name="RhoadsClin14" /><ref name="El-KarehImpact12">{{cite journal |title=Impact of automated alerts on follow-up of post-discharge microbiology results: a cluster randomized controlled trial |journal=Journal of General Internal Medicine |author=El-Kareh, R.; Roy, C.; Williams, D.H. et al. |volume=27 |issue=10 |pages=1243-50 |year=2012 |doi=10.1007/s11606-012-1986-8 |pmid=22278302 |pmc=PMC3445692}}</ref> Like all laboratory information systems, the microbiology laboratory information system must be secure, user-friendly, and able to interact with other information systems. However, there are several unique features of microbiology that are not used in other [[Clinical laboratory|clinical laboratories]], i.e., tracking multiple drifts, laboratory electronic notes, reporting results, and taking the preliminary and final results into account.<ref name="RhoadsClin14" />

The strategic plan of development of e-health has been defined and is being implemented.<ref name="OrdrePlan17">{{cite web |url=http://doczz.fr/doc/3118472/pdncs-ci---order-national-des-des-decins-de-ivoire-divoire |title=Plan Strategique de Cybersante |author=Ordre National Des Medecins de Côte d’Ivoire |date=2017 |accessdate=15 January 2018}}</ref> All health facilities have to implement an electronic information system for better management of data generated by their activities. 

The purpose of this project was to set up a laboratory information system (LIS) at Institute Pasteur of Côte d’Ivoire to collect specific data for ''Mycobacterium tuberculosis''. This LIS will allow the recording of the data resulting from the activities of the laboratory. It should also allow for the generation of results that are ultimately given to the patient as well as the generation of reports on the activities of the laboratory. Finally, an analysis of the impact of this new system in the laboratory routine was carried out. 

==Methods==
===Design===
Designing a laboratory information system requires an understanding of the [[workflow]] and the processes implemented. The data collection and recording sheet was the starting point for this work as the first objective, which was to build a system capable of recording the data and results from the laboratory’s activities. This data sheet is a key element in the activities of the laboratory since all patient [[information]] such as socio-demographic data, information on the samples, the preliminary and final results, and the notes of the various examinations are notified. This sheet was previously reorganized by the epidemiology unit. Then, from this new form and a series of interviews with biologists, some improvements were made. It was noted that in the paper recording system used before, the biological monitoring of a patient throughout his/her treatment was not possible. This feature was thus integrated into the new system. After analysis of all data, an application with conceptual, logic, and physical characteristics was designed using the Merise method in the open source tool MySQL Workbench.<ref name="MatheronComprendre03">{{cite book |title=Comprendre Merise: Outils conceptuels et organisationnels |author=Matheron, J.P. |publisher=Eyrolles |edition=10th |year=2003 |isbn=9782212075021}}</ref><ref name="MySQLWorkbench">{{cite web |url=https://www.mysql.com/fr/products/workbench/ |title=MySQL Workbench |publisher=Oracle Corporation |accessdate=04 October 2017}}</ref>

===Architecture and system features===
We opted for a web-based application used in the company’s intranet. It should be noted that the project was entirely based on Java technology. The design of the application was based on the Apache Struts 2.0 framework<ref name="ApacheStruts">{{cite web |url=https://struts.apache.org/ |title=Apache Struts |publisher=Apache Software Foundation |accessdate=04 October 2017}}</ref>, which defined a controller-view-template three-layer design. The database connection layer uses Hibernate<ref name="Hibernate">{{cite web |url=http://
hibernate.org/ |title=Hibernate |publisher=Red Hat, Inc |date=04 May 2018}}</ref>, which is an object-relational mapping (ORM) open-source solution that facilitates the development of the persistence layer; this database connection layer is also based on Java Database Connectivity (JDBC) for some modules of the application. The production of PDF reports was possible by the use of the JasperReports Library.<ref name="JRLib">{{cite web |url=https://community.jaspersoft.com/project/jasperreports-library |title=JasperReports Library |publisher=TIBCO Software, Inc |accessdate=16 January 2018}}</ref> The reports in the Excel format required the libraries of the Apache POI project.<ref name="ApachePOI">{{cite web |title=Apache POI |publisher=Apache Software Foundation |accessdate=10 May 2018}}</ref> The Java Enterprise Edition of Glassfish 4.1<ref name="GlassFish">{{cite web |url=https://javaee.github.io/glassfish |title=GlassFish: The Open Source Java EE Reference Implementation |author=Oracle Corporation |work=Github |accessdate=14 January 2019}}</ref> deployment server in its free version was used to host the application, and the [[MySQL]] 5.1 database management system (DBMS) was used to manage the database. The MySQL DBMS and Glassfish were installed on an HP ProLiant server running on a UNIX CentOS 6.7 OS. All the client machines were PC-type computers. All web browsers could be used as web clients for the application, though with a preference for Google Chrome; browsers such as Internet Explorer, Safari, and Firefox do not fully support the “date” and “time” input types.<ref name="PatreonDateAndTime">{{cite web |url=https://caniuse.com/#feat=input-datetime |title=Date and time input types |work=Can I use |publisher=Patreon |accessdate=14 January 2019}}</ref> The data stored in the database benefited from automatic backups to an external hard drive, and replication of this external hard drive was done at the end of the week. The source code of the application as well as the different steps of the implementation was documented to allow future maintenance. The user interface was modeled to be fairly similar to the original paper form. System access management was also taken into account in the implementation. The system modules are accessible according to the rights assigned by the administrator. 

===On-site system installation and user training===
The server housing the executable files of the information system and the database was installed in a room which was secure and protected from the weather. A high capacity UPS was connected to this server to prevent the system from shutting down in the event of a power outage. The client computers comprised the ordinary service computers. The application was available on the corporate intranet from a web browser. 

Training of six members of the laboratory staff was conducted in half a day. The assimilation took place quite quickly because the members of the laboratory all had good notions of the computer tool. Consultations were often sought when certain aspects had been forgotten when using the system. After each update, a short information session was organized to share the new features, after which use of the software continued without interruption. Biologists' use of the LIS often resulted in the discovery of bugs, which were later corrected; suggestions and comments were often made by users to improve this information system.

===Qualitative assessment===
The management of patients with tuberculosis involves regular biological tests. Monitoring of the analyses over time for a patient becomes problematic, which is also the case with the search for information on a sample, as well as the completion of activity reports and the delivery of results. The information system put in place should be able to improve the realization of these tasks on a daily basis. 

After 12 months of usage, we evaluated the acceptability of this information system and the impact of implementation on the functioning of the laboratory by different users of the system, namely a data manager, two technicians, two engineers and a biologist who had to use the software continuously. This evaluation was based on the Likert scale.<ref name="DemeuseEchelles08">{{cite book |chapter=Chapter 5.3 Echelles de Likert ou méthode des classements additionnés |title=Introduction aux théories et aux méthodes de la mesure en sciences psychologiques et en sciences de l'éducation |author=Demeuse, M. |pages=213–18 |year=2008 |url=http://iredu.u-bourgogne.fr/images/stories/Documents/Cours_disponibles/Demeuse/Cours/p5.3.pdf |format=PDF |accessdate=04 January 2018}}</ref> To do this, we administered a questionnaire to selected the staff members. The interviewees were to choose one response from the five possible responses given for each of the questions which included: Strongly Agree (5), Agree (4), Neither Agree or Disagree (3), Disagree (2), and Strongly Disagree (1). Summary statistics were generated from the responses obtained. 

==Results==
===Results of the system launch===
The system in place has been in use since the January 1, 2017. By the end of the year, 3,892 patients were registered in the LIS, with 4,811 visits and 6,083 collected samples recorded. Of the registered patients, 805 made at least two visits to the laboratory. In this information system, 93.9% (185/197) of the entry fields from patient and visit cards are fields with drop-down lists of those pre-recorded at the level of the administration module. These mechanisms were put in place to avoid the errors inherent in free text field filling. LIS allowed the patient folder creation as well as the creation of visit cards related to requests for examinations. These visit sheets were linked to the same record for a patient, which helps to monitor his/her condition (Figures 1, 2, 3). 


[[File:Fig1 Koné JofHlthManInfo2019 6-1.png|800px]]
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{| 
 | STYLE="vertical-align:top;"|
{| border="0" cellpadding="5" cellspacing="0" width="800px"
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Figure 1.''' This page for creating a new patient record</blockquote>
 |- 
|}
|}

[[File:Fig2 Koné JofHlthManInfo2019 6-1.png|800px]]
{{clear}}
{| 
 | STYLE="vertical-align:top;"|
{| border="0" cellpadding="5" cellspacing="0" width="800px"
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Figure 2.''' Patient card</blockquote>
 |- 
|}
|}

[[File:Fig3 Koné JofHlthManInfo2019 6-1.png|800px]]
{{clear}}
{| 
 | STYLE="vertical-align:top;"|
{| border="0" cellpadding="5" cellspacing="0" width="800px"
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Figure 3.''' Visit card</blockquote>
 |- 
|}
|}

The printing of the results intended for the patients requires preliminary validation by rhe biologist responsible for test results; otherwise, the request for printing is not executed. Six laboratory-delivered results could be printed, including microscopy, Genexpert, solid and/or fluid culture, genotypic test, standard antibiogram, and extended antibiogram. In the interests of quality assurance of the laboratory, the second impression for the same result carries the duplicate mark, so during this period, 6,075 printed results were obtained, which included 3,415 microscopy examinations, 1,591 Genexpert and LPA tests, 35 culture samples, 90 classical antibiogram, and five expanded. 

A dashboard system allows the calculation of indicators for the monitoring of laboratory activities and also provides indicators on the state of the health of the patients. These dashboards generate indicators for activities, including microscopy, Genexpert, culture in liquids and solids media, LPA, and antibiotic sensitivity (antibiogram) for a period defined by a time interval to complete. It also allows you to generate an Excel spreadsheet, the list of samples with associated information such as sample number, methods, and test results (Figures 4, 5). 


[[File:Fig4 Koné JofHlthManInfo2019 6-1.png|800px]]
{{clear}}
{| 
 | STYLE="vertical-align:top;"|
{| border="0" cellpadding="5" cellspacing="0" width="800px"
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Figure 4.''' Dashboard of microscopy</blockquote>
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[[File:Fig5 Koné JofHlthManInfo2019 6-1.png|800px]]
{{clear}}
{| 
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{| border="0" cellpadding="5" cellspacing="0" width="800px"
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  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Figure 5.''' Dashboard of LPA</blockquote>
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===Perception and usability of the system===
The questionnaire was administered to the laboratory staff. Table 1 details the results obtained for these five questions. Regarding the assertions, they’re saying “the user feels comfortable with the LIS,” “LIS allows security and quick access to information,” “the LIS improves the quality of the work in the laboratory,” and “the user considers to switch to exclusive use of the electronics for managing the laboratory data”; 100% (6/6) responded favorably. One in six found that LIS did not save time in performing data management tasks.

{| 
 | STYLE="vertical-align:top;"|
{| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="100%"
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;" colspan="6"|'''Table 1.''' Results of the evaluation of the acceptability and impact of the implementation of the information system on the functioning of the laboratory
 |- 
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Strongly Agree
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Agree
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Neither Agree or Disagree
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Disagree
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Strongly Disagree
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|I am completely comfortable with LIS
  | style="background-color:white; padding-left:10px; padding-right:10px;"|5 (25)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|1 (4)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|LIS saves time in completing tasks
  | style="background-color:white; padding-left:10px; padding-right:10px;"|5 (25)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|1 (2)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|The LIS allows access to information quickly and securely
  | style="background-color:white; padding-left:10px; padding-right:10px;"|6 (30)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|LIS improves the overall quality of work
  | style="background-color:white; padding-left:10px; padding-right:10px;"|5 (25)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|1 (4)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
 |-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|I plan to move to the exclusive use of the LIS for laboratory data management
  | style="background-color:white; padding-left:10px; padding-right:10px;"|5 (25)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|1 (4)
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
  | style="background-color:white; padding-left:10px; padding-right:10px;"|0
 |-
|}
|} 


==References==
{{Reflist|colwidth=30em}}

==Notes==
This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. We also added PMCID and DOI when they were missing from the original reference. Under "Architecture and system features," the original article had a poorly punctuated and confusing sentence about browser support for date and time input types; it has been updated to be more correct, with a citation added. The URL to GlassFish was updated to show the 4.x versions.

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