ABSTRACT
BACKGROUND: Testing, traceability, and isolation actions are a central strategy defined by the World Health Organization to contain the COVID-19 pandemic. In this sense, the countries have had difficulties in counting the number of people infected with SARS-CoV-2. Errors in reporting results are a common factor, as well as the lack of interoperability between laboratories and governments. Approaches aimed at sending spreadsheets via email expose patients' privacy and have increased the probability of errors due to retyping, which generates a delay in the notification of results. OBJECTIVE: This study aims to design and develop an interoperable platform to report polymerase chain reaction (PCR) SARS-CoV-2 tests from laboratories to the Chilean government. METHODS: The methodology to design and develop the interoperable platform was comprised of six well-structured stages: (1) creation of a minimum data set for PCR SARS-CoV-2 tests, (2) modeling processes and end points where institutions interchange information, (3) standards and interoperability design, (4) software development, (5) software testing, and (6) software implementation. RESULTS: The interoperable Fast Healthcare Interoperability Resources (FHIR) platform to report PCR SARS-CoV-2 tests from laboratories to the Chilean government was successfully implemented. The platform was designed, developed, tested, and implemented following a structured methodology. The platform's performance to 1000 requests resulted in a response time of 240 milliseconds, throughput of 28.3 requests per second, and process management time of 131 milliseconds. The security was assured through a private network exclusive to the Ministry of Health to ensure confidentiality and integrity. The authorization and authentication of laboratories were implemented with a JavaScript Object Notation Web Token. All the PCR SARS-CoV-2 tests were accessible through an application programming interface gateway with valid credentials and the right access control list. CONCLUSIONS: The platform was implemented and is currently being used by UC Christus Laboratory. The platform is secure. It was tested adequately for confidentiality, secure authorization, authentication, and message integrity. This platform simplifies the reporting of PCR SARS-CoV-2 tests and reduces the time and probability of mistakes in counting positive cases. The interoperable solution with FHIR is working successfully and is open for the community, laboratories, and any institution that needs to report PCR SARS-CoV-2 tests.
ABSTRACT
Helicobacter pylori es una bacteria que coloniza la mucosa del estómago produciendo enfermedades gástricas crónicas. Las cepas que expresan el factor de virulencia CagA se unen al epitelio gástrico e inyectan en él esta proteína, la cual es activada por fosforilación en residuos de tirosina ubicados en el motivo EPIYA. Dependiendo del número y tipo de motivo EPIYA (EPIYA-A, B, C y D), se inducen transformaciones celulares que juegan un papel importante en el desarrollo de enfermedades gastroduodenales asociadas con H. pylori. El objetivo de este trabajo fue determinar la frecuencia de las variantes de EPIYA en cepas de H. pylori cagA positivas de la región centroccidental de Venezuela. Se estudiaron 81 muestras de ADN extraídas de biopsias gástricas tomadas de individuos con gastritis crónica. El tipo de motivo EPIYA fue determinado por PCR y secuenciación. Solamente se detectaron variantes de EPIYA descritas para países occidentales: ABC (58,0%), ABCC (38,3%) y ABCCC (3,7%). La baja prevalencia detectada de cepas de H. pylori con tres repeticiones de EPIYA-C, las cuales se conocen por generar un mayor riesgo a cáncer gástrico, puede encontrase entre las razones que expliquen la escasa incidencia de cambios histológicos severos en las muestras de gastritis crónica analizadas.
Abstract: Helicobacter pylori is a bacterium that colonizes stomach mucous tissue producing chronic gastric disease. The strains that express the CagA virulence factor adhere to the gastric epithelium and inject this protein, which is activated by phosphorilation at tyrosine residues located in the EPIYA motif. Depending on the number and type of EPIYA motif (EPIYA-A, B, C, and D), cellular transformations are induced which play an important role in the development of H. pylori associated gastro duodenal diseases. The objective of this work was to determine the frequency of the EPIYA variants in cagA positive H. pylori strains from the center-occidental region of Venezuela. The study included 81 DNA samples extracted from gastric biopsies taken from individuals with chronic gastritis. The type of EPIYA motif was determined by PCR and sequencing. Only EPIYA variants described for occidental countries were detected: ABC (58.0%), ABCC (38.3%) and ABCCC (3.7%). The low prevalence of H. pylori strains with three EPIYA-C repetitions detected, which are known to generate a higher gastric cancer risk, could be one of the reasons that explain the low incidence of severe histological changes in the chronic gastric samples analyzed.
