Padronização e validação de métodos moleculares (qPCR e LAMP) para detecção de Escherichia coli em urina

Abstract

The gold standard for the identification of an etiologic agent in the diagnosis of urinary tract infection is urine culture. However, this method is dependent on bacterial growth and the bacterial identification by an experienced microbiologist. Because of this, molecular methods such as qPCR and LAMP are viable to reduce identification time, and delivering results with higher sensitivity, specificity, and easier interpretation. This work aimed to evaluate the use of qPCR and LAMP technologies as methods for detection of Escherichia coli in the urine of inpatients from Walter Cantídio University Hospital (HUWC - UFC/EBSERH). We collected 94 urine samples from patients over 18 years old who were admitted at HUWC - UFC/EBSERH during the period from October 2021 to October 2022. For DNA extraction, the heat extraction method was used. To determine sensitivity, specificity, and predictive values, the results of each molecular test were compared to the urine culture reports and evaluated using chi-square contingency analysis and Fisher's exact test, additionally Cohen’s Kappa score were determined as well. A total of 94 samples were collected and tested for the detection of E. coli, the qPCR obtained a positive predicted value (PPV) of 33.33%, negative predicted value (NPV) of 100%, sensitivity of 100%, specificity of 91.11% and kappa score of 0,466. While LAMP showed 61.54% for PPV, 100.00% of NPV, 100% sensitivity, 94.19% of specificity and kappa score of 0,734. For qPCR and LAMP, we were able to perform the validation and standardization of the respective molecular tests for detection of E. coli in urine. However, for use in diagnosis, it is still necessary to carry out a more robust validation with clinical samples, thus leaving the possibilities of exploring the identification of several other bacteria of clinical importance in different body fluids.