Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil.

In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.

Effect on Antimicrobial Resistance of a Policy Restricting Over-the-Counter Antimicrobial Sales in a Large Metropolitan Area, São Paulo, Brazil.

Although restricting over-the-counter (OTC) antimicrobial drug sales is recommended globally, no data track its effect on antimicrobial resistance (AMR) in bacteria. We evaluated the effect of a national policy restricting OTC antimicrobial sales, put in place in November 2010, on AMR in a metropolitan region of São Paulo, Brazil. We reviewed associations between antimicrobial sales from private pharmacies and AMR in 404,558 Escherichia coli and 5,797 Streptococcus pneumoniae isolates using a dynamic regression model based on a Bayesian approach. After policy implementation, a substantial drop in AMR in both bacterial species followed decreased amoxicillin and trimethoprim/sulfamethoxazole sales. Conversely, increased ciprofloxacin sales were associated with increased ciprofloxacin resistance, and extended spectrum ß-lactamases-positive E. coli isolates and azithromycin sales increases after 2013 were associated with increased erythromycin resistance in S. pneumoniae isolates. These findings suggest that restricting OTC antimicrobial sales may influence patterns of AMR, but multifaceted approaches are needed to avoid unintended consequences.

Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020.

In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.

Clinical Applications of Point-of-Care Testing in Different Conditions.

BACKGROUND: The use of point-of-care testing (POCT) in different clinical applications is justified by the fact that the time to release the result is shortened, allowing the physician to define the diagnosis and most appropriate therapy in a shorter time. However, the negative aspects must also be highlighted and studied so that we can move forward with the use of these devices. These negative aspects include greater analytical imprecision compared to laboratory automation, the variability between different equipment from different manufacturers, the risk of inappropriate use, a low level of global regulation, higher costs compared with laboratory testing and cost ineffectiveness in terms of health care. Methods and. RESULTS: This review presents some clinical applications of POCT in different scenarios, such as for diabetes mellitus, infectious diseases, pediatrics, and chronic kidney disease, among others. CONCLUSIONS: We hope to see a global consensus on an acceptable quality standard for performing POCT that is adaptable, practical, and cost effective in primary care settings, ensuring patient safety, and minimizing the risk of harm.

Point-of-Care Testing: General Aspects.

Point-of-Care Testing (POCT) has been highlighted in the health care sector in recent decades. On the other hand, due to its low demand, POCT is at a disadvantage compared to conventional equipment, since its cost is inversely proportional to the volume of use. In addition, for the implementation of POCT to succeed, it is essential to rely on the work of a multidisciplinary team. The awareness of health professionals of the importance of each step is perhaps the critical success factor. The trend towards the continuous advancement of the use of POCT and the great potential of its contributions reinforce the need to implement quality management tools, including performance indicators, to ensure their results. This review presents some advantages and disadvantages concerning POCT and the real need to use it. A worldwide call for the availability of easy-to-use health technologies that are increasingly closer to the final user is one of the main reasons for this focus.

QuantiFERON-CMV as a Predictor of CMV Events During Preemptive Therapy in CMV-seropositive Kidney Transplant Recipients.

BACKGROUND: Prevention of cytomegalovirus (CMV) infection after kidney transplantation is costly and burdensome. METHODS: Given its promising utility in risk stratification, we evaluated the use of QuantiFERON-CMV (QFCMV) and additional clinical variables in this prospective cohort study to predict the first clinically significant CMV infection (CS-CMV, ranging from asymptomatic viremia requiring treatment to CMV disease) in the first posttransplant year. A cost-effectiveness analysis for guided prevention was done. RESULTS: One hundred adult kidney transplant recipients, CMV IgG + , were given basiliximab induction and maintained on steroid/mycophenolate/tacrolimus with weekly CMV monitoring. Thirty-nine patients developed CS-CMV infection (viral syndrome, n = 1; end-organ disease, n = 9; and asymptomatic viremia, n = 29). A nonreactive or indeterminate QFCMV result using the standard threshold around day 30 (but not before transplant) was associated with CS-CMV rates of 50% and 75%, respectively. A higher QFCMV threshold for reactivity (>1.0 IU interferon-γ/mL) outperformed the manufacturer's standard (>0.2 IU interferon-γ/mL) in predicting protection but still allowed a 16% incidence of CS-CMV. The combination of recipient age and type of donor, along with posttransplant QFCMV resulted in a prediction model that increased the negative predictive value from 84% (QFCMV alone) to 93%. QFCMV-guided preemptive therapy was of lower cost than preemptive therapy alone ( P < 0.001, probabilistic sensitivity analysis) and was cost-effective (incremental net monetary benefit of 210 USD) assuming willingness-to-pay of 2000 USD to avoid 1 CMV disease. CONCLUSIONS: Guided CMV prevention by the prediction model with QFCMV is cost-effective and would spare from CMV surveillance in 42% of patients with low risk for CS-CMV.

Chromosomal microarray analyses from 5778 patients with neurodevelopmental disorders and congenital anomalies in Brazil.

Chromosomal microarray analysis (CMA) has been recommended and practiced routinely since 2010 both in the USA and Europe as the first-tier cytogenetic test for patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. However, in Brazil, the use of CMA is still limited, due to its high cost and complexity in integrating the results from both the private and public health systems. Although Brazil has one of the world's largest single-payer public healthcare systems, nearly all patients referred for CMA come from the private sector, resulting in only a small number of CMA studies in Brazilian cohorts. To date, this study is by far the largest Brazilian cohort (n = 5788) studied by CMA and is derived from a joint collaboration formed by the University of São Paulo and three private genetic diagnostic centers to investigate the genetic bases of neurodevelopmental disorders and congenital abnormalities. We identified 2,279 clinically relevant CNVs in 1886 patients, not including the 26 cases of UPD found. Among detected CNVs, the corresponding frequency of each category was 55.6% Pathogenic, 4.4% Likely Pathogenic and 40% VUS. The diagnostic yield, by taking into account Pathogenic, Likely Pathogenic and UPDs, was 19.7%. Since the rational for the classification is mostly based on Mendelian or highly penetrant variants, it was not surprising that a second event was detected in 26% of those cases of predisposition syndromes. Although it is common practice to investigate the inheritance of VUS in most laboratories around the world to determine the inheritance of the variant, our results indicate an extremely low cost-benefit of this approach, and strongly suggest that in cases of a limited budget, investigation of the parents of VUS carriers using CMA should not be prioritized.

Dynamics of SARS-CoV-2 Variants of Concern in Brazil, Early 2021.

Brazil is the country with the second-largest number of deaths due to the coronavirus disease-2019 (COVID-19). Two variants of concern (VOCs), Alpha (B.1.1.7) and Gamma (P.1), were first detected in December 2020. While Alpha expanded within an expected rate in January and February 2021, its prevalence among new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases started to decrease in March, which coincided with the explosion of Gamma variant incidence all over the country, being responsible for more than 95% of the new cases over the following months. A significantly higher viral load [i.e., mean cycle threshold (Ct) values] for Gamma in comparison to non-VOC samples was verified by the analysis of a large data set of routine reverse transcription-PCR (RT-PCR) exams. Moreover, the rate of reinfections greatly increased from March 2021 onward, reinforcing the enhanced ability of Gamma to escape the immune response. It is difficult to predict the outcomes of competition between variants since local factors like frequency of introduction and vaccine coverage play a key role. Genomic surveillance is of uttermost importance for the mitigation of the pandemic.

Conceitos de automação na medicina laboratorial: revisão de literatura / Concepts in laboratory medicine automation: literature review

Nas últimas décadas, a introdução da automação na medicina laboratorial foi destacada como a espinha dorsal na busca de eficiência e viabilidade das empresas atuantes nesse setor e expandiu-se em todas as fases dos processos no laboratório clínico: pré-analítica, analítica e pós-analítica. A implementação de um processo de automação laboratorial deve levar em consideração o posicionamento estratégico da empresa e sua forma de atuação. Diferentes modelos de processos automatizados funcionam para diferentes negócios, definidos pelo mix de exames, volume de processamento, atributos estratégicos necessários, capacidade de investimento, entre outros. Este artigo tem como principal objetivo apresentar uma breve revisão dos processos automatizados disponíveis em medicina laboratorial.

In the last decades, the introduction of automation in laboratory medicine has played a major role in the search for efficiency and viability promoted by enterprises from this sector. Additionally, it has been expanded to all phases and processes within clinical laboratories: pre-analytical, analytical and post-analytical. Automation program implementation must take into account the company's strategic planning and business approach. Different automated processes cater for different business platforms, which are defined by test mix, workflow volume, required strategic characteristics, investment capacity, among others. This article aims at briefly reviewing the automation processes available in laboratory medicine.

Tendências em medicina laboratorial / Trends in laboratory medicine

A patologia clínica/medicina laboratorial é uma especialidade direcionada à realização de exames complementares no auxílio ao diagnóstico, com impacto nos diferentes estágios da cadeia de saúde: prevenção, diagnóstico, prognóstico e acompanhamento terapêutico. Diversos elementos apontam para maior utilização da medicina diagnóstica no futuro. Para discutirmos as principais tendências na medicina laboratorial, descrevemos os fatores que colaboram e são fundamentais para o crescimento desse mercado denominados, neste estudo, drivers de crescimento. As principais tendências que terão forte impacto na medicina laboratorial, e que serão descritas neste artigo, são: ferramentas de gestão, inserção de novos testes no mercado e rol de procedimentos, qualidade dos serviços em medicina diagnóstica, modelos de operação, automação, consolidação e integração, tecnologia da informação, medicina personalizada e genética. Sabemos que a medicina diagnóstica demonstra sua importância ao participar de 70 por cento das decisões clínicas, absorvendo uma pequena parte dos custos em saúde (cerca de 10 por cento). Todas as tendências analisadas neste trabalho apontam para um crescimento na utilização dos exames laboratoriais e também para sua importância na cadeia de saúde. Esse novo posicionamento, somado às novas expectativas de alta resolubilidade, pressiona o mercado e as companhias que o compõem a buscar mudanças e novas estratégias de atuação.

Clinical pathology/laboratory medicine, a specialty focused on performing complementary tests to aid diagnosis, has impact upon several stages of health care: prevention, diagnosis, prognosis, and therapeutic management. There are several factors that will foster the use of laboratory medicine in the future. In order to discuss the main trends in laboratory medicine, this article describes the major factors that have promoted growth in this market, which herein are referred to as growth drivers. The major trends that will cause substantial impact on laboratory medicine are: management tools, inclusion of new tests and procedures, service quality, operational models, automation, consolidation and integration, information technology, personalized and genetic medicine. Laboratory medicine occupies a pivotal role in 70 percent of all clinical decisions with minimal healthcare costs of approximately 10 percent. All trends discussed herein sustain an increase in the use of laboratory tests as well as its importance in health care. Both this new model and the expectation of optimal solutions have led the market to search for changes and new management strategies.

Fatores competitivos de produção em medicina diagnóstica: da área técnica ao mercado: [revisão] / Production strategic factors in diagnostic medicine: from technical floor to the market: [review]

A medicina diagnóstica é, hoje, um conglomerado de especialidades direcionadas à realização de exames complementares no auxílio ao diagnóstico. A maior competitividade do mercado fez com que os gestores realizassem os denominados trade offs entre diferentes fatores estratégicos de produção - qualidade, confiabilidade, flexibilidade, velocidade e custo -, com o objetivo de definir o posicionamento ante a contribuição da área de produção para a organização. A determinação dos fatores escolhidos, diante das expectativas dos clientes e de um benchmarking com a concorrência, analisados de forma sistemática, define o posicionamento estratégico da organização. Para sedimentar os conceitos defendidos neste artigo, uma simulação de um caso de definição da estratégia da área de produção é apresentada.

Diagnostic Medicine is currently a pool of medical specialties oriented to conduct complementary tests for clinical diagnostics. The higher market competitiveness has led management teams to make trade offs among strategic factors such as quality, reliability, flexibility, velocity and costs with the aim to define the contribution of the production area to the company. The determination of these factors based on clients' expectations, benchmarking and subject to systematical analysis define the company strategy. The simulation of a production area strategy planning is presented to demonstrate the concepts discussed in this article.