New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing.

BACKGROUND: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB. OBJECTIVE: To describe TB transmission dynamics and drug resistance profiles in PP using whole-genome sequencing (WGS). METHODS: This was a retrospective study of Mycobacterium tuberculosis cultivated from people incarcerated in 55 prisons between 2016 and 2019; only one isolate per prisoner was included. Information about movement from one prison to another was tracked. Clinical information was collected, and WGS was performed on isolates obtained at the time of TB diagnosis. RESULTS: Among 134 prisoners included in the study, we detected 16 clusters with a total of 58 (43%) cases of M. tuberculosis. Clusters ranged from two to seven isolates with five or fewer single nucleotide polymorphism (SNP) differences, suggesting a recent transmission. Six (4.4%) isolates were resistant to at least one anti-TB drug. Two of these clustered together and showed resistance to rifampicin, isoniazid, and fluoroquinolones, with 100% concordance between WGS and phenotypic drug-susceptibility testing. Prisoners with clustered isolates had a high amount of movement between prisons (two to eight moves) during the study period. CONCLUSIONS: WGS demonstrated the recent transmission of TB within prisons in Brazil. The high movement among prisoners seems to be related to the transmission of the same M. tuberculosis strain within the prison system. Screening for TB before and after the movement of prisoners using rapid molecular tests could play a role in reducing transmission.

New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing

ABSTRACT Background: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB. Objective: To describe TB transmission dynamics and drug resistance profiles in PP using whole-genome sequencing (WGS). Methods: This was a retrospective study of Mycobacterium tuberculosis cultivated from people incarcerated in 55 prisons between 2016 and 2019; only one isolate per prisoner was included. Information about movement from one prison to another was tracked. Clinical information was collected, and WGS was performed on isolates obtained at the time of TB diagnosis. Results: Among 134 prisoners included in the study, we detected 16 clusters with a total of 58 (43%) cases of M. tuberculosis. Clusters ranged from two to seven isolates with five or fewer single nucleotide polymorphism (SNP) differences, suggesting a recent transmission. Six (4.4%) isolates were resistant to at least one anti-TB drug. Two of these clustered together and showed resistance to rifampicin, isoniazid, and fluoroquinolones, with 100% concordance between WGS and phenotypic drug-susceptibility testing. Prisoners with clustered isolates had a high amount of movement between prisons (two to eight moves) during the study period. Conclusions: WGS demonstrated the recent transmission of TB within prisons in Brazil. The high movement among prisoners seems to be related to the transmission of the same M. tuberculosis strain within the prison system. Screening for TB before and after the movement of prisoners using rapid molecular tests could play a role in reducing transmission.

Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia.

To date, blood banks apply routine diagnosis to a specific spectrum of transfusion-transmitted viruses. Even though this measure is considered highly efficient to control their transmission, the threat imposed by emerging viruses is increasing globally, which can impact transfusion safety, especially in the light of the accelerated viral discovery by novel sequencing technologies. One of the most important groups of patients, who may indicate the presence of emerging viruses in the field of blood transfusion, is the group of individuals who receive multiple transfusions due to hereditary hemoglobinopathies. It is possible that they harbor unknown or unsuspected parenterally-transmitted viruses. In order to elucidate this, nucleic acids from 30 patients with beta-thalassemia were analyzed by Illumina next-generation sequencing and bioinformatics analysis. Three major viral families: Anelloviridae, Flaviviridae and Hepadnaviridae were identified. Among them, anelloviruses were the most representative, being detected with high number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C), Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV and HCV detection was expected due to the high seroprevalence in patients with beta thalassemia. Our results do not confirm the presence of emerging or unsuspected viruses threatening the transfusion safety at present, but can be used to actively search for viruses that threaten blood transfusion safety. We believe that the application of viral metagenomics in multiple-transfused patients is highly useful to monitor possible viral transfusion threats and for the annotation of their virome composition.

The first five-year evaluation of cystic fibrosis neonatal screening program in São Paulo State, Brazil.

The Hospital of the Ribeirão Preto Medical School, University of São Paulo is one of the three screening centers in São Paulo State, Brazil, and has included a test for cystic fibrosis (CF) since February 6, 2010, by a court order. We evaluated the first five years of this CF-newborn screening program. The original immunoreactive trypsinogen (IRT)/IRT screening protocol was adopted in Brazil. A total of 173,571 newborns were screened, 1,922 (1.1%) of whom showed IRT1 ≥ 70ng/mL. Of these, 1,795 (93.4%) collected IRT2, with elevated results (IRT2 ≥ 70ng/mL) in 102 of them (5.2%). We identified a total of 26 CF cases during this period, including three CF cases that were not detected by the CF-newborn screening. The incidence of the disease among the screened babies was 1:6,675 newborns screened. Median age at the initial evaluation was 42 days, comparable to that of neonates screened with the IRT/DNA protocol. Almost all infants with CF already exhibited some manifestations of the disease during the neonatal period. The mutation most frequently detected in the CF cases was F508del. These findings suggest the early age at the beginning of treatment at our center was due to the effort of the persons involved in the program regarding an effective active search. Considering the false negative results of CF-newborn screening and the early onset of clinical manifestations of the disease in this study, pediatricians should be aware of the diagnosis of CF even in children with negative test.

The first five-year evaluation of cystic fibrosis neonatal screening program in São Paulo State, Brazil / Uma avaliação dos primeiros cinco anos do programa de triagem neonatal da fibrose cística no Estado de São Paulo, Brasil / Una evaluación de los primeros cinco años del programa de cribado neonatal de fibrosis cística en el Estado de São Paulo, Brasil

The Hospital of the Ribeirão Preto Medical School, University of São Paulo is one of the three screening centers in São Paulo State, Brazil, and has included a test for cystic fibrosis (CF) since February 6, 2010, by a court order. We evaluated the first five years of this CF-newborn screening program. The original immunoreactive trypsinogen (IRT)/IRT screening protocol was adopted in Brazil. A total of 173,571 newborns were screened, 1,922 (1.1%) of whom showed IRT1 ≥ 70ng/mL. Of these, 1,795 (93.4%) collected IRT2, with elevated results (IRT2 ≥ 70ng/mL) in 102 of them (5.2%). We identified a total of 26 CF cases during this period, including three CF cases that were not detected by the CF-newborn screening. The incidence of the disease among the screened babies was 1:6,675 newborns screened. Median age at the initial evaluation was 42 days, comparable to that of neonates screened with the IRT/DNA protocol. Almost all infants with CF already exhibited some manifestations of the disease during the neonatal period. The mutation most frequently detected in the CF cases was F508del. These findings suggest the early age at the beginning of treatment at our center was due to the effort of the persons involved in the program regarding an effective active search. Considering the false negative results of CF-newborn screening and the early onset of clinical manifestations of the disease in this study, pediatricians should be aware of the diagnosis of CF even in children with negative test.

O Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo é um dos três centros de triagem da fibrose cística (FC) no estado de São Paulo, tendo incluído esse teste desde 6 de fevereiro de 2010, a partir de uma liminar judicial. O estudo avalia os primeiros cinco anos desse programa de triagem neonatal da FC. O Brasil adota o protocolo de triagem original, com o tripsinogênio imunorreativo (IRT)/IRT. Foram triados um total de 173.571 recém-nascidos, dos quais 1.922 (1,1%) mostraram IRT ≥ 70ng/mL. Destes, 1.795 (93,4%) tiveram amostras coletadas para IRT2, com resultados elevados (IRT2 ≥ 70ng/mL) em 102 deles (5,2%). Identificamos um total de 26 casos de FC durante esse período, inclusive 3 casos de FC que não foram detectados com a triagem neonatal. A incidência da FC foi de 1 caso em cada 6.675 recém-nascidos triados. A idade mediana na avaliação inicial foi 42 dias, comparável à idade de recém-nascidos triados com o protocolo IRT/DNA. Quase todos os lactentes com FC já exibiam algumas manifestações da doença durante o período neonatal. A mutação mais comum nos casos de FC foi a F508del. Os resultados em nosso centro indicam que a idade precoce no início do tratamento foi devido aos esforços do programa na implementação de uma busca ativa eficaz. Considerando os resultados falsos-negativos no programa de triagem neonatal para FC e o início precoce das manifestações clínicas da doença neste estudo, os pediatras devem estar cientes da possibilidade de diagnóstico de FC, mesmo em crianças com teste negativo.

El Hospital das Clínicas de la Facultad de Medicina de Ribeirão Preto, São Paulo Universidad es uno de los tres centros de cribado de fibrosis cística (FC) en el estado de São Paulo, incluyendo este test desde el 6 de febrero de 2010, debido a una medida cautelar judicial. El estudio evalúa los primeros cinco años de este programa de cribado neonatal de FC. Brasil adopta el protocolo de cribado original, con el tripsinógeno inmunorreactivo (TIR)/IRT. Se cribaron un total de 173.571 recién nacidos, de los cuales 1.922 (1,1%) mostraron IRT ≥ 70ng/mL. De estos, se obtuvieron 1.795 (93,4%) muestras recogidas para IRT2, con resultados elevados (IRT2 ≥ 70ng/mL) en 102 de ellos (5,2%). Identificamos un total de 26 casos de FC durante ese período, inclusive 3 casos de FC que no fueron detectados con el cribado neonatal. La incidencia de la FC fue de 1 caso por cada 6.675 recién-nacidos cribados. La edad media en la evaluación inicial fue 42 días, comparable a la edad de recién nacidos cribados con el protocolo IRT/DNA. Casi todos los lactantes con FC ya manifestaban algunos síntomas de la enfermedad durante el período neonatal. La mutación más común en los casos de FC era el F508del. Los resultados en nuestro centro indican que la edad precoz en el inicio del tratamiento se debía a los esfuerzos del programa en la implementación de una búsqueda activa eficaz. Considerando los resultados falsos-negativos en el programa de cribado neonatal para FC, y el inicio precoz de las manifestaciones clínicas de la enfermedad en este estudio, los pediatras deben ser conscientes de la posibilidad de diagnóstico de FC, incluso en niños con test negativo.

Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction.

The dermatophyte Trichophyton rubrum is the major fungal pathogen of skin, hair, and nails that uses keratinized substrates as the primary nutrients during infection. Few strategies are available that permit a better understanding of the molecular mechanisms involved in the interaction of T. rubrum with the host because of the limitations of models mimicking this interaction. Dual RNA-seq is a powerful tool to unravel this complex interaction since it enables simultaneous evaluation of the transcriptome of two organisms. Using this technology in an in vitro model of co-culture, this study evaluated the transcriptional profile of genes involved in fungus-host interactions in 24 h. Our data demonstrated the induction of glyoxylate cycle genes, ERG6 and TERG_00916, which encodes a carboxylic acid transporter that may improve the assimilation of nutrients and fungal survival in the host. Furthermore, genes encoding keratinolytic proteases were also induced. In human keratinocytes (HaCat) cells, the SLC11A1, RNASE7, and CSF2 genes were induced and the products of these genes are known to have antimicrobial activity. In addition, the FLG and KRT1 genes involved in the epithelial barrier integrity were inhibited. This analysis showed the modulation of important genes involved in T. rubrum⁻host interaction, which could represent potential antifungal targets for the treatment of dermatophytoses.

Polymorphisms in chronic rhinosinusitis with nasal polyps - a systematic review / Polimorfismos na rinossinusite crônica com pólipos nasais - uma revisão sistemática

Abstract Introduction: Chronic rhinosinusitis with nasal polyps is a multifactorial disease with a complex pathophysiology involving multiple genetic and environmental factors. Objective: The purpose of this work review is to focus on the importance of genetic studies in chronic rhinosinusitis with nasal polyps besides the several barriers that exists for its understanding. Methods: A systematic review on studies of association between single nucleotide polymorphisms and chronic rhinosinusitis with nasal polyps based on a PubMed/Medline and Periódicos CAPES search of all articles published between January 2005 and January 2015 was made. The search was guided on studies containing the terms polymorphisms, rhinosinusitis, and polyps. Results: Two studies found an association of MMP-9 and MMP-2 polymorphisms and chronic rhinosinusitis with nasal polyps, but not in patients with recurrent nasal polyps. Other studies found an association of nasal polyps with MMP-9 polymorphisms, but not with MMP-2 ones. There is evidence of an association of LTC4S, NOS2A, PTGDR, MET, COX-2, OSF-2, and LF polymorphisms and the risk of developing nasal polyps, especially when combined with chronic allergic rhinitis and asthma. Conclusion: Genetic studies on chronic rhinosinusitis with nasal polyps are promising and may offer insights into its pathophysiology, which is likely affected by multiple genetic factors.

Resumo Introdução: A rinossinusite crônica com pólipos nasais é uma doença multifatorial com uma fisiopatologia complexa envolvendo múltiplos fatores genéticos e ambientais. Objetivo: O objetivo deste trabalho é enfatizar a importância dos estudos genéticos na rinossinusite crônica com pólipos nasais, além das diversas barreiras existentes para sua compreensão. Método: Realizou-se uma revisão sistemática de estudos de associação entre polimorfismos de nucleotídeo único e rinossinusite crônica com pólipos nasais com base em uma busca feita nos bancos de dados PubMed/Medline e Periódicos CAPES de todos os artigos publicados entre janeiro de 2005 e janeiro de 2015. A busca foi direcionada à estudos contendo os termos polimorfismos, rinossinusite e pólipos. Resultados: Dois estudos encontraram uma associação entre os polimorfismos MMP-9 e MMP-2 e rinossinusite crônica com pólipos nasais, mas não em pacientes com pólipos nasais recorrentes. Outros estudos encontraram uma associação de pólipos nasais com polimorfismos MMP-9, mas não com MMP-2. Existem evidências de uma associação dos polimorfismos LTC4S, NOS2A, PTGDR, MET, COX-2, OSF-2 e LF e o risco de desenvolver pólipos nasais, especialmente quando combinados com rinite alérgica crônica e asma. Conclusão: Estudos genéticos sobre rinossinusite crônica com pólipos nasais são promissores e podem oferecer conhecimento sobre sua fisiopatologia, que é provavelmente afetada por múltiplos fatores genéticos.

Comparison of gene expression profile between blood cells and white adipose tissue of patients with obesity

INTRODUCTION: Gene expression analyses from peripheral blood mononuclear cells (PBMC) and white adipose tissue are conflicting. It seems that results from single tissue are not enough to explain how changes affect humans as a complex biological system. OBJECTIVE: The aim of this study was to compare, from obesity subjects, PBMC and white adipose tissue gene expression that regulates adipogenesis (perilipin 1 [PLIN1], adrenoreceptor beta 3 [ADRB3] and peroxisome proliferator-activated receptor [PPARG2]) and the energy metabolism (uncoupling protein UCP1, UCP2 and UCP3) process. METHODS: This study enrolled 35 obese patients, with a body mass index (BMI) > 40 kg/m2 (obesity group [OG]), and ten eutrophic health subjects, 18 > BMI > 24.9 kg/m2 (control group [CG]). Anthropometric and body composition data were assessed at recruitment using standardized protocols. Samples of peripheral blood and subcutaneous adipose tissue (biopsy) were collected to analyze gene expression by RT-qPCR technique. For statistical analysis, we used the Shapiro-Wilk test and Wilcoxon tests by the SPSS software version 20.0; a p < 0.05 significance level was adopted. RESULTS: There were significant differences of PLIN1, ADRB3, PPARG2 and UCP3 expression between blood against adipose tissue samples, showing that these genes are upregulated in adipose tissue. UCP2 expression was upregulated in PBMC. CONCLUSION: The PLIN1, ADRB3, PPARG2 and UCP3 genes were preferentially expressed in adipose tissue. However, UCP2 was upregulated in PBMC, suggesting that this gene may be assessed in a peripheral blood cell, which is easily accessible, safe and practical.

Polymorphisms in chronic rhinosinusitis with nasal polyps - a systematic review.

INTRODUCTION: Chronic rhinosinusitis with nasal polyps is a multifactorial disease with a complex pathophysiology involving multiple genetic and environmental factors. OBJECTIVE: The purpose of this work review is to focus on the importance of genetic studies in chronic rhinosinusitis with nasal polyps besides the several barriers that exists for its understanding. METHODS: A systematic review on studies of association between single nucleotide polymorphisms and chronic rhinosinusitis with nasal polyps based on a PubMed/Medline and Periódicos CAPES search of all articles published between January 2005 and January 2015 was made. The search was guided on studies containing the terms polymorphisms, rhinosinusitis, and polyps. RESULTS: Two studies found an association of MMP-9 and MMP-2 polymorphisms and chronic rhinosinusitis with nasal polyps, but not in patients with recurrent nasal polyps. Other studies found an association of nasal polyps with MMP-9 polymorphisms, but not with MMP-2 ones. There is evidence of an association of LTC4S, NOS2A, PTGDR, MET, COX-2, OSF-2, and LF polymorphisms and the risk of developing nasal polyps, especially when combined with chronic allergic rhinitis and asthma. CONCLUSION: Genetic studies on chronic rhinosinusitis with nasal polyps are promising and may offer insights into its pathophysiology, which is likely affected by multiple genetic factors.

DNA methylation analysis of the tumor suppressor gene CDKN2B in Brazilian leukemia patients

The aim of this work was to evaluate the methylation profile of the p15 (CDKN2B) gene in Brazilian patients with leukemia and to correlate the CDKN2B gene expression with the percentage of methylated CpG dinucleotides in its promoter region. Thirty-one samples from six patients with acute lymphocytic leukemia (ALL), four with chronic myeloid leukemia (CML), and 21 with acute myeloid leukemia (AML) were evaluated by MSP (Methylation-Specific PCR). The CDKN2B gene was found to be methylated in four (67 percent) of the six ALL samples and in 16 (76 percent) of the 21 AML samples, but in none of the four CML samples analyzed. We observed a correlation between the CDKN2B mRNA expression (RT-PCR) and the percentage of methylated CpG dinucleotides. Therefore, this study in Brazilian patients confirms that the CDKN2B gene is methylated in the majority of leukemia patients.

Avaliação eletroforética, cromatográfica e molecular da Hb D Los Angeles no Brasil / Electrophoretical, chromatographic and molecular valuations of Hb D Los Angeles in Brazil

A variante de hemoglobina (Hb) D mais comum, Hb D Los Angeles ou D Punjab, é originada de uma transversão GAA->CAA no códon 121 da globina beta; essa mutação resulta na substituição do ácido glutâmico por glutamina na proteína. É a terceira variante de hemoglobina mais freqüente da população brasileira. Como as hemoglobinas D apresentam migração similar à hemoglobina S em pH alcalino, e com a hemoglobina A em pH ácido, são necessários vários testes para o correto diagnóstico. No presente estudo objetivou-se relacionar os diferentes procedimentos laboratoriais de rotina diagnóstica, além da análise molecular, para estabelecer o perfil de Hb D Los Angeles no Brasil. Foram analisados 47 indivíduos da população brasileira com provável Hb D Los Angeles, por vários procedimentos eletroforéticos em diferentes condições de pH, além da cromatografia líquida de alta pressão, e testes moleculares para confirmação da mutação. Foram encontrados quatro tipos de combinações de hemoglobinas: 42 indivíduos portadores de hemoglobina AD Los Angeles, dois indivíduos com doença de Hb S/D Los Angeles, dois indivíduos com Hb D Los Angeles e talassemia beta e um indivíduo com Hb D Los Angeles e Hb Lepore. Os indivíduos heterozigotos para D Los Angeles são assintomáticos, entretanto, em associação com outras variantes e talassemias podem apresentar graus variáveis de manifestações clínicas. Os resultados apresentados enfatizaram a necessidade da associação de várias metodologias para a identificação da Hb D Los Angeles, além de auxiliar na elucidação de combinações raras

The most common Hb D variant, the Hb D-Los Angeles,also know as Hb D-Punjab, originates through aGAA¨CAA change at the 121 codon of the ƒÀ globingene; this mutation results in the replacement ofglutamic acid for glutamine in the protein. It is thethird most common hemoglobin variant in theBrazilian population. This variant has electrophoreticmigration in alkaline pHs similar to Hb S and identicalmigration to hemoglobin A in acidic pHs. Thus, severaltechniques are necessary for its correct diagnosis. Thepurpose of this work was to relate the differentlaboratorial techniques and molecular analyses to determinethe profile of Hb D Los Angeles in Brazil. Fortysevenindividuals from the Brazilian population withHb D Los Angeles were studied. Multiple electrophoresisin several experimental conditions were carried out,in addition to high performance liquid chromatography (HPLC) and molecular analysis to confirm thismutation. Four compound heterozygotes were observed:42 individuals heterozygous Hb AD Los Angeles, twowith Hb S/D Los Angeles disease, two individuals withHb D Los Angeles and beta-thalassemia and one withHb D Los Angeles and Hb Lepore. The heterozygoushemoglobin D Los Angeles is asymptomatic, even thoughits association with other variants and thalassemias maypresent varying degrees of clinical manifestations. Theresults presented emphasize the significance of theassociation of different laboratorial techniques for DLos Angeles diagnosis, and help to elucidate rarecombinations.

Diagnóstico laboratorial de hemoglobinas semelhantes à HbS / Laboratorial diagnosis for hemoglobin like HbS

A hemoglobina S (HbS) está presente na populaçäo brasileira com prevalência variável, dependente dos grupos raciais formadores de cada regiäo. A migraçäo eletroforética em pH alcalino apresenta similaridade com outras hemoglobinas, e estudos complementares para sua correta caracterizaçäo säo necessários. No presente estudo objetivamos traçar um fluxograma com as metodologias disponíveis para a caracterizaçäo da hemoglobina S e das hemoglobinas que apresentam migraçäo semelhante em pH alcalino. No período de janeiro a junho de 2000, analisamos amostras de sangue com suspeita de hemoglobina S encaminhadas ao Laboratório de Hemoglobinas da Unesp. Caracterizamos diferentes mutantes e formas interativas com hemoglobina S, por procedimentos eletroforéticos, em variados pH, análises citológicas e testes bioquímicos específicos. Os procedimentos de análise aplicados resultaram em orientaçäo fornecida aos laboratórios de rotina sobre como proceder no diagnóstico laboratorial destas alteraçöes de hemoglobina. Desta forma contribuímos para um melhor conhecimento sobre a variabilidade genética das hemoglobinas em nossa populaçäo, auxiliando no acompanhamento clínico e no aconselhamento genético das hemoglobinopatias com fisiopatologia relacionada à alteraçäo

Hemoglobin J Rovigo (*53 ALA ==> ASP) is not associated with an *-globin gene deletion

Uma paciente de descendência italiana exibia uma hemoglobina anormal com migraçäo eletroforética rápida correspondendo a 30% do total de hemoglobina. A análise cromatográfica mostrou tratar-se de alteraçäo das cadeias *; pela digestäo trípica seguida de análise por HPLC foi identificada como Hb J Rovigo (* 53 Ala ==> Asp). A análise do DNA da paciente após a digestäo com enzima BamHI produziu um único fragmento de 14 kb. Esses resultados demonstram que a mutaçäo da Hb J Rovigo näo está associada à *-talassemia, ou seja, ocorre em um cromossomo 16 onde está presente um par de genes *