SARS-CoV-2 intralineage variation and temporal patterns of COVID-19 risk factors in three cities of southeastern Brazil: Age, sex, and race.

The Santo André Regional Center from Adolfo Lutz Institute evaluated 91 537 samples by reverse transcription-polymerase chain reaction (RT-PCR) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from March 2020 to April 2021. The age, sex, and race of patients from three cities in southeastern Brazil, namely São Bernardo do Campo (SBC), Diadema, and Mauá were assessed in association to the rate of positive results using generalized linear models. Circulating lineages were obtained from GISAID and intralineage genetic variation was investigated employing Lasergene software. A declining number of reported cases around October to November 2020 separate two epidemic waves in the three cities. Mauá differed by the highest positive RT-PCR scores in January and February. GISAID classification of 38 SARS-CoV-2 complete genomic sequences showed the circulation of lineages P.1, B.1.1.28, P.2, B.1.1.332; P.1, P.2, B.1.1.28, B.1.1.33; and P.1, P.2 in SBC, Diadema and Mauá, respectively. Intralineage variation revealed a significant amino-acid substitution in the ORF3a encoding protein (A33S) present in four out of six (67%) P.1 Mauá isolates. As ORF3a encodes a nonselective Ca2+ permeable cation channel, supposed to interfere in airway homeostasis, specific mutations could increase its pathogenic effect resulting in a higher number of symptomatic individuals explaining why the second wave was more intense in Mauá city.

Recurrent community-acquired pneumococcal meningitis in adults with and without identified predisposing factors.

Bacterial meningitis is still a significant public health concern, with high morbidity and mortality rates. Despite this, it is still a rare event that requires the bacterial invasion of the meninges. However, some predisposing factors can trigger recurrent episodes of meningitis. This study is aimed at determining the clinical characteristics and the molecular epidemiology of episodes of recurrent community-acquired meningitis with and without predisposing factors. For this purpose, we performed a retrospective study of our laboratory database during the period of 2010 to 2020. Additionally, using molecular tools developed in our previous works, the epidemiology of the pathogens causing these episodes was analyzed using cerebrospinal fluid samples, especially in the absence of isolated strains. We observed a total of 1,779 meningitis cases and 230 were caused by Streptococcus pneumoniae. Of those, 16 were recurrent meningitis episodes (16/1,779; 0.9%) from seven patients. Pneumococcus was the main agent responsible in these recurrent episodes and only two episodes were caused by Haemophilus influenzae. The mean age of these patients was 20 years old and three had predisposing factors which could have led to contracting meningitis. The samples presented different pneumococcal serotypes. Most of them were non-vaccine-covered serotypes and antibiotic susceptible strains. Therefore, it was demonstrated how the practical employment of molecular tools, developed for research, when applied in the routine of diagnosis, can provide important information for epidemiological surveillance. Furthermore, it was shown how pneumococcus was the leading cause of recurrent community-acquired meningitis without predisposing factors, suggesting that pneumococcal vaccination may be necessary, even in those groups of individuals considered to be less susceptible.

Multiplex real-time PCR using SYBR Green: Unspecific intercalating dye to detect antimicrobial resistance genes of Streptococcus pneumoniae in cerebrospinal fluid.

Meningitis caused by Streptococcus pneumoniae is still a disease of great impact on Public health, which requires immediate diagnosis and treatment. However, the culture of clinical specimens is often negative and antibiotic susceptibility testing (AST) must be performed with isolated strains. Multiplex real-time polymerase chain reaction (qPCR) has high sensitivity and specificity, produces faster results to identify the pathogen, and it can also be an important tool to identify resistance antibiotic genes earlier than AST, especially in the absence of an isolated strain. This study developed a multiplex qPCR assay, using SYBR Green as a nonspecific dye, to detect antibiotic resistance genes to predict pneumococcal susceptibility/resistance in cerebrospinal fluid (CSF) samples from meningitis patients. From 2017 to 2020, CSF samples were cultured and analyzed by qPCR to detect the main three bacteria causing meningitis. Isolated and reference strains were applied in SYBR Green qPCR multiplex to detect pbp2b, ermB, and mef genes, and the results were compared with the AST. Pneumococcal-positive CSF samples (lytA-positive gene) without isolated strains were also tested to evaluate the antimicrobial susceptibility profile in the region from 2014 to 2020. From the received 873 CSF samples; 263 were cultivated, 149 were lytA-positive in the qPCR, and 25 produced viable isolated pneumococci strains, which were evaluated by AST. Melting temperature for each gene and the acceptance criteria were determined (pbp2b: 78.24-79.86; ermB: 80.88-82.56; mef: 74.85-76.34 ºC). A total of 48/51 strains presented a genetic profile in agreement with the AST results. Resistant strains to erythromycin and clindamycin were ermB-positive, and two were also mef-positive, indicating both resistance mechanisms were present. In the retrospective study of the genetic profile of resistance, 82 lytA-positive CSF samples plus 4 strains were applied in the SYBR Green qPCR multiplex: 51% of samples presented the wild genotype (pbp2b positive and ermB/mef negative); 15% were negative for all the three evaluated, indicating pneumococci resistant to penicillin; and 17% represented the multidrug-resistant pneumococci (pbp2b negative and ermB positive or pbp2b negative and ermB and mef positive). Therefore, SYBR Green qPCR multiplex proved to be a reliable tool to identify resistance genes in S. pneumoniae and would be less expensive than multiplex qPCR using specific probes. This could be easily introduced into the routine of diagnostic laboratories and provide a strong presumption of pneumococcal resistance, especially in the absence of isolated strains.

Fragment detection of Coleopteran and Triatomine insects in experimentally contaminated acai pulp and sugarcane juice.

INTRODUCTION: Oral transmission of acute Chagas disease is an emerging public health concern. This study aimed to detect insect fragments in experimentally contaminated food, by comparing triatomines with other insects. METHODS: Food samples were experimentally contaminated with insects, processed to recover their fragments by light filth, and analyzed by microscopy and Polymerase Chain Reaction (PCR). RESULTS: Morphological differences between coleopteran and triatomine insects were observed in microscopic images. PCR was efficient in amplifying Triatominae DNA in the experimentally contaminated food. CONCLUSIONS: This methodology could be utilized by food analysts to identify possible insect contamination in food samples.

Detection of virulence factors in coagulase-negative Staphylococcus spp. strains isolated from Emmental cheese / Detecção de fatores de virulência em cepas de Staphylococcus spp. coagulase negativos isoladas de queijo Emmental

Food prepared with products derived from animals are involved in most cases of staphylococcal poisoning; therefore, the research of Staphylococcus spp. in Emmental cheese is more applicable. The objective of this study was to identify coagulase-negative Staphylococcus spp. (CNS) in cheese using biochemical and molecular techniques to detect the presence of nine genes responsible for the production of enterotoxins. From 180 samples analyzed, 204 CNS strains were obtained and identified as being 46 (22.6%) S. saprophyticus strains, 27 (13.2%) S. hominis spp. hominis strains, 22 (10.8%) S. sciuri strains, 21 (10.3%) S. xylosus strains, 19 (9.3%) S. epidermidis strains, 19 (9.3%) S. haemolyticus strains, 17 (8.3%) S. lentus strains, 17 (8.3%) S. warneri strains, 11 (5.4%) S. equorum strains and 5 (2.5%) S. cohnni . Using the PCRm protocol, 14 (6.9%) strains with the presence of the genes on the enterotoxin E (SEE)11 (78.6%), J (SEJ) 1 (7%), C (SEC) 1 (7%) and I (SEI) 1 (7%) were detected. Based on the results, the type of package is not interfered of growth and isolated that Staphylococcus spp. in cheese. It was observed that bacteria capacity to produce coagulase cannot be understood as an indicative of enterotoxigenicity; therefore, the CNS should be considered as a target of importance in the epidemiology of staphylococcal intoxications. It can be concluded that CNS need to be included in bacterial foodborne disease research, since the genes responsible for the production of toxins were detected and none of the studied samples presented Staphylococcus spp. counting above the limits allowed by legislation.(AU)

Os alimentos preparados com produtos de origem animal são os mais envolvidos em casos de intoxicação alimentar estafilocócica; portanto a pesquisa do Staphylococcus spp. em queijos tipo Emmental é relevante. O objetivo foi isolar e identificar espécies de Staphylococcus coagulase negativas (CNS)de queijo Emmental acondicionado em vários tipos de embalagem, por meio de técnicas bacteriológicas e bioquímicas e detectar, por PCR, a presença de nove genes responsáveis pela produção de enterotoxinas. Das 180 amostras, foram isoladas 204 cepas de CNS, que foram identificadas por provas bioquímicas como: 46 (22,6%) S. saprophyticus, 27 (13,2%) S. hominis spp. hominis, 22 (10,8%) S. sciuri, 21 (10,3%) S. xylosus, 19 (9,3%) S. epidermidis , 19 (9,3%) S. haemolyticus , 17 (8,3%) S. lentus , 17 (8,3%) S. warneri , 11(5,4%) S. equorum e 5 (2,5%) S. cohnii . Na PCR multiplex, em 14 (6,9%) isolados foi detectada a presença dos genes para enterotoxina E (SEE), em 11 (78,6%) J (SEJ), em 1 (7%) C (SEC) e em 1 (7%) I (SEI). Com base nos resultados, o tipo de embalagem não interferiu na multiplicação dos Staphylococcus spp. isolados dos queijos. Neste estudo, verificou-se que a capacidade para a produção de coagulase pela bactéria não pode ser concebida como indicativa de enterotoxigenicidade, portanto devem-se considerar os CNS como objeto de importância na epidemiologia das intoxicações estafilocócicas, fazendo-se necessária a atenção com relação à pesquisa dos CNS nos alimentos, uma vez que foram detectados genes responsáveis pela produção de toxinas, e nenhuma das amostras apresentou contagem para Staphylococcus spp. acima do limite permitido pela legislação.(AU)

Fragment detection of coleopteran and triatomine insects in experimentally contaminated acai pulp and sugarcane juice

INTRODUCTION: Oral transmission of acute Chagas disease is an emerging public health concern. This study aimed to detect insect fragments in experimentally contaminated food, by comparing triatomines with other insects. METHODS: Food samples were experimentally contaminated with insects, processed to recover their fragments by light filth, and analyzed by microscopy and Polymerase Chain Reaction (PCR). RESULTS: Morphological differences between coleopteran and triatomine insects were observed in microscopic images. PCR was efficient in amplifying Triatominae DNA in the experimentally contaminated food. CONCLUSIONS: This methodology could be utilized by food analysts to identify possible insect contamination in food samples. (AU)

Indicadores microscópicos de qualidade de molhos tipo ketchup / Microscopic quality indicators of ketchup sauces

O tomate (Solanum lycopersicum) é um produto agrícola importante no mundo inteiro e também o vegetal mais consumido no Brasil. O ketchup especificamente, é um produto a base de tomate, utilizado comumente para acompanhar pratos prontos, sanduíches e saladas. Foram analisadas 30 amostras de 13 marcas diferentes, com lotes e validades aleatórios, no período de julho a outubro de 2013, adquiridas no comércio do grande ABC, para pesquisa de sujidades leves. Os resultados revelaram que 6 amostras (20%) continham pelo de roedor e 26 (86,6%) apresentaram fragmentos de insetos. Os resultados foram também analisados e discutidos de acordo com as legislações RDC n° 175/2003, Portaria n° 326/1997 e RDC n°14/2014. Conclui- se que as condições higienicossanitárias do ketchup se encontram comprometidas tendo em vista a alta porcentagem de amostras com a presença de matérias estranhas. Faz- -se necessário um monitoramento constante desse tipo de alimento a fim de oferecer à população um produto seguro e de boa qualidade.

Alimentos embalados que compõem as cestas básicas: avaliação microscópica e da rotulagem / Packaged foods composing the basic baskets: microscopic and labeling assessment

Cesta básica é um conjunto de bens, composto de gêneros alimentícios e produtos de higiene pessoal e de limpeza, suficientes para determinada família pelo período de 30 dias. No presente trabalho as condições higiênicas e da rotulagem foram analisadas em 130 produtos alimentícios embalados e componentes das cestas básicas comercializadas nas regiões de abrangência do Instituto Adolfo Lutz Central e Regionais. Foram identificados os elementos histológicos, cascas e paus, assim como matérias estranhas e filamentos micelianos. As Resoluções RDC nº 259/2002, 359 e 360/2003, da ANVISA/MS e Lei nº 10.674/2003 foram utilizadas para a avaliação da rotulagem. Nas análises histológicas, 6,1% foram insatisfatórias e 71,0% apresentaram matérias estranhas, cujos achados estão em desacordo com a Resolução RDC nº 175/2003da ANVISA/MS e Portaria nº 326/1997 da SVS/MS. Ademais, 100% estavam em desacordo com pelo menos uma das legislações utilizadas para avaliar os rótulos das embalagens. Os dados obtidos poderão subsidiar as ações das Vigilâncias Sanitárias, contribuir na melhoria dos produtos e, consequentemente, proteger a saúde da população.

A “basic basket” is a kit of commodities including food items and products for personal hygiene and cleaning,sufficient for a determined family for a period of 30 days. This study evaluated the hygienic conditions andlabeling of 130 packaged food products assembled in the “basic baskets”, which are marketed in the regionscomprised by the Central & Regional Laboratories of Adolfo Lutz Institute. Histological elements, skins andsticks, and also foreign matter and mold were found. The labeling assessment was based on Resolutions RDCnº 259/2002 and nos 359 & 360/2003 of ANVISA/MS (Sanitary Surveillance Agency/Ministry of Health/Brazil) and the Law nº 10,674/2003 recommendations. On histological analyses 6.1% were unsatisfactory,71% presented foreign matter, which did not comply with Resolution RDC nº 175/2003 of ANVISA/MSand Decree nº 326/1997 of SVS/MS; 100% failed to comply with at least one of the legislations used forevaluating the information contained on the label. These findings will provide subsidy for the regulatoryactions, contributing to improve the products quality, and consequently to protect the health of population.

Observações macro e microscópicas de matérias estranhas em alimentos, segundo denúncias do consumidor, no período de 1997 a 2001 nas regiões de Campinas e Santo André / SP / Observations macro and microscopic of strange matters in sustenances, second denunciations of the consumer, in the period from 1997 to 2001 in the regions of Campinas and Santo André / SP

Estudo realizado pelo Instituto Adolfo Lutz (IAL) - Laboratórios Regionais de Campinas e Santo André, no período de 1997 a 2001, com objetivo de avaliar a freqüência de produtos condenados por matérias estranhas através de denúncias do consumidor. Das 473 amostras estudadas de vários grupos de alimentos, 241 foram realizadas pelo IAL- Campinas e 232 pelo IAL-Santo André. As amostras foram analisadas macroscopicamente e nos casos em que esta análise não foi conclusiva, seguiu-se a metodologia descrita por Rodrigues, Atui, Correia & outros, (1999). Os grupos de alimentos condenados com maior freqüência, segundo denúncias do consumidor foram água mineral, produtos de panificação, bebidas não alcoólicas, biscoitos, leite e derivados e embutidos. As matérias estranhas mais comumente observadas e o número de amostras que foram identificadas nas análises foram: fungos (96), insetos (58), larvas de insetos (24) e fragmentos de insetos (22). A análise microscópica tem sido importante como indicador de boas normas de produção evidenciando as condições higiênicas do produto.