Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning.

MOTIVATION: The genome-wide discovery of microRNAs (miRNAs) involves identifying sequences having the highest chance of being a novel miRNA precursor (pre-miRNA), within all the possible sequences in a complete genome. The known pre-miRNAs are usually just a few in comparison to the millions of candidates that have to be analyzed. This is of particular interest in non-model species and recently sequenced genomes, where the challenge is to find potential pre-miRNAs only from the sequenced genome. The task is unfeasible without the help of computational methods, such as deep learning. However, it is still very difficult to find an accurate predictor, with a low false positive rate in this genome-wide context. Although there are many available tools, these have not been tested in realistic conditions, with sequences from whole genomes and the high class imbalance inherent to such data. RESULTS: In this work, we review six recent methods for tackling this problem with machine learning. We compare the models in five genome-wide datasets: Arabidopsis thaliana, Caenorhabditis elegans, Anopheles gambiae, Drosophila melanogaster, Homo sapiens. The models have been designed for the pre-miRNAs prediction task, where there is a class of interest that is significantly underrepresented (the known pre-miRNAs) with respect to a very large number of unlabeled samples. It was found that for the smaller genomes and smaller imbalances, all methods perform in a similar way. However, for larger datasets such as the H. sapiens genome, it was found that deep learning approaches using raw information from the sequences reached the best scores, achieving low numbers of false positives. AVAILABILITY: The source code to reproduce these results is in: http://sourceforge.net/projects/sourcesinc/files/gwmirna Additionally, the datasets are freely available in: https://sourceforge.net/projects/sourcesinc/files/mirdata.

Novel SARS-CoV-2 encoded small RNAs in the passage to humans.

MOTIVATION: The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease 2019. This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. RESULTS: We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprograming of the new host upon infection. AVAILABILITY AND IMPLEMENTATION: https://github.com/sinc-lab/sarscov2-mirna-discovery. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Estudio multicéntrico de disfunción vaginal de la Red Nacional de Laboratorios BACOVA de la República Argentina: prevalencia, influencia de factores seleccionados, evaluación clínica y distribución de casos por región / Multicenter study on vaginal dysfunction of the National Network of BACOVA Laboratories in Argentina: prevalence, influence of selected factors, clinical evaluation and case distribution by region / Estudo multicêntrico de disfunção vaginal da Rede Nacional de Laboratórios BACOVA da República Argentina: prevalência, influência de fatores selecionados, avaliação clínica e distribuição dos casos por região

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Abstract The aims of this study were to update the prevalence of vaginal dysfunction (VD) in non-pregnant women of childbearing age, pregnant women and menopausal women, to analyse microbiological aspects, to evaluate the influence of parity and contraception in the vaginal microenvironment, to analyse case studies, and to compare the prevalence in the five regions of Argentina: Northeast, Northwest, Centre, Cuyo and South. Eight thousand three hundred twenty-four (8324) vaginal content samples of patients from 39 institutions, examined between May 2019 and June 2020, were prospectively and consecutively studied. The samples were analysed applying the standardized BAVACO-VIR methodology (study of the balance of vaginal content and genital inflammatory response). Of the 8324 samples, 5947 (71.5%) corresponded to women of childbearing age; 1627 (19.5%) to pregnant women and 750 (9.0%) to menopausal women. The most frequent basic vaginal state (BVS) in the three groups was BVS I with normal microbiota, accounting for 33.5% of the entire studied population. Moreover, 66.5% of vaginal dysfunction states were detected. In the pregnant women and menopausal women group there was a significant increase in the frequency of normal BVS I, in contrast with the group of women of childbearing age, where a significant increase of vaginosis and vaginitis was observed. In asymptomatic women, a predominance of BVS I was detected in the three groups. In symptomatic women, there was a predominance of BVS II and V in pregnant women, of BVS II, IV and V in women of childbearing age, and of BVS III and V in menopausal women. Asymptomatic VD was detected in 56.6% of pregnant women, 62.8% of women of childbearing age and 50.9% of menopausal women. A significantly positive association was detected between the presence of yeasts and BVS II and V and the presence of trichomonas and BVS V. The multiparity history variable showed a statistically significant positive association with BVS V and a negative association with BVS I. With regard to contraception, in women who used hormonal contraceptives it was observed that oral contraceptives increased the frequency of BVS I and II and decreased the frequency of BVS III, IV and V of VD; in those who used an intradermal device, there was a decrease in the frequency of BVS I, II and III and an increase in the frequency of BVS IV and V, whereas in women using injectable contraceptives, there was no association. The intrauterine device decreased the frequency of BVS I and II and increased the frequency of BVS V; the condom increased the frequency of BVS IV and the rhythm method decreased the frequency of BVS II. In BVS I, a decrease in the frequency of signs and symptoms was detected. The prevalence of VD in some regions accounted for values over 80%, a higher figure than that described at the national and international levels, which reflects the poor and insufficient action in Sexual and Reproductive Health. The high percentage of asymptomatic women with VD highlights the importance of studying the vaginal content, even in the absence of symptoms. A history of multiparity and contraception showed a link with vaginal function, reflecting the importance of considering this fact in a gynecological evaluation. Although the relationship of BVS with signs and symptoms does not constitute a diagnostic tool, it contributes to the understanding of pathogenic mechanisms.

Resumo Os objetivos deste estudo foram: atualizar a prevalência de disfunção vaginal (DV) em mulheres não grávidas em idade fértil (MEF), mulheres grávidas (EMB) e mulheres menopausadas (MPN), analisar aspectos microbiológicos, avaliar a influência da paridade e contracepção no microambiente vaginal, analisar quadros clínicos e comparar as prevalências das 5 regiões do nosso país: Nordeste, Noroeste, Centro, Cuyo e Sur. 8324 conteúdos vaginais de pacientes de 39 instituições, que compareceram entre maio de 2019 e junho de 2020, foram estudados prospectiva e facilitadoconsecutivamente. As amostras foram analisadas aplicando-se a metodologia padronizada BACOVA-ERIGE (estudo do equilíbrio do conteúdo vaginal e resposta inflamatória genital). Das 8324 amostras de conteúdo vaginal, 5947 (71,5%) corresponderam às MEF; 1627 (19,5%) às EMB e 750 (9,0%) às MNP. O estado vaginal básico (EVB) mais frequente nos três grupos foi EVB I de microbiota normal e representou 33,5% de toda a população global. Foram detectados 66,5% dos estados de disfunção vaginal. No grupo EMB e MNP, um aumento significativo na frequência de EVB I normal foi registrado, em contraste com o grupo MEF, onde foi reconhecido um aumento significativo de EVB de vaginose e vaginite. Em mulheres assintomáticas, foi detectado predomínio de EVB I nos três grupos. Em mulheres sintomáticas foi detetado: nas EMB, predomínio de EVB II e V; nas MEF, predominância de EVB II, IV e V, e nas MNP, predominância de EVB III e V. 56,6% das EMB, 62,8% das MEF e 50,9% das MNP apresentaram DV na ausência de sintomas. Foi detectada associação significativamente positiva entre a presença de leveduras e EVB II e V e a presença de tricomonas e EVB V. A variável antecedente de multiparidade apresentou associação positiva estatisticamente significativa com EVB V e associação negativa com EVB I. Em relação à contracepção, observou-se em mulheres que usavam anticoncepcionais hormonais, que os anticoncepcionais orais aumentaram a frequência de EVB I e II e diminuíram a frequência de EVB III, IV e V de DV; Em mulheres com dispositivo intradérmico, foi observada uma diminuição na frequência de EVB I, II e III e um aumento na frequência de EVB IV e V, e finalmente em mulheres com anticoncepcionais injetáveis, nenhuma associação foi demonstrada. O dispositivo intrauterino diminuiu a frequência de EVB I e II e aumentou a frequência de EVB V; o preservativo aumentou a frequência de EVB IV e o método do ritmo diminuiu a frequência de EVB II. Na EVB I, foi detectada diminuição da frequência de sinais e sintomas. A prevalência de DV em algumas regiões ultrapassou valores de 80%, valor superior ao descrito a nível nacional e internacional, o que reflete a atuação precária e insuficiente em Saúde Sexual e Reprodutiva. O alto percentual de mulheres assintomáticas com DV demonstra a importância da realização do estudo do conteúdo vaginal, mesmo na ausência de sintomas. A história de multiparidade e contracepção mostrou ligação com a função vaginal, refletindo a importância da sua consideração na avaliação ginecológica. Embora a relação da EVB com os sinais e sintomas não constitua uma ferramenta diagnóstica, ela contribui para o entendimento dos mecanismos patogênicos.

Deep Neural Architectures for Highly Imbalanced Data in Bioinformatics.

In the postgenome era, many problems in bioinformatics have arisen due to the generation of large amounts of imbalanced data. In particular, the computational classification of precursor microRNA (pre-miRNA) involves a high imbalance in the classes. For this task, a classifier is trained to identify RNA sequences having the highest chance of being miRNA precursors. The big issue is that well-known pre-miRNAs are usually just a few in comparison to the hundreds of thousands of candidate sequences in a genome, which results in highly imbalanced data. This imbalance has a strong influence on most standard classifiers and, if not properly addressed, the classifier is not able to work properly in a real-life scenario. This work provides a comparative assessment of recent deep neural architectures for dealing with the large imbalanced data issue in the classification of pre-miRNAs. We present and analyze recent architectures in a benchmark framework with genomes of animals and plants, with increasing imbalance ratios up to 1:2000. We also propose a new graphical way for comparing classifiers performance in the context of high-class imbalance. The comparative results obtained show that, at a very high imbalance, deep belief neural networks can provide the best performance.

Alternative use of miRNA-biogenesis co-factors in plants at low temperatures.

Plants use molecular mechanisms to sense temperatures, trigger quick adaptive responses and thereby cope with environmental changes. MicroRNAs (miRNAs) are key regulators of plant development under such conditions. The catalytic action of DICER LIKE 1 (DCL1), in conjunction with HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE), produces miRNAs from double-stranded RNAs. As plants lack a stable internal temperature to which enzymatic reactions could be optimized during evolution, reactions such as miRNA processing have to be adjusted to fluctuating environmental temperatures. Here, we report that with decreasing ambient temperature, the plant miRNA biogenesis machinery becomes more robust, producing miRNAs even in the absence of the key DCL1 co-factors HYL1 and SE. This reduces the morphological and reproductive defects of se and hyl1 mutants, restoring seed production. Using small RNA-sequencing and bioinformatics analyses, we have identified specific miRNAs that become HYL1/SE independent for their production in response to temperature decrease. We found that the secondary structure of primary miRNAs is key for this temperature recovery. This finding may have evolutionary implications as a potential adaptation-driving mechanism to a changing climate.

Identification and expression profiling of microRNAs in Hymenolepis.

Tapeworms (cestodes) of the genus Hymenolepis are the causative agents of hymenolepiasis, a neglected zoonotic disease. Hymenolepis nana is the most prevalent human tapeworm, especially affecting children. The genomes of Hymenolepis microstoma and H. nana have been recently sequenced and assembled. MicroRNAs (miRNAs), a class of small non-coding RNAs, are principle regulators of gene expression at the post-transcriptional level and are involved in many different biological processes. In previous work, we experimentally identified miRNA genes in the cestodes Echinococcus, Taenia and Mesocestoides. However, current knowledge about miRNAs in Hymenolepis is limited. In this work we described for the first known time the expression profile of the miRNA complement in H. microstoma, and discovered miRNAs in H. nana. We found a reduced complement of 37 evolutionarily conserved miRNAs, putatively reflecting their low morphological complexity and parasitic lifestyle. We found high expression of a few miRNAs in the larval stage of H. microstoma that are conserved in other cestodes, suggesting that these miRNAs may have important roles in development, survival and for host-parasite interplay. We performed a comparative analysis of the identified miRNAs across the Cestoda and showed that most of the miRNAs in Hymenolepis are located in intergenic regions, implying that they are independently transcribed. We found a Hymenolepis-specific cluster composed of three members of the mir-36 family. Also, we found that one of the neighboring genes of mir-10 was a Hox gene as in most bilaterial species. This study provides a valuable resource for further experimental research in cestode biology that might lead to improved detection and control of these neglected parasites. The comprehensive identification and expression analysis of Hymenolepis miRNAs can help to identify novel biomarkers for diagnosis and/or novel therapeutic targets for the control of hymenolepiasis.

Predicting novel microRNA: a comprehensive comparison of machine learning approaches.

MOTIVATION: The importance of microRNAs (miRNAs) is widely recognized in the community nowadays because these short segments of RNA can play several roles in almost all biological processes. The computational prediction of novel miRNAs involves training a classifier for identifying sequences having the highest chance of being precursors of miRNAs (pre-miRNAs). The big issue with this task is that well-known pre-miRNAs are usually few in comparison with the hundreds of thousands of candidate sequences in a genome, which results in high class imbalance. This imbalance has a strong influence on most standard classifiers, and if not properly addressed in the model and the experiments, not only performance reported can be completely unrealistic but also the classifier will not be able to work properly for pre-miRNA prediction. Besides, another important issue is that for most of the machine learning (ML) approaches already used (supervised methods), it is necessary to have both positive and negative examples. The selection of positive examples is straightforward (well-known pre-miRNAs). However, it is difficult to build a representative set of negative examples because they should be sequences with hairpin structure that do not contain a pre-miRNA. RESULTS: This review provides a comprehensive study and comparative assessment of methods from these two ML approaches for dealing with the prediction of novel pre-miRNAs: supervised and unsupervised training. We present and analyze the ML proposals that have appeared during the past 10 years in literature. They have been compared in several prediction tasks involving two model genomes and increasing imbalance levels. This work provides a review of existing ML approaches for pre-miRNA prediction and fair comparisons of the classifiers with same features and data sets, instead of just a revision of published software tools. The results and the discussion can help the community to select the most adequate bioinformatics approach according to the prediction task at hand. The comparative results obtained suggest that from low to mid-imbalance levels between classes, supervised methods can be the best. However, at very high imbalance levels, closer to real case scenarios, models including unsupervised and deep learning can provide better performance.

Computational Prediction of Novel miRNAs from Genome-Wide Data.

The computational prediction of novel microRNAs (miRNAs) within a full genome involves identifying sequences having the highest chance of being bona fide miRNA precursors (pre-miRNAs). These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are usually only a few in comparison to the hundreds of thousands of potential candidates to miRNA that have to be analyzed. Although the selection of positive labeled examples is straightforward, it is very difficult to build a set of negative examples in order to obtain a good set of training samples for a supervised method. In this chapter we describe an approach to this problem, based on the unsupervised clustering of unlabeled sequences from genome-wide data, and the well-known miRNA precursors for the organism under study. Therefore, the protocol developed allows for quick identification of the best candidates to miRNA as those sequences clustered together with known precursors.

High Class-Imbalance in pre-miRNA Prediction: A Novel Approach Based on deepSOM.

The computational prediction of novel microRNA within a full genome involves identifying sequences having the highest chance of being a miRNA precursor (pre-miRNA). These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are usually only a few in comparison to the hundreds of thousands of potential candidates to miRNA that have to be analyzed, which makes this task a high class-imbalance classification problem. The classical way of approaching it has been training a binary classifier in a supervised manner, using well-known pre-miRNAs as positive class and artificially defining the negative class. However, although the selection of positive labeled examples is straightforward, it is very difficult to build a set of negative examples in order to obtain a good set of training samples for a supervised method. In this work, we propose a novel and effective way of approaching this problem using machine learning, without the definition of negative examples. The proposal is based on clustering unlabeled sequences of a genome together with well-known miRNA precursors for the organism under study, which allows for the quick identification of the best candidates to miRNA as those sequences clustered with known precursors. Furthermore, we propose a deep model to overcome the problem of having very few positive class labels. They are always maintained in the deep levels as positive class while less likely pre-miRNA sequences are filtered level after level. Our approach has been compared with other methods for pre-miRNAs prediction in several species, showing effective predictivity of novel miRNAs. Additionally, we will show that our approach has a lower training time and allows for a better graphical navegability and interpretation of the results. A web-demo interface to try deepSOM is available at http://fich.unl.edu.ar/sinc/web-demo/deepsom/.

miRNAfe: A comprehensive tool for feature extraction in microRNA prediction.

miRNAfe is a comprehensive tool to extract features from RNA sequences. It is freely available as a web service, allowing a single access point to almost all state-of-the-art feature extraction methods used today in a variety of works from different authors. It has a very simple user interface, where the user only needs to load a file containing the input sequences and select the features to extract. As a result, the user obtains a text file with the features extracted, which can be used to analyze the sequences or as input to a miRNA prediction software. The tool can calculate up to 80 features where many of them are multidimensional arrays. In order to simplify the web interface, the features have been divided into six pre-defined groups, each one providing information about: primary sequence, secondary structure, thermodynamic stability, statistical stability, conservation between genomes of different species and substrings analysis of the sequences. Additionally, pre-trained classifiers are provided for prediction in different species. All algorithms to extract the features have been validated, comparing the results with the ones obtained from software of the original authors. The source code is freely available for academic use under GPL license at http://sourceforge.net/projects/sourcesinc/files/mirnafe/0.90/. A user-friendly access is provided as web interface at http://fich.unl.edu.ar/sinc/web-demo/mirnafe/. A more configurable web interface can be accessed at http://fich.unl.edu.ar/sinc/web-demo/mirnafe-full/.

Portación nasal de Staphylococcus aureus en individuos de la comunidad: factores epidemiológicos / Nasal carriage of Staphylococcus aureus in community individuals: epidemiological factors / Carreamento nasal de Staphylococcus aureus em indivíduos da comunidade: fatores epidemiológicos

La portación nasal de Staphylococcus aureus (SAU) en individuos sanos confirma su diseminación, constituye una fuente potencial de infección y se la relaciona con patologías atópicas. El objetivo del trabajo fue determinar la prevalencia de colonización nasal de SAU en individuos de la comunidad, sus respectivos patrones de resistencia antimicrobiana (PRA) y su asociación con factores epidemiológicos. Se realizó un estudio en 150 hisopados nasales. Se identificaron los aislados de SAU por métodos convencionales, y se evaluó su sensibilidad antimicrobiana por el método de difusión con discos de Kirby-Bauer y en cepas de Staphylococcus aureus resistentes a meticilina (SAMR) se confirmó la presencia del gen mec A y se investigó el gen lpv codificante de la toxina de Panton y Valentine (LPV) por PCR. Se analizó su asociación con factores epidemiológicos (lesiones, rinitis, etc.) con el programa SPSS. Se obtuvieron 119 aislamientos de SAU (79%) con 12 PRA. Las PCR de las cepas SAMR fueron positivas para el gen mec A y negativas para el gen lpv. Estadísticamente se detectó asociación de colonización nasal con sexo masculino y rinitis. Se concluye que la prevalencia de portación nasal de SAU en la comunidad fue elevada y mayor en varones. Los aislamientos multirresistentes y SAMR- LPV (-) sugieren relación hospitalaria y su diseminación a la comunidad. Es importante el hallazgo de la asociación epidemiológica con rinitis, la cual confirma vinculación con patologías atópicas.(AU)

Nasal carriage of Staphylococcus aureus (SAU) in healthy individuals confirms its spreading, constitutes a potential infection source and is related to atopic pathologies. The objetive was to determine the prevalence of SAU nasal carriage in community individuals, its antimicrobial resistance patterns (ARP) and its association with epidemiological factors. A total of 150 nasal swabs were studied, where SAU isolates were identified by conventional methods and their antimicrobial sensitivity was evaluated by disk diffusion Kirby Bauer test. In addition, the presence of mec A gene was confirmed and the lpv gene coding for Panton-Valentine toxin (PVL) was investigated by PCR in methicillin resistant Staphylococcus aureus (MRSA) strains. Its association with epidemiological factors (injuries, rhinitis, etc) was analyzed with SPSS program. One hundred and nineteen (79%) SAU isolates with 12 ARP were obtained. PCR assays of MRSA strains were positive for the mec A gene and negative for the lpv gene. Association between nasal colonization and both male sex and rhinitis was detected statistically. It can be concluded that high prevalence of SAU nasal carriage was found in the community, mainly in males. Multiresistant isolates and lpv (-) MRSA suggest a hospital-acquired infection with subsequent dissemination to the community. The epidemiological association with rhinitis, which confirms the link with atopic pathologies, deserves to be highlighted.(AU)

O carreamento nasal de Staphylococcus aureus (SAU) em individuos saudáveis confirma sua disseminagao, constitui uma fonte potencial de infecgao e é relacionada com patologias atópicas. O objetivo do trabalho foi determinar a prevalencia de colonizagao nasal de SAU em individuos da comunidade, seus respectivos padróes de resistencia antimicrobiana (PRA) e sua associagao com fatores epidemiológicos. Foi realizado um estudo em 150 esfregagos nasais. Identificaramse os isolados de SA U por métodos convencionais, e foi avaliada sua sensibilidade antimicrobiana pelo método de difusao com discos de Kirby-Bauer e em cepas de Staphylococcus aureus resistentes a meticilina (SAMR) foi confirmada a presenga do gene mec A e se investigou o gene lpv codificante da toxina de Panton - Valentine (LPV) por PCR. Foi analisada sua associagao com fatores epidemiológicos (lesóes, rinite, etc.) com o programa SPSS. Obtiveramse 119 isolamentos de SAU (79%) com 12 PRA. As PCR das cepas SAMR foram positivas para o gene mec A e negativas para o gene lpv. Estatisticamente se detectou associagao de colonizagao nasal com sexo masculino e rinite. Concluise que a prevalencia de carreamento nasal de SAU na comunidade foi elevada e maior em homens. Os isolamentos multirresistentes e SAMR- LPV (-) sugerem relagao hospitalar e sua disseminagao para a comunidade. E importante o achado da associagao epidemiológica com rinite, a qual confirma vinculagao com patologias atópicas.(AU)

Portación nasal de Staphylococcus aureus en individuos de la comunidad: factores epidemiológicos / Nasal carriage of Staphylococcus aureus in community individuals: epidemiological factors / Carreamento nasal de Staphylococcus aureus em indivíduos da comunidade: fatores epidemiológicos

La portación nasal de Staphylococcus aureus (SAU) en individuos sanos confirma su diseminación, constituye una fuente potencial de infección y se la relaciona con patologías atópicas. El objetivo del trabajo fue determinar la prevalencia de colonización nasal de SAU en individuos de la comunidad, sus respectivos patrones de resistencia antimicrobiana (PRA) y su asociación con factores epidemiológicos. Se realizó un estudio en 150 hisopados nasales. Se identificaron los aislados de SAU por métodos convencionales, y se evaluó su sensibilidad antimicrobiana por el método de difusión con discos de Kirby-Bauer y en cepas de Staphylococcus aureus resistentes a meticilina (SAMR) se confirmó la presencia del gen mec A y se investigó el gen lpv codificante de la toxina de Panton y Valentine (LPV) por PCR. Se analizó su asociación con factores epidemiológicos (lesiones, rinitis, etc.) con el programa SPSS. Se obtuvieron 119 aislamientos de SAU (79%) con 12 PRA. Las PCR de las cepas SAMR fueron positivas para el gen mec A y negativas para el gen lpv. Estadísticamente se detectó asociación de colonización nasal con sexo masculino y rinitis. Se concluye que la prevalencia de portación nasal de SAU en la comunidad fue elevada y mayor en varones. Los aislamientos multirresistentes y SAMR- LPV (-) sugieren relación hospitalaria y su diseminación a la comunidad. Es importante el hallazgo de la asociación epidemiológica con rinitis, la cual confirma vinculación con patologías atópicas.(AU)

Nasal carriage of Staphylococcus aureus (SAU) in healthy individuals confirms its spreading, constitutes a potential infection source and is related to atopic pathologies. The objetive was to determine the prevalence of SAU nasal carriage in community individuals, its antimicrobial resistance patterns (ARP) and its association with epidemiological factors. A total of 150 nasal swabs were studied, where SAU isolates were identified by conventional methods and their antimicrobial sensitivity was evaluated by disk diffusion Kirby Bauer test. In addition, the presence of mec A gene was confirmed and the lpv gene coding for Panton-Valentine toxin (PVL) was investigated by PCR in methicillin resistant Staphylococcus aureus (MRSA) strains. Its association with epidemiological factors (injuries, rhinitis, etc) was analyzed with SPSS program. One hundred and nineteen (79%) SAU isolates with 12 ARP were obtained. PCR assays of MRSA strains were positive for the mec A gene and negative for the lpv gene. Association between nasal colonization and both male sex and rhinitis was detected statistically. It can be concluded that high prevalence of SAU nasal carriage was found in the community, mainly in males. Multiresistant isolates and lpv (-) MRSA suggest a hospital-acquired infection with subsequent dissemination to the community. The epidemiological association with rhinitis, which confirms the link with atopic pathologies, deserves to be highlighted.(AU)

O carreamento nasal de Staphylococcus aureus (SAU) em individuos saudáveis confirma sua disseminagao, constitui uma fonte potencial de infecgao e é relacionada com patologias atópicas. O objetivo do trabalho foi determinar a prevalencia de colonizagao nasal de SAU em individuos da comunidade, seus respectivos padróes de resistencia antimicrobiana (PRA) e sua associagao com fatores epidemiológicos. Foi realizado um estudo em 150 esfregagos nasais. Identificaramse os isolados de SA U por métodos convencionais, e foi avaliada sua sensibilidade antimicrobiana pelo método de difusao com discos de Kirby-Bauer e em cepas de Staphylococcus aureus resistentes a meticilina (SAMR) foi confirmada a presenga do gene mec A e se investigou o gene lpv codificante da toxina de Panton - Valentine (LPV) por PCR. Foi analisada sua associagao com fatores epidemiológicos (lesóes, rinite, etc.) com o programa SPSS. Obtiveramse 119 isolamentos de SAU (79%) com 12 PRA. As PCR das cepas SAMR foram positivas para o gene mec A e negativas para o gene lpv. Estatisticamente se detectou associagao de colonizagao nasal com sexo masculino e rinite. Concluise que a prevalencia de carreamento nasal de SAU na comunidade foi elevada e maior em homens. Os isolamentos multirresistentes e SAMR- LPV (-) sugerem relagao hospitalar e sua disseminagao para a comunidade. E importante o achado da associagao epidemiológica com rinite, a qual confirma vinculagao com patologias atópicas.(AU)

Portación nasal de Staphylococcus aureus en individuos de la comunidad: factores epidemiológicos / Nasal carriage of Staphylococcus aureus in community individuals: epidemiological factors / Carreamento nasal de Staphylococcus aureus em indivíduos da comunidade: fatores epidemiológicos

La portación nasal de Staphylococcus aureus (SAU) en individuos sanos confirma su diseminación, constituye una fuente potencial de infección y se la relaciona con patologías atópicas. El objetivo del trabajo fue determinar la prevalencia de colonización nasal de SAU en individuos de la comunidad, sus respectivos patrones de resistencia antimicrobiana (PRA) y su asociación con factores epidemiológicos. Se realizó un estudio en 150 hisopados nasales. Se identificaron los aislados de SAU por métodos convencionales, y se evaluó su sensibilidad antimicrobiana por el método de difusión con discos de Kirby-Bauer y en cepas de Staphylococcus aureus resistentes a meticilina (SAMR) se confirmó la presencia del gen mec A y se investigó el gen lpv codificante de la toxina de Panton y Valentine (LPV) por PCR. Se analizó su asociación con factores epidemiológicos (lesiones, rinitis, etc.) con el programa SPSS. Se obtuvieron 119 aislamientos de SAU (79%) con 12 PRA. Las PCR de las cepas SAMR fueron positivas para el gen mec A y negativas para el gen lpv. Estadísticamente se detectó asociación de colonización nasal con sexo masculino y rinitis. Se concluye que la prevalencia de portación nasal de SAU en la comunidad fue elevada y mayor en varones. Los aislamientos multirresistentes y SAMR- LPV (-) sugieren relación hospitalaria y su diseminación a la comunidad. Es importante el hallazgo de la asociación epidemiológica con rinitis, la cual confirma vinculación con patologías atópicas.

Nasal carriage of Staphylococcus aureus (SAU) in healthy individuals confirms its spreading, constitutes a potential infection source and is related to atopic pathologies. The objetive was to determine the prevalence of SAU nasal carriage in community individuals, its antimicrobial resistance patterns (ARP) and its association with epidemiological factors. A total of 150 nasal swabs were studied, where SAU isolates were identified by conventional methods and their antimicrobial sensitivity was evaluated by disk diffusion Kirby Bauer test. In addition, the presence of mec A gene was confirmed and the lpv gene coding for Panton-Valentine toxin (PVL) was investigated by PCR in methicillin resistant Staphylococcus aureus (MRSA) strains. Its association with epidemiological factors (injuries, rhinitis, etc) was analyzed with SPSS program. One hundred and nineteen (79%) SAU isolates with 12 ARP were obtained. PCR assays of MRSA strains were positive for the mec A gene and negative for the lpv gene. Association between nasal colonization and both male sex and rhinitis was detected statistically. It can be concluded that high prevalence of SAU nasal carriage was found in the community, mainly in males. Multiresistant isolates and lpv (-) MRSA suggest a hospital-acquired infection with subsequent dissemination to the community. The epidemiological association with rhinitis, which confirms the link with atopic pathologies, deserves to be highlighted.

O carreamento nasal de Staphylococcus aureus (SAU) em individuos saudáveis confirma sua disseminagao, constitui uma fonte potencial de infecgao e é relacionada com patologias atópicas. O objetivo do trabalho foi determinar a prevalencia de colonizagao nasal de SAU em individuos da comunidade, seus respectivos padróes de resistencia antimicrobiana (PRA) e sua associagao com fatores epidemiológicos. Foi realizado um estudo em 150 esfregagos nasais. Identificaramse os isolados de SA U por métodos convencionais, e foi avaliada sua sensibilidade antimicrobiana pelo método de difusao com discos de Kirby-Bauer e em cepas de Staphylococcus aureus resistentes a meticilina (SAMR) foi confirmada a presenga do gene mec A e se investigou o gene lpv codificante da toxina de Panton - Valentine (LPV) por PCR. Foi analisada sua associagao com fatores epidemiológicos (lesóes, rinite, etc.) com o programa SPSS. Obtiveramse 119 isolamentos de SAU (79%) com 12 PRA. As PCR das cepas SAMR foram positivas para o gene mec A e negativas para o gene lpv. Estatisticamente se detectou associagao de colonizagao nasal com sexo masculino e rinite. Concluise que a prevalencia de carreamento nasal de SAU na comunidade foi elevada e maior em homens. Os isolamentos multirresistentes e SAMR- LPV (-) sugerem relagao hospitalar e sua disseminagao para a comunidade. É importante o achado da associagao epidemiológica com rinite, a qual confirma vinculagao com patologias atópicas.