Molecular Epidemiology of Plasmodium species in Conflicted Federally Administered Tribal Area (FATA) Pakistan / Epidemiologia molecular de espécies de plasmódio em área tribal sob administração federal em conflito do Paquistão

Military conflicts have been significant obstacles in detecting and treating infectious disease diseases due to the diminished public health infrastructure, resulting in malaria endemicity. A variety of violent and destructive incidents were experienced by FATA (Federally Administered Tribal Areas). It was a struggle to pursue an epidemiological analysis due to continuing conflict and Talibanization. Clinical isolates were collected from Bajaur, Mohmand, Khyber, Orakzai agencies from May 2017 to May 2018. For Giemsa staining, full blood EDTA blood samples have been collected from symptomatic participants. Malaria-positive microscopy isolates were spotted on filter papers for future Plasmodial molecular detection by nested polymerase chain reaction (nPCR) of small subunit ribosomal ribonucleic acid (ssrRNA) genes specific primers. Since reconfirming the nPCR, a malariometric study of 762 patients found 679 positive malaria cases. Plasmodium vivax was 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) were with mixed-species infection (P. vivax plus P. falciparum), and 83 were declared negative by PCR. Among the five agencies of FATA, Khyber agency has the highest malaria incidence (19%) with followed by P. vivax (19%) and P. falciparum (4.1%). In contrast, Kurram has about (14%), including (10.8%) P. vivax and (2.7%) P. falciparum cases, the lowest malaria epidemiology. Surprisingly, no significant differences in the distribution of mixed-species infection among all five agencies. P. falciparum and P. vivax were two prevalent FATA malaria species in Pakistan's war-torn area. To overcome this rising incidence of malaria, this study recommends that initiating malaria awareness campaigns in school should be supported by public health agencies and malaria related education locally, targeting children and parents alike.

Os conflitos militares têm sido obstáculos significativos na detecção e tratamento de doenças infecciosas devido à diminuição da infraestrutura de saúde pública, resultando na endemicidade da malária. Uma variedade de incidentes violentos e destrutivos foi vivida pelas FATA (áreas tribais administradas pelo governo federal). Foi uma luta busca ruma análise epidemiológica devido ao conflito contínuo e à talibanização. Isolados clínicos foram coletados de agências Bajaur, Mohmand, Khyber e Orakzai, de maio de 2017 a maio de 2018. Para a coloração de Giemsa, amostras de sangue completo com EDTA foram coletadas de participantes sintomáticos. Isolados de microscopia positivos para malária foram colocados em papéis de filtro para futura detecção molecular plasmódica por reação em cadeia da polimerase aninhada (nPCR) de primers específicos de genes de subunidade ribossômica de ácido ribonucleico (ssrRNA). Desde a reconfirmação do nPCR, um estudo malariométrico de 762 pacientes encontrou 679 casos positivos de malária. Plasmodium vivax foi 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) eram com infecção de espécies mistas (P. vivax mais P. falciparum) e 83 foram declarados negativos por PCR. Entre as cinco agências da FATA, a agência Khyber tem a maior incidência de malária (19%), seguida por P. vivax (19%) e P. falciparum (4,1%). Em contraste, Kurram tem cerca de 14%, incluindo 10,8% casos de P. vivax e 2,7% P. falciparum, a epidemiologia de malária mais baixa. Surpreendentemente, não há diferenças significativas na distribuição da infecção de espécies mistas entre todas as cinco agências. P. falciparum e P. vivax foram duas espécies prevalentes de malária FATA na área devastada pela guerra no Paquistão. Para superar essa incidência crescente de malária, este estudo recomenda que o início de campanhas de conscientização sobre a malária na escola deve ser apoiado por agências de saúde pública e educação relacionada com a malária localmente, visando crianças e pais.

Molecular Epidemiology of Plasmodium species in Conflicted Federally Administered Tribal Area (FATA) Pakistan

Abstract Military conflicts have been significant obstacles in detecting and treating infectious disease diseases due to the diminished public health infrastructure, resulting in malaria endemicity. A variety of violent and destructive incidents were experienced by FATA (Federally Administered Tribal Areas). It was a struggle to pursue an epidemiological analysis due to continuing conflict and Talibanization. Clinical isolates were collected from Bajaur, Mohmand, Khyber, Orakzai agencies from May 2017 to May 2018. For Giemsa staining, full blood EDTA blood samples have been collected from symptomatic participants. Malaria-positive microscopy isolates were spotted on filter papers for future Plasmodial molecular detection by nested polymerase chain reaction (nPCR) of small subunit ribosomal ribonucleic acid (ssrRNA) genes specific primers. Since reconfirming the nPCR, a malariometric study of 762 patients found 679 positive malaria cases. Plasmodium vivax was 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) were with mixed-species infection (P. vivax plus P. falciparum), and 83 were declared negative by PCR. Among the five agencies of FATA, Khyber agency has the highest malaria incidence (19%) with followed by P. vivax (19%) and P. falciparum (4.1%). In contrast, Kurram has about (14%), including (10.8%) P. vivax and (2.7%) P. falciparum cases, the lowest malaria epidemiology. Surprisingly, no significant differences in the distribution of mixed-species infection among all five agencies. P. falciparum and P. vivax were two prevalent FATA malaria species in Pakistans war-torn area. To overcome this rising incidence of malaria, this study recommends that initiating malaria awareness campaigns in school should be supported by public health agencies and malaria-related education locally, targeting children and parents alike.

Resumo Os conflitos militares têm sido obstáculos significativos na detecção e tratamento de doenças infecciosas devido à diminuição da infraestrutura de saúde pública, resultando na endemicidade da malária. Uma variedade de incidentes violentos e destrutivos foi vivida pelas FATA (áreas tribais administradas pelo governo federal). Foi uma luta buscar uma análise epidemiológica devido ao conflito contínuo e à talibanização. Isolados clínicos foram coletados de agências Bajaur, Mohmand, Khyber e Orakzai, de maio de 2017 a maio de 2018. Para a coloração de Giemsa, amostras de sangue completo com EDTA foram coletadas de participantes sintomáticos. Isolados de microscopia positivos para malária foram colocados em papéis de filtro para futura detecção molecular plasmódica por reação em cadeia da polimerase aninhada (nPCR) de primers específicos de genes de subunidade ribossômica de ácido ribonucleico (ssrRNA). Desde a reconfirmação do nPCR, um estudo malariométrico de 762 pacientes encontrou 679 casos positivos de malária. Plasmodium vivax foi 523 (77%), Plasmodium falciparum 121 (18%), 35 (5%) eram com infecção de espécies mistas (P. vivax mais P. falciparum) e 83 foram declarados negativos por PCR. Entre as cinco agências da FATA, a agência Khyber tem a maior incidência de malária (19%), seguida por P. vivax (19%) e P. falciparum (4,1%). Em contraste, Kurram tem cerca de 14%, incluindo 10,8% casos de P. vivax e 2,7% P. falciparum, a epidemiologia de malária mais baixa. Surpreendentemente, não há diferenças significativas na distribuição da infecção de espécies mistas entre todas as cinco agências. P. falciparum e P. vivax foram duas espécies prevalentes de malária FATA na área devastada pela guerra no Paquistão. Para superar essa incidência crescente de malária, este estudo recomenda que o início de campanhas de conscientização sobre a malária na escola deve ser apoiado por agências de saúde pública e educação relacionada com a malária localmente, visando crianças e pais.

Detección clonal de cepas parentales de streptococcus agalactiae Lehmann y Neumann por amplificación aleatoria de ADN polimórfico / Clonal detection of streptococcus agalactiae Lehmann and Neumann parental strains by random amplification of polymorphic DNA

RESUMEN Streptococcus agalactiae (SGB) produce infecciones invasivas en neonatos siendo la transmisión materna la más frecuente. Estudios epidemiológicos utilizan técnicas moleculares que evalúan la diversidad genética, entre ellas la de amplificación aleatoria de ADN polimórfico (RAPD) que resulta ser accesible, sensible y utiliza cebadores arbitrarios para amplificar segmentos polimórficos de ADN mediante PCR. El objetivo fue determinar la relación clonal entre aislamientos de SGB recuperados de madres y sus respectivos recién nacidos. Se estudiaron por RAPD cuatro parejas de aislamientos de SGB obtenidos de hisopados vagino-rectales de madres y de hemocultivos de sus neonatos. Se utilizaron los cebadores OPS11, OPB17 y OPB18 para seleccionar uno con capacidad de discriminar entre cepas no relacionadas genéticamente. Se utilizó la fórmula de Hunter-Gaston que establece el índice de discriminación (D), cuando D>0,90 se considera que los aislamientos pertenecen a clones diferentes. Los perfiles de amplificación para los ocho aislamientos, empleando independientemente cada cebador, permitieron calcular un D=1 para OPS11, y D=0,84 para OPB17 y OPB18. Por lo tanto, OPS11 fue seleccionado para el estudio de la relación clonal de los aislamientos, encontrándose perfiles de amplificación similares por RAPD para cada par de cepas madre-recién nacido. Se observaron diferentes perfiles de amplificación entre los pares de cepas madre-recién nacido, lo que revela la discriminación entre cepas no relacionadas, resultados confirmados por electroforesis en campo pulsante (PFGE). Estos resultados indican transmisión vertical para cada caso estudiado y robustez del cebador OPS11. Se encontraron condiciones apropiadas del ensayo de RAPD, lo que es útil para estudios epidemiológicos.

ABSTRACT Streptococcus agalactiae (GBS) causes invasive infections in newborns, being the most frequent the maternal transmission. Epidemiological studies use molecular techniques that assess genetic diversity, including random amplification of polymorphic DNA (RAPD) that is found to be accessible, sensitive and uses arbitrary primers to amplify polymorphic segments of DNA by PCR. The objective was to determine the clonal relationship between GBS strains recovered from mothers and their respective newborns. Four pairs of GBS isolates obtained from vaginal-rectal swabs of mothers and blood cultures of their newborns were studied with RAPD. Primers OPS11, OPB17 and OPB18 were used to select one with the ability to discriminate between non-genetically related strains. The Hunter-Gaston formula that establishes the discrimination index (D) was used; when D>0.90, it is considered that the isolates belong to different clones. The amplification profiles for the eight isolates, using each primer independently, allowed to calculate a D=1 for OPS11, and D=0.84 for OPB17 and OPB18. Therefore, OPS11 was selected for the study of the clonal relationship of the isolates, and similar amplification profiles were found by RAPD for each mother-newborn pair of GBS isolates. Different amplification profiles were observed between pairs of mother-newborn strains, which reveals the discrimination between unrelated strains, confirmed by pulsating field electrophoresis (PFGE). These results indicated vertical transmission for each studied case and robustness of the OPS11 primer. Appropriate conditions of the RAPD trial were found, which is useful for epidemiological studies.

Estructura genética de cepas de Mycobacterium tuberculosis farmacorresistentes en Perú con base en haplotipos obtenidos de un ensayo de sonda lineal / Genetic structure of drug-resistant strains of Mycobacterium tuberculosis in Peru based on haplotypes obtained from a linear probe assay

RESUMEN Objetivo. Determinar la estructura genética de las cepas drogorresistentes de Mycobacterium tuberculosis que circularon en todo el Perú durante los años 2011-2015 a través de haplotipos obtenidos de un ensayo con sondas en línea. Materiales y métodos. Se analizaron 6589 muestras que ingresaron al Instituto Nacional de Salud para el diagnóstico rutinario mediante el ensayo GenoType® MTBDRplus v2, durante el periodo de estudio. Se crearon haplotipos resistentes mediante la concatenación de 21 sitios polimórficos de los genes evaluados por el ensayo con sondas en línea, y se realizó el análisis de asociación con fenotipos obtenidos por el método de proporciones agar 7H10. Resultados. Las mutaciones de mayores frecuencias fueron: rpoB S531L (55,4%) y rpoB D516V (18,5%) para la resistencia a rifampicina, y katG S315T (59,5%) e inhA c-15t (25,7%) para la resistencia a isoniacida. Se obtuvieron 13 haplotipos representativos (87,8% de muestras analizadas) de los cuales seis correspondieron al genotipo multidrogorresistente, cuatro al genotipo monorresistente a isoniacida y tres al genotipo monorresistente a rifampicina. Dieciocho departamentos, y la provincia del Callao, presentaron una alta diversidad haplotípica; cuatro presentaron moderada diversidad y dos presentaron baja diversidad. Conclusiones. Existe una alta diversidad haplotípica en la mayoría de los departamentos, además de una concentración de las cepas de Mycobacterium tuberculosis drogorresistentes en las ciudades de Lima y Callao. Asimismo, las cepas de Mycobacterium tuberculosis con perfil drogorresistente que circulan en el Perú contienen principalmente los marcadores genéticos de mayor prevalencia a nivel mundial asociados con la resistencia frente a rifampicina e isoniacida.

ABSTRACT Objective. To determine the genetic structure of drug-resistant strains of Mycobacterium tuberculosis that circulated throughout Peru during the years 2011-2015, by using haplotypes obtained from a line probe assay. Materials and methods. A total of 6589 samples that were admitted to the Instituto Nacional de Salud for routine diagnosis using the GenoType® MTBDRplus v2 assay were analyzed during the study period. Resistant haplotypes were created by concatenating 21 polymorphic sites of the evaluated genes using the line probe assay; and the association analysis was carried out with phenotypes obtained by the 7H10 agar ratio method. Results. The most frequent mutations were: rpoB S531L (55.4%) and rpoB D516V (18.5%) for rifampicin resistance, and katG S315T (59.5%) and inhA c-15t (25.7%) for isoniazid resistance. We obtained 13 representative haplotypes (87.8% of analyzed samples), 6 corresponded to the multidrug-resistant genotype, 4 to the isoniazid mono-resistant genotype and 3 to the rifampicin mono-resistant genotype. Eighteen regions and the province of Callao showed high haplotype diversity; four showed moderate diversity and two showed low diversity. Conclusions. Most regions showed high haplotype diversity; in addition, most drug-resistant strains of Mycobacterium tuberculosis were concentrated in the cities of Lima and Callao. Likewise, drug-resistant Mycobacterium tuberculosis strains circulating in Peru mainly contain the genetic markers with the highest prevalence worldwide, which are associated with resistance to rifampicin and isoniazid.

GENETIC DIVERSITY OF Lutzomyia (Nyssomyia) intermedia IN AN ENDEMIC AREA OF AMERICAN CUTANEOUS LEISHMANIASIS, STATE OF PARANÁ, BRAZIL / Diversidad genética de Lutzomyia (Nyssomyia) intermedia en un área endémica de leishmaniasis cutánea americana del estado de Paraná, Brasil

ABSTRACT Lutzomyia intermedia (Diptera: Psychodidae) features as one of the main vectors that are involved in the transmission of American cutaneous leishmaniasis (ACL) in the Neotropical region. However, genetic studies involving this taxon are still incipient and important for understanding the level of variability of different populations, their role, and implications as vectors. The aim of this study was to determine the level of genetic diversity of L. intermedia present in the Ribeira River Valley, an area of ACL transmission in the state of Paraná, Brazil, through the Random amplified polymorphic DNA (RAPD). Two municipalities were chosen to collect sand flies: Cerro Azul (new transmission area of the ACL) and Adrianópolis (endemic area of the ACL). The insects were captured in the house, in the peridomicile and in the wild (forest). Two of the used markers made it possible to estimate the polymorphism of the studied populations, resulting in 40 genotypes, most of them from peridomicile. The dendrogram generated by the analysis with the primer A10 showed different degrees of similarity, suggesting that there may be gene flow in the studied populations. The Principal Coordinate Analysis (PCO) with the A2 primer, was useful in grouping L. intermedia according to its ecological and geographical origin. There was no distinction between the lineages composing the L. intermedia complex. The results of this study, with the record of great genotypic diversity in L. intermedia, may contribute to explain the maintenance of the life cycle of Leishmania braziliensis (Kinetoplastida: Trypanosomatidae) in the region.

RESUMEN Lutzomyia intermedia (Diptera: Psychodidae) es uno de los principales vectores que participan en la transmisión de leishmaniasis cutánea americana (LCA) en la región Neotropical. A pesar de que aún los estudios genéticos que involucran a este taxón son incipientes, tienen una gran importancia para comprender el nivel de variabilidad de las diferentes poblaciones y sus implicaciones en su papel vectorial. El objetivo de este estudio fue determinar el nivel de diversidad genética de L. intermedia presente en el Valle del Río Ribeira, área de transmisión de LCA en el estado de Paraná, Brasil, mediante RAPD (ADN polimórfico amplificado aleatoriamente). Los flebótomos fueron recolectados en los municipios Cerro Azul (nueva área de transmisión de LCA) y Adrianópolis (área endémica de LCA), donde fueron capturados en ambientes residenciales, en el peridomicilio y en el bosque. Dos de los marcadores utilizados permitieron estimar el polimorfismo en las poblaciones estudiadas con la obtención de 40 genotipos, la mayoría de ellos en el peridomicilio. El dendrograma generado por el análisis con el cebador A10 mostró diferentes grados de similitud, lo que sugiere que puede haber flujo gènico en las poblaciones. El Análisis de Coordenadas Principales (PCO) con el cebador A2 fue útil para agrupar L. intermedia según su origen ecológico y geográfico. No hubo distinción entre los linajes que componen el complejo L. intermedia. Los resultados de este estudio, con el registro de gran diversidad genotipica en L. intermedia, pueden contribuir a explicar el mantenimiento del ciclo biológico de Leishmania braziliensis (Kinetoplastida: Trypanosomatidae) en la región.

Diversidad genómica en SARS-CoV-2: Mutaciones y variantes / Genomic diversity in SARS-CoV-2: Mutations and variants

Introducción: La variabilidad genética del SARS-CoV-2 ha incrementado notablemente desde que se declaró la pandemia, lo que le ha permitido representar un continuo desafió para las políticas de salud destinadas a su control. Objetivo. Describir la nomenclatura genómica utilizada para la comunicación general y científica sobre el SARS-CoV-2, así como describir las mutaciones, evolución, origen y variantes del virus. Material y Metodos. Se realizó una revisión narrativa de literatura, para el cual se realizó una búsqueda y análisis de la información hasta el 15 de diciembre de 2021. Se revisaron 74 fuentes seleccionados desde las bases de datos MEDLINE/ PubMed, SciELO, LILACS y páginas web oficiales; sin restricciones de idioma. Resultados. Las mutaciones son cambios en la secuencia de nucleótidos del genoma viral, que, al producir afectación de la dinámica epidemiológica en una población, dan lugar a variantes, y estos a su vez a clados diferenciados. Entre las variantes de interés destacan Lambda y Mu, identificadas por primera vez en Perú y Colombia, respectivamente. Mientras que, las variantes de preocupación, en orden cronológico, son la Alfa (británica), Beta (sudafricana), Gamma (brasilera), Delta (india) y recientemente Ómicron. Conclusiones. Se concluye que la diversidad genómica del SARS-CoV-2 se debe a su elevada tasa de mutaciones que pueden constituirse en variantes y clados. La mejor comprensión de esta diversidad permite tomar medidas de control más eficaces, guiando el desarrollo y uso de vacunas, terapias, diagnóstico y políticas en salud.

Introduction: The genetic variability of SARS-CoV-2 has increased markedly since the pandemic was declared, allowing it to pose a continuing challenge to health policies aimed at its control. Objective. To describe the genomic nomenclature used for general and scientific communication about SARS-CoV-2, as well as to describe the mutations, evolution, origin and variants of the virus. Material and Methods. A narrative literature review was conducted, for which a search and analysis of the information was performed until December 15, 2021. Seventy-four selected sources were reviewed from MEDLINE/PubMed, SciELO, LILACS databases and official web pages; without language restrictions. Results. Mutations are changes in the nucleotide sequence of the viral genome, which, by affecting the epidemiological dynamics in a population, give rise to variants, and these in turn to differentiated clades. Among the variants of interest are Lambda and Mu, identified for the first time in Peru and Colombia, respectively. Meanwhile, the variants of concern, in chronological order, are Alpha (British), Beta (South African), Gamma (Brazilian), Delta (Indian) and recently Omicron. Conclusions. It is concluded that the genomic diversity of SARS-CoV-2 is due to its high rate of mutations that can constitute variants and clades. A better understanding of this diversity allows more effective control measures to be taken, guiding the development and use of vaccines, therapies, diagnostics and health policies.

HELICOBACTER PYLORI cagA VIRULENCE GENE AND SEVERE ESOGASTRODUODENAL DISEASES: IS THERE AN ASSOCIATION? / Gene de virulência cagA de Helicobacter pylori e doenças esogastroduodenais severas: existe uma associação?

ABSTRACT BACKGROUND: Helicobacter pylori colonizes approximately half of the world's human population. Its presence in the gastric mucosa is associated with an increased risk of gastric adenocarcinoma, gastric lymphoma, and peptic ulcer disease. In Brazil, the high prevalence of H. pylori infection is a serious health problem. H. pylori virulence factors are associated with an increased risk of serious gastrointestinal disorders. The cagA gene encodes a cytotoxin-A-associated antigen (CagA) that is involved in bacterial pathogenicity. H. pylori strains carrying the cag pathogenicity island (cag-PAI) are significantly associated with severe clinical outcomes and histopathological changes. OBJECTIVE: The present study aims to investigate the prevalence of the cagA gene among H. pylori isolates from patients with different gastric pathologies. Further, the study hopes to verify its association with clinical outcomes. In addition, phylogenetic analysis was performed on cagA-positive H. pylori strains from patients with severe and non-severe diseases. METHODS: Gastric specimens were collected through a biopsy from 117 patients with different esogastroduodenal diseases. DNA was extracted from these gastric specimens and the polymerase chain reaction was performed to amplify the gene fragments corresponding to the 16S ribosomal RNA and cagA genes using specific primers. The polymerase chain reaction products of selected samples positive for cagA were sequenced. The sequences were aligned with reference sequences from the National Center for Biotechnology Information (NCBI) (Bethesda/USA), and a phylogenetic tree was constructed. RESULTS: H. pylori was detected in 65.9% (77/117) of Brazilian patients with different gastroduodenal disorders. Overall, 80.5% (62/77) of the strains were cagA-positive. The ages of patients with cagA-positive strains (15 males and 47 females) ranged from 18 to 74 years. The lesions were categorized as non-severe and severe according to the endoscopic and histopathological reports the most prevalent non-severe esogastroduodenal lesion was gastritis 54/77 (70.12%), followed by esophagitis 12/77 (15.58%) and duodenitis 12/77 (15.58%). In contrast, the most prevalent severe lesions were atrophy 7/77 (9.09%), followed by metaplasia 3/77 (3.86%) and gastric adenocarcinoma 2/77 (2.59%). Phylogenetic analyses performed with the partial sequences of the cagA gene obtained from local strains were grouped in the same clade. No differences in phylogenetic distribution was detected between severe and non-severe diseases. CONCLUSION: The cagA gene is highly prevalent among H. pylori isolates from gastric lesions in Brazilian patients. The presence of the cagA gene was not considered a marker of the severity of esogastroduodenal lesions in the present study. This is the first study to investigate the phylogenetic population structure of H. pylori strains in a Brazilian capital, which may improve our understanding of the clinical outcome of H. pylori infection.

RESUMO CONTEXTO: Helicobacter pylori coloniza aproximadamente metade da população humana mundial. A presença do microrganismo na mucosa gástrica está associada a um risco aumentado de adenocarcinoma gástrico, linfoma gástrico e úlcera péptica. No Brasil, a alta prevalência de infecção por H. pylori é um grave problema de saúde. Os fatores de virulência de H. pylori estão associados a risco aumentado de distúrbios gastrointestinais severos. O gene cagA codifica um antígeno associado à citotoxina A (CagA) que está envolvido na patogenicidade bacteriana. As cepas de H. pylori portadoras da ilha de patogenicidade cag (cag-PAI) estão significativamente associadas a desfechos clínicos severos e alterações histopatológicas. OBJETIVO: O presente estudo tem como objetivo investigar a prevalência do gene cagA entre isolados de H. pylori de pacientes com diferentes desordens gástricas, bem como verificar sua associação com desfechos clínicos. Além disso, a análise filogenética foi realizada em cepas de H. pylori cagA-positivas de pacientes com doenças severas e não severas. MÉTODOS: Amostras gástricas foram coletadas por meio de biópsia gástrica de 117 pacientes com diferentes doenças esogastroduodenais. O DNA foi extraído das amostras e utilizado para amplificar os fragmentos gênicos correspondentes aos genes RNA ribossomal 16S e cagA, através da reação em cadeia da polimerase. Os produtos da reação em cadeia da polimerase de amostras selecionadas positivas para cagA foram sequenciados e as sequências foram alinhadas com sequências de referência do National Center for Biotechnology Information (NCBI) (Bethesda/EUA). As análises filogenéticas foram realizadas a partir do sequenciamento e construção da árvore filogenética. RESULTADOS: H. pylori foi detectado em 65,9% (77/117) dos pacientes brasileiros com diferentes distúrbios gastroduodenais. No total, 80,5% (62/77) das cepas foram cagA-positivas. As idades dos pacientes com cepas cagA-positivas (15 homens e 47 mulheres) variaram de 18 a 74 anos. As lesões foram categorizadas como não severas e severas de acordo com o laudo endoscópico e histopatológico. A lesão esogastroduodenal não severa mais prevalente foi gastrite 54/77 (70,12%), seguida de esofagite 12/77 (15,58%) e duodenite 12/77 (15,58%). Em contraste, as lesões severas mais prevalentes foram atrofia 7/77 (9,09%), seguida de metaplasia 3/77 (3,86%) e adenocarcinoma gástrico 2/77 (2,59%). As análises filogenéticas realizadas com as sequências parciais do gene cagA obtidas de cepas locais foram agrupadas no mesmo clado. Nenhuma diferença na distribuição filogenética foi detectada entre doenças severas e não severas. CONCLUSÃO: O gene cagA é altamente prevalente entre isolados de H. pylori de lesões gástricas em pacientes brasileiros. A presença do gene cagA não foi considerada um marcador de severidade das lesões esogastroduodenais no presente estudo. Este é o primeiro estudo a investigar a estrutura filogenética da população de cepas de H. pylori em uma capital brasileira. Esses resultados irão contribuir para o entendimento sobre o desfecho clínico da infecção por H. pylori.

Caracterización de Escherichia coli D7111 productora de ß-LACTAMASA TEM-176 / Characterization of Escherichia coli D7111 producing the ß-LACTAMASA TEM-176

RESUMEN El presente reporte es la descripción original de bla TEM-176. Se caracterizaron los mecanismos de resistencia a antimicrobianos de un aislamiento de Escherichia coli enterotoxigénica, determinándose la resistencia a 22 antimicrobianos categorizados en 15 grupos diferentes mediante difusión en agar, estableciéndose grupo filogenético, mecanismos de resistencia y presencia de integrones de Clase 1 y 2 mediante PCR. Integrones y genes de resistencia a β-lactámicos fueron secuenciados. El aislamiento del grupo filogenético A, mostró resistencia o sensibilidad disminuida a ampicilina, amoxicilina más ácido clavulánico, ácido nalidíxico, ciprofloxacino, estreptomicina, kanamicina, tetraciclina, trimetoprim, sulfisoxazol, cotrimoxazol, azitromicina y nitrofurantoina, detectándose la presencia de bla TEM, aadA1/2, aphA1, sul3, tet(A) y un integron de Clase 2 conteniendo un gen dfrA1. La resistencia a quinolonas se relacionó con la substitución Ser83Ala. La secuencia de TEM mostró la substitución Ala222Val, la cual a la fecha no había sido descrita, reportándose como una nueva β-lactamasa, con el nombre de bla TEM-176.

ABSTRACT The present report is the original description of bla TEM-176. The mechanisms of resistance to antimicrobial agents were determined in an enterotoxigenic Escherichia coli, determining the susceptibility to 22 antimicrobials classified in 15 different groups by agar diffusion and establishing the phylogenetic group, mechanisms of resistance and presence of Class 1 and 2 integrons. Integrons and β-lactam resistance genes were sequenced. The isolate, belonging to phylogenetic group A, showed the presence of resistance or diminished susceptibility to a ampicillin, amoxicillin plus clavulanic acid, nalidíxic acid, ciprofloxacin, streptomycin, kanamycin, tetracycline, trimethoprim, sulfisoxazole, cotrimoxazole, azithromycin and nitrofurantoin, carrying bla TEM, aadA1/2, aphA1, sul3, tet(A) and a Class 2 integron containing a dfrA1 gene. Quinolone resistance was related to the substitution Ser83Ala. The TEM sequencing showed the presence of the new substitution Ala222Val, which led to the description of the new β-lactamase bla TEM-176.

Caracterización de Escherichia coli D7111 productora de ß-LACTAMASA TEM-176 / Characterization of Escherichia coli D7111 producing the ß-LACTAMASE TEM-176

RESUMEN El presente reporte es la descripción original de bla TEM-176. Se caracterizaron los mecanismos de resistencia a antimicrobianos de un aislamiento de Escherichia coli enterotoxigénica, determinándose la resistencia a 22 antimicrobianos categorizados en 15 grupos diferentes mediante difusión en agar, estableciéndose grupo filogenético, mecanismos de resistencia y presencia de integrones de Clase 1 y 2 mediante PCR. Integrones y genes de resistencia a β-lactámicos fueron secuenciados. El aislamiento del grupo filogenético A, mostró resistencia o sensibilidad disminuida a ampicilina, amoxicilina más ácido clavulánico, ácido nalidíxico, ciprofloxacino, estreptomicina, kanamicina, tetraciclina, trimetoprim, sulfisoxazol, cotrimoxazol, azitromicina y nitrofurantoina, detectándose la presencia de bla TEM, aadA1/2, aphA1, sul3, tet(A) y un integron de Clase 2 conteniendo un gen dfrA1. La resistencia a quinolonas se relacionó con la substitución Ser83Ala. La secuencia de TEM mostró la substitución Ala222Val, la cual a la fecha no había sido descrita, reportándose como una nueva β-lactamasa, con el nombre de bla TEM-176.

ABSTRACT The present report is the original description of bla TEM-176. The mechanisms of resistance to antimicrobial agents were determined in an enterotoxigenic Escherichia coli, determining the susceptibility to 22 antimicrobials classified in 15 different groups by agar diffusion and establishing the phylogenetic group, mechanisms of resistance and presence of Class 1 and 2 integrons. Integrons and β-lactam resistance genes were sequenced. The isolate, belonging to phylogenetic group A, showed the presence of resistance or diminished susceptibility to a ampicillin, amoxicillin plus clavulanic acid, nalidíxic acid, ciprofloxacin, streptomycin, kanamycin, tetracycline, trimethoprim, sulfisoxazole, cotrimoxazole, azithromycin and nitrofurantoin, carrying bla TEM, aadA1/2, aphA1, sul3, tet(A) and a Class 2 integron containing a dfrA1 gene. Quinolone resistance was related to the substitution Ser83Ala. The TEM sequencing showed the presence of the new substitution Ala222Val, which led to the description of the new β-lactamase bla TEM-176.

Uso de genomas de SARS-CoV -2 para la estimación del número reproductivo efectivo (Rt) en Perú durante marzo y abril del 2020

La comprensión de la COVID-19, provocada por el coronavirus de tipo 2 (SARS-CoV-2) causante de síndrome respiratorio agudo severo, utilizando un enfoque multidisciplinario, es esencial para mejorar la toma de decisiones basadas en evidencia. Se estimó el número reproductivo efectivo (Rt) en Perú a partir de 113 genomas completos generados por el Instituto Nacional de Salud (INS) del Perú almacenados en la base de datos pública GISAID. La tendencia mostrada por el Rt durante marzo y abril del 2020 fue similar a otras estimaciones epidemiológicas. El Rt disminuyó considerablemente durante la primera quincena de marzo, alcanzando su menor valor la semana posterior al inicio de la cuarentena, pero aumentó moderadamente desde la quincena de abril. Se discute las implicancias de las medidas tempranas tomadas para mitigar la transmisión. La vigilancia genómica será una herramienta necesaria para conocer la transmisión y evolución del virus, y complementará la información epidemiológica.

The understanding of COVID-19, caused by the SARS-CoV-2, is essential to improve evidence-based public health policies. The effective reproductive number (Rt) in Peru was estimated using information from 113 complete genomes sequenced by the Instituto Nacional de Salud del Perú (INS), available in the GISAID public database. The Rt trend during March and April of 2020 was found to be similar to results from other epidemiological reports. The Rt decreased during the first two weeks of March. Its lowest value was reported during the week after the quarantine began. The Rt increased moderately after the second week of April. The implication of early decisions taken to mitigate the transmission are discussed. Genomic surveillance will be necessary to understand the transmission and evolution of SARS-CoV-2 in Peru, and will complement the epidemiological information.

Genotipos de Echinococcus granulosus en hidatidosis humana alrededor del mundo: revisión sistemática / Echinococcus granulosus genotypes verified in human hydatid disease around the world: systematic review

Resumen Introducción: La evidencia sobre las características genotípicas de la infección por Echinococcus granulosus en humanos es escasa. Objetivo: Desarrollar un resumen de la evidencia disponible respecto a genotipos de E. granulosus verificados en hidatidosis humana en el mundo. Material y Métodos: Revisión sistemática. Se incluyeron artículos relacionados con genotipos de E. granulosus, en humanos, sin restricción de lenguaje ni método de secuenciación; publicados entre 1990-2019. Se realizó una búsqueda sistemática en WoS, EMBASE, MEDLINE, SCOPUS, Trip Database, BIREME, SciELO, LILACS, IBECS y OPS-OMS. Las variables en estudio fueron: año de publicación, país de origen, número de muestras, órganos parasitados, marcador molecular utilizado y genotipo identificado. Se aplicó estadística descriptiva. Resultados: Se identificaron 701 artículos relacionados; 62 cumplieron los criterios de selección, representando 1.511 muestras. La evidencia existente fue publicada entre 1994 y 2019 y proviene principalmente de Irán (45,2%). El método de secuenciación más utilizado fue amplificación por reacción de polimerasa en cadena más secuenciación tipo Sanger con genotipificación del gen cox1 (79,0%). Los genotipos identificados con mayor frecuencia fueron G1 (49,1%) y el complejo G1/G3 (32,2%). Conclusión: Las publicaciones relacionadas con genotipos de E. granulosus en humanos son escasas y heterogéneas. Eg G1 representa la mayor parte de la carga global mundial.

Abstract Background: The evidence regarding genotypic characteristics of Echinococcus granulosus infection in humans worldwide is scarce. Aim: To develop a synthesis of the available evidence regarding genotypes of E. granulosus verified in humans worldwide. Methods: Systematic review. Articles related with genotypes of E. granulosus, in humans, without language neither genotyped method restriction, published between 1990-2019 were included. A systematic in WoS, EMBASE, MEDLINE, SCOPUS, Trip Database, BIREME, SciELO, LILACS, IBECS, and PAHO-WHO was carried out. In study variables were year of publication, country, number of samples, host and parasite organs, genotype identified, molecular marker and genes. Descriptive statistics were applied. Results: 701 related articles were identified; 62 fulfilled selection criteria, representing 1,511 samples. The existing evidence was published between 1994 and 2019; and mainly comes from Iran (45.2%). The most commonly used sequencing method was PCR amplification and Sanger type sequencing with partial or total genotyping of the cox1 gene. Genotyped method most frequently used was cox1 (79,0%). Genotypes most frequently identified were G1 and G1/G3 complex (49.1% and 32.2%). Conclusions: Publications related to genotypes of Eg in humans are scarce, heterogeneous, and presenting differing results. Eg G1/G3 accounts for most of the global burden worldwide.

Epidemiología molecular del virus del sarampión en la región de las Américas: Panorama actual / Molecular Epidemiology Of The Measles Virus In The Region Of The Americas: Current Overview

Tras su erradicación en la región de las Américas en el 2016, ha reemergido y el número de casos va en progresivo aumento. Objetivo: Profundizar y actualizar los aspectos más importantes de la epidermiología molecular del virus sarampión en las Américas. Métodos: La búsqueda y análisis de la información se realizó en un periodo de cinco meses (primero de noviembre de 2019 al 31 de marzo de 2020) para lo cual se emplearon las siguientes palabras: measles, epidemiology molecular, América,outbreak, genotype, epidemic, en las bases de datos PubMed, Hinari, SciELO y Medline. Así mismo, se tomaron en cuenta los informes epidemiológicos de la Organización Panamericana De La Salud (OPS)y entidades gubernamentales de distintos países de América. Resultados: Dos linajes del genotipo D8están diseminándose ampliamente en la región de las Américas. Y aunque aún no podemos conocer el impacto de la actual pandemia producida por el SARS-CoV-2, la baja tasa de inmunización, los elevados movimientos migratorios antes del 2020, factores socioculturales y religiosos sumados a la crisis socia y política que afectan a algunos países de la región, están contribuyendo a que este problema sea creciente. Conclusión: La revisión brinda el conocimiento de la epidemiología molecular del virus. Su empleo y correcta interpretación permitirá establecer un adecuado manejo y medidas de contención con el fin de recuperar la condición de enfermedad erradicada en las Américas.

Introduction: Measles is one of the most contagious diseases that affect humans. After its eradicationin the Americas region in 2016, it has reemerged and the number of cases is progressively increasing..Objective: To deepen and update the most important aspects of the measles virus molecularepidermiology in the Americas. Methods: The search and analysis of the information was carriedout over a period of five months (November 1, 2019 to March 31, 2020) for which the following wordswere used: measles, molecular epidemiology, America, outbreak, genotype, epidemic, in the PubMed,Hinari, SciELO and Medline databases Likewise, the epidemiological reports of the Pan American HealthOrganization (PAHO) and government entities from different countries of America were taken intoaccount. Results: Two lineages of the D8 genotype are spreading widely in the Americas region. Andalthough we still cannot know the impact of the current pandemic produced by the SARS-CoV-2, thelow immunization rate, the high migratory movements before 2020, socio-cultural and religious factorsadded to the social and political crisis that affect to some countries in the region, they are helping toincrease this problem. Conclusion: The review provides knowledge of the molecular epidemiologyof the virus. Its use and correct interpretation will allow establishing adequate management andcontainment measures in order to recover the eradicated disease condition in the Americas.

Epidemiología molecular de Klebsiella pneumoniae resistentes a los antibióticos betalactámicos aislados de centros asistenciales del estado Aragua-Venezuela / Molecular epidemiology of Klebsiella pneumoniae resistant to beta-lactams antibiotics isolated from health centers of Aragua State-Venezuela

La resistencia de K. pneumoniae a los antibióticos ß-lactámicos es un problema de salud pública. El objetivo fue caracterizar por epidemiología molecular aislados de K. pneumoniae resistentes a los antibióticos ß-lactámicos en cuatro Centros Asistenciales del Estado Aragua y establecer asociaciones entre los genotipos con la resistencia y las variables epidemiológicas. Se procesaron 72 cepas de K. pneumoniae y su resistencia a ß-lactámicos se realizó según las directrices del CLSI. Para la detección fenotípica de ß-lactamasa de Espectro Extendido (BLEE) se usó la sinergia de doble disco, mientras que para detectar metalobetalactamasa (MBLs), carbapemenasas (KPC) y AmpC inducible se utilizaron las combinaciones de discos de EDTA/imipenem/meropenem, ácido fenilborónico/meropenem/imipenem y piperacilina tazobactam/ceftazidima/Imipenem/cefoxitin respectivamente. La tipificación molecular se realizó por la reacción en cadena de la polimerasa de las secuencias repetitivas extragénicas palindrómicas. Solo 35 cepas (48,6%) fueron resistentes a todos los ß-lactámicos. El 34,29%; 31,43% y 31,43% resultaron ser productoras de BLEE, KPC y MBLs respectivamente, y 2,86% AmpC inducible. Se identificaron siete genotipos, donde el tipo B agrupó 23 cepas idénticas que se diseminan clonalmente. Se encontró una relación estadísticamente significativa entre el genotipo, la edad y el género. En conclusión, K. pneumoniae es altamente resistente a los antibióticos ß-lactámicos

K. pneumoniae resistance to ß-lactam antibiotics is a public health problem. The objective was to characterize by molecular epidemiology isolates of K. pneumoniae resistant to ß-lactams in four Health Centers of the Aragua State and establish the association between genotypes with resistance and epidemiological variables. 72 strains of K. pneumoniae were processed and their resistance to ß-lactams was performed according to the CLSI guidelines. Double disc synergy was used for phenotypic detection of Extended Spectrum ß-lactamase or ESBL. Combinations of EDTA/imipenem/meropenem; phenylboronic acid/meropenem/imipenem and piperacillin tazobactam/ ceftazidime/Imipenem/cefoxitin were used to detect metallo-beta-lactamase or MBLs, carbapenemases (KPC) and inducible AmpC respectively. Molecular typing was performed by polymerase chain reaction of palindromic extragenic repetitive sequences. Only 35 strains (48.6%) were resistant to all ß-lactams. 34.29%; 31.43% and 31.43% turned out to be ESBL, KPC and MBLs respectively, and 2.86% inducible AmpC. Seven genotypes were identified, where type B grouped 23 genetically identical strains and clonally spreaded. A statistically significant relationship was found between genotype, age and gender. In conclusion, K. pneumoniae is highly resistant to ß-lactams

Tipificación del cassette cromosómico estafilocócico de Staphylococcus aureus resistentes al meticilino en el estado de Aragua, Venezuela / Typification of the staphylococcal chromosome cassette of methicillin-resistant Staphylococcus aureus in the state of Aragua, Venezuela

RESUMEN Objetivos: Tipificar el casette SCCmec en cepas de Staphylococcus aureus resistentes a meticilino (SARM) en aislados clínicos de centros de salud del Estado Aragua-Venezuela y comparar la presencia de los genotipos SCCmec entre los centros de salud del estado y según el tipo de infección. Materiales y métodos: Durante enero y agosto de 2015 se estudiaron 81 cepas SARM de cuatro centros de salud del estado de Aragua en Venezuela. La resistencia al meticilino se midió con el método de Kirby-Bauer con discos de oxacilina (1 µgr) y cefoxitina (30 µgr). El gen mecA y el SCCmec se analizaron por la técnica de reacción en cadena de polimerasa múltiple. Resultados: 55 aislados (67,9%) amplificaron el gen mecA, y 24 cepas (43,6%) amplificaron el SCCmec. El SCCmec I fue el más frecuente, seguido de SCCmecIV y SCCmec III, representaron el 62,5%, 25% y 12,5%, respectivamente. El SCCmec I fue predominante en el centro de salud A (80%), mientras que el SCCmec IV se encontró en el centro de salud B (60%) y C (100%). En el centro de salud D, 50% resultó ser SCCmec I y 50% SCCmec IVd. Se encontró relación entre el SCCmec y el centro de salud con significancia estadística. En infecciones de piel y tejidos blandos y en las respiratorias predominó el SCCmec I con 63,2% y 50% respectivamente. Conclusiones: La frecuencia de SCCmec I y IV permitirá establecer nuevas medidas en el uso y control de la resistencia a los antibióticos.

ABSTRACT Objective: Typify the SCCmec cassette in methicillin-resistant strains of Staphylococcus aureus in clinical isolates from health centers in the State of Aragua-Venezuela and compare the presence of SCCmec genotypes among the state health centers and according to the type of infection. Materials and methods: 81 MRSA strains from four health centers of the Aragua-Venezuela State were studied. Methicillin resistance was performed with the Kirby-Bauer method with oxacillin (1 µg) and cefoxitin (30 µg) disks. The mecA gene and SCCmec were analyzed by the multiple PCR technique. Results: Only 55 isolates (67.9%) amplified the mecA gene, and 24 strains (43.6%) amplified SCCmec. SCCmec type I was the most frequency, followed by SCCmec IV and SCCmec III, representing 62.5%, 25% and 12.5%, respectively. SCCmec I was predominant in health center A (80%), while in B and C 60% and 100% respectively were SCCmec IV. At health center D, 50% turned out to be SCCmec I and 50% SCCmec IVd. A relationship was found between the SCCmec and the health center with statistical significance. SCCmec I predominated in skin and soft tissue and respiratory infections with 63.2% and 50%, respectively. There was no association between genotype and type of infection with a p value greater than 0.05. Conclusions: The prevalence of SCCmec I and IV will allow establishing new measures in the use of antibiotics and epidemiological control.

Polymorphism in GRHL2 gene may contribute to noise-induced hearing loss susceptibility: a meta-analysis / Polimorfismo no gene GRHL2 pode contribuir para a suscetibilidade à perda auditivainduzida por ruído: uma metanálise

Abstract Instruction: Noise-induced hearing loss is a leading occupational disease caused by gene-environment interaction. The Grainy Like 2, GRHL2, is a candidate gene. In this regard, many studies have evaluated the association between GRHL2 and noise-induced hearing loss, although the results are ambiguous and conflicting. Objective: The purpose of this study was to identify a precise estimation of the association between rs3735715 polymorphism in GRHL2 gene and susceptibility of noise-induced hearing loss. Methods: A comprehensive search was performed to collect data up to July 8, 2018. Finally, 4 eligible articles were included in this meta-analysis comprising 2410 subjects. The pooled odds ratios with 95% confidence intervals were used to evaluate the strength of the association. Results: Significant association was found in the overall population in the dominant model (GA/AA vs. GG, odds ratio = 0.707, 95% confidence interval = 0.594-0.841) and allele model (G allele vs. A allele, odds ratio = 1.189, 95% confidence interval = 1.062-1.333). When stratified by source of the subjects, we also found association between rs3735715 and noise-induced hearing loss risk in the dominant model (GA/AA vs. GG, odds ratio = 0.634, 95% confidence interval = 0.514-0.783) and allele model (G allele vs. A allele, odds ratio = 1.206, 95% confidence interval = 1.054-1.379). Conclusion: Rs3735715 polymorphism in GRHL2 gene may influence the susceptibility of noise-induced hearing loss. Additional large, well-designed and functional studies are needed to confirm this association in different populations.

Resumo Introdução: Perda auditiva induzida por ruído é uma das principais doenças ocupacionais causadas pela interação gene-ambiente. O Grainy Like 2, ou GRHL2 é um gene que tem sido considerado como candidato. Nesse sentido, muitos estudos avaliaram a associação entre o GRHL2 e perda auditiva induzida por ruído, embora os resultados sejam ambíguos e conflitantes. Objetivo: Identificar uma estimativa precisa da associação entre o polimorfismo rs3735715 no gene GRHL2 e a suscetibilidade à perda auditiva induzida por ruído. Método: Uma pesquisa abrangente foi feita para coletar dados até 8 de julho de 2018. No fim, quatro artigos elegíveis foram incluídos nesta metanálise, abrangeram 2.410 indivíduos. As odds ratios agrupadas com intervalos de confiança de 95% foram usadas para avaliar a força da associação. Resultados: Uma associação significante foi encontrada na população geral no modelo de dominância (GA/AA vs. GG, odds ratio = 0,707, intervalo de confiança 95% = 0,594-0,841) e modelo de alelo (alelo G vs. alelo A; odds ratio = 1,189, intervalo de confiança 95% = 1,062 a 1,333). Quando estratificados pelo local de trabalho dos indivíduos, também encontramos associação entre rs3735715 e risco de perda auditiva induzida por ruído no modelo de dominância (GA/AA vs. GG, odds ratio = 0,634, intervalo de confiança 95% = 0,514 ± 0,783) e modelo de alelo (alelo G vs. alelo A; odds ratio = 1,206, intervalo de confiança 95% = 1,054- 1,379). Conclusão: O polimorfismo Rs3735715 no gene GRHL2 pode influenciar a suscetibilidade à perda auditiva induzida por ruído. Estudos adicionais, amplos, bem desenhados e funcionais são necessários para confirmar essa associação em diferentes populações.

Prevalencia y caracterización genotípica de cepas de Staphylococcus aureus resistente a meticilina aisladas en un hospital regional mexicano / Prevalence and genotypic characterization of methicillin-resistant strains of Staphylococcus aureus isolated in a Mexican regional hospital

Resumen Introducción: Staphylococcus aureus es uno de los patógenos con mayor prevalencia en el mundo, asociado a una alta tasa de mortalidad y un rápido desarrollo de resistencia a los antimicrobianos. A pesar de su patogenicidad, su seguimiento epidemiológico en México es escaso. Objetivo: Analizar la epidemiología molecular local y determinar el origen clonal de cepas resistentes a meticilina (RM) aisladas de pacientes internados en el Hospital Central "Dr. Ignacio Morones Prieto". Métodos: Se llevó a cabo un estudio prospectivo de corte transversal, de julio a diciembre de 2016. La caracterización de las cepas se realizó mediante genotipificación Spa, la determinación por RPC punto final de la frecuencia de genes de virulencia específicos y su antibiograma. Resultados: A partir de estos datos, se obtuvo que la prevalencia de S. aureus RM fue de 25,7%, destacando la presencia del tipo Spa t895 en 76% de las cepas resistentes y un patrón similar de susceptibilidad a antimicrobianos. Conclusión: Los resultados de este estudio indican que la prevalencia regional de SARM no se ha modificado en los últimos 10 años y proporcionan información valiosa del origen clonal y los factores de virulencia de las cepas de S. aureus aisladas en la región.

Abstract Background: Staphylococcus aureus is one of most prevalent pathogens in the world associated with a high mortality rate and a rapid development of resistance to antibiotics. Despite its pathogenicity, epidemiological monitoring in Mexico is scarce. Aim: To analyze the local molecular epidemiology and determine the clonal origin of methicillin-resistant (MR) strains isolated from patients admitted to Hospital "Dr. Ignacio Morones Prieto". Methods: A cross-sectional prospective study was carried out from July to December 2016. The characterization of the strains was carried out by Spa genotyping, frequency of specific virulence genes by PCR and antibiogram. Results: The prevalence of MRSA was 25.7%, highlighting the presence of the Spa type t895 in 76% of the resistant strains and a similar pattern of susceptibility to antibiotics. Conclusion: The results of this study indicate that the regional prevalence of MRSA has not changed in the last 10 years and provide valuable information on the clonal origin and the virulence factors of the strains of S. aureus isolated in the region.

Characterization of clinical isolates of Mycobacterium tuberculosis from indigenous peoples of Colombia / Caracterización de aislamientos clínicos de Mycobacterium tuberculosis de pueblos indígenas de Colombia

ABSTRACT Introduction: Tuberculosis continues to be a public health priority. Indigenous peoples are vulnerable groups with cultural determinants that increase the risk of the disease. Objective: To determine molecular epidemiology and phenotypical features and of Mycobacterium tuberculosis isolates from indigenous people in Colombia during the period from 2009 to 2014. Materials and methods: We conducted an analytical observational study; we analyzed 234 isolates to determine their patterns of sensitivity to antituberculosis drugs and their molecular structures by spoligotyping. Results: The isolates came from 41 indigenous groups, predominantly the Wayúu (13.10%) and Emberá Chamí (11.35%). We found 102 spoligotypes distributed among seven genetic families (37.2% LAM, 15.8% Haarlem, 8.1% T, 3.4% U, 2.6% S, 2.1% X, and 0.9%, Beijing). The association analysis showed that the non-clustered isolates were related to prior treatment, relapse, orphan spoligotypes, and the Beijing family. The H family presented an association with the Arhuaco and Camëntŝá indigenous groups, the U family was associated with the Wounaan group, and the T family was associated with the Motilón Barí group. Conclusions: This is the first national study on M. tuberculosis characterization in indigenous groups. The study evidenced that diagnosis in indigenous people is late. We described 53% of orphan patterns that could be typical of the Colombian indigenous population. The high percentage of grouping by spoligotyping (62%) could indicate cases of active transmission, a situation that should be corroborated using a second genotyping marker. A new Beijing spoligotype (Beijing-like SIT 406) was identified in Colombia.

RESUMEN Introducción. La tuberculosis es prioridad de salud pública. Los pueblos indígenas son vulnerables debido a los factores culturales determinantes que aumentan el riesgo de tuberculosis. Objetivo. Determinar la epidemiologia molecular y las características fenotípicas de los aislamientos de Mycobacterium tuberculosis de pueblos indígenas de Colombia entre 2009 y 2014. Materiales y métodos. Se hizo un estudio observacional analítico; se analizaron 234 aislamientos para determinar la sensibilidad a los fármacos antituberculosos y la estructura molecular usando spoligotyping. La información epidemiológica se recolectó utilizando el formato único de vigilancia de micobacterias. Resultados. Los aislamientos provenían de 41 grupos indígenas, principalmente los wayúu (13,10 %) y emberá chamí (11,35 %). Se encontraron 102 genotipos distribuidos en siete familias genéticas (37,2 %, LAM; 15,8 %, Haarlem; 8,1 %, T; 3,4 %, U; 2,6 %, S; 2,1 %, X, y 0,9%, Beijing). El análisis de asociación mostró que los aislamientos no agrupados se asociaron con el tratamiento previo, las recaídas, los genotipos huérfanos y la familia Beijing. La familia H presentó una asociación con los grupos indígenas arhuaco y camëntŝá, la familia U se asoció con el grupo wounaan y la familia T con el grupo motilón barí. Conclusiones. Este es el primer estudio nacional de caracterización de M. tuberculosis en grupos indígenas. Se evidenció que el diagnóstico en indígenas es tardío, y que 53 % de los patrones huérfanos podrían ser típicos de la población indígena colombiana. El alto porcentaje de agrupamiento por spoligotyping (62%) podría indicar casos de transmisión activa, una situación que debe ser corroborada usando un segundo marcador de genotipificación. Se identificó un nuevo genotipo (Beijing-like SIT 406) en Colombia.

Infecciones por Escherichia coli productora de toxina Shiga O121: H19 en pacientes atendidos en Mar del Plata / Infections caused by Escherichia coli producing Shiga O121: H19 toxin in patients treated in Mar del Plata

Escherichia coli productora de toxina Shiga (STEC) O157:H7 es el serotipo más frecuentemente identificado como agente causal de colitis hemorrágica y síndrome urémico hemolítico (SUH), aunque se han descripto más de 100 serotipos con potencial patogénico similar. El objetivo del trabajo fue describir casos de enfermedad humana asociados a la infección por STEC O121:H19, atendidos en la ciudad de Mar del Plata y establecer la relación genética de los aislamientos mediante técnicas de epidemiología molecular. Se observó un amplio espectro en la severidad clínica de los ocho casos estudiados: dos fueron asintomáticos (contactos de SUH), un paciente tuvo diarrea sanguinolenta, y cinco presentaron SUH. Uno de los pacientes con SUH falleció. Las cepas O121:H19 portadoras del genotipo stx2a/eae/ehxA fueron sensibles a los antibióticos ensayados y presentaron por electroforesis en gel de campo pulsado (Xbal-PFGE) distintos patrones de macrorrestricción, con similitud del 84,25%. El patrón AREXKX01.0072, detectado en un SUH y en su contacto, es nuevo en la Base de Datos Nacional de STEC no-O157 de la Argentina. La utilización de métodos estandarizados de detección y tipificación de STEC permite a los laboratorios de referencia monitorear la frecuencia temporal y la distribución geográfica de las cepas circulantes para la prevención y control de estos patógenos asociados a enfermedad humana.

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is the most frequent serotype identified as causative agent of sporadic cases and outbreaks of diarrhea with or without blood, hemorrhagic colitis and hemolytic uremic syndrome (HUS), although more than 100 serotypes have been described of similar pathogenic potential. The aim of the study was to describe cases of human disease associated with STEC O121:H19 infections, assisted in Mar del Plata City, and to establish the genetic relationship of the isolates by molecular epidemiology techniques. A wide spectrum was observed in the clinical severity of the eight cases studied: two were asymptomatic (contacts of HUS), one patient had bloody diarrhea, and five cases presented HUS. One HUS case died. All STEC O121:H19 strains carried the stx2a/eae/ehxA genotype, were sensitive to all antibiotics tested and showed different macrorestriction patterns by pulsed-field gel electrophoresis (Xbal-PFGE), with 84.25% similarity. The pattern AREXKX01.0072, detected in a HUS case and in his contact, is new in the Argentine National Database of non-O157 STEC. The use of standardized methods for detection and typing of STEC allows reference laboratories to monitor the temporal frequency and geographical distribution of circulating strains for the prevention and control of these pathogens associated with human diseases.

Escherichia coli produtora de toxina Shiga (STEC) O157:H7 é o sorotipo mais frequentemente identificado como o agente causador de colite hemorrágica e síndrome hemolítica urêmica (SHU), embora tenham sido descritas mais de 100 sorotipos com potencial patogênico semelhantes. O objectivo foi o de descrever os casos de doença humana associadas com a infecção por STEC O121:H19, assistido, na cidade de Mar del Plata e estabelecer relação genética de isolados utilizando epidemiologia molecular. Um amplo espectro foi observado na severidade clínica dos oito casos estudados, dois eram assintomáticos (contacto SHU), uma paciente teve diarreia com sangue, e cinco tiveram SHU. Um caso de SHU faleceu. As cepas O121:H19 portaram o genótipo stx2a/eae/ehxA, foram sensíveis aos antibióticos testados e apresentaram, por eletroforese em gel de campo pulsado (Xbal-PFGE), diferentes padrões de macrorestrição, com similaridade de 84,25%. O padrão AREXKX01.0072 detectado em SHU e em seu contato, é novo para a Base de Dados Nacional de STEC não-O157 na Argentina. O uso de métodos padrão de detecção e tipagem de STEC permite os laboratórios de referência monitorar frequência temporal e distribuição geográfica de estirpes circulantes para a prevenção e controlo destes agentes patogénicos associados com a doença humana.

Molecular association of pathogenicity and resistance to multiple antimicrobials in Acinetobacter baumannii strains recovered from patients with diverse infectious diseases / Associação molecular de fatores de patogenicidade e resistência a múltiplos antimicrobianos em linhagens de Acinetobacter baumannii recuperados de pacientes com doenças infecciosas diversas

ABSTRACT INTRODUCTION: The success of Acinetobacter baumannii infections can be attributed to its various virulence factors and antimicrobial resistance mechanisms. OBJECTIVE: To evaluate the presence and correlation between different resistance and virulence factors in clinical A. baumannii strains. METHODS: Study conducted at a University Hospital in Belo Horizonte, Minas Gerais, Brazil. The confirmation of Acinetobacter baumannii-calcoaceticus complex was performed by detecting the blaOXA-51 gene through the polymerase chain reaction (PCR), as well as the search for genes: blaOXA-23, 24, 58, 143, blaVIM-1, csuE, ompA and ISAba1. Antimicrobials and metallo-betalactamase (MβL) expression were evaluated by E-test®; and genetic diversity, by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Biofilm formation was classified into four categories according to the mean optical density obtained. RESULTS: 98.4% (61/62) of the strains were resistant to meropenem; 71%, to ceftazidime; and 61.3%, to ampicillin-sulbactam; while 98.4% were sensitive to polymyxin B; and 48.4%, to tigecycline. The production of MβL was detected in 95.2% of the strains. The blaOXA-51 gene was detected in all strains tested; blaVIM-1, in 83.9%; and ISAba1, in 90.3%. On the other hand, the csuE and ompA genes were present in 43.5% and 53.2% of the strains, respectively. CONCLUSION: There was a possible correlation between gentamicin resistant samples and those that were positive for the ompA gene. The csuE gene correlated positively with ISAba1.

RESUMO INTRODUÇÃO: O sucesso das infecções por Acinetobacter baumannii pode ser atribuído a seus vários fatores de virulência e a mecanismos de resistência a antimicrobianos. OBJETIVO: Avaliar a presença e a correlação entre diferentes fatores de resistência e virulência em amostras clínicas de A. baumannii. MÉTODOS: Estudo conduzido em um hospital universitário em Belo Horizonte, Minas Gerais, Brasil. A confirmação do complexo Acinetobacter baumannii-calcoaceticus foi realizada pela detecção do gene blaOXA-51, por meio da reação em cadeia da polimerase (PCR), assim como a pesquisa dos genes: blaOXA-23, 24, 58, 143, blaVIM-1, csuE, ompA e ISAba1. Os antimicrobianos e a expressão das metalobetalactamases (MβL) foram avaliados pelo E-test®; e a diversidade genética, por enterobacterial repetitive intergenic consensus (ERIC)-PCR. A formação de biofilme foi classificada em quatro categorias de acordo com a média da densidade ótica obtida. RESULTADOS: Do total de amostras, 98, 4% (61/62) foram resistentes ao meropenem; 71%, a ceftazidime; e 61, 3%, a ampicilina-sulbactam; enquanto 98, 4% foram sensíveis a polimixina B; e 48, 4%, a tigeciclina. A produção de MβL foi detectada em 95, 2% das amostras. O gene blaOXA-51 foi detectado em todas as amostras testadas; blaVIM-1, em 83, 9%; e ISAba1, em 90, 3%. Por outro lado, os genes csuE e ompA estiveram presentes em 43, 5% e 53, 2% das amostras, respectivamente. CONCLUSÃO: Houve uma possível correlação entre as amostras resistentes a gentamicina e aquelas positivas para o gene ompA. O gene csuE correlacionou-se positivamente com ISAba1.

Molecular characterization of Cryptosporidium parvum and Cryptosporidium hominis GP60 subtypes worldwide / Caracterización molecular de los subtipos de la GP60 de Cryptosporidium parvum y Cryptosporidium hominis alrededor del mundo

ABSTRACT Cryptosporidium is a zoonotic parasite very important in animal health as well as in public health. It is because this is one of the main causes of diarrhea in children, calves, lambs and other variety of youth mammalians in a lot of countries. The globalization has enabled the exchange of biological material in different regions worldwide, encouraging the spread of diseases and exposure to these biological agents to different environmental conditions, inducing adaptation through genetic changes. Based in the polymorphism of the gene for GP60, this review intended to present the distribution of Cryptosporidium parvum and Cryptosporidium hominis in humans and calves worldwide. The subtype that affects cattle more frequently corresponds to IIaA15G2R; while the subtype most frequently isolated from human samples is IaA19G2.

RESUMEN Cryptosporidium es un parásito zoonótico muy importante en salud animal así como en salud pública. Esto se debe a que el parásito se constituye en una de las principales causas de diarrea en niños, terneros, corderos y una gran variedad de mamíferos jóvenes en una gran cantidad de países. Debido a que la globalización ha permitido el intercambio de material biológico en diferentes regiones alrededor del mundo, se ha favorecido la propagación de enfermedades y se han expuesto a los agentes biológicos a diferentes condiciones ambientales, induciendo así la adaptación a través de cambios genéticos. Con base en el polimorfismo del gen GP60, esta revisión pretende presentar la distribución de Cryptosporidium parvum y Cryptosporidium hominis en humanos y terneros alrededor del mundo. El subtipo que afecta con mayor frecuencia al ganado vacuno corresponde a IIaA15G2R1; en tanto que el subtipo aislado con mayor frecuencia a partir de las muestras humanas es IaA19G2.