Detection and differentiation of Entamoeba histolytica and Entamoeba dispar in clinical samples through PCR-denaturing gradient gel electrophoresis

Amebiasis is one of the twenty major causes of disease in Mexico; however, the diagnosis is difficult due to limitations of conventional microscopy-based techniques. In this study, we analyzed stool samples using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to differentiate between Entamoeba histolytica (pathogenic) and E. dispar (non-pathogenic). The target for the PCR amplification was a small region (228 bp) of the adh112 gene selected to increase the sensitivity of the test. The study involved 62 stool samples that were collected from individuals with complaints of gastrointestinal discomfort. Of the 62 samples, 10 (16.1%) were positive for E. histolytica while 52 (83.9%) were negative. No sample was positive for E. dispar. These results were validated by nested PCR-RFLP (restriction fragment length polymorphism) and suggest that PCR-DGGE is a promising tool to differentiate among Entamoeba infections, contributing to determine the specific treatment for patients infected with E. histolytica, and therefore, avoiding unnecessary treatment of patients infected with the non-pathogenic E. dispar.

Variación diurna de la composición bacterioplanctónica y daño en el ADN de la comunidad microbiana de una laguna oligotrófica de los Andes / Diurnal variation in bacterioplankton composition and DNA damage in the microbial community from an Andean

La Laguna Azul es un ambiente oligotrófi co localizado a 4560 m de altura y sometido a elevados niveles de radiación solar. La composición de su comunidad bacterioplanctónica fue analizada empleando la técnica de electroforesis en gradiente desnaturalizante y se investigó el impacto de la radiación ultravioleta cuantifi cando los dímeros de pirimidina (CPD). Además, se expusieron simultáneamente cultivos puros de Acinetobacter johnsonii A2 y Rhodococcus sp. A5 para estudiar la acumulación de CPD. El análisis de los geles mostró siete secuencias pertenecientes a Alpha-proteobacteria (1 banda), Beta-proteobacteria (1 banda), Bacteroidetes (2 bandas), Actinobacteria (1 banda) y Firmicutes (1 banda). A lo largo del día se observaron cambios mínimos en la composición de la comunidad y no se detectaron CPD. A. johnsonii A2 presentó un daño bajo mientras que Rhodococcus sp. A5 no presentó daño en su ADN, sugiriendo que la comunidad bacteriana está muy bien adaptada a este ambiente altamente irradiado

Laguna Azul is an oligotrophic lake situated at 4,560 m above sea level and subject to a high level of solar radiation. Bacterioplankton community composition (BCC) was analysed by denaturing gradient gel electrophoresis and the impact of solar ultraviolet radiation was assessed by measuring cyclobutane pyrimidine dimers (CPD). Furthermore, pure cultures of Acinetobacter johnsonii A2 and Rhodococcus sp. A5 were exposed simultaneously and CPD accumulation was studied. Gel analyses generated a total of 7 sequences belonging to Alpha-proteobacteria (1 band), Beta-proteobacteria (1 band), Bacteroidetes (2 bands), Actinobacteria (1 band), and Firmicutes (1 band). DGGE profi les showed minimal changes in BCC and no CPD was detected even though a high level of damage was found in biodosimeters. A. johnsonii A2 showed low level of DNA damage while Rhodococcus sp. A5 exhibited high resistance since no CPD were detected under natural UV-B exposure, suggesting that the bacterial community is well adapted to this highly solar irradiated environment

Variación diurna en la composición del bacterioplancton y daño del ADN en la comunidad microbiana de un lago oligotrófico andino / Diurnal variation in bacterioplankton composition and DNA damage in the microbial community from an Andean oligotrophic lake

Laguna Azul is an oligotrophic lake situated at 4,560 m above sea level and subject to a high level of solar radiation. Bacterioplankton community composition (BCC) was analysed by denaturing gradient gel electrophoresis and the impact of solar ultraviolet radiation was assessed by measuring cyclobutane pyrimidine dimers (CPD). Furthermore, pure cultures of Acinetobacter johnsonii A2 and Rhodococcus sp. A5 were exposed simultaneously and CPD accumulation was studied. Gel analyses generated a total of 7 sequences belonging to Alpha-proteobacteria (1 band), Beta-proteobacteria (1 band), Bacteroidetes (2 bands), Actinobacteria (1 band), and Firmicutes (1 band). DGGE profiles showed minimal changes in BCC and no CPD was detected even though a high level of damage was found in biodosimeters. A. johnsonii A2 showed low level of DNA damage while Rhodococcus sp. A5 exhibited high resistance since no CPD were detected under natural UV-B exposure, suggesting that the bacterial community is well adapted to this highly solar irradiated environment.

La Laguna Azul es un ambiente oligotrófico localizado a 4560m de altura y sometido a elevados niveles de radiación solar. La composición de su comunidad bacterioplanctónica fue analizada empleando la técnica de electroforesis en gradiente desnaturalizante y se investigó el impacto de la radiación ultravioleta cuantificando los dímeros de pirimidina (CPD). Además, se expusieron simultáneamente cultivos puros de Acinetobacter johnsonii A2 y Rhodococcus sp. A5 para estudiar la acumulación de CPD. El análisis de los geles mostró siete secuencias pertenecientes a Alpha-proteobacteria (1 banda), Beta-proteobacteria (1 banda), Bacteroidetes (2 bandas), Actinobacteria (1 banda) y Firmicutes (1 banda). A lo largo del día se observaron cambios mínimos en la composición de la comunidad y no se detectaron CPD. A. johnsonii A2 presentó un daño bajo mientras que Rhodococcus sp. A5 no presentó daño en su ADN, sugiriendo que la comunidad bacteriana está muy bien adaptada a este ambiente altamente irradiado

The Milk Borne Pathogens of Raw Milk from Some Egyptian Farms in Different Seasons.

Milk has good quality protein and is a unique substance in that it is consumed as fluid milk with minimal processing and also it is the raw material used to manufacture a wide variety of products. Milk is susceptible to contamination by many pathogenic microorganisms, which result in infection and threat to consumer’s health. The aim of this study was to determinate occurrence of pathogenic microorganisms in raw milk in four seasons from different locations in Egypt, the obtained counts results showed that the samples gave the lowest Total Plate Count (TPC) of 3x105cfu/ml in winter’s samples. While, the summer's sample showed the highest TPC of 5.8x107cfu/ml. E. coli count ranged from 2x102cfu/ml to 5.8x 105cfu/ml which the lowest count was noticed in winter’s samples. Staphylococcal count ranged from 2.7 x 103cfu/ml (winter sample) to1.28 x 106cfu/ml (another sample in the same season). These results indicated poor hygienic standard of raw milk from uncontrolled environments and the increased public health risk of those consuming raw milk from such uncontrolled sources and all these tests consume time but with Cultureindependent methods that are based on protocols where total DNA (or RNA) is directly extracted from the substrate it can save time. Coupled with a global analysis, these methods make it possible to study the total diversity from the bulk extract in a single step.

Avaliação da comunidade microbiana, com ênfase para a espécie Enterococus faecalis, em dentes decíduos com necrose pulpar através de técnicas fenotípicas e moleculares / Evaluation of microbiota with emphasis on species of Enterococcus faecalis, in primary teeth root canals with pulp necrosis, using conventional and molecular microbiological techniques

Infecção endodôntica em dentes decíduos tem sido pouca avaliada, apesar da influência destes sobre a dentição permanente. No presente estudo foi avaliada a microbiota, com ênfase na espécie de Enterococcus faecalis, de canais radiculares de dentes decíduos com diagnóstico de necrose pulpar, utilizando-se técnicas microbiológicas convencionais e moleculares. Para tanto, um estudo do tipo seccional, clínico e laboratorial foi desenvolvido, sendo a coleta do material endodôntico realizada na clínica de Odontopediatria da Faculdade de Odontologia da UFRJ. Para o estudo, 244 crianças saudáveis foram examinadas no período de um ano, e destas, 43 se enquadravam nos critérios de inclusão. O material foi coletado do canal radicular utilizando-se cones estéreis de papel, dos quais dois foram inoculados em caldo seletivo-indicador Enterococcosel e os outros dois em TSB-DMSO sob congelamento a -20º C. A identificação de E. faecalis foi realizada a partir do cultivo inicial no caldo e subcultivo em agar sangue para observação de colônias bacterianas características. Testes bioquímicos e enzimáticos e a Reação em Cadeia da Polimerase (PCR) para o gene do rRNA 16S também foram utilizados para identificação da espécie. A técnica de Eletroforese em Gel com Gradiente Desnaturante (DGGE) foi utilizada para avaliação do perfil da comunidade microbiana presentes nos espécimes clínicos. Os resultados mostraram que dos 43 espécimes clínicos obtidos, 18 foram excluídos devido à contaminação no controle. Entre os 25 casos estudados, 10 foram positivos no caldo de enterococcosel, sendo cinco (20%) positivos para a espécie E. faecalis nos testes fenotípicos e na PCR. Outros cinco espécimes foram positivos no caldo, mas as amostras bacterianas não apresentaram bioquímica compatível com a espécie E. faecalis, e foram então submetidas ao seqüenciamento de um fragmento do gene do rRNA 16S. Foram identificados Lactobacillus plantarum (4 amostras) e Lactobacillus rhamnosus (1 amostra). Não houve relação dos dados clínicos com a presença de E. faecalis (p > 0,05). A técnica de DGGE mostrou uma comunidade polimicrobiana nos 25 espécimes analisados e, considerando-se o número de bandas no gel, um número ≥ 20 foi relacionado com pacientes com idade ≤ 4 anos e  20 bandas com pacientes com mais de 4 anos de idade (p  0,05). Relação significativa também foi observada entre idade  4 anos e cárie em dente posterior, assim como entre idade  4 anos e cárie em dente anterior. Trauma como causa de infecção endodôntica foi significativa entre crianças com 4 anos de idade. Os resultados demostram a presença de E. faecalis em infecções endodônticas com necrose pulpar em dentição decídua, confirmando sua presença na cavidade oral destes pacientes. Adicionalmente, a técnica de DGGE mostrou uma comunidade polimicrobiana, indicando associação entre idade do paciente e doença cárie.

Endodontic infections in primary teeth have been poorly evaluated despite their influence on permanent dentition. In the present study we assessed the microbiota, with emphasis on species of Enterococcus faecalis, in primary teeth root canals with pulp necrosis, using conventional and molecular microbiological techniques. Thus, a cross-sectional study of clinical and laboratory data was developed. The material was collected at the endodontic clinic of Pediatric Dentistry, Faculty of Dentistry, UFRJ. For the study, 244 healthy children were examined during one year, and of these, 43 met the inclusion criteria. Material was collected from root canals using sterile paper cones. Four paper cones were used for each canal: two were inoculated in the selective broth indicator Enterococcosel and anothers two placed in TSB-DMSO and frozen at -20 ° C until required. Identification of E. faecalis was initially made using culture in broth and subculture on blood agar for observational characteristics of bacterial colonies. Biochemical and enzymatic analysis as well as Polymerase Chain Reaction (PCR) for the 16S rRNA gene were also used for species identification. The Gradient Gel Electrophoresis Agents denaturants (DGGE) technique was used to assess the profile of the microbial communities present in the clinical specimens. Eighteen (18) of the 43 clinical specimens obtained were excluded due to contamination. Among the 25 cases studied, 10 were positive for the species E. faecalis in Enterococcosel broth, five (20%) were positive in the phenotypic tests and PCR. Another five specimens were positive in the broth medium, but the bacterial samples showed no biochemical species compatible with E. faecalis, and so were subjected to sequencing of a fragment of the 16S rRNA gene. Lactobacillus plantarum were identified (4 samples) and Lactobacillus rhamnosus (1 sample). There was no statistically significant correlation of clinical data with the presence of E. faecalis (p> 0.05). The DGGE analysis showed a community polymicrobial. About 20 bands or more were associated with patients ≤ 4 years old and that lesser 20 bands were associated with patients over 4 years old (p  0,05). A significant relationship was also found between patients > 4 years old and caries in posterior teeth, as well as between patients  4 years and anterior tooth caries. Trauma as the cause of endodontic infection was significant among children  4 years old. The results show the presence of E. faecalis in endodontic infections with pulp necrosis in the primary dentition, confirming its presence in the oral cavity of patients. Additionally, DGGE showed a polymicrobial community in 25 samples obtained, suggesting an association between patient age and tooth decay.

Polymorphism study of small nuclear ribonucleoprotein polypeptide N gene rs220030 by DGGE / 法医学杂志

OBJECTIVE@#To analyze the polymorphism of rs220030, a SNP which is located in the promoter region of small nuclear ribonucleoprotein polypeptide N (SNRPN) gene in the Chinese Han population and to obtain the data of population genetics.@*METHODS@#The denaturing gradient gel electrophoresis (DGGE) method was applied to detect the polymorphism of rs220030 in 100 unrelated and healthy individuals from the Shanghai Han population. The genotyping result of this SNP was confirmed by TaqMan assay in some typical samples.@*RESULTS@#DGGE results showed 4 bands for CT heterozygote, and 1 band for CC or TT homozygote, and those results were confirmed by The TaqMan SNP genotyping assays. Genotyping results showed 34 individuals with CC, 41 with CT and 25 with TT of rs220030. The allele frequencies for C and T were 0.545 and 0.455, respectively. H was 0.500, PIC was 0.373, DP was 0.654, and PE was 0.186. The distribution of genotype frequencies were in Hardy-Weinberg equilibrium.@*CONCLUSION@#DGGE is a quick and effective method in the analysis of SNP polymorphism in small population. Statistical parameters of rs220030 for forensic evaluation meet the requirements for forensic identification and paternity testing.