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Electron. j. biotechnol ; 45: 53-59, May 15, 2020. tab, ilus
Article in English | LILACS | ID: biblio-1177447


BACKGROUND: Helicobacter pylori is a chronic pathogenic bacteria that causes gastric mucosal damage through various host-related and pathogen-related factors. Thus, a single gene research cannot fully explain its pathogenicity. PURPOSE OF STUDY: It is necessary to establish a Helicobacter pylori pathogenic gene transcription factor regulatory network (TFRN) and study its central nodes. RESULTS: The expression data of Helicobacter pylori pathogenic genes were obtained through GEO Datasets of NCBI. The genes were screened using linear model-empirical Bayesian statistics in R language Limma package combined with the conventional t-test; the results identified 1231 differentially expressed genes. The functional analysis (gene ontology-analysis) and signal pathway analysis (pathway-analysis) of differentially expressed genes were performed using the DAVID and KEGG databases, respectively. The pathogenic gene regulatory network was constructed by integrating transcriptional regulatory element database (TRED); the disease-related analysis of the pathogenic genes was conducted using the DAVID annotation tool. Five pathogenic genes (Nos2, Il5, Colla1, Tnf, and Nfkb1) and their transcription factors (Jun, Cebpa, Egrl, Ppara, and Il6) were found to suppress the host immune function and enhance the pathogenicity of Helicobacter pylori by regulating the host immune system. CONCLUSIONS: This effect was largely mediated via three signaling pathways: Tnf pathway, PI3K Akt pathway, and Jak­STAT pathway. The pathogenicity of Helicobacter pylori is closely related to the body's immune and inflammatory system. A better understanding of the correlation of the pathogenic factors with the host immune and inflammatory factors may help to determine the precise pathogenic mechanism of H. pylori infection.

Helicobacter pylori/genetics , Helicobacter pylori/pathogenicity , Computational Biology , Transcription Factors , Cytokines , Virulence Factors , Gastritis/immunology , Gastritis/microbiology , Genes, Bacterial , Immune System , Inflammation
Article in English | WPRIM | ID: wpr-829019


Objective@#Our objective was to investigate the occurrence of opportunistic pathogens and characterize the bacterial community structures in the water system of a pulmonary hospital.@*Methods@#The water samples were collected from automatic and manual faucets in the consulting room, treatment room, dressing room, respiratory ward, and other non-medical rooms in three buildings of the hospital. Quantitative polymerase chain reaction was used to quantify the load of several waterborne opportunistic pathogens and related microorganisms, including spp., spp., and . Illumina sequencing targeting 16S rRNA genes was performed to profile bacterial communities.@*Results@#The occurrence rates of spp., spp., and were 100%, 100%, and 76%, respectively in all samples. Higher occurrence rates of were observed in the outpatient service building (building 1, 91.7%) and respiration department and wards (building 2, 80%) than in the office building (building 3), where no was found. were more abundant in automatic faucets (average 2.21 × 10 gene copies/L) than in manual faucets (average 1.03 × 10 gene copies/mL) ( < 0.01). , , , , , and were the dominant bacterial phyla. Disinfectant residuals, nitrate, and temperature were found to be the key environmental factors driving microbial community structure shifts in water systems.@*Conclusion@#This study revealed a high level of colonization of water faucets by opportunistic pathogens and provided insight into the characteristics of microbial communities in a hospital water system and approaches to reduce risks of microbial contamination.

China , Drinking Water , Microbiology , Genes, Bacterial , Hospitals , Legionella , Microbiota , Mycobacterium , Mycobacterium avium , RNA, Bacterial , RNA, Ribosomal, 16S , Water Quality , Water Supply
Braz. j. biol ; 79(4): 625-628, Nov. 2019. tab
Article in English | LILACS | ID: biblio-1001470


Abstract The isolation of Escherichia coli from food is a major concern. Pathogenic strains of these bacteria cause diseases which range from diarrhea to hemolytic-uremic syndrome. Therefore the virulence genes in E. coli isolates from the mussel ( Mytella guyanensis) commercialized in Cachoeira, Bahia, Brazil were investigated. Samples were purchased from four vendors: two from supermarkets and two from fair outlets. They were conditioned into isothermal boxes with reusable ice and transported to the laboratory for analysis. E. coli strains were isolated in eosin methylene blue agar, preserved in brain-heart infusion medium with 15% glycerol and stored at -20 °C, after microbiological analysis. Virulence genes in the isolated strains were identified by specific primers, with Polymerase Chain Reaction. Twenty-four isolates were obtained, with a prevalence of elt gene, typical from enterotoxigenic infection, in 75% of the isolates. The stx and bfpA genes, prevalent in enterohemorragic and enteropathogenic E. coli, respectively, were not detected. The occurrence of elt virulence-related gene in the E. coli isolates of Mytella guyanensis reveals urgent improvement in food processing, including good handling practices, adequate storage and cooking before consumption, to ensure consumer's health.

Resumo O isolamento de Escherichia coli a partir de alimentos é uma grande preocupação, pois cepas patogênicas desta bactéria podem causar desde diarreia até síndrome hemolítico-urêmica. Diante do exposto, o objetivo do trabalho foi pesquisar genes de virulência em isolados de Escherichia coli provenientes do sururu Mytella guyanensis comercializado na cidade de Cachoeira, Bahia, Brasil. As amostras foram adquiridas de quatro comerciantes, sendo duas de mercados e duas em pontos de venda na feira livre da cidade de Cachoeira, acondicionadas em caixas isotérmicas com gelo reutilizável e transportadas até o laboratório para a análise. Após a análise microbiológica, as cepas de Escherichia coli foram isoladas em ágar Eosina Azul de Metileno e preservadas em caldo Brian Heart Infusion e glicerol a 15% e mantidas a - 20° C. A identificação dos genes de virulência nas cepas isoladas foi realizada utilizando primers específicos, por meio da Reação em Cadeia da Polimerase. Foram obtidos 24 isolados de Escherichia coli, destes a prevalência do gene elt , característico de Escherichia coli enterotoxigênica, foi de 75% dos isolados. Não houve a detecção dos genes stx e bfpA nos isolados, os quais são prevalentes nas cepas de Escherichia coli enterohemorrágica e Escherichia coli enteropatogênica, respectivamente. A presença do gene elt relacionado à virulência de Escherichia coli nos isolados de Mytella guyanensis revela a necessidade da melhoria no processamento, incluindo boas práticas de manipulação, armazenamento adequado e cocção previa ao consumo, visando a garantia da saúde do consumidor.

Animals , Seafood/microbiology , Virulence Factors , Escherichia coli/genetics , Mytilidae/microbiology , Food Microbiology , Genes, Bacterial , Brazil
Electron. j. biotechnol ; 42: 30-41, Nov. 2019. tab, graf, ilus
Article in English | LILACS | ID: biblio-1087456


Background: Gene expression analysis via microarray is widely used in phytobacteria to validate differential gene expression associated with virulence or to compare biological profiles of wild type and mutant strains. Here, we employed DNA microarrays to study the early stages of the infection process (24, 72 and 120 h post-inoculation) of Xanthomonas citri subsp. citri (Xac) infecting Citrus sinensis to interrogate the expression profiles of hypothetical genes. Results: Under infective conditions, 446 genes were up- and 306 downregulated. Outstanding among genes upregulated during infection were those involved in synthesizing the Type 3 Secretion System and effectors, xanthan gum and quorum-sensing induction, and flagellum synthesis and regulation. Additionally, 161 hypothetical genes were up- and 100 were downregulated, 49 of which are known to have a significant biological role. To understand hypothetical gene co-regulation or -expression, nine expression profiles including 158 genes were identified during the three infection phases. Of these, 47 hypothetical genes were identified as having expression profiles associated with at least one connected to a gene associated with adaptation and virulence. Conclusions: Expression patterns of six differentially expressed genes were validated by quantitative reverse transcription polymerase chain reaction, thus demonstrating the effectiveness of this tool in global gene expression analysis in Xac.

Xanthomonas/genetics , Xanthomonas/pathogenicity , Citrus sinensis/microbiology , Virulence , Xanthomonas/growth & development , Gene Expression , Reverse Transcriptase Polymerase Chain Reaction , Oligonucleotide Array Sequence Analysis , Transcriptome , Type III Secretion Systems , Genes, Bacterial
Rev. chil. infectol ; 36(4): 455-460, ago. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1042662


Resumen Introducción: El método de difusión de doble disco se presenta como una alternativa diagnóstica que permite identificar aislados de Staphylococcus aureus susceptibles a clindamicina, ante el aumento de resistencia a meticilina, reduciendo así la posibilidad de fallo en el tratamiento. Objetivo: Determinar la frecuencia de resistencia a clindamicina inducida por eritromicina en S. aureus resistentes a meticilina (SARM) aislados de niños paraguayos. Materiales y Métodos: Estudio observacional, descriptivo, de corte transversal. Se colectaron 145 aislados S. aureus que causaron infecciones de piel y tejidos blandos y osteo-articulares en pacientes pediátricos del Hospital Central del Instituto de Previsión Social en el período de diciembre-2012 a noviembre-2013. La resistencia a clindamicina se determinó por métodos automatizados y de difusión de doble disco. Se realizó reacción de polimerasa en cadena para genes ermA, ermB, ermC y msrA de aislados representativos. Resultados: La resistencia global a meticilina y clindamicina fue de 67 y 13%, respectivamente (11% atribuible al mecanismo de resistencia a clindamicina inducible). Los genes ermC y msrA fueron detectados individualmente en 25 y 17% de los aislados, respectivamente, mientras que un aislado presentó ambos genes en simultáneo. Discusión: La frecuencia de mecanismo de resistencia inducible a clindamicina señala la importancia de los métodos de difusión de doble disco en la práctica microbiológica, así como se encuentran en los límites de puntos de cortes considerados como aceptables para el uso de este antimicrobiano para infecciones cutáneas y osteo-articulares causadas por SARM.

Background: The double disc diffusion method is an alternative diagnostic that allows the identification of Staphylococcus aureus isolates apparently susceptible to clindamycin but that may develop resistance due to an induction phenomena, mainly asociated to the increase in resistance to methicillin, thus increasing the possibility of failure in the treatment. Aim: To determine the frequency of induced clindamycin resistance in methicillin-resistant S. aureus (MRSA) isolated from Paraguayan children. Materials and Methods: In this cross sectional study, we collected 145 S. aureus isolates that caused skin and soft tissue and osteoarticular infections in pediatric patients of the Central Hospital I.P.S. in the period from December-2012 to November-2013. Resistance to clindamycin was determined by automated methods and double disc diffusion. PCR was performed for ermA, ermB, ermC and msrA genes from representative isolates. Results: The global resistance to methicillin and clindamycin was 67 and 13%, respectively (11% attributable to the inducible mechanism). The ermC and msrA genes were detected individually in 25 and 17% of the isolates respectively while an isolate presented both genes simultaneously. Discussion: The frequency of inducible resistance to clindamycin indicates the importance of double disc diffusion methods in microbiological practice, as well as being within the cut off points considered acceptable for the use of this antibiotic for skin infections. and osteoarticular caused by MRSA.

Humans , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Staphylococcal Infections/microbiology , Clindamycin/pharmacology , Drug Resistance, Bacterial/genetics , Methicillin-Resistant Staphylococcus aureus/drug effects , Anti-Bacterial Agents/pharmacology , Paraguay , Polymerase Chain Reaction , Cross-Sectional Studies , Drug Resistance, Bacterial/drug effects , Disk Diffusion Antimicrobial Tests , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Genes, Bacterial
Braz. j. med. biol. res ; 52(3): e8186, 2019. tab, graf
Article in English | LILACS | ID: biblio-989465


Klebsiella pneumoniae is one of the main pathogenic bacteria that causes nosocomial infections, such as pneumonia, urinary tract infection, and sepsis. Therefore, the rapid and accurate detection of K. pneumoniae is important for the timely treatment of infectious patients. This study aimed to establish a loop-mediated isothermal amplification (LAMP) method for the rapid and sensitive detection of K. pneumoniae-specific gene ureR_1 (Gene ID: 11847803). The ureR_1 gene was obtained through local and online BLAST, and the specific primers were designed for its detection. Positive reactions were observed on all 140 K. pneumoniae clinical isolates while all the 82 non-K. pneumoniae clinical isolates were negative. Plasmids with the specific gene and the mouse blood with K. pneumoniae were used for sensitivity analysis. The detection limit of the LAMP was 1 bacterium/reaction. The results showed that the LAMP targeted to ureR_1 is a fast, specific, sensitive, inexpensive, and suitable method for the detection of K. pneumoniae.

Nucleic Acid Amplification Techniques/methods , Genes, Bacterial , Klebsiella pneumoniae/genetics , Plasmids/isolation & purification , Plasmids/genetics , Temperature , Time Factors , Polymerase Chain Reaction/methods , Reproducibility of Results , Sequence Analysis, DNA , DNA Primers/isolation & purification , DNA Primers/genetics , Limit of Detection , Klebsiella pneumoniae/isolation & purification
Article in Chinese | WPRIM | ID: wpr-771515


Ralstonia solanacearum strain PRS-84 used in this study was isolated from diseased Pogostemon cablin plants in our previous study.The competent cells of R.solanacearum strain PRS-84 were transformed by electroporation with Tn5 transposon and then were plated on TTC agar plates containing kanamycin to select for kanamycin-resistant colonies.The detection of kanamycin-resistant gene in kanamycin-resistant colonies was performed by PCR.Further,the flanking fragments of Tn5 transposon insertion site in the mutants were amplified by inverse PCR,and the flanking fragments were sequenced and analyzed.The results indicated that the kanamycin-resistant colonies were obtained in the transformation experiment of R.solanacearum strain PRS-84 by electroporation with Tn5 transposon.A specific band of approximately 700 bp was amplified by PCR from kanamycin-resistant colonies.The flanking sequences of Tn5 transposon insertion site in the transformants were obtained by inverse PCR.After sequencing and sequence analysis of Tn5 transposon insertion site in mutants,we preliminarily speculated that the Tn5 transposon inserted in the typ A gene,rec O gene and gid A gene in three mutants,respectively.A random mutagenesis system of R.solanacearum strain PRS-84 by electroporation with Tn5 transposon has been established,and the Tn5 insertion mutants have been obtained.This study might facilitate the creation of mutant library and the discovery of the virulence gene of R.solanacearum isolated from P.cablin.

DNA Transposable Elements , Electroporation , Genes, Bacterial , Mutagenesis, Insertional , Pogostemon , Microbiology , Ralstonia solanacearum , Genetics , Virulence
Arq. gastroenterol ; 55(4): 390-396, Oct.-Dec. 2018. tab, graf
Article in English | LILACS | ID: biblio-983850


ABSTRACT BACKGROUND: Enteroaggregative Escherichia coli (EAEC) is one of the main acute and chronic diarrhea causes both in children and adults, mainly in developing countries. OBJECTIVE: The aim of the present study is to characterize EAEC strains isolated from faecal samples and to identify genes potentially contributing to virulence, biofilm production and antimicrobial resistance in children admitted to a pediatric hospital in Porto Velho, Rondônia State. METHODS: The total of 1,625 E. coli specimens were isolated from 591 children in the age group 6 years or younger who were hospitalized in Cosme and Damião Children Hospital in Porto Velho, between February 2010 and February 2012, with acute gastroenteritis. Colonies suggestive of E. coli were subjected to polymerase chain reaction testing in order to identify the virulence factors. The in vitro adhesion assays using HEp-2 adherence were tests. Biofilm detection through spectrophotometry and antimicrobial susceptibility tests were conducted in the disk diffusion method. RESULTS: The mentioned study examined 591 stool samples from children with diarrhea. Diarrheogenic E. coli was found in 27.4% (162/591) of the children. EAEC was the diarreagenic E. coli most frequently associated with diarrhea 52.4% (85/162), which was followed by enteropathogenic E. coli 43.8% (71/162), enterotoxigenic E. coli 2.4% (4/162), and enterohemorrhagic E. coli 1.2% (2/162). The aggR gene was detected in 63.5% (54/85) of EAEC isolates; moreover, statistically significant correlation was observed among typical EAEC (aggR) and aatA (P<0.0001), irp2 (P=0.0357) and shf (P=0.0328). It was recorded that 69% (59/85) of the 85 analyzed EAEC strains were biofilm producers; 73% (43/59) of the biofilm producers carried the aggR gene versus 42.3% (11/26) of non-producers (P=0.0135). In addition, there was association between the aatA gene and biofilm production; 61% (36/59) of the samples presented producer strains, versus 19.2% (5/26) of non-producers (P<0.0004). Antibiotic sensitivity test evidenced that most EAEC were ampicillin 70.6% (60/85), sulfamethoxazole 60% (51/85), tetracycline 44.7% (38/85) and cefotaxime 22.4% (19/85) resistant. CONCLUSION: As far as it is known, the present study is pioneer in Northern Brazil to investigate EAEC virulence factors and to show the antimicrobial susceptibility of EAEC strains isolated from children with diarrhea.

RESUMO CONTEXTO: A Escherichia coli enteroagregativa (EAEC) é um dos principais agentes causadores de diarreia aguda e crônica em crianças e adultos, principalmente em países em desenvolvimento. OBJETIVO: Caracterizar cepas de EAEC isoladas de amostras fecais e identificar genes que potencialmente contribuem para a virulência, produção de biofilme e resistência antimicrobiana em crianças internadas em um hospital pediátrico em Porto Velho, Rondônia. MÉTODOS: Um total de 1.625 cepas de E. coli foram isolados de 591 crianças com gastroenterite aguda na faixa etária de 6 anos que foram internadas no Hospital Infantil Cosme e Damião na cidade de Porto Velho, entre fevereiro de 2010 e fevereiro de 2012. Colônias sugestivas de E. coli foram submetidas a reação em cadeia da polimerase para identificação de fatores de virulência. O ensaio de adesão in vitro foi desenvolvido com célula HEp-2. A detecção de biofilme foi realizada através do teste de espectrofotometria e os testes de susceptibilidade aos antimicrobiana foram realizados através do método de difusão em disco. RESULTADOS: A E. coli diarreiogênica foi encontrada em 27,4% (162/591) das crianças e a EAEC foi a E. coli diarreiogênica mais frequentemente associada à diarreia com 52,4% (85/162), seguida pela E. coli enteropatogênica 43,8% (71/162), E. coli enterotoxigênica 2,4% (4/162) e E. coli enterohemorrágica 1,2% (2/162). O gene aggR foi detectado em 63,5% (54/85) dos isolados de EAEC com correlação estatisticamente significante entre esse gene com os genes aatA (P<0,0001), irp2 (P=0,0357) e shf (P=0,0328). Neste estudo 69% (59/85) das cepas de EAEC eram produtoras de biofilme, destas 73% (43/59) possuíam o gene aggR, ao passo que entre as não produtoras 42,3% (11/26) possuíam o gene (P=0,0135). Essa associação também foi observada com o gene aatA, presente em 61% (36/59) das cepas produtoras e em 19,2% (5/26) das não produtoras (P<0,0004). O teste de sensibilidade aos antibimicrobianos evidenciou que a maioria das EAEC eram resistentes a ampicilina 70,6% (60/85), ao sulfametoxazol 60% (51/85), a tetraciclina 44,7% (38/85) e a cefotaxima 22,4% (19/85). CONCLUSÃO: Este é o primeiro estudo no Norte do Brasil sobre a investigação dos fatores de virulência de EAEC mostrando a susceptibilidade antimicrobiana de cepas de EAEC isoladas de crianças com diarreia.

Humans , Male , Female , Infant , Child, Preschool , Biofilms/growth & development , Diarrhea/microbiology , Escherichia coli/isolation & purification , Escherichia coli/physiology , Escherichia coli Infections/microbiology , Virulence/genetics , Brazil/epidemiology , Microbial Sensitivity Tests , Polymerase Chain Reaction , Prevalence , Diarrhea/epidemiology , Escherichia coli/drug effects , Escherichia coli Infections/epidemiology , Feces/microbiology , Genes, Bacterial/genetics
Braz. j. biol ; 78(3): 421-428, Aug. 2018. tab, graf
Article in English | LILACS | ID: biblio-951563


Abstract Wolbachia (Hertig) endosymbionts are extensively studied in a wide range of organisms and are known to be transmitted through the egg cytoplasm to the offsping. Wolbachia may cause several types of reproductive modifications in arthropods. In Trichogramma species, parthenogenesis-inducing Wolbachia bacteria allow females wasps to produce daughters from unfertilized eggs and these bacteria are present in at least 9% of all Trichogramma species. Phylogenetic studies have led to the subdivision of the Wolbachia clade in five supergroups (A, B, C, D and E) and Wolbachia from Trichogramma belong to supergroup B. Here, using the wsp gene, four groups of Wolbachia that infect Trichogramma species were distinguished and the addition of a new group "Ato" was suggested due to the addition of Wolbachia from Trichogramma atopovirilia (Oatman and Platner). Specific primers were designed and tested for the "Ato" group. Seventy-five percent of all evaluated Wolbachia strains from Trichogramma fell within "Sib" group.

Resumo Endosimbiontes do gênero Wolbachia (Hertig) são extensivamente estudados em uma ampla gama de organismos e são conhecidos por serem transmitidos via citoplasma do ovo hospedeiro para seu descendente. Wolbachia pode causar vários tipos de alterações reprodutivas nos artrópodes. Nas espécies de Trichogramma, a reprodução partenogenética induzida por Wolbachia, possibilita as fêmeas dos parasitoides a produção de fêmeas a partir de ovos não fertilizados e estas bactérias estão presentes em pelo menos 9% de todas as espécies de Trichogramma. Estudos filogenéticos têm levado a subdivisão do clado Wolbachia em cinco supergrupos (A, B, C, D and E). Wolbachia em Trichogramma pertence ao supergrupo B. Com o gene wsp foi possível se distinguir quatro grupos de Wolbachia que infectam Trichogramma e adicionar um novo grupo (Ato) devido a inclusão de Wolbachia detectada em Trichogramma atopovirilia (Oatman and Platner, 1983). Primers específicos foram construídos e testados para o grupo "Ato". Setenta e cinco por cento de todas as linhagens de Wolbachia que infectam Trichogramma se enquadraram dentro do grupo "Sib".

Animals , Female , Bacterial Outer Membrane Proteins/metabolism , Wasps/microbiology , DNA Primers/genetics , Alphaproteobacteria/metabolism , Wolbachia/genetics , Genes, Bacterial/genetics , Phylogeny , Reproduction , Species Specificity , Symbiosis , Wasps/genetics
Rev. Soc. Bras. Med. Trop ; 51(5): 603-609, Sept.-Oct. 2018. tab, graf
Article in English | LILACS | ID: biblio-957466


Abstract INTRODUCTION: The behavior of methicillin-resistant Staphylococcus aureus (MRSA) isolated from central venous catheter-related infection was evaluated to determine its biofilm potential, antimicrobial resistance, and adhesion genes. METHODS: A total of 1,156 central venous catheters (CVC) were evaluated to screen for pathogens. Antimicrobial sensitivity, biofilm formation potential, and molecular analysis of MRSA were examined following standard guidelines. RESULTS: Of the 1,156 samples, 882 (76%) were colonized by bacteria or candida. Among the infected patients, 69% were male and 36% were female with median age of 32 years. Staphylococcus aureus infected 39% (344/882) of CVCs in patients. Of the 59% (208/344) of patients with MRSA, 57% had community acquired MRSA and 43% had hospital acquired MRSA. Linezolid and vancomycin killed 100% of MRSA; resistance levels to fusidic acid, doxycycline, clindamycin, azithromycin, amikacin, trimethoprim-sulfamethoxazole, gentamycin, tobramycin, and ofloxacin were 21%, 42%, 66%, 68%, 72%, 85%, 95%, 97%, and 98% respectively. Strong biofilm was produced by 23% of samples, moderate by 27%, and weak by 50% of MRSA. The presence of adhesion genes, sdrC and sdrD (90%), eno (87%), fnbA (80%), clfA and sdrE (67%), fnbB, sdrD (61%), and cna (51%), in most MRSA samples suggested that the adhesion genes are associated with biofilm synthesis. CONCLUSIONS: The superbug MRSA is a major cause of CVC-related infection. Antibiotic resistance to major classes of antibiotics and biofilm formation potential enhanced superbug MRSA virulence, leading to complicated infection. MRSA causes infection in hospitals, communities, and livestock.

Humans , Male , Female , Child , Adolescent , Adult , Young Adult , Staphylococcal Infections/microbiology , Cross Infection/microbiology , Community-Acquired Infections/microbiology , Biofilms/growth & development , Methicillin-Resistant Staphylococcus aureus/physiology , Catheter-Related Infections/microbiology , Anti-Bacterial Agents/pharmacology , Bacterial Adhesion/genetics , Microbial Sensitivity Tests , Biofilms/drug effects , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Methicillin-Resistant Staphylococcus aureus/drug effects , Genes, Bacterial/genetics , Middle Aged
Braz. j. infect. dis ; 22(5): 438-441, Sept.-Oct. 2018. tab, graf
Article in English | LILACS | ID: biblio-1039218


ABSTRACT Acinetobacter baumannii is one of the most frequent Gram-negative opportunistic pathogens associated with hospital-acquired infection worldwide. We briefly describe A. baumannii isolates that were recovered from surrounding ICU bed surfaces, exhibiting multidrug resistance phenotype and belonging to some widely spread clonal complexes of clinical A. baumannii isolates.

Beds/microbiology , Drug Resistance, Multiple, Bacterial/genetics , Acinetobacter baumannii/isolation & purification , Intensive Care Units , Bacteria/isolation & purification , Bacteria/drug effects , Brazil , Microbial Sensitivity Tests , Cross Infection/microbiology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/genetics , Tertiary Care Centers , Genes, Bacterial
Electron. j. biotechnol ; 34: 83-90, july. 2018. tab, ilus, graf
Article in English | LILACS | ID: biblio-1047375


Background: Although the functional redundancy of catechol 1,2-dioxygenase (C12O) genes has been reported in several microorganisms, limited enzymes were characterised, let alone the advantage of the coexistence of the multiple copies of C12O genes. Results: In this study, four novel C12O genes, designated catA, catAI, catAII and catAIII, in the naphthalene-degrading strain Pseudomonas putida ND6, were cloned and characterised. Phylogenetic analysis of their deduced amino acid sequences revealed that the four C12O isozymes each formed independent subtrees, together with homologues from other organisms. All four enzymes exhibited maximum activity at pH 7.4 and higher activity in alkaline than in acidic conditions. Furthermore, CatA, CatAI and CatAIII were maximally active at a temperature of 45°C, whereas a higher optimum temperature was observed for CatAII at a temperature of 50°C. CatAI exhibited superior temperature stability compared with the other three C12O isozymes, and kinetic analysis indicated similar enzyme activities for CatA, CatAI and CatAII, whereas that of CatAIII was lower. Significantly, among metal ions tested, only Cu2+ substantially inhibited the activity of these C12O isozymes, thus indicating that they have potential to facilitate bioremediation in environments polluted with aromatics in the presence of metals. Moreover, gene expression analysis at the mRNA level and determination of enzyme activity clearly indicated that the redundancy of the catA genes has increased the levels of C12O. Conclusion: The results clearly imply that the redundancy of catA genes increases the available amount of C12O in P. putida ND6, which would be beneficial for survival in challenging environments.

Pseudomonas putida/enzymology , Pseudomonas putida/genetics , Catechol 1,2-Dioxygenase/genetics , Temperature , Biodegradation, Environmental , Cloning, Molecular , Catechol 1,2-Dioxygenase/analysis , Catechol 1,2-Dioxygenase/metabolism , Genes, Bacterial , Hydrogen-Ion Concentration , Isoenzymes , Metals
Arq. gastroenterol ; 55(2): 122-127, Apr.-June 2018. tab, graf
Article in English | LILACS | ID: biblio-950513


ABSTRACT BACKGROUND: The association between infection with Helicobacter pylori and different gastroduodenal diseases is related to bacterial, host and environmental factors. Studies have demonstrated an association between the genetic diversity of H. pylori, especially in the vacA and cagA genes, and the development of digestive diseases such as peptic ulcer and gastric cancer. In addition, the nature of the host inflammatory response may explain these different manifestations of infection caused by this microorganism. In this respect, host factors that regulate the immune and inflammatory responses involving the functional interaction of H. pylori infection with different components of the immune system, particularly T cells, in gastroduodenal diseases still need further investigation. OBJECTIVE: To characterize the immune response, including immunity induced by infection with H. pylori, especially virulent strains (vacA alleles and cagA gene), by analyzing the cytokine profile and T-cell population present in gastroduodenal diseases in a Brazilian population. METHODS: In a prospective study, gastric biopsies were collected from 554 patients with different gastroduodenal diseases for histological analysis and for the determination of bacterial genotype and cytokine production (IL-4, IL-10, IFN-γ and IL-12) by ELISA. RESULTS: The predominant genotype of the H. pylori strains isolated from the patients studied was s1m1cagA+, which was more common among patients with gastric ulcer, duodenal ulcer and gastric cancer. A significant association was observed between the s1m1cagA+ genotype and a higher degree of inflammation, higher neutrophil activity and the development of intestinal metaplasia. The gastric concentrations of IFN-γ and IL-12 were significantly higher in patients infected with H. pylori than in uninfected individuals. Higher levels of these cytokines were detected in patients with gastric ulcer and cancer, while the levels of IL-4 and IL-10 in the gastric mucosa were lower in these patients. In addition, IFN-γ and IL-12 concentrations in gastric biopsies were higher in patients infected with the virulent s1m1cagA+ genotype. In contrast, IL-4 and IL-10 levels were higher in tissue infected with s2m2cagA in gastric biopsies. CONCLUSION: Our study shows that the interaction between the type of infectious strain and the Th1 immune response can influence and perpetuate gastric inflammation, and thus contributes to the development of the different clinical manifestations of H. pylori infection.

RESUMO CONTEXTO: A associação da infecção por Helicobacter pylori com diferentes doenças gastroduodenais pode estar associada a fatores bacterianos, do hospedeiro e do ambiente. Nesse contexto, estudos têm demonstrado que a diversidade genética do H. pylori, sobretudo nos genes vacA e cagA, está associada ao desenvolvimento de doenças gastroduodenais como a úlcera péptica e o câncer gástrico. Além disso, a natureza da resposta inflamatória do hospedeiro pode explicar essas diferentes manifestações da infecção por esse microrganismo. Portanto, fatores do hospedeiro que regulam as respostas imunológica e inflamatória, envolvendo a interação funcional da infecção por H. pylori com diferentes membros do compartimento imunológico, especialmente respostas imunes de células T nas doenças gastroduodenais, ainda precisam ser melhor estudados. OBJETIVO: Caracterizar a resposta imune, incluindo imunidade induzida por infecção pelo H. pylori, especialmente com cepas virulentas de H. pylori (alelos vacA e gene cagA), através da análise do perfil de citocinas e da caracterização da população de células T presentes em doenças gastroduodenais em nossa população. MÉTODOS: Em um estudo prospectivo, foram coletadas biópsias gástricas de 554 pacientes portadores das diferentes doenças gastroduodenais. Nas amostras biológicas destes pacientes foi realizada a determinação do genótipo bacteriano e a detecção das citocinas IL-4, IL-10, INF-γ e IL-12 através do método Elisa. Foram obtidas biópsias gástricas para avaliação histológica. RESULTADOS: Observamos que o genótipo predominante nas cepas de H. pylori isoladas dos pacientes estudados foi s1m1cagA positivo, sendo mais frequentes entre os pacientes com úlcera gástrica, úlcera duodenal e câncer gástrico. Houve associação significativa das cepas com o genótipo s1m1cagA positivo com maior grau de inflamação, atividade neutrofílica e desenvolvimento de metaplasia intestinal. As concentrações gástricas de INF-γ e IL-12 foram significativamente mais elevadas em pacientes infectados pelo H. pylori do que nos não infectados. Foram detectados níveis mais elevados dessas citocinas nos portadores de úlcera e câncer gástrico, sendo que nesses pacientes foram observados níveis mais baixos de IL-4 e IL-10 na mucosa gástrica. Além disso, as concentrações de INF-γ e IL-12 em biópsias gástricas, foram mais elevadas nos pacientes portadores das cepas bacterianas virulentas s1m1cagA+. Contrariamente, os níveis de IL-4 e IL-10 foram maiores em tecido infectado por cepas s2m2cagA. Pacientes com maior grau de inflamação, de atividade neutrofílica e presença de metaplasia intestinal, apresentaram níveis mais elevados de INF-γ e IL-12 e uma concentração mais baixa de IL-4 e IL-10 nas biópsias gástricas. CONCLUSÃO: Nosso estudo demonstra que a interação entre o tipo de cepa infectante e resposta imunológica com perfil Th1, podem influenciar e perpetuar a inflamação gástrica contribuindo para o desenvolvimento de diferentes manifestações clínicas na infecção pelo H. pylori.

Humans , Male , Female , Adolescent , Adult , Aged , Aged, 80 and over , Young Adult , Stomach Neoplasms/immunology , Helicobacter pylori/genetics , Helicobacter Infections/immunology , Duodenal Ulcer/immunology , Gastric Mucosa/immunology , Gastritis/immunology , Stomach Neoplasms/microbiology , Bacterial Proteins/genetics , DNA, Bacterial , Polymerase Chain Reaction , Prospective Studies , Cytokines/biosynthesis , Helicobacter pylori/isolation & purification , Helicobacter Infections/microbiology , Duodenal Ulcer/microbiology , Gastric Mucosa/microbiology , Gastric Mucosa/pathology , Gastritis/microbiology , Genes, Bacterial/immunology , Genotype , Middle Aged , Antigens, Bacterial/genetics
Rev. chil. infectol ; 35(2): 147-154, abr. 2018. tab, graf
Article in Spanish | LILACS | ID: biblio-959424


Resumen Introducción: La resistencia de enterobacterias a quinolonas se ha difundido por el mundo, fenómeno presente también en Venezuela. El mecanismo de esta resistencia pudiera estar mediado por genes incluidos en el cromosoma bacteriano o transmitirse en el interior de plásmidos. Objetivo: Evaluar la resistencia a quino-lonas, codificada por genes qnr, presentes en cepas de enterobacterias, aisladas en el Hospital Universitario de Cumaná, Venezuela. Métodos: A las cepas obtenidas se les realizaron pruebas de susceptibilidad antimicrobiana a quinolonas, β-lactámicos y aminoglucósidos. La presencia del gen qnr se determinó por RPC. Las enterobacterias portadoras del gen qnr fueron sometidas al proceso de conjugación bacteriana para comprobar su capacidad de transferencia. A las transconjugantes obtenidas se les realizó pruebas de susceptibilidad antimicrobiana y RPC para comprobar la transferencia de los genes. Resultados: Se encontraron elevados porcentajes de resistencia antimicrobiana a quinolonas y betalactámicos. El 33,6% de las cepas eran portadoras del gen qnrB, y 0,9% del gen qnrA. Se obtuvieron 23 cepas transconjugantes; de éstas, 20 portaban el gen qnrB, no se observó la presencia de qnrA. Discusión: En conclusión, el elevado porcentaje de genes qnr encontrado en las enterobacterias aisladas, y comprobada la presencia de éstos en plásmidos transferibles, complica la aplicación de tratamientos basados en quinolonas y fluoroquinolonas, por lo que es recomendable el uso racional de estos antimicrobianos, y proponer la rotación de la terapia antimicrobiana, a fin de evitar la selección de cepas resistentes.

Background: Enterobacteria resistant to quinolones is increasing worldwide, including Venezuela. The mechanism for this resistance could be due to genes included in the chromosome or in transmissible plasmids. Aim: To evaluate the resistance to quinolones, coded by qnr genes present in enterobacteria species, isolated in the University Hospital of Cumana, Venezuela. Methods: Antimicrobial susceptibility tests to quinolones, beta-lactams and aminoglycosides were carried out to all the isolates. The presence of qnr genes were determined by PCR. The isolates carrying the qnr genes were used for bacterial conjugation tests to determine the presence of transferable plasmids. Antimicrobial susceptibility tests and PCR were carried out in the transconjugants to verify the transfer of the genes. Results: High levels of antimicrobial resistance to quinolones and beta-lactams were found among the isolates. We found that 33.6% of the isolates carry the qnrB gene and 0.9% qnr A gene. Of the 23 transconjugants, 20 showed to have qnrB gene, but none qnrA. Discussion: We concluded that the high frequency of qnr genes found in the enterobacteria isolates and their presence on transferable plasmids, complicate the use of quinolones for the treatment of bacterial infections, thus, a treatment plan should be designed with the rational use and the rotation of different types of antimicrobials, in order to avoid the selection of increasingly resistant strains.

Plasmids , Quinolones/pharmacology , beta-Lactam Resistance/genetics , Drug Resistance, Bacterial/genetics , Enterobacteriaceae/genetics , Enterobacteriaceae Infections/genetics , Gram-Negative Bacteria/genetics , Anti-Bacterial Agents/pharmacology , Venezuela , beta-Lactamases/genetics , DNA, Bacterial/genetics , Microbial Sensitivity Tests , Polymerase Chain Reaction , Sequence Analysis, DNA , Escherichia coli Proteins , Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/microbiology , Genes, Bacterial , Gram-Negative Bacteria/classification , Hospitals, University
Salud pública Méx ; 60(1): 29-40, Jan.-Feb. 2018. tab, graf
Article in English | LILACS | ID: biblio-903844


Abstract: Objective: To compare the genetic determinants involved in plant colonization or virulence in the reported genomes of K. variicola, K. quasipneumoniae and K. pneumoniae. Materials and methods: In silico comparisons and Jaccard analysis of genomic data were used. Fimbrial genes were detected by PCR. Biological assays were performed with plant and clinical isolates. Results: Plant colonization genes such as cellulases, catalases and hemagglutinins were mainly present in K. variicola genomes. Chromosomal β-lactamases were characteristic of this species and had been previously misclassified. K. variicola and K. pneumoniae isolates produced plant hormones. Conclusions: A mosaic distribution of different virulence- and plant-associated genes was found in K. variicola and in K. quasipneumoniae genomes. Some plant colonizing genes were found mainly in K. variicola genomes. The term plantanosis is proposed for plant-borne human infections.

Resumen: Objetivo: Comparar genes de colonización de plantas o de virulencia en los genomas reportados de K. variicola, K. quasipneumoniae y K. pneumoniae. Material y métodos: Se utilizaron análisis in silico y de Jaccard. Por PCR se detectaron genes de fimbrias. Se realizaron ensayos biológicos con aislados de plantas y clínicos. Resultados: Los genes de colonización de plantas como celulasas, catalasas y hemaglutininas se encontraron principalmente en genomas de K. variicola. Las β-lactamasas cromosómicas son características de la especie y en algunos casos estaban mal clasificadas. K. variicola y K. pneumoniae producen hormonas vegetales. Conclusiones: Se encontró una distribución en mosaico de los genes de asociación con plantas y de virulencia en K. variicola y K. quasipneumoniae. Principalmente en K. variicola se encontraron algunos genes involucrados en la colonización de plantas. Se propone el término plantanosis para las infecciones humanas de origen vegetal.

Humans , Plants/microbiology , Klebsiella Infections/microbiology , Klebsiella/physiology , Bacterial Proteins/physiology , Bacterial Proteins/genetics , Virulence/genetics , Computer Simulation , Disease Reservoirs , Adaptation, Biological/genetics , Genome, Bacterial , Drug Resistance, Multiple, Bacterial , Gene Ontology , Genes, Bacterial , Klebsiella/enzymology , Klebsiella/genetics , Klebsiella/pathogenicity
Mem. Inst. Oswaldo Cruz ; 113(10): e180192, 2018. tab, graf
Article in English | LILACS | ID: biblio-1040581


Raoultella planticola is an emerging zoonotic pathogen that is associated with rare but life-threatening cases of bacteremia, biliary tract infections, and urinary tract infections. Moreover, increasing antimicrobial resistance in the organism poses a potential threat to public health. In spite of its importance as a human pathogen, the genome of R. planticola remains largely unexplored and little is known about its virulence factors. Although lipopolysaccharides has been detected in R. planticola and implicated in the virulence in earlier studies, the genetic background is unknown. Here, we report the complete genome and comparative analysis of the multidrug-resistant clinical isolate R. planticola GODA. The complete genome sequence of R. planticola GODA was sequenced using single-molecule real-time DNA sequencing. Comparative genomic analysis reveals distinct capsular polysaccharide synthesis gene clusters in R. planticola GODA. In addition, we found bla TEM-57 and multiple transporters related to multidrug resistance. The availability of genomic data in open databases of this emerging zoonotic pathogen, in tandem with our comparative study, provides better understanding of R. planticola and the basis for future work.

Polysaccharides, Bacterial/biosynthesis , Genome, Bacterial/genetics , Enterobacteriaceae/genetics , Genes, Bacterial/genetics , Polysaccharides, Bacterial/genetics , Bacterial Capsules/genetics , Enterobacteriaceae/classification
Rev. chil. infectol ; 35(1): 7-14, 2018. tab, graf
Article in Spanish | LILACS | ID: biblio-899771


Resumen Desde el inicio de la era antimicrobiana se han ido seleccionando gradualmente cepas de Staphylococcus aureus resistentes a antimicrobianos de amplio uso clínico. Es así como en 1960 se describen en Inglaterra las primeras cepas resistentes a meticilina, y algunos años después son informadas en hospitales de Chile. Actualmente, S. aureus resistente a penicilinas antiestafilocóccicas es endémico en los hospitales de nuestro país y del mundo, siendo responsable de una alta morbimortalidad. La resistencia es mediada habitualmente por la síntesis de una nueva transpeptidasa, denominada PBP2a o PBP2' que posee menos afinidad por el β-lactámico, y es la que mantiene la síntesis de peptidoglicano en presencia del antimicrobiano. Esta nueva enzima se encuentra codificada en el gen mecA, a su vez inserto en un cassette cromosomal con estructura de isla genómica, de los cuales existen varios tipos y subtipos. La resistencia a meticilina se encuentra regulada, principalmente, por un mecanismo de inducción de la expresión del gen en presencia del β-lactámico, a través de un receptor de membrana y un represor de la expresión. Si bien se han descrito mecanismos generadores de resistencia a meticilina mec independientes, son categóricamente menos frecuentes.

Staphylococcus aureus isolates resistant to several antimicrobials have been gradually emerged since the beginning of the antibiotic era. Consequently, the first isolation of methicillin-resistant S. aureus occurred in 1960, which was described a few years later in Chile. Currently, S. aureus resistant to antistaphylococcal penicillins is endemic in Chilean hospitals and worldwide, being responsible for a high burden of morbidity and mortality. This resistance is mediated by the expression of a new transpeptidase, named PBP2a or PBP2', which possesses lower affinity for the β-lactam antibiotics, allowing the synthesis of peptidoglycan even in presence of these antimicrobial agents. This new enzyme is encoded by the mecA gene, itself embedded in a chromosomal cassette displaying a genomic island structure, of which there are several types and subtypes. Methicillin resistance is mainly regulated by an induction mechanism activated in the presence of β-lactams, through a membrane receptor and a repressor of the gene expression. Although mec-independent methicillin resistance mechanisms have been described, they are clearly infrequent.

Bacterial Proteins/genetics , Genetic Structures/genetics , Penicillin-Binding Proteins/genetics , Methicillin-Resistant Staphylococcus aureus/genetics , Bacterial Proteins/drug effects , Molecular Structure , Chromosomes, Bacterial/drug effects , Penicillin-Binding Proteins/drug effects , Methicillin-Resistant Staphylococcus aureus/drug effects , Genes, Bacterial/drug effects , Methicillin/pharmacology , Methicillin/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry
Frontiers of Medicine ; (4): 196-205, 2018.
Article in English | WPRIM | ID: wpr-772750


We employed a multiplex polymerase chain reaction (PCR) coupled with capillary electrophoresis (mPCR-CE) targeting six Clostridium difficile genes, including tpi, tcdA, tcdB, cdtA, cdtB, and a deletion in tcdC for simultaneous detection and characterization of toxigenic C. difficile directly from fecal specimens. The mPCR-CE had a limit of detection of 10 colony-forming units per reaction with no cross-reactions with other related bacterial genes. Clinical validation was performed on 354 consecutively collected stool specimens from patients with suspected C. difficile infection and 45 isolates. The results were compared with a reference standard combined with BD MAX Cdiff, real-time cell analysis assay (RTCA), and mPCR-CE. The toxigenic C. difficile species were detected in 36 isolates and 45 stool specimens by the mPCR-CE, which provided a positive rate of 20.3% (81/399). The mPCR-CE had a specificity of 97.2% and a sensitivity of 96.0%, which was higher than RTCA (x = 5.67, P = 0.017) but lower than BD MAX Cdiff (P = 0.245). Among the 45 strains, 44 (97.8%) were determined as nonribotype 027 by the mPCR-CE, which was fully agreed with PCR ribotyping. Even though ribotypes 017 (n = 8, 17.8%), 001 (n = 6, 13.3%), and 012 (n = 7, 15.6%) were predominant in this region, ribotype 027 was an important genotype monitored routinely. The mPCR-CE provided an alternative diagnosis tool for the simultaneous detection of toxigenic C. difficile in stool and potentially differentiated between RT027 and non-RT027.

Clostridium Infections , Diagnosis , Clostridioides difficile , Genetics , Electrophoresis, Capillary , Feces , Microbiology , Genes, Bacterial , Humans , Polymerase Chain Reaction , Ribotyping , Sensitivity and Specificity
Article in English | WPRIM | ID: wpr-776069


Enterotoxigenic Escherichia coli (ETEC) causes neonatal and post-weaning diarrhea in pigs. In order to determine the risk factors, rectal/fecal swabs and visceral organs obtained from pig farms in two regions of South Africa were analyzed microbiologically against risk variables. Seventy-two percent of young pigs were found to be positive for ETEC toxin genes; estB (38.9%), estB/STAP (25%), and estB/LT (13.9%) were dominant. Risk factors for ETEC-diarrhea in pigs include: leaving sick piglets in a pen with healthy piglets [odds ratio (OR) = 33.52; P < 0.0001]; water spillage in pen (OR = 42.87; P < 0.0001); hypothermic piglets (OR = 7.29; P < 0.0001); runt piglets in pen with healthy littermates (OR = 3.65; P < 0.0001); and prolonged use of antibiotics (OR = 3.05; P = 0.05).

Animals , Animals, Newborn , Diarrhea , Epidemiology , Microbiology , Escherichia coli , Genetics , Escherichia coli Infections , Epidemiology , Microbiology , Genes, Bacterial , Prevalence , Rectum , Microbiology , Risk Factors , South Africa , Swine , Swine Diseases , Epidemiology , Microbiology , Weaning
Mycobiology ; : 224-235, 2018.
Article in English | WPRIM | ID: wpr-729776


Temperature is an important environmental factor that can greatly influence the cultivation of Auricularia cornea. In this study, lignin peroxidase, laccase, manganese peroxidase, and cellulose in A. cornea fruiting bodies were tested under five different temperatures (20 °C, 25 °C, 30 °C, 35 °C, and 40 °C) in three different culture periods (10 days, 20 days and 30 days). In addition, the V4 region of bacterial 16S rRNA genes in the substrate of A. cornea cultivated for 30 days at different temperatures were sequenced using next-generation sequencing technology to explore the structure and diversity of bacterial communities in the substrate. Temperature and culture days had a significant effect on the activities of the four enzymes, and changes in activity were not synchronized with changes in temperature and culture days. Overall, we obtained 487,694 sequences from 15 samples and assigned them to 16 bacterial phyla. Bacterial community composition and structure in the substrate changed when the temperature was above 35 °C. The relative abundances of some bacteria were significantly affected by temperature. A total of 35 genera at five temperatures in the substrate were correlated, and 41 functional pathways were predicted in the study. Bacterial genes associated with the membrane transport pathway had the highest average abundance (16.16%), and this increased at 35 °C and 40 °C. Generally, different temperatures had impacts on the physiological activity of A. cornea and the bacterial community in the substrate; therefore, the data presented herein should facilitate cultivation of A. cornea.

Bacteria , Cellulose , Cornea , Fruit , Genes, Bacterial , Genes, rRNA , Laccase , Lignin , Manganese , Membranes , Peroxidase