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1.
Gene ; 715: 144008, 2019 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-31362038

RESUMO

Deinococcus radiodurans is a model microorganism used for studies on DNA repair and antioxidation due to its extraordinary tolerance to ionizing radiation and other DNA-damaging agents. Various transcriptome analyses have revealed that hundreds of genes are induced and that many other genes are repressed during recovery of D. radiodurans following irradiation, suggesting that gene regulation is of great importance for the extreme resistance of this microorganism to ionizing radiation. In this article, we focus on some reported strategies that are employed by D. radiodurans to regulate the genes implicated in its extreme tolerance to ionizing radiation for a comprehensive understanding of the reasons this bacterium can survive such extraordinary stress. We expect this review to shed light on potential radioprotective agents and applications for use in a range of fields.


Assuntos
Reparo do DNA/efeitos da radiação , DNA Bacteriano/metabolismo , Deinococcus/metabolismo , Regulação Bacteriana da Expressão Gênica/efeitos da radiação , Tolerância a Radiação , Radiação Ionizante , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Dano ao DNA , DNA Bacteriano/genética , Deinococcus/genética
2.
BMC Infect Dis ; 19(1): 542, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31221109

RESUMO

BACKGROUND: Tuberculosis rapid molecular assays, including GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit®, are highly sensitive and specific. Such performance does not automatically translate in improved disease control and highly depends on their use, local epidemiology and the diagnostic algorithms they're implemented within. We evaluate the performance of both assays and assess their impact on additional cases notification when implemented within WHO recommended tuberculosis diagnostic algorithms in Madagascar. METHODS: Five hundred forty eight presumptive pulmonary tuberculosis patients were prospectively recruited between November 2013 and December 2014 in Antananarivo, Madagascar, a high TB incidence sub-Saharan African urban setting. Both molecular assays were evaluated as first line or add-on testing following negative smear microscopy. Based on locally defined assay performance characteristics we measure the impact of both assays and WHO-recommended diagnostic algorithms on additional tuberculosis case notifications. RESULTS: High sensitivity and specificity was confirmed for both GeneXpert MTB/RIF® (86.6% (95% CI 81.1-90.7%) and 97.4% (95% CI 94.9-98.8%)) and Loopamp MTBC Detection Kit® (84.6% (95% CI 78.9-89.0%) and 98.4% (95% CI 96.2-99.4%)). Implementation of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® increased tuberculosis diagnostic algorithms sensitivity from 73.6% (95% CI 67.1-79.3%) up to 88.1% (95% CI 82.8-91.9%). This increase was highest when molecular assays were used as add-on testing following negative smear microscopy. As add-on testing, GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® respectively improved case detection by 23.8 and 21.2% (p < 0.05). CONCLUSION: Including GeneXpert MTB/RIF® or Loopamp MTBC Detection Kit® molecular assays for TB detection on sputum samples from presumptive TB cases can significantly increase case notification in TB diagnostic centers. The TB case detection rate is further increased when those tests are use as second-line follow-on testing following negative smear microscopy results. A country wide scale-up and digital integration of molecular-based TB diagnosis assays shows promises for TB control in Madagascar.


Assuntos
Mycobacterium tuberculosis/genética , Técnicas de Amplificação de Ácido Nucleico/métodos , Tuberculose Pulmonar/diagnóstico , Adulto , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Feminino , Humanos , Madagáscar , Masculino , Pessoa de Meia-Idade , Mycobacterium tuberculosis/isolamento & purificação , Kit de Reagentes para Diagnóstico , Sensibilidade e Especificidade , Escarro/microbiologia , Tuberculose Pulmonar/microbiologia
3.
BMC Infect Dis ; 19(1): 553, 2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31234780

RESUMO

BACKGROUND: Kazakhstan remains a high-burden TB prevalence country with a concomitent high-burden of multi-drug resistant tuberculosis. For this reason, we performed an in depth genetic diversity and population structure characterization of Mycobacterium tuberculosis complex (MTC) genetic diversity in Kazakhstan with both patient and community benefit. METHODS: A convenience sample of 700 MTC DNA cultures extracts from 630 tuberculosis patients recruited from 12 out of 14 regions in Kazakhstan, between 2010 and 2015, was independently studied by high-throughput hybridization-based methods, TB-SPRINT (59-Plex, n = 700), TB-SNPID (50-Plex, n = 543). DNA from 391 clinical isolates was successfully typed by two methods. To resolve the population structure of drug-resistant clades in more detail two complementary assays were run on the L2 isolates: an IS6110-NTF insertion site typing assay and a SigE SNP polymorphism assay. RESULTS: Strains belonged to L2/Beijing and L4/Euro-American sublineages; L2/Beijing prevalence totaled almost 80%. 50% of all samples were resistant to RIF and to INH., Subtyping showed that: (1) all L2/Beijing were "modern" Beijing and (2) most of these belonged to the previously described 94-32 sublineage (Central Asian/Russian), (3) at least two populations of the Central Asian/Russian sublineages are circulating in Kazakhstan, with different evolutionary dynamics. CONCLUSIONS: For the first time, the global genetic diversity and population structure of M. tuberculosis genotypes circulating in Kazakhstan was obtained and compared to previous local studies. Results suggest a region-specific spread of a very limited number of L2/Beijing clonal complexes in Kazakhstan many strongly associated with an MDR phenotype.


Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico , Adulto , Idoso , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Evolução Molecular , Variação Genética , Genótipo , Humanos , Cazaquistão/epidemiologia , Masculino , Pessoa de Meia-Idade , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/isolamento & purificação , Técnicas de Amplificação de Ácido Nucleico/métodos , Hibridização de Ácido Nucleico/métodos , Fenótipo , Prevalência , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Adulto Jovem
4.
BMC Infect Dis ; 19(1): 561, 2019 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-31248368

RESUMO

BACKGROUND: In a context of increasing use of Nucleic Acid Amplification Test, diagnoses of Neisseria gonorrhoeae and Chlamydia trachomatis infections among men increased in Europe and USA since 2007. We aimed to describe trends in the incidence of male urethritis in France between 2007 and 2017. METHODS: We analysed male urethritis clinical cases reported by the French GPs' Sentinelles network. RESULTS: GPs reported 1944 cases of male urethritis during the study period. The estimated annual incidence rates in men aged 15 years and older remained stable between 226 cases per 100,000 seen in 2007 and 196 in 2017 (P value = 0.9). A third-generation cephalosporin with macrolide or tetracycline was prescribed in 17.5% of cases in 2009 (27/154) and 32.4% in 2017 (47/145) (P value = 0.0327). CONCLUSIONS: The incidence rates for adult male urethritis diagnosed in primary care have remained stable since 2007 in France in contrast with the increasing trend of Neisseria gonorrhoeae and Chlamydia trachomatis infections based on microbiological surveillance. Using stable clinical definition for male urethritis seems essential to follow correctly epidemiological dynamic.


Assuntos
Chlamydia trachomatis/genética , Neisseria gonorrhoeae/genética , Trichomonas vaginalis/genética , Uretrite/diagnóstico , Adolescente , Adulto , Idoso , Antibacterianos/uso terapêutico , Cefalosporinas/uso terapêutico , Chlamydia trachomatis/isolamento & purificação , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , França/epidemiologia , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Neisseria gonorrhoeae/isolamento & purificação , Técnicas de Amplificação de Ácido Nucleico , Trichomonas vaginalis/isolamento & purificação , Uretrite/tratamento farmacológico , Uretrite/epidemiologia , Uretrite/microbiologia , Adulto Jovem
5.
BMC Infect Dis ; 19(1): 563, 2019 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-31248383

RESUMO

BACKGROUND: Rapid and accurate diagnosis of childhood tuberculosis (TB) is challenging because children are often unable to produce the sputum sample required for conventional tests. Stool is an alternative sample type that is easy to collect from children, and studies investigating the use of stool for molecular detection of Mycobacterium tuberculosis (Mtb) have led to promising results. Our objective was to evaluate stool as an alternative specimen to sputum for Mtb detection in children. We did so using the TruTip workstation (Akonni Biosystems), a novel automated lysis and extraction platform. METHODS: We tested stool samples from 259 children aged 0-14 years old, in Lima, Peru who presented with TB symptoms. Following extraction with TruTip, we detected the presence of Mtb DNA by IS6110 real-time PCR. We calculated assay sensitivity in two groups: (1) children with culture confirmed TB (N = 22); and (2) children with clinically-diagnosed unconfirmed TB (N = 84). We calculated specificity among children in whom TB was ruled out (N = 153). Among children who were diagnosed with TB, we examined factors associated with a positive stool test. RESULTS: Assay sensitivity was 59% (95% confidence interval [CI]: 39-80%) and 1.2% (95% CI: 0.0-6.5%) in children with culture-confirmed and clinically-diagnosed unconfirmed TB, respectively, and specificity was 97% (95% CI: 93-99%). The assay detected Mtb in stool of 7/7 children with smear-positive TB (100% sensitivity; 95% CI: 59-100%), and in 6/15 of children with smear-negative, culture-confirmed TB (40% sensitivity; 95% CI: 16-68%). Older age, smear positivity, culture positivity, ability to produce sputum and cavitary disease were associated with a positive stool result. CONCLUSION: Testing of stool samples with the TruTip workstation and IS6110 amplification yielded sensitivity and specificity estimates comparable to other tests such as Xpert. Future work should include detection of resistance using the TruTip closed amplification system and assay optimization to improve sensitivity in children with low bacillary loads.


Assuntos
Fezes/microbiologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , Tuberculose/diagnóstico , Adolescente , Criança , Pré-Escolar , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/isolamento & purificação , Peru , Sensibilidade e Especificidade , Tuberculose/microbiologia
6.
Emerg Microbes Infect ; 8(1): 857-865, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31169081

RESUMO

Ciprofloxacin resistance in Salmonella has been increasingly reported due to the emergence and dissemination of multiple Plasmid-Mediated Quinolone Resistance (PMQR) determinants, which are mainly located in non-conjugative plasmids or chromosome. In this study, we aimed to depict the molecular mechanisms underlying the rare phenomenon of horizontal transfer of ciprofloxacin resistance phenotype in Salmonella by conjugation experiments, S1-PFGE and complete plasmid sequencing. Two types of non-conjugative plasmids, namely an IncX1 type carrying a qnrS1 gene, and an IncH1 plasmid carrying the oqxAB-qnrS gene, both ciprofloxacin resistance determinants in Salmonella, were recovered from two Salmonella strains. Importantly, these non-conjugative plasmids could be fused with a novel Incl1 type conjugative helper plasmid, which could target insertion sequence (IS) elements located in the non-conjugative, ciprofloxacin-resistance-encoding plasmid through replicative transcription, eventually forming a hybrid conjugative plasmid transmissible among members of Enterobacteriaceae. Since our data showed that such conjugative helper plasmids are commonly detectable among clinical Salmonella strains, particularly S. Typhimurium, fusion events leading to generation and enhanced dissemination of conjugative ciprofloxacin resistance-encoding plasmids in Salmonella are expected to result in a sharp increase in the incidence of resistance to fluoroquinolone, the key choice for treating life-threatening Salmonella infections, thereby posing a serious public health threat.


Assuntos
Antibacterianos/farmacologia , Ciprofloxacino/farmacologia , Conjugação Genética , Farmacorresistência Bacteriana , Plasmídeos/genética , Salmonella/efeitos dos fármacos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/metabolismo , Humanos , Testes de Sensibilidade Microbiana , Plasmídeos/metabolismo , Salmonella/genética , Salmonella/metabolismo , Infecções por Salmonella/microbiologia
7.
Nat Commun ; 10(1): 1731, 2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31043596

RESUMO

Systemic sclerosis (SSc) is a chronic autoimmune disease characterized by fibrosis and vasculopathy. CXCL4 represents an early serum biomarker of severe SSc and likely contributes to inflammation via chemokine signaling pathways, but the exact role of CXCL4 in SSc pathogenesis is unclear. Here, we elucidate an unanticipated mechanism for CXCL4-mediated immune amplification in SSc, in which CXCL4 organizes "self" and microbial DNA into liquid crystalline immune complexes that amplify TLR9-mediated plasmacytoid dendritic cell (pDC)-hyperactivation and interferon-α production. Surprisingly, this activity does not require CXCR3, the CXCL4 receptor. Importantly, we find that CXCL4-DNA complexes are present in vivo and correlate with type I interferon (IFN-I) in SSc blood, and that CXCL4-positive skin pDCs coexpress IFN-I-related genes. Thus, we establish a direct link between CXCL4 overexpression and the IFN-I-gene signature in SSc and outline a paradigm in which chemokines can drastically modulate innate immune receptors without being direct agonists.


Assuntos
DNA Bacteriano/metabolismo , Interferon-alfa/metabolismo , Fator Plaquetário 4/metabolismo , Escleroderma Sistêmico/imunologia , Receptor Toll-Like 9/metabolismo , Adulto , Idoso , Biópsia , Estudos de Casos e Controles , DNA Bacteriano/imunologia , Células Dendríticas/imunologia , Células Dendríticas/metabolismo , Feminino , Voluntários Saudáveis , Humanos , Interferon-alfa/imunologia , Cristais Líquidos , Masculino , Pessoa de Meia-Idade , Fator Plaquetário 4/imunologia , Receptores CXCR3/imunologia , Receptores CXCR3/metabolismo , Escleroderma Sistêmico/microbiologia , Escleroderma Sistêmico/patologia , Pele/citologia , Pele/imunologia , Pele/microbiologia , Pele/patologia , Receptor Toll-Like 9/imunologia
8.
Food Chem ; 292: 336-345, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31054683

RESUMO

Biochemical effects of the water soluble fiber fraction of sugarcane bagasse (BSF) fermented in the colon was examined to evaluate its potential health promoting effects. A feeding experiment involving Fischer 344 rats, was conducted with 3 experimental diets containing, cellulose (CON), a commercial xylo-oligosaccharide (XYO) and BSF (BGS). Cumulative feed intake was significantly lower in XYO group while cecal weight was significantly higher. Acetic and propionic acid contents in the cecal content were significantly higher in the BGS and XYO, respectively. Total short chain fatty acid content was significantly higher in BGS and XYO resulting significantly lower cecal pH. Beneficial bacteria such as Bifidobacterium, Blautia, Akkermansia and Roseburia abundance was significantly higher in the XYO and BGS groups. Further, mucin and immunoglobulin-A contents were significantly higher in BGS group compared to CON group. Thus, BSF exhibited its ability to enhance the intestinal and systemic health upon fermentation in the colon.


Assuntos
Bactérias/metabolismo , Ceco/microbiologia , Fibras na Dieta/análise , Saccharum/metabolismo , Amônia/análise , Animais , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Bifidobacterium/genética , Bifidobacterium/crescimento & desenvolvimento , Ceco/química , Ceco/metabolismo , Celulose/química , Cromatografia Líquida de Alta Pressão , DNA Bacteriano/química , DNA Bacteriano/metabolismo , Ácidos Graxos Voláteis/análise , Ácidos Graxos Voláteis/química , Masculino , Modelos Animais , Oligossacarídeos/química , Análise de Componente Principal , Ratos , Ratos Endogâmicos F344 , Água/química
9.
BMC Infect Dis ; 19(1): 358, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31035964

RESUMO

BACKGROUND: Necrotizing fasciitis is a deep infection of the fascia and subcutaneous tissue with a high mortality rate. Meningitis is an infection of the membranes surrounding the brain with a likewise high mortality rate. Streptococcus pneumoniae is the most frequent cause of bacterial meningitis and it is an extremely rare cause of necrotizing fasciitis. Different subcapsular serotypes of S. pneumoniae are known to have diverse virulence. The serotype 9 N is associated with a high risk of death. CASE PRESENTATION: We report a case of a previously healthy 68-year-old female who presented at our clinic with complaints of pain in her left calf since having experienced a very painful leg cramp 3 weeks prior. Within a few hours after admission, she developed fever, neck stiffness and an altered mental state. Concurrently, the pain in her leg worsened. Upon further examination it was found that she suffered from both meningitis and necrotizing fasciitis due to S. pneumoniae, serotype 9 N. The patient survived and avoided leg amputation. CONCLUSIONS: The patient suffered from two very lethal infections simultaneously. Both of them were caused by S. pneumoniae. We believe that her favorable outcome was, a result of prompt surgical intervention and appropriate antibiotic treatment. Our case underlines the importance of continuous reevaluation of the symptoms and clinical findings in patients with unclear causes of severe illness, especially if the patient's condition changes.


Assuntos
Fasciite Necrosante/diagnóstico , Meningite/diagnóstico , Streptococcus pneumoniae/genética , Idoso , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Fasciite Necrosante/microbiologia , Fasciite Necrosante/terapia , Feminino , Humanos , Meningite/tratamento farmacológico , Meningite/microbiologia , Sorogrupo , Transplante de Pele , Streptococcus pneumoniae/isolamento & purificação
10.
BMC Infect Dis ; 19(1): 357, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31035966

RESUMO

BACKGROUND: Overcrowding, reduced nurse to patient ratio, limited distance between incubators and absence of microbiological surveillance have been shown to promote spread of multidrug-resistant gram-negative organisms (MDRGN) in patients with birthweight < 1500 g. Patients > 1500 g treated on an intermediate care unit are unrepresented in recent literature. We therefore intended to present data obtained from a short-term overcrowded neonatal intermediate care unit (NIMCU) at a level III (international categorization) perinatal center at University Hospital Frankfurt, Germany. METHODS: During a 25 day overcrowding (OV) and 28 day post-overcrowding period (POST-OV) on NIMCU, epidemiological data obtained from continuously hold microbiological surveillance were investigated and compared to the last 12 months of ward-regular bed occupancy preceding OV (PRAE-OV). RESULTS: During OV, the number of patients simultaneously treated at the NIMCU increased from 18 to 22, resulting in a reduced bed-to-bed space. Nurse: patient ratio was 4:22 during OV compared to 3:18 during PRAE-OV. Cumulative incidence of MDRGN was 4.7% in OV and 2.4% POST-OV compared to 4.8% to PRAE-OV, respectively, without any significant variations. During OV and POST-OV, septic episodes due to MDRGN were not observed. In one case, potential nosocomial transmission of Enterobacter cloacae resistant to Piperacillin and 3rd/4th generation cephalosporins was observed. CONCLUSIONS: Prevention of nosocomial spread of MDRGN in an overcrowded NIMCU is based on staff's diligent training and adequate staffing. Concise microbiological surveillance should be guaranteed to escort through overcrowding periods. In our setting, impact of bed-to-bed distance on MDRGN transmission seemed to be less strong.


Assuntos
Infecção Hospitalar/diagnóstico , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Bactérias Gram-Negativas/diagnóstico , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Enterobacter cloacae/genética , Enterobacter cloacae/isolamento & purificação , Feminino , Alemanha/epidemiologia , Infecções por Bactérias Gram-Negativas/epidemiologia , Infecções por Bactérias Gram-Negativas/microbiologia , Hospitais Universitários , Humanos , Incidência , Lactente , Recém-Nascido , Unidades de Terapia Intensiva Neonatal , Masculino
11.
BMC Infect Dis ; 19(1): 361, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-31039738

RESUMO

BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease (IBD) that is widely identified worldwide. This study aimed to investigate the phenotypic characterization and molecular typing of Clostridium difficile isolates among patients with UC at an inflammatory bowel disease clinic in Iran. METHODS: In this cross-sectional study, conducted from April 2015 to December 2015, 85 UC patients were assessed for C.difficile infection (CDI). C. difficile isolates were characterized based on their toxin profile and antimicrobial resistance pattern. Multi-locus sequence typing analysis (MLST) and PCR ribotyping were performed to define the genetic relationships between different lineages of toxigenic strains. RESULTS: The prevalence of C. difficile isolates was 31.8% (27/85) in patients, of those 15 patients (17.6%) had CDI. Three different sequence types (STs) identified based on MLST among the toxigenic isolates, that is ST54 (33.3%), ST2 (53.3%), and ST37 (13.6%). C. difficile strains were divided into four different PCR-ribotypes (012, 014, 017 and IR1). The most common ribotype was 014 accounting for 48.3% (7/15) of all strains. The strains isolated during the first episode and recurrence of CDI usually belonged to PCR ribotype 014 (ST2). A high rate of CDI recurrence (14.1%, 12/85) experienced in UC patients. Colonization of the gastrointestinal tract with non-toxigenic C. difficile strains was frequent among patients with mild disease. All C. difficile isolates were susceptible to metronidazole, and vancomycin, 86 and 67% of isolates were resistant to clindamycin and erythromycin respectively. There was no correlation between the toxin type and antibiotic resistance (p > 0.05). CONCLUSION: Overall CDI is rather prevalent in UC patients. All patients with CDI experienced moderate to severe disease and exposed to different antimicrobial and anti-inflammatory agents. Close monitoring and appropriate management including early detection and fast treatment of CDI will improve UC outcomes.


Assuntos
Infecções por Clostridium/diagnóstico , Colite Ulcerativa/diagnóstico , Fezes/microbiologia , Adulto , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Anti-Inflamatórios/uso terapêutico , Infecções por Clostridium/tratamento farmacológico , Infecções por Clostridium/microbiologia , Clostridium difficile/efeitos dos fármacos , Clostridium difficile/genética , Clostridium difficile/isolamento & purificação , Colite Ulcerativa/tratamento farmacológico , Colite Ulcerativa/microbiologia , Estudos Transversais , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Farmacorresistência Bacteriana , Feminino , Trato Gastrointestinal/microbiologia , Humanos , Modelos Logísticos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Recidiva , Ribotipagem
12.
BMC Infect Dis ; 19(1): 366, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-31039752

RESUMO

BACKGROUND: Independent of HIV infection, extrapulmonary TB (EPTB) risk is increased in women, persons of black race or foreign birth, and by genetic variants in vitamin D receptor (VDR), interleukin-1 beta (IL-1ß), and toll-like receptor (TLR)-2; functional correlates are unclear. We evaluated macrophage expression of VDR, TLR2, cathelicidin, and TNF-α, and production of IL-1ß in HIV-seronegative persons with previous EPTB, previous pulmonary TB, latent M. tuberculosis infection, and uninfected TB contacts. Persons with previous pleural TB were excluded due to enhanced immune responses at the site of disease. METHODS: Macrophages were stimulated with TLR-2 agonist M. tuberculosis lipoprotein (LpqH), live and gamma-irradiated M. tuberculosis. RESULTS: M. tuberculosis - infected macrophages from persons with previous EPTB had increased VDR expression (29.17 relative value unit increase in median expression vs. uninfected contacts, after adjusting for foreign-born status; P = 0.02). Macrophages from persons with previous EPTB had a 38.88 µg/mL increase in median IL-1ß production after stimulation with LpqH compared to uninfected contacts (P = 0.01); the effect was similar (44.99 µg/mL) but not statistically significant after controlling for foreign-born status. Median 25-hydroxyvitamin D levels were low but not significantly different between groups. CONCLUSIONS: There was increased macrophage expression of VDR after stimulation with live M. tuberculosis in persons with previous extrapulmonary TB. If post-treatment VDR expression reflects expression prior to disease, it may identify persons at risk for extrapulmonary TB.


Assuntos
Macrófagos/metabolismo , Mycobacterium tuberculosis/fisiologia , Receptores de Calcitriol/metabolismo , Tuberculose/patologia , Adulto , Idoso , Proteínas de Bactérias/imunologia , Estudos de Casos e Controles , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Feminino , Raios gama , Expressão Gênica , Humanos , Interleucina-1beta/análise , Macrófagos/citologia , Macrófagos/microbiologia , Masculino , Pessoa de Meia-Idade , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/efeitos da radiação , Receptores de Calcitriol/genética , Receptor 2 Toll-Like/agonistas , Tuberculose/imunologia , Vitamina D/análogos & derivados , Vitamina D/sangue
13.
BMC Infect Dis ; 19(1): 371, 2019 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-31046692

RESUMO

BACKGROUND: There is an ongoing outbreak of Mycobacterium chimaera infections among patients exposed to contaminated heater-cooler devices used during cardiac surgery. Recognition of M. chimaera infection is hampered by its long latency and non-specific symptoms. Standard diagnostic methods using acid-fast bacilli (AFB) culture often require invasive sampling, have low sensitivity, and can take weeks to result. We describe the performance of a plasma-based next-generation sequencing test (plasma NGS) for the diagnosis of M. chimaera infection. METHODS: We conducted a retrospective study of 10 patients with a history of cardiac surgery who developed invasive M. chimaera infection and underwent testing by plasma NGS between February 2017 and April 2018. RESULTS: Plasma NGS detected M. chimaera in 9 of 10 patients (90%) with invasive disease in a median of 4 days from specimen collection, including all 8 patients with disseminated infection. In 7 of these 9 cases (78%), plasma NGS was the first test to provide microbiologic confirmation of M. chimaera infection. In contrast, AFB cultures required a median of 20 days to turn positive, and the median time for confirmation of M. chimaera was 41 days. Of 24 AFB blood cultures obtained in this cohort, only 4 (17%) were positive. Invasive procedures were performed in 90% of cases, and in 5 patients (50%), mycobacterial growth was achieved only by culture of these deep sites. CONCLUSIONS: Plasma NGS can accurately detect M. chimaera noninvasively and significantly faster than AFB culture, making it a promising new diagnostic tool.


Assuntos
Infecções por Mycobacterium/diagnóstico , Mycobacterium/genética , Idoso , DNA Bacteriano/sangue , DNA Bacteriano/metabolismo , Surtos de Doenças , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Mycobacterium/isolamento & purificação , Infecções por Mycobacterium/microbiologia , Estudos Retrospectivos , Análise de Sequência de DNA
14.
Nat Commun ; 10(1): 2194, 2019 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-31097704

RESUMO

Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower-density origin of replication and an ultrathin flexible string of DNA at the terminus of replication. At the single-cell level, the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells.


Assuntos
Cromossomos Bacterianos/química , DNA Bacteriano/química , DNA Circular/química , Escherichia coli/genética , Genoma Bacteriano , Proteínas Cromossômicas não Histona/metabolismo , Cromossomos Bacterianos/metabolismo , Replicação do DNA , DNA Bacteriano/metabolismo , DNA Circular/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Microscopia Intravital/instrumentação , Microscopia Intravital/métodos , Microscopia de Fluorescência/instrumentação , Microscopia de Fluorescência/métodos , Conformação de Ácido Nucleico , Análise de Célula Única/instrumentação , Análise de Célula Única/métodos
15.
Nat Chem Biol ; 15(6): 607-614, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31101917

RESUMO

Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. Recently, UdgX, an unconventional UDG with extremely tight binding to DNA containing uracil, was discovered. The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. H109 functions as a nucleophile to attack the oxocarbenium ion, substituting for the catalytic water molecule found in other UDGs. To our knowledge, this change from a catalytic water attack to a direct nucleophilic attack by the histidine residue is unprecedented. UdgX utilizes a unique mechanism of protecting cytotoxic abasic sites from exposure to the cellular environment.


Assuntos
Dano ao DNA , DNA Bacteriano/metabolismo , Mycobacterium smegmatis/enzimologia , Uracila-DNA Glicosidase/metabolismo , Uracila/metabolismo , Sítios de Ligação , Biocatálise , Modelos Moleculares , Conformação Proteica , Uracila-DNA Glicosidase/química , Uracila-DNA Glicosidase/genética
16.
Nat Chem Biol ; 15(7): 690-698, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31110305

RESUMO

Two-component systems (TCSs) are the largest family of multi-step signal transduction pathways and valuable sensors for synthetic biology. However, most TCSs remain uncharacterized or difficult to harness for applications. Major challenges are that many TCS output promoters are unknown, subject to cross-regulation, or silent in heterologous hosts. Here, we demonstrate that the two largest families of response regulator DNA-binding domains can be interchanged with remarkable flexibility, enabling the corresponding TCSs to be rewired to synthetic output promoters. We exploit this plasticity to eliminate cross-regulation, un-silence a gram-negative TCS in a gram-positive host, and engineer a system with over 1,300-fold activation. Finally, we apply DNA-binding domain swapping to screen uncharacterized Shewanella oneidensis TCSs in Escherichia coli, leading to the discovery of a previously uncharacterized pH sensor. This work should accelerate fundamental TCS studies and enable the engineering of a large family of genetically encoded sensors with diverse applications.


Assuntos
DNA Bacteriano/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Engenharia Genética , Shewanella/genética , Shewanella/metabolismo , DNA Bacteriano/genética
17.
BMC Infect Dis ; 19(1): 412, 2019 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-31088383

RESUMO

BACKGROUND: Brucellosis is a systemic infectious disease frequently associated with osteoarticular involvement. While sacroiliitis is a common manifestation of brucellosis, septic osteoarthritis is less frequent. Here, we report two cases of septic osteoarthritis caused by Brucella melitensis. CASE PRESENTATION: Both patients had a history of contact with goats before admission. Upon clinical examination, they showed marked pain and limited movement in the hip. Imaging findings revealed obvious osteonecrosis of the right femoral head. Inflammatory markers, including erythrocyte sedimentation rate and C-reactive protein level, were elevated. The tube agglutination test results of both patients were positive (1:160 and 1:200). Real-time polymerase chain reaction analysis of synovial fluid revealed the presence of B. melitensis. We deduced that septic osteoarthritis could explain these clinical and radiological findings. Both patients were followed-up for 12 months. They returned to their normal routine after completing a standard antibiotic regimen, including doxycycline (100 mg, daily) and rifampicin (600 mg), for 6 weeks. CONCLUSIONS: Brucellar hip arthritis is a serious clinical manifestation of brucellosis, presenting mainly as marked joint pain and limited mobility. It is characterized by joint effusion, synovitis, and soft-tissue swelling on magnetic resonance images. Physicians should consider brucellosis as one of the differential diagnoses of arthritis.


Assuntos
Brucelose/diagnóstico , Osteoartrite do Quadril/diagnóstico , Adulto , Animais , Antibacterianos/uso terapêutico , Sedimentação Sanguínea , Brucella melitensis/genética , Brucella melitensis/isolamento & purificação , Brucelose/tratamento farmacológico , Brucelose/microbiologia , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Diagnóstico Diferencial , Doxiciclina/uso terapêutico , Cabras , Quadril/diagnóstico por imagem , Humanos , Imagem por Ressonância Magnética , Masculino , Osteoartrite do Quadril/tratamento farmacológico , Osteoartrite do Quadril/microbiologia , Reação em Cadeia da Polimerase , Rifampina/uso terapêutico , Sinovite/etiologia
18.
BMC Infect Dis ; 19(1): 423, 2019 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-31092207

RESUMO

BACKGROUND: Determining the etiology of pneumonia is essential to guide public health interventions. Diagnostic test results, including from polymerase chain reaction (PCR) assays of upper respiratory tract specimens, have been used to estimate prevalence of pneumococcal pneumonia. However limitations in test sensitivity and specificity and the specimen types available make establishing a definitive diagnosis challenging. Prevalence estimates for pneumococcal pneumonia could be biased in the absence of a true gold standard reference test for detecting Streptococcus pneumoniae. METHODS: We conducted a case control study to identify etiologies of community acquired pneumonia (CAP) from April 2014 through August 2015 in Thailand. We estimated the prevalence of pneumococcal pneumonia among adults hospitalized for CAP using Bayesian latent class models (BLCMs) incorporating results of real-time polymerase chain reaction (qPCR) testing of upper respiratory tract specimens and a urine antigen test (UAT) from cases and controls. We compared the prevalence estimate to conventional analyses using only UAT as a reference test. RESULTS: The estimated prevalence of pneumococcal pneumonia was 8% (95% CI: 5-11%) by conventional analyses. By BLCM, we estimated the prevalence to be 10% (95% CrI: 7-16%) using binary qPCR and UAT results, and 11% (95% CrI: 7-17%) using binary UAT results and qPCR cycle threshold (Ct) values. CONCLUSIONS: BLCM suggests a > 25% higher prevalence of pneumococcal pneumonia than estimated by a conventional approach assuming UAT as a gold standard reference test. Higher quantities of pneumococcal DNA in the upper respiratory tract were associated with pneumococcal pneumonia in adults but the addition of a second specific pneumococcal test was required to accurately estimate disease status and prevalence. By incorporating the inherent uncertainty of diagnostic tests, BLCM can obtain more reliable estimates of disease status and improve understanding of underlying etiology.


Assuntos
Infecções Comunitárias Adquiridas/diagnóstico , Pneumopatias/diagnóstico , Adulto , Idoso , Antígenos de Bactérias/urina , Teorema de Bayes , Estudos de Casos e Controles , Infecções Comunitárias Adquiridas/microbiologia , Infecções Comunitárias Adquiridas/patologia , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Feminino , Humanos , Pneumopatias/epidemiologia , Pneumopatias/patologia , Masculino , Pessoa de Meia-Idade , Nasofaringe/microbiologia , Prevalência , Reação em Cadeia da Polimerase em Tempo Real , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação , Tailândia/epidemiologia
19.
BMC Infect Dis ; 19(1): 347, 2019 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-31029099

RESUMO

BACKGROUND: Pooling sputum specimens is one potential strategy for reducing the cost of using Xpert MTB/RIF, a rapid polymerase chain reaction (PCR)-based test, for the diagnosis of pulmonary tuberculosis. We sought to compare the sensitivity of two alternative method of pooling. METHODS: Patients referred for assessment for TB, whose initial sputum was Xpert MTB positive, were recruited and their sputum specimens were pooled for analysis with sputum specimens that were Xpert MTB negative. Two alternative pooling strategies were employed: one in which the concentration of sample reagent (buffer) was maintained at 2:1 (standard), in accordance with the manufacturer's instructions, and another in which the concentration of sample reagent was reduced to 1:1. RESULTS: We tested 101 Xpert MTB positive sputum specimens. Among these, 96% of valid test results (95% confidence interval (CI) 89-99%) were positive using the "standard buffer method". Using the "reduced buffer pooling" method 94% of valid test results (95% CI 87-98%) were positive. McNemar's test for the difference in paired proportions did not reach statistical significance (P = 0.56). CONCLUSION: We have confirmed that pooling of two sputum specimens for testing in a single cartridge is a valid method of reducing the number of cartridges required when using Xpert MTB to detect pulmonary tuberculosis. Two alternative pooling strategies tested here yielded similar results. TRIAL REGISTRATION: The present study was conducted within the Active Casefinding in Tuberculosis (ACT3) Trial. The ACT3 Trial had been registered with Australian and New Zealand Clinical Trials Register on 8th April, 2014. The trial registration number is ACTRN12614000372684 . (Retrospectively registered).


Assuntos
Mycobacterium tuberculosis/genética , Escarro/microbiologia , Tuberculose/diagnóstico , Estudos Transversais , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Humanos , Mycobacterium tuberculosis/isolamento & purificação , Reação em Cadeia da Polimerase/métodos , Kit de Reagentes para Diagnóstico , Sensibilidade e Especificidade
20.
Food Chem ; 289: 177-186, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-30955601

RESUMO

This study applied an in vitro fermentation model, whereby the catabolism of Porphyra haitanensis polysaccharides (PHP) was monitored coupled with the variations of microbiota composition and the concentration of short-chain fatty acids (SCFAs), so as to assess the effects of PHP on human intestinal microbiota. After 24 h anaerobic incubation, the level of microflora diversity increased significantly, as the microbiome structure was reshaped through promotion of intestinal probiotics proliferation and inhibition of pathogens growth. Besides, the final concentration of total SCFAs increased to 32.32 ±â€¯1.81 mmol/L, and contained high amounts of acetic, propionic and butyric acid. Furthermore, the molecular weight of PHP decreased from 2.623 × 105 g/mol to 2.308 × 104 g/mol. The degree of polymerization of oligosaccharide products ranged from 2 to 9, with the main linkage patterns being 1 → 3 and 1 → 4 linked Galp. The current study provides new insight on the probiotic activity of PHP within the human gastrointestinal tract.


Assuntos
Microbioma Gastrointestinal , Porphyra/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Ácido Butírico/metabolismo , Cromatografia Líquida de Alta Pressão , DNA Bacteriano/análise , DNA Bacteriano/metabolismo , Ácidos Graxos Voláteis/metabolismo , Fezes/microbiologia , Galactose/análogos & derivados , Galactose/análise , Cromatografia Gasosa-Espectrometria de Massas , Microbioma Gastrointestinal/efeitos dos fármacos , Humanos , Intestinos/microbiologia , Monossacarídeos/análise , Polissacarídeos/farmacologia , Porphyra/química
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