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1.
Acta Vet Scand ; 61(1): 25, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146786

RESUMO

BACKGROUND: Although artificial insemination (AI) was developed as a means of controlling disease transmission, pathogens can still be transmitted to females in semen used for AI. In addition, bacteria can cause deterioration in sperm quality during storage. Semen becomes contaminated by the male's normal bacterial flora as it passes out of the reproductive tract but potential pathogens may also contaminate the semen. Therefore, semen samples from stallions to be used for AI are tested before the breeding season to minimize transmission of pathogens to inseminated mares. In Sweden, semen samples are tested at the National Veterinary Institute, Uppsala (SVA). For the present study, a retrospective analysis was made of potentially pathogenic bacteria isolated from samples submitted to the SVA from 2007 to 2017. RESULTS: In our study, Taylorella equigenitalis was found infrequently (53 out of 25,512 samples), representing 11 out of 2308 stallions. If T. equigenitalis was detected, the stallions were treated with antibiotics and re-tested later in the same year. Klebsiella pneumoniae and beta haemolytic streptococci were the most commonly found potential pathogens, whereas Pseudomonas aeruginosa was also isolated occasionally. There were considerable differences in the number of species isolated each year. CONCLUSIONS: Potential pathogens were identified in relatively few of the samples submitted to SVA during this period, with T. equigenitalis not being identified since 2015. Of the other potential pathogens, K. pneumoniae and beta haemolytic streptococci were the most common. The information is relevant for determining guidelines on the testing and treatment of stallions before breeding.


Assuntos
Infecções Bacterianas/veterinária , Fenômenos Fisiológicos Bacterianos , Líquidos Corporais/microbiologia , Genitália Masculina/microbiologia , Doenças dos Cavalos/microbiologia , Infecções do Sistema Genital/veterinária , Sêmen/microbiologia , Animais , Antibacterianos/uso terapêutico , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/tratamento farmacológico , Infecções Bacterianas/microbiologia , Doenças dos Cavalos/diagnóstico , Doenças dos Cavalos/tratamento farmacológico , Cavalos , Inseminação Artificial , Masculino , Infecções do Sistema Genital/diagnóstico , Infecções do Sistema Genital/tratamento farmacológico , Infecções do Sistema Genital/microbiologia , Suécia
2.
Ann Biol Clin (Paris) ; 77(3): 295-305, 2019 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-30977732

RESUMO

Liquid wastes from clinical biology automated systems are currently evacuated in the urban network after chemical treatment to eliminate a possible risk of infection. Since these wastes are ecotoxic because of the presence of numerous chemical reagents, we studied their intrinsic microbicidal power towards a selection of infectious agents widely found in clinical specimens. The objective was to determine if an additional anti-infectious treatment before elimination is necessary. Thus, we evaluated the bactericidal effect of liquid wastes of several automated systems towards four bacterial species (Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Enterococcus faecalis) and their virucidal activity against a non-enveloped virus, resistant in the environment (adenovirus). This effect was determined for different exposure times. Our results showed that the antibacterial activity was highly variable depending on the waste-bacteria pair considered (varying from no activity to complete sterilization of a strong bacterial inoculum). The liquid wastes were on the other hand globally inactive towards adenovirus.


Assuntos
Anti-Infecciosos/isolamento & purificação , Técnicas de Laboratório Clínico , Resíduos de Serviços de Saúde , Esgotos/análise , Esterilização , Antibacterianos/isolamento & purificação , Antibacterianos/farmacologia , Anti-Infecciosos/farmacologia , Antivirais/isolamento & purificação , Antivirais/farmacocinética , Automação Laboratorial/instrumentação , Automação Laboratorial/métodos , Biodegradação Ambiental , Líquidos Corporais/microbiologia , Líquidos Corporais/virologia , Técnicas de Laboratório Clínico/instrumentação , Técnicas de Laboratório Clínico/métodos , França , Humanos , Laboratórios/normas , Testes de Sensibilidade Microbiana , Esgotos/microbiologia , Esterilização/métodos , Esterilização/normas , Purificação da Água/métodos , Purificação da Água/normas
3.
Anaerobe ; 56: 40-45, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30738138

RESUMO

In the present study, we investigated the potential of Bifidobacterium spp., isolated from ruminal fluid samples from buffaloes (Bubalus bubalis) for conjugated linoleic acid (CLA) production. A total of 294 isolates were obtained from 86 ruminal fluid samples using Bifidus Selective Medium (BSM) medium, and based on phospoketolase assay, 24 isolates were presumptively confirmed to be Bifidobacterium species. Further, the isolates were confirmed morphologically, biochemically and by PCR assays for genus specific (16s rDNA) and transaldolase genes. All 24 strains were positive for conversion of linoleic acid (LA) to CLA by spectrophotometric screening. Gas chromatographic analysis showed that the strains produced cis9, trans11 and tran10, cis12 CLA isomers in LA-supplemented deMan-Rogosa-Sharpe (MRS) broth. The strains were identified as B. thermophilum (n = 21) and B. pseudolongum (n = 3) based on 16 rDNA sequence analysis. The study shows that Bifidobacterium spp., present in the rumens of buffaloes produce CLA from LA and the strains may have the potential to be used as probiotics to enhance the nutraceutical value of ruminant food products.


Assuntos
Bifidobacterium/isolamento & purificação , Bifidobacterium/metabolismo , Búfalos , Ácidos Linoleicos Conjugados/metabolismo , Rúmen/microbiologia , Animais , Técnicas Bacteriológicas , Bifidobacterium/classificação , Bifidobacterium/genética , Líquidos Corporais/microbiologia , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Transaldolase/genética
4.
Leg Med (Tokyo) ; 36: 73-80, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30419494

RESUMO

According to the Human Microbiome Project (HMP), a healthy human body contains ten times more microbes than human cells. Microbial communities colonize different organs of the body, playing fundamental roles both in human health and disease. Despite the vast scientific knowledge of the role of microbial communities in a living body, little is known at present about microbial changes occurring after death, thus leading many authors to investigate the composition of the thanatomicrobiome and its potential applications in the forensic field. The aim of the following review is to provide a general overview of the advances of postmortem microbiology research, mainly focusing on the role of microbiological investigations carried out on internal organs and fluids. To this end, a total of 19 studies have been sistematically reviewed, each one chosen according to specific inclusion/exclusion criteria. The selected studies assess the contribution of contamination, postmortem transmigration and agonal spread to microbial isolation from dead body samples, and shed light on the role of postmortem microbiological investigations in several forensic fields, such as cause of death or PMI determination.


Assuntos
Líquidos Corporais/microbiologia , Encéfalo/microbiologia , Sistema Digestório/microbiologia , Medicina Legal , Coração/microbiologia , Microbiota , Mudanças Depois da Morte , Pele/microbiologia , Adulto , Idoso , Causas de Morte , Bases de Dados Bibliográficas , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fatores de Tempo
6.
Microbiologyopen ; 8(3): e00661, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-29931836

RESUMO

Three previously unidentified Gram-positive anaerobic coccoid bacteria, strains KhD-2T , KHD4T , and Kh-D5T , isolated from a vaginal swab, were characterized using the taxonogenomics concept. The phylogenic analysis, phenotypic characteristics, and genotypic data presented in this report attest that these three bacteria are distinct from previously known bacterial species with standing in nomenclature and represent three new Peptoniphilus species. Strain KhD-2T is most closely related to Peptoniphilus sp. DNF00840 and Peptoniphilus harei (99.7% and 98.2% identity, respectively); strain KHD4T to Peptoniphilus lacrimalis (96%) and strain Kh-D5T to Peptoniphilus coxii (97.2%). Strains KhD-2T , KHD4T , and Kh-D5T DNA G+C contents are, respectively, 34.23%, 31.87%, and 49.38%; their major fatty acid was C16:0 (41.6%, 32.0%, and 36.4%, respectively). We propose that strains KhD-2T (=CSUR P0125 = DSM 101742), KHD4T (=CSUR P0110 = CECT 9308), and Kh-D5T (=CSUR P2271 = DSM 101839) be the type strains of the new species for which the names Peptoniphilus vaginalis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilu pacaensis sp. nov., are proposed, respectively.


Assuntos
Técnicas de Tipagem Bacteriana , Líquidos Corporais/microbiologia , Firmicutes/classificação , Firmicutes/isolamento & purificação , Vaginose Bacteriana/microbiologia , Adulto , Anaerobiose , Composição de Bases , Citosol/química , Ácidos Graxos/análise , Feminino , Firmicutes/genética , Firmicutes/fisiologia , Humanos , Filogenia , Homologia de Sequência do Ácido Nucleico
7.
Diagn Microbiol Infect Dis ; 93(1): 22-23, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30213466

RESUMO

The FilmArray Blood Culture Identification Panel was validated for nonblood sterile site specimens with clinical impact of rapid identification compared to conventional diagnostics. The panel accurately identified target organisms from 98% of positive broth cultures a median 1.1 day faster than conventional techniques (P < 0.0001) with potential clinical impact in 22% of cases.


Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/patologia , Técnicas Bacteriológicas/métodos , Infecções Bacterianas/líquido cefalorraquidiano , Biópsia , Líquidos Corporais/microbiologia , Testes Diagnósticos de Rotina , Humanos , Técnicas de Diagnóstico Molecular , Sensibilidade e Especificidade , Fatores de Tempo
8.
Diagn Microbiol Infect Dis ; 93(3): 183-187, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30420211

RESUMO

Transformation is one of the mechanisms of acquisition of foreign genetic material leading to the emergence of multidrug resistant (MDR) bacteria. Recently, human serum albumin (HSA) was shown to specifically increase transformation frequency in the nosocomial pathogen Acinetobacter baumannii. To further assess the relevance of HSA as a possible modulator of A. baumannii transformation in host-pathogen interactions, in this work we examined the effect of different human fluids. We observed a significant increase in transformation frequencies in the presence of pleural fluid, whole blood cells and liquid ascites, and to a lesser extent with urine. The observed effects correlate with both HSA and bacterial content found in the assayed patient fluids. Taken together, these results are in agreement with our previous findings that highlight HSA as a possible host signal with the ability to trigger natural transformation in A. baumannii.


Assuntos
Acinetobacter baumannii/genética , Líquidos Corporais/fisiologia , Transformação Bacteriana/genética , Infecções por Acinetobacter/microbiologia , Líquidos Corporais/química , Líquidos Corporais/microbiologia , DNA/genética , Competência de Transformação por DNA/genética , Expressão Gênica , Transferência Genética Horizontal/genética , Genes Bacterianos/genética , Humanos , Albumina Sérica Humana/análise
9.
J Nippon Med Sch ; 85(6): 302-308, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30568055

RESUMO

BACKGROUND: Antibiotic resistance of pathogenic bacteria is well recognized among clinicians; however, studies that directly evaluate the bacterial resistance to commonly used disinfectants in clinical settings are lacking. Currently available reports focus on the resistance of single strains to single disinfectants and do not adequately examine the degree of resistance and cross-resistance to antimicrobials in the large-scale clinical use of disinfectants. METHODS: We investigated the resistance capacity to 11 antibiotics and 7 chemical disinfectants by bacterial strains collected from body fluids of patients in 10 hospitals in Beijing, China over a 1-year period. Bacterial resistance to disinfectants was tested using minimum inhibitory concentration and minimum bactericidal concentration using agar dilution methods based on commercially available reference strains. RESULTS: A total of 1,104 pathogenic strains were identified, of which 23% were Gram-positive bacteria, 74% were Gram-negative bacteria, and 3% were fungi. Overall, resistance to antibiotics for the most common strains was significantly higher than their resistance to disinfectants. The least effective antibiotics and disinfectants were aztreonam and glutaral, respectively, exhibiting the highest overall resistance rates; while amikacin and alcohol had the lowest resistance rates. Consistently, Acinetobacter baumannii exhibited the most resistance, while Escherichia coli had the least resistance for both antibiotics and disinfectants. CONCLUSIONS: Based on the pathogen spectrum for bacterial infective pathogens evaluated in this study, as well as the status quo of their resistance to antimicrobial agents and common clinical disinfectants, it is essential for healthcare professionals to pay attention not only to the standardized use of antimicrobial agents but also to the rational application of disinfectants.


Assuntos
Anti-Infecciosos/farmacologia , Bactérias/efeitos dos fármacos , Infecções Bacterianas/prevenção & controle , Desinfetantes/farmacologia , Farmacorresistência Bacteriana/efeitos dos fármacos , Anti-Infecciosos/classificação , Bactérias/classificação , Bactérias/patogenicidade , Infecções Bacterianas/microbiologia , Pequim , Líquidos Corporais/microbiologia , Desinfetantes/classificação , Humanos , Testes de Sensibilidade Microbiana , Virulência
10.
Exp Lung Res ; 44(4-5): 201-210, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30465452

RESUMO

AIM OF THE STUDY: The pulmonary microbiota is important for both normal homeostasis and the progression of disease, and may be affected by aspiration of gastric fluid. The aim of this study was to investigate changes in the lung microbiota induced by aspiration of gastric fluid in a laboratory rat model. MATERIAL AND METHODS: Using the intratracheal application method, male rats received aspiration with 0.9% normal saline (n = 11); gastric fluid (n = 24) or sterilized (gamma-irradiated) gastric fluid (n = 12) once-weekly for four weeks. On the fifth week, the animals were sacrificed, and the microbiota of the lung was assessed by 16S ribosomal RNA gene sequencing. RESULTS: Lungs without aspiration and lungs after aspiration with normal saline had similar microbial compositions, dominated by bacteria of the genera Serratia, Ralstonia and Brucella. Evaluation of the microbiota following aspiration of gastric fluid revealed a much different profile that was dominated by bacteria from the genera Romboutsia and Turicibacter and largely independent of sterilization of the gastric fluid. CONCLUSION: In a laboratory rat model, aspiration with gastric fluid caused a substantial shift of the lung microbiota that could be characterized as a shift from Proteobacteria towards Firmicutes, possibly of enteric origin. Bacteria contained in the gastric fluid are not apparently responsible for this change.


Assuntos
Pulmão/microbiologia , Microbiota , Aspiração Respiratória/microbiologia , Animais , Líquidos Corporais/microbiologia , Firmicutes/genética , Firmicutes/isolamento & purificação , Masculino , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/análise , Ratos , Estômago/microbiologia
12.
J Microbiol Methods ; 155: 78-81, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30448215

RESUMO

We investigated the efficacy of syringe filters and membrane filters with different pore sizes for recovering Campylobacter. A syringe filter with a 0.45 µm pore size achieved the highest recovery rate (0.29%), while polycarbonate membrane filters with pore sizes of 0.6 µm and 0.4 µm recovered less Campylobacter, at 0.01% and 1.3 × 10-3%, respectively. We also tested 601 diarrheic stool samples using membrane and syringe filtration methods. A total of 23 Campylobacter jejuni/coli were isolated from both syringe and membrane filtration; nine and one were isolated from only syringe or only membrane filtration, respectively (p < .05). The syringe filtration technique was better than membrane filtration for the isolation of Campylobacter.


Assuntos
Técnicas Bacteriológicas/métodos , Campylobacter/isolamento & purificação , Fezes/microbiologia , Filtração/instrumentação , Filtração/métodos , Seringas , Líquidos Corporais/microbiologia , Campylobacter/patogenicidade , Infecções por Campylobacter/diagnóstico , Infecções por Campylobacter/microbiologia , Campylobacter jejuni/isolamento & purificação , Campylobacter jejuni/patogenicidade , Diarreia/microbiologia , Humanos , Cimento de Policarboxilato , Sensibilidade e Especificidade
13.
J Aquat Anim Health ; 30(4): 325-331, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30336511

RESUMO

Coelomic fluid aspiration has been utilized in echinoderms in research and clinical settings. Detailed procedural descriptions for coelomic fluid sampling in sea urchins (class Echinoidea) are lacking, and samples are prone to contamination. The objectives of this study were to (1) standardize a technique for coelomic fluid collection in long-spined sea urchin Diadema antillarum that optimizes the diagnostic quality of the sample utilizing diagnostic imaging, (2) identify coelomic fluid bacterial isolates (using Biolog GEN III MicroLog and 16s rDNA sequencing), and (3) compare positive cultures to animal weight, holding time prior to sampling, water temperature, and gross fluid appearance. Seventy Diadema antillarum from the Florida Keys collected in two groups (March and September 2015) were utilized. Positive cultures for bacterial contamination were identified in 5% and 44%, respectively, of animals in the sampling groups. Vibrio spp. was the predominant genus identified. Positive cultures were more frequent in the group with smaller-sized animals, increased holding times, and elevated water temperatures. Deviation from clear-pink gross coelomic fluid appearance did not reliably predict bacterial contamination. A standardized technique for coelomocentesis was defined. The use of the proposed coelomocentesis methodology may facilitate improved health evaluations of sea urchins and may be applicable to research, conservation efforts, and disease investigations.


Assuntos
Líquidos Corporais/microbiologia , Ouriços-do-Mar/microbiologia , Animais , Bactérias/isolamento & purificação , Técnicas Bacteriológicas , Peso Corporal , Florida , Imagem por Ressonância Magnética , RNA Ribossômico 16S , Temperatura Ambiente , Tomografia Computadorizada por Raios X , Ultrassonografia , Vibrio/isolamento & purificação
14.
J Med Microbiol ; 67(12): 1747-1752, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30325299

RESUMO

PURPOSE: In May 2017 we were notified of a cluster of Yersinia enterocolitica-positive isolates from Liverpool. The purpose of this work was to investigate this cluster of cases and find a possible common source. We combined epidemiological information with whole-genome sequencing (WGS) results, which indicated that these cases were unlikely to be from the same source. This investigation provides evidence that WGS could be used to investigate future clusters of Y. enterocolitica cases. METHODS: A case was defined as a person with a laboratory-confirmed isolate of Y. enterocolitica, sampled in 2017, who is a resident in Liverpool local authority at the time of sampling. Faecal samples were cultured at the local laboratory and presumptive isolates of Yersinia sp. were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Positive isolates were whole-genome sequenced by the reference laboratory. RESULTS: Nine cases were identified, which was significantly greater (P<0.0001) than the average number of cases in this area from the last 10 years. Six cases were female (66.67 %) and the ages of the patients ranged from 20 to 81 (median 54). The sample dates ranged from 29 April to 1 August 2017. The WGS results showed that Y. enterocolitica isolates belonged to different sequence types. CONCLUSION: This was the first time that WGS was used to investigate a cluster of Y. enterocolitica cases; the cases were clustered in time, person and place, but the WGS results indicate that these cases were not from the same source. This result informed the Outbreak Control Team's decision-making and resulted in the investigation being closed.


Assuntos
Genoma Bacteriano/genética , Yersiniose/diagnóstico , Yersiniose/epidemiologia , Yersinia enterocolitica/genética , Yersinia enterocolitica/isolamento & purificação , Adulto , Idoso , Idoso de 80 Anos ou mais , Líquidos Corporais/microbiologia , Líquido da Lavagem Broncoalveolar/microbiologia , Cidades , Demografia , Fezes/microbiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Pâncreas , Reto/microbiologia , Reino Unido/epidemiologia , Sequenciamento Completo do Genoma , Adulto Jovem
15.
Clin Chem ; 64(12): 1743-1752, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30237148

RESUMO

BACKGROUND: A recent study has reported that the microbiota in endometrial fluid of patients receiving in vitro fertilization and embryo transfer (IVF-ET) may predict implantation and pregnancy rates. However, studies are lacking that simultaneously compare the microbiota between endometrial fluid and tissue samples. Whether the microbiota composition in endometrial fluid reflects that in the endometrial tissue remains unclear. METHODS: We systematically profiled the microbiota in endometrial fluid and tissue samples of IVF-ET patients using massively parallel sequencing. The bacterial 16S ribosomal RNA gene (V4 region) was PCR-amplified. Sequencing reads with >98% nucleotide identity were clustered as a bacterial taxon. To account for the different number of reads per sample, we normalized the read counts of each taxon before comparing its relative abundances across samples. RESULTS: Thirteen taxa, including Verrucomicrobiaceae, Brevundimonas, Achromobacter, Exiguobacterium, and Flavobacterium, were consistently detected only in endometrial tissue samples but not fluid samples. Eight taxa were detected in fluid but not tissue. Twenty-two taxa were differentially abundant between fluid and tissue samples (adjusted P values, 4.1 × 10-25 to 0.025). The numbers of taxa identified per 1000 sequencing reads, diversity, and evenness in fluid samples were smaller than those in tissue samples. CONCLUSIONS: Our data suggest that the microbiota composition in endometrial fluid does not fully reflect that in endometrial tissue. Sampling from both endometrial fluid and biopsy allows a more comprehensive view of microbial colonization. Further efforts are needed to identify the preanalytical effects, including sampling sites, methods, and sequencing depth, on profiling endometrial microbiota.


Assuntos
Aborto Habitual/microbiologia , Bactérias/genética , Endométrio/microbiologia , Microbiota/fisiologia , Adulto , Líquidos Corporais/microbiologia , Feminino , Fertilização In Vitro , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Microbiota/genética , RNA Ribossômico 16S/genética
16.
Rev Esp Quimioter ; 31(5): 439-442, 2018 Oct.
Artigo em Espanhol | MEDLINE | ID: mdl-30251525

RESUMO

OBJECTIVE: Kingella kingae is a common colonizer of the oropharynx in children that may lead to invasive infection, mainly osteoarticular infections. Invasive infections occur almost exclusively in young children, fundamentally fewer than two years old. K. kingae infections in children are probably underdiagnosed due to the difficulty in growing in routine cultures and the absence of systematic realization of molecular techniques to identify it. It is the most common bacteria involved in childhood osteoarticular infections in recent series and increasingly being recognized in Spain. We report our experience on the epidemiological and clinical characteristics of osteoarticular infections in children in recent years. METHODS: Retrospective analysis of septic arthritis by K. kingae identified by PCR in joint fluid in children during 2010-2016. Epidemiological, clinical and laboratory characteristics are presented. RESULTS: Five arthritis by K. kingae were identified, all of them in ≤6 years old children. Median leukocytes, CRP and ESR were 12950 leukocytes/µL, 4.84 mg/dL and 58 mm/h respectively, and 61,322 leukocytes /µL in joint fluid. All patients evolved favorably. CONCLUSIONS: Osteoarticular infections by K. kingae in children usually present low increase of inflammatory markers despite being invasive infections. The development of PCR in sterile samples has greatly improved the diagnostic yield of K. kingae infections improving the management of osteoarthritis in children.


Assuntos
Artrite Infecciosa/etiologia , Artrite Infecciosa/microbiologia , Kingella kingae , Infecções por Neisseriaceae/complicações , Infecções por Neisseriaceae/microbiologia , Líquidos Corporais/microbiologia , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Articulações , Masculino , Osteomielite/microbiologia , Reação em Cadeia da Polimerase , Estudos Retrospectivos
17.
Sci Rep ; 8(1): 13767, 2018 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-30213965

RESUMO

High throughput sequencing has been proposed as a one-stop solution for diagnostics and molecular typing directly from patient samples, allowing timely and appropriate implementation of measures for treatment, infection prevention and control. However, it is unclear how the variety of available methods impacts the end results. We applied shotgun metagenomics on diverse types of patient samples using three different methods to deplete human DNA prior to DNA extraction. Libraries were prepared and sequenced with Illumina chemistry. Data was analyzed using methods likely to be available in clinical microbiology laboratories using genomics. The results of microbial identification were compared to standard culture-based microbiological methods. On average, 75% of the reads corresponded to human DNA, being a major determinant in the analysis outcome. None of the kits was clearly superior suggesting that the initial ratio between host and microbial DNA or other sample characteristics were the major determinants of the proportion of microbial reads. Most pathogens identified by culture were also identified through metagenomics, but substantial differences were noted between the taxonomic classification tools. In two cases the high number of human reads resulted in insufficient sequencing depth of bacterial DNA for identification. In three samples, we could infer the probable multilocus sequence type of the most abundant species. The tools and databases used for taxonomic classification and antimicrobial resistance identification had a key impact on the results, recommending that efforts need to be aimed at standardization of the analysis methods if metagenomics is to be used routinely in clinical microbiology.


Assuntos
Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Tipagem Molecular/métodos , Líquidos Corporais/microbiologia , Farmacorresistência Bacteriana/genética , Humanos , Testes de Sensibilidade Microbiana , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
18.
Bioinspir Biomim ; 13(6): 065001, 2018 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-30141414

RESUMO

In this work, two antifouling polymer brushes were tested at different shear stress conditions to evaluate their performance in reducing the initial adhesion of Escherichia coli. Assays were performed using a parallel plate flow chamber and a shear stress range between 0.005 and 0.056 Pa. These shear stress values are found in different locations in the human body where biomedical devices are placed. The poly(MeOEGMA) and poly(HPMA) brushes were characterized and it was shown that they can reduce initial adhesion up to 90% when compared to glass. Importantly, the performance of these surfaces was not affected by the shear stress, which is an indication that they do not collapse under this shear stress range. The brushes displayed a similar behavior despite the differences in their chemical composition and surface energy. Both surfaces have shown ultra-low adsorption of macromolecules from the medium when tested with relevant biological fluids (urine and serum). This indicates that these surfaces can potentially be used in biomedical devices to reduce initial bacterial colonization and eventually reduce biofilm formation on these devices.


Assuntos
Aderência Bacteriana/fisiologia , Polímeros/química , Resistência ao Cisalhamento/fisiologia , Biofilmes/crescimento & desenvolvimento , Líquidos Corporais/microbiologia , Escherichia coli , Humanos , Estresse Mecânico , Propriedades de Superfície
19.
BMC Infect Dis ; 18(1): 284, 2018 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-29940951

RESUMO

BACKGROUND: Tuberculous pleurisy (TP) presents a diagnostic problem due to the limitations of traditional diagnostic methods. Different studies with the Xpert MTB/RIF assay have drawn variable conclusions about its values in TP diagnosis. We conducted a meta-analysis to assess whether the Xpert MTB/RIF assay is appropriate for the diagnosis of TP using pleural fluid samples. METHODS: A systematic search of four literature databases in English and Chinese language was performed to identify studies involving the use of Xpert MTB/RIF in patients with TP confirmed by plural biopsy and/or mycobacterial culture. Pooled sensitivity, specificity and accordance proportion were calculated, and the forest plots were generated to assess the accuracy of Xpert MTB/RIF for TP diagnosis. RESULTS: We identified 23 studies meeting our inclusion criteria. The pooled sensitivity and specificity of Xpert MTB/RIF were 30% (95% CI: 21-42%, I2 = 87.93%) and 99% (95% CI: 97-100%, I2 = 96.20%), respectively, and the area under the SROC curve (AUC) of Xpert MTB/RIF was 0.86 (95% CI: 0.83-0.89). Compared with drug susceptibility testing (DST), the pooled accordance rate of Xpert MTB/RIF in detecting rifampicin-susceptible cases and rifampicin-resistant cases was 99% (95% CI: 95-104%, I2 = 8.7%) and 94% (95% CI: 86-102%), respectively. CONCLUSIONS: Our analysis suggests that the Xpert MTB/RIF assay is of limited value as a screening test for TP but has a high potential for confirming TP diagnosis and differentiating TP from non-TB diseases using pleural fluid samples.


Assuntos
Antibióticos Antituberculose/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Rifampina/farmacologia , Tuberculose Pleural/diagnóstico , Líquidos Corporais/microbiologia , Farmacorresistência Bacteriana/efeitos dos fármacos , Humanos , Testes de Sensibilidade Microbiana , Sensibilidade e Especificidade , Tuberculose Pleural/microbiologia
20.
Microbiome ; 6(1): 87, 2018 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-29751830

RESUMO

Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It is unknown if the developing fetus is exposed to a community of viruses (virome). Given the debate over the existence of an intra-amniotic microbial community and the importance of understanding how the infant gut is populated, we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies using next-generation sequencing methods. Contrary to expectations, the bacterial microbiota of amniotic fluid was indistinguishable from contamination controls. Viral reads were sparse in the amniotic fluid, and we found no evidence of a core viral community across samples.


Assuntos
Líquido Amniótico/microbiologia , Líquido Amniótico/virologia , Bactérias/classificação , Líquidos Corporais/microbiologia , Líquidos Corporais/virologia , Microbiota/genética , Vírus/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Gravidez , Vírus/genética , Vírus/isolamento & purificação
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