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1.
Clin Lab Med ; 40(4): 459-472, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33121615

RESUMO

Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.


Assuntos
Controle de Doenças Transmissíveis/métodos , Coronavirus , Surtos de Doenças/prevenção & controle , Técnicas Microbiológicas/métodos , Infecções Respiratórias , Serviços de Laboratório Clínico , Coronavirus/classificação , Coronavirus/genética , Coronavirus/isolamento & purificação , Coronavirus/patogenicidade , Humanos , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/virologia , Sequenciamento Completo do Genoma
2.
PLoS One ; 15(8): e0237748, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32866195

RESUMO

Soil microbiota are considered a source of undiscovered bioactive compounds, yet cultivation of most bacteria within a sample remains generally unsuccessful. Two main reasons behind the unculturability of bacteria are the presence of cells in a viable but not culturable state (such as dormant cells) and the failure to provide the necessary growth requirements in vitro (leading to the classification of some bacterial taxa as yet-to-be-cultured). The present work focuses on the development of a single procedure that helps distinguish between both phenomena of unculturability based on viability staining coupled with flow cytometry and fluorescence-activated cell sorting. In the selected soil sample, the success rate of cultured bacteria was doubled by selecting viable and metabolically active bacteria. It was determined that most of the uncultured fraction was not dormant or dead but likely required different growth conditions. It was also determined that the staining process introduced changes in the taxonomic composition of the outgrown bacterial biomass, which should be considered for further developments. This research shows the potential of flow cytometry and fluorescence-activated cell sorting applied to soil samples to improve the success rate of bacterial cultivation by estimating the proportion of dormant and yet-to-be-cultured bacteria and by directly excluding dormant cells from being inoculated into growth media.


Assuntos
Bactérias/crescimento & desenvolvimento , Técnicas Microbiológicas/métodos , Microbiota/fisiologia , Microbiologia do Solo , Bactérias/química , Bactérias/genética , Biomassa , Separação Celular/métodos , Meios de Cultura , DNA Bacteriano/isolamento & purificação , Estudos de Viabilidade , Citometria de Fluxo/métodos , Corantes Fluorescentes/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Coloração e Rotulagem/métodos
3.
Rev. esp. med. legal ; 46(3): 127-138, jul.-sept. 2020. ilus, tab, mapas, graf
Artigo em Espanhol | IBECS | ID: ibc-192314

RESUMO

En este artículo se revisan los aspectos microbiológicos de la infección COVID-19 y se presentan las recomendaciones sobre los análisis que deben realizarse en casos forenses. En primer lugar se analizan las características taxonómicas del virus, su relación con la familia Coronaviridae y su estructura genética. Se presentan brevemente las características clínicas y patológicas de la infección COVID-19, así como las coinfecciones que pueden asociarse a este virus. En el diagnóstico de laboratorio se describen la PCR -técnica de elección en la fase aguda de la infección-, los estudios antigénicos y los estudios serológicos. Finalmente se detallan los principales objetivos para los estudios microbiológicos en fallecidos en relación con la pandemia COVID-19 y se describen los principales análisis microbiológicos post mortem a realizar en fallecidos en el ámbito forense. Los estudios microbiológicos deben estar dirigidos tanto a la detección del SARS-CoV-2 como a la de las coinfecciones, que también podrían contribuir a la causa de muerte


We review the microbiological aspects of COVID-19 infection and present the microbiological studies that should be performed in forensic cases. We describe the taxonomic characteristics of the virus, its relationship with the Coronaviridae family and its genetic structure. We briefly present the clinical and pathological characteristics of COVID-19 infection, as well as the co-infections that could be associated with this virus. In the laboratory, PCR is a first-choice technique in the acute phase of the infection, together with antigen and serological studies. Finally, we describe the main objectives of microbiological studies in the deceased in relation to the COVID-19 pandemic, as well as the main post-mortem microbiological analysis to be carried out in the medico-legal context. The microbiological analysis should aim to detect both SARS-CoV-2 and coinfections, which may also contribute to the cause of death


Assuntos
Humanos , Infecções por Coronavirus/mortalidade , Síndrome Respiratória Aguda Grave/mortalidade , Pneumonia Viral/mortalidade , Atestado de Óbito/legislação & jurisprudência , Causas de Morte , Vírus da SARS/isolamento & purificação , Genoma Viral , Infecções por Coronavirus/diagnóstico , Ciências Forenses/métodos , Técnicas Microbiológicas/métodos , Pandemias/legislação & jurisprudência
4.
APMIS ; 128(10): 552-557, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32794590

RESUMO

Barbour-Stoenner-Kelly II (BSK-II) and BSK-H media were used for cultivation and isolation of fastidious Borrelia species - the causative agents of Lyme borreliosis. Culture media have a limited shelf life and require adequate storage. Our goal was to assess how the growth of Borrelia would be affected by prolonged storage of media and inadequate storage conditions (BSK-H stored at +4 °C for 2.5 years and BSK-II stored at -20 °C for 11 years). Growth of different Borrelia afzelii, Borrelia garinii, Borrelia lusitaniae and Borrelia valaisiana strains was assessed during 2 weeks of incubation at 33 °C. Monitored parameters included cell count per mL, morphology and motility. The results of this study have shown weaker growth of borrelia strains in BSK-H at +4 °C (median final cell number of 1.5 × 106 /mL) than in BSK-II at -20 °C (median final cell number of 7.75 × 106 /mL) and in fresh BSK-H media (median final cell number of 8.95 × 106 /mL). Duration of storage of media had no impact on Borrelia morphology and motility. Our results indicate that temperature of -20 °C is optimal for long-term storage of medium, BSK-II stored for 11 years provided effective support to growth of Borrelia and may be employed for cultivation.


Assuntos
Borrelia burgdorferi/crescimento & desenvolvimento , Meios de Cultura , Técnicas Microbiológicas/métodos , Técnicas Microbiológicas/normas
5.
Emerg Microbes Infect ; 9(1): 1671-1681, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32623963

RESUMO

Infectious diseases still remain one of the biggest challenges for human health. Accurate and early detection of infectious pathogens are crucial for transmission control, clinical diagnosis, and therapy. For a traditional reason, most immunological and microbiological laboratories are equipped with instruments designated for antibody-based assays in detection of infectious pathogens or clinical diagnosis. Emerging aptamer-based technologies have pushed a shift from antibody-based to aptamer-based assays due to equal specificity, even better sensitivity, lower manufacturing cost and more flexibility in amending for chemiluminescent, electrochemical or fluorescent detection in a multifaceted and high throughput fashion in comparison of aptamer-based to antibody-based assays. The nature of aptamer-based technologies is particularly suitable for point-of-care testing in remote areas at warm or hot atmosphere, and mass screening for potential infection in pandemic of emerging infectious agents, such as SARS-CoV or SARS-CoV-2 in an epicentre or other regions. This review intends to summarize currently available aptamer-based technologies in detection of bacterial, viral, and protozoan pathogens for research and clinical application. It is anticipated that potential technologies will be further optimized and validated for clinical translation in meeting increasing demands for prompt, precise, and reliable detection of specific pathogens in various atmospheric conditions.


Assuntos
Técnicas Microbiológicas/métodos , Técnica de Seleção de Aptâmeros/métodos , Animais , Bactérias/isolamento & purificação , Humanos , Parasitos/isolamento & purificação , Vírus/isolamento & purificação
6.
Appl Environ Microbiol ; 86(17)2020 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-32591382

RESUMO

Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large scale are required. In this study, we further optimized the analysis of buccal swab samples as a proxy for direct bacterial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the inverse Simpson's diversity, Shannon's evenness, and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding (P < 0.05), suggesting that this time point was optimal for representative sampling. In addition, the random forest classifier was able to accurately identify nonrumen taxa, including 10 oral and putative feed-associated taxa. Two highly prevalent (>60%) taxa in buccal and rumen samples had significant variance in relative abundances between sampling methods but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants but also further validates and refines buccal swabbing as a method to assess the rumen bacterial in large herds.IMPORTANCE The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of noninvasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.


Assuntos
Bovinos/microbiologia , Bochecha/microbiologia , Microbioma Gastrointestinal , Técnicas Microbiológicas/veterinária , Animais , Técnicas Microbiológicas/métodos , Rúmen/microbiologia , Amostragem
7.
J Med Microbiol ; 69(7): 944-948, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32490795

RESUMO

Introduction. Polymicrobial infections including yeasts and bacteria are not rare and patients with polymicrobial bloodstream infection have higher early and overall case fatality rates. The diagnosis of invasive fungal and bacterial infections is mainly based on blood culture.Aim. The aim was to reveal the effect of concomitant bacteraemia on the detection of fungi from blood cultures in the presence of polymicrobial bloodstream infections involving Candida and non-Candida fungi and to show the superiority of blood culture bottles including selective fungal media in such situations.Methodology. Twenty-four polymicrobial bloodstream infection models - involving one fungus and one bacterium - were constituted by using clinical blood culture isolates (Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans, Candida glabrata, Fusarium solani and Trichosporon asahii). The Plus Aerobic/F (PAF) and Mycosis IC/F (MICF) culture bottles were used with the BACTEC 9240 device. After a bottle signalled positive, direct microscopic examination and subcultures on agar plates were performed.Results. All of fungi that were inoculated alone and in combination were detected by both direct microscopic examination and subcultures on agar plates from MICF bottles, whereas direct microscopic examination only revealed the bacterial agents from PAF bottles including combinations. Furthermore, fungal growth was hidden by bacterial growth on blood agar subcultures from PAF bottles including combinations of F. solani, C. glabrata or T. asahii with bacteria.Conclusion. Blood culture bottles including selective fungal media that can allow selective growth of fungi and earlier detection of some species should be preferred in addition to non-selective blood culture bottles, especially in specific patient populations. Further, the use of selective agar plates such as inhibitory mould agar may contribute to the solution of this problem in clinical laboratories.


Assuntos
Bacteriemia/diagnóstico , Hemocultura/métodos , Bacteriemia/sangue , Bacteriemia/microbiologia , Bactérias/crescimento & desenvolvimento , Bactérias/isolamento & purificação , Infecções Bacterianas/sangue , Infecções Bacterianas/diagnóstico , Candida/isolamento & purificação , Candidemia/sangue , Candidemia/diagnóstico , Candidemia/microbiologia , Meios de Cultura , Fungos/crescimento & desenvolvimento , Fungos/isolamento & purificação , Humanos , Técnicas Microbiológicas/métodos , Micoses/sangue , Micoses/diagnóstico
10.
Lett Appl Microbiol ; 71(4): 330-336, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32506499

RESUMO

The deferred antagonism technique has been utilized for several decades for detecting antibiosis activity. Most protocols require the elimination of antibiotic-producing cells by exposing them to chloroform vapour, UV radiation or filter sterilizing the filtrate steps that require additional time and expense to complete. We provide a modified approach to current soft agar overlay practices, which involves addition of antibiotics to the soft agar overlay to inhibit growth of the producer but not the indicator strain. This technique can be used to reproducibly and efficiently screen for antibiotic production with ease. We demonstrate the effectiveness of this technique with three bacterial systems: inhibition of the bacterial spot of tomato pathogen, Xanthomonas euvesicatoria, by its pathogenic competitor Xanthomonas perforans; and inhibition of the fire blight pathogen, Erwinia amylovora, by Pantoea vagans C9-1 or Pseudomonas fluorescens A506. SIGNIFICANCE AND IMPACT OF THE STUDY: Deferred antagonism assays are used commonly to observe antibiotic production by micro-organisms. Killing or removing the producer cells prior to introduction of the indicator strain is a standard practice but requires additional time and special handling procedures. We evaluated a modification of the assay, where the overlay medium is amended with an antibiotic to which the indicator strain is resistant and the producer strain is sensitive. This modification obviates extra steps to kill the producer strain prior to overlaying with the indicator strain and provides a rapid, consistent and cost-effective method to detect antibiosis.


Assuntos
Antibiose , Erwinia amylovora/fisiologia , Técnicas Microbiológicas/métodos , Pantoea/fisiologia , Pseudomonas fluorescens/fisiologia , Xanthomonas/fisiologia , Lycopersicon esculentum/microbiologia , Doenças das Plantas/microbiologia , Xanthomonas/crescimento & desenvolvimento
11.
J Vis Exp ; (159)2020 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-32449734

RESUMO

Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of movement. Here we demonstrate a combination of three of these methodologies. Motility in soft agar is the oldest, offering a strong selection for isolating gain-of-function suppressor mutations in motility-impaired strains, where motility is restored through a second mutation. The cell-tethering technique, first employed to demonstrate the rotary nature of the flagellar motor, can be used to assess the impact of signaling effectors on the motor speed and its ability to switch rotational direction. The "border-crossing" assay is more recent, where swimming bacteria can be primed to transition into moving collectively as a swarm. In combination, these protocols represent a systematic and powerful approach to identifying components of the motility machinery, and to characterizing their role in different facets of swimming and swarming. They can be easily adapted to study motility in other bacterial species.


Assuntos
Escherichia coli/fisiologia , Flagelos/metabolismo , Técnicas Microbiológicas/métodos , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Genes Supressores , Movimento , Mutação/genética
12.
J Vis Exp ; (159)2020 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-32449732

RESUMO

Microbial behaviors, such as motility and chemotaxis (the ability of a cell to alter its movement in response to a chemical gradient), are widespread across the bacterial and archaeal domains. Chemotaxis can result in substantial resource acquisition advantages in heterogeneous environments. It also plays a crucial role in symbiotic interactions, disease, and global processes, such as biogeochemical cycling. However, current techniques restrict chemotaxis research to the laboratory and are not easily applicable in the field. Presented here is a step-by-step protocol for the deployment of the in situ chemotaxis assay (ISCA), a device that enables robust interrogation of microbial chemotaxis directly in the natural environment. The ISCA is a microfluidic device consisting of a 20 well array, in which chemicals of interest can be loaded. Once deployed in aqueous environments, chemicals diffuse out of the wells, creating concentration gradients that microbes sense and respond to by swimming into the wells via chemotaxis. The well contents can then be sampled and used to (1) quantify strength of the chemotactic responses to specific compounds through flow cytometry, (2) isolate and culture responsive microorganisms, and (3) characterize the identity and genomic potential of the responding populations through molecular techniques. The ISCA is a flexible platform that can be deployed in any system with an aqueous phase, including marine, freshwater, and soil environments.


Assuntos
Organismos Aquáticos/fisiologia , Quimiotaxia , Ecossistema , Técnicas Microbiológicas/métodos , Citometria de Fluxo , Dispositivos Lab-On-A-Chip , Técnicas Microbiológicas/instrumentação
13.
BMC Infect Dis ; 20(1): 303, 2020 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-32321447

RESUMO

BACKGROUND: This study aimed to establish and evaluate a simultaneous amplification and testing method for detection of extra-pulmonary tuberculosis (EPTB). METHODS: From January 2016 and December 2017 the pus or surgical excision from the lesions of inpatients admitted from Chongqing Public Health Treatment Center were collected. According to the clinical diagnosis, the samples were divided into two groups including EPTB (Group A) and other diseases excluded from tuberculosis diseases (Group B). Simultaneous detection of Mycobacterium tuberculosis (MTB) used Roche culture method, liquid culture method and simultaneous amplification and testing (SAT) method. The sensitivity and specificity of the SAT method were compared with culture methods and clinical diagnosis of EPTB. RESULTS: For 433 EPTB specimens and 49 non-TB specimens, the simultaneous amplification and testing tuberculosis (SAT-TB) results correlated with 80.5% (388/482 specimens) of the culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of EPTB were 83.6, 79.4, 59.4, and 93.0%, respectively, compared to culture methods. Compared with the clinical diagnosis of patients, the sensitivity and specificity of the SAT-TB test were 41.6 and 100%, respectively, the cultures test were 29.3 and 98.0%. CONCLUSIONS: SAT test is a simple and rapid test with high specificity which may enhance the detection of EPTB. SAT-TB is a higher clinical diagnosis value for EPTB in clinical microbiology laboratories.


Assuntos
Corantes Fluorescentes/análise , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Tuberculose/diagnóstico , Reações Falso-Negativas , Fluorescência , Corantes Fluorescentes/metabolismo , Humanos , Técnicas Microbiológicas/métodos , Testes Imediatos , Valor Preditivo dos Testes , Sensibilidade e Especificidade , Fatores de Tempo , Tuberculose/microbiologia
14.
Ann Biol Clin (Paris) ; 78(2): 139-146, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-32319942

RESUMO

The pre-analytical step of the cytobacteriological examination of urine (CBEU) is one of the most critical in microbiology. The objectives of our study were to determine the rate of urinary contamination and to analyze the factors that would facilitate this in order to propose solutions to this problem. METHOD: This is a 26-month descriptive study including all CBEU requests to our laboratory. Urine was treated in accordance with the recommendations of the medical microbiology recommendations. Urine was considered contaminated in the case of polymorphic culture with at least three different types of germs with a count from 103 CFU/mL. RESULTS: We collected 16,412 CBEU requests. Urine was contaminated in 4,830 cases (29.43%). Of the contaminated urine, 39.23% (n=1,895) was from emergency departments, 79.44% (n=3,837) was collected in the middle of the stream, 69.83% (n=3,373) was from a female patient and 16.34% (n=789) was from children under the age of 5. DISCUSSION AND CONCLUSION: To reduce urine contamination, quality instructions describing sampling procedures should be available and samples in the middle of the stream and through the collection adhesive bags should be replaced by sus-pubic puncture samples in children, whenever the profit/risk ratio of this method is favourable.


Assuntos
Urinálise/normas , Infecções Urinárias/diagnóstico , Coleta de Urina/normas , Urina/microbiologia , Adolescente , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Reações Falso-Positivas , Feminino , Hospitais Universitários , Humanos , Lactente , Recém-Nascido , Masculino , Técnicas Microbiológicas/métodos , Técnicas Microbiológicas/normas , Pessoa de Meia-Idade , Marrocos/epidemiologia , Fase Pré-Analítica/normas , Fase Pré-Analítica/estatística & dados numéricos , Estudos Retrospectivos , Fatores Sexuais , Urinálise/métodos , Urinálise/estatística & dados numéricos , Infecções Urinárias/epidemiologia , Infecções Urinárias/microbiologia , Coleta de Urina/métodos , Coleta de Urina/estatística & dados numéricos , Adulto Jovem
15.
PLoS Negl Trop Dis ; 14(4): e0008087, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32330127

RESUMO

There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,799 stool samples from children aged 2-12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to double-slide Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for Trichuris trichiura. Ascaris lumbricoides prevalence was lower using qPCR, and 26% of samples classified as A. lumbricoides positive by Kato-Katz were negative by qPCR. Amplicon sequencing of the 18S rDNA from 10 samples confirmed that A. lumbricoides was absent in samples classified as positive by Kato-Katz and negative by qPCR. The sensitivity of Kato-Katz was 49% for A. lumbricoides, 32% for hookworm, and 52% for T. trichiura; the sensitivity of qPCR was 79% for A. lumbricoides, 93% for hookworm, and 90% for T. trichiura. Specificity was ≥ 97% for both tests for all STH except for Kato-Katz for A. lumbricoides (specificity = 68%). There were moderate negative, monotonic correlations between qPCR cycle quantification values and eggs per gram quantified by Kato-Katz. While it is widely assumed that double-slide Kato-Katz has few false positives, our results indicate otherwise and highlight inherent limitations of the Kato-Katz technique. qPCR had higher sensitivity than Kato-Katz in this low intensity infection setting.


Assuntos
Helmintíase/diagnóstico , Enteropatias Parasitárias/diagnóstico , Técnicas Microbiológicas/métodos , Técnicas de Diagnóstico Molecular/métodos , Reação em Cadeia da Polimerase em Tempo Real/métodos , Ancylostomatoidea/isolamento & purificação , Animais , Ascaris lumbricoides/isolamento & purificação , Bangladesh , Criança , Pré-Escolar , DNA de Helmintos/genética , DNA Ribossômico/genética , Fezes/parasitologia , Feminino , Humanos , Lactente , Masculino , RNA Ribossômico 18S/genética , População Rural , Sensibilidade e Especificidade , Trichuris/isolamento & purificação
16.
PLoS One ; 15(3): e0230338, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32182283

RESUMO

The aim of this study was to evaluate the diagnostic performance of immunochromatographic tests (ICTs) for the detection of Mycoplasma pneumoniae. Medline/Pubmed, Embase, the Cochrane Library, and ISI Web of Science were searched through June 12, 2019 for relevant studies that used ICTs for the detection of M. pneumoniae infection with polymerase chain reaction (PCR) or microbial culturing as reference standards. Pooled diagnostic accuracy with 95% confidence interval (CI) was calculated using a bivariate random effects model. We also constructed summary receiver operating characteristic curves and calculated the area under the curve (AUC). Statistical heterogeneity was evaluated by χ2 test or Cochrane's Q test. Thirteen studies including 2,235 samples were included in the meta-analysis. The pooled sensitivity and specificity for diagnosing M. pneumoniae infection were 0.70 (95% CI: 0.59-0.79) and 0.92 (95% CI: 0.87-0.95), respectively. The positive likelihood ratio (LR) was 8.94 (95% CI: 4.90-14.80), negative LR 0.33 (95% CI: 0.22-0.46), diagnostic odds ratio 29.20 (95% CI: 10.70-64.20), and AUC 0.904. In subgroup analysis, ICTs demonstrated similar pooled sensitivities and specificities in populations of children only and mixed populations (children + adults). Specimens obtained from oropharyngeal swabs exhibited a higher sensitivity and specificity than those of nasopharyngeal swab. Moreover, pooled estimates of sensitivity and accuracy for studies using PCR as a reference standard were higher than those using culture. The pooled sensitivity and specificity of Ribotest Mycoplasma®, the commercial kit most commonly used in the included studies, were 0.66 and 0.89, respectively. Overall, ICT is a rapid user-friendly method for diagnosing M. pneumoniae infection with moderate sensitivity, high specificity, and high accuracy. This suggests that ICT may be useful in the diagnostic workup of M. pneumoniae infection; however, additional studies are needed for evaluating the potential impact of ICT in clinical practice.


Assuntos
Cromatografia de Afinidade/normas , Testes Diagnósticos de Rotina/normas , Mycoplasma pneumoniae/isolamento & purificação , Pneumonia por Mycoplasma/diagnóstico , Adulto , Criança , Testes Diagnósticos de Rotina/métodos , Humanos , Técnicas Microbiológicas/métodos , Técnicas Microbiológicas/normas , Mycoplasma pneumoniae/imunologia , Orofaringe/microbiologia , Pneumonia por Mycoplasma/imunologia , Pneumonia por Mycoplasma/microbiologia , Reação em Cadeia da Polimerase/normas , Curva ROC , Padrões de Referência
17.
Med Mycol J ; 61(1): 1-5, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32115443

RESUMO

Effects of the type of microplates and solvent for preparation of caspofungin (CPFG) on antifungal susceptibility testing of CPFG against clinical isolates of Candida albicans, Candida glabrata, and Candida krusei (20 strains each) by broth microdilution method according to the Clinical and Laboratory Standards Institute were evaluated. When CPFG was dissolved in water, MICs against the three Candida species decreased 3.1-6.0-fold in surface-untreated microplates compared to those in treated microplates. When CPFG was dissolved in dimethyl sulfoxide, MICs against the three Candida species decreased 1.3-2.5-fold in surface-untreated microplates compared to those in treated microplates. Differences in MICs according to the type of solvent did not exceed the difference for one dilution interval (0.5-2-fold MIC ratio) regardless of whether the microplate surface was treated or not. These findings suggest that differences in CPFG MICs may depend mainly on the type of surface treatment of assay microplates.


Assuntos
Antifúngicos/farmacologia , Candida/efeitos dos fármacos , Caspofungina/farmacologia , Técnicas Microbiológicas/métodos , Solventes , Farmacorresistência Fúngica
18.
Actas dermo-sifiliogr. (Ed. impr.) ; 111(2): 135-142, mar. 2020. ilus, tab, graf
Artigo em Espanhol | IBECS | ID: ibc-191503

RESUMO

INTRODUCCIÓN: La sífilis es una infección de transmisión sexual (ITS) producida por el Treponema pallidum subespecie pallidum, bacteria difícil de cultivar por lo que se requieren técnicas serológicas para su diagnóstico. La aparición de nuevas pruebas treponémicas (PT) automatizadas ha supuesto un cambio en el algoritmo diagnóstico de la sífilis, el cual tradicionalmente se iniciaba con una prueba no treponémica (PNT). Presentamos 15 casos de sífilis primarias detectadas gracias a la utilización de las nuevas PT automatizadas y realizamos una revisión de las técnicas microbiológicas en el diagnóstico de la sífilis precoz. MATERIAL Y MÉTODOS: Se recogieron todos los casos de sífilis diagnosticados en nuestro servicio desde enero de 2013 hasta septiembre de 2018. Se seleccionaron los pacientes con PNT negativas, Rapid Plasma Reagin (RPR) en particular. RESULTADOS: De un total de 158 pacientes diagnosticados de sífilis en este periodo, 15 presentaron PNT (RPR) negativas y de estos 15, todos excepto uno presentaron PT positivas. Catorce casos eran varones, con un rango de edad desde 22 a 60 años. Además, a 8 pacientes se les realizó reacción en cadena de la polimerasa (PCR) del exudado de la úlcera, siendo en todos ellos positiva. Los 15 pacientes fueron tratados con una dosis única de penicilina G benzatina 2,4 MUI. CONCLUSIÓN: resaltamos la utilidad de las nuevas técnicas serológicas automatizadas, Chemiluminiscence Inmunoassay (CLIA) y Automated Treponema Pallidum Enzime linked Inmunoassay (EIA) y apoyamos su implantación como pruebas de screening en el diagnóstico de sífilis, dado su sensibilidad diagnóstica, su rapidez y su bajo coste


BACKGROUND: Syphilis is a sexually transmitted infection caused by Treponema pallidum, subspecies pallidum. As these bacteria are difficult to culture, syphilis must be diagnosed by serologic testing. The introduction of automated treponemal tests has led to changes in the traditional diagnostic algorithm for syphilis, which began with a nontreponemal test. We present 15 cases of primary syphilis detected using these new tools and review the microbiologic techniques used for the diagnosis of early syphilis. MATERIAL AND METHODS: We examined all cases of syphilis diagnosed in our department between January 2013 and September 2018 and selected patients with negative nontreponemal (rapid plasma reagin [RPR]) tests. RESULTS: Of the 158 patients diagnosed with syphilis during the study period, 15 had a negative RPR test, and 14 of them had a positive treponemal test. Fourteen of the patients were men and ages ranged from 22 to 60 years. Polymerase chain reaction was used to detect T pallidum in the lesion exudate from 8 patients and was positive in all cases. The 15 patients were treated with a single injection of 2.4 million units of benzathine penicillin G. CONCLUSIÓN: Chemiluminescence immunoassays and T pallidum automated enzyme-linked immunoassays are useful in the diagnosis of early syphilis, and we believe that they should be adopted as screening tools given their diagnostic sensitivity, speed, and low cost


Assuntos
Humanos , Masculino , Adulto , Pessoa de Meia-Idade , Sorodiagnóstico da Sífilis/métodos , Sífilis/diagnóstico , Sorodiagnóstico da Sífilis , Treponema pallidum/isolamento & purificação , Microscopia/métodos , Técnicas Microbiológicas/métodos , Reação em Cadeia da Polimerase
19.
PLoS One ; 15(3): e0226467, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32203515

RESUMO

The aim of this study was to compare the Candida bromcresol green (BCG) medium with the chromogenic (CHROM) Brilliance Candida agar and Sabouraud dextrose agar (SDA) media in regard to their capability of detecting Candida isolates from mono- or dual-species cultures. We prepared Candida isolates' suspensions to obtain mono-species (n = 18) or dual-species (n = 153) culture plates per each medium, and three readers independently observed 513 plates at 24-h, 48-h and 72-h incubation time. We scored reading results as correct, over or under detection compared to the expected species number(s). BCG showed significantly higher correct-detection and lower under-detection rates for all Candida species when observed by at least one reader. At 24-h reading, 12 mono-species cultures had correct (or over) detections in all media, whereas 106, 60 and 78 dual-species cultures had correct (or over) detections in BCG, CHROM or SDA, respectively. BCG provides the basis for an accurate laboratory diagnosis of Candida infections.


Assuntos
Ágar/química , Candida/isolamento & purificação , Candidíase/diagnóstico , Meios de Cultura/química , Indicadores e Reagentes/química , Candidíase/microbiologia , Humanos , Técnicas Microbiológicas/métodos
20.
Artigo em Inglês | MEDLINE | ID: mdl-31952364

RESUMO

Respiratory viruses are a common cause of respiratory tract infection (RTI), particularly in neonates and children. Rapid and accurate diagnosis of viral infections could improve clinical outcomes and reduce the use of antibiotics and treatment sessions. Advances in diagnostic technology contribute to the accurate detection of viruses. We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. Fifteen respiratory viruses were included in our investigation: respiratory syncytial virus A/B (RSV), influenza virus A (FluA) and influenza virus B (FluB), human metapneumovirus (MPV), enterovirus (EV), human parainfluenza virus (PIV) types 1-4, human rhinovirus (RV), human coronavirus OC43, NL63, and 229E, human adenovirus (ADV), and human bocavirus (Boca). In total, 474 specimens were collected and tested. Respiratory viruses were detected more frequently by PCR (357, 75.3%) than they were by traditional tests (229, 49.3%). The leading pathogens were RSV (113, 23.8%), RV (72, 15.2%), PIV3 (53, 11.2%), FluA (51, 10.8%), and ADV (48, 10.1%). For children younger than 5 years, RSV and RV were most prevalent; for children older than 5 years, FluA and ADV were the most frequently detected. Of the specimens, 25.8% (92/357) were coinfected with two or more viruses. RV, Boca, PIV2, FluB, and PIV4 had higher rates of coinfection; MPV and PIV1 had the lowest rates of coinfection (9.1% and 5.3%). To conclude, the detection power of PCR was better than that of traditional antigen tests and virus cultures when considering the detection of respiratory viruses. RSV and RV were the leading viral pathogens identified in the respiratory specimens. One-quarter of the positive specimens were coinfected with two or more viruses. In the future, further application of PCR may contribute to the rapid and accurate diagnosis of respiratory viruses and could improve patient outcomes.


Assuntos
Técnicas Microbiológicas/métodos , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Viroses/diagnóstico , Viroses/virologia , Criança , Pré-Escolar , Coinfecção , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Técnicas Microbiológicas/normas , Reação em Cadeia da Polimerase em Tempo Real
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