<html> 1. Sangue Cultura Caldos Bandeira como &quot;positiva&quot; <ol><li> Retire a garrafa de hemocultura sinalizou a partir do contínuo monitoramento do gabinete de incubação e coloque-o em uma cabine de segurança biológica. Nota: Os frascos podem conter microorganismos perigosos e precauções universais precisam ser seguidas. Devido ao risco de aerossóis infecciosos em amostragem, todos os procedimentos de amostragem deve ser realizada em um Biossegurança Classe II câmara de fluxo laminar. </li></ol> 2. Gram Stain é preparado <ol><li> Prepare uma coloração de Gram do caldo de cultura de sangue sinalizada conforme protocolos institucionais locais. Nota: Quando organismos Gram negativos são identificados em microscopia o caldo de cultura do sangue é processada de acordo com o seguinte método. Quando os organismos Gram-positivas são identificadas, um método molecular alternativa visando a identificação genética e marcadores de resistência é aplicada ao caldo (não abordados neste artigo) 13. </li></ol>e &quot;&gt; 3. Transferência de Cultura de sangue sinalizadas Caldo de um tubo de separação do soro <ol><li> Misture suavemente o frasco de cultura de sangue invertendo 2-3x. </li><li> Dentro da cabine de segurança biológica anexar uma seringa de 10 ml para um dispositivo de transferência de sangue de segurança. </li><li> Anexar o dispositivo de transferência de sangue para o frasco de cultura de sangue e retirar 5 ml de caldo dentro da seringa. Transferir o caldo BC aspirado para um tubo de separação de soro. </li></ol> 4. Concentração de Sangue cultura Caldo <ol><li> Centrifuga-se o tubo de separação de soro a 1250 x g durante 15 min, que remove um grande volume de células vermelhas do sangue. </li><li> Aspirar e desprezar o sobrenadante utilizando uma pipeta de transferência estéril tendo o cuidado de deixar cerca de 1 ml de creme leucocitário imediatamente acima da interface gel / fluido. Nota: As garrafas aeróbias mostram uma clara separação das células vermelhas do sangue para o fundo do tubo com a interface gel / fluido aparecendo uma cor branca opaca. Em contraste, quandoaplicado ao caldo de cultura do sangue anaeróbio lítico a interface gel / fluido aparece como uma cor vermelho escuro, devido aos componentes de glóbulos vermelhos lisados ​​permanecendo suspensas no sobrenadante. </li></ol> 5. Repita os passos de lavagem Centrifugação <ol><li> Agitar suavemente as últimas 1 ml de buffy coat fluido acima da interface de gel com uma pipeta estéril e então transferir todo o volume para um tubo de microcentrífuga de 1,5 ml. Centrifuga-se o tubo de novo a 288 xg durante 30 seg. </li><li> Transferir o sobrenadante utilizando uma pipeta de 1 ml descartável de plástico de transferência para um novo tubo de microcentrifugação de 1,5 mL e rejeitar o tubo com o sedimento. Nota: É essencial nesta fase que seja tomado cuidado para evitar a transferência do sedimento. Isto é particularmente importante para um espécime a ser processado a partir da garrafa BC anaeróbico como o sobrenadante permanece pigmentado e o sedimento nem sempre é vista claramente. </li></ol> 6. Lise de células residuais </p&gt; <ol><li> Centrifugar as amostras a 18.407 xg durante 1 min e, em seguida, aspirado (e descarte) do sobrenadante utilizando uma pipeta fina de transferência de ponta para deixar o mínimo de líquido residual quanto possível, sem perturbar o sedimento. </li><li> Ressuspender o sedimento residual em 1 ml de DNAse e RNAse estéril livre de água por pipetagem cima e para baixo. Nota: Alguns autores descreveram o uso de soluções de álcool em vez de água estéril para ressuspender o sedimento que torna as bactérias não-viáveis. </li><li> Centrifugar a solução ressuspensas a 18.407 xg durante 1 min. </li></ol> 7. Extração de Proteínas de Bactérias <ol><li> Aspirar e desprezar o sobrenadante, novamente por meio de aspiração com uma pipeta de ponta fina assegurar que tanto líquido quanto possível seja removida. </li><li> Ressuspender o sedimento em 10 mL de ácido fórmico (70% v / v). Nota: O ácido fórmico pode afetar o corpo, se for inalado ou se entrar em contacto com a pele. Ao preparar ou manipular soluções é recommended que o pessoal usar um gabinete de fumo, além de equipamentos de proteção individual. </li><li> Misturar bem utilizando a pipeta para assegurar uma solução homogénea ressuspensas. Com a ponta da pipeta para perturbar fisicamente o sedimento pode ser necessário para assegurar uma solução mais homogénea. </li></ol> 8. Preparação de MALDI-TOF-alvo Placa <ol><li> Inocular um prato limpo alvo de MALDI-TOF com 2 mL da suspensão preparada por local alvo. Prepare três sítios-alvo para cada amostra para superar o problema ocasional de não lê. </li><li> Permitir que a placa-alvo MALDI-TOF para secar. A taxa de secagem pode ser aumentada colocando o prato na extremidade do exaustor de fumos para maximizar o fluxo de ar ao longo da placa. </li><li> Overlay cada local seco com 1 ul da solução de matriz (10 mg / ml de ácido α-ciano-4-hidroxicinâmico (HCCA), 50% de acetonitrilo, ácido trifluoroacético a 2,5%). Nota: solução de matriz pode afectar o corpo se inalada ou se entra em Contact com a pele. Ao preparar ou manipular soluções recomenda-se que o pessoal usar um gabinete de fumo, além de equipamentos de proteção individual. </li><li> Permitir que a placa alvo de MALDI-TOF para secar sobre a extremidade da câmara de exaustão tal como descrito acima. Certifique-se de uma preparação homogênea preenche cada um dos pontos de destino na placa. </li></ol> 9. Lugar MALDI-TOF-alvo Placa para o Espectrômetro de Massa <ol><li> Insira a placa-alvo MALDI-TOF para espectrômetro de massa MALDI-TOF. Verifique se a placa está sentado nivelado com as placas de mola. Nota: não insira a placa alvo até que todos os pontos-alvo estão secos. </li><li> Verifique se a borracha de vedação está limpa de fiapos, poeira e cabelo para permitir que as condições de vácuo exigidas pode ser criado. </li><li> Feche a tampa fase MALDI-TOF e pressione o botão &quot;in / out&quot; na parte da frente do instrumento. A tampa agora irá bloquear e permitir que o vácuo necessário para ser criado. </li></ol> 10. MALDI-TOF MS Spectra Aquisição <ol><li> Abra o MALDI Biotipagem e software FlexControl. </li><li> Dentro do software Typing selecione &quot;nova classificação&quot; no menu suspenso chamado &quot;arquivo&quot;. Nomeie o projeto e em seguida, selecione &quot;novo&quot;. Selecione &quot;Next&quot; para concluir a instalação do software de digitação. </li><li> Dentro da janela do software de Controle identificar o gráfico na tela da placa-alvo. Destaque os pontos-alvo MALDI-TOF que estão em uso, movendo o mouse sobre os pontos inoculados, mantendo pressionado o botão esquerdo do mouse. </li><li> Use o botão direito do mouse para clicar em qualquer lugar nas posições de destino selecionadas e, em seguida, selecione &quot;adicionar Analitos&quot; a partir do menu suspenso. </li><li> Adicionar hemocultivos detalhes de identificação para a coluna &quot;ID&quot; para cada um dos pontos de destino e clique em &quot;next&quot; quando terminar. </li><li> Selecione a opção &quot;taxonomia&quot; banco de dados espectros comercial e selecione &quot;Avançar&quot;. Nota: Labotórios pode utilizar adicional in-house ou bases de dados comerciais para aumentar o número de espectros de referência. </li><li> Clique em &quot;Finish&quot; e MALDI-TOF MS começará gerar espectros. Nota: As configurações de MALDI-TOF foram conforme as definições do fabricante (modo linear positivo, 60 freqüências de laser Hz, 20 kV de tensão de aceleração, 16,7 kV de tensão IS2, 170 ns de atraso extração e 2,000-20,137 faixa m / z). </li><li> Se o software de controlo de MALDI não permite gerar picos, aquisição manual dos espectros podem ser realizados (método não descrito). </li></ol> 11. Análise Pós Interpretação de MALDI-TOF MS Scores <ol><li> Uma vez que os espectros são adquiridos e análise estiver concluída, selecione o botão &quot;+&quot; ao lado de identificação das espécies sobre o software de digitação para expandir a lista de identificação para cada alvo. </li><li> Estude os top 5 identificações, observando se o top 5 são semelhantes. Discordantes top 5 gêneros com pontuação ≥ 1,7 do mesmo alvolocal levantou a possibilidade de caldos mistos. Nota: tecnologia MALDI-TOF tem pouca sensibilidade para a detecção de caldos mistos. Por exemplo, quando um caldo contém espécies mista uma pontuação elevada confiança pode ser identificado por apenas uma das espécies mistas. </li><li> Quando uma pontuação ≥ 2,0 é anotado para o maior jogo em um local de destino, informar a espécie. </li><li> Quando a maior pontuação em um ponto alvo é ≥ 1,7, mas &lt;2,0, informe apenas os gêneros. Se os critérios adicionais dos top 5 identificações são concordantes, em seguida, informar ao nível de espécie. </li></ol> 12. Remoção de MALDI-TOF-alvo Placa <ol><li> Quando todos os espectros são de imprensa completo o botão &quot;in / out&quot; na máquina MALDI-TOF. </li><li> Abra o MALDI-TOF placa-alvo recipiente e retire a placa de alvo MALDI-TOF. </li><li> Se estiver usando uma placa-alvo MALDI-TOF reutilizável, limpar todos os pontos de destino usando álcool e armazenar a placa de MALDI-TOF na RT, uma vez que está limpa e seca. </li></ol>

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Os autores declaram que não têm interesses financeiros concorrentes.

É importante quando se aplica MALDI-TOF MS para caldo de cultura de sangue que as etapas de pós centrifugação são realizados com o cuidado suficiente para não remixar os componentes separados. É particularmente importante para remover os constituintes de culturas de sangue e as proteínas celulares humanas, incluindo a hemoglobina, o que pode produzir picos interferindo com o espectro de MALDI-TOF. Embora MS fabrica recomendo cortar de pontuação ≥ 2,0 para as espécies e ≥ 1,7 p...

Os pacientes com infecção de corrente sanguínea (BSI), devido a bactérias continuam a ter alta taxa de mortalidade intra-hospitalar, que vão 6-48% 1. A entrega de antibiótico empírico adequado promove a sobrevivência e no subgrupo de pacientes com sepse grave, a cada hora de atraso para a terapêutica adequada se relaciona à diminuição da sobrevivência de 2,3. Assim, um objectivo-chave do laboratório clínico é detectar rapidamente, identificar e comunicar a presença de bactérias em hemoculturas para informar as decisões clínicas. Tem sido demonstrado que o laboratório microbiológico tem a maior influência sobre a terapia antimicrobiana no momento de relatar a coloração de Gram e 4 recentemente, um estudo de observação demonstraram que o tempo de dessorção a laser assistida por matriz / ionização de voo de espectrometria de massa (MALDI-TOF MS) realizado diretamente em caldos de cultura de sangue influenciar a prescrição em mais de um terço da BSI causada por bactérias Gram negativas 5. 6,7. A tecnologia está agora bem estabelecida e tem sido integrado em muitos laboratórios para a identificação rápida e precisa dos microorganismos isolados em 6,8 meios sólidos. A aplicação direta de MALDI-TOF MS para hemocultura (BC) caldo que sinalizaram &quot;positivo&quot; para microorganismos apela para os clínicos e gestores de laboratório por causa do potencial para obter a identificação precoce de microorganismos com baixo custo. A utilidade clínica da aplicação directa de MALDI-TOF MS para caldo de cultura de sangue tem sido limitada pela ampla gama de sensibilidades observadas quando comparado com os métodos baseados cultura fenotípica padrão de identificação, com relatos de uma identificação bem sucedida de bactérias Gram-negativas variam 47-98,9 9-11%. A variação na sensibilidade provávelrelaciona-se com a composição BC caldo, a concentração bacteriana inicial, a variação dos métodos de preparação da amostra, bem como a gama de organismos gram-negativos encontrados em populações de estudo 9. Em comparação com estes outros protocolos publicados pelo método aqui apresentado evita a utilização de etanol, cloreto de amónio ou (não-matriz) acetonitrilo adicional. Como resultado, o pellet bacteriano permanecerá viável (até o ponto de extração de proteínas) permitindo potenciais métodos de análise fenotípica de susceptibilidade para ser aplicado diretamente a estes organismos em caldo. Além disso, o método apresentado tem sido mostrado a ser barato, fiável e rápida, com a identificação de bactérias disponíveis dentro de 25 min dos resultados de cultura de sangue Gram mancha, com o mínimo &#39;mãos no tempo 12. Este método é um protocolo simples em casa spin-lise utilizando extração ácido fórmico aplicados diretamente para caldos de cultura de sangue positivos para identificar Gram negativo bacteria com tecnologia de MALDI-TOF MS.

<table border="0" cellpadding="0" cellspacing="0" width="1319">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:275px;">BACTEC Plus Aerobic/F Medium</td>
			<td style="width:307px;">Becton Dickinson; BD, Franklin Lakes, NJ, USA</td>
			<td align="right" style="width:188px;">442192</td>
			<td style="width:551px;"></td>
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			<td height="20" style="height:20px;">BACTEC Lytic/10 Anaerobic /F Medium</td>
			<td>Becton Dickinson; BD, Franklin Lakes, NJ, USA</td>
			<td align="right">442265</td>
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			<td height="20" style="height:20px;">BACTEC Peds Plus Medium</td>
			<td>Becton Dickinson; BD, Franklin Lakes, NJ, USA</td>
			<td align="right">442194</td>
			<td></td>
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			<td height="20" style="height:20px;">Vacutainer - Blood transfer device</td>
			<td>Becton Dickinson; BD, Franklin Lakes, NJ, USA</td>
			<td align="right">364880</td>
			<td>Single use sampling device reducing the risk of needlestick injury</td>
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			<td height="20" style="height:20px;">Vacutainer SST 5.0mL, Advance plus</td>
			<td>Becton Dickinson; BD, Franklin Lakes, NJ, USA</td>
			<td align="right">367954</td>
			<td>Serum separating tube</td>
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			<td height="20" style="height:20px;">Syringe 10 mL</td>
			<td>Becton Dickinson; BD, Franklin Lakes, NJ, USA</td>
			<td align="right">302143</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Transfer pipette</td>
			<td>Samco, USA</td>
			<td>222-20S</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Transfer pipette (fine tipped)</td>
			<td>Samco, USA</td>
			<td>232-20S</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Microcentrifuge tube (2.0 mL)</td>
			<td>Eppendorf, Hamburg, Germany</td>
			<td>0030.120.094</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Sterile water (DNAse and RNAse free)</td>
			<td>Life Technologies, Carlsbad, California, USA</td>
			<td>10977-015</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Formic acid</td>
			<td>Sigma-Aldrich, St. Louis, Missouri, USA</td>
			<td>F0507</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Matrix solution&#160;</td>
			<td>Bruker Daltonics, Bremen Germany</td>
			<td align="right">285074</td>
			<td>10 mg/ml &#945;-cyano-4-hydroxycinnamic acid, 50% acetonitrile, 2.5% trifluoroacetic acid</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Benchtop microflex LT MALDI-TOF MS</td>
			<td>Bruker Daltonics, Bremen Germany</td>
			<td></td>
			<td>Utilizing BioTyper 3.1 (Build 65) and FlexControl 3.3 (Build 99) software</td>
		</tr>
	</tbody>
</table>

rapid identification of gram negative bacteria from blood culture broth using maldi-tof mass spectrometry

Um papel importante do laboratório de microbiologia clínica é proporcionar a rápida identificação de bactérias que causam infecção na corrente sanguínea. Identificação tradicional exige a sub-cultura do sinalizou caldo de cultura de sangue com a identificação disponível somente depois colônias em agar sólido amadureceram. MALDI-TOF MS é um método fiável, rápido para a identificação da maioria das bactérias clinicamente relevantes, quando aplicado para colónias em meios sólidos. A aplicação de MALDI-TOF MS diretamente ao caldo de cultura de sangue é uma abordagem atraente, pois tem potencial para acelerar a identificação de espécies de bactérias e melhorar a gestão clínica. No entanto, um problema importante para superar é a remoção de pré-análise de interferentes resinas, proteínas e hemoglobina contidos em amostras de cultura do sangue, que, se não for removido, interferem com os espectros de MS e pode resultar em pontuações suficientes ou baixos de identificação de discriminação. Além disso, é necessário concentrar a bactériaia para desenvolver espectros de qualidade suficiente. O método apresentado descreve a concentração, purificação e extração de bactérias Gram negativas que permitem a identificação precoce de bactérias a partir de um caldo de cultura de sangue sinalizado.

A MALDI-TOF MS espectros gerados são comparados com a base de dados de espectros de referência integrada. A pontuação logarítmica é atribuído pela confiança do jogo entre o isolado de teste eo banco de dados de referência isola, com a recomendação de uma pontuação ≥ 1.7 necessário para provável identificação ao nível de gêneros (Figura 1) e ≥ 2.0 para provável identificação de espécies (Figura 2). Comunicar ao nível de espécie, quando a pontuação ≥ 1,7 e...

Watch this Scientific Journal Video about Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry at JoVE.com

Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

A aplicação de matriz assistida por laser de dessorção / ionização por tempo de voo (MALDI-TOF), espectrometria de massa (MS) directamente ao caldo de cultura do sangue acelera a identificação de bactérias. O método apresentado é um método rápido e fiável para a identificação de bactérias Gram-negativas directamente do caldo de cultura do sangue.

Rápida identificação de bactérias gram-negativas de Sangue Cultura Caldo Usando MALDI-TOF Espectrometria de Massa

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional ...

rapid-identification-gram-negative-bacteria-from-blood-culture-broth

Research

JoVE Journal

Immunology and Infection

23.8K visualizações.  Westmead Hospital.  A aplicação de matriz assistida por laser de dessorção / ionização por tempo de voo (MALDI-TOF), espectrometria de massa (MS) directamente ao caldo de cultura do sangue acelera a identificação de bactérias. O método apresentado é um método rápido e fiável para a identificação de bactérias Gram-negativas directamente do caldo de cultura do sangue. 

Vídeo: Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

A 1.5 Hour Procedure for Identification of Enterococcus Species Directly from Blood Cultures

Enterococci are a common cause of bacteremia with E. faecalis being the predominant species followed by E. faecium. Because resistance to ampicillin and vancomycin in E. faecalis is still uncommon compared to resistance in E. faecium, the development of rapid tests allowing differentiation between enterococcal species is important for appropriate therapy and resistance surveillance. The E. faecalis OE PNA FISH assay (AdvanDx, Woburn, MA) uses species-specific peptide nucleic acid (PNA) probes in a fluorescence in situ hybridization format and offers a time to results of 1.5 hours and the potential of providing important information for species-specific treatment. Multicenter studies were performed to assess the performance of the 1.5 hour E. faecalis/OE PNA FISH procedure compared to the original 2.5 hour assay procedure and to standard bacteriology methods for the identification of enterococci directly from a positive blood culture bottle.

A 1.5 Hour Procedure for Identification of Enterococcus Species Directly from Blood Cultures

A rapid protocol for the direct identification of Enterococcus faecalis and other Enterococcus species from a positive blood culture using a Peptide Nucleic Acid fluorescent in situ hybridization assay (PNA FISH).

Um Procedimento de 1,5 horas para a Identificação de Enterococcus Espécies Diretamente de hemoculturas

Enterococci are a common cause of bacteremia with E. faecalis being the predominant species followed by E. faecium.  Because resistance to ampicillin and ...

Imunologia e Infecção

Purification and Visualization of Lipopolysaccharide from Gram-negative Bacteria by Hot Aqueous-phenol Extraction

Lipopolysaccharide (LPS) is a major component of Gram-negative bacterial outer membranes. It is a tripartite molecule consisting of lipid A, which is embedded in the outer membrane, a core oligosaccharide and repeating O-antigen units that extend outward from the surface of the cell1, 2. LPS is an immunodominant molecule that is important for the virulence and pathogenesis of many bacterial species, including Pseudomonas aeruginosa, Salmonella species, and Escherichia coli3-5, and differences in LPS O-antigen composition form the basis for serotyping of strains. LPS is involved in attachment to host cells at the initiation of infection and provides protection from complement-mediated killing; strains that lack LPS can be attenuated for virulence6-8. For these reasons, it is important to visualize LPS, particularly from clinical isolates. Visualizing LPS banding patterns and recognition by specific antibodies can be useful tools to identify strain lineages and to characterize various mutants. 
In this report, we describe a hot aqueous-phenol method for the isolation and purification of LPS from Gram-negative bacterial cells. This protocol allows for the extraction of LPS away from nucleic acids and proteins that can interfere with visualization of LPS that occurs with shorter, less intensive extraction methods9. LPS prepared this way can be separated by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and directly stained using carbohydrate/glycoprotein stains or standard silver staining methods. Many anti-sera to LPS contain antibodies that cross-react with outer membrane proteins or other antigenic targets that can hinder reactivity observed following Western immunoblot of SDS-PAGE-separated crude cell lysates. Protease treatment of crude cell lysates alone is not always an effective way of removing this background using this or other visualization methods. Further, extensive protease treatment in an attempt to remove this background can lead to poor quality LPS that is not well resolved by any of the aforementioned methods. For these reasons, we believe that the following protocol, adapted from Westpahl and Jann10, is ideal for LPS extraction.

We describe a modified hot aqueous-phenol extraction method for purifying lipopolysaccharide (LPS) from Gram-negative bacteria. Once extracted, the LPS can be subsequently analyzed by SDS-PAGE and visualized by direct staining or Western immunoblot.

Purificação e visualização de lipopolissacarídeo de bactérias Gram-negativas por extracção aquosa de fenol-Hot

Lipopolysaccharide (LPS)  is a major component of Gram-negative bacterial outer membranes. It is a tripartite molecule consisting of  lipid A, which is ...

Detection of Bacteria Using Fluorogenic DNAzymes

Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses each and every year. Prevention of such outbreaks and minimization of the impact of an ongoing epidemic place an ever-increasing demand for analytical methods that can accurately identify culprit pathogens at the earliest stage. Although there is a large array of effective methods for pathogen detection, none of them can satisfy all the following five premier requirements embodied for an ideal detection method: high specificity (detecting only the bacterium of interest), high sensitivity (capable of detecting as low as a single live bacterial cell), short time-to-results (minutes to hours), great operational simplicity (no need for lengthy sampling procedures and the use of specialized equipment), and cost effectiveness. For example, classical microbiological methods are highly specific but require a long time (days to weeks) to acquire a definitive result.1 PCR- and antibody-based techniques offer shorter waiting times (hours to days), but they require the use of expensive reagents and/or sophisticated equipment.2-4 Consequently, there is still a great demand for scientific research towards developing innovative bacterial detection methods that offer improved characteristics in one or more of the aforementioned requirements. Our laboratory is interested in examining the potential of DNAzymes as a novel class of molecular probes for biosensing applications including bacterial detection.5
DNAzymes (also known as deoxyribozymes or DNA enzymes) are man-made single-stranded DNA molecules with the capability of catalyzing chemical reactions.6-8 These molecules can be isolated from a vast random-sequence DNA pool (which contains as many as 1016 individual sequences) by a process known as "in vitro selection" or "SELEX" (systematic evolution of ligands by exponential enrichment).9-16 These special DNA molecules have been widely examined in recent years as molecular tools for biosensing applications.6-8
Our laboratory has established in vitro selection procedures for isolating RNA-cleaving fluorescent DNAzymes (RFDs; Fig. 1) and investigated the use of RFDs as analytical tools.17-29 RFDs catalyze the cleavage of a DNA-RNA chimeric substrate at a single ribonucleotide junction (R) that is flanked by a fluorophore (F) and a quencher (Q). The close proximity of F and Q renders the uncleaved substrate minimal fluorescence. However, the cleavage event leads to the separation of F and Q, which is accompanied by significant increase of fluorescence intensity.
More recently, we developed a method of isolating RFDs for bacterial detection.5 These special RFDs were isolated to "light up" in the presence of the crude extracellular mixture (CEM) left behind by a specific type of bacteria in their environment or in the media they are cultured (Fig. 1). The use of crude mixture circumvents the tedious process of purifying and identifying a suitable target from the microbe of interest for biosensor development (which could take months or years to complete). The use of extracellular targets means the assaying procedure is simple because there is no need for steps to obtain intracellular targets.
Using the above approach, we derived an RFD that cleaves its substrate (FS1; Fig. 2A) only in the presence of the CEM produced by E. coli (CEM-EC).5 This E. coli-sensing RFD, named RFD-EC1 (Fig. 2A), was found to be strictly responsive to CEM-EC but nonresponsive to CEMs from a host of other bacteria (Fig. 3).
Here we present the key experimental procedures for setting up E. coli detection assays using RFD-EC1 and representative results.

We have recently reported a novel approach for generating fluorogenic DNAzyme probes that can be applied to set up a simple, "mix-and-read" fluorescent assay for bacterial detection. These special DNA probes catalyze the cleavage of a chromophore-modified DNA-RNA chimeric substrate in the presence of crude extracellular mixture (CEM) produced by a specific bacterium, thereby translating bacterial detection into fluorescence signal generation. In this report we will describe key experimental procedures where a specific DNAzyme probe denoted "RFD-EC1" is employed for the detection of the model bacterium, Escherichia coli (E. coli).

Detecção de bactérias utilizando DNAzymes fluorogénicas

Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses ...

Whole-cell MALDI-TOF Mass Spectrometry is an Accurate and Rapid Method to Analyze Different Modes of Macrophage Activation

MALDI-TOF is an extensively used mass spectrometry technique in chemistry and biochemistry. It has been also applied in medicine to identify molecules and biomarkers. Recently, it has been used in microbiology for the routine identification of bacteria grown from clinical samples, without preparation or fractionation steps. We and others have applied this whole-cell MALDI-TOF mass spectrometry technique successfully to eukaryotic cells. Current applications range from cell type identification to quality control assessment of cell culture and diagnostic applications. Here, we describe its use to explore the various polarization phenotypes of macrophages in response to cytokines or heat-killed bacteria. It allowed the identification of macrophage-specific fingerprints that are representative of the diversity of proteomic responses of macrophages. This application illustrates the accuracy and simplicity of the method. The protocol we described here may be useful for studying the immune host response in pathological conditions or may be extended to wider diagnostic applications.

This protocol describes the use of whole-cell MALDI-TOF mass spectrometry on eukaryotic cells. Here, we illustrate the accuracy of this technique by analyzing the multiple activation states of macrophages in response to their microenvironment.

De células inteiras MALDI-TOF espectrometria de massa é um método rápido e preciso para analisar os diferentes modos de ativação de macrófagos

MALDI-TOF is an extensively used mass spectrometry technique in chemistry and biochemistry. It has been also applied in medicine to identify molecules and ...

Isolation of Double Negative &#945;&#946; T Cells from the Kidney

There is currently no standard protocol for the isolation of DN T cells from the non-lymphoid tissues despite their increasingly reported involvement in various immune responses. DN T cells are a unique immune cell type that has been implicated in regulating immune and autoimmune responses and tolerance to allotransplants1-6. DN T cells are, however, rare in peripheral blood and secondary lymphoid organs (spleen and lymph nodes), but are major residents of the normal kidney. Very little is known about their pathophysiologic function7 due to their paucity in the periphery. We recently described a comprehensive phenotypic and functional analysis of this population in the kidney8 in steady state and during ischemia reperfusion injury. Analysis of DN T cell function will be greatly enhanced by developing a protocol for their isolation from the kidney.
Here, we describe a novel protocol that allows isolation of highly pure ab CD4+ CD8+ T cells and DN T cells from the murine kidney. Briefly, we digest kidney tissue using collagenase and isolate kidney mononuclear cells (KMNC) by density gradient. This is followed by two steps to enrich hematopoietic T cells from 3% to 70% from KMNC. The first step consists of a positive selection of hematopoietic cells using a CD45+ isolation kit. In the second step, DN T cells are negatively isolated by removal of non-desired cells using CD4, CD8, and MHC class II monoclonal antibodies and CD1d &#945;-galcer tetramer. This strategy leads to a population of more than 90% pure DN T cells. Surface staining with the above mentioned antibodies followed by FACs analysis is used to confirm purity.

Isolation of Double Negative &amp;#945;&amp;#946; T Cells from the Kidney

DNabT cells are rare among peripheral T cells; however, they are abundant in certain non-lymphoid tissues. Difficulty of isolating DN T cells from non-lymphoid tissue hinders their functional analysis despite increasing recognized pathophysiologic significance. We describe a novel protocol for isolation of highly purified DN T cells from murine kidney.

Isolamento de duplas Células αβ T negativa do Rim

There is currently no standard protocol for the isolation of DN T cells from the non-lymphoid tissues despite their increasingly reported involvement in ...

Preparation of a Blood Culture Pellet for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections.

A rapid bacterial pellet preparation from a positive blood culture can be used as a sample for applications such as identification by MALDI-TOF, Gram staining, antibiotic susceptibility testing and PCR-based test. The results can be rapidly communicated to clinicians to improve the outcome of patients suffering from bloodstream infections.

Preparação de uma Cultura Pellet sangue para rápida identificação bacteriana e Antibiótico Teste à Susceptibilidade

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a ...

A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically

Antimicrobial susceptibility testing (AST) is performed to assess the in vitro activity of antimicrobial agents against various bacteria. The AST results, which are expressed as minimum inhibitory concentrations (MICs) are used in research for antimicrobial development and monitoring of resistance development and in the clinical setting for antimicrobial therapy guidance. Dalbavancin is a semi-synthetic lipoglycopeptide antimicrobial agent that was approved in May 2014 by the Food and Drug Administration (FDA) for the treatment of acute bacterial skin and skin structure infections caused by Gram-positive organisms. The advantage of dalbavancin over current anti-staphylococcal therapies is its long half-life, which allows for once-weekly dosing. Dalbavancin has activity against Staphylococcus aureus (including both methicillin-susceptible S. aureus [MSSA] and methicillin-resistant S. aureus [MRSA]), coagulase-negative staphylococci, Streptococcus pneumoniae, Streptococcus anginosus group, &#946;-hemolytic streptococci and vancomycin susceptible enterococci. Similar to other recent lipoglycopeptide agents, optimization of CLSI and ISO broth susceptibility test methods includes the use of dimethyl sulfoxide (DMSO) as a solvent when preparing stock solutions and polysorbate 80 (P80) to alleviate adherence of the agent to plastic. Prior to the clinical studies and during the initial development of dalbavancin, susceptibility studies were not performed with the use of P-80 and MIC results tended to be 2-4 fold higher and similarly higher MIC results were obtained with the agar dilution susceptibility method. Dalbavancin was first included in CLSI broth microdilution methodology tables in 2005 and amended in 2006 to clarify use of DMSO and P-80. The broth microdilution (BMD) procedure shown here is specific to dalbavancin and is in accordance with the CLSI and ISO methods, with step-by-step detail and focus on the critical steps added for clarity.

A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically

Here, we present a protocol for determination of dalbavancin susceptibility of clinically relevant Gram-positive bacteria using a broth microdilution reference methodology.

Um método de microdiluição em caldo de referência para Dalbavancin<em&gt; In Vitro</em&gt; Teste à Susceptibilidade de bactérias que crescem aeròbia

Antimicrobial susceptibility testing (AST) is performed to assess the in vitro activity of antimicrobial agents against various bacteria. The AST results, ...

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in immunocompromised patients. In most cases only few data, mostly published as case reports, are available which investigate the role of such pathogens as an infectious agent. Therefore, in order to clarify the pathogenic character of such microorganisms, it is necessary to conduct epidemiologic studies which include large numbers of these bacteria. The methods used in such a surveillance study have to meet the following criteria: the identification of the strains has to be accurate according to the valid nomenclature, they should be easy to handle (robustness), economical in routine diagnostics and they have to generate comparable results among different laboratories. Generally, there are three strategies for identifying bacterial strains in a routine setting: 1) phenotypic identification characterizing the biochemical and metabolic properties of the bacteria, 2) molecular techniques such as 16S rRNA gene sequencing and 3) mass spectrometry as a novel proteome based approach. Since mass spectrometry and molecular approaches are the most promising tools for identifying a large variety of bacterial species, these two methods are described. Advances, limitations and potential problems when using these techniques are discussed.

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and molecular techniques (16S rRNA gene sequencing) permit the identification of rare bacterial pathogens in routine diagnostics. The goal of this protocol lies in the combination of both techniques which leads to more accurate and reliable data.

Identificação de patógenos bacterianos raras, seqüência do gene 16rRNA e MALDI-TOF MS

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in ...

Culture of Macrophage Colony-stimulating Factor Differentiated Human Monocyte-derived Macrophages

A protocol is presented for cell culture of macrophage colony-stimulating factor (M-CSF) differentiated human monocyte-derived macrophages. For initiation of experiments, fresh or frozen monocytes are cultured in flasks for 1 week with M-CSF to induce their differentiation into macrophages. Then, the macrophages can be harvested and seeded into culture wells at required cell densities for carrying out experiments. The use of defined numbers of macrophages rather than defined numbers of monocytes to initiate macrophage cultures for experiments yields macrophage cultures in which the desired cell density can be more consistently attained. Use of cryopreserved monocytes reduces dependency on donor availability and produces more homogeneous macrophage cultures.

A protocol is presented for cell culture of macrophage colony-stimulating factor (M-CSF) differentiated human monocyte-derived macrophages. The protocol utilizes cryopreservation of monocytes coupled with their bulk differentiation into macrophages. Then harvested macrophages can then be seeded into culture wells at required cell densities for carrying out experiments.

Cultura de macrófagos macrófagos Colony estimulante fator diferenciado Humano monócitos derivados

A protocol is presented for cell culture of macrophage colony-stimulating factor (M-CSF) differentiated human monocyte-derived macrophages. For initiation ...

Dextran Enhances the Lentiviral Transduction Efficiency of Murine and Human Primary NK Cells

The efficient transduction of specific genes into natural killer (NK) cells has been a major challenge. Successful transductions are critical to defining the role of the gene of interest in the development, differentiation, and function of NK cells. Recent advances related to chimeric antigen receptors (CARs) in cancer immunotherapy accentuate the need for an efficient method to deliver exogenous genes to effector lymphocytes. The efficiencies of lentiviral-mediated gene transductions into primary human or mouse NK cells remain significantly low, which is a major limiting factor. Recent advances using cationic polymers, such as polybrene, show an improved gene transduction efficiency in T cells. However, these products failed to improve the transduction efficiencies of NK cells. This work shows that dextran, a branched glucan polysaccharide, significantly improves the transduction efficiency of human and mouse primary NK cells. This highly reproducible transduction methodology provides a competent tool for transducing human primary NK cells, which can vastly improve clinical gene delivery applications and thus NK cell-based cancer immunotherapy.

The goal of this study was to formulate technologies that allow for successful gene transduction in primary natural killer (NK) cells. The dextran-mediated lentiviral transduction of human or mouse primary NK cells results in higher gene expression efficiencies. This method of gene transduction will vastly improve NK cell genetic manipulation.

Dextran aumenta a eficiência de Lentivirus transdução das células NK primário murino e humano

The efficient transduction of specific genes into natural killer (NK) cells has been a major challenge. Successful transductions are critical to defining ...