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Limited Applicability of Direct Fluorescent-Antibody Testing for Bordetella sp. and Legionella sp. Specimens for the Clinical Microbiology Laboratory▿

She, Rosemary C.; Billetdeaux, Erick; Phansalkar, Amit R.; Petti, Cathy A.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
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The rapid diagnosis of infections with Bordetella and Legionella species is important for patient management. With observed increases in direct fluorescent-antibody (DFA) testing volumes, we retrospectively compared the performance characteristics of DFA testing to those of culture and PCR. For Bordetella sp., samples were classified as positive by DFA testing (184 [3%] of 6,195 samples) and culture (150 [2%] of 6,251 samples) significantly less often than by PCR (2,557 [10%] of 26,929 samples). Of 360 samples tested by both DFA and PCR methods, 81 (16 by DFA testing and 79 by PCR) were determined to be positive for Bordetella, with a sensitivity and specificity of DFA testing of 18% and 99%, respectively. Of 1,426 samples tested by both DFA and culture methods, 48 (44 by DFA testing and 15 by culture) were determined to be positive for Bordetella, with a sensitivity and specificity of DFA testing of 73% and 98%, respectively. For Legionella sp., samples were identified as positive by DFA testing (31 [0.25%] of 12,597 samples) and culture (85 [0.6%] of 13,572 samples) significantly less often than by PCR (27 [4%] of 716 samples). Of 62 samples tested by both DFA and PCR methods, none were positive for Legionella sp. by DFA testing and 3 were positive by PCR. Of 3...

Multicenter Evaluation of the BD Phoenix Automated Microbiology System for Antimicrobial Susceptibility Testing of Streptococcus Species▿

Richter, Sandra S.; Howard, Wanita J.; Weinstein, Melvin P.; Bruckner, David A.; Hindler, Janet F.; Saubolle, Michael; Doern, Gary V.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
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This multicenter study evaluated the BD Phoenix Automated Microbiology System STREP panel (BD Diagnostic Systems). Antimicrobial susceptibility testing (AST) with 13 agents was performed on 2,013 streptococci (938 Streptococcus pneumoniae isolates; 396 group B streptococci [GBS]; 369 viridans group streptococci [VGS]; 290 beta-hemolytic streptococcus groups A, C, and G; and 20 other streptococci) with the Phoenix system and a broth microdilution reference method. Clinical and challenge isolates were tested against cefepime, cefotaxime (CTX), ceftriaxone (CTR), clindamycin (CLI), erythromycin (ERY), gatifloxacin, levofloxacin, linezolid, meropenem, penicillin (PEN), tetracycline (TET), trimethoprim-sulfamethoxazole, and vancomycin. Clinical isolates with major errors or very major errors (VMEs) were retested in duplicate by both methods. The final results for clinical isolates showed the following trends. For all of the organism-antimicrobial agent combinations tested, categorical agreement (CA) was 92 to 100%, with one exception—VGS-PEN (87% CA; all errors were minor). For S. pneumoniae, there was one major error with CLI (0.1%) and one or two VMEs with CTX (4%), CTR (4.5%), ERY (0.9%), and TET (0.7%). For groups A, C, and G, the CA was 97 to 100% and the only VMEs were resolved by additional reference laboratory testing. For GBS...

Variability of Bacterial Biofilms of the “Tina” Wood Vats Used in the Ragusano Cheese-Making Process▿

Licitra, G.; Ogier, J. C.; Parayre, S.; Pediliggieri, C.; Carnemolla, T. M.; Falentin, H.; Madec, M. N.; Carpino, S.; Lortal, S.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Ragusano cheese is a “protected denomination of origin” cheese made in the Hyblean region of Sicily from raw milk using traditional wooden tools, without starter. To explore the Ragusano bacterial ecosystem, molecular fingerprinting was conducted at different times during the ripening and biofilms from the wooden vats called “tinas” were investigated. Raw milks collected at two farm sites, one on the mountain and one at sea level, were processed to produce Ragusano cheese. Raw milk, curd before and after cooking, curd at stretching time (cheese 0 time), and cheese samples (4 and 7 months) were analyzed by PCR-temporal temperature gel electrophoresis (PCR-TTGE) and by classical enumeration microbiology. With the use of universal primers, PCR-TTGE revealed many differences between the raw milk profiles, but also notable common bands identified as Streptococcus thermophilus, Lactobacillus lactis, Lactobacillus delbrueckii, and Enterococcus faecium. After the stretching, TTGE profiles revealed three to five dominant species only through the entire process of ripening. In the biofilms of the two tinas used, one to five species were detected, S. thermophilus being predominant in both. Biofilms from five other tinas were also analyzed by PCR-TTGE...

Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows▿ †

Zinger, L.; Coissac, E.; Choler, P.; Geremia, R. A.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Understanding how microbial community structure and diversity respond to environmental conditions is one of the main challenges in environmental microbiology. However, there is often confusion between determining the phylogenetic structure of microbial communities and assessing the distribution and diversity of molecular operational taxonomic units (MOTUs) in these communities. This has led to the use of sequence analysis tools such as multiple alignments and hierarchical clustering that are not adapted to the analysis of large and diverse data sets and not always justified for characterization of MOTUs. Here, we developed an approach combining a pairwise alignment algorithm and graph partitioning by using MCL (Markov clustering) in order to generate discrete groups for nuclear large-subunit rRNA gene and internal transcript spacer 1 sequence data sets obtained from a yearly monitoring study of two spatially close but ecologically contrasting alpine soils (namely, early and late snowmelt locations). We compared MCL with a classical single-linkage method (Ccomps) and showed that MCL reduced bias such as the chaining effect. Using MCL, we characterized fungal communities in early and late snowmelt locations. We found contrasting distributions of MOTUs in the two soils...

Cryptic Lineages of the Genus Escherichia▿ † ‡

Walk, Seth T.; Alm, Elizabeth W.; Gordon, David M.; Ram, Jeffrey L.; Toranzos, Gary A.; Tiedje, James M.; Whittam, Thomas S.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Extended multilocus sequence typing (MLST) analysis of atypical Escherichia isolates was used to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. Analysis of individual housekeeping loci showed that E. coli and its sister clade, CI, remain largely indistinguishable and represent nascent evolutionary lineages. Conversely, clades of similar age (CIII and CIV) were found to be phylogenetically distinct. When all Escherichia lineages (named and unnamed) were evaluated, we found evidence that Escherichia fergusonii has evolved at an accelerated rate compared to E. coli, CI, CIII, CIV, and CV, suggesting that this species is younger than estimated by the molecular clock method. Although the five novel clades were phylogenetically distinct, we were unable to identify a discriminating biochemical marker for all but one of them (CIII) with traditional phenotypic profiling. CIII had a statistically different phenotype from E. coli that resulted from the loss of sucrose and sorbitol fermentation and lysine utilization. The lack of phenotypic distinction has likely hindered the ability to differentiate these clades from typical E. coli, and so their ecological significance and importance for applied and clinical microbiology are yet to be determined. However...

Design of an Experimental Viscoelastic Food Model System for Studying Zygosaccharomyces bailii Spoilage in Acidic Sauces▿

Mertens, L.; Geeraerd, A. H.; Dang, T. D. T.; Vermeulen, A.; Serneels, K.; Van Derlinden, E.; Cappuyns, A. M.; Moldenaers, P.; Debevere, J.; Devlieghere, F.; Van Impe, J. F.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Within the field of predictive microbiology, the number of studies that quantify the effect of food structure on microbial behavior is very limited. This is mainly due to impracticalities related to the use of a nonliquid growth medium. In this study, an experimental food model system for studying yeast spoilage in acid sauces was developed by selecting a suitable thickening/gelling agent. In a first step, a variety of thickening/gelling agents was screened, with respect to the main physicochemical (pH, water activity, and acetic acid and sugar concentrations) and rheological (weak gel viscoelastic behavior and presence of a yield stress) characteristics of acid sauces. Second, the rheological behavior of the selected thickening/gelling agent, Carbopol 980, was extensively studied within the following range of conditions: pH 4.0 to 5.0, acetic acid concentration of 0 to 1.0% (vol/vol), glycerol concentration of 0 to 15% (wt/vol), and Carbopol concentration of 1.0 to 1.5% (wt/vol). Finally, the applicability of the model system was illustrated by performing growth experiments in microtiter plates for Zygosaccharomyces bailii at 0, 0.5, 1.0, and 1.5% (wt/vol) Carbopol, 5% (wt/vol) glycerol, 0% (vol/vol) acetic acid, and pH 5.0. A shift from planktonic growth to growth in colonies was observed when the Carbopol concentration increased from 0.5 to 1.0%. The applicability of the model system was illustrated by estimating μmax at 0.5% Carbopol from absorbance detection times.

Internal Transcribed Spacer Region Sequence Heterogeneity in Rhizopus microsporus: Implications for Molecular Diagnosis in Clinical Microbiology Laboratories ▿

Woo, Patrick C. Y.; Leung, Shui-Yee; To, Kelvin K. W.; Chan, Jasper F. W.; Ngan, Antonio H. Y.; Cheng, Vincent C. C.; Lau, Susanna K. P.; Yuen, Kwok-Yung
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Although internal transcribed spacer region (ITS) sequence heterogeneity has been reported in a few fungal species, it has very rarely been reported in pathogenic fungi and has never been described in Mucorales, causes of the highly fatal mucormycosis. In a recent outbreak investigation of intestinal mucormycosis due to Rhizopus microsporus infection in patients with hematological malignancies, PCR of the ITS of four of the 28 R. microsporus strains, P11, P12, D3-1, and D4-1, showed thick bands at about 700 bp. Direct sequencing of the purified bands showed frequent double peaks along all of the sequence traces and occasional triple peaks for P12, D3-1, and D4-1. The thick bands of the four R. microsporus strains were purified and cloned. Sequencing of 10 clones for each strain revealed two different ITS sequences for P11 and three different ITS sequences for P12, D3-1, and D4-1. Variations in ITS sequence among the different ribosomal DNA (rDNA) operons in the same strain were observed in only ITS1 and ITS2 and not the 5.8S rDNA region. One copy of P11, P12, and D4-1, respectively, and one copy of P11, P12, D3-1, and D4-1, respectively, showed identical sequences. This represents the first evidence of ITS sequence heterogeneity in Mucorales. ITS sequence heterogeneity is an obstacle to molecular identification and genotyping of fungi in clinical microbiology laboratories. When thick bands and double peaks are observed during PCR sequencing of a gene target...

Spatially Resolved Characterization of Water and Ion Incorporation in Bacillus Spores▿

Ghosal, Sutapa; Leighton, Terrance J.; Wheeler, Katherine E.; Hutcheon, Ian D.; Weber, Peter K.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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We present the first direct visualization and quantification of water and ion uptake into the core of individual dormant Bacillus thuringiensis subsp. israelensis (B. thuringiensis subsp. israelensis) endospores. Isotopic and elemental gradients in the B. thuringiensis subsp. israelensis spores show the permeation and incorporation of deuterium in deuterated water (D2O) and solvated ions throughout individual spores, including the spore core. Under hydrated conditions, incorporation into a spore occurs on a time scale of minutes, with subsequent uptake of the permeating species continuing over a period of days. The distribution of available adsorption sites is shown to vary with the permeating species. Adsorption sites for Li+, Cs+, and Cl− are more abundant within the spore outer structures (exosporium, coat, and cortex) relative to the core, while F− adsorption sites are more abundant in the core. The results presented here demonstrate that elemental abundance and distribution in dormant spores are influenced by the ambient environment. As such, this study highlights the importance of understanding how microbial elemental and isotopic signatures can be altered postproduction, including during sample preparation for analysis, and therefore...

Multiple-Locus Variable-Number Tandem-Repeat Analysis of the Swine Dysentery Pathogen, Brachyspira hyodysenteriae▿ †

Hidalgo, Álvaro; Carvajal, Ana; La, Tom; Naharro, Germán; Rubio, Pedro; Phillips, Nyree D.; Hampson, David J.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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The spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe colonic infection of pigs that has a considerable economic impact in many swine-producing countries. In spite of its importance, knowledge about the global epidemiology and population structure of B. hyodysenteriae is limited. Progress in this area has been hampered by the lack of a low-cost, portable, and discriminatory method for strain typing. The aim of the current study was to develop and test a multiple-locus variable-number tandem-repeat analysis (MLVA) method that could be used in basic veterinary diagnostic microbiology laboratories equipped with PCR technology or in more advanced laboratories with access to capillary electrophoresis. Based on eight loci, and when performed on isolates from different farms in different countries, as well as type and reference strains, the MLVA technique developed was highly discriminatory (Hunter and Gaston discriminatory index, 0.938 [95% confidence interval, 0.9175 to 0.9584]) while retaining a high phylogenetic value. Using the technique, the species was shown to be diverse (44 MLVA types from 172 isolates and strains), although isolates were stable in herds over time. The population structure appeared to be clonal. The finding of B. hyodysenteriae MLVA type 3 in piggeries in three European countries...

Granule Formation Mechanisms within an Aerobic Wastewater System for Phosphorus Removal▿ †

Barr, Jeremy J.; Cook, Andrew E.; Bond, Phillip L.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Granular sludge is a novel alternative for the treatment of wastewater and offers numerous operational and economic advantages over conventional floccular-sludge systems. The majority of research on granular sludge has focused on optimization of engineering aspects relating to reactor operation with little emphasis on the fundamental microbiology. In this study, we hypothesize two novel mechanisms for granule formation as observed in three laboratory scale sequencing batch reactors operating for biological phosphorus removal and treating two different types of wastewater. During the initial stages of granulation, two distinct granule types (white and yellow) were distinguished within the mixed microbial population. White granules appeared as compact, smooth, dense aggregates dominated by 97.5% “Candidatus Accumulibacter phosphatis,” and yellow granules appeared as loose, rough, irregular aggregates with a mixed microbial population of 12.3% “Candidatus Accumulibacter phosphatis” and 57.9% “Candidatus Competibacter phosphatis,” among other bacteria. Microscopy showed white granules as homogeneous microbial aggregates and yellow granules as segregated, microcolony-like aggregates, with phylogenetic analysis suggesting that the granule types are likely not a result of strain-associated differences. The microbial community composition and arrangement suggest different formation mechanisms occur for each granule type. White granules are hypothesized to form by outgrowth from a single microcolony into a granule dominated by one bacterial type...

Cultivation-Independent Analysis of Bacteria in IDEXX Quanti-Tray/2000 Fecal Indicator Assays ▿

Sercu, Bram; Van De Werfhorst, Laurie C.; Murray, Jill L. S.; Holden, Patricia A.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
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Monitoring microbiological water quality is important for protecting water resources and the health of swimmers. Routine monitoring relies on cultivating fecal indicator bacteria (FIB), frequently using defined substrate technology. Defined substrate technology is designed to specifically enrich for FIB, but a complete understanding of the assay microbiology requires culture-independent analysis of the enrichments. This study aimed to identify bacteria in positive wells of Colilert and Enterolert Quanti-Tray/2000 (IDEXX Laboratories) FIB assays in environmental water samples and to quantify the degree of false-positive results for samples from an urban creek by molecular methods. Pooled Escherichia coli- and Enterococcus-positive Quanti-Tray/2000 enrichments, either from urban creek dry weather flow or municipal sewage, harbored diverse bacterial populations based on 16S rRNA gene sequences and terminal restriction fragment length polymorphism analyses. Target taxa (coliforms or enterococci) and nontarget taxa (Vibrio spp., Shewanella spp., Bacteroidetes, and Clostridium spp.) were identified in pooled and individual positive Colilert and Enterolert wells based on terminal restriction fragments that were in common with those generated in silico from clone sequences. False-positive rates of between 4 and 23% occurred for the urban creek samples...

Comparison of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometer to BD Phoenix Automated Microbiology System for Identification of Gram-Negative Bacilli▿

Saffert, Ryan T.; Cunningham, Scott A.; Ihde, Sherry M.; Monson Jobe, Kristine E.; Mandrekar, Jayawant; Patel, Robin
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2011 Português
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We compared the BD Phoenix automated microbiology system to the Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) system for identification of Gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. The BD Phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. The Bruker Biotyper correctly identified 408 (93%) and 360 (82%) isolates to the genus and species level, respectively. The 440 isolates were grouped into common (308) and infrequent (132) isolates in the clinical laboratory. For the 308 common isolates, the BD Phoenix and Bruker Biotyper correctly identified 294 (95%) and 296 (96%) of the isolates to the genus level, respectively. For species identification, the BD Phoenix and Bruker Biotyper correctly identified 93% of the common isolates (285 and 286, respectively). In contrast, for the 132 infrequent isolates, the Bruker Biotyper correctly identified 112 (85%) and 74 (56%) isolates to the genus and species level, respectively, compared to the BD Phoenix, which identified only 69 (52%) and 45 (34%) isolates to the genus and species level, respectively. Statistically...

Expert Systems in Clinical Microbiology

Winstanley, Trevor; Courvalin, Patrice
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /07/2011 Português
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Summary: This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the “big three”: Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically.

Molecular Definition of Vaginal Microbiota in East African Commercial Sex Workers ▿ †

Schellenberg, John J.; Links, Matthew G.; Hill, Janet E.; Dumonceaux, Tim J.; Kimani, Joshua; Jaoko, Walter; Wachihi, Charles; Mungai, Jane Njeri; Peters, Geoffrey A.; Tyler, Shaun; Graham, Morag; Severini, Alberto; Fowke, Keith R.; Ball, T. Blake; Plumme
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /06/2011 Português
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Resistance to HIV infection in a cohort of commercial sex workers living in Nairobi, Kenya, is linked to mucosal and antiinflammatory factors that may be influenced by the vaginal microbiota. Since bacterial vaginosis (BV), a polymicrobial dysbiosis characterized by low levels of protective Lactobacillus organisms, is an established risk factor for HIV infection, we investigated whether vaginal microbiology was associated with HIV-exposed seronegative (HESN) or HIV-seropositive (HIV+) status in this cohort. A subset of 44 individuals was selected for deep-sequencing analysis based on the chaperonin 60 (cpn60) universal target (UT), including HESN individuals (n = 16), other HIV-seronegative controls (HIV-N, n = 16), and HIV+ individuals (n = 12). Our findings indicate exceptionally high phylogenetic resolution of the cpn60 UT using reads as short as 200 bp, with 54 species in 29 genera detected in this group. Contrary to our initial hypothesis, few differences between HESN and HIV-N women were observed. Several HIV+ women had distinct profiles dominated by Escherichia coli. The deep-sequencing phylogenetic profile of the vaginal microbiota corresponds closely to BV+ and BV− diagnoses by microscopy, elucidating BV at the molecular level. A cluster of samples with intermediate abundance of Lactobacillus and dominant Gardnerella was identified...

Life, Death, and In-Between: Meanings and Methods in Microbiology▿

Davey, Hazel M.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /08/2011 Português
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Determination of microbial viability by the plate count method is routine in microbiology laboratories worldwide. However, limitations of the technique, particularly with respect to environmental microorganisms, are widely recognized. Many alternatives based upon viability staining have been proposed, and these are often combined with techniques such as image analysis and flow cytometry. The plethora of choices, however, adds to confusion when selecting a method. Commercial staining kits aim to simplify the performance of microbial viability determination but often still need adaptation to the specific organism of interest and/or the instruments available to the researcher. This review explores the meaning of microbial viability and offers guidance in the selection and interpretation of viability testing methods.

A Critical Appraisal of the Role of the Clinical Microbiology Laboratory in Diagnosis of Invasive Fungal Infections

Klutts, J. Stacey; Robinson-Dunn, Barbara
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2011 Português
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The incidence of invasive fungal infections (IFIs) continues to rise in industrialized countries, primarily due to both increasingly potent iatrogenic immunosuppression and immunocompromising therapies aimed at treating hematologic malignancies. As this situation continues to evolve, the clinical microbiology laboratory has few new, innovative methodologies to diagnose these serious infections and existing methods lack sensitivity. This represents a difficult clinical situation for health care providers, as they are left to rely on clinical instincts for the management of patients with potential IFIs, as mycology test results are not consistently reliable. The goals of this session of Camp Clin Micro (CCM) were to critically assess currently available methods and practices for diagnosing IFIs, to discuss the potential of current investigational methods, to evaluate the role of antifungal susceptibility testing, and finally to identify action items that can help move the field of diagnostic mycology in a direction that will improve our ability to identify IFIs in a timely manner. This is meant to be not a comprehensive overview of the diagnosis of IFIs but rather a detailed account of the discussion at CCM among clinical microbiologists with experience in diagnostic mycology and knowledge of the literature.

Efficient Biostimulation of Native and Introduced Quorum-Quenching Rhodococcus erythropolis Populations Is Revealed by a Combination of Analytical Chemistry, Microbiology, and Pyrosequencing

Cirou, Amélie; Mondy, Samuel; An, Shu; Charrier, Amélie; Sarrazin, Amélie; Thoison, Odile; DuBow, Michael; Faure, Denis
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /01/2012 Português
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Degradation of the quorum-sensing (QS) signals known as N-acylhomoserine lactones (AHL) by soil bacteria may be useful as a beneficial trait for protecting crops, such as potato plants, against the worldwide pathogen Pectobacterium. In this work, analytical chemistry and microbial and molecular approaches were combined to explore and compare biostimulation of native and introduced AHL-degrading Rhodococcus erythropolis populations in the rhizosphere of potato plants cultivated in farm greenhouses under hydroponic conditions. We first identified gamma-heptalactone (GHL) as a novel biostimulating agent that efficiently promotes plant root colonization by AHL-degrading R. erythropolis population. We also characterized an AHL-degrading biocontrol R. erythropolis isolate, R138, which was introduced in the potato rhizosphere. Moreover, root colonization by AHL-degrading bacteria receiving different combinations of GHL and R138 treatments was compared by using a cultivation-based approach (percentage of AHL-degrading bacteria), pyrosequencing of PCR-amplified rrs loci (total bacterial community), and quantitative PCR (qPCR) of the qsdA gene, which encodes an AHL lactonase in R. erythropolis. Higher densities of the AHL-degrading R. erythropolis population in the rhizosphere were observed when GHL treatment was associated with biocontrol strain R138. Under this condition...

How Should Long-Term Tunneled Central Venous Catheters Be Managed in Microbiology Laboratories in Order To Provide an Accurate Diagnosis of Colonization?

Guembe, M.; Martín-Rabadán, P.; Echenagusia, A.; Camúñez, F.; Rodríguez-Rosales, G.; Simó, G.; Echenagusia, M.; Bouza, E.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2012 Português
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Guidelines recommend the roll-plate technique for short-term central venous catheter (CVC) tip cultures. However, the issue of whether the roll-plate technique is better than the sonication method for long-term CVCs remains unresolved. In addition, no data are available for predicting the value of direct Gram staining in anticipating catheter colonization or catheter-related bloodstream infection (CRBSI) in these long-term CVCs. Our objectives were to compare the roll-plate technique and the sonication method and to define the validity values of Gram staining for the prediction of colonization and CRBSI in patients with long-term tunneled CVCs. During the study period, all tunneled CVCs removed at our institution were prospectively and routinely sent to the microbiology laboratory for Gram staining (first) and tip culture (the Maki technique and sonication, in a random order). We received 149 tunneled CVCs, 39 (26.2%) of which were colonized and 11 (7.4%) of which were associated with CRBSI. Overall, the roll-plate method detected 94.9% of the colonized catheters, whereas sonication detected only 43.6% (P < 0.001). The validity values of Gram staining for the detection of colonization and CRBSI were as follows: a sensitivity of 35.9% to 60.0%...

Microbiology, ecology, and application of the nitrite-dependent anaerobic methane oxidation process

Shen, Li-Dong; He, Zhan-Fei; Zhu, Qun; Chen, Dong-Qing; Lou, Li-Ping; Xu, Xiang-Yang; Zheng, Ping; Hu, Bao-Lan
Fonte: Frontiers Research Foundation Publicador: Frontiers Research Foundation
Tipo: Artigo de Revista Científica
Publicado em 27/07/2012 Português
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Nitrite-dependent anaerobic methane oxidation (n-damo), which couples the anaerobic oxidation of methane to denitrification, is a recently discovered process mediated by “Candidatus Methylomirabilis oxyfera.” M. oxyfera is affiliated with the “NC10” phylum, a phylum having no members in pure culture. Based on the isotopic labeling experiments, it is hypothesized that M. oxyfera has an unusual intra-aerobic pathway for the production of oxygen via the dismutation of nitric oxide into dinitrogen gas and oxygen. In addition, the bacterial species has a unique ultrastructure that is distinct from that of other previously described microorganisms. M. oxyfera-like sequences have been recovered from different natural habitats, suggesting that the n-damo process potentially contributes to global carbon and nitrogen cycles. The n-damo process is a process that can reduce the greenhouse effect, as methane is more effective in heat-trapping than carbon dioxide. The n-damo process, which uses methane instead of organic matter to drive denitrification, is also an economical nitrogen removal process because methane is a relatively inexpensive electron donor. This mini-review summarizes the peculiar microbiology of M. oxyfera and discusses the potential ecological importance and engineering application of the n-damo process.

Performances of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Rapid Identification of Bacteria in Routine Clinical Microbiology

Dubois, Damien; Grare, Marion; Prere, Marie-Françoise; Segonds, Christine; Marty, Nicole; Oswald, Eric
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /08/2012 Português
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Rapid and cost-effective matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based systems will replace conventional phenotypic methods for routine identification of bacteria. We report here the first evaluation of the new MALDI-TOF MS-based Vitek MS system in a large clinical microbiology laboratory. This system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. We have tested 767 routine clinical isolates representative of 50 genera and 124 species. Vitek MS-based identifications were performed by means of a single deposit on a MALDI disposable target without any prior extraction step and compared with reference identifications obtained mainly with the VITEK2 phenotypic system; if the identifications were discordant, molecular techniques provided reference identifications. The Vitek MS system provided 96.2% correct identifications to the species level (86.7%), to the genus level (8.2%), or within a range of species belonging to different genera (1.3%). Conversely, 1.3% of isolates were misidentified and 2.5% were unidentified, partly because the species was not included in the database; a second deposit provided a successful identification for 0.8% of isolates unidentified with the first deposit. The Vitek MS system is a simple...