Phylogeny and structural insights of lipase from Halopseudomonas maritima sp. nov., isolated from sea sand / Filogenia y conocimientos estructurales de la lipasa de Halopseudomonas maritima sp. nov., aislado de la arena del mar

A Gram-negative, aerobic bacterial strain RR6T was isolated from the sea sand to produce lipase and proposed as a novel species of Halopseudomonas. The optimum growth occurred at 28–37 °C, and the pH was 6.0–8.0. The optimum growth occurred at 3.0 -6.5% (w/v) NaCl. The major cellular fatty acids were C10:0 3OH, C12:0, C16:1 ω7c/16:1 ω6c, 18:1 ω7c and/or 18:1 ω6c, and C16:0. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid, and unidentified lipids. The genome is 3.93 Mb, and the G + C content is 61.3%. The 16S rRNA gene sequences shared 99.73–99.87% sequence similarity with the closely related type strains of Halopseudomonas. The average nucleotide identity and average amino acid identity of strain RR6T with reference type strains were below 95–96%, and the corresponding in-silico DNA–DNA hybridization values were below 70%. Strain RR6T clustered with Halopseudomonas gallaeciensis V113T and Halopseudomonas pachastrellae CCUG 46540 T in the phylogenetic tree. Further, lipase produced by this bacterium belongs to α/β hydrolase lipase family and exhibits structural similarity to the lactonizing lipase. Based on the polyphasic analysis, the new isolates RR6T represent a novel species of Halopseudomonas for which Halopseudomonas maritima sp. nov. is proposed. The type strain is RR6T (= NBRC 115418 T = TBRC 15628 T).(AU)

Characterization of the fecal microbiota in gastrointestinal cancer patients and healthy people

BackgroundThe incidence and mortality of gastrointestinal (GI) tumors are high in China. Some studies suggest that the gut microbiota is related to the occurrence and development of tumors. At present, there are no prospective studies based on the correlation between gastrointestinal tumors and gut microbiota in the Chinese population. The objective of this report is to characterize the fecal microbiota in healthy control participants and patients with esophageal cancer, gastric cancer, and colorectal cancer.MethodsPatients with locally advanced or metastatic esophageal, gastric, and colorectal cancer were enrolled, and healthy people were included as controls. 16S rRNA sequencing was used to analyze the characteristics of fecal microbiota. PICRUSt software was used for functional prediction.ResultsSignificant differences in the composition and abundance of fecal microbiota were identified between gastrointestinal cancer patients (n = 130) and healthy controls (n = 147). The abundance of Faecalibacterium prausnitzii, Clostridium clostridioforme and Bifidobacterium adolescent in tumor groups were all significantly lower than in the control group (P < 0.05). The levels of Blautia producta and R. faecis in the gastric (n = 46) and colorectal cancer (n = 44) groups were significantly lower than those in the control group (P < 0.05). The level of Butyricicoccus pullicaecorum in the esophageal cancer (n = 40) and gastric cancer groups was significantly lower than that in the control group (P < 0.05).

Evaluation of Vitek-MS(TM) and Microflex LT(TM) commercial systems for identification of Acinetobacter calcoaceticus-baumannii complex / Evaluación de los sistemas comerciales Vitek(R) MS y Microflex(R) LT para la identificación del complejo Acinetobacter calcoaceticus-baumannii

INTRODUCTION: Acinetobacter is a genus that comprises a group of opportunistic pathogens responsible for a variety of nosocomial infections. The Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex includes some species of clinical importance, mainly A. baumannii, A. pittii and A. nosocomialis, which share phenotypic similarities that make it very difficult to distinguish between them using a phenotypic approach. The aim of this study was to evaluate two commercial matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems for the identification of different Acinetobacter species, with a special focus among those belonging to the Acb complex. METHODS: One hundred and fifty-six Acinetobacter spp. clinical strains, identified by amplified ribosomal DNA restriction analysis (ARDRA) and rpoB gene sequencing, were analysed by two different MALDI-TOF systems. RESULTS: Considering only the 144 strains of the Acb complex evaluated in this study, the Vitek-MS(TM) and Microflex LT(TM) systems correctly identified 129 (89.6%) and 143 (99.3%) strains, respectively. CONCLUSION: After analysing 156 strains belonging to Acinetobacter spp., both Vitek-MS(TM) and Microflex LT(TM) proved to be rapid and accurate systems for the identification of Acb complex species showing a good correlation. However, both manufacturers should improve their databases to include new species in them

INTRODUCCIÓN: Acinetobacter es un género que comprende un grupo de patógenos oportunistas responsables de varias infecciones nosocomiales. El complejo Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) reúne algunas especies de importancia clínica, principalmente A. baumannii, A. pittii y A. nosocomialis, que comparten similitudes fenotípicas que hacen muy difícil poder discriminar entre ellas utilizando un enfoque fenotípico. El objetivo de este estudio fue evaluar 2 sistemas comerciales de espectrometría de masas de ionización por láser asistido con una matriz (MALDI-TOF MS) para la identificación de diferentes especies de Acinetobacter, con un enfoque especial entre los que pertenecen al complejo Acb. MÉTODOS: Analizamos 156 cepas clínicas de Acinetobacter spp., identificadas mediante análisis de restricción de ADN ribosomal amplificado (ARDRA) y secuenciación del gen rpoB, por 2 sistemas diferentes de MALDI-TOF. RESULTADOS: Teniendo en cuenta solo las 144 cepas del complejo Acb evaluadas en este estudio, los sistemas Vitek(R) MS y Microflex(R) LT identificaron correctamente 129 (89,6%) y 143 (99,3%) cepas, respectivamente. CONCLUSIÓN: Después de analizar 156 cepas pertenecientes a Acinetobacter spp., Vitek(R) MS y Microflex(R) LT demostraron ser sistemas rápidos y precisos para la identificación de especies del complejo Acb mostrando una buena correlación. Sin embargo, ambos fabricantes deberían mejorar sus bases de datos incluyendo nuevas especies en ellas

First identification of blaNDM-1 carbapenemase in blaOXA-94-producing Acinetobacter baumannii ST85 in Spain / Detección por primera vez en España de la carbapenemasa blaNDM-1 en Acinetobacter baumannii ST85 productor de blaOXA-94

INTRODUCTION: NDM-1 carbapenemase is spreading rapidly all over the world, but this metallo-beta-lactamase has just been detected for the first time in an Acinetobacter baumannii (Ab) isolate of the ST85 clone in Spain. The aim of this study was to characterize a NDM-1-producing carbapenem-resistant A. baumannii (CR-Ab) isolate submitted to the Andalusian PIRASOA [infection prevention program] referral laboratory. METHODS: Carbapenemases were detected by PCR and Sanger DNA sequencing. Whole genome sequencing was performed by NGS (Miseq, Illumina). Resistance genes were identified with RESfinder, while MLSTfinder was used for sequence typing (ST). The genetic location of blaNDM-1 was determined by nuclease S-1/PFGE/hybridization with specific probe. RESULTS: The isolate was susceptible to amikacin and tigecycline and belonged to the ST85 clone. blaOXA-94 and blaNDM-1 were identified by PCR and Sanger DNA sequencing, respectively. The resistance genes aadB, blaADC-25, blaNDM-1, blaOXA-94, msr(E), mph(E) and floR,sul2 were identified by NGS. The chromosome of the isolate contained a defective Tn125 transposon with blaNDM-1 flanked by the insertion sequences ISAbA125 and ISAba14. The blaNDM-1 gene was only detected in the chromosomal DNA. CONCLUSION: This is the first time that blaNDM-1 has been detected and characterized in a blaOXA-94-producing CR-Ab isolate belonging to the ST85 clone in Spain

INTRODUCCIÓN: La carbapenemasa NDM-1 se está diseminando rápidamente por todo el mundo, pero esta metalo-beta-lactamasa se detecta por primera vez en un aislado de A. baumannii del clon ST85 procedente de España. El objetivo de este estudio es caracterizar un aislado de A. baumannii resistente a carbapenémicos productor de NDM-1 remitido al laboratorio de referencia PIRASOA de Andalucía. MÉTODOS: La detección de carbapenemasas se realizó mediante PCR y secuenciación de ADN Sanger. La secuenciación del genoma completo se realizó mediante NGS (MiSeq, Illumina). La detección de genes de resistencia y el secuenciotipo (ST) se obtuvo mediante ResFinder y MLSTFinder, respectivamente. La localización de blaNDM-1 se determinó utilizando el método de la nucleasa S1/PFGE/hibridación con sonda específica. RESULTADOS: El aislado era sensible a amikacina y tigeciclina, y pertenecía al clon ST85. Se identificaron las variantes blaOXA-94 y blaNDM-1, respectivamente, mediante PCR y secuenciación Sanger. Mediante secuenciación masiva se detectaron los genes de resistencia aadB, blaADC-25, blaNDM-1, blaOXA-94, msr(E), mph(E), floR y sul2. El aislado contenía en su cromosoma un transposón defectivo de tipo Tn125 con blaNDM-1 flanqueado por las secuencias de inserción ISAbA125 y ISAba14. El gen blaNDM-1 solo se detectó en el ADN cromosómico. CONCLUSIÓN: En este estudio se detecta y se caracteriza por primera vez en España blaNDM-1 en un aislado de A. baumannii resistente a carbapenémicos productor de blaOXA-94 y perteneciente al clon ST85

Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses

Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized the microbial communities using 16S rRNA gene sequences from DNA isolated from halite at various locations and correlated these to geographic distance in the Uyuni salt flat (Bolivia). Sequences from each site were analyzed to determine any spatial patterns of diversity, as well as to describe the microbial communities. Results suggest that different taxa are able to disperse over Uyuni's surface crust regardless of distance. As expected, ubiquitous taxa included members of Halobacteriaceae such as Haloarcula, Halorubrum, Halorhabdus, Halolamina, and halophilic bacteria Salinibacter, Halorhodospira, and unclassified members of the Gammaproteobacteria. Archaeal communities were homogeneous across the salt flat. In contrast, bacterial communities present strong local variations which could be attributed to external factors. Likely sources for these variations are the Rio Grande river influent in the south shore and the Tunupa volcano influencing the northern area

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Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle)

The objective of the present study was to isolate Actinobacteria, preferably Streptomyces spp. from the rhizosphere soils of three ethno-medicinal plants collected in Serbia (Papaver rhoeas, Matricaria chamomilla, and Urtica dioica) and to screen their antifungal activity against Candida spp. Overall, 103 sporulating isolates were collected from rhizosphere soil samples and determined as Streptomyces spp. Two different media and two extraction procedures were used to facilitate identification of antifungals. Overall, 412 crude cell extracts were tested against Candida albicans using disk diffusion assays, with 42% (43/103) of the strains showing the ability to produce antifungal agents. Also, extracts inhibited growth of important human pathogens: Candida krusei, Candida parapsilosis, and Candida glabrata. Based on the established degree and range of antifungal activity, nine isolates, confirmed as streptomycetes by 16S rRNA sequencing, were selected for further testing. Their ability to inhibit Candida growth in liquid culture, to inhibit biofilm formation, and to disperse pre-formed biofilms was assessed with active concentrations from 8 to 250 μg/mL. High-performance liquid chromatographic profiles of extracts derived from selected strains were recorded, revealing moderate metabolic diversity. Our results proved that rhizosphere soil of ethno-medicinal plants is a prolific source of streptomycetes, producers of potentially new antifungal compounds

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High diversity and novelty of Actinobacteria isolated from the coastal zone of the geographically remote young volcanic Easter Island, Chile

Easter Island is an isolated volcanic island in the Pacific Ocean. Despite the extended knowledge about its origin, flora, and fauna, little is known about the bacterial diversity inhabiting this territory. Due to its isolation, Easter Island can be considered as a suitable place to evaluate microbial diversity in a geographically isolated context, what could shed light on actinobacterial occurrence, distribution, and potential novelty. In the present study, we performed a comprehensive analysis of marine Actinobacteria diversity of Easter Island by studying a large number of coastal sampling sites, which were inoculated into a broad spectrum of different culture media, where most important variations in composition included carbon and nitrogen substrates, in addition to salinity. The isolates were characterized on the basis of 16S ribosomal RNA gene sequencing and phylogenetic analysis. High actinobacterial diversity was recovered with a total of 163 pure cultures of Actinobacteria representing 72 phylotypes and 20 genera, which were unevenly distributed in different locations of the island and sample sources. The phylogenetic evaluation indicated a high degree of novelty showing that 45% of the isolates might represent new taxa. The most abundant genera in the different samples were Micromonospora, Streptomyces, Salinispora, and Dietzia. Two aspects appear of primary importance in regard to the high degree of novelty and diversity of Actinobacteria found. First, the application of various culture media significantly increased the number of species and genera obtained. Second, the geographical isolation is considered to be of importance regarding the actinobacterial novelty found

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Perfil bacteriano del biofilm dental supragingival en niños con dentición temporal y mixta temprana utilizando la técnica de secuenciación de próxima generación (HOMINGS) / Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique

OBJETIVO: Describir el perfil bacteriano del biofilm supragingival de niños con dentición temporal (NDT) y dentición mixta temprana (NDMT), con la técnica de secuenciación de próxima generación HOMINGS. MÉTODO: Se realizó un estudio descriptivo comparativo con 30 niños de 5 a 7 años de edad sistémicamente sanos de escuelas públicas de Cartagena (Colombia). Todos los participantes estaban libres de caries, según los criterios del Sistema Internacional de Detección y Evaluación de Caries (ICDAS II) y sin experiencia de caries según el índice de dientes cariados, perdidos y obturados (DCPO). Se recolectaron muestras de biofilm supragingival. Se extrajo el ADN bacteriano y se usó para su análisis mediante HOMINGS (identificación de microorganismos orales humanos utilizando secuenciación de próxima generación) basado en la secuenciación de la región V3-V4 del gen 16S rRNA con la plataforma Illumina MiSeq. RESULTADOS: Se identificaron 360 especies específicas y 65 géneros específicos de las sondas: Streptococcus, Actinomyces, Veillonella y Fusobacterium (29,2% del total de ADN bacteriano presente), mientras que en el grupo de dentición mixta temprana se encontraban Streptococcus, Leptotrichia, TM7 y Porphyromonas (24,5% del ADN bacteriano presente). Las especies bacterianas con mayor abundancia relativa en el microbioma oral de biofilm de NDT fueron Streptococcus sanguinis, Rothia aeria, Gemella haemolysans, mientras que en NDMT fueron S. sanguinis, Leptotrichia sp. HOT-417, Leptotrichia sp. HOT-498. El índice de diversidad de Shannon fue 2,77 (DE = 0,26) para NDT y 3,01 (DE = 0,39) para NDMT (p = 0,06). CONCLUSIONES: El análisis del perfil bacteriano del biofilm dental supragingival en niños con NDMT mediante HOMINGS mostró baja diversidad microbiológica tanto en presencia como en abundancia relativa a nivel de género y de especies bacterianas

OBJECTIVE: Tdescribe the bacterial profile of the supragingival biofilm of children with temporary dentition (CTD) and early mixed dentition (CEMD), with the next-generation sequencing (HOMINGS) technique. METHOD: A comparative descriptive study was carried out with 30 systemically healthy children aged between 5 and 7 years old from public schools in Cartagena-Colombia. All participants were caries-free applying the criteria of the International Caries Detection and Assessment System (ICDAS II) and had no caries experience according to the Decayed, Missing and Filled Teeth (DMFT) index. Supragingival biofilm samples were collected. Bacterial DNA was extracted and used for analysis using HOMINGS (Human Oral Microbe Identification using Next-Generation Sequencing) based on the sequencing of the V3-V4 region of the 16S rRNA gene using the Illumina MiSeq platform (V3-V4 primers). RESULTS: A total of 360 species-specific and 65 genus-specific probes were identified. The bacterial genus most predominant in CTD were Streptococcus, Actinomyces, Veillonella and Fusobacterium (29.2% of all bacterial DNA present), while in CEMD the most predominant were Streptococcus, Leptotrichia, TM7 and Porphyromonas (24.5% of all bacterial DNA present). The bacterial species with the highest relative abundance in the oral biofilm microbiome from CTD were Streptococcus sanguinis, Rothia aeria, Gemella haemolysans, while in CEMD they were S. sanguinis, Leptotrichia spp. HOT-417 and Leptotrichia spp. HOT-498. The Shannon diversity index was 2.77 (SD = 0.26) for CTD and 3.01 (SD = 0.39) for CEMD (P = 0.06). CONCLUSIONS: The analysis of the bacterial profile of the supragingival dental biofilm in children with DMFT, by means of HOMINGS showed low microbiological diversity both in presence and in relative abundance in terms of genus as well as bacterial species

Evaluation of the DNA microarray "AMR Direct Flow Chip Kit" for detection of antimicrobial resistance genes from Gram-positive and Gram-negative bacterial isolated colonies / Evaluación de una micromatriz de ADN "AMR Direct Flow Chip Kit" para la detección de genes de resistencia antimicrobiana de bacterias grampositivas y gramnegativas a partir de colonias aisladas

INTRODUCTION: The AMR Direct Flow Chip assay allows the simultaneous detection of a large variety of antibiotic resistance genetic markers. To assess this kit's performance, we use isolated colonies as starting material. The assay has been approved by the European Economic Area as a suitable device for in vitro diagnosis (CE IVD) using clinical specimens. METHODS: A total of 210 bacterial isolates harbouring either one or more antimicrobial resistance genes including plasmid-encoded extended-spectrum β-lactamases (SHV, CTX-M) and carbapenemases (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP, and OXA), mecA, vanA and vanB, and 30 controls were included. RESULTS: The assay displayed a sensitivity and specificity of 100% for all target genes included in the array. CONCLUSION: The AMR Direct Flow Chip Kit is an accurate assay for detecting genes which commonly confer resistance to β-lactams and vancomycin from isolated colonies in culture of Gram-positive and Gram-negative bacteria

INTRODUCCIÓN: El ensayo "AMR Direct Flow Chip Kit" permite detectar simultáneamente la presencia de una gran variedad de marcadores genotípicos de resistencia bacteriana. Evaluamos su rendimiento utilizando colonias aisladas como material de partida. El ensayo aludido ha sido aprobado por el Área Económica Europea como un dispositivo adecuado para el diagnóstico in vitro (CE IVD) utilizando muestras clínicas. MÉTODOS: El estudio ha incluido 210 aislados bacterianos con uno o más genes de resistencia a los antimicrobianos, incluidos genes plasmídicos que codifican β-lactamasas de espectro extendido (SHV y CTX-M) y carbapenemasas (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP y OXA), mecA, vanA y vanB, y 30 controles. RESULTADOS: El ensayo mostró una sensibilidad y especificidad del 100% para todos los genes diana incluidos en la matriz. CONCLUSIÓN: El «AMR Direct Flow Chip Kit» es un ensayo fiable para la detección de genes que comúnmente confieren resistencia a β-lactámicos y vancomicina en bacterias grampositivas y gramnegativas a partir de colonias aisladas en cultivo

Reduced Akkermansia muciniphila and Faecalibacterium prausnitzii levels in the gut microbiota of children with allergic asthma

Introduction and objectives: The amounts of Akkermansia muciniphila and Faecalibacterium prausnitzii in gut microbiota are reduced in patients with allergic diseases compared to healthy controls. We aimed to quantify levels of A. muciniphila and F. prausnitzii amounts using real-time quantitative PCR (qPCR) in the gut microbiota of children with allergic asthma and in healthy controls. Materials and methods: In total, 92 children between the ages of three and eight who were diagnosed with asthma and 88 healthy children were included in the study and bacterial DNA was isolated from the stool samples using the stool DNA isolation Kit. qPCR assays were studied with the microbial DNA qPCR Kit for A. muciniphila and microbial DNA qPCR Kit for F. prausnitzii. Results: Both bacterial species showed a reduction in the patient group compared to healthy controls. A. muciniphila and F. prausnitzii were found to be 5.45 ± 0.004, 6.74 ± 0.01 and 5.71 ± 0.002, 7.28 ± 0.009 in the stool samples of the asthma and healthy control groups, respectively. Conclusions: F. prausnitzii and A. muciniphila may have induced anti-inflammatory cytokine IL-10 and prevented the secretion of pro-inflammatory cytokines like IL-12. These findings suggest that A. muciniphila and F. prausnitzii may suppress inflammation through its secreted metabolites

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Targeted 16S rRNA amplicon analysis reveals the diversity of bacterial communities in carwash effluents

This study aimed to analyze the bacterial diversity in carwash effluents and to determine their potential for use in microbial degradation of environmental contaminants. Nine carwash effluent samples were collected for physicochemical and bacterial community diversity analysis using multi-digital probes and 16S rRNA gene amplicon sequencing respectively. The pH of all effluent samples was neutral to slightly alkaline. Oil and grease concentrations ranged from 15.3 to 49.7 mg/L. 16S gene amplicon sequencing of the nine samples produced 45,934-sequence reads, which translated to 13 bacterial phyla, 26 classes, and 43 genera. The most dominant phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Fusobacteria. Canonical correspondence analysis (CCA) showed that the distribution of the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Verrucomicrobia was influenced by the presence of oil and grease, total petroleum hydrocarbons-gasoline range organics (GRO-TPH), and metals species (Pb, Cu, and Zn). The dominant bacterial genera found in the present study were previously proven to biodegrade hydrocarbons, and their presence in carwash effluents could bode well for in situ natural bioremediation of these contaminated sites

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Strategical isolation of efficient chicken feather-degrading bacterial strains from tea plantation soil sample

Chicken feather waste is generally insufficiently utilized despite its high content of protein, constituting an environmental issue. Biodegradation of the waste with enabling microbes provides an advantageous option among the available solutions. In this study, an efficient whole feather-degrading strain was strategically isolated from a soil sample taken from a local tea plantation that has little or nothing to do with feathers. The strain was identified as Bacillus thuringiensis (designated as FDB-10) according to the cloned complete 16S rRNA sequence. The FDB-10 could efficiently degrade briefly heat-treated whole feather (102 °C, 5 min; up to 90% of a maximum concentration of 30 g/L) in a salt medium supplemented with 0.1 g/L yeast extract within 24 h (37°C, 150 rpm). Addition of carbon sources (glycerol, glucose, starch, Tween 20, Tween 80, 1.25 g/L as glycerol) to the fermentation medium could improve the degradation. However, significant inhibition could be observed when the added carbon source reached the amount usually adopted in the investigation of carbon source preference (1%). Nitrogen source (NH4Cl, (NH4)2SO4, peptone) adversely influenced the performance of the strain. When the molar concentrations of NH4+ were equal for the two salt, the inhibitory effect on degradation of whole feathers was similar. Entirely different from other reported feather-degrading strains showing a preference to melanin-free feather substrates, the strain isolated in this study could degrade melanin-containing feather equally efficiently, and higher protease activity could be detected in the digest mix. As a plus, the strain could degrade feathers in rice wash produced in daily cooking, indicating its potential use in the simultaneous treatment of rice cooker wastewater produced by a rice processing plant. All these results imply that the FDB-10 is a strain with great potential in the biodegradation of feather waste

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Flocculating, emulsification and metal sorption properties of a partial characterized novel exopolysaccharide produced by Rhizobium tropici SRA1 isolated from Psophocarpus tetragonolobus (L) DC

A novel exopolysaccharide (EPS) was produced by a bacterium which was isolated from Psophocarpus tetragonolobus (L) D.C. and identified as 99% Rhizobium tropici SRA1 by 16S rDNA sequencing. The flocculating performances along with emulsifying activity began simultaneously with the growth and the production of EPS and reached its utmost at 28 h. EPS was purified via chilled ethanol precipitation followed by dialysis and lyophilization. The existence of hydroxyl, methoxyl, and carboxylic functional groups were confirmed by Fourier transform infrared (FT-IR) spectrum. EPS was found to be compose of 82.44% neutral sugar and 15.93% uronic acid. The average molecular weight of the exopolysaccharide was estimated as ~1.8×105. Gas-liquid chromatography indicated the presence of glucose and galactose at a molar ratio of 3:1 in EPS. In the pH range of 3-5 with EPS dosage of 15 mg/l at 30 °C, cation-independent flocculation greater than 90% was observed. Emulsification indices (E24) of EPS were observed as 86.66%, 83.33%, 76.66%, and 73.33% with olive oil, kerosene, toluene, and n-hexane respectively. Biosorption of Cu K [45.69 wt%], Cu L [05.67 wt%], Co K [15.58 wt%], and Co L [11.72 wt%] by EPS was confirmed by energy-dispersive X-ray spectroscopy (EDS). This report on the flocculating, emulsifying, and metal sorption properties of EPS produced by R. tropici SRA1 is unique in the literature

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Identification of two pesticide-tolerant bacteria isolated from Medicago sativa nodule useful for organic soil phytostabilization

Plant-microbe interactions such as rhizobacteria legumes are interesting in organic farming that has undergone significant expansion in the world. The organic agriculture is as an environment-friendly technique and a sustainable alternative to intensive agricultural system. Three types of soil were chosen, organic (ORG), conventional (CON), and fallow land (NA) to isolate soil bacteria-nodulating Medicago sativa, in order to develop microbial inoculants for use in agricultural sustainable system. Soil analysis revealed significant higher amounts of total nitrogen, organic carbon, total phosphorus, and matter detected in ORG. As for heavy metals, ORG showed high Cu content due to the authorized chemical use in organic farming. A sample of 130 bacteria was isolated from Medicago sativa nodule, genetically characterized by PCR/RFLP of ribosomal 16S RNAs, and a great dominance of Sinorhizobium meliloti (88.4%, 73.8%, and 55.5%) is obtained among NA-, CON-, and ORG-managed soils, respectively. The ORG showed the high bacterial diversity with 13.3% of non-identified strains. The resistance against five pesticides (Prosper, Cuivox, Fungastop, Nimbecidine, and Maneb) revealed a maximum of inhibitory concentration about 10 mg l−1 of Prosper, 12 mg l−1 of Cuivox, 6 ml l−1 of Fungastop, 7.5 ml l−1of Nimbecidine, and 25 ml l−1 of Maneb. The analysis of the symbiotic properties and plant growth-promoting potential revealed two efficient strains significantly increased alfalfa dry weight through producing siderophores, phosphorus, and indole acetic acid (13.6 mg ml−1 and 19.9 mg ml−1 respectively). Hence, we identify two tolerant and efficient strains, Achromobacter spanium and Serratia plymuthica, isolated from Medicago sativa nodule with valuable potential able to phytostabilize pesticide-contaminated soils

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Reporting identification of Acinetobacter spp genomic species: A nationwide proficiency study in Spain / Capacidad de los laboratorios españoles para identificar las genoespecies de Acinetobacter spp: estudio nacional multicéntrico español

Acinetobacter baumannii is the most important genomic species of Acinetobacter from a clinical and epidemiological point of view. Nevertheless, genomic species other than A. baumannii are increasingly recognized as nosocomial pathogens. Molecular methods of identification (genotypic and proteomic assays) are more accurate and reliable and have greater discriminatory power than phenotypic methods. Eleven genomic species of Acinetobacter spp. (8 A. baumannii, 1 A. pittii, 1 A. nosocomialis and 1 A. lwoffii) with different antimicrobial resistance phenotypes and mechanisms of resistance to antimicrobial agents were sent to 48 participating Spanish centers to evaluate their ability for correct identification at the genomic species level. Identification of the genomic species was performed at the two Clinical Microbiology reference laboratories (Hospital Universitario Virgen Macarena, Seville, Spain; and Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain) by partial DNA sequencing of the rpoB gene and MALDI-TOF. The mean percentage of agreement was 76.1%. Fifty percent of CC-01 (A. pittii) and 50% of CC-02 (A. nosocomialis) identification results were reported as A. baumannii. Discrepancies by type of systems used for identification were: MicroScan WA (51.1%), Vitek 2 (19.5%), MALDI-TOF (18.0%), Phoenix (4.5%), Wider (3.8%) and API 20 NE (3.0%). In conclusion, clinical microbiology laboratories must improve their ability to correctly identify the most prevalent non A. baumannii genomic species

Acinetobacter baumannii es la genoespecie de Acinetobacter más importante desde el punto de vista clínico y epidemiológico. No obstante, otras genoespecies distintas de A. baumannii están adquiriendo cada vez mayor importancia como patógeno nosocomial. Los métodos moleculares (genotípicos y proteómicos) usados para la identificación de genoespecies de Acinetobacter son más precisos, fiables, y tienen mayor poder de discriminación que los métodos fenotípicos. En este estudio se incluyen 11 genoespecies de Acinetobacter spp. (8 A. baumannii, 1 A. pittii, 1 A. nosocomialis y 1 A. lwoffii) con diferentes fenotipos de resistencia y mecanismos de resistencia antimicrobiana. Los aislados se enviaron a 48 centros españoles participantes para evaluar su capacidad para identificar correctamente la genoespecie de Acinetobacter. Las identificaciones de referencia se realizaron en 2 Laboratorios de Microbiología Clínica (Hospital Universitario Virgen Macarena, Sevilla, España; Complejo Hospitalario Universitario de A Coruña, A Coruña, España) mediante secuenciación parcial del gen rpoB y MALDI-TOF. El porcentaje medio de concordancia fue del 76,1%. El 50% de los resultados de identificación del control CC-01 (A. pittii) y el 50% de los resultados de identificación del control CC-02 (A. nosocomialis) se informaron como A. baumannii. Considerando el tipo de sistema de identificación usado las discrepancias fueron: MicroScan/WA (51,1%), Vitek 2 (19,5%), MALDI-TOF (18,0%), Phoenix (4,5%), Wider (3,8%) y API 20 NE (3,0%). En conclusión, los laboratorios españoles de microbiología clínica deben mejorar su capacidad para identificar correctamente las genoespecies de Acinetobacter distintas de A. baumannii que son más prevalentes

Identification of a new variant of Chlamydia trachomatis in Mexico / Identificación de nueva variante de Chlamydia trachomatis en México

Introduction: Chlamydia trachomatis is one of the main etiological agents of sexually transmitted infections worldwide. In 2006, a Swedish variant of C. trachomatis (Swedish-nvCT), which has a deletion of 377bp in the plasmid, was reported. In Latin America, Swedish-nvCT infections have not been reported. We investigated the presence of Swedish-nvCT in women with infertility in Mexico. Methods: Swedish-nvCT was searched in 69 C. trachomatis positive samples from 2339 endocervical specimens. We designed PCR primers to identify the deletion in the plasmid in the ORF1, and the presence of a repeated 44 bp in the ORF3. The sample with the deletion was genotyped with the genes of the major outer membrane protein A (ompA) and the polymorphic membrane protein (pmpH). Results: The deletion was detected in one of the 69 samples positive C. trachomatis of 2339 endocervical exudates. The nucleotide sequence analysis of the ompA shows a high degree of similarity with the Swedish nvCT (98%), however the variant found belongs to serovar D. The nucleotide sequence of the pmpH gene associates to the variant found in the genitourinary pathotype of the Swedish-nvCT but in different clusters. Conclusions: Our results revealed the presence of a new variant of C. trachomatis in Mexican patients. This variant found in Mexico belongs to serovar D based on the in silico analysis of the ompA and pmpH genes and differs to the Swedish-nvCT (serovars E). For these variants of C. trachomatis that have been found it is necessary to carry out a more detailed analysis, although the role of this mutation has not been demonstrated in the pathogenesis

Introducción: Chlamydia trachomatis es una de las principales bacterias que causan infecciones de transmisión sexual en todo el mundo. En 2006 se informó de una variante sueca de C. trachomatis (nvCT-sueca), que tiene una deleción de 377 bp en su plásmido. En América Latina no se ha informado de infecciones por la nvCT-sueca. El propósito de esta investigación fue la búsqueda de la nvCT-sueca en mujeres mexicanas con infertilidad. Métodos: Se analizaron 69 muestras positivas para C. trachomatis de 2.339 muestras endocervicales. Se diseñaron cebadores que identificaron la deleción de 377 pb en ORF1, y detección de un tándem de 44 pb repetidos en ORF3, como ocurre en la nvCT-sueca. Las muestras con la deleción fueron genotipificadas mediante los genes de la proteína principal de la membrana externa A (ompA) y de la proteína polimórfica de membrana H (pmpH). Resultados: La deleción se detectó en una de las 69 muestras (1,44%). El análisis de la secuencia del gen ompA mostró un alto grado de similitud con la nvCT-sueca (98%). Sin embargo, la variante encontrada perteneció al serovar D. La secuencia del gen pmpH se asoció al patotipo genitourinario, pero en diferentes clusters al de la nvCT-sueca. Conclusiones: Los resultados revelaron la presencia de una nueva variante de C. trachomatis en México con delección y que pertenece al serovar D con base al análisis in silico de los genes ompA y pmpH, y que difiere de la nvCT-sueca (serovares E). Se requiere conocer su prevalencia en México y en América Latina

Effect of symbiotic supplementation on fecal calprotectin levels and lactic acid bacteria, Bifidobacteria, Escherichia coli and Salmonella DNA in patients with cervical cancer / Efecto de la suplementación con simbióticos sobre los niveles de calprotectina fecal y ADN de bacterias ácido lácticas, Bifidobacteria, Escherichia coli y Salmonella en pacientes con cáncer cervical

Background: patients with cervical cancer (CC) receiving chemotherapy and radiotherapy have several gastrointestinal adverse effects. Objective: to evaluate the effect of dietary symbiotic supplementation on fecal calprotectin (FCP), bacterial DNA levels, and gastrointestinal adverse effects in patients with CC. Methods: clinical, controlled, randomized, double-blind trial. Patients consumed symbiotics or placebo three times a day for seven weeks. FCP was assessed by Elisa method. DNA from probiotic and pathogenic bacteria were determined by quantitative real-time polymerase chain reaction. Diarrheal evacuations were evaluated with the Bristol stool form scale and nausea and vomiting were measured using the scale of the National Institute of Cancerology of the United States. Results: after a seven-week treatment, FCP concentration was lower in the symbiotic group compared to the control group (p < 0.001). Stool consistency in the placebo and symbiotic groups was similar at baseline. A significant improvement in stool consistency was obtained in both groups at the end of the intervention (p < 0.001). The concentrations and total proportions of the probiotic and pathogenic bacteria were similar in both groups. Nausea significantly diminished in both groups (p < 0.001) at the end of the trial. Furthermore, the symbiotic group had a statistically significant decrease in the frequency and intensity of vomiting when compared to the control group (p < 0.001). Conclusions: the symbiotic treatment decreases significantly the FCP levels and the frequency and intensity of vomiting in patients with CC

Introducción: los pacientes con cáncer cervical (CC) tratados con quimioterapia y radioterapia tienen frecuentemente efectos gastrointestinales adversos (EGA). Objetivo: evaluar el efecto de la suplementación dietética con simbióticos en la calprotectina fecal (FCP), el DNA bacteriano y sobre los EGA en pacientes con CC. Métodos: se realizó un ensayo clínico, aleatorizado y doble ciego. Los pacientes ingirieron simbióticos o placebo tres veces al día durante siete semanas. La FCP se evaluó mediante el método de ELISA. El ADN bacteriano se cuantificó mediante PCR en tiempo real. Las evacuaciones se evaluaron con la escala de Bristol y las náuseas y los vómitos se cuantificaron utilizando la escala del Instituto Nacional de Cancerología (USA). Resultados: después de siete semanas de tratamiento, la concentración de FCP fue menor en el grupo tratado con simbióticos en comparación al grupo control (p < 0,001). La consistencia de las heces en los grupos tratados con placebo y simbióticos fue similar al inicio del estudio. Se obtuvo una mejora significativa en la consistencia de las heces en ambos grupos al final de la intervención (p < 0,001). Los niveles de las bacterias probióticas y patogénicas fueron similares en ambos grupos. Los casos de náuseas disminuyeron en ambos grupos (p < 0,001) y el grupo tratado con simbióticos tuvo una disminución significativa en la frecuencia e intensidad de los vómitos en comparación al grupo control (p < 0,001). Conclusiones: el tratamiento simbiótico disminuye significativamente los niveles de FCP y la frecuencia e intensidad del vómito en pacientes con CC

Borrelia miyamotoi: Should this pathogen be considered for the diagnosis of tick-borne infectious diseases in Spain? / Borrelia miyamotoi: ¿un patógeno a tener en cuenta en el diagnóstico de enfermedades transmitidas por garrapatas en España?

INTRODUCTION: Borrelia miyamotoi is a tick-borne pathogen belonging to the relapsing fever group. It had not been reported from Spain, but its wide distribution and the presence of the tick-vector (Ixodes ricinus) made us suspect its circulation. The aim of this study was to investigate the presence of Borrelia spp. in I. ricinus in Spain. METHODS: A total of 652 I. ricinus nymphs collected in northern Spain were processed. The DNA was extracted using incubations with ammonium hydroxide. Borrelia spp. DNA was amplified using Borrelia-specific PCR assays (glpQ, 16S rRNA and flagellin genes). RESULTS: B. miyamotoi was amplified in 4 specimens, and Borrelia burgdorferi sensu lato in 27 (8 Borrelia afzelii, 7 Borrelia garinii, 8 Borrelia lusitaniae, 3 Borrelia valaisiana and 1 B. burgdorferi sensu stricto). CONCLUSION: B. miyamotoi should be considered in the differential diagnoses of patients with confirmed or suspected tick-bite in Spanish endemic areas for Lyme disease

INTRODUCCIÓN: Borrelia miyamotoi, patógeno del grupo de las fiebres recurrentes transmitido por garrapatas, no había sido encontrado en España. Su amplia distribución y la presencia del vector (Ixodes ricinus) nos hizo sospechar su circulación. El objeto del estudio fue investigar la presencia de Borrelia spp. en I. ricinus de España. MÉTODOS: Se procesaron 652 ninfas recogidas en el norte de España. El ADN se extrajo mediante incubaciones de amonio. Se llevaron a cabo PCR específicas para la amplificación de ADN de Borrelia spp. (genes glpQ, ARNr 16S y flagelina). RESULTADOS: Se amplificó B. miyamotoi en 4 ejemplares y Borrelia burgdorferi sensu lato en 27 (8 Borrelia afzelii, 7 Borrelia garinii, 8 Borrelia lusitaniae, 3 Borrelia valaisiana y 1 Borrelia burgdorferi sensu stricto). CONCLUSIÓN: B. miyamotoi debe ser considerado en el diagnóstico diferencial de pacientes con picadura o posible picadura de garrapata en zonas endémicas de enfermedad de Lyme

Molecular characterization of KPC-producing Klebsiella pneumoniae isolated from patients in a Public Hospital in Caracas, Venezuela / Caracterización molecular de aislados de Klebsiella pneumoniaeproductores de carbapenemasas tipo KPC provenientes de pacientes de un hospital público en Caracas, Venezuela

Introduction: Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria are amongst the most important causative agents of nosocomial infections worldwide. Isolates of this bacterium have been identified in Venezuela but little is known about their local spread. The aim of this study was to perform the molecular characterization of KPC-producing strains isolated from 2012 to 2013 in a public hospital in Caracas, Venezuela. Methods: Twenty-two K. pneumoniae clinical isolates phenotypically classified as KPC producing were subjected to PCR screening for the presence of blaKPC genes and their location within transposon Tn4401. The blaKPC PCR product was sequenced to identify the KPC alleles. Genotypic analysis was performed by means of repetitive extragenic palindromic PCR (rep-PCR) and Multi Locus Sequence Typing (MLST). Finally, conjugation and electroporation assays were used to determine whether the blaKPC genes were found in plasmids. Results: All isolates contained the blaKPC-2 variant, and 21 of the 22 were associated with the Tn4401b isoform. The strains were distributed in 8 sequence types (ST), three of which were new. Conjugation and electroporation assays indicated that 95.5% (n=21/22) of the isolates contained the blaKPC gene in plasmids. Conclusions: This study on circulating bacterial strains and the identification of KPC alleles may help to understand the routes of dissemination and control their spread within this hospital (AU)

Introducción: Klebsiella pneumoniae productora de carbapenemasas tipo KPC es uno de los principales agentes causantes de infecciones nosocomiales a nivel mundial. En Venezuela se han identificado aislados de esta bacteria, sin embargo, se conoce poco sobre su dispersión. El objetivo de este estudio fue realizar la caracterización molecular de aislados de K. pneumoniae productores de KPC provenientes de un hospital público en Caracas, Venezuela, durante los años 2012 y 2013. Métodos: Se analizaron 22 aislados de K. pneumoniae clasificados fenotípicamente como productores de KPC, se les realizó la detección del gen blaKPC así como su ubicación en el transposón Tn4401 mediante PCR. El producto de PCR del gen blaKPC se secuenció para identificar los alelos circulantes. El análisis genotípico se realizó empleando las técnicas de amplificación por PCR de las secuencias repetidas extragénicas palindrómicas (rep-PCR) y la secuenciación de múltiples loci (MLST). Mediante ensayos de conjugación o electroporación, se determinó si los genes blaKPC se encontraban en plásmidos. Resultados: Los 22 aislados contenían una variante del gen blaKPC-2 pero 21 de ellos estaban asociados a la isoforma Tn4401b y se distribuyeron en 8 secuencias tipo (ST), siendo tres de ellas nuevas. Los ensayos de conjugación y electroporación indicaron que el 95,5% (n=21/22) de los aislados portaban al gen blaKPC en plásmidos. Conclusión: El estudio de aislados clínicos circulantes así como la identificación de los alelos del gen blaKPC podría ayudar a conocer las rutas de diseminación y a controlar su propagación en este hospital (AU)