Broad-Range Detection of Microorganisms Directly from Bronchoalveolar Lavage Specimens by PCR/Electrospray Ionization-Mass Spectrometry

PubMed Central

Ullberg, Måns; Lüthje, Petra; Mölling, Paula; Strålin, Kristoffer

2017-01-01

The clinical demand on rapid microbiological diagnostic is constantly increasing. PCR coupled to electrospray ionization-mass spectrometry, PCR/ESI-MS, offers detection and identification of over 750 bacteria and Candida species directly from clinical specimens within 6 hours. In this study, we investigated the clinical performance of the IRIDICA BAC LRT Assay for detection of bacterial pathogens in 121 bronchoalveolar lavage (BAL) samples that were received consecutively at our bacterial laboratory for BAL culture. Commensal or pathogenic microorganisms were detected in 118/121 (98%) BAL samples by PCR/ESI-MS, while in 104/121 (86%) samples by routine culture (P<0.01). Detection of potentially pathogenic microorganisms by PCR/ESI-MS was evaluated in comparison with conventional culture-based or molecular methods. The agreement between positive findings was overall good. Most Staphylococcus aureus-positive PCR/ESI-MS results were confirmed by culture or species-specific PCR (27/33, 82%). The identity of Streptococcus pneumoniae could however be confirmed for only 6/17 (35%) PCR/ESI-MS-positive samples. Non-cultivable and fastidious pathogens, which were not covered by standard culture procedures were readily detected by PCR/ESI-MS, including Legionella pneumophila, Bordetella pertussis, Norcadia species and Mycoplasma pneumoniae. In conclusion, PCR/ESI-MS detected a broad range of potential pathogens with equal or superior sensitivity compared to conventional methods within few hours directly from BAL samples. This novel method might thus provide a relevant tool for diagnostics in critically ill patients. PMID:28085931

White and blue light induce reduction in susceptibility to minocycline and tigecycline in Acinetobacter spp. and other bacteria of clinical importance.

PubMed

Ramírez, María Soledad; Traglia, German Matías; Pérez, Jorgelina Fernanda; Müller, Gabriela Leticia; Martínez, María Florencia; Golic, Adrián Ezequiel; Mussi, María Alejandra

2015-05-01

Minocycline (MIN) and tigecycline (TIG) are antibiotics currently used for treatment of multidrug-resistant nosocomial pathogens. In this work, we show that blue light, as well as white light, modulates susceptibility to these antibiotics in a temperature-dependent manner. The modulation of susceptibility by light depends on the content of iron; an increase in iron results in a reduction in antibiotic susceptibility both under light and in the dark, though the effect is more pronounced in the latter condition. We further provide insights into the mechanism by showing that reduction in susceptibility to MIN and TIG induced by light is likely triggered by the generation of (1)O2, which, by a yet unknown mechanism, would ultimately lead to the activation of resistance genes such as those coding for the efflux pump AdeABC. The clinical relevance of these results may lie in surface-exposed wound infections, given the exposure to light in addition to the relatively low temperatures recorded in this type of lesion. We further show that the modulation of antibiotic susceptibility occurs not only in Acinetobacter baumannii but also in other micro-organisms of clinical relevance such as Escherichia coli and Staphylococcus aureus. Overall, our findings allow us to suggest that MIN and TIG antibiotic treatments may be improved by the inclusion of an iron chelator, in addition to keeping the wounds in the dark, a condition that would increase the effectiveness in the control of infections involving these micro-organisms. © 2015 The Authors.

Pre-sporulation stages of Streptomyces differentiation: state-of-the-art and future perspectives

PubMed Central

Yagüe, Paula; López-García, Maria T.; Rioseras, Beatriz; Sánchez, Jesús; Manteca, Ángel

2013-01-01

Streptomycetes comprise very important industrial bacteria, producing two-thirds of all clinically relevant secondary metabolites. They are mycelial microorganisms with complex developmental cycles that include programmed cell death (PCD) and sporulation. Industrial fermentations are usually performed in liquid cultures (large bioreactors), conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that there was no differentiation. In this work, we review the current knowledge on Streptomyces pre-sporulation stages of Streptomyces differentiation. PMID:23496097

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance

NASA Astrophysics Data System (ADS)

Kuzyakov, Yakov; Xu, Xingliang

2014-05-01

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 15N-labelling studies that investigated 15N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on Km (Michaelis constant) and Vmax (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower Km values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (Vmax) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms.

Standards for gene therapy clinical trials based on pro-active risk assessment in a London NHS Teaching Hospital Trust.

PubMed

Bamford, K B; Wood, S; Shaw, R J

2005-02-01

Conducting gene therapy clinical trials with genetically modified organisms as the vectors presents unique safety and infection control issues. The area is governed by a range of legislation and guidelines, some unique to this field, as well as those pertinent to any area of clinical work. The relevant regulations covering gene therapy using genetically modified vectors are reviewed and illustrated with the approach taken by a large teaching hospital NHS Trust. Key elements were Trust-wide communication and involvement of staff in a pro-active approach to risk management, with specific emphasis on staff training and engagement, waste management, audit and record keeping. This process has led to the development of proposed standards for clinical trials involving genetically modified micro-organisms.

Enhancing the Antibiotic Antibacterial Effect by Sub Lethal Tellurite Concentrations: Tellurite and Cefotaxime Act Synergistically in Escherichia coli

PubMed Central

Molina-Quiroz, Roberto C.; Muñoz-Villagrán, Claudia M.; de la Torre, Erick; Tantaleán, Juan C.; Vásquez, Claudio C.; Pérez-Donoso, José M.

2012-01-01

The emergence of antibiotic-resistant pathogenic bacteria during the last decades has become a public health concern worldwide. Aiming to explore new alternatives to treat antibiotic-resistant bacteria and given that the tellurium oxyanion tellurite is highly toxic for most microorganisms, we evaluated the ability of sub lethal tellurite concentrations to strengthen the effect of several antibiotics. Tellurite, at nM or µM concentrations, increased importantly the toxicity of defined antibacterials. This was observed with both Gram negative and Gram positive bacteria, irrespective of the antibiotic or tellurite tolerance of the particular microorganism. The tellurite-mediated antibiotic-potentiating effect occurs in laboratory and clinical, uropathogenic Escherichia coli, especially with antibiotics disturbing the cell wall (ampicillin, cefotaxime) or protein synthesis (tetracycline, chloramphenicol, gentamicin). In particular, the effect of tellurite on the activity of the clinically-relevant, third-generation cephalosporin (cefotaxime), was evaluated. Cell viability assays showed that tellurite and cefotaxime act synergistically against E. coli. In conclusion, using tellurite like an adjuvant could be of great help to cope with several multi-resistant pathogens. PMID:22536386

Cytological Findings of 140 Bile Samples from Dogs and Cats and Associated Clinical Pathological Data.

PubMed

Peters, L M; Glanemann, B; Garden, O A; Szladovits, B

2016-01-01

Cholecystocentesis can be part of the diagnostic workup of hepatobiliary disease in small animals, but literature on cytological evaluation of bile is scant. To determine the diagnostic utility of cytological assessment of bile aspirates. Fifty-six and 78 client-owned dogs and cats, respectively, with bile collected by cholecystocentesis and submitted to our diagnostic laboratory between 1999 and 2014. Retrospective study describing cytological findings of bile, concurrent bacterial culture results, hematological and serum biochemical data, gallbladder biopsy results, as well as final diagnosis and complications after cholecystocentesis. Infectious agents were found in 30% of canine and 22% of feline bile aspirates, and inflammation in 5% and 19% respectively. Presence of microorganisms was more often detected on cytological examination (24%) than by culture (21%). The most common bacterial isolates were Escherichia coli and Enterococcus spp., isolated from 14.8% and 6.7% of cultured samples respectively. Only increased canine pancreatic lipase immunoreactivity concentration (cPLI) was significantly associated with the presence of microorganisms, inflammatory cells, or both in bile. Clinically relevant complications of cholecystocentesis occurred in 2 dogs. The majority of the animals undergoing cholecystocentesis suffered from hepatic, pancreatic, gastrointestinal disease, or a combination thereof. Cytological examination of bile is inexpensive and straightforward, and yields diagnostically relevant information that precedes and complements bacterial culture. Copyright © 2015 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids

PubMed Central

Pazos-Perez, Nicolas; Pazos, Elena; Catala, Carme; Mir-Simon, Bernat; Gómez-de Pedro, Sara; Sagales, Juan; Villanueva, Carlos; Vila, Jordi; Soriano, Alex; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

2016-01-01

Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints. PMID:27364357

The global dispersion of pathogenic microorganisms by dust storms and its relevance to agriculture: Chapter 1

USGS Publications Warehouse

Gonzalez-Martin, Cristina; Teigell-Perez, Nuria; Valladares, Basilio; Griffin, Dale W.

2014-01-01

Dust storms move an estimated 500–5000 Tg of soil through Earth’s atmosphere every year. Dust-storm transport of topsoils may have positive effects such as fertilization of aquatic and terrestrial ecosystems and the evolution of soils in proximal and distal environments. Negative effects may include the stripping of nutrient-rich topsoils from source regions, sandblasting of plant life in downwind environments, the fertilization of harmful algal blooms, and the transport of toxins (e.g., metals, pesticides, herbicides, etc.) and pathogenic microorganisms. With respect to the long-range dispersion of microorganisms and more specifically pathogens, research is just beginning to demonstrate the quantity and diversity of organisms that can survive this type of transport. Most studies to date have utilized different assays to identify microorganisms and microbial communities using predominately culture-based, and more recently nonculture-based, methodologies. There is a clear need for international-scale research efforts that apply standardized methods to advance this field of science. Here we present a review of dust-borne microorganisms with a focus on their relevance to agronomy.

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance.

PubMed

Kuzyakov, Yakov; Xu, Xingliang

2013-05-01

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 (15)N-labelling studies that investigated (15)N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on K(m) (Michaelis constant) and V(max) (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower K(m) values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (V(max)) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Secondary metabolites from marine-derived microorganisms.

PubMed

Chen, Gang; Wang, Hai-Feng; Pei, Yue-Hu

2014-01-01

In the search for novel and bioactive molecules for drug discovery, marine-derived natural resources, especially marine microorganisms are becoming an important and interesting research area. This study covers the literature published after 2008 on secondary metabolites of marine-derived microorganisms. The emphasis was on new compounds with the relevant biological activities, strain information, and country of origin. New compounds without biological activity were not included.

Antimicrobial efficacy of eucalyptus oil and 1,8-cineole alone and in combination with chlorhexidine digluconate against microorganisms grown in planktonic and biofilm cultures.

PubMed

Hendry, E R; Worthington, T; Conway, B R; Lambert, P A

2009-12-01

Effective disinfection and antisepsis is pivotal in preventing infections within the healthcare setting. Chlorhexidine digluconate (CHG) is a widely used disinfectant/antiseptic possessing broad-spectrum antimicrobial activity; however, its penetration into bacterial biofilms and human skin is poor. The aim of this study was to investigate the antimicrobial efficacy of crude eucalyptus oil (EO) and its main component 1,8-cineole (a recognized permeation enhancer), alone and in combination with CHG, against a panel of clinically relevant microorganisms grown in planktonic and biofilm cultures. MICs and minimum bactericidal/fungicidal concentrations were determined for each microorganism grown in suspension and biofilm using microbroth dilution and ATP bioluminescence, respectively. Chequerboard assays were used to determine synergistic, indifferent or antagonistic interactions between CHG and EO or 1,8-cineole. Antimicrobial activity was demonstrated by CHG, EO and 1,8-cineole; however, CHG was significantly more active against microorganisms in both planktonic and biofilm modes of growth (P < 0.05). Crude EO was significantly more efficacious against microorganisms grown in suspension compared with 1,8-cineole (P < 0.05). Synergistic activity was demonstrated between CHG and both EO and 1,8-cineole against suspensions of Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Escherichia coli and Candida albicans, and biofilm cultures of MRSA and Pseudomonas aeruginosa. In conclusion, CHG may be combined with either crude EO or its major component 1,8-cineole for enhanced, synergistic antimicrobial activity against a wide range of microorganisms in planktonic and biofilm modes of growth; however, the superior antimicrobial efficacy associated with crude EO alone, compared with 1,8-cineole, favours its combination with CHG.

Surface Disinfectants for Burn Units Evaluated by a New Double Method, Using Microorganisms Recently Isolated From Patients, on a Surface Germ-Carrier Model.

PubMed

Herruzo, Rafael; Vizcaino, Maria Jose; Herruzo, Irene; Sanchez, Manuel

Assessment methods of surface disinfection based on international standards (Environmental Protection Agency, European Norms, etc) do not correspond to hospital reality. New evaluation methods of surfaces disinfection are proposed to choose the most suitable disinfectant to act against clinically relevant microorganisms detected on the surfaces of burn units. 1) "Immediate effect": 6 products were compared using a glass germ-carrier and 20 recently isolated microorganisms from different patients in the intensive care units. Disinfectants were applied with microfiber cloths. Log10 reductions were calculated for colony forming units produced after 15 minutes of disinfectant application. 2) "Residual effect": the glass germ-carriers were previously impregnated with one of the studied disinfectants. After a 30-minute wait period, they were then contaminated with 1 microorganism (from the 20 above-mentioned). After 15 minutes, the disinfectant was inhibited and the log10 reduction of colony forming units was assessed. The immediate effect (disinfection and microorganism dragging and transferring from the surface to the cloth) produced complete elimination of the inoculums for all products used except one (a diluted quaternary ammonium). The average residual effect found on the 20 microorganisms was moderate: 2 to 3 log10 colony forming unit reduction with chlorine dioxide or 0.5% chlorhexidine (and lower with the other products), obtaining surfaces refractory to recontamination, at least, during 30 minutes. Two tests should be performed before advising surface disinfectant: 1) direct effect and 2) residual efficacy. These characteristics should be considered when a new surface disinfectant is chosen. Chlorine dioxide has a similar or better direct effect than sodium hypochlorite and a similar residual effect than chlorhexidine.

Antimicrobial Compounds from Marine Invertebrates-Derived Microorganisms.

PubMed

Liu, Juan; Jung, Jee H; Liu, Yonghong

2016-01-01

It is known that marine invertebrates, including sponges, tunicates, cnidaria or mollusks, host affluent and various communities of symbiotic microorganisms. The microorganisms associated with the invertebrates metabolized various biologically active compounds, which could be an important resource for the discovery and development of potentially novel drugs. In this review, the new compounds with antimicrobial activity isolated from marine invertebrate-derived microorganisms in the last decade (2004-2014) will be presented, with focus on the relevant antimicrobial activities, origin of isolation, and information of strain species. New compounds without antimicrobial activity were not revealed.

The Danish Microbiology Database (MiBa) 2010 to 2013.

PubMed

Voldstedlund, M; Haarh, M; Mølbak, K

2014-01-09

The Danish Microbiology Database (MiBa) is a national database that receives copies of reports from all Danish departments of clinical microbiology. The database was launched in order to provide healthcare personnel with nationwide access to microbiology reports and to enable real-time surveillance of communicable diseases and microorganisms. The establishment and management of MiBa has been a collaborative process among stakeholders, and the present paper summarises lessons learned from this nationwide endeavour which may be relevant to similar projects in the rapidly changing landscape of health informatics.

Consensus and contentious statements on the use of probiotics in clinical practice: a South East Asian Gastro-neuro Motility Association Working Team Report.

PubMed

Gwee, Kok-Ann; Lee, Warren Wei-Rhen; Ling, Khoon Lin; Ooi, Choon Jin; Quak, Seng Hock; Dan, Yock Young; Siah, Kewin Tien-Ho; Huang, James Guoxian; Chua, Andrew Seng Boon; Hilmi, Ida Normiha; Raja Affendi, R A; Ong, Christina; Simadibrata, Marcellus; Abdullah, Murdani; Sollano, Jose D; Leelakusolvong, Somchai; Gonlachanvit, Sutep; Lee, Yeong Yeh; Ricaforte-Campos, Jane D; Yin, Yee Kian; Chong, Kuck-Meng; Wong, Chong Yuen

2018-04-26

The concept of consuming microorganisms in the treatment of a medical condition and in health maintenance has gained much traction, giving rise to an abundance of medical claims, and of health supplements. We identified relevant clinical questions on the therapeutic use of probiotics and reviewed the literature in irritable bowel syndrome, inflammatory bowel disease, impaired intestinal immunity, liver disease, intestinal infections and common childhood digestive disorders. Statements were developed to address these clinical questions. A panel of experienced clinicians was tasked to critically evaluate and debate the available data. Both consensus and contentious statements are presented to provide to clinicians a perspective on the potential of probiotics, and importantly their limitations. This article is protected by copyright. All rights reserved.

[Survival of probiotic microorganisms in the conditions in vitro imitating the process of human digestion].

PubMed

Darmov, I V; Chicherin, I Iu; Pogorel'skiĭ, I P; Lundovskikh, I A

2011-01-01

Assessment of survival bifidobacteria and lactobacteria under the conditions in vitro, simulating digestion in human stomach and intestine, and study of survival probiotic and indigenous microorganisms in co-cultivation on solid nutrient medium. Probiotic microorganisms from commercial preparations Bifidobacterin and Lactobacterin, clinical isolates lactobacillus (Lactobacillus acidophilus No 1, L. brevis No 2) were used in experiments. Survival study of probiotic microorganisms was performed on a model in vitro, simulating the process of digestion in the human body. Assessment of the relationship of probiotic microorganisms and indigenous microorganisms was carried out in co-cultivation in vitro on solid nutrient medium. A significant reduction in the number of viable probiotic microorganisms during their incubation in model media was set as well as suppression of probiotic microorganisms growth by cultures of a clinical strains of lactobacillus, corresponding to biocompatibility by type "host against probiotic". While choosing probiotics in the treatment of dysbacterioses the character of relationship between probiotic microorganisms and indigenous microorganisms of a patient is recommended to be preliminarily tested. Also microorganisms of own microflora should be stimulated using modern prebiotics.

Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

PubMed Central

Papadimitriou, Konstantinos; Zoumpopoulou, Georgia; Foligné, Benoit; Alexandraki, Voula; Kazou, Maria; Pot, Bruno; Tsakalidou, Effie

2015-01-01

Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms. PMID:25741323

Pre-sporulation stages of Streptomyces differentiation: state-of-the-art and future perspectives.

PubMed

Yagüe, Paula; López-García, Maria T; Rioseras, Beatriz; Sánchez, Jesús; Manteca, Angel

2013-05-01

Streptomycetes comprise very important industrial bacteria, producing two-thirds of all clinically relevant secondary metabolites. They are mycelial microorganisms with complex developmental cycles that include programmed cell death (PCD) and sporulation. Industrial fermentations are usually performed in liquid cultures (large bioreactors), conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that there was no differentiation. In this work, we review the current knowledge on Streptomyces pre-sporulation stages of Streptomyces differentiation. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Let microorganisms do the talking, let us talk more about microorganisms.

PubMed

Nai, Corrado; Magrini, Boris; Offe, Julia

2016-01-01

Microorganisms are of uttermost importance, yet in the eyes of the general public they are often associated with dirt and diseases. At the same time, microbiologists have access to and comprehensive knowledge of just a tiny minority of the microbial diversity existing in nature. In this commentary, we present these issues of public misconception and scientific limitations and their possible consequences, and propose ways to overcome them. A particular interest is directed toward the secondary metabolism of filamentous fungi as well as novel outreach activities, including so-called "science slams" and interactions between the arts and the sciences, to raise awareness about the relevance of microorganisms.

The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

PubMed Central

Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

2005-01-01

Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms

PubMed Central

Price, Travis K.; Dune, Tanaka; Hilt, Evann E.; Thomas-White, Krystal J.; Kliethermes, Stephanie; Brincat, Cynthia; Brubaker, Linda; Wolfe, Alan J.

2016-01-01

Enhanced quantitative urine culture (EQUC) detects live microorganisms in the vast majority of urine specimens reported as “no growth” by the standard urine culture protocol. Here, we evaluated an expanded set of EQUC conditions (expanded-spectrum EQUC) to identify an optimal version that provides a more complete description of uropathogens in women experiencing urinary tract infection (UTI)-like symptoms. One hundred fifty adult urogynecology patient-participants were characterized using a self-completed validated UTI symptom assessment (UTISA) questionnaire and asked “Do you feel you have a UTI?” Women responding negatively were recruited into the no-UTI cohort, while women responding affirmatively were recruited into the UTI cohort; the latter cohort was reassessed with the UTISA questionnaire 3 to 7 days later. Baseline catheterized urine samples were plated using both standard urine culture and expanded-spectrum EQUC protocols: standard urine culture inoculated at 1 μl onto 2 agars incubated aerobically; expanded-spectrum EQUC inoculated at three different volumes of urine onto 7 combinations of agars and environments. Compared to expanded-spectrum EQUC, standard urine culture missed 67% of uropathogens overall and 50% in participants with severe urinary symptoms. Thirty-six percent of participants with missed uropathogens reported no symptom resolution after treatment by standard urine culture results. Optimal detection of uropathogens could be achieved using the following: 100 μl of urine plated onto blood (blood agar plate [BAP]), colistin-nalidixic acid (CNA), and MacConkey agars in 5% CO2 for 48 h. This streamlined EQUC protocol achieved 84% uropathogen detection relative to 33% detection by standard urine culture. The streamlined EQUC protocol improves detection of uropathogens that are likely relevant for symptomatic women, giving clinicians the opportunity to receive additional information not currently reported using standard urine culture techniques. PMID:26962083

Respiratory infections due to nontuberculous mycobacterias.

PubMed

Máiz Carro, Luis; Barbero Herranz, Esther; Nieto Royo, Rosa

2018-03-09

The most common infections caused by nontuberculous mycobacteria (NTM) are lung infections. The microorganisms causing these infections most frequently are Mycobacterium avium complex, Mycobacterium kansasii and Mycobacterium abscessus complex. Their incidence has increased in the last three decades. After identifying an NTM in the respiratory tract, clinical and radiological aspects must be considered to determine if isolations are clinically relevant. Predisposing conditions that could contribute to infection must also be investigated. Pulmonary disease due to NTM is presented in three clinical forms: a) pneumonitis due to hypersensitivity; b) fibrocavitary form; and c) nodular-bronchiectasic. The diagnosis of respiratory disease due to NTM does not make it obligatory to immediately initiate treatment. Before initiating the latter, other factors must be considered, such as age, comorbidities, life expectancy, due to the prolonged nature of treatments, with potential side effects and, in many cases, only a slight response to the treatment. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

PubMed

Alcaide, F; Amlerová, J; Bou, G; Ceyssens, P J; Coll, P; Corcoran, D; Fangous, M-S; González-Álvarez, I; Gorton, R; Greub, G; Hery-Arnaud, G; Hrábak, J; Ingebretsen, A; Lucey, B; Marekoviċ, I; Mediavilla-Gradolph, C; Monté, M R; O'Connor, J; O'Mahony, J; Opota, O; O'Reilly, B; Orth-Höller, D; Oviaño, M; Palacios, J J; Palop, B; Pranada, A B; Quiroga, L; Rodríguez-Temporal, D; Ruiz-Serrano, M J; Tudó, G; Van den Bossche, A; van Ingen, J; Rodriguez-Sanchez, B

2018-06-01

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Protease expression by microorganisms and its relevance to crucial physiological/pathological events.

PubMed

Dos Santos, André Luis Souza

2011-03-26

The treatment of infections caused by fungi and trypanosomatids is difficult due to the eukaryotic nature of these microbial cells, which are similar in several biochemical and genetic aspects to host cells. Aggravating this scenario, very few antifungal and anti-trypanosomatidal agents are in clinical use and, therefore, therapy is limited by drug safety considerations and their narrow spectrum of activity, efficacy and resistance. The search for new bioactive agents against fungi and trypanosomatids has been expanded because progress in biochemistry and molecular biology has led to a better understanding of important and essential pathways in these microorganisms including nutrition, growth, proliferation, signaling, differentiation and death. In this context, proteolytic enzymes produced by these eukaryotic microorganisms are appointed and, in some cases, proven to be excellent targets for searching novel natural and/or synthetic pharmacological compounds, in order to cure or prevent invasive fungal/trypanosomatid diseases. With this task in mind, our research group and others have focused on aspartic-type proteases, since the activity of this class of hydrolytic enzymes is directly implicated in several facets of basic biological processes of both fungal and trypanosomatid cells as well as due to the participation in numerous events of interaction between these microorganisms and host structures. In the present paper, a concise revision of the beneficial effects of aspartic protease inhibitors, with emphasis on the aspartic protease inhibitors used in the anti-human immunodeficiency virus therapy, will be presented and discussed using our experience with the following microbial models: the yeast Candida albicans, the filamentous fungus Fonsecaea pedrosoi and the protozoan trypanosomatid Leishmania amazonensis.

Humus-reducing microorganisms and their valuable contribution in environmental processes.

PubMed

Martinez, Claudia M; Alvarez, Luis H; Celis, Lourdes B; Cervantes, Francisco J

2013-12-01

Humus constitutes a very abundant class of organic compounds that are chemically heterogeneous and widely distributed in terrestrial and aquatic environments. Evidence accumulated during the last decades indicating that humic substances play relevant roles on the transport, fate, and redox conversion of organic and inorganic compounds both in chemically and microbially driven reactions. The present review underlines the contribution of humus-reducing microorganisms in relevant environmental processes such as biodegradation of recalcitrant pollutants and mitigation of greenhouse gases emission in anoxic ecosystems, redox conversion of industrial contaminants in anaerobic wastewater treatment systems, and on the microbial production of nanocatalysts and alternative energy sources.

PubMed Central

Combaz-Söhnchen, Nina; Kuhn, Annette

2017-01-01

Mycoplasma species relevant to the urogenital tract include mycoplasma hominis, mycoplasma genitalia and ureaplasma urealyticum. Their occurrence in the context of urogynaecological disease has been demonstrated in urethritis, cystitis and upper renal tract infections. Their role in hyperactive bladder and interstitial cystitis/painful bladder syndrome is controversial. All the above-mentioned microorganisms can occur as commensals or as potential pathogens. In most cases their role in any particular pathology cannot be proven, only presumed. The aim of this systematic review was to summarise current knowledge on the influence of mycoplasma and ureaplasma in urogynaecological pathology and to provide clinical guidance on diagnosis (when and how is pathogen detection indicated?) and treatment. 377 relevant articles were analysed. In summary: a urethral swab for PCR analysis of the three bacteria should be performed in the context of symptomatic sterile leukocyturia, chronic urethritis and suspected hyperactive bladder or interstitial cystitis/painful bladder syndrome. Symptomatic women should be treated strictly according to results of the antibiogram. PMID:29269957

[ACTIVITY OF ANTIMICROBIAL NANOSTRUCTURED BARRIER LAYERS BASED ON POLYETHYLENETEREPHTHALATE IN RELATION TO CLINICAL STRAINES OF MICROORGANISMS FOR SICK PERSONS OF GASTROENTEROLOGICAL PROFILE].

PubMed

Elinson, V M; Rusanova, E V; Vasilenko, I A; Lyamin, A N; Kostyuchenko, L N

2015-01-01

Homeostasis transgressions of enteral medium including disbiotic ones are often accompanying deseases of digestive tract. Espessially it touches upon sick persons connected with probe nourishing. One of the way for solving this problem is normalization of digestion microflore by means of wares with nanotechnological modifications of walls (probes, stomic tubes) which provide them antimicrobial properties and assist to normalization of digestive microbiotis and enteral homeostasis completely. The aim to study is research of antimicrobial activity of of nanostructured barrier layers based on polyethyleneterephthalate (PET) in relation to clinical straines of microorganisms. For barrier layer creation the approach on the base of methods of ion-plasma technology was used including ion-plasma treatment (nanostructuring) of the surface by ions noble and chemically active gases and following formation nanodimensional carbon films on the surface/ For the study of antimicrobial activity in relation to clinical straines of microorganisms we used the technique which allowed to establish the influence of parting degree of microorganisms suspension and time for samples exposing and microorganisms adsorbed on the surface. In experiment clinical straines obtained from different materials were used: Staphylococcus Hly+ and Calbicans--from pharyngeal mucosa, E. coli--from feces, K.pneumoniae--from urine. Sharing out and species identification of microorganisms were fulfilled according with legasy documents. In results of the study itwas obtained not only the presence of staticticaly confirmed antimicrobial activity of PET samples with nanostructured barrier layers in relation to different stimulators of nosocomical infections but also the influence of different factors connected with formation of nanostructured layers and consequently based with them physicochemical characteristics such as, in particular, surface energy, surface relief parameters, surface charg and others, as well as influence of microorganisms nature onto the interaction of between barrier layers and microorganisms.

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments

PubMed Central

Finkelshtein, Alin; Roth, Dalit

2015-01-01

ABSTRACT Swarming bacteria are challenged by the need to invade hostile environments. Swarms of the flagellated bacterium Paenibacillus vortex can collectively transport other microorganisms. Here we show that P. vortex can invade toxic environments by carrying antibiotic-degrading bacteria; this transport is mediated by a specialized, phenotypic subpopulation utilizing a process not dependent on cargo motility. Swarms of beta-lactam antibiotic (BLA)-sensitive P. vortex used beta-lactamase-producing, resistant, cargo bacteria to detoxify BLAs in their path. In the presence of BLAs, both transporter and cargo bacteria gained from this temporary cooperation; there was a positive correlation between BLA resistance and dispersal. P. vortex transported only the most beneficial antibiotic-resistant cargo (including environmental and clinical isolates) in a sustained way. P. vortex displayed a bet-hedging strategy that promoted the colonization of nontoxic niches by P. vortex alone; when detoxifying cargo bacteria were not needed, they were lost. This work has relevance for the dispersal of antibiotic-resistant microorganisms and for strategies for asymmetric cooperation with agricultural and medical implications. PMID:25968641

Measuring micro-organism gas production

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Pearson, A. O.; Mills, S. M.

1973-01-01

Transducer, which senses pressure buildup, is easy to assemble and use, and rate of gas produced can be measured automatically and accurately. Method can be used in research, in clinical laboratories, and for environmental pollution studies because of its ability to detect and quantify rapidly the number of gas-producing microorganisms in water, beverages, and clinical samples.

[THE TRUE OR FALSE BACTERIEMIA: THE SIGNIFICANCE OF EVALUATION CRITERIA OF CLINICAL SIGNIFICANCE OF POSITIVE HEMOCULTURE].

PubMed

Bagirova, N S

2015-08-01

The diagnostic of infections of blood flow using technique of hemofermentation (blood inoculation) is one of the most significant functions of laboratory of clinical microbiology. The effectiveness of the given technique depends on many factors, including criteria of evaluation of clinical significance of episode of bacteriemia and isolated microorganism applied by physician-microbiologist. The intelligent analysis of received results is needed. The physician-microbiologist has to determine if microorganism isolated from given blood sample, is a genuine agent of infections of bloodflow or it is only effect of contamination of analyzed sample at certain stage. The article presents data concerning taxonomic structure of microorganisms isolated under episodes of bacteriemia of adult oncologic hematologic patients during 2005-2013. The criteria of evaluation of clinical significance of episode of bacteriemia and isolated microorganism are described. The given criteria are developed in the N.N. Blokhin Russian oncological research center and are applied since 1977. The cases of contamination and genuine bacteriemia are established. The comparative analysis of international data and results of one's own study are carried out.

Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: intact cell vs. extraction method.

PubMed

Ferreira, L; Sánchez-Juanes, F; Muñoz-Bellido, J L; González-Buitrago, J M

2011-07-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a fast and reliable technology for the identification of microorganisms with proteomics approaches. Here, we compare an intact cell method and a protein extraction method before application on the MALDI plate for the direct identification of microorganisms in both urine and blood culture samples from clinical microbiology laboratories. The results show that the intact cell method provides excellent results for urine and is a good initial method for blood cultures. The extraction method complements the intact cell method, improving microorganism identification from blood culture. Thus, we consider that MALDI-TOF MS performed directly on urine and blood culture samples, with the protocols that we propose, is a suitable technique for microorganism identification, as compared with the routine methods used in the clinical microbiology laboratory. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World.

PubMed

Chisanga, Malama; Muhamadali, Howbeer; Ellis, David I; Goodacre, Royston

2018-01-01

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.

Magnetohydrodynamics Nanofluid Flow Containing Gyrotactic Microorganisms Propagating Over a Stretching Surface by Successive Taylor Series Linearization Method

NASA Astrophysics Data System (ADS)

Shahid, A.; Zhou, Z.; Bhatti, M. M.; Tripathi, D.

2018-03-01

Nanofluid dynamics with magnetohydrodynamics has tremendously contributed in industrial applications recently since presence of nanoparticle in base fluids enhances the specific chemical and physical properties. Owing to the relevance of nanofluid dynamics, we analyze the nanofluid flow in the presence of gyrotactic microorganism and magnetohydrodynamics through a stretching/shrinking plate. The impacts of chemical reaction and thermal radiation on flow characteristics are also studied. To simplify the governing equations of microorganisms, velocity, concentration and temperature, the similarity transformations are employed. The couple governing equations are numerically solved using Successive Taylor Series Linearization Method (STSLM). The velocity profile, motile microorganism density profile, concentration profile, temperature profile as well as Nusselt number, skin friction coefficient, Sherwood number and density number of motile microorganisms are discussed using tables and graphs against all the sundry parameters. A numerical comparison is also given for Nusselt number, Sherwood number, skin friction, and density number of motile microorganisms with previously published results to validate the present model. The results show that Nusselt number, Sherwood number and density number diminish with increasing the magnetic field effects.

[Microorganisms responsible of nosocomial infections in the Mexican Social Security Institute].

PubMed

Arias-Flores, Rafael; Rosado-Quiab, Ulises; Vargas-Valerio, Alfredo; Grajales-Muñiz, Concepción

2016-01-01

The prevention and control of the nosocomial infections involve the knowledge of the most frequent type of microorganism isolated. In Mexico there are not national statistics to identify the main microorganisms that cause a nosocomial infection. It was conducted an analysis of all the culture results of the nosocomial infections reported by the Sistema de Vigilancia Epidemiológica Hospitalaria (Epidemiological Surveillance System) of the Instituto Mexicano del Seguro Social during the year 2013. The most frequent and relevant microorganisms were reported. 48 377 results from cultures of nosocomial infections were studied. Of these 13 207 (27.3 %) were from 25 high specialty medical units and 35 170 (72.6 %) from 197 second level medical units. The most frequently isolated microorganism was Escherichia coli with 8192 results (16.9 %), followed by the group of Coagulase-negative Staphylococci with 6771 cultures (14 %) and Pseudomonas aeruginosa with 5275 results (19.9 %). Slight differences between levels of care and specialized hospitals were observed. This study identifies the Escherichia coli, the group of Coagulase-negative Staphylococci and the Pseudomonas aeruginosa as the main microorganisms to prevent.

Raman spectroscopic studies on bacteria

NASA Astrophysics Data System (ADS)

Maquelin, Kees; Choo-Smith, Lin-P'ing; Endtz, Hubert P.; Bruining, Hajo A.; Puppels, Gerwin J.

2000-11-01

Routine clinical microbiological identification of pathogenic micro-organisms is largely based on nutritional and biochemical tests. Laboratory results can be presented to a clinician after 2 - 3 days for most clinically relevant micro- organisms. Most of this time is required to obtain pure cultures and enough biomass for the tests to be performed. In the case of severely ill patients, this unavoidable time delay associated with such identification procedures can be fatal. A novel identification method based on confocal Raman microspectroscopy will be presented. With this method it is possible to obtain Raman spectra directly from microbial microcolonies on the solid culture medium, which have developed after only 6 hours of culturing for most commonly encountered organisms. Not only does this technique enable rapid (same day) identifications, but also preserves the sample allowing it to be double-checked with traditional tests. This, combined with the speed and minimal sample handling indicate that confocal Raman microspectroscopy has much potential as a powerful new tool in clinical diagnostic microbiology.

Status of microbial based cleaning products in statutory regulations and ecolabelling in Europe, the USA, and Canada.

PubMed

Spök, Armin; Arvanitakis, George; McClung, Gwendolyn

2018-06-01

Cleaning products containing living microorganisms as active ingredients are increasingly being used in household, professional and industrial cleaning applications. Microorganisms can degrade soiling associated with dirt, food residues, and grease by enzymatic and metabolic action and out-compete microorganisms associated with odor problems. Their potential for odor control seems to result in a competitive advantage over conventional chemically-based cleaning products. Moreover, producers of microbial-based cleaning products (MBCPs) claim that their products are less harmful to the environment. These promising prospects have triggered interest from consumer and environmental organizations, professional users, and regulators in understanding if there are also possible negative health and environmental impacts which require attention and how the safety of these products is ensured. Unfortunately, there is little information on these issues in the public domain. Moreover, regulatory oversight in Europe is essentially limited to pathogenic properties in the context of worker protection. Canada, in contrast, has a regulatory framework in place to assess risks to human health and the environment from the manufacture, import and/or use of new microorganisms contained in MBCPs. In the absence of mandatory standards, safety assessment and hygienic practices seem to vary considerably across companies. Recently developed ecolabelling standards are - for the time being - the only option for transparent compliance to minimum standards in terms of safety as well as assessments of manufacturer information by third parties. These standards highlight in particular the need for precise taxonomic information for assessing the pathogenic properties and the need to ensure the absence of potentially harmful microorganisms as contaminants. Ecolabelling standards are, however, voluntary and do not cover all relevant safety issues. In order to develop a more comprehensive set of mandatory standards for health and safety, a number of areas would benefit from further research (e.g. the role in plant pathogenicity and other environmental properties of the microorganisms used; the relevance of chronic exposure to dusts and aerosols containing vegetative cells and spores; the relevance of strains which belong to species known to include opportunistic pathogens and possible hazards for particularly sensitive risk groups). Improved knowledge in these areas will contribute to a predictable level of product safety. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Bacterial contamination and stethoscope disinfection practices: a cross-sectional survey of healthcare workers in Karachi, Pakistan.

PubMed

Rao, Danish Ahmed; Aman, Aiysha; Muhammad Mubeen, Syed; Shah, Ahmed

2017-07-01

Stethoscopes routinely used for clinical examination of patients may potentially transfer micro-organisms and cause iatrogenic infections. This study was undertaken to detect the presence of microorganisms on stethoscopes used clinically in hospitals of Karachi, Pakistan and to ascertain the infection control practices of healthcare workers (HCWs). In a cross-sectional study, 118 samples were collected from public and private institutions. Samples were tested for the presence and sensitivity of pathogenic microorganisms. Microorganisms were found on diaphragms of 33/64 (51.6%) and 19/57 (33.3%) stethoscopes in public and private sector hospitals, respectively. Methycillin resistance was identified in all staphylococcally contaminated samples. Only 33 (18%) respondents reported cleaning their stethoscopes regularly. We highlight the need for more and better on-the-job routines for decontaminating stethoscopes among HCWs in Karachi.

Nutraceuticals for Skin Care: A Comprehensive Review of Human Clinical Studies.

PubMed

Pérez-Sánchez, Almudena; Barrajón-Catalán, Enrique; Herranz-López, María; Micol, Vicente

2018-03-24

The skin is the body's largest organ, it participates in sensitivity and offers protection against microorganisms, chemicals and ultraviolet (UV) radiation. Consequently, the skin may suffer alterations such as photo-ageing, immune dysfunction and inflammation which may significantly affect human health. Nutraceuticals represent a promising strategy for preventing, delaying, or minimising premature ageing of the skin and also to alleviate certain skin disorders. Among them, bioactive peptides and oligosaccharides, plant polyphenols, carotenoids, vitamins and polyunsaturated fatty acids are the most widely used ingredients. Supplementation with these products has shown evidence of having an effect on the signs of ageing and protection against UV radiation ageing in several human trials. In this review, the most relevant human studies on skin nutraceuticals are evaluated and the statistical resolution, biological relevance of their results, and, the trial protocols are discussed. In conclusion, quality and rigorousness of the trials must be improved to build credible scientific evidence for skin nutraceuticals and to establish a cause-effect relationship between the ingredients the beneficial effects for the skin.

Host-microbe interactions in distal airways: relevance to chronic airway diseases.

PubMed

Martin, Clémence; Burgel, Pierre-Régis; Lepage, Patricia; Andréjak, Claire; de Blic, Jacques; Bourdin, Arnaud; Brouard, Jacques; Chanez, Pascal; Dalphin, Jean-Charles; Deslée, Gaetan; Deschildre, Antoine; Gosset, Philippe; Touqui, Lhousseine; Dusser, Daniel

2015-03-01

This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways. Copyright ©ERS 2015.

Clinical Infectious Outcomes Associated with Biofilm-related Infections: a Retrospective Chart Review

DTIC Science & Technology

2015-06-07

Chronic infections, Risk factors, Trauma-related infections, Burn Background The ability of microorganisms to form biofilms, a sessile mode of growth...patients [8]. With the present study, clinical information recovered from chart review was able to differentiate colonizing from infecting organisms...potential influences. Utilization of a randomly selected sample had conse- quences in microorganism representation as well as demographics. Species were

Waterborne microorganisms and biofilms related to hospital infections: strategies for prevention and control in healthcare facilities.

PubMed

Capelletti, Raquel Vannucci; Moraes, Ângela Maria

2016-02-01

Water is the main stimulus for the development of microorganisms, and its flow has an important role in the spreading of contaminants. In hospitals, the water distribution system requires special attention since it can be a source of pathogens, including those in the form of biofilms often correlated with resistance of microorganisms to various treatments. In this paper, information relevant to cases of nosocomial infections involving water circuits as a source of contaminants is compiled, with emphasis on the importance of microbiological control strategies to prevent the installation, spreading and growth of microorganisms in hospitals. An overview of the worldwide situation is provided, with emphasis on Brazilian hospitals. Different approaches normally used to control the occurrence of nosocomial infections due to waterborne contaminants are analyzed, and the use of the polysaccharide chitosan for this specific application is briefly discussed.

Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

PubMed

Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

2015-12-01

Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

Microbiological aspects related to the feasibility of PEF technology for food pasteurization.

PubMed

Saldaña, G; Álvarez, I; Condón, S; Raso, J

2014-01-01

Processing unit operations that seek to inactivate harmful microorganisms are of primary importance in ascertaining the safety of food. The capability of pulsed electric fields (PEF) to inactivate vegetative cells of microorganisms at temperatures below those used in thermal processing makes this technology very attractive as a nonthermal pasteurization process for the food industry. Commercial exploitation of this technology for food pasteurization requires the identification of the most PEF-resistant microorganisms that are of concern to public health. Then, the treatment conditions applicable at industrial scale that would reduce the population of these microorganisms to a level that guarantees food safety must be defined. The objective of this paper is to critically compile recent, relevant knowledge with the purpose of enhancing the feasibility of using PEF technology for food pasteurization and underlining the required research for designing PEF pasteurization processes.

Microorganisms present on peripheral intravenous needleless connectors in the clinical environment.

PubMed

Slater, Karen; Cooke, Marie; Whitby, Michael; Fullerton, Fiona; Douglas, Joel; Hay, Jennine; Rickard, Claire

2017-08-01

The aim of this study was to quantify culturable microorganisms on needleless connectors (NCs) attached to peripheral intravenous catheters in hospitalized adult medical patients. Half (50%) of 40 NCs were contaminated with microorganisms commonly found on the skin or mouth. Staphylococcus capitis and Staphylococcus epidermidis were most commonly isolated. Emergency department insertion and higher patient dependency were statistically associated with positive NC microorganism growth. These results reaffirm the need for NC decontamination prior to access. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

[New aspects of safety assessment and food contamination with antibiotics of tetracycline group in the light of harmonization of hygienic standards in Russia and Customs Union with the international standards].

PubMed

Onishchenko, G G; Sheveleva, S A; Khotimchenko, S A

2012-01-01

To address the issue of harmonization of Russian MRLs for tetracycline in food and on the basis of the tasks of preserving the value of hygienic standard for the more restrictive level than similar standards of the Codex Alimentarius Commission in this survey we analyzed the evidences of the negative effects of subingibitory amounts of these antibiotics (lying below the MIC for clinically relevant microorganisms). The inadequacy of the microbiological JECFA ADI and the necessity of using of methodology of analyzing the effects of biological active substances in small doses for assessing the risk of food contamination of tetracycline subingibitory concentrations were demonstrated. Current scientific information on the functions of antibiotics as signaling molecules in the microbial world and the role of tetracycline as a leading factor in the regulation of transcription in microorganisms and activation of the horizontal transfer of resistance genes transferred to the family of conjugative transposons Tn916-Tn1545 also was reviewed in paper. Evidence-based data regarding the basic contribution of subingibitory concentrations of tetracycline in the spread of worst transmissible type of antibiotic resistance and the formation of new pathogens, associated with it, are represented. To reduce the risk of direct adverse effects on microbial ecosystem in the human body and its habitat, and to minimize the indirect risk of new infections, the necessity of saving the current Russian level residues of tetracycline (< or = 0.01 mg/kg of product), which is low by contrast to the Codex MRLs (< or = 0.1-1.2 mg/kg), was proved. Tetracycline concentrations in food, regulated in Russian Federation, below 0.1 MIC for clinically significant microorganisms which aren't capable to initiation of the above described negative changes.

Lectins and their application to clinical microbiology.

PubMed Central

Slifkin, M; Doyle, R J

1990-01-01

Lectins are generally associated with plant or animal components, selectively bind carbohydrates, and interact with procaryotic and eucaryotic cells. Lectins have various specificities that are associated with their ability to interact with acetylaminocarbohydrates, aminocarbohydrates, sialic acids, hexoses, pentoses, and as other carbohydrates. Microbial surfaces generally contain many of the sugar residues that react with lectins. Lectins are presently used in the clinical laboratory to type blood cells and are used in a wide spectrum of applications, including, in part, as carriers of chemotherapeutic agents, as mitogens, for fractionation of animal cells, and for investigations of cellular surfaces. Numerous studies have shown that lectins can be used to identify rapidly certain microorganisms isolated from a clinical specimen or directly in a clinical specimen. Lectins have been demonstrated to be important diagnostic reagents in the major realms of clinical microbiology. Thus, they have been applied in bacteriology, mycology, mycobacteriology, and virology for the identification and/or differentiation of various microorganisms. Lectins have been used successfully as epidemiologic as well as taxonomic markers of specific microorganisms. Lectins provide the clinical microbiologist with cost-effective and potential diagnostic reagents. This review describes the applications of lectins in clinical microbiology. Images PMID:2200603

Antimicrobial activity of jasmine oil against oral microorganisms

NASA Astrophysics Data System (ADS)

Thaweboon, S.; Thaweboon, B.; Kaypetch, R.

2018-02-01

Jasmine sambac is a species of jasmine indigenous to the tropical and warm temperature regions in particular West and Southeast Asia. Essential oil extracted from the flowers of J. sambac has been shown to have anti-oxidant activity. However, very little information regarding antimicrobial activity especially oral microorganisms exists. Objective: To investigate antimicrobial effect of essential oil extracted from flowers of J. sambac against various oral microorganisms. Materials and Methods: Oral microbial strains used in the study were Streptococcus mutans KPSK2, Staphylococcus aureus ATCC 5638, Lactobacillus casei ATCC 6363, Klebsiella pneumoniae (clinical isolate), Escherichia coli ATCC 25922, Candida albicans ATCC 10231, Candida krusei ATCC 6258, Candida parapsilosis ATCC 22019, Candida tropicalis (clinical isolate), Candida glabrata ATCC 90030, Candida pseudotropicalis (clinical isolate) and Candida stellatoidia (clinical isolate). The potential of microbial growth inhibition of the oil was firstly screened by Kirby-Bauer disk diffusion method and then the minimum inhibitory concentration (MIC) was determined by agar dilution method. Results: Jasmine oil showed antimicrobial activities against S. mutans, L. casei, E. coli and all strains of Candida species with the zones of inhibition ranging from 9 to 26 mm and MIC values of 0.19-1.56 %v/v. Conclusion: Results from the present study are scientific evidence to demonstrate that jasmine oil could be employed as a natural antimicrobial agent against oral microorganisms.

[Community-acquired pneumonia--from medical technologist].

PubMed

Yamanaka, Kiyoharu

2002-07-01

The main causative microorganisms of Community-acquired pneumonia are Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus. Especially the causative microorganisms affecting whole body basic disease, persons of advanced age, and alcoholic patients are Moraxella catarrhalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Candida spp., Cryptococcus spp., Aspergillus spp., Pneumocystis carinii and anaerobic bacteria. Other microorganisms involved in epidemic disease, action condition (travel around hot springs etc.) and pet breeding environments are Mycoplasma pneumoniae, Legionella pnumophila, Chlamydia spp., respiratory syncytial virus, influenza virus, and adeno virus. We suggest methods of advancing the microscopic and microbiological examination and report, and quickly obtaining clinical information and extracting the clinical specimen. We also describe the inspection method for a case "Legionella pneumonia" that was discussed during this symposium.

A Rat Model of Central Venous Catheter to Study Establishment of Long-Term Bacterial Biofilm and Related Acute and Chronic Infections

PubMed Central

Chauhan, Ashwini; Lebeaux, David; Decante, Benoit; Kriegel, Irene; Escande, Marie-Christine; Ghigo, Jean-Marc; Beloin, Christophe

2012-01-01

Formation of resilient biofilms on medical devices colonized by pathogenic microorganisms is a major cause of health-care associated infection. While in vitro biofilm analyses led to promising anti-biofilm approaches, little is known about their translation to in vivo situations and on host contribution to the in vivo dynamics of infections on medical devices. Here we have developed an in vivo model of long-term bacterial biofilm infections in a pediatric totally implantable venous access port (TIVAP) surgically placed in adult rats. Using non-invasive and quantitative bioluminescence, we studied TIVAP contamination by clinically relevant pathogens, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Staphylococcus epidermidis, and we demonstrated that TIVAP bacterial populations display typical biofilm phenotypes. In our study, we showed that immunocompetent rats were able to control the colonization and clear the bloodstream infection except for up to 30% that suffered systemic infection and death whereas none of the immunosuppressed rats survived the infection. Besides, we mimicked some clinically relevant TIVAP associated complications such as port-pocket infection and hematogenous route of colonization. Finally, by assessing an optimized antibiotic lock therapy, we established that our in vivo model enables to assess innovative therapeutic strategies against bacterial biofilm infections. PMID:22615964

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics.

PubMed

Gibson, Glenn R; Hutkins, Robert; Sanders, Mary Ellen; Prescott, Susan L; Reimer, Raylene A; Salminen, Seppo J; Scott, Karen; Stanton, Catherine; Swanson, Kelly S; Cani, Patrice D; Verbeke, Kristin; Reid, Gregor

2017-08-01

In December 2016, a panel of experts in microbiology, nutrition and clinical research was convened by the International Scientific Association for Probiotics and Prebiotics to review the definition and scope of prebiotics. Consistent with the original embodiment of prebiotics, but aware of the latest scientific and clinical developments, the panel updated the definition of a prebiotic: a substrate that is selectively utilized by host microorganisms conferring a health benefit. This definition expands the concept of prebiotics to possibly include non-carbohydrate substances, applications to body sites other than the gastrointestinal tract, and diverse categories other than food. The requirement for selective microbiota-mediated mechanisms was retained. Beneficial health effects must be documented for a substance to be considered a prebiotic. The consensus definition applies also to prebiotics for use by animals, in which microbiota-focused strategies to maintain health and prevent disease is as relevant as for humans. Ultimately, the goal of this Consensus Statement is to engender appropriate use of the term 'prebiotic' by relevant stakeholders so that consistency and clarity can be achieved in research reports, product marketing and regulatory oversight of the category. To this end, we have reviewed several aspects of prebiotic science including its development, health benefits and legislation.

Biological permeable reactive barriers coupled with electrokinetic soil flushing for the treatment of diesel-polluted clay soil.

PubMed

Mena, Esperanza; Ruiz, Clara; Villaseñor, José; Rodrigo, Manuel A; Cañizares, Pablo

2015-01-01

Removal of diesel from spiked kaolin has been studied in the laboratory using coupled electrokinetic soil flushing (EKSF) and bioremediation through an innovative biological permeable reactive barriers (Bio-PRBs) positioned between electrode wells. The results show that this technology is efficient in the removal of pollutants and allows the soil to maintain the appropriate conditions for microorganism growth in terms of pH, temperature, and nutrients. At the same time, EKSF was demonstrated to be a very interesting technology for transporting pollutants, microorganisms and nutrients, although results indicate that careful management is necessary to avoid the depletion of nutrients, which are effectively transported by electro-migration. After two weeks of operation, 30% of pollutants are removed and energy consumption is under 70 kWh m(-3). Main fluxes (electroosmosis and evaporation) and changes in the most relevant parameters (nutrients, diesel, microorganisms, surfactants, moisture conductivity and pH) during treatment and in a complete post-study analysis are studied to give a comprehensive description of the most relevant processes occurring in the soil (pollutant transport and biodegradation). Copyright © 2014 Elsevier B.V. All rights reserved.

Microbiology and atmospheric processes: research challenges concerning the impact of airborne micro-organisms on the atmosphere and climate

NASA Astrophysics Data System (ADS)

Morris, C. E.; Sands, D. C.; Bardin, M.; Jaenicke, R.; Vogel, B.; Leyronas, C.; Ariya, P. A.; Psenner, R.

2011-01-01

For the past 200 years, the field of aerobiology has explored the abundance, diversity, survival and transport of micro-organisms in the atmosphere. Micro-organisms have been explored as passive and severely stressed riders of atmospheric transport systems. Recently, an interest in the active roles of these micro-organisms has emerged along with proposals that the atmosphere is a global biome for microbial metabolic activity and perhaps even multiplication. As part of a series of papers on the sources, distribution and roles in atmospheric processes of biological particles in the atmosphere, here we describe the pertinence of questions relating to the potential roles that air-borne micro-organisms might play in meteorological phenomena. For the upcoming era of research on the role of air-borne micro-organisms in meteorological phenomena, one important challenge is to go beyond descriptions of abundance of micro-organisms in the atmosphere toward an understanding of their dynamics in terms of both biological and physico-chemical properties and of the relevant transport processes at different scales. Another challenge is to develop this understanding under contexts pertinent to their potential role in processes related to atmospheric chemistry, the formation of clouds, precipitation and radiative forcing. This will require truly interdisciplinary approaches involving collaborators from the biological and physical sciences, from disciplines as disparate as agronomy, microbial genetics and atmosphere physics, for example.

Capillary electromigration separation of proteins and microorganisms dynamically modified by chromophoric nonionogenic surfactant.

PubMed

Horká, Marie; Růzicka, Filip; Holá, Veronika; Kahle, Vladislav; Moravcová, Dana; Slais, Karel

2009-08-15

A chromophoric nonionogenic surfactant poly(ethylene glycol) 3-(2-hydroxy-5-n-octylphenylazo)-benzoate, HOPAB, has been prepared and used as a buffer additive for a dynamic modification of proteins and/or microorganisms including Escherichia coli , Staphylococcus epidermidis (biofilm-positive and biofilm-negative), and the strains of yeast cells Candida albicans and Candida parapsilosis (biofilm-positive and biofilm-negative) during a capillary electrophoresis and a capillary isoelectric focusing (CIEF) with UV detection at 326 nm. Values of isoelectric points of labeled proteins and microorganisms have been calculated using UV-detectable pI markers and have been found comparable with pI of the native compounds. Minimum detectable amount has been assessed lower than picograms of proteins and lower than a hundred cells injected into a separation capillary. The introduced labeling method facilitates CIEF separation of microorganisms from the clinical sample of the infected urine at their clinically important levels in the pH gradient pH range of 2-5 and their subsequent cultivation. At the same time, it has enabled the determination of albumin in human urine as a major clinical marker of urinary tract infections and kidney diseases.

Mould routine identification in the clinical laboratory by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Cassagne, Carole; Ranque, Stéphane; Normand, Anne-Cécile; Fourquet, Patrick; Thiebault, Sandrine; Planard, Chantal; Hendrickx, Marijke; Piarroux, Renaud

2011-01-01

MALDI-TOF MS recently emerged as a valuable identification tool for bacteria and yeasts and revolutionized the daily clinical laboratory routine. But it has not been established for routine mould identification. This study aimed to validate a standardized procedure for MALDI-TOF MS-based mould identification in clinical laboratory. First, pre-extraction and extraction procedures were optimized. With this standardized procedure, a 143 mould strains reference spectra library was built. Then, the mould isolates cultured from sequential clinical samples were prospectively subjected to this MALDI-TOF MS based-identification assay. MALDI-TOF MS-based identification was considered correct if it was concordant with the phenotypic identification; otherwise, the gold standard was DNA sequence comparison-based identification. The optimized procedure comprised a culture on sabouraud-gentamicin-chloramphenicol agar followed by a chemical extraction of the fungal colonies with formic acid and acetonitril. The identification was done using a reference database built with references from at least four culture replicates. For five months, 197 clinical isolates were analyzed; 20 were excluded because they were not identified at the species level. MALDI-TOF MS-based approach correctly identified 87% (154/177) of the isolates analyzed in a routine clinical laboratory activity. It failed in 12% (21/177), whose species were not represented in the reference library. MALDI-TOF MS-based identification was correct in 154 out of the remaining 156 isolates. One Beauveria bassiana was not identified and one Rhizopus oryzae was misidentified as Mucor circinelloides. This work's seminal finding is that a standardized procedure can also be used for MALDI-TOF MS-based identification of a wide array of clinically relevant mould species. It thus makes it possible to identify moulds in the routine clinical laboratory setting and opens new avenues for the development of an integrated MALDI-TOF MS-based solution for the identification of any clinically relevant microorganism.

Applications of mid-infrared spectroscopy in the clinical laboratory setting.

PubMed

De Bruyne, Sander; Speeckaert, Marijn M; Delanghe, Joris R

2018-01-01

Fourier transform mid-infrared (MIR-FTIR) spectroscopy is a nondestructive, label-free, highly sensitive and specific technique that provides complete information on the chemical composition of biological samples. The technique both can offer fundamental structural information and serve as a quantitative analysis tool. Therefore, it has many potential applications in different fields of clinical laboratory science. Although considerable technological progress has been made to promote biomedical applications of this powerful analytical technique, most clinical laboratory analyses are based on spectroscopic measurements in the visible or ultraviolet (UV) spectrum and the potential role of FTIR spectroscopy still remains unexplored. In this review, we present some general principles of FTIR spectroscopy as a useful method to study molecules in specimens by MIR radiation together with a short overview of methods to interpret spectral data. We aim at illustrating the wide range of potential applications of the proposed technique in the clinical laboratory setting with a focus on its advantages and limitations and discussing the future directions. The reviewed applications of MIR spectroscopy include (1) quantification of clinical parameters in body fluids, (2) diagnosis and monitoring of cancer and other diseases by analysis of body fluids, cells, and tissues, (3) classification of clinically relevant microorganisms, and (4) analysis of kidney stones, nails, and faecal fat.

[Necroscopic findings in patients with acquired immunodeficiency syndrome].

PubMed

Netto, J G; Collarile, D C; Borges, A F; Biancalana, M L; Stefano, H N

1990-01-01

The summaries of clinical data and the autopsy materials of 58 patients who died of acquired immunodeficiency syndrome were reviewed to study the spectrum of the pathologic features of this disease in a general hospital. Histologic sections of all organs were routinely obtained. The most affected organs were the lungs and encephalo, those responsible for the immediate cause of death. There were 11 types of microorganisms and 3 types of tumors. Among the microorganisms, the most frequent was the cytomegalovirus and, among tumors, Kaposi's sarcoma. The microorganisms were frequently associated, mainly in the central nervous system. There was also an association of microorganisms with tumors. Many patients presented with suppurative inflammation. Besides these lesions, a lymphocytic depletion of lymphoid organs was observed. The spectrum of pathologic changes in AIDS is vast, and pathologists should be aware of this fact to accurately diagnose the lesions they find. The morphologic lesions are neither unique nor specific for this syndrome, but in this clinical and immunologic setting they are characteristic. It became clear that several microorganisms and tumors sometimes can only be discovered by autopsy, which is an irrefutable proof that despite the modern technology, autopsy is unavoidable for the knowledge of the pathogeny of a disease.

Molecular diagnosis of bloodstream infections in onco-haematology patients with PCR/ESI-MS technology.

PubMed

Jordana-Lluch, Elena; Rivaya, Belén; Marcó, Clara; Giménez, Montserrat; Quesada, Mª Dolores; Escobedo, Agustín; Batlle, Montserrat; Martró, Elisa; Ausina, Vicente

2017-02-01

Onco-haematological patients are prone to develop infections, and antibiotic prophylaxis may lead to negative blood cultures. Thus, the microbiological diagnosis and subsequent administration of a targeted antimicrobial therapy is often difficult. The goal of this study was to evaluate the usefulness of IRIDICA (PCR/ESI-MS technology) for the molecular diagnosis of bloodstream infections in this patient group. A total of 463 whole blood specimens from different sepsis episodes in 429 patients were analysed using the PCR/ESI-MS platform, comparing the results with those of blood culture and other clinically relevant information. The sensitivity of PCR/ESI-MS by specimen (excluding polymicrobial infections, n = 25) in comparison with blood culture was 64.3% overall, 69.0% in oncological patients, and 59.3% in haematological patients. When comparing with a clinical infection criterion, overall sensitivity rose to 74.7%, being higher in oncological patients (80.0%) than in haematological patients (67.7%). Thirty-one microorganisms isolated by culture were not detected by IRIDICA, whereas 42 clinically relevant pathogens not isolated by culture were detected moleculary. PCR/ESI-MS offers a reliable identification of pathogens directly from whole blood. While additional studies are needed to confirm our findings, the system showed a lower sensitivity in onco-haematological patients in comparison with previously reported results in patients from the Intensive Care Unit. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

[Infectious complications in patients undergoing a heart transplant].

PubMed

Bouza, E; Muñoz, P

1995-01-01

Infectious complications are, with rejection, the main cause of morbidity and mortality in heart transplantation recipients. Adequate management of these patients requires an adequate knowledge of risk factors, of most common infectious syndromes and of relevant microorganism, as long as of their resistance pattern. Among the first group, we may mention lower respiratory tract infections, mediastinitis and meningitis, and among the microorganisms, Citomegalovirus, Aspergillus and Toxoplasma gondii. The impressive development of diagnostical techniques and of prophylactic and therapeutical possibilities suggest the convenience of a multidisciplinar approach to these complications.

Antimicrobial Photodynamic Therapy as an Adjunct for Clinical Partial Removal of Deciduous Carious Tissue: A Minimally Invasive Approach.

PubMed

Ornellas, Pâmela O; Antunes, Leonardo S; Motta, Paula C; Mendonça, Caroline; Póvoa, Helvécio; Fontes, Karla; Iorio, Natalia; Antunes, Lívia A A

2018-06-20

This study aimed to evaluate the use of antimicrobial photodynamic therapy (aPDT) as an adjunct for minimally invasive treatment (partial removal of carious tissue - PRCT) of deciduous carious tissue evaluating its efficacy in reducing microorganisms. For that, a clinical study was design including children with deciduous molars with active deep caries lesions (DCL). PRCT was performed and remaining dentin was treated with 100 μg/mL methylene blue solution (5 min) and than irradiated with a low power laser emitting red light (InGaAIP - indium gallium aluminum phosphide; λ = 660nm; 100mW; 300 J/cm²; 90s; 9J). The colony forming units (CFU) count after PRCT and after PRCT + aPDT/mg of dentin were compared for total microorganisms, including Candida spp., the mutans streptococci group, Streptococcus spp. and Lactobacillus spp. The dentin was classified (color, consistency and humidity). The microbial reduction varied from 69.88% to 86.29% and was significantly observed for total microorganisms, mutans streptococci, Streptococcus spp. and Lactobacillus spp (p<0.001). The dentin type did not influence reduction of microorganisms (p>0.05). The aPDT presents a promising future for clinical use as an adjunct for the reduction of microorganisms in PRCT of DCL in all kinds of dentin. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Comparison of methods for the identification of microorganisms isolated from blood cultures.

PubMed

Monteiro, Aydir Cecília Marinho; Fortaleza, Carlos Magno Castelo Branco; Ferreira, Adriano Martison; Cavalcante, Ricardo de Souza; Mondelli, Alessandro Lia; Bagagli, Eduardo; da Cunha, Maria de Lourdes Ribeiro de Souza

2016-08-05

Bloodstream infections are responsible for thousands of deaths each year. The rapid identification of the microorganisms causing these infections permits correct therapeutic management that will improve the prognosis of the patient. In an attempt to reduce the time spent on this step, microorganism identification devices have been developed, including the VITEK(®) 2 system, which is currently used in routine clinical microbiology laboratories. This study evaluated the accuracy of the VITEK(®) 2 system in the identification of 400 microorganisms isolated from blood cultures and compared the results to those obtained with conventional phenotypic and genotypic methods. In parallel to the phenotypic identification methods, the DNA of these microorganisms was extracted directly from the blood culture bottles for genotypic identification by the polymerase chain reaction (PCR) and DNA sequencing. The automated VITEK(®) 2 system correctly identified 94.7 % (379/400) of the isolates. The YST and GN cards resulted in 100 % correct identifications of yeasts (15/15) and Gram-negative bacilli (165/165), respectively. The GP card correctly identified 92.6 % (199/215) of Gram-positive cocci, while the ANC card was unable to correctly identify any Gram-positive bacilli (0/5). The performance of the VITEK(®) 2 system was considered acceptable and statistical analysis showed that the system is a suitable option for routine clinical microbiology laboratories to identify different microorganisms.

[Potential antimicrobial drug interactions in clinical practice: consequences of polypharmacy and multidrug resistance].

PubMed

Martínez-Múgica, Cristina

2015-12-01

Polypharmacy is a growing problem nowadays, which can increase the risk of potential drug interactions, and result in a loss of effectiveness. This is particularly relevant to the anti-infective therapy, especially when infection is produced by resistant bacteria, because therapeutic options are limited and interactions can cause treatment failure. All antimicrobial prescriptions were retrospectively reviewed during a week in the Pharmacy Department, in order to detect potential drug-interactions and analysing their clinical significance. A total of 314 antimicrobial prescriptions from 151 patients were checked. There was at least one potential interaction detected in 40% of patients, being more frequent and severe in those infected with multidrug-resistant microorganisms. Drugs most commonly involved were quinolones, azoles, linezolid and vancomycin. Potential drug interactions with antimicrobial agents are a frequent problem that can result in a loss of effectiveness. This is why they should be detected and avoided when possible, in order to optimize antimicrobial therapy, especially in case of multidrug resistant infections.

Impact of an oil-based lubricant on the effectiveness of the sterilization processes .

PubMed

Rutala, William A; Gergen, Maria F; Weber, David J

2008-01-01

Surgical instruments, including hinged instruments, were inoculated with test microorganisms (ie, methicillin-resistant Staphylococcus aureus, approximately 2 x 10(6) colony-forming units [cfu]; Pseudomonas aeruginosa, approximately 3 x 10(6) cfu; Escherichia coli, approximately 2 x 10(5) cfu; vancomycin-resistant enterococci, 1 x 10(5) cfu; Geobacillus stearothermophilus spores, 2 x 10(5) cfu or more; or Bacillus atrophaeus spores, 9 x 10(4) cfu or more), coated with an oil-based lubricant (hydraulic fluid), subjected to a sterilization process, and then samples from the instruments were cultured. We found that the oil-based lubricant did not alter the effectiveness of the sterilization process because high numbers of clinically relevant bacteria and standard test spores (which are relatively resistant to the sterilization process) were inactivated.

In situ antimicrobial behavior of materials with copper-based additives in a hospital environment.

PubMed

Palza, Humberto; Nuñez, Mauricio; Bastías, Roberto; Delgado, Katherine

2018-06-01

Copper and its alloys are effective antimicrobial surface materials in the laboratory and in clinical trials. Copper has been used in the healthcare setting to reduce environmental contamination, and thus prevent healthcare-associated infections, complementing traditional protocols. The addition of copper nanoparticles to polymer/plastic matrices can also produce antimicrobial materials, as confirmed under laboratory conditions. However, there is a lack of studies validating the antimicrobial effects of these nanocomposite materials in clinical trials. To satisfy this issue, plastic waiting room chairs with embedded metal copper nanoparticles, and metal hospital IV pools coated with an organic paint with nanostructured zeolite/copper particles were produced and tested in a hospital environment. These prototypes were sampled once weekly for 10 weeks and the viable microorganisms were analysed and compared with the copper-free materials. In the waiting rooms, chairs with copper reduced by around 73% the total viable microorganisms present, showing activity regardless of the microorganism tested. Although there were only low levels of microorganisms in the IV pools installed in operating rooms because of rigorous hygiene protocols, samples with copper presented lower total viable microorganisms than unfilled materials. Some results did not have statistical significance because of the low load of microorganisms; however, during at least three weeks the IV pools with copper had reduced levels of microorganisms by a statistically significant 50%. These findings show for the first time the feasibility of utilizing the antimicrobial property of copper by adding nanosized fillers to other materials in a hospital environment. Copyright © 2018 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Natural Diversity in Heat Resistance of Bacteria and Bacterial Spores: Impact on Food Safety and Quality.

PubMed

den Besten, Heidy M W; Wells-Bennik, Marjon H J; Zwietering, Marcel H

2018-03-25

Heat treatments are widely used in food processing often with the aim of reducing or eliminating spoilage microorganisms and pathogens in food products. The efficacy of applying heat to control microorganisms is challenged by the natural diversity of microorganisms with respect to their heat robustness. This review gives an overview of the variations in heat resistances of various species and strains, describes modeling approaches to quantify heat robustness, and addresses the relevance and impact of the natural diversity of microorganisms when assessing heat inactivation. This comparison of heat resistances of microorganisms facilitates the evaluation of which (groups of) organisms might be troublesome in a production process in which heat treatment is critical to reducing the microbial contaminants, and also allows fine-tuning of the process parameters. Various sources of microbiological variability are discussed and compared for a range of species, including spore-forming and non-spore-forming pathogens and spoilage organisms. This benchmarking of variability factors gives crucial information about the most important factors that should be included in risk assessments to realistically predict heat inactivation of bacteria and spores as part of the measures for controlling shelf life and safety of food products.

Anaerobic psychrophiles from Alaska, Antarctica, and Patagonia: implications to possible life on Mars and Europa

NASA Astrophysics Data System (ADS)

Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph D.

2002-02-01

Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryopreserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 degree(s)C. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep-sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica. The microbial extremophiles recovered from permafrost, ice, cold pools and deep-sea sediments may provide information relevant to the question of how and where we should search for evidence of extant or extinct microbial life elsewhere in the Cosmos.

Anaerobic Psychrophiles from Alaska, Antarctica, and Patagonia: Implications to Possible Life on Mars and Europa

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph

2002-01-01

Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryopreserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 C. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep-sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica. The microbial extremophiles recovered from permafrost, ice, cold pools and deep-sea sediments may provide information relevant to the question of how and where we should search for evidence of extant or extinct microbial life elsewhere in the Cosmos.

Anaerobic Psychrophiles from Alaska, Antarctica, and Patagonia: Implications to Possible Life on Mars and Europa

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Pikuta, Elena V.; Marsic, Damien; Ng, Joseph; Six, N. Frank (Technical Monitor)

2001-01-01

Microorganisms preserved within the permafrost, glaciers, and polar ice sheets of planet Earth provide analogs for microbial life forms that may be encountered in ice or permafrost of Mars, Europa, Callisto, Ganymede, asteroids, comets or other frozen worlds in the Cosmos. The psychrophilic and psychrotolerant microbes of the terrestrial cryosphere help establish the thermal and temporal limitations of life on Earth and provide clues to where and how we should search for evidence of life elsewhere in the Universe. For this reason, the cold-loving microorganisms are directly relevant to Astrobiology. Cryo-preserved microorganisms can remain viable (in deep anabiosis) in permafrost and ice for millions of years. Permafrost, ice wedges, pingos, glaciers, and polar ice sheets may contain intact ancient DNA, lipids, enzymes, proteins, genes, and even frozen and yet viable ancient microbiota. Some microorganisms carry out metabolic processes in water films and brine, acidic, or alkaline channels in permafrost or ice at temperatures far below 0 T. Complex microbial communities live in snow, ice-bubbles, cryoconite holes on glaciers and ancient microbial ecosystems are cryopreserved within the permafrost, glaciers, and polar caps. In the Astrobiology group of the NASA Marshall Space Flight Center and the University of Alabama at Huntsville, we have employed advanced techniques for the isolation, culture, and phylogenetic analysis of many types of microbial extremophiles. We have also used the Environmental Scanning Electron Microscope to study the morphology, ultra-microstructure and chemical composition of microorganisms in ancient permafrost and ice. We discuss several interesting and novel anaerobic microorganisms that we have isolated and cultured from the Pleistocene ice of the Fox Tunnel of Alaska, guano of the Magellanic Penguin, deep sea sediments from the vicinity of the Rainbow Hydrothermal Vent and enrichment cultures from ice of the Patriot Hills of Antarctica. The microbial extremophiles recovered from permafrost, ice, cold pools and deep sea sediments may provide information relevant to the question of how and where we should search for evidence of extant or extinct microbial life elsewhere in the Cosmos.

Nutraceuticals for Skin Care: A Comprehensive Review of Human Clinical Studies

PubMed Central

Pérez-Sánchez, Almudena; Micol, Vicente

2018-01-01

The skin is the body’s largest organ, it participates in sensitivity and offers protection against microorganisms, chemicals and ultraviolet (UV) radiation. Consequently, the skin may suffer alterations such as photo-ageing, immune dysfunction and inflammation which may significantly affect human health. Nutraceuticals represent a promising strategy for preventing, delaying, or minimising premature ageing of the skin and also to alleviate certain skin disorders. Among them, bioactive peptides and oligosaccharides, plant polyphenols, carotenoids, vitamins and polyunsaturated fatty acids are the most widely used ingredients. Supplementation with these products has shown evidence of having an effect on the signs of ageing and protection against UV radiation ageing in several human trials. In this review, the most relevant human studies on skin nutraceuticals are evaluated and the statistical resolution, biological relevance of their results, and, the trial protocols are discussed. In conclusion, quality and rigorousness of the trials must be improved to build credible scientific evidence for skin nutraceuticals and to establish a cause-effect relationship between the ingredients the beneficial effects for the skin. PMID:29587342

Invasion of vascular cells in vitro by Porphyromonas endodontalis.

PubMed

Dorn, B R; Harris, L J; Wujick, C T; Vertucci, F J; Progulske-Fox, A

2002-04-01

The objective of this study was to determine whether laboratory strains and clinical isolates of microorganisms associated with root canal infections can invade primary cultures of cardiovascular cells. Quantitative levels of bacterial invasion of human coronary artery endothelial cells (HCAEC) and coronary artery smooth muscle cells (CASMC) were measured using a standard antibiotic protection assay. Transmission electron microscopy was used to confirm and visualize internalization within the vascular cells. Of the laboratory and clinical strains tested, only P. endodontalis ATCC 35406 was invasive in an antibiotic protection assay using HCAEC and CASMC. Invasion of P. endodontalis ATCC 35406 was confirmed by transmission electron microscopy. Certain microorganisms associated with endodontic infections are invasive. If bacterial invasion of the vasculature contributes to the pathogenesis of cardiovascular disease, then microorganisms in the pulp chamber represent potential pathogens.

Antimicrobial potential of Australian macrofungi extracts against foodborne and other pathogens.

PubMed

Bala, Neeraj; Aitken, Elizabeth A B; Cusack, Andrew; Steadman, Kathryn J

2012-03-01

Basidiomycetous macrofungi have therapeutic potential due to antimicrobial activity but little information is available for Australian macrofungi. Therefore, the present study investigated 12 Australian basidiomycetous macrofungi, previously shown to have promising activity against Staphylococcus aureus and Escherichia coli, for their antimicrobial potential against a range of other clinically relevant micro-organisms. Fruiting bodies were collected from across Queensland, Australia, freeze-dried and sequentially extracted with water and ethanol. The crude extracts were tested at 10 mg/mL and 1 mg/mL against six pathogens including two Gram-positive and two Gram-negative bacteria along with two fungi using a high throughput 96-well microplate bioassay. A degree of specificity in activity was exhibited by the water extract of Ramaria sp. (Gomphaceae) and the ethanol extracts of Psathyrella sp. (Psathyrellaceae) and Hohenbuehelia sp., which inhibited the growth of the two fungal pathogens used in the assay. Similarly, the ethanol extract of Fomitopsis lilacinogilva (Fomitopsidaceae) was active against the Gram-positive bacteria B. cereus only. Activity against a wider range of the microorganisms used in the assay was exhibited by the ethanol extract of Ramaria sp. and the water extract of Hohenbuehelia sp. (Pleurotaceae). These macrofungi can serve as new sources for the discovery and development of much needed new antimicrobials. Copyright © 2011 John Wiley & Sons, Ltd.

Detection of Legionella pneumophila on clinical samples and susceptibility assessment by flow cytometry.

PubMed

Faria-Ramos, I; Costa-de-Oliveira, S; Barbosa, J; Cardoso, A; Santos-Antunes, J; Rodrigues, A G; Pina-Vaz, C

2012-12-01

Culture in selective media represents the standard diagnostic method to confirm Legionella pneumophila infection, despite requiring a prolonged incubation period; antigen detection by immunofluorescence (IFS) and molecular techniques are also available, but they do not allow antimicrobial susceptibility evaluation. Our objective was to optimise flow cytometry (FC) protocols for the detection of L. pneumophila in respiratory samples and for susceptibility evaluation to first-line drugs. In order to optimise the FC protocol, a specific monoclonal antibody, conjugated with fluorescein isothiocyanate (FITC), was incubated with type strain L. pneumophila ATCC 33152. The limit of detection was established by analysing serial dilutions of bacterial suspension; specificity was assayed using mixtures of prokaryotic and eukaryotic microorganisms. The optimised FC protocol was used to assess 50 respiratory samples and compared with IFS evaluation. The susceptibility profile to erythromycin, ciprofloxacin and levofloxacin was evaluated by FC using propidium iodide and SYBR Green fluorescent dyes; the results were compared with the Etest afterwards. The optimal specific antibody concentration was 20 μg/ml; 10(2)/ml Legionella organisms were detected by this protocol and no cross-reactions with other microorganisms were detected. The five positive respiratory samples (10 %) determined by IFS were also detected by FC, showing 100 % correlation. After 1 h of incubation at 37 °C with different antimicrobials, SYBR Green staining could discriminate between treated and non-treated cells. A novel flow cytometric approach for the detection of L. pneumophila from clinical samples and susceptibility evaluation is now available, representing an important step forward for the diagnosis of this very relevant agent.

Standardized Procedures for Use of Nucleic Acid-Based Tools

EPA Science Inventory

Groundwater and soil samples are frequently analyzed using molecular biological tools (MBTs) to detect unique genetic biomarkers associated with Dehalococcoides (Dhc) and other environmentally relevant microorganisms. The results of these analyses are increasingly used b...

Microbial degradation of terrigenous dissolved organic matter and potential consequences for carbon cycling in brown-water streams.

PubMed

Fasching, Christina; Behounek, Barbara; Singer, Gabriel A; Battin, Tom J

2014-05-15

Streams receive substantial terrestrial deliveries of dissolved organic matter (DOM). The chromophoric (CDOM) fraction of terrestrial deliveries confers the brown colour to streamwater, often understood as browning, and plays a central role in aquatic photochemistry and is generally considered resistant to microbial metabolism. To assess the relevance of terrigenous DOM for carbon fluxes mediated by stream microorganisms, we determined the bioavailable fraction of DOM and microbial carbon use efficiency (CUE), and related these measures to partial pressure of CO2 in headwater streams spanning across a browning gradient. Fluorescence and absorbance analyses revealed high molecular weight and aromaticity, and elevated contributions from humic-like components to characterize terrestrial CDOM. We found that microorganisms metabolized this material at the cost of low CUE and shifted its composition (from fluorescence and absorbance) towards less aromatic and low-molecular weight compounds. Respiration (from CUE) was related to CO2 supersaturation in streams and this relationship was modulated by DOM composition. Our findings imply that terrigenous DOM is respired by microorganisms rather than incorporated into their biomass, and that this channelizes terrigenous carbon to the pool of CO2 potentially outgassing from streams into the atmosphere. This finding may gain relevance as major terrigenous carbon stores become mobilized and browning progresses.

Microbial degradation of terrigenous dissolved organic matter and potential consequences for carbon cycling in brown-water streams

PubMed Central

Fasching, Christina; Behounek, Barbara; Singer, Gabriel A.; Battin, Tom J.

2014-01-01

Streams receive substantial terrestrial deliveries of dissolved organic matter (DOM). The chromophoric (CDOM) fraction of terrestrial deliveries confers the brown colour to streamwater, often understood as browning, and plays a central role in aquatic photochemistry and is generally considered resistant to microbial metabolism. To assess the relevance of terrigenous DOM for carbon fluxes mediated by stream microorganisms, we determined the bioavailable fraction of DOM and microbial carbon use efficiency (CUE), and related these measures to partial pressure of CO2 in headwater streams spanning across a browning gradient. Fluorescence and absorbance analyses revealed high molecular weight and aromaticity, and elevated contributions from humic-like components to characterize terrestrial CDOM. We found that microorganisms metabolized this material at the cost of low CUE and shifted its composition (from fluorescence and absorbance) towards less aromatic and low-molecular weight compounds. Respiration (from CUE) was related to CO2 supersaturation in streams and this relationship was modulated by DOM composition. Our findings imply that terrigenous DOM is respired by microorganisms rather than incorporated into their biomass, and that this channelizes terrigenous carbon to the pool of CO2 potentially outgassing from streams into the atmosphere. This finding may gain relevance as major terrigenous carbon stores become mobilized and browning progresses. PMID:24828296

Microbiology and atmospheric processes: an upcoming era of research on bio-meteorology

NASA Astrophysics Data System (ADS)

Morris, C. E.; Sands, D. C.; Bardin, M.; Jaenicke, R.; Vogel, B.; Leyronas, C.; Ariya, P. A.; Psenner, R.

2008-01-01

For the past 200 years, the field of aerobiology has explored the abundance, diversity, survival and transport of micro-organisms in the atmosphere. Micro-organisms have been explored as passive and severely stressed riders of atmospheric transport systems. Recently, an interest in the active roles of these micro-organisms has emerged along with proposals that the atmosphere is a global biome for microbial metabolic activity and perhaps even multiplication. As part of a series of papers on the sources, distribution and roles in atmospheric processes of biological particles in the atmosphere, here we describe the pertinence of questions relating to the potential roles that air-borne micro-organisms might play in meteorological phenomena. For the upcoming era of research on the role of air-borne micro-organisms in meteorological phenomena, one important challenge is to go beyond descriptions of abundance of micro-organisms in the atmosphere toward an understanding of their dynamics in terms of both biological and physico-chemical properties and of the relevant transport processes at different scales. Another challenge is to develop this understanding under contexts pertinent to their potential role in processes related to atmospheric chemistry, the formation of clouds, precipitation and radiative forcing. This will require truly interdisciplinary approaches involving collaborators from the biological and physical sciences, from disciplines as disparate as agronomy, microbial genetics and atmosphere physics, for example.

[Efficacy of probiotic feed additives: guidelines for the evaluation of the efficiency of microorganisms in dogs, cats, and horses].

PubMed

Lahrssen, M; Zentek, J

2002-01-01

Probiotic microorganisms are frequently in use as feed additives for farm and pet animals. For admission for the common market products have to be tested according to the feed additive directive 70/524/EC. The dossier for admission has to comprise data of efficiency as laid down in the directive 87/153/EC. During the last years it became obvious after the evaluation of several dossiers, that no definitive criteria for the assessment of efficacy were available for dogs, cats and horses (84/153/EC). Aspects like the promotion of animal production are not relevant in this context. Therefore, the European commission launched the directive for the evaluation of efficacy of microorganisms for dogs, cats and horses, that supports the evaluation of microbial feed additives and which is described in this paper.

Compost supplementation with nutrients and microorganisms in composting process.

PubMed

Sánchez, Óscar J; Ospina, Diego A; Montoya, Sandra

2017-11-01

The composting is an aerobic, microorganism-mediated, solid-state fermentation process by which different organic materials are transformed into more stable compounds. The product obtained is the compost, which contributes to the improvement of physical, chemical and microbiological properties of the soil. However, the compost usage in agriculture is constrained because of its long-time action and reduced supply of nutrients to the crops. To enhance the content of nutrients assimilable by the plants in the compost, its supplementation with nutrients and inoculation with microorganisms have been proposed. The objective of this work was to review the state of the art on compost supplementation with nutrients and the role played by the microorganisms involved (or added) in their transformation during the composting process. The phases of composting are briefly compiled and different strategies for supplementation are analyzed. The utilization of nitrogenous materials and addition of microorganisms fixing nitrogen from the atmosphere or oxidizing ammonia into more assimilable for plants nitrogenous forms are analyzed. Several strategies for nitrogen conservation during composting are presented as well. The supplementation with phosphorus and utilization of microorganisms solubilizing phosphorus and potassium are also discussed. Main groups of microorganisms relevant during the composting process are described as well as most important strategies to identify them. In general, the development of this type of nutrient-enriched bio-inputs requires research and development not only in the supplementation of compost itself, but also in the isolation and identification of microorganisms and genes allowing the degradation and conversion of nitrogenous substances and materials containing potassium and phosphorus present in the feedstocks undergoing the composting process. In this sense, most important research trends and strategies to increase nutrient content in the compost are provided in this work. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid Microbial Sample Preparation from Blood Using a Novel Concentration Device

PubMed Central

Boardman, Anna K.; Campbell, Jennifer; Wirz, Holger; Sharon, Andre; Sauer-Budge, Alexis F.

2015-01-01

Appropriate care for bacteremic patients is dictated by the amount of time needed for an accurate diagnosis. However, the concentration of microbes in the blood is extremely low in these patients (1–100 CFU/mL), traditionally requiring growth (blood culture) or amplification (e.g., PCR) for detection. Current culture-based methods can take a minimum of two days, while faster methods like PCR require a sample free of inhibitors (i.e., blood components). Though commercial kits exist for the removal of blood from these samples, they typically capture only DNA, thereby necessitating the use of blood culture for antimicrobial testing. Here, we report a novel, scaled-up sample preparation protocol carried out in a new microbial concentration device. The process can efficiently lyse 10 mL of bacteremic blood while maintaining the microorganisms’ viability, giving a 30‑μL final output volume. A suite of six microorganisms (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, and Candida albicans) at a range of clinically relevant concentrations was tested. All of the microorganisms had recoveries greater than 55% at the highest tested concentration of 100 CFU/mL, with three of them having over 70% recovery. At the lowest tested concentration of 3 CFU/mL, two microorganisms had recoveries of ca. 40–50% while the other four gave recoveries greater than 70%. Using a Taqman assay for methicillin-sensitive S. aureus (MSSA)to prove the feasibility of downstream analysis, we show that our microbial pellets are clean enough for PCR amplification. PCR testing of 56 spiked-positive and negative samples gave a specificity of 0.97 and a sensitivity of 0.96, showing that our sample preparation protocol holds great promise for the rapid diagnosis of bacteremia directly from a primary sample. PMID:25675242

[Mass spectrometry in the clinical microbiology laboratory].

PubMed

Jordana-Lluch, Elena; Martró Català, Elisa; Ausina Ruiz, Vicente

2012-12-01

Infectious diseases are still a cause of high mortality and morbidity rates. Current microbiological diagnostic methods are based on culture and phenotypic identification of isolated microorganisms, which can be obtained in about 24-48 h. Given that the microbiological identification is of major importance for patient management, new diagnostic methods are needed in order to detect and identify microorganisms in a timely and accurate manner. Over the last few years, several molecular techniques based on the amplification of microbial nucleic acids have been developed with the aim of reducing the time needed for the identification of the microorganisms involved in different infectious processes. On the other hand, mass spectrometry has emerged as a rapid and consistent alternative to conventional methods for microorganism identification. This review describes the most widely used mass spectrometry technologies -matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization time-of-flight (ESI-TOF)-, both for protein and nucleic acid analysis, as well as the commercial platforms available. Related publications of most interest in clinical microbiology are also reviewed. Copyright © 2011 Elsevier España, S.L. All rights reserved.

[Microorganism test systems and antibiograms useful for the proper use of antibacterial agents].

PubMed

Takahashi, Shunji

2010-07-01

Antimicrobial agents are used for the accurate diagnosis of infectious diseases and effective implementation of antibacterial chemotherapy. The role of microbiological technologists is to provide data from microorganism tests useful for rapid infection treatment. Gram strain can be used to observe microorganisms and neutrophils from specimens of a patient. It is also possible to estimate the kinds of microorganism. If bacterial infectious disease is negative, there is no need for antibacterial chemotherapy. The applied dose of antibacterial agents is different in every hospital. Also, there is a difference in the percentage antibacterial agent susceptibility of isolates. Antibiograms must be created to investigate local factors. For empiric therapy, antibiograms are useful when choosing antibacterial agents showing marked efficacy against the clinical isolate. Microorganism test systems which are useful for the proper use of antibacterial agents are necessary to facilitate safe antibacterial chemotherapy and prevent the development of resistant bacteria. We report a microorganism test system employed at the Sapporo City General Hospital.

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

PubMed Central

Naccache, Samia N.; Federman, Scot; Veeraraghavan, Narayanan; Zaharia, Matei; Lee, Deanna; Samayoa, Erik; Bouquet, Jerome; Greninger, Alexander L.; Luk, Ka-Cheung; Enge, Barryett; Wadford, Debra A.; Messenger, Sharon L.; Genrich, Gillian L.; Pellegrino, Kristen; Grard, Gilda; Leroy, Eric; Schneider, Bradley S.; Fair, Joseph N.; Martínez, Miguel A.; Isa, Pavel; Crump, John A.; DeRisi, Joseph L.; Sittler, Taylor; Hackett, John; Miller, Steve; Chiu, Charles Y.

2014-01-01

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7–500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times. PMID:24899342

Comparison of acridine orange and Gram stains for detection of microorganisms in cerebrospinal fluid and other clinical specimens.

PubMed Central

Lauer, B A; Reller, L B; Mirrett, S

1981-01-01

Acridine orange, a fluorochrome strain, is potentially superior to the Gram stain in the direct microscopic examination of clinical specimens because it gives striking differential staining between bacteria and background cells and debris. Its value in clinical laboratories was evaluated by testing 209 cerebrospinal fluids and 288 other body fluids, tissues, and exudates by both techniques. Smears were made in duplicate, fixed with methanol, stained, and examined without knowledge of the result of the companion smear or culture. Overall, acridine orange was slightly more sensitive than the Gram stain (acridine orange, 59.9%; Gram stain, 55.8%) and equally specific in detecting microorganisms. One smear was falsely positive by the Gram stain; none was falsely positive by the acridine orange stain. We conclude that acridine orange staining is a sensitive method for screening clinical specimens and reviewing selected specimens that are purulent, but negative by the Gram stain. Bloody fluids, thick exudates, and other normally difficult-to-read specimens were easily and quickly examined. We recommend, however, that positive smears be reexamined with the Gram stain to confirm the result and determine the Gram reaction of the microorganisms. PMID:6168652

Mannose-binding lectin binds to a range of clinically relevant microorganisms and promotes complement deposition.

PubMed

Neth, O; Jack, D L; Dodds, A W; Holzel, H; Klein, N J; Turner, M W

2000-02-01

Mannose-binding lectin (MBL) is a collagenous serum lectin believed to be of importance in innate immunity. Genetically determined low levels of the protein are known to predispose to infections. In this study the binding of purified MBL to pathogens isolated from immunocompromised children was investigated by flow cytometry. Diverse Candida species, Aspergillus fumigatus, Staphylococcus aureus, and beta-hemolytic group A streptococci exhibited strong binding of MBL, whereas Escherichia coli, Klebsiella species, and Haemophilus influenzae type b were characterized by heterogeneous binding patterns. In contrast, beta-hemolytic group B streptococci, Streptococcus pneumoniae, and Staphylococcus epidermidis showed low levels of binding. Bound MBL was able to promote C4 deposition in a concentration-dependent manner. We conclude that MBL may be of importance in first-line immune defense against several important pathogens.

Local oxygen therapy for treating acute necrotizing periodontal disease in smokers.

PubMed

Gaggl, Alexander J; Rainer, Heribert; Grund, Eveline; Chiari, Friedrich M

2006-01-01

The main aim of treatment for acute necrotizing periodontal disease is fast and effective reduction of anaerobic destructive microorganisms to avoid periodontal damage. The effect of adjunctive local oxygen therapy in the treatment of necrotizing periodontal disease was examined in this study. Thirty patients with acute necrotizing periodontal disease were treated with the systemic antibiotics amoxicillin, clavulanic acid, and metronidazole. In 15 out of 30 patients, adjunctive local oxygen therapy was administered. The patients were followed from the first to 10th day of treatment with clinical and bacteriological examinations. The clinical examination registered gingival bleeding, periodontal probing depth, and attachment loss; to follow up microbiological colonization of the periodontal sulcus, five representative bacteria were registered by a semiquantitative DNA polymerase chain reaction test. In both groups of patients, colonization with Prevotella intermedia, Tannerella forsythensis, and Treponema denticola was initially positive. None of these three microorganisms were completely eradicated in any of the patients in the group without oxygen therapy within the first 10 days of treatment. In the group with adjunctive oxygen therapy, all patients either showed a reduction in or complete eradication of the microorganisms, resulting in more rapid clinical restitution with less periodontal destruction. Adjunctive oxygen therapy results in early eradication of pathogenic anaerobic microorganisms in cases of acute necrotizing periodontal disease. The damage to periodontal tissue is reduced.

Bio-recovery of non-essential heavy metals by intra- and extracellular mechanisms in free-living microorganisms.

PubMed

García-García, Jorge D; Sánchez-Thomas, Rosina; Moreno-Sánchez, Rafael

2016-01-01

Free-living microorganisms may become suitable models for recovery of non-essential and essential heavy metals from wastewater bodies and soils by using and enhancing their accumulating and/or leaching abilities. This review analyzes the variety of different mechanisms developed mainly in bacteria, protists and microalgae to accumulate heavy metals, being the most relevant those involving phytochelatin and metallothionein biosyntheses; phosphate/polyphosphate metabolism; compartmentalization of heavy metal-complexes into vacuoles, chloroplasts and mitochondria; and secretion of malate and other organic acids. Cyanide biosynthesis for extra-cellular heavy metal bioleaching is also examined. These metabolic/cellular processes are herein analyzed at the transcriptional, kinetic and metabolic levels to provide mechanistic basis for developing genetically engineered microorganisms with greater capacities and efficiencies for heavy metal recovery, recycling of heavy metals, biosensing of metal ions, and engineering of metalloenzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

Fast Selective Detection of Pyocyanin Using Cyclic Voltammetry

PubMed Central

Alatraktchi, Fatima AlZahra’a; Breum Andersen, Sandra; Krogh Johansen, Helle; Molin, Søren; Svendsen, Winnie E.

2016-01-01

Pyocyanin is a virulence factor uniquely produced by the pathogen Pseudomonas aeruginosa. The fast and selective detection of pyocyanin in clinical samples can reveal important information about the presence of this microorganism in patients. Electrochemical sensing of the redox-active pyocyanin is a route to directly quantify pyocyanin in real time and in situ in hospitals and clinics. The selective quantification of pyocyanin is, however, limited by other redox-active compounds existing in human fluids and by other metabolites produced by pathogenic bacteria. Here we present a direct selective method to detect pyocyanin in a complex electroactive environment using commercially available electrodes. It is shown that cyclic voltammetry measurements between −1.0 V to 1.0 V reveal a potential detection window of pyocyanin of 0.58–0.82 V that is unaffected by other redox-active interferents. The linear quantification of pyocyanin has an R2 value of 0.991 across the clinically relevant concentration range of 2–100 µM. The proposed method was tested on human saliva showing a standard deviation of 2.5% ± 1% (n = 5) from the known added pyocyanin concentration to the samples. This inexpensive procedure is suggested for clinical use in monitoring the presence and state of P. aeruginosa infection in patients. PMID:27007376

Fast Selective Detection of Pyocyanin Using Cyclic Voltammetry.

PubMed

Alatraktchi, Fatima AlZahra'a; Andersen, Sandra Breum; Johansen, Helle Krogh; Molin, Søren; Svendsen, Winnie E

2016-03-19

Pyocyanin is a virulence factor uniquely produced by the pathogen Pseudomonas aeruginosa. The fast and selective detection of pyocyanin in clinical samples can reveal important information about the presence of this microorganism in patients. Electrochemical sensing of the redox-active pyocyanin is a route to directly quantify pyocyanin in real time and in situ in hospitals and clinics. The selective quantification of pyocyanin is, however, limited by other redox-active compounds existing in human fluids and by other metabolites produced by pathogenic bacteria. Here we present a direct selective method to detect pyocyanin in a complex electroactive environment using commercially available electrodes. It is shown that cyclic voltammetry measurements between -1.0 V to 1.0 V reveal a potential detection window of pyocyanin of 0.58-0.82 V that is unaffected by other redox-active interferents. The linear quantification of pyocyanin has an R² value of 0.991 across the clinically relevant concentration range of 2-100 µM. The proposed method was tested on human saliva showing a standard deviation of 2.5% ± 1% (n = 5) from the known added pyocyanin concentration to the samples. This inexpensive procedure is suggested for clinical use in monitoring the presence and state of P. aeruginosa infection in patients.

Pulsed electric field processing of different fruit juices: impact of pH and temperature on inactivation of spoilage and pathogenic micro-organisms.

PubMed

Timmermans, R A H; Nierop Groot, M N; Nederhoff, A L; van Boekel, M A J S; Matser, A M; Mastwijk, H C

2014-03-03

Pulsed electrical field (PEF) technology can be used for the inactivation of micro-organisms and therefore for preservation of food products. It is a mild technology compared to thermal pasteurization because a lower temperature is used during processing, leading to a better retention of the quality. In this study, pathogenic and spoilage micro-organisms relevant in refrigerated fruit juices were studied to determine the impact of process parameters and juice composition on the effectiveness of the PEF process to inactivate the micro-organisms. Experiments were performed using a continuous-flow PEF system at an electrical field strength of 20 kV/cm with variable frequencies to evaluate the inactivation of Salmonella Panama, Escherichia coli, Listeria monocytogenes and Saccharomyces cerevisiae in apple, orange and watermelon juices. Kinetic data showed that under the same conditions, S. cerevisiae was the most sensitive micro-organism, followed by S. Panama and E. coli, which displayed comparable inactivation kinetics. L. monocytogenes was the most resistant micro-organism towards the treatment conditions tested. A synergistic effect between temperature and electric pulses was observed at inlet temperatures above 35 °C, hence less energy for inactivation was required at higher temperatures. Different juice matrices resulted in a different degree of inactivation, predominantly determined by pH. The survival curves were nonlinear and could satisfactorily be modeled with the Weibull model. Copyright © 2013 Elsevier B.V. All rights reserved.

[Complicated urinary tract infections--from the perspective of the medical technologist].

PubMed

Nagasawa, Zenzo

2002-07-01

We would like to propose re-establishment of the protocol for ordering a clinical microbiology laboratory test after a bedside screening test using urine reagent strip when urinary tract infection is suspected. Media for isolation shall be chosen by the clinical microbiology laboratory after checking turbidity and microscopic examination of the urine specimen. In cases of complicated urinary tract infections, quantitative culture should be performed to investigate changes in the number of microorganism to grasp condition of super infection. In such infections, there are many cases in which multiple microorganism growth including glucose non-fermenting gram-negative bacilli can be recognized. Therefore, it is necessary to inspect colonies on media as long as possible (24 hrs culture may be short in some cases). The protocol for microorganism identification and susceptibility test for such specimen varies in each laboratory, considering the Health Insurance Point System (reimbursement system by MHW). It is necessary to communicate with physicians and to refer to past results to proceed with the laboratory test properly. Therefore, a Certified Clinical Microbiology Medical Technologist is needed and the role played by such staff is important.

Clinical characteristics and outcomes of the meningitides in systemic lupus erythematosus.

PubMed

Baizabal-Carvallo, José Fidel; Delgadillo-Márquez, German; Estañol, Bruno; García-Ramos, Guillermo

2009-01-01

The meningitides are rare but well-identified complications in patients with systemic lupus erythematosus (SLE). To determine the clinical characteristics, risk factors, prevalence and outcomes of the meningitides (septic and aseptic) in patients with SLE. From January 1988 to December 2006, we identified patients with SLE and septic or aseptic meningitis. We identified 25 episodes of meningitis in 23 patients with SLE, from a total of 1,411 SLE patients (1.63%); in 15 out of 25 episodes, a microorganism was identified. Mycobacterium tuberculosis, Listeria monocytogenes and Criptococcus neoformans represented the main microorganisms. In 10 episodes, aseptic meningitis was diagnosed. Lymphopenia, steroid use, chronic damage and systemic activity of SLE were frequent in both kinds of meningitis. Although the clinical presentation did not differ significantly, patients with septic meningitis had more residual neurological deficits (p = 0.04). Meningitis was observed in about 1.6% of the patients with SLE; in 40% of the cases, no microorganism could be isolated. A residual neurological deficit was more common in patients with septic meningitis. Copyright (c) 2008 S. Karger AG, Basel.

The Biogeography of Putative Microbial Antibiotic Production

PubMed Central

Bryant, Jessica A.; Charkoudian, Louise K.; Docherty, Kathryn M.; Jones, Evan; Kembel, Steven W.; Green, Jessica L.; Bohannan, Brendan J. M.

2015-01-01

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics. PMID:26102275

High pressure inactivation of relevant target microorganisms in poultry meat products and the evaluation of pressure-induced protein denaturation of marinated poultry under different high pressure treatments

NASA Astrophysics Data System (ADS)

Schmidgall, Johanna; Hertel, Christian; Bindrich, Ute; Heinz, Volker; Toepfl, Stefan

2011-03-01

In this study, the possibility of extending shelf life of marinated poultry meat products by high pressure processing was evaluated. Relevant spoilage and pathogenic strains were selected and used as target microorganisms (MOs) for challenge experiments. Meat and brine were inoculated with MOs and treated at 450 MPa, 4 °C for 3 min. The results of inactivation show a decreasing pressure tolerance in the series Lactobacillus > Arcobacter > Carnobacterium > Bacillus cereus > Brochothrix thermosphacta > Listeria monocytogenes. Leuconostoc gelidum exhibited the highest pressure tolerance in meat. A protective effect of poultry meat was found for L. sakei and L. gelidum. In parallel, the influence of different marinade formulations (pH, carbonates, citrates) on protein structure changes during a pressure treatment was investigated. Addition of sodium carbonate shows a protection against denaturation of myofibrillar proteins and provides a maximum water-holding capacity. Caustic marinades allowed a higher retention of product characteristics than low-pH marinades.

Safety of the Surrogate Microorganism Enterococcus faecium NRRL B-2354 for Use in Thermal Process Validation

PubMed Central

Kopit, Lauren M.; Kim, Eun Bae; Siezen, Roland J.; Harris, Linda J.

2014-01-01

Enterococcus faecium NRRL B-2354 is a surrogate microorganism used in place of pathogens for validation of thermal processing technologies and systems. We evaluated the safety of strain NRRL B-2354 based on its genomic and functional characteristics. The genome of E. faecium NRRL B-2354 was sequenced and found to comprise a 2,635,572-bp chromosome and a 214,319-bp megaplasmid. A total of 2,639 coding sequences were identified, including 45 genes unique to this strain. Hierarchical clustering of the NRRL B-2354 genome with 126 other E. faecium genomes as well as pbp5 locus comparisons and multilocus sequence typing (MLST) showed that the genotype of this strain is most similar to commensal, or community-associated, strains of this species. E. faecium NRRL B-2354 lacks antibiotic resistance genes, and both NRRL B-2354 and its clonal relative ATCC 8459 are sensitive to clinically relevant antibiotics. This organism also lacks, or contains nonfunctional copies of, enterococcal virulence genes including acm, cyl, the ebp operon, esp, gelE, hyl, IS16, and associated phenotypes. It does contain scm, sagA, efaA, and pilA, although either these genes were not expressed or their roles in enterococcal virulence are not well understood. Compared with the clinical strains TX0082 and 1,231,502, E. faecium NRRL B-2354 was more resistant to acidic conditions (pH 2.4) and high temperatures (60°C) and was able to grow in 8% ethanol. These findings support the continued use of E. faecium NRRL B-2354 in thermal process validation of food products. PMID:24413604

Microbiological survey of commercial tattoo and permanent makeup inks available in the United States.

PubMed

Nho, S W; Kim, S-J; Kweon, O; Howard, P C; Moon, M S; Sadrieh, N K; Cerniglia, C E

2018-05-01

Tattooing and use of permanent makeup (PMU) has dramatically increased over the last decade, with a concomitant increase in ink-related infections. The aim of this study was to determine whether micro-organisms are present, and if so, the number and their identification in the commercial tattoo and PMU inks available in the United States. We surveyed 85 unopened tattoo and PMU inks, purchased from 13 companies. We incubated 100 μl of ink samples on trypticase soy agar plates for bacterial growth, 7H10 Middlebrook medium for mycobacterial growth, and Sabouraud dextrose medium for fungal growth. In total, 42 inks were contaminated with micro-organisms (49%). Thirty-three inks were contaminated with bacteria, 2 inks with fungi, and 7 inks had both bacterial and fungal growth. Mycobacteria were not detected in any of the examined tattoo and PMU inks. In 26 inks, microbial concentrations ranged between 10 1 and 10 3 CFU per ml, but higher counts (>10 3 CFU per ml) were recorded in 16 inks. We identified 83 bacteria by their 16S rDNA sequences, including 20 genera and 49 species. Strains of Bacillus spp. (53%) were dominant, followed by Lysinibacillus fusiformis (7%) and Pseudomonas aeruginosa (5%). Thirty-four (41%) possibly clinically relevant strains were identified, including P. aeruginosa, Dermacoccus barathri and Roseomonas mucosa, some of which have been previously reported to be associated with human skin infections. The results indicate that commercial tattoo and PMU inks on the US market surveyed in this study contain a wide range of micro-organisms, including pathogenic bacteria. Microbial contaminants in tattoo and PMU inks are an emerging safety concern for public health. This study provides evidence that microbial contamination of tattoo and PMU inks available in the United States is more common than previously thought and highlights the importance of monitoring these products for potentially pathogenic micro-organisms. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Pneumonia due to Enterobacter cancerogenus infection.

PubMed

Demir, Tülin; Baran, Gamze; Buyukguclu, Tuncay; Sezgin, Fikriye Milletli; Kaymaz, Haci

2014-11-01

Enterobacter cancerogenus (formerly known as CDC Enteric Group 19; synonym with Enterobacter taylorae) has rarely been associated with human infections, and little is known regarding the epidemiology and clinical significance of this organism. We describe a community-acquired pneumonia case in a 44-year-old female due to E. cancerogenus. Identification and antimicrobial susceptibility of the microorganism was performed by the automatized VITEK 2 Compact system (bioMerieux, France). The clinical case suggests that E. cancerogenus is a potentially pathogenic microorganism in determined circumstances; underlying diseases such as bronchial asthma, empiric antibiotic treatment, wounds, diagnostic, or therapeutic instruments.

Selective decontamination of the digestive tract in gastrointestinal surgery: useful in infection prevention? A systematic review.

PubMed

Abis, Gabor S A; Stockmann, Hein B A C; van Egmond, Marjolein; Bonjer, Hendrik J; Vandenbroucke-Grauls, Christina M J E; Oosterling, Steven J

2013-12-01

Gastrointestinal surgery is associated with a high incidence of infectious complications. Selective decontamination of the digestive tract is an antimicrobial prophylaxis regimen that aims to eradicate gastrointestinal carriage of potentially pathogenic microorganisms and represents an adjunct to regular prophylaxis in surgery. Relevant studies were identified using bibliographic searches of MEDLINE, EMBASE, and the Cochrane database (period from 1970 to November 1, 2012). Only studies investigating selective decontamination of the digestive tract in gastrointestinal surgery were included. Two randomized clinical trials and one retrospective case-control trial showed significant benefit in terms of infectious complications and anastomotic leakage in colorectal surgery. Two randomized controlled trials in esophageal surgery and two randomized clinical trials in gastric surgery reported lower levels of infectious complications. Selective decontamination of the digestive tract reduces infections following esophageal, gastric, and colorectal surgeries and also appears to have beneficial effects on anastomotic leakage in colorectal surgery. We believe these results provide the basis for a large multicenter prospective study to investigate the role of selective decontamination of the digestive tract in colorectal surgery.

The predominant bacteria isolated from radicular cysts

PubMed Central

2013-01-01

Purpose To detect predominant bacteria associated with radicular cysts and discuss in light of the literature. Material and methods Clinical materials were obtained from 35 radicular cysts by aspiration. Cultures were made from clinical materials by modern laboratory techniques, they underwent microbiologic analysis. Results The following are microorganisms isolated from cultures: Streptococcus milleri Group (SMG) (23.8%) [Streptococcus constellatus (19.1%) and Streptococcus anginosus (4.7%)], Streptococcus sanguis (14.3%), Streptococcus mitis (4.7%), Streptococcus cremoris (4.7%), Peptostreptococcus pevotii (4.7%), Prevotella buccae (4.7%), Prevotella intermedia (4.7%), Actinomyces meyeri (4.7%), Actinomyces viscosus (4.7%), Propionibacterium propionicum (4.7%), Bacteroides capillosus (4.7%), Staphylococcus hominis (4.7%), Rothia denticariosa (4.7%), Gemella haemolysans (4.7%), and Fusobacterium nucleatum (4.7%). Conclusions Results of this study demonstrated that radicular cysts show a great variety of anaerobic and facultative anaerobic bacterial flora. It was observed that all isolated microorganisms were the types commonly found in oral flora. Although no specific microorganism was found, Streptococcus spp. bacteria (47.5%) – especially SMG (23.8%) – were predominantly found in the microorganisms isolated. Furthermore, radicular cysts might be polymicrobial originated. Although radicular cyst is an inflammatory cyst, some radicular cyst fluids might be sterile. PMID:24011184

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

PubMed

McIntyre, Alexa B R; Ounit, Rachid; Afshinnekoo, Ebrahim; Prill, Robert J; Hénaff, Elizabeth; Alexander, Noah; Minot, Samuel S; Danko, David; Foox, Jonathan; Ahsanuddin, Sofia; Tighe, Scott; Hasan, Nur A; Subramanian, Poorani; Moffat, Kelly; Levy, Shawn; Lonardi, Stefano; Greenfield, Nick; Colwell, Rita R; Rosen, Gail L; Mason, Christopher E

2017-09-21

One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.

Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS).

PubMed

Barberino, Maria Goreth; Silva, Marcio de Oliveira; Arraes, Ana Carolina Palmeiras; Correia, Luís Cláudio; Mendes, Ana Verena

Bloodstream infections (BSIs) are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30-70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94%) species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43%) of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85%) of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI. Copyright © 2017 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

Biogeography in the Air: Fungal Diversity over Land and Oceans

EPA Science Inventory

Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on...

Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production.

PubMed

Robertsen, Helene Lunde; Weber, Tilmann; Kim, Hyun Uk; Lee, Sang Yup

2018-01-01

Streptomycetes are known for their inherent ability to produce pharmaceutically relevant secondary metabolites. Discovery of medically useful, yet novel compounds has become a great challenge due to frequent rediscovery of known compounds and a consequent decline in the number of relevant clinical trials in the last decades. A paradigm shift took place when the first whole genome sequences of streptomycetes became available, from which silent or "cryptic" biosynthetic gene clusters (BGCs) were discovered. Cryptic BGCs reveal a so far untapped potential of the microorganisms for the production of novel compounds, which has spurred new efforts in understanding the complex regulation between primary and secondary metabolism. This new trend has been accompanied with development of new computational resources (genome and compound mining tools), generation of various high-quality omics data, establishment of molecular tools, and other strain engineering strategies. They all come together to enable systems metabolic engineering of streptomycetes, allowing more systematic and efficient strain development. In this review, the authors present recent progresses within systems metabolic engineering of streptomycetes for uncovering their hidden potential to produce novel compounds and for the improved production of secondary metabolites. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxacilin-resistant Coagulase-negative staphylococci (CoNS) bacteremia in a general hospital at São Paulo city, Brasil

PubMed Central

d’Azevedo, P.A.; Secchi, C.; Antunes, A.L.S.; Sales, T.; Silva, F.M.; Tranchesi, R.; Pignatari, A.C.C.

2008-01-01

In the last decades, coagulase-negative staphylococci (CoNS), especially Staphylococcus epidermidis have become an important cause of bloodstream infections. In addition, rates of methicillin-resistance among CoNS have increased substantially, leading to the use of glicopeptides for therapy. The objective of this study was to evaluate eleven consecutives clinically relevant cases of oxacillin-resistant CoNS bacteremia in a general hospital localized in São Paulo city, Brazil. Five different species were identified by different phenotypic methods, including S. epidermidis (5), S. haemolyticus (3), S. hominis (1), S. warneri (1) and S. cohnii subsp urealyticus (1). A variety of Pulsed Field Gel Electrophoresis profiles was observed by macrorestriction DNA analysis in S. epidermidis isolates, but two of three S. haemolyticus isolates presented the same profile. These data indicated the heterogeneity of the CoNS isolates, suggesting that horizontal dissemination of these microorganisms in the investigated hospital was not frequent. One S. epidermidis and one S. haemolyticus isolates were resistant to teicoplanin and susceptible to vancomycin. The selective pressure due to the use of teicoplanin in this hospital is relevant. PMID:24031279

Nanofluid slip flow over a stretching cylinder with Schmidt and Péclet number effects

NASA Astrophysics Data System (ADS)

Md Basir, Md Faisal; Uddin, M. J.; Md. Ismail, A. I.; Bég, O. Anwar

2016-05-01

A mathematical model is presented for three-dimensional unsteady boundary layer slip flow of Newtonian nanofluids containing gyrotactic microorganisms over a stretching cylinder. Both hydrodynamic and thermal slips are included. By applying suitable similarity transformations, the governing equations are transformed into a set of nonlinear ordinary differential equations with appropriate boundary conditions. The transformed nonlinear ordinary differential boundary value problem is then solved using the Runge-Kutta-Fehlberg fourth-fifth order numerical method in Maple 18 symbolic software. The effects of the controlling parameters on the dimensionless velocity, temperature, nanoparticle volume fractions and microorganism motile density functions have been illustrated graphically. Comparisons of the present paper with the existing published results indicate good agreement and supports the validity and the accuracy of our numerical computations. Increasing bioconvection Schmidt number is observed to depress motile micro-organism density function. Increasing thermal slip parameter leads to a decrease in temperature. Thermal slip also exerts a strong influence on nano-particle concentration. The flow is accelerated with positive unsteadiness parameter (accelerating cylinder) and temperature and micro-organism density function are also increased. However nano-particle concentration is reduced with positive unsteadiness parameter. Increasing hydrodynamic slip is observed to boost temperatures and micro-organism density whereas it decelerates the flow and reduces nano-particle concentrations. The study is relevant to nano-biopolymer manufacturing processes.

Methods for determining the antimicrobial susceptibility of mycobacteria.

PubMed

Alcaide, Fernando; Esteban, Jaime; González-Martin, Julià; Palacios, Juan-José

2017-10-01

Mycobacteria are a large group of microorganisms, multiple species of which are major causes of morbidity and mortality, such as tuberculosis and leprosy. At present, the emergence and spread of multidrug-resistant strains of Mycobacterium tuberculosis complex are one of the most serious health problems worldwide. Furthermore, in contrast to M. tuberculosis and Mycobacterium leprae, non-tuberculous mycobacteria (NTM) are more frequently isolated and, in many cases, treatment is based on drug susceptibility testing. This article is a review of the different methods to determine the in vitro drug susceptibility of M. tuberculosis complex and the most relevant NTM isolates. The molecular techniques currently used for rapid detection of resistance of clinical specimens are also analysed. Copyright © 2016 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Ticks collected from humans, domestic animals, and wildlife in Yucatan, Mexico

USDA-ARS?s Scientific Manuscript database

Domestic animals and wildlife play important roles as reservoirs of zoonotic pathogens that are transmitted to humans by ticks. Besides their role as vectors of several classes of microorganisms of veterinary and public health relevance, ticks also burden human and animal populations through their o...

Transfer rates of enteric microorganisms in recycled water during machine clothes washing.

PubMed

O'Toole, Joanne; Sinclair, Martha; Leder, Karin

2009-03-01

Approximately 15% of overall Australian household water usage is in the laundry; hence, a significant reduction in household drinking water demand could be achieved if potable-quality water used for clothes washing is replaced with recycled water. To investigate the microbiological safety of using recycled water in washing machines, bacteriophages MS-2 and PRD-1, Escherichia coli, and Cryptosporidium parvum oocysts were used in a series of experiments to investigate the transfer efficiency of enteric microorganisms from washing machine water to objects including hands, environmental surfaces, air, and fabric swatches. By determining the transference efficiency, it is possible to estimate the numbers of microorganisms that the user will be exposed to if recycled water with various levels of residual microorganisms is used in washing machines. Results, expressed as transfer rates to a given surface area per object, showed that the mean transfer efficiency of E. coli, bacteriophages MS-2 and PRD-1, and C. parvum oocysts from seeded water to fabric swatches ranged from 0.001% to 0.090%. Greatest exposure to microorganisms occurred through direct contact of hands with seeded water and via hand contact with contaminated fabric swatches. No microorganisms were detected in the air samples during the washing machine spin cycle, and transfer rates of bacteriophages from water to environmental surfaces were 100-fold less than from water directly to hands. Findings from this study provide relevant information that can be used to refine regulations governing recycled water and to allay public concerns about the use of recycled water.

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.

PubMed

Naccache, Samia N; Federman, Scot; Veeraraghavan, Narayanan; Zaharia, Matei; Lee, Deanna; Samayoa, Erik; Bouquet, Jerome; Greninger, Alexander L; Luk, Ka-Cheung; Enge, Barryett; Wadford, Debra A; Messenger, Sharon L; Genrich, Gillian L; Pellegrino, Kristen; Grard, Gilda; Leroy, Eric; Schneider, Bradley S; Fair, Joseph N; Martínez, Miguel A; Isa, Pavel; Crump, John A; DeRisi, Joseph L; Sittler, Taylor; Hackett, John; Miller, Steve; Chiu, Charles Y

2014-07-01

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen identification"), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times. © 2014 Naccache et al.; Published by Cold Spring Harbor Laboratory Press.

Rapid Characterization of Microorganisms by Mass Spectrometry—What Can Be Learned and How?

NASA Astrophysics Data System (ADS)

Fenselau, Catherine C.

2013-08-01

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method—everything has a mass—and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Rapid characterization of microorganisms by mass spectrometry--what can be learned and how?

PubMed

Fenselau, Catherine C

2013-08-01

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method--everything has a mass--and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Diagnosis of bacteremia in febrile neutropenic episodes in children with cancer: microbiologic and molecular approach.

PubMed

Santolaya, María E; Farfán, Mauricio J; De La Maza, Verónica; Cociña, Manuela; Santelices, Felipe; Alvarez, Ana M; Avilés, Carmen L; Becker, Ana; O'Ryan, Miguel; Román, Paulina; Salgado, Carmen; Silva, Pamela; Topelberg, Santiago; Tordecilla, Juan; Varas, Mónica; Villarroel, Milena; Viviani, Tamara; Zubieta, Marcela; Torres, Juan P

2011-11-01

Bacterial isolation using conventional microbiologic techniques rarely surpasses 25% in children with clinical and laboratory findings indicative of an invasive bacterial infection. The aim of this study was to determine the role of real-time polymerase chain reaction (RT-PCR) from whole blood samples compared with automated blood cultures (BC) in detection of relevant microorganisms causing bacteremia in episodes of high-risk febrile neutropenia (HRFN) in children with cancer. Children presenting with HRFN at 6 hospitals in Santiago, Chile, were invited to participate. Blood samples were obtained at admission for BC, and at admission and 24 hours for RT-PCR targeting DNA of Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa causing bacteremia in children with HRFN. A total of 177 HRFN episodes were evaluated from May 2009 to August 2010, of which 29 (16.3%) had positive BC, 9 (5%) positive for 1 of the 3 selected bacterial species: 5 for E. coli, 3 for S. aureus, and 1 for P. aeruginosa. RT-PCR detected 39 bacteria in 36 episodes (20%): 14 E. coli, 20 S. aureus, and 5 P. aeruginosa. The sensitivity, specificity, and positive and negative predictive values of RT-PCR compared with BC were 56%, 80%, 13%, and 97%. The final clinical diagnosis was compatible with an invasive bacterial infection in 30/36 (83%) RT-PCR-positive episodes. In our series, RT-PCR significantly improved detection of the most relevant bacteria associated with HRFN episodes. Large number of patients and close clinical monitoring, in addition to improved RT-PCR techniques will be required to fully recommend RT-PCR-based diagnosis for the routine workup of children with cancer, fever, and neutropenia.

The Antarctic cryptoendolithic ecosystem: relevance to exobiology.

PubMed

Friedmann, E I; Ocampo-Friedmann, R

1984-01-01

Cryptoendolithic microorganisms in the Antarctic desert live inside porous sandstone rocks, protected by a thin rock crust. While the rock surface is abiotic, the microclimate inside the rock is comparatively mild. These organisms may have descended from early, pre-glaciation Antarctic life forms and thus may represent the last outpost of life in a gradually deteriorating environment. Assuming that life once arose on Mars, it is conceivable that, following the loss of water, the last of surviving organisms withdrew to similar insulated microenvironments. Because such microscopic pockets have little connection with the outside environment, their detection may be difficult. The chances that the Viking lander could sample cryptoendolithic microorganisms in the Antarctic desert would be infinitesimal.

The Antarctic cryptoendolithic ecosystem - Relevance to exobiology

NASA Technical Reports Server (NTRS)

Friedmann, E. I.; Ocampo-Friedmann, R.

1984-01-01

Cryptoendolithic microorganisms in the Antarctic desert live inside porous sandstone rocks, protected by a thin rock crust. While the rock surface is abiotic, the microclimate inside the rock is comparatively mild. These organisms may have descended from early, pre-glaciation Antarctic life forms and thus may represent the last outpost of life in a gradually deteriorating environment. Assuming that life once arose on Mars, it is conceivable that, following the loss of water, the last of surviving organisms withdrew to similar insulated microenvironments. Because such microscopic pockets have little connection with the outside environment, their detection may be difficult. The chances that the Viking lander could sample cryptoendolithic microorganisms in the Antarctic desert would be infinitesimal.

Profiles and technological requirements of urogenital probiotics.

PubMed

Nader-Macías, María Elena Fátima; Juárez Tomás, María Silvina

2015-09-15

Probiotics, defined as live microorganisms that, when administered in adequate amounts, confer a health benefit on the host, are considered a valid and novel alternative for the prevention and treatment of female urogenital tract infections. Lactobacilli, the predominant microorganisms of the healthy human vaginal microbiome, can be included as active pharmaceutical ingredients in probiotics products. Several requirements must be considered or criteria fulfilled during the development of a probiotic product or formula for the female urogenital tract. This review deals with the main selection criteria for urogenital probiotic microorganisms: host specificity, potential beneficial properties, functional specifications, technological characteristics and clinical trials used to test their effect on certain physiological and pathological conditions. Further studies are required to complement the current knowledge and support the clinical applications of probiotics in the urogenital tract. This therapy will allow the restoration of the ecological equilibrium of the urogenital tract microbiome as well as the recovery of the sexual and reproductive health of women. Copyright © 2015 Elsevier B.V. All rights reserved.

Production of oils and fats by oleaginous microorganisms with an emphasis given to the potential of the nonconventional yeast Yarrowia lipolytica.

PubMed

Carsanba, E; Papanikolaou, S; Erten, H

2018-05-15

Recently, there has been a great upsurge of interest in studies related to several aspects of microbial lipid production, which is one of the top topics in relevant research fields due to the high demand of these fatty materials in food, medical, oleochemical and biofuel industries. Lipid accumulation by the so-called "oleaginous microorganisms" can generate more than 20% w/w of oil in dry biomass and is governed by a plethora of parameters, such as medium pH, incubation temperature, nutrient limitation and C/N (carbon/nitrogen) ratio, which drastically affect the lipid production bioprocess. Until now, considerable work has been undertaken to find the cheapest substrate to enable lipid fermentation by oleaginous microorganisms. This review principally details information regarding microbial lipids, suitable production conditions and focuses attention on using the yeast Yarrowia lipolytica to achieve these objectives. Lipid production by this yeast is discussed and the necessary conditions and suitable substrates are reviewed.

Mixed convection in gravity-driven thin film non-Newtonian nanofluids flow with gyrotactic microorganisms

NASA Astrophysics Data System (ADS)

Khan, Noor Saeed; Gul, Taza; Khan, Muhammad Altaf; Bonyah, Ebenezer; Islam, Saeed

Mixed convection in gravity-driven non-Newtonian nanofluid films (Casson and Williamson) flow containing both nanoparticles and gyrotactic microorganisms along a convectively heated vertical surface is investigated. The actively controlled nanofluid model boundary conditions are used to explore the liquid films flow. The study exhibits an analytical approach for the non-Newtonian thin film nanofluids bioconvection based on physical mechanisms responsible for the nanoparticles and the base fluid, such as Brownian motion and thermophoresis. Both the fluids have almost the same behaviors for the effects of all the pertinent parameters except the effect of Schmidt number on the microorganism density function where the effect is opposite. Ordinary differential equations together with the boundary conditions are obtained through similarity variables from the governing equations of the problem, which are solved by HAM (Homotopy Analysis Method). The solution is expressed through graphs and illustrated which show the influences of all the parameters. The study is relevant to novel microbial fuel cell technologies combining the nanofluid with bioconvection phenomena.

Methods to preserve potentially toxigenic fungi.

PubMed

Guimarães, Lucas Costa; Fernandes, Ana Paula; Chalfoun, Sara Maria; Batista, Luís Roberto

2014-01-01

Microorganisms are a source of many high-value compounds which are useful to every living being, such as humans, plants and animals. Since the process of isolating and improving a microorganism can be lengthy and expensive, preserving the obtained characteristic is of paramount importance, so the process does not need to be repeated. Fungi are eukaryotic, achlorophyllous, heterotrophic organisms, usually filamentous, absorb their food, can be either macro or microscopic, propagate themselves by means of spores and store glycogen as a source of storage. Fungi, while infesting food, may produce toxic substances such as mycotoxins. The great genetic diversity of the Kingdom Fungi renders the preservation of fungal cultures for many years relevant. Several international reference mycological culture collections are maintained in many countries. The methodologies that are most fit for preserving microorganisms for extended periods are based on lowering the metabolism until it reaches a stage of artificial dormancy. The goal of this study was to analyze three methods for potentially toxigenic fungal conservation (Castellani's, continuous subculture and lyophilization) and to identify the best among them.

Identification of Emerging Human Mastitis Pathogens by MALDI-TOF and Assessment of Their Antibiotic Resistance Patterns

PubMed Central

Marín, María; Arroyo, Rebeca; Espinosa-Martos, Irene; Fernández, Leónides; Rodríguez, Juan M.

2017-01-01

Lactational mastitis constitutes one of the main causes of undesired weaning, depriving the mother–infant pair from the benefits of breastfeeding; therefore, this condition should be considered a relevant public health issue. The role of specific microorganisms remains unclear since human milk cultures and antibiotic susceptibility testing (AST) are not routinely performed, despite the fact that this would be key to ensure an early and effective diagnosis and treatment. The objective of this study was to describe the culturable microbial diversity in 647 milk samples from breastfeeding women with clinical symptoms of mastitis by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF) VITEK MS technology and to analyze the antimicrobial susceptibility profiles of a collection of isolates from these samples by the VITEK 2 AST system. Staphylococcus epidermidis was the most common species isolated from mastitis samples (87.6%), while Staphylococcus aureus was detected in 22.1%. Streptococci constituted the second (68.6%) most prevalent bacterial group, with Streptococcus mitis/oralis, Streptococcus salivarius, and Streptococcus parasanguinis detected with frequencies of 40.8, 36.8, and 14.4%, respectively. The antibiotic susceptibility profiles of 642 staphylococcal isolates indicated a remarkable resistance to benzylpenicillin (88.3%) and erythromycin (67.3%) with differences between species. A high percentage of Staphylococcus isolates were resistant to at least one antibiotic (Staphylococcus hominis, 100%; S. epidermidis, 98.2%; S. aureus, 92.9%; Staphylococcus lugdunensis, 90.5%) and the percentage of multidrug-resistance (MDR) isolates was noticeable (S. hominis, 81%; S. epidermidis, 64.4%; S. aureus, 11.5%; S. lugdunensis, 10.5%). In relation to streptococcal isolates (n = 524), AST revealed high or moderate percentages of resistance to erythromycin (68.7%), benzylpenicillin (63.7%), ampicillin (51.5%), and tetracycline (30.8%). Antibiotic resistance to at least one antibiotic was detected in 97.6% of S. parasanguinis, 92.6% of S. salivarius, 83.3% of S. mitis/oralis, and 72.4% of Streptococcus vestibularis isolates. A significant number of MDR streptococcal isolates was also found (S. parasanguinis, 51.2%; S. salivarius, 39.3%; S. mitis/oralis, 34.6%; and S. vestibularis, 19%). The results highlight the important role of coagulase-negative staphylococci and streptococci as human mastitis-causing agents. Moreover, the high rates of antimicrobial resistance among these microorganisms must be contemplated as an issue of clinical relevance in relation to treatment options. PMID:28747897

Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting.

PubMed

Muhamadali, Howbeer; Subaihi, Abdu; Mohammadtaheri, Mahsa; Xu, Yun; Ellis, David I; Ramanathan, Rajesh; Bansal, Vipul; Goodacre, Royston

2016-08-15

Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the most suitable for the analysis of mixed cultures in future studies. Furthermore, our results suggest that while each of these spectroscopic approaches may favour different organisms (sample types), when combined, they would provide complementary and more in-depth knowledge (structural and/or metabolic state) of biological systems. To the best of our knowledge, this is the first time that such a comparative and combined spectroscopic study (using FT-IR, Raman and SERS) has been carried out on microbial samples.

Iron management and production of electricity by microorganisms.

PubMed

Folgosa, Filipe; Tavares, Pedro; Pereira, Alice S

2015-10-01

The increasing dependency on fossil fuels has driven researchers to seek for alternative energy sources. Renewable energy sources such as sunlight, wind, or water are the most common. However, since the 1990s, other sources for energy production have been studied. The use of microorganisms such as bacteria or archaea to produce energy is currently in great progress. These present several advantages even when compared with other renewable energy sources. Besides the energy production, they are also involved in bioremediation such as the removal of heavy metal contaminants from soils or wastewaters. Several research groups have demonstrated that these organisms are able to interact with electrodes via heme and non-heme iron proteins. Therefore, the role of iron as well as iron metabolism in these species must be of enormous relevance. Recently, the influence of cellular iron regulation by Fur in the Geobacter sulfurreducens growth and ability to produce energy was demonstrated. In this review, we aim to briefly describe the most relevant proteins involved in the iron metabolism of bacteria and archaea and relate them and their biological function with the ability of selected organisms to produce energy.

Yeast‐insect associations: It takes guts

PubMed Central

2018-01-01

Abstract Insects interact with microorganisms in several situations, ranging from the accidental interaction to locate attractive food or the acquisition of essential nutrients missing in the main food source. Despite a wealth of studies recently focused on bacteria, the interactions between insects and yeasts have relevant implications for both of the parties involved. The insect intestine shows several structural and physiological differences among species, but it is generally a hostile environment for many microorganisms, selecting against the most sensitive and at the same time guaranteeing a less competitive environment to resistant ones. An intensive characterization of the interactions between yeasts and insects has highlighted their relevance not only for attraction to food but also for the insect's development and behaviour. Conversely, some yeasts have been shown to benefit from interactions with insects, in some cases by being carried among different environments. In addition, the insect intestine may provide a place to reside for prolonged periods and possibly mate or generate sexual forms able to mate once back in the external environments. YEA‐May‐17‐0084.R3 PMID:29363168

Bioactive secondary metabolites from marine microbes for drug discovery.

PubMed

Nikapitiya, Chamilani

2012-01-01

The isolation and extraction of novel bioactive secondary metabolites from marine microorganisms have a biomedical potential for future drug discovery as the oceans cover 70% of the planet's surface and life on earth originates from sea. Wide range of novel bioactive secondary metabolites exhibiting pharmacodynamic properties has been isolated from marine microorganisms and many to be discovered. The compounds isolated from marine organisms (macro and micro) are important in their natural form and also as templates for synthetic modifications for the treatments for variety of deadly to minor diseases. Many technical issues are yet to overcome before wide-scale bioprospecting of marine microorganisms becomes a reality. This chapter focuses on some novel secondary metabolites having antitumor, antivirus, enzyme inhibitor, and other bioactive properties identified and isolated from marine microorganisms including bacteria, actinomycetes, fungi, and cyanobacteria, which could serve as potentials for drug discovery after their clinical trials. Copyright © 2012 Elsevier Inc. All rights reserved.

The stethoscope in the Emergency Department: a vector of infection?

PubMed Central

Núñez, S.; Moreno, A.; Green, K.; Villar, J.

2000-01-01

The purposes of this study were to determine whether microorganisms can be isolated from the membranes of stethoscopes used by clinicians and nurses, and to analyse whether or not the degree of bacterial colonization could be reduced with different cleaning methods. We designed a transversal before-after study in which 122 stethoscopes were examined. Coagulase negative staphylococci (which are also potentially pathogenic microorganisms) were isolated together with 13 other potentially pathogenic microorganisms, including S. aureus, Acinetobacter sp. and Enterobacter agglomerans. The most effective antiseptic was propyl alcohol. Analysis of the cleaning habits of the Emergency Department (ED) staff, showed that 45% cleaned the stethoscope annually or never. The isolation of potentially pathogenic microorganisms suggests that the stethoscope must be considered as a potential vector of infection not only in the ED but also in other hospital wards and out-patient clinics. PMID:10813148

Atmospheric Sampling of Microorganisms with UAS

NASA Astrophysics Data System (ADS)

Schmale, D. G., III

2017-12-01

Many microorganisms relevant to crops, domestic animals, and humans are transported over long distances through the atmosphere. Some of these atmospheric microbes catalyze the freezing of water at higher temperatures and facilitate the onset of precipitation. A few have crossed continents. New technologies are needed to study the movement of microorganisms in the atmosphere. We have used unmanned aircraft systems (UAS) to study the transport of microorganisms tens to hundreds of meters above the ground. These UAS are equipped with unique devices for collecting microbes in the atmosphere during flight. Autonomous systems enable teams of UAS to perform complex atmospheric sampling tasks, and coordinate flight missions with one another. Data collected with UAS can be used to validate and improve disease forecasting models along highways in the sky, connecting transport scales across farms, states, and continents. Though terrestrial environments are often considered a major contributor to atmospheric microbial aerosols, little is known about aquatic sources of microbial aerosols. Droplets containing microorganisms can aerosolize from the water surface, liberating them into the atmosphere. We are using teams of unmanned surface vehicles (USVs) and UAS to study the aerosolization of microbes from aquatic environments. Controlled flume studies using highspeed video have allowed us to observe unique aerosolization phenomena that can launch microbes out of the water and into the air. Unmanned systems may be used to excite the next generation of biologists and engineers, and raise important ethical considerations about the future of human-robot interactions.

Bioleaching in brackish waters--effect of chloride ions on the acidophile population and proteomes of model species.

PubMed

Zammit, Carla M; Mangold, Stefanie; Jonna, Venkateswara rao; Mutch, Lesley A; Watling, Helen R; Dopson, Mark; Watkin, Elizabeth L J

2012-01-01

High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L(-1) NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.

[Frequency of yeasts in vaginal fluid of women with and without clinical suspicion of vulvovaginal candidiasis].

PubMed

Andrioli, João Luciano; Oliveira, Gílvia Simone Andrade; Barreto, Cilene Souza; Sousa, Zulane Lima; Oliveira, Maria Cristina Haun de; Cazorla, Irene Mauricio; Fontana, Renato

2009-06-01

to study vulvovaginal candidiasis from the vaginal fluid of women with and without clinical suspicion, identifying the frequency of Candida spp., and associating it with intrinsic and extrinsic risk factors. a total of 286 samples from patients attended in private practices and public health units from August 2005 to August 2007 were collected, being 121 women under clinical suspicion and 165, without. The samples were collected with sterile swabs, taken to the laboratory in 0.85% physiological solution, and then seeded in CHROMagar Candida and in 4% agar Sabourad with chloramphenicol. Classical identification procedures were carried out: macro and micromorphology, zymogram and auxanogram. Data obtained were analyzed by frequency tests and contingency tables (chi2). a total of 47.9% of the women under clinical suspicion got confirmation of candidiasis by the laboratorial tests. Among the patients without clinical suspicion (Control Group), 78.2% were vulvovaginal candidiasis negative according to the laboratorial tests. Candida albicans was the prevalent strain in 74.5% of the cases. There were significant differences among the positive cases, according to the patients from the two cities evaluated (p<0.05). Clothing was one differential aspect found among the two populations studied. the presence of predisposing factors does not necessarily define vulvovaginal candidiasis. Geographical localization has shown to be a relevant factor in the distribution of events. The type of clothing may be one of the reasons for it. Culture of samples from the vaginal contents, followed by microorganisms' identification, can be important.

Proteome-based bacterial identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS): A revolutionary shift in clinical diagnostic microbiology.

PubMed

Nomura, Fumio

2015-06-01

Rapid and accurate identification of microorganisms, a prerequisite for appropriate patient care and infection control, is a critical function of any clinical microbiology laboratory. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a quick and reliable method for identification of microorganisms, including bacteria, yeast, molds, and mycobacteria. Indeed, there has been a revolutionary shift in clinical diagnostic microbiology. In the present review, the state of the art and advantages of MALDI-TOF MS-based bacterial identification are described. The potential of this innovative technology for use in strain typing and detection of antibiotic resistance is also discussed. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Multifunctional sample preparation kit and on-chip quantitative nucleic acid sequence-based amplification tests for microbial detection.

PubMed

Zhao, Xinyan; Dong, Tao

2012-10-16

This study reports a quantitative nucleic acid sequence-based amplification (Q-NASBA) microfluidic platform composed of a membrane-based sampling module, a sample preparation cassette, and a 24-channel Q-NASBA chip for environmental investigations on aquatic microorganisms. This low-cost and highly efficient sampling module, having seamless connection with the subsequent steps of sample preparation and quantitative detection, is designed for the collection of microbial communities from aquatic environments. Eight kinds of commercial membrane filters are relevantly analyzed using Saccharomyces cerevisiae, Escherichia coli, and Staphylococcus aureus as model microorganisms. After the microorganisms are concentrated on the membrane filters, the retentate can be easily conserved in a transport medium (TM) buffer and sent to a remote laboratory. A Q-NASBA-oriented sample preparation cassette is originally designed to extract DNA/RNA molecules directly from the captured cells on the membranes. Sequentially, the extract is analyzed within Q-NASBA chips that are compatible with common microplate readers in laboratories. Particularly, a novel analytical algorithmic method is developed for simple but robust on-chip Q-NASBA assays. The reported multifunctional microfluidic system could detect a few microorganisms quantitatively and simultaneously. Further research should be conducted to simplify and standardize ecological investigations on aquatic environments.

Survival, DNA Integrity, and Ultrastructural Damage in Antarctic Cryptoendolithic Eukaryotic Microorganisms Exposed to Ionizing Radiation.

PubMed

Pacelli, Claudia; Selbmann, Laura; Zucconi, Laura; Raguse, Marina; Moeller, Ralf; Shuryak, Igor; Onofri, Silvano

2017-02-01

Life dispersal between planets, planetary protection, and the search for biosignatures are main topics in astrobiology. Under the umbrella of the STARLIFE project, three Antarctic endolithic microorganisms, the melanized fungus Cryomyces antarcticus CCFEE 515, a hyaline strain of Umbilicaria sp. (CCFEE 6113, lichenized fungus), and a Stichococcus sp. strain (C45A, green alga), were exposed to high doses of space-relevant gamma radiation ( 60 Co), up to 117.07 kGy. After irradiation survival, DNA integrity and ultrastructural damage were tested. The first was assessed by clonogenic test; viability and dose responses were reasonably described by the linear-quadratic formalism. DNA integrity was evaluated by PCR, and ultrastructural damage was observed by transmission electron microscopy. The most resistant among the tested organisms was C. antarcticus both in terms of colony formation and DNA preservation. Besides, results clearly demonstrate that DNA was well detectable in all the tested organisms even when microorganisms were dead. This high resistance provides support for the use of DNA as a possible biosignature during the next exploration campaigns. Implication in planetary protection and contamination during long-term space travel are put forward. Key Words: Biosignatures-Ionizing radiation-DNA integrity-Eukaryotic microorganisms-Fingerprinting-Mars exploration. Astrobiology 17, 126-135.

Pseudo-outbreak of Cupriavidus pauculus infection at an outpatient clinic related to rinsing culturette swabs in tap water.

PubMed

Balada-Llasat, Joan-Miquel; Elkins, Camille; Swyers, Lettie; Bannerman, Tammy; Pancholi, Preeti

2010-07-01

Cupriavidus pauculus is a water microorganism rarely isolated from clinical specimens. We describe a pseudo-outbreak in which multiple strains that were associated with moistening of culturette swabs with tap water were isolated from a single clinic before collecting the patient specimen.

Personal Hygiene and Vulvovaginitis in Prepubertal Children.

PubMed

Cemek, Fatıma; Odabaş, Dursun; Şenel, Ünal; Kocaman, Ayşe Tuba

2016-06-01

To determine and compare clinical and microbiological features of vulvovaginitis in prepubertal girls. Vulvovaginitis is the most common gynecological problem of childhood. DESIGN, SETTING, PARTICIPANTS, INTERVENTIONS, AND MAIN OUTCOME MEASURES: This study involved 45 girls from 2-12 (5.38 ± 2.9) years old; and 26 girls from 3-12 (5.72 ± 3.1) years old as a control group. Anamnesis and physical examination were followed by vaginal smear, urine culture, and stool analyses from both groups, and the personal hygiene status and education level of the mother were determined. The most common symptoms among the patients were vaginal discharge (44.4%, vulvar erythema (37.8%), and vaginal itch (24.4%). Microorganisms, isolated from vaginal smears, were detected in 48.9% of the patients. Escherichia coli was shown in the urine culture of 3 patients with vulvovaginitis (6.70%). In microscopic stool analysis parasites were detected (45.9%). We found some relevant personal hygiene factors, such as wiping back to front (42.9%), cleaning by herself after defecation (89.3%), using toilet paper (60.7%) and wet wipes (21.4%), and bathing standing (14.3%) and sitting (46.4%) among patients. The questionnaire also showed that the children wore tight clothing (35.7%). Our findings suggest that vulvovaginitis in prepubertal girls is related not only to microorganisms but also poor personal hygiene, the educational status of mothers, and specific irritants. Copyright © 2015 North American Society for Pediatric and Adolescent Gynecology. Published by Elsevier Inc. All rights reserved.

The role of lactobacilli and probiotics in maintaining vaginal health.

PubMed

Borges, Sandra; Silva, Joana; Teixeira, Paula

2014-03-01

The vaginal microbiota of healthy women consists typically of a diversity of anaerobic and aerobic microorganisms. Lactobacilli are the most prevalent and often numerically dominant microorganisms and are relevant as a barrier to infection. The capacity of lactobacilli to adhere and compete for adhesion sites in the vaginal epithelium and the capacity to produce antimicrobial compounds (hydrogen peroxide, lactic acid, bacteriocin-like substances), are important in the impairment of colonization by pathogens. This review summarizes the role of lactic acid bacteria in preventing illness of the host, including bacterial vaginosis, yeast vaginitis, urinary tract infection and sexually transmitted diseases. The administration of probiotics that colonize the vaginal tract can be important in maintaining a normal urogenital health and also to prevent or treat infections.

Genetic engineering of microorganisms for biodiesel production

PubMed Central

Lin, Hui; Wang, Qun; Shen, Qi; Zhan, Jumei; Zhao, Yuhua

2013-01-01

Biodiesel, as one type of renewable energy, is an ideal substitute for petroleum-based diesel fuel and is usually made from triacylglycerides by transesterification with alcohols. Biodiesel production based on microbial fermentation aiming to establish more efficient, less-cost and sustainable biodiesel production strategies is under current investigation by various start-up biotechnology companies and research centers. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. Here, we present an overview of principal microorganisms used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples. PMID:23222170

Genetic engineering of microorganisms for biodiesel production.

PubMed

Lin, Hui; Wang, Qun; Shen, Qi; Zhan, Jumei; Zhao, Yuhua

2013-01-01

Biodiesel, as one type of renewable energy, is an ideal substitute for petroleum-based diesel fuel and is usually made from triacylglycerides by transesterification with alcohols. Biodiesel production based on microbial fermentation aiming to establish more efficient, less-cost and sustainable biodiesel production strategies is under current investigation by various start-up biotechnology companies and research centers. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. Here, we present an overview of principal microorganisms used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples.

Strain improvement of industrially important microorganisms based on resistance to toxic metabolites and abiotic stress.

PubMed

Fiedurek, Jan; Trytek, Mariusz; Szczodrak, Janusz

2017-06-01

Improvement of the biosynthetic capabilities of industrially relevant microbes to produce desired metabolites in higher quantities is one of the important topics of modern biotechnology. In this article, different strategies of improvement of mutated microbial strains are briefly described. This is followed by the first comprehensive review of the literature on obtaining high yielding microorganisms, that is, mutants exhibiting resistance to antimetabolites, nutritional repression, and abiotic stresses as well as tolerance to solvents and toxic substrates or products. Furthermore, the efficiency of the microbial metabolites produced by improved microbial strains, advantages, and limitations, as well as future prospects for strategies of strain development are discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Medical Service Clinical Laboratory Procedures--Bacteriology.

ERIC Educational Resources Information Center

Department of the Army, Washington, DC.

This manual presents laboratory procedures for the differentiation and identification of disease agents from clinical materials. Included are procedures for the collection of specimens, preparation of culture media, pure culture methods, cultivation of the microorganisms in natural and simulated natural environments, and procedures in…

Evaluation of a Mixing versus a Cycling Strategy of Antibiotic Use in Critically-Ill Medical Patients: Impact on Acquisition of Resistant Microorganisms and Clinical Outcomes.

PubMed

Cobos-Trigueros, Nazaret; Solé, Mar; Castro, Pedro; Torres, Jorge Luis; Rinaudo, Mariano; De Lazzari, Elisa; Morata, Laura; Hernández, Cristina; Fernández, Sara; Soriano, Alex; Nicolás, José María; Mensa, Josep; Vila, Jordi; Martínez, José Antonio

2016-01-01

To compare the effect of two strategies of antibiotic use (mixing vs. cycling) on the acquisition of resistant microorganisms, infections and other clinical outcomes. Prospective cohort study in an 8-bed intensive care unit during 35- months in which a mixing-cycling policy of antipseudomonal beta-lactams (meropenem, ceftazidime/piperacillin-tazobactam) and fluoroquinolones was operative. Nasopharyngeal and rectal swabs and respiratory secretions were obtained within 48h of admission and thrice weekly thereafter. Target microorganisms included methicillin-resistant S. aureus, vancomycin-resistant enterococci, third-generation cephalosporin-resistant Enterobacteriaceae and non-fermenters. A total of 409 (42%) patients were included in mixing and 560 (58%) in cycling. Exposure to ceftazidime/piperacillin-tazobactam and fluoroquinolones was significantly higher in mixing while exposure to meropenem was higher in cycling, although overall use of antipseudomonals was not significantly different (37.5/100 patient-days vs. 38.1/100 patient-days). There was a barely higher acquisition rate of microorganisms during mixing, but this difference lost its significance when the cases due to an exogenous Burkholderia cepacia outbreak were excluded (19.3% vs. 15.4%, OR 0.8, CI 0.5-1.1). Acquisition of Pseudomonas aeruginosa resistant to the intervention antibiotics or with multiple-drug resistance was similar. There were no significant differences between mixing and cycling in the proportion of patients acquiring any infection (16.6% vs. 14.5%, OR 0.9, CI 0.6-1.2), any infection due to target microorganisms (5.9% vs. 5.2%, OR 0.9, CI 0.5-1.5), length of stay (median 5 d for both groups) or mortality (13.9 vs. 14.3%, OR 1.03, CI 0.7-1.3). A cycling strategy of antibiotic use with a 6-week cycle duration is similar to mixing in terms of acquisition of resistant microorganisms, infections, length of stay and mortality.

Antibacterial, modulatory activity of antibiotics and toxicity from Rhinella jimi (Stevaux, 2002) (Anura: Bufonidae) glandular secretions.

PubMed

Sales, Débora Lima; Morais-Braga, Maria Flaviana Bezerra; Santos, Antonia Thassya Lucas Dos; Machado, Antonio Judson Targino; Araujo Filho, João Antonio de; Dias, Diógenes de Queiroz; Cunha, Francisco Assis Bezerra da; Saraiva, Rogério de Aquino; Menezes, Irwin Rose Alencar de; Coutinho, Henrique Douglas Melo; Costa, José Galberto Martins; Ferreira, Felipe Silva; Alves, Rômulo Romeu da Nóbrega; Almeida, Waltécio de Oliveira

2017-08-01

The increase in microorganisms with resistance to medications has caused a strong preoccupation within the medical and scientific community. Animal toxins studies, such as parotoid glandular secretions from amphibians, possesses a great potential in the development of drugs, such as antimicrobials, as these possess bioactive compounds. It was evaluated Rhinella jimi (Stevaux, 2002) glandular secretions against standard and multi-resistant bacterial strains; the effect of secretions combined with drugs; and determined the toxicity using two biologic in vivo models, and a in vitro model with mice livers. Standard strains were used for the determination of the Minimum Inhibitory Concentration (MIC), while for the modulatory activity of antibiotics, the clinical isolates Escherichia coli 06, Pseudomonas aeruginosa 03 and Staphylococcus aureus 10 were used. Modulatory activity was evaluated by the broth microdilution method with aminoglycosides and β-lactams as target antibiotics. The secretions in association with the antibiotics have a significant reduction in MIC, both the aminoglycosides and β-lactams. The toxicity and cytotoxicity results were lower than the values used in the modulation. R. jimi glandular secretions demonstrated clinically relevant results regarding the modulation of the tested antimicrobials. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Appearance of colonies of Prototheca on CHROMagar Candida medium.

PubMed

Casal, M; Linares, M J; Solís, F; Rodríguez, F C

1997-01-01

The microorganisms capable of producing opportunist infections include the yeast-like organisms of the genus Candida, and the unicellular algae of the genus Prototheca, which share common features and can, therefore, lead to confusion. Their colonies are almost identical and they grow in the same culture media used routinely in mycology. CHROMagar Candida is a new chromogenic differential isolation medium that facilitates the presumptive differentiation of some of the most clinically important yeast-like organisms. To our knowledge, the use of CHROMagar Candida with Prototheca spp. has not been reported in the literature. This report describes the growth of 151 strains of Prototheca on CHROMagar Candida compared to the growth of a total of 326 well-characterized yeast organisms of the genera Candida, Cryptococcus, Trichosporon, Geotrichum, and Saccharomyces. It is clinically relevant to note that algae of the genus Prototheca (P. wickerhamii, P. zopfii, and P. stagnora) and of the genus Candida parapsilosis produced similar cream-colored colonies on CHROMagar Candida medium. Based on their growth on CHROMagar, a new species of Candida is described, C. zeylanoides, which has blue-green colonies. The colonies of two species of Trichosporon are also differentiated: the blue-green colonies of T. beigelii and the pink colonies of T. capitatum.

[Role of bacteria associated with sexually transmitted infections in the etiology of lower urinary tract infection in primary care].

PubMed

González-Pedraza, Alberto; Ortiz, Catalina; Mota, Ricardo; Dávila, Rocío; Dickinson, Eloísa

2003-02-01

Urinary tract infections (UTI) are the second most frequent type of infectious pathology treated in primary care clinics. The participation of microorganisms associated with sexually transmitted infection has been reported as a cause of UTI; nevertheless this concept is still controversial. To gather data on this subject, we carried out a search for Gardnerella vaginalis, Ureaplasma urealyticum, Mycoplasma hominis and Streptococcus agalactiae besides the common microorganisms involved in UTI. A total of 1507 urine cultures from patients with a clinical diagnosis of low UTI were analyzed. Samples were inoculated onto 5% sheep blood agar and McConkey agar, as well as HBT medium for G. vaginalis, and U9B broth and agar E broth for M. hominis and U. urealyticum. The following parameters were analyzed as possible risk factors: age, sex, pregnancy and diabetes status. RESULTS. There were 436 (28.9%) positive urine cultures. Escherichia coli was isolated in 44.34% of cases. Microorganisms associated with sexually transmitted disease were found in 162 (37%): G. vaginalis (25.7%), U. urealyticum (5.9%), S. agalactiae (3.4%) and M. hominis (2%). UTI were more frequent among the 20 to 40 year-old age group, in women and in diabetic patients. Microorganisms associated with sexually transmitted disease were found in a large percentage of cultures, indicating the need for studies to clarify their role in the etiology of UTI.

[Detection of biofilm formation by selected pathogens relevant to the food industry].

PubMed

Šilhová-Hrušková, L; Moťková, P; Šilha, D; Vytřasová, J

2015-09-01

Detection of biofilm formation by microbial pathogens relevant to the food industry and comparison of biofilm formation under different conditions of culture. The following microorganisms were selected for the study: Staphylococcus aureus, Listeria innocua, Listeria ivanovii, Cronobacter sakazakii, Cronobacter muytjensii, Arcobacter butzleri, Arcobacter cryaerophilus, Campylobacter jejuni, and Campylobacter coli. To detect biofilm formation the microtiter plate assay, as described by Christensen and culture on stainless steel coupons were used. The biofilm forming capacity was confirmed in all microorganisms tested, both on the microtiter plates and stainless steel coupons. Biofilm formation was influenced by the culture medium, material used, and culture duration as well as by the test microorganism. It was found that different species and strains of the same genus differ in biofilm formation. Differences were also found between the collection strains and isolates from the environment. Some bacteria tended to form biofilm more readily on the surface of the polyethylene microtiter plates and less readily on stainless steel coupons while others appeared to have an opposite tendency. Some pathogens were able to increase the planktonic cell density in the initial suspension even by three orders of magnitude within 72 hours while producing plenty of biofilm. The study of biofilm formation by high risk pathogens is of utmost importance, not only to the food industry. From the obtained results, it is evident that bacterial biofilms form rapidly (within 24 hours in the present study). Due to their architecture, these biofilms are difficult to eradicate, and therefore, it is crucial to prevent biofilm formation.

Antibiotic Management of Lung Infections in Cystic Fibrosis. II. Nontuberculous Mycobacteria, Anaerobic Bacteria, and Fungi

PubMed Central

Aksamit, Timothy R.; Chotirmall, Sanjay H.; Dasenbrook, Elliott C.; Elborn, J. Stuart; LiPuma, John J.; Ranganathan, Sarath C.; Waters, Valerie J.; Ratjen, Felix A.

2014-01-01

Airway infections are a key component of cystic fibrosis (CF) lung disease. Whereas the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including methicillin-resistant Staphylococcus aureus, gram-negative bacterial infections, and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria, and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in patients with CF, but differentiation between colonization and infection is difficult clinically as coinfection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected in CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens. Although the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in patients with CF and treatment should be considered. At present, however there remains limited information on how best to select patients who could benefit from antifungal therapy. PMID:25167882

Antibiotic management of lung infections in cystic fibrosis. II. Nontuberculous mycobacteria, anaerobic bacteria, and fungi.

PubMed

Chmiel, James F; Aksamit, Timothy R; Chotirmall, Sanjay H; Dasenbrook, Elliott C; Elborn, J Stuart; LiPuma, John J; Ranganathan, Sarath C; Waters, Valerie J; Ratjen, Felix A

2014-10-01

Airway infections are a key component of cystic fibrosis (CF) lung disease. Whereas the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including methicillin-resistant Staphylococcus aureus, gram-negative bacterial infections, and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria, and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in patients with CF, but differentiation between colonization and infection is difficult clinically as coinfection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected in CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens. Although the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in patients with CF and treatment should be considered. At present, however there remains limited information on how best to select patients who could benefit from antifungal therapy.

Inflammatory Responses, Spirometry, and Quality of Life in Subjects With Bronchiectasis Exacerbations.

PubMed

Guan, Wei-Jie; Gao, Yong-Hua; Xu, Gang; Lin, Zhi-Ya; Tang, Yan; Li, Hui-Min; Lin, Zhi-Min; Jiang, Mei; Zheng, Jin-Ping; Chen, Rong-Chang; Zhong, Nan-Shan

2015-08-01

Bronchiectasis exacerbations are critical events characterized by worsened symptoms and signs (ie, cough frequency, sputum volume, malaise). Our goal was to examine variations in airway and systemic inflammation, spirometry, and quality of life during steady state, bronchiectasis exacerbations, and convalescence (1 week following a 2-week antibiotic treatment) to determine whether potentially pathogenic microorganisms, including Pseudomonas aeruginosa, were associated with poorer conditions during bronchiectasis exacerbations. Peripheral blood and sputum were sampled to detect inflammatory mediators and bacterial densities. Spirometry and quality of life (St George Respiratory Questionnaire [SGRQ]) were assessed during the 3 stages. Forty-eight subjects with bronchiectasis (43.2 ± 14.2 y of age) were analyzed. No notable differences in species and density of potentially pathogenic microorganisms were found during bronchiectasis exacerbations. Except for CXCL8 and tumor necrosis factor alpha (TNF-α), serum inflammation was heightened during bronchiectasis exacerbations and recovered during convalescence. Even though sputum TNF-α was markedly higher during bronchiectasis exacerbations and remained heightened during convalescence, the variations in miscellaneous sputum markers were unremarkable. Bronchiectasis exacerbations were associated with notably higher SGRQ symptom and total scores, which recovered during convalescence. FVC, FEV1, and maximum mid-expiratory flow worsened during bronchiectasis exacerbations (median change from baseline of -2.2%, -0.8%, and -1.3%) and recovered during convalescence (median change from baseline of 0.6%, 0.7%, and -0.7%). Compared with no bacterial isolation, potentially pathogenic microorganism or P. aeruginosa isolation at baseline did not result in poorer clinical condition during bronchiectasis exacerbations. Bronchiectasis exacerbations are characterized by heightened inflammatory responses and poorer quality of life and spirometry, but not by increased bacterial density, which applies for subjects with and without potentially pathogenic microorganism isolation when clinically stable. (ClinicalTrials.gov registration NCT01761214.). Copyright © 2015 by Daedalus Enterprises.

Host-Microbiome Cross-talk in Oral Mucositis

PubMed Central

Vasconcelos, R.M.; Sanfilippo, N.; Paster, B.J.; Kerr, A.R.; Li, Y.; Ramalho, L.; Queiroz, E.L.; Smith, B.; Sonis, S.T.; Corby, P.M.

2016-01-01

Oral mucositis (OM) is among the most common, painful, and debilitating toxicities of cancer regimen–related treatment, resulting in the formation of ulcers, which are susceptible to increased colonization of microorganisms. Novel discoveries in OM have focused on understanding the host-microbial interactions, because current pathways have shown that major virulence factors from microorganisms have the potential to contribute to the development of OM and may even prolong the existence of already established ulcerations, affecting tissue healing. Additional comprehensive and disciplined clinical investigation is needed to carefully characterize the relationship between the clinical trajectory of OM, the local levels of inflammatory changes (both clinical and molecular), and the ebb and flow of the oral microbiota. Answering such questions will increase our knowledge of the mechanisms engaged by the oral immune system in response to mucositis, facilitating their translation into novel therapeutic approaches. In doing so, directed clinical strategies can be developed that specifically target those times and tissues that are most susceptible to intervention. PMID:27053118

Hydrogel-forming Microneedle Arrays Exhibit Antimicrobial Properties: Potential for Enhanced Patient Safety

PubMed Central

Donnelly, Ryan F.; Singh, Thakur Raghu Raj; Alkilani, Ahlam Zaid; McCrudden, Maelíosa T.C.; O’Mahony, Conor; Armstrong, Keith; McLoone, Nabla; Kole, Prashant; Woolfson, A. David

2014-01-01

We describe, for the first time, the microbial characterisation of hydrogel-forming polymeric microneedle arrays and the potential for passage of microorganisms into skin following microneedle penetration. Uniquely, we also present insights into the storage stability of these hydroscopic formulations, from physical and microbiological viewpoints, and examine clinical performance and safety in human volunteers. Experiments employing excised porcine skin and radiolabelled microorganisms showed that microorganisms can penetrate skin beyond the stratum corneum following microneedle puncture. Indeed, the numbers of microorganisms crossing the stratum corneum following microneedle puncture was greater than 105 cfu in each case. However, no microorganisms crossed the epidermal skin. When using a 21G hypodermic needle, more than 104 microorganisms penetrated into the viable tissue and 106 cfu of C. albicans and S. epidermidis completely crossed the epidermal skin in 24 h. The hydrogel-forming materials contained no microorganisms following de-moulding and exhibited no microbial growth during storage, while also maintaining their mechanical strength, apart from when stored at relative humidities of 86%. No microbial penetration through the swelling microneedles was detectable, while human volunteer studies confirmed that skin or systemic infection is highly unlikely when polymeric microneedles are used for transdermal drug delivery. Since no pharmacopoeial standards currently exist for microneedle-based products, the exact requirements for a proprietary product based on hydrogel-forming microneedles are at present unclear. However, we are currently working towards a comprehensive specification set for this microneedle system that may inform future developments in this regard. PMID:23644043

[Applications of MALDI-TOF technology in clinical microbiology].

PubMed

Suarez, S; Nassif, X; Ferroni, A

2015-02-01

Until now, the identification of micro-organisms has been based on the cultural and biochemical characteristics of bacterial and fungal species. Recently, Mass Spectrometry type Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF MS) was developed in clinical microbiology laboratories. This new technology allows identification of micro-organisms directly from colonies of bacteria and fungi within few minutes. In addition, it can be used to identify germs directly from positive blood culture bottles or directly from urine samples. Other ways are being explored to expand the use of MALDI-TOF in clinical microbiology laboratories. Indeed, some studies propose to detect bacterial antibiotic resistance while others compare strains within species for faster strain typing. The main objective of this review is to update data from the recent literature for different applications of MALDI-TOF technique in microbiological diagnostic routine. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Microbiological Contamination of Drugs during Their Administration for Anesthesia in the Operating Room.

PubMed

Gargiulo, Derryn A; Mitchell, Simon J; Sheridan, Janie; Short, Timothy G; Swift, Simon; Torrie, Jane; Webster, Craig S; Merry, Alan F

2016-04-01

The aseptic techniques of anesthesiologists in the preparation and administration of injected medications have not been extensively investigated, but emerging data demonstrate that inadvertent lapses in aseptic technique may be an important contributor to surgical site and other postoperative infections. A prospective, open, microbiological audit of 303 cases in which anesthesiologists were asked to inject all bolus drugs, except propofol and antibiotics, through a 0.2-µm filter was performed. The authors cultured microorganisms, if present, from the 0.2-µm filter unit and from the residual contents of the syringes used for drawing up or administering drugs. Participating anesthesiologists rated ease of use of the filters after each case. Twenty-three anesthesiologists each anesthetized up to 25 adult patients. The authors isolated microorganisms from filter units in 19 (6.3%) of 300 cases (3 cases were excluded), including Staphylococcus capitis, Staphylococcus warneri, Staphylococcus epidermidis, Staphylococcus haemolyticus, Micrococcus luteus/lylae, Corynebacterium, and Bacillus species. The authors collected used syringes at the end of each case and grew microorganisms from residual drug in 55 of these 2,318 (2.4%) syringes including all the aforementioned microorganisms and also Kocuria kristinae, Staphylococcus aureus, and Staphylococcus hominus. Participants' average rating of ease of use of the filter units was 3.5 out of 10 (0 being very easy and 10 being very difficult). Microorganisms with the potential to cause infection are being injected (presumably inadvertently) into some patients during the administration of intravenous drugs by bolus during anesthesia. The relevance of this finding to postoperative infections warrants further investigation.

Impact of polymicrobial biofilms in catheter-associated urinary tract infections.

PubMed

Azevedo, Andreia S; Almeida, Carina; Melo, Luís F; Azevedo, Nuno F

2017-08-01

Recent reports have demonstrated that most biofilms involved in catheter-associated urinary tract infections are polymicrobial communities, with pathogenic microorganisms (e.g. Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and uncommon microorganisms (e.g. Delftia tsuruhatensis, Achromobacter xylosoxidans) frequently co-inhabiting the same urinary catheter. However, little is known about the interactions that occur between different microorganisms and how they impact biofilm formation and infection outcome. This lack of knowledge affects CAUTIs management as uncommon bacteria action can, for instance, influence the rate at which pathogens adhere and grow, as well as affect the overall biofilm resistance to antibiotics. Another relevant aspect is the understanding of factors that drive a single pathogenic bacterium to become prevalent in a polymicrobial community and subsequently cause infection. In this review, a general overview about the IMDs-associated biofilm infections is provided, with an emphasis on the pathophysiology and the microbiome composition of CAUTIs. Based on the available literature, it is clear that more research about the microbiome interaction, mechanisms of biofilm formation and of antimicrobial tolerance of the polymicrobial consortium are required to better understand and treat these infections.

An Immunological Strategy To Monitor In Situ the Phosphate Starvation State in Thiobacillus ferrooxidans

PubMed Central

Varela, Patricia; Levicán, Gloria; Rivera, Francisco; Jerez, Carlos A.

1998-01-01

Thiobacillus ferrooxidans is one of the chemolithoautotrophic bacteria important in industrial biomining operations. During the process of ore bioleaching, the microorganisms are subjected to several stressing conditions, including the lack of some essential nutrients, which can affect the rates and yields of bioleaching. When T. ferrooxidans is starved for phosphate, the cells respond by inducing the synthesis of several proteins, some of which are outer membrane proteins of high molecular weight (70,000 to 80,000). These proteins were considered to be potential markers of the phosphate starvation state of these microorganisms. We developed a single-cell immunofluorescence assay that allowed monitoring of the phosphate starvation condition of this biomining microorganism by measuring the increased expression of the surface proteins. In the presence of low levels of arsenate (2 mM), the growth of phosphate-starved T. ferrooxidans cells was greatly inhibited compared to that of control nonstarved cells. Therefore, the determination of the phosphorus nutritional state is particularly relevant when arsenic compounds are solubilized during the bioleaching of different ores. PMID:9835593

Short communication: Quantification of the transmission of microorganisms to milk via dirt attached to the exterior of teats.

PubMed

Vissers, M M M; Driehuis, F; Te Giffel, M C; De Jong, P; Lankveld, J M G

2007-08-01

Pathogens and spoilage microorganisms can be transmitted to milk via dirt (e.g., feces, bedding material, soil, or a combination of these) attached to the exterior of the cows' teats. To determine the relevance of this pathway and to perform quantitative microbial risk analysis of the microbial contamination of farm tank milk (FTM), it is important to know the amount of dirt transmitted to milk via the exterior of teats. In this study at 11 randomly selected Dutch farms the amount of dirt transmitted to milk via the exterior of teats is determined using spores of mesophilic aerobic bacteria as a marker for transmitted dirt. The amount of transmitted dirt to milk varied among farms from approximately 3 to 300 mg/L, with an average of 59 mg/L. The usefulness of the data for microbial risk analyses is briefly illustrated using the contamination of FTM with spores of butyric acid bacteria as a case study. In a similar way the data can be used to identify measures to control the contamination of FTM with other microorganisms or chemical residues.

The Evolving Nature of Infective Endocarditis in Spain: A Population-Based Study (2003 to 2014).

PubMed

Olmos, Carmen; Vilacosta, Isidre; Fernández-Pérez, Cristina; Bernal, José L; Ferrera, Carlos; García-Arribas, Daniel; Pérez-García, Carlos N; San Román, J Alberto; Maroto, Luis; Macaya, Carlos; Elola, Francisco J

2017-12-05

Little information exists regarding population-based epidemiological changes in infective endocarditis (IE) in Europe. This study sought to analyze temporal trends in IE in Spain from 2003 to 2014. This retrospective, population-based, temporal trend study analyzed the incidence, epidemiological and clinical characteristics, and outcome of all patients discharged from hospitals included in the Spanish National Health System with a diagnosis of IE, from January 2003 to December 2014. Overall, 16,867 episodes of IE were identified during the study period, 66.3% in men. The rate of IE significantly increased, from 2.72 in 2003 to 3.49 per 100,000 person-years in 2014, and this rise was higher among older adults. The most frequent microorganisms were staphylococci (28.7%), followed by streptococci (20.4%) and enterococci (13.1%). Twenty-three percent of patients underwent cardiac surgery. The in-hospital mortality rate was 20.4%. Throughout the study period, the proportion of patients with previously known heart valve disease and diabetes mellitus significantly increased, whereas the prevalence of intravenous drug use decreased. Regarding microorganisms, Staphylococcus aureus and streptococci slightly declined, whereas coagulase-negative staphylococci and enterococci consistently increased over the years. In-hospital complications and cardiac surgery rates significantly increased across the years. The risk-adjusted in-hospital mortality rate diminished (0.2% per year) during the study period. The incidence of IE episodes significantly increased over the decade of the study period, particularly among older adults. Relevant changes in clinical and microbiological profile included older patients with more comorbidity and a rise in enterococci and coagulase-negative staphylococcal infections. Adjusted mortality rates slightly declined over the study period. Copyright © 2017 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates.

PubMed

Ercan, Onur; Bisschops, Markus M M; Overkamp, Wout; Jørgensen, Thomas R; Ram, Arthur F; Smid, Eddy J; Pronk, Jack T; Kuipers, Oscar P; Daran-Lapujade, Pascale; Kleerebezem, Michiel

2015-09-01

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms Lactobacillus plantarum, Lactococcus lactis, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus niger. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Analytical considerations and dimensionless analysis for a description of particle interactions in high pressure processes

NASA Astrophysics Data System (ADS)

Rauh, Cornelia; Delgado, Antonio

2010-12-01

High pressures of up to several hundreds of MPa are utilized in a wide range of applications in chemical, bio-, and food engineering, aiming at selective control of (bio-)chemical reactions. Non-uniformity of process conditions may threaten the safety and quality of the resulting products because processing conditions such as pressure, temperature, and treatment history are crucial for the course of (bio-)chemical reactions. Therefore, thermofluid-dynamical phenomena during the high pressure process have to be examined, and numerical tools to predict process uniformity and to optimize the processes have to be developed. Recently applied mathematical models and numerical simulations of laboratory and industrial scale high pressure processes investigating the mentioned crucial phenomena are based on continuum balancing models of thermofluid dynamics. Nevertheless, biological systems are complex fluids containing the relevant (bio-)chemical compounds (enzymes and microorganisms). These compounds are particles that interact with the surrounding medium and between each other. This contribution deals with thermofluid-dynamical interactions of the relevant particulate (bio-)chemical compounds (enzymes and microorganisms) with the surrounding fluid. By consideration of characteristic time and length scales and particle forces, the motion of the (bio-)chemical compounds is characterized.

Systems medicine: a new approach to clinical practice.

PubMed

Cardinal-Fernández, Pablo; Nin, Nicolás; Ruíz-Cabello, Jesús; Lorente, José A

2014-10-01

Most respiratory diseases are considered complex diseases as their susceptibility and outcomes are determined by the interaction between host-dependent factors (genetic factors, comorbidities, etc.) and environmental factors (exposure to microorganisms or allergens, treatments received, etc.) The reductionist approach in the study of diseases has been of fundamental importance for the understanding of the different components of a system. Systems biology or systems medicine is a complementary approach aimed at analyzing the interactions between the different components within one organizational level (genome, transcriptome, proteome), and then between the different levels. Systems medicine is currently used for the interpretation and understanding of the pathogenesis and pathophysiology of different diseases, biomarker discovery, design of innovative therapeutic targets, and the drawing up of computational models for different biological processes. In this review we discuss the most relevant concepts of the theory underlying systems medicine, as well as its applications in the various biological processes in humans. Copyright © 2013 SEPAR. Published by Elsevier Espana. All rights reserved.

Nanobioimaging and sensing of infectious diseases.

PubMed

Tallury, Padmavathy; Malhotra, Astha; Byrne, Logan M; Santra, Swadeshmukul

2010-03-18

New methods to identify trace amount of infectious pathogens rapidly, accurately and with high sensitivity are in constant demand to prevent epidemics and loss of lives. Early detection of these pathogens to prevent, treat and contain the spread of infections is crucial. Therefore, there is a need and urgency for sensitive, specific, accurate, easy-to-use diagnostic tests. Versatile biofunctionalized engineered nanomaterials are proving to be promising in meeting these needs in diagnosing the pathogens in food, blood and clinical samples. The unique optical and magnetic properties of the nanoscale materials have been put to use for the diagnostics. In this review, we focus on the developments of the fluorescent nanoparticles, metallic nanostructures and superparamagnetic nanoparticles for bioimaging and detection of infectious microorganisms. The various nanodiagnostic assays developed to image, detect and capture infectious virus and bacteria in solutions, food or biological samples in vitro and in vivo are presented and their relevance to developing countries is discussed. Copyright 2009 Elsevier B.V. All rights reserved.

High-resolution microcontact printing and transfer of massive arrays of microorganisms on planar and compartmentalized nanoporous aluminium oxide.

PubMed

Ingham, Colin; Bomer, Johan; Sprenkels, Ad; van den Berg, Albert; de Vos, Willem; van Hylckama Vlieg, Johan

2010-06-07

Handling microorganisms in high throughput and their deployment into miniaturized platforms presents significant challenges. Contact printing can be used to create dense arrays of viable microorganisms. Such "living arrays", potentially with multiple identical replicates, are useful in the selection of improved industrial microorganisms, screening antimicrobials, clinical diagnostics, strain storage, and for research into microbial genetics. A high throughput method to print microorganisms at high density was devised, employing a microscope and a stamp with a massive array of PDMS pins. Viable bacteria (Lactobacillus plantarum, Esherichia coli), yeast (Candida albicans) and fungal spores (Aspergillus fumigatus) were deposited onto porous aluminium oxide (PAO) using arrays of pins with areas from 5 x 5 to 20 x 20 microm. Printing onto PAO with up to 8100 pins of 20 x 20 microm area with 3 replicates was achieved. Printing with up to 200 pins onto PAO culture chips (divided into 40 x 40 microm culture areas) allowed inoculation followed by effective segregation of microcolonies during outgrowth. Additionally, it was possible to print mixtures of C. albicans and spores of A. fumigatus with a degree of selectivity by capture onto a chemically modified PAO surface. High resolution printing of microorganisms within segregated compartments and on functionalized PAO surfaces has significant advantages over what is possible on semi-solid surfaces such as agar.

Determining the relationship between atherosclerosis and periodontopathogenic microorganisms in chronic periodontitis patients.

PubMed

Bozoglan, Alihan; Ertugrul, Abdullah Seckin; Taspınar, Mehmet; Yuzbasioglu, Betul

2017-05-01

The aim of this study is to determine the relationship between atherosclerosis and periodontopathogenic microorganisms in chronic periodontitis patients following periodontal treatment. A total of 40 patients were included in the study. 20 of these patients diagnosed with atherosclerosis and chronic periodontitis formed the test group. The remaining 20 patients were systemically healthy patients diagnosed with chronic periodontitis and formed the control group. All patients had nonsurgical periodontal treatment. The periodontopathogenic microorganism levels were determined at baseline and at 6 months in microbial dental plaque samples and WBC, LDL, HDL, PLT, fibrinogen, creatinine and hs-CRP levels were determined by blood samples. Statistically significant reduction has been achieved in clinical periodontal parameters following non-surgical periodontal treatment in test and control groups. Following periodontal treatment, WBC, LDL, PLT, fibrinogen, creatinine and hs-CRP levels significantly decreased and HDL levels significantly increased in both test and control groups. Similarly, the periodontopathogenic microorganism levels significantly decreased following periodontal treatment in the test and control groups. A statistically significant positive correlation has been determined between the periodontopathogenic microorganism levels and WBC, LDL, PLT, fibrinogen, creatinine, and hs-CRP levels in the test group. The association between hs-CRP, WBC, LDL, PLT, fibrinogen, creatinine, and the amount of periodontopathogenic microorganisms indicates the possibility that periodontal treatment could decrease the risk atherosclerosis. More studies must be conducted in order for these results to be supported.

Development and maintenance of intestinal regulatory T cells.

PubMed

Tanoue, Takeshi; Atarashi, Koji; Honda, Kenya

2016-05-01

Gut-resident forkhead box P3 (FOXP3)(+)CD4(+) regulatory T cells (Treg cells) are distinct from those in other organs and have gut-specific phenotypes and functions. Whereas Treg cells in other organs have T cell receptors (TCRs) specific for self antigens, intestinal Treg cells have a distinct set of TCRs that are specific for intestinal antigens, and these cells have pivotal roles in the suppression of immune responses against harmless dietary antigens and commensal microorganisms. The differentiation, migration and maintenance of intestinal Treg cells are controlled by specific signals from the local environment. In particular, certain members of the microbiota continuously provide antigens and immunoregulatory small molecules that modulate intestinal Treg cells. Understanding the development and the maintenance of intestinal Treg cells provides important insights into disease-relevant host-microorganism interactions.

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms.

PubMed

Sibanda, Timothy; Selvarajan, Ramganesh; Tekere, Memory

2017-05-01

Synthetic extreme environments like carwash effluent tanks and drains are potential sources of biotechnologically important microorganisms and molecules which have, however, remained unexplored. Using culture- and molecular-based methods, a total of 17 bacterial isolates belonging to the genera Shewanella, Proteus, Paenibacillus, Enterobacter and Citrobacter, Aeromonas, Pseudomonas and Pantoea were identified. Hydrocarbon utilization and enzyme production screening assays showed that Aeromonas sp. CAC11, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 and Citrobacter sp. PCW7 were able to degrade benzanthracene, naphthalene and diesel oil, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 could produce cellulase enzyme, while Proteus sp. BPS2, Pseudomonas sp. SAS8 and Proteus sp. CAL3 could produce lipase. GC-MS analysis of bacterial secondary metabolites resulted in identification of 107 different compounds produced by Proteus sp. BPS2, Paenibacillus sp. CAC12, Pseudomonas sp. SAS8, Proteus sp. CAL3 and Paenibacillus sp. CAC13. Most of the compounds identified by both GC-MS and LC-MS have previously been determined to have antibacterial, antifungal and/or anticancer properties. Further, microbial metabolites which have previously been known to be produced only by plants or microorganisms found in natural extreme environments were also identified in this study. This research has revealed the immense bioresource potential of microorganisms inhabiting synthetic extreme environments. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

PubMed Central

Rahi, Praveen; Prakash, Om; Shouche, Yogesh S.

2016-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies. PMID:27625644

Microbial diversity and interactions in subgingival biofilm communities.

PubMed

Diaz, Patricia I

2012-01-01

The human subgingival environment is a complex environmental niche where microorganisms from the three domains of life meet to form diverse biofilm communities that exist in close proximity to the host. Bacteria constitute the most abundant, diverse and ultimately well-studied component of these communities with about 500 bacterial taxa reported to occur in this niche. Cultivation and molecular approaches are revealing the breadth and depth of subgingival biofilm diversity as part of an effort to understand the subgingival microbiome, the collection of microorganisms that inhabit the gingival crevices. Although these investigations are constructing a pretty detailed taxonomical census of subgingival microbial communities, including inter-subject and temporal variability in community structure, as well as differences according to periodontal health status, we are still at the front steps in terms of understanding community function. Clinical studies that evaluate community structure need to be coupled with biologically relevant models that allow evaluation of the ecological determinants of subgingival biofilm maturation. Functional characteristics of subgingival biofilm communities that still need to be clarified include main metabolic processes that support microbial communities, identification of keystone species, microbial interactions and signaling events that lead to community maturation and the relationship of different communities with the host. This manuscript presents a summary of our current understanding of subgingival microbial diversity and an overview of experimental models used to dissect the functional characteristics of subgingival communities. Future coupling of 'omics'-based approaches with such models will facilitate a better understanding of subgingival ecology opening opportunities for community manipulation. Copyright © 2012 S. Karger AG, Basel.

Bubble Shuttle: A newly discovered transport mechanism, which transfers microorganisms from the sediment into the water column

NASA Astrophysics Data System (ADS)

Schmale, O.; Stolle, C.; Leifer, I.; Schneider von Deimling, J.; Kiesslich, K.; Krause, S.; Frahm, A.; Treude, T.

2013-12-01

The diversity and abundance of methanotrophic microorganisms is well studied in the aquatic environment, indicating their importance in biogeochemical cycling of methane in the sediment and the water column. However, whether methanotrophs are distinct populations in these habitats or are exchanged between benthic and pelagic environments, remains an open question. Therefore, field studies were conducted at the 'Rostocker Seep' site (Coal Oil Point seep area, California, USA) to test our hypothesis that methane-oxidizing microorganisms can be transported by gas bubbles from the sediment into the water column. The natural methane emanating location 'Rostocker Seep' showed a strong surface water oversaturation in methane with respect to the atmospheric equilibrium. Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) analyzes were performed to determine the abundance of aerobic and anaerobic methanotrophic microorganisms. Aerobic methane oxidizing bacteria were detected in the sediment and the water column, whereas anaerobic methanotrophs were detected exclusively in the sediment. The key device of the project was the newly developed "Bubble Catcher" used to collect naturally emanating gas bubbles at the sea floor together with particles attached to the bubble surface rim. Bubble Catcher experiments were carried out directly above a natural bubble release spot and on a reference site at which artificially released gas bubbles were caught, which had no contact with the sediment. CARD-FISH analyzes showed that aerobic methane oxidizing bacteria were transported by gas bubbles from the sediment into the water column. In contrast anaerobic methanotrophs were not detected in the bubble catcher. Further results indicate that this newly discovered Bubble Shuttle transport mechanism might influence the distribution pattern of methanotrophic microorganisms in the water column and even at the air-sea interface. Methane seep areas are often characterized by an elevated abundance of methane-oxidizing microorganisms, which consume a considerable amount of methane before it escapes into the atmosphere. Based on our study we hypothesize that the Bubble Shuttle transport mechanism contributes to this pelagic methane sink by a sediment-water column transfer of methane oxidizing microorganisms. Furthermore, this Bubble Shuttle may influence the methanotrophic community in the water column after massive short-term submarine inputs of methane (e.g. release of methane from bore holes). Especially in deep-sea regions, where the abundance of methane oxidizing microorganisms in the water column is low in general, Bubble Shuttle may inject a relevant amount of methane oxidizing microorganisms into the water column during massive inputs, supporting indirectly the turnover of this greenhouse active trace gas in the submarine environment.

Biomachining: metal etching via microorganisms.

PubMed

Díaz-Tena, Estíbaliz; Barona, Astrid; Gallastegui, Gorka; Rodríguez, Adrián; López de Lacalle, L Norberto; Elías, Ana

2017-05-01

The use of microorganisms to remove metal from a workpiece is known as biological machining or biomachining, and it has gained in both importance and scientific relevance over the past decade. Conversely to mechanical methods, the use of readily available microorganisms is low-energy consuming, and no thermal damage is caused during biomachining. The performance of this sustainable process is assessed by the material removal rate, and certain parameters have to be controlled for manufacturing the machined part with the desired surface finish. Although the variety of microorganisms is scarce, cell concentration or density plays an important role in the process. There is a need to control the temperature to maintain microorganism activity at its optimum, and a suitable shaking rate provides an efficient contact between the workpiece and the biological medium. The system's tolerance to the sharp changes in pH is quite limited, and in many cases, an acid medium has to be maintained for effective performance. This process is highly dependent on the type of metal being removed. Consequently, the operating parameters need to be determined on a case-by-case basis. The biomachining time is another variable with a direct impact on the removal rate. This biological technique can be used for machining simple and complex shapes, such as series of linear, circular, and square micropatterns on different metal surfaces. The optimal biomachining process should be fast enough to ensure high production, a smooth and homogenous surface finish and, in sum, a high-quality piece. As a result of the high global demand for micro-components, biomachining provides an effective and sustainable alternative. However, its industrial-scale implementation is still pending.

Assessment of the scalability of a microtiter plate system for screening of oleaginous microorganisms.

PubMed

Kosa, Gergely; Vuoristo, Kiira S; Horn, Svein Jarle; Zimmermann, Boris; Afseth, Nils Kristian; Kohler, Achim; Shapaval, Volha

2018-06-01

Recent developments in molecular biology and metabolic engineering have resulted in a large increase in the number of strains that need to be tested, positioning high-throughput screening of microorganisms as an important step in bioprocess development. Scalability is crucial for performing reliable screening of microorganisms. Most of the scalability studies from microplate screening systems to controlled stirred-tank bioreactors have been performed so far with unicellular microorganisms. We have compared cultivation of industrially relevant oleaginous filamentous fungi and microalga in a Duetz-microtiter plate system to benchtop and pre-pilot bioreactors. Maximal glucose consumption rate, biomass concentration, lipid content of the biomass, biomass, and lipid yield values showed good scalability for Mucor circinelloides (less than 20% differences) and Mortierella alpina (less than 30% differences) filamentous fungi. Maximal glucose consumption and biomass production rates were identical for Crypthecodinium cohnii in microtiter plate and benchtop bioreactor. Most likely due to shear stress sensitivity of this microalga in stirred bioreactor, biomass concentration and lipid content of biomass were significantly higher in the microtiter plate system than in the benchtop bioreactor. Still, fermentation results obtained in the Duetz-microtiter plate system for Crypthecodinium cohnii are encouraging compared to what has been reported in literature. Good reproducibility (coefficient of variation less than 15% for biomass growth, glucose consumption, lipid content, and pH) were achieved in the Duetz-microtiter plate system for Mucor circinelloides and Crypthecodinium cohnii. Mortierella alpina cultivation reproducibility might be improved with inoculation optimization. In conclusion, we have presented suitability of the Duetz-microtiter plate system for the reproducible, scalable, and cost-efficient high-throughput screening of oleaginous microorganisms.

Use of in-vitro experimental results to model in-situ experiments: bio-denitrification under geological disposal conditions.

PubMed

Masuda, Kaoru; Murakami, Hiroshi; Kurimoto, Yoshitaka; Kato, Osamu; Kato, Ko; Honda, Akira

2013-01-01

Some of the low level radioactive wastes from reprocessing of spent nuclear fuels contain nitrates. Nitrates can be present in the form of soluble salts and can be reduced by various reactions. Among them, reduction by metal compounds and microorganisms seems to be important in the underground repository. Reduction by microorganism is more important in near field area than inside the repository because high pH and extremely high salt concentration would prevent microorganism activities. In the near field, pH is more moderate (pH is around 8) and salt concentration is lower. However, the electron donor may be limited there and it might be the control factor for microorganism's denitrification activities. In this study, in-vitro experiments of the nitrate reduction reaction were conducted using model organic materials purported to exist in underground conditions relevant to geological disposal. Two kinds of organic materials were selected. A super plasticizer was selected as being representative of the geological disposal system and humic acid was selected as being representative of pre-existing organic materials in the bedrock. Nitrates were reduced almost to N2 gas in the existence of super plasticizer. In the case of humic acids, although nitrates were reduced, the rate was much lower and, in this case, dead organism was used as an electron donor instead of humic acids. A reaction model was developed based on the in-vitro experiments and verified by running simulations against data obtained from in-situ experiments using actual groundwaters and microorganisms. The simulation showed a good correlation with the experimental data and contributes to the understanding of microbially mediated denitrification in geological disposal systems.

A brief introduction to the model microswimmer Chlamydomonas reinhardtii

NASA Astrophysics Data System (ADS)

Jeanneret, Raphaël; Contino, Matteo; Polin, Marco

2016-11-01

The unicellular biflagellate green alga Chlamydomonas reinhardtii has been an important model system in biology for decades, and in recent years it has started to attract growing attention also within the biophysics community. Here we provide a concise review of some of the aspects of Chlamydomonas biology and biophysics most immediately relevant to physicists that might be interested in starting to work with this versatile microorganism.

Microbiologic study of soft contact lenses after laser subepithelial keratectomy for myopia.

PubMed

Hondur, Ahmet; Bilgihan, Kamil; Cirak, Meltem Yalinay; Dogan, Ozgur; Erdinc, Alper; Hasanreisoglu, Berati

2008-01-01

To evaluate the extent and agents of bacterial contamination of bandage disposable soft contact lenses after laser subepithelial keratectomy (LASEK) and to correlate the findings with clinical data. Disposable soft contact lenses were collected from 52 eyes of 26 consecutive patients treated with LASEK for myopia. The patients were treated with a fixed combination of tobramycin and diclofenac until epithelial closure. The lenses were removed on the fourth or fifth postoperative day with sterile forceps and immediately placed in sterile tubes containing culture media brain-heart infusion broth. The lenses were evaluated for microbial colonization. Of the 52 contact lenses analyzed, six (11.5%) had positive cultures. However, no clinical finding of infection was noted. Isolated microorganisms were coagulase-negative staphylococci (two lenses), Stenotrophomonas maltophilia (two lenses), Acinetobacter species (one lens), and Aeromonas hydrophila (one lens). Except for one case, the microorganisms were sensitive to the administered antibiotic. The risk of infectious keratitis after LASEK seems to be low. Except for staphylococci, the isolated microorganisms have not been previously reported to colonize the ocular surface or cause keratitis after refractive surgery. These findings may suggest a changing trend of potentially infectious agents after surface ablation.

[Formation of microbial biofilms in causative agents of acute and chronic pyelonephritis].

PubMed

Lagun, L V; Atanasova, Iu V; Tapal'skiĭ, D V

2013-01-01

Study the intensity of formation of microbial biofilms by Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus strains isolated during various forms of pyelonephritis. 150 clinical isolates of microorganisms isolated from urine ofpatientswith acute and chronic pyelonephritiswere included into the study. Determination of intensity of film-formation was carried out by staining of the formed biofilms by crystal violet with consequent extraction of the dye and measurement of its concentration in washout solution. Among causative agents ofpyelonephritis P. aeruginosa isolates had the maximum film-forming ability. The intensity of biofilm formation of these isolates was 2-3 time higher than staphylococcus and enterobacteria strains. Strains isolated from patients with chronic pyelonephritis by ability to form biofilms significantly surpassed strains isolated from acute pyelonephritis patients. A higher ability to form microbial biofilms for microorganisms--causative agents of pyelonephritis progressing against the background ofurolithiasis was noted. The ability to form biofilms is determined by both causative agent species and character of the infectious process in which this microorganism participates. Intensive formation of biofilms by E. coli, P. aeruginosa, K. pneumoniae, S. aureus clinical isolates may be an important factor of chronization of urinary tract infections.

Relevance of microbial coculture fermentations in biotechnology.

PubMed

Bader, J; Mast-Gerlach, E; Popović, M K; Bajpai, R; Stahl, U

2010-08-01

The purpose of this article is to review coculture fermentations in industrial biotechnology. Examples for the advantageous utilization of cocultures instead of single cultivations include the production of bulk chemicals, enzymes, food additives, antimicrobial substances and microbial fuel cells. Coculture fermentations may result in increased yield, improved control of product qualities and the possibility of utilizing cheaper substrates. Cocultivation of different micro-organisms may also help to identify and develop new biotechnological substances. The relevance of coculture fermentations and the potential of improving existing processes as well as the production of new chemical compounds in industrial biotechnology are pointed out here by means of more than 35 examples.

Application of the MALDI Biotyper to clinical microbiology: progress and potential.

PubMed

Kostrzewa, Markus

2018-03-01

The introduction of the MALDI Biotyper in laboratories substantially changed microbiology practice, this has been called a revolution. The system accelerated diagnostic while costs were reduced and accuracy was increased. In just a few years MALDI-TOF MS became the first-line identification tool for microorganisms. Ten years after its introduction, more than 2000 MALDI Biotyper systems are installed in laboratories which are performing routine diagnostic, and the number is still increasing. Areas covered: This article summarises changes in clinical microbiology introduced by the MALDI Biotyper and its effects, as it has been published in peer reviewed articles found in PubMed. Further, the potential of novel developments to increase the value of the system is described. Expert commentary: The MALDI Biotyper has significantly improved clinical microbiology in the area of microorganism identification. Now new developments and applications, e.g. for typing and resistance testing, might further increase its value in clinical microbiology. The systems might get the central diagnostic analyser which is getting integrated into the widely automated microbiology laboratories of the future.

Optimizing identification of clinically relevant Gram-positive organisms by use of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system.

PubMed

McElvania Tekippe, Erin; Shuey, Sunni; Winkler, David W; Butler, Meghan A; Burnham, Carey-Ann D

2013-05-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including "heavy" (H) and "light" (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or "score." We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS.

Optimizing Identification of Clinically Relevant Gram-Positive Organisms by Use of the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System

PubMed Central

McElvania TeKippe, Erin; Shuey, Sunni; Winkler, David W.; Butler, Meghan A.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including “heavy” (H) and “light” (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or “score.” We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS. PMID:23426925

Effect of the antimicrobial photodynamic therapy on microorganism reduction in deep caries lesions: a systematic review and meta-analysis.

PubMed

Ornellas, Pâmela Oliveira; Antunes, Leonardo Dos Santos; Fontes, Karla Bianca Fernandes da Costa; Póvoa, Helvécio Cardoso Corrêa; Küchler, Erika Calvano; Iorio, Natalia Lopes Pontes; Antunes, Lívia Azeredo Alves

2016-09-01

This study aimed to perform a systematic review to assess the effectiveness of antimicrobial photodynamic therapy (aPDT) in the reduction of microorganisms in deep carious lesions. An electronic search was conducted in Pubmed, Web of Science, Scopus, Lilacs, and Cochrane Library, followed by a manual search. The MeSH terms, MeSH synonyms, related terms, and free terms were used in the search. As eligibility criteria, only clinical studies were included. Initially, 227 articles were identified in the electronic search, and 152 studies remained after analysis and exclusion of the duplicated studies; 6 remained after application of the eligibility criteria; and 3 additional studies were found in the manual search. After access to the full articles, three were excluded, leaving six for evaluation by the criteria of the Cochrane Collaboration’s tool for assessing risk of bias. Of these, five had some risk of punctuated bias. All results from the selected studies showed a significant reduction of microorganisms in deep carious lesions for both primary and permanent teeth. The meta-analysis demonstrated a significant reduction in microorganism counts in all analyses (p<0.00001). Based on these findings, there is scientific evidence emphasizing the effectiveness of aPDT in reducing microorganisms in deep carious lesions.

Effect of the antimicrobial photodynamic therapy on microorganism reduction in deep caries lesions: a systematic review and meta-analysis

NASA Astrophysics Data System (ADS)

Ornellas, Pâmela Oliveira; Antunes, Leonardo Santos; Fontes, Karla Bianca Fernandes da Costa; Póvoa, Helvécio Cardoso Corrêa; Küchler, Erika Calvano; Iorio, Natalia Lopes Pontes; Antunes, Lívia Azeredo Alves

2016-09-01

This study aimed to perform a systematic review to assess the effectiveness of antimicrobial photodynamic therapy (aPDT) in the reduction of microorganisms in deep carious lesions. An electronic search was conducted in Pubmed, Web of Science, Scopus, Lilacs, and Cochrane Library, followed by a manual search. The MeSH terms, MeSH synonyms, related terms, and free terms were used in the search. As eligibility criteria, only clinical studies were included. Initially, 227 articles were identified in the electronic search, and 152 studies remained after analysis and exclusion of the duplicated studies; 6 remained after application of the eligibility criteria; and 3 additional studies were found in the manual search. After access to the full articles, three were excluded, leaving six for evaluation by the criteria of the Cochrane Collaboration's tool for assessing risk of bias. Of these, five had some risk of punctuated bias. All results from the selected studies showed a significant reduction of microorganisms in deep carious lesions for both primary and permanent teeth. The meta-analysis demonstrated a significant reduction in microorganism counts in all analyses (p<0.00001). Based on these findings, there is scientific evidence emphasizing the effectiveness of aPDT in reducing microorganisms in deep carious lesions.

Cyst infection in autosomal dominant polycystic kidney disease: causative microorganisms and susceptibility to lipid-soluble antibiotics.

PubMed

Suwabe, T; Araoka, H; Ubara, Y; Kikuchi, K; Hazue, R; Mise, K; Hamanoue, S; Ueno, T; Sumida, K; Hayami, N; Hoshino, J; Imafuku, A; Kawada, M; Hiramatsu, R; Hasegawa, E; Sawa, N; Takaichi, K

2015-07-01

Cyst infection is a frequent and serious complication of autosomal dominant polycystic kidney disease (ADPKD). Lipid-soluble antibiotics like fluoroquinolones show good penetration into cysts and are recommended for cyst infection, but causative microorganisms are often resistant to these agents. This study investigated the profile of the microorganisms causing cyst infection in ADPKD, their susceptibility to lipid-soluble antibiotics, and clinical outcomes. This retrospective study reviewed all ADPKD patients admitted to Toranomon Hospital with a diagnosis of cyst infection from January 2004 to March 2014. All patients who underwent cyst drainage and had positive cyst fluid cultures were enrolled. Patients with positive blood cultures who satisfied our criteria for cyst infection or probable infection were also enrolled. There were 99 episodes with positive cyst fluid cultures and 93 episodes with positive blood cultures. The majority of patients were on dialysis. The death rate was high when infection was caused by multiple microorganisms or when there were multiple infected cysts. Gram-negative bacteria accounted for 74-79 % of the isolates in all groups, except for patients with positive hepatic cyst fluid cultures. The susceptibility of Escherichia coli to fluoroquinolones was very low in patients with hepatic cyst infection, especially those with frequent episodes and those with hepatomegaly. Fungi were detected in two episodes. Fluoroquinolone-resistant microorganisms showed a high prevalence in cyst infection. It is important to identify causative microorganisms to avoid the overuse of fluoroquinolones and to improve the outcome of cyst infection in ADPKD.

Clinical relevance vs. statistical significance: Using neck outcomes in patients with temporomandibular disorders as an example.

PubMed

Armijo-Olivo, Susan; Warren, Sharon; Fuentes, Jorge; Magee, David J

2011-12-01

Statistical significance has been used extensively to evaluate the results of research studies. Nevertheless, it offers only limited information to clinicians. The assessment of clinical relevance can facilitate the interpretation of the research results into clinical practice. The objective of this study was to explore different methods to evaluate the clinical relevance of the results using a cross-sectional study as an example comparing different neck outcomes between subjects with temporomandibular disorders and healthy controls. Subjects were compared for head and cervical posture, maximal cervical muscle strength, endurance of the cervical flexor and extensor muscles, and electromyographic activity of the cervical flexor muscles during the CranioCervical Flexion Test (CCFT). The evaluation of clinical relevance of the results was performed based on the effect size (ES), minimal important difference (MID), and clinical judgement. The results of this study show that it is possible to have statistical significance without having clinical relevance, to have both statistical significance and clinical relevance, to have clinical relevance without having statistical significance, or to have neither statistical significance nor clinical relevance. The evaluation of clinical relevance in clinical research is crucial to simplify the transfer of knowledge from research into practice. Clinical researchers should present the clinical relevance of their results. Copyright © 2011 Elsevier Ltd. All rights reserved.

Biotechnical use of polymerase chain reaction for microbiological analysis of biological samples.

PubMed

Lantz, P G; Abu al-Soud, W; Knutsson, R; Hahn-Hägerdal, B; Rådström, P

2000-01-01

Since its introduction in the mid-80s, polymerase chain reaction (PCR) technology has been recognised as a rapid, sensitive and specific molecular diagnostic tool for the analysis of micro-organisms in clinical, environmental and food samples. Although this technique can be extremely effective with pure solutions of nucleic acids, it's sensitivity may be reduced dramatically when applied directly to biological samples. This review describes PCR technology as a microbial detection method, PCR inhibitors in biological samples and various sample preparation techniques that can be used to facilitate PCR detection, by either separating the micro-organisms from PCR inhibitors and/or by concentrating the micro-organisms to detectable concentrations. Parts of this review are updated and based on a doctoral thesis by Lantz [1] and on a review discussing methods to overcome PCR inhibition in foods [2].

Microneedle arrays allow lower microbial penetration than hypodermic needles in vitro.

PubMed

Donnelly, Ryan F; Singh, Thakur Raghu Raj; Tunney, Michael M; Morrow, Desmond I J; McCarron, Paul A; O'Mahony, Conor; Woolfson, A David

2009-11-01

In this study we determined, for the first time, the ability of microorganisms to traverse microneedle-induced holes using two different in vitro models. When employing Silescol membranes, the numbers of Candida albicans, Pseudomonas aeruginosa and Staphylococcus epidermidis crossing the membranes were an order of magnitude lower when the membranes were punctured by microneedles rather than a 21G hypodermic needle. Apart from the movement of C. albicans across hypodermic needle-punctured membranes, where 40.2% of the microbial load on control membranes permeated the barrier over 24 h, the numbers of permeating microorganisms was less than 5% of the original microbial load on control membranes. Experiments employing excised porcine skin and radiolabelled microorganisms showed that the numbers of microorganisms penetrating skin beyond the stratum corneum were approximately an order of magnitude greater than the numbers crossing Silescol membranes in the corresponding experiments. Approximately 10(3) cfu of each microorganism adhered to hypodermic needles during insertion. The numbers of microorganisms adhering to MN arrays were an order of magnitude higher in each case. We have shown here that microneedle puncture resulted in significantly less microbial penetration than did hypodermic needle puncture and that no microorganisms crossed the viable epidermis in microneedle-punctured skin, in contrast to needle-punctured skin. Given the antimicrobial properties of skin, it is, therefore, likely that application of microneedle arrays to skin in an appropriate manner would not cause either local or systemic infection in normal circumstances in immune-competent patients. In supporting widespread clinical use of microneedle-based delivery systems, appropriate animal studies are now needed to conclusively demonstrate this in vivo. Safety in patients will be enhanced by aseptic or sterile manufacture and by fabricating microneedles from self-disabling materials (e.g. dissolving or biodegradable polymers) to prevent inappropriate or accidental reuse.

Development of a Quantitative TaqMan{trademark}-PCR Assay and Feasibility of Atmosphoric Collection for Coccidioides Immits for Ecological Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daniels, J I; Wilson, W J; DeSantis, T Z

2002-02-01

Understanding and then modeling the complex relationships between environmental, climatological, and biological systems can present great opportunities for developing effective strategies to prevent outbreaks of environmentally linked infectious disease. For example, a report from the American Academy of Microbiology (Rose et al., 2001) points out that including climatic signals and ecological triggers into the decision making process for disease management, is going to be essential for developing a proactive approach for protecting public health, and circumventing the practice of having to wait for clinical cases to appear before any action is taken. To meet this grand challenge, specific and sensitivemore » analytical techniques and effective collection devices are required for finding the microorganisms of concern in environmentally relevant media (air, soil, water, vegetation, etc.), and a multidisciplinary approach is needed for evaluating all of the environmental and biological data and building the applicable predictive models. In this study, the unique capabilities in biotechnology and environmental science available at Lawrence Livermore National Laboratory (LLNL) are combined with the distinguished and highly regarded expertise for clinically investigating and treating infectious disease at the Department of Microbiology and Immunology in the School of Medicine of the University of California, Davis, in order to develop, standardize, validate, and test safely the feasibility of applying advanced polymerase chain reaction (PCR) technology and new air-sample collection media that would be appropriate for addressing comprehensively the environmentally linked, medically important infectious disease Valley Fever (coccidioidomycosis). The responsible agent for this disease is the airborne spore (arthroconidia) of the pathogenic fungus Coccidioides immitis, which is a microorganism that is endemic to California, Arizona, and the southwestern United States, and also is identified as a select (biological) agent in the federal Anti-Terrorist and Effective Death Penalty Act. Successful demonstration of these tools in this study will place this multidisciplinary team in a credible position to proceed with additional research designed to determine the climatic signals and ecological triggers that would be associated with the presence of this microorganism environmentally and that would correlate with subsequent outbreaks of Valley Fever clinically. Results from such future research would then provide the information needed for environmental intervention of the disease occurrence, well before clinical cases appear. The technology and modeling developed for such a study also could be used for determining the ecology of other environmentally linked, medically important infectious diseases that occur naturally or that might be introduced deliberately into environmental media indoors or outside. The following approach was taken to achieve the technological objectives of this study. First, the protocols for the TaqMan{trademark}-PCR assay were enhanced to achieve the superior specificity and sensitivity required for quantifying, from a DNA signature, those C. immitis spores that are present in calibration samples (consisting of known quantities of pure culture inoculated onto air-filter concentrate, and then removed, and the DNA extracted) and those that are present within the calibration range on air filters obtained from the field and handled similarly. Second, the feasibility of using advanced nuclepore air-filter media to collect the spores from ambient air in C immitis endemic areas in the Central Valley of California was evaluated. These membranes permit the physics of high-volume air sampling to be used to filter larger amounts of air than previously possible for detecting airborne microorganisms. Thus, the higher volume of air flow improves the likelihood of capturing on the filter any C. immitis spores resuspended from nearby soil, where this microorganism grows prior to sporulation, and where its exact location can be elusive under any environmental conditions. Finally, experiments were conducted in the Department of Microbiology and Immunology at the School of Medicine of the University of California, Davis (UCD), to demonstrate that C. immitis spores can be killed, whether in pure culture or on air-filter media, to ensure safe handling during laboratory processing and analyses.« less

Spontaneous regression of tumour and the role of microbial infection – possibilities for cancer treatment

PubMed Central

Cervinkova, Monika

2016-01-01

This review deals with the role of microorganisms in spontaneous regression of a tumour. Spontaneous cancer regression is a phenomenon that has been described for many centuries. One of the most well known methods of inducing spontaneous regression of cancer is the application of Coley’s toxin (heat-killed Streptococcus pyogenes and Serratia marcescens), which has been used for the successful treatment of sarcomas, carcinomas, lymphomas, myelomas and melanomas. In clinical practice, the use of Bacillus Calmette-Guérin vaccine for the treatment of superficial urinary bladder cancer is the most common instance of the application of microorganisms for the treatment of cancer. This review provides further information on other tested bacteria – Clostridium spp., Bifidobacterium spp., Lactobacillus spp. and Salmonella spp. – in this field of study. Among new age methods, bactofection, alternative gene therapy, combination bacteriolytic therapy and bacteria-directed enzyme prodrug therapy are some of the potential cancer treatment modalities that use microorganisms. We have also provided information about the interconnection among microorganisms, immune system response, and the possible mechanisms involved in the spontaneous regression of tumours. PMID:26813865

Spontaneous regression of tumour and the role of microbial infection--possibilities for cancer treatment.

PubMed

Kucerova, Petra; Cervinkova, Monika

2016-04-01

This review deals with the role of microorganisms in spontaneous regression of a tumour. Spontaneous cancer regression is a phenomenon that has been described for many centuries. One of the most well known methods of inducing spontaneous regression of cancer is the application of Coley's toxin (heat-killed Streptococcus pyogenes and Serratia marcescens), which has been used for the successful treatment of sarcomas, carcinomas, lymphomas, myelomas and melanomas. In clinical practice, the use of Bacillus Calmette-Guérin vaccine for the treatment of superficial urinary bladder cancer is the most common instance of the application of microorganisms for the treatment of cancer. This review provides further information on other tested bacteria--Clostridium spp., Bifidobacterium spp., Lactobacillus spp. and Salmonella spp.--in this field of study. Among new age methods, bactofection, alternative gene therapy, combination bacteriolytic therapy and bacteria-directed enzyme prodrug therapy are some of the potential cancer treatment modalities that use microorganisms. We have also provided information about the interconnection among microorganisms, immune system response, and the possible mechanisms involved in the spontaneous regression of tumours.

The role of natural environments in the evolution of resistance traits in pathogenic bacteria.

PubMed

Martinez, Jose L

2009-07-22

Antibiotics are among the most valuable compounds used for fighting human diseases. Unfortunately, pathogenic bacteria have evolved towards resistance. One important and frequently forgotten aspect of antibiotics and their resistance genes is that they evolved in non-clinical (natural) environments before the use of antibiotics by humans. Given that the biosphere is mainly formed by micro-organisms, learning the functional role of antibiotics and their resistance elements in nature has relevant implications both for human health and from an ecological perspective. Recent works have suggested that some antibiotics may serve for signalling purposes at the low concentrations probably found in natural ecosystems, whereas some antibiotic resistance genes were originally selected in their hosts for metabolic purposes or for signal trafficking. However, the high concentrations of antibiotics released in specific habitats (for instance, clinical settings) as a consequence of human activity can shift those functional roles. The pollution of natural ecosystems by antibiotics and resistance genes might have consequences for the evolution of the microbiosphere. Whereas antibiotics produce transient and usually local challenges in microbial communities, antibiotic resistance genes present in gene-transfer units can spread in nature with consequences for human health and the evolution of environmental microbiota that are largely ignored.

Activation, Impaired Tumor Necrosis Factor-α Production, and Deficiency of Circulating Mucosal-Associated Invariant T Cells in Patients with Scrub Typhus.

PubMed

Kang, Seung-Ji; Jin, Hye-Mi; Won, Eun Jeong; Cho, Young-Nan; Jung, Hyun-Ju; Kwon, Yong-Soo; Kee, Hae Jin; Ju, Jae Kyun; Kim, Jung-Chul; Kim, Uh Jin; Jang, Hee-Chang; Jung, Sook-In; Kee, Seung-Jung; Park, Yong-Wook

2016-07-01

Mucosal-associated invariant T (MAIT) cells contribute to protection against certain microorganism infections. However, little is known about the role of MAIT cells in Orientia tsutsugamushi infection. Hence, the aims of this study were to examine the level and function of MAIT cells in patients with scrub typhus and to evaluate the clinical relevance of MAIT cell levels. Thirty-eight patients with scrub typhus and 53 health control subjects were enrolled in the study. The patients were further divided into subgroups according to disease severity. MAIT cell level and function in the peripheral blood were measured by flow cytometry. Circulating MAIT cell levels were found to be significantly reduced in scrub typhus patients. MAIT cell deficiency reflects a variety of clinical conditions. In particular, MAT cell levels reflect disease severity. MAIT cells in scrub typhus patients displayed impaired tumor necrosis factor (TNF)-α production, which was restored during the remission phase. In addition, the impaired production of TNF-α by MAIT cells was associated with elevated CD69 expression. This study shows that circulating MAIT cells are activated, numerically deficient, and functionally impaired in TNF-α production in patients with scrub typhus. These abnormalities possibly contribute to immune system dysregulation in scrub typhus infection.

Survival, DNA Integrity, and Ultrastructural Damage in Antarctic Cryptoendolithic Eukaryotic Microorganisms Exposed to Ionizing Radiation

NASA Astrophysics Data System (ADS)

Pacelli, Claudia; Selbmann, Laura; Zucconi, Laura; Raguse, Marina; Moeller, Ralf; Shuryak, Igor; Onofri, Silvano

2017-02-01

Life dispersal between planets, planetary protection, and the search for biosignatures are main topics in astrobiology. Under the umbrella of the STARLIFE project, three Antarctic endolithic microorganisms, the melanized fungus Cryomyces antarcticus CCFEE 515, a hyaline strain of Umbilicaria sp. (CCFEE 6113, lichenized fungus), and a Stichococcus sp. strain (C45A, green alga), were exposed to high doses of space-relevant gamma radiation (60Co), up to 117.07 kGy. After irradiation survival, DNA integrity and ultrastructural damage were tested. The first was assessed by clonogenic test; viability and dose responses were reasonably described by the linear-quadratic formalism. DNA integrity was evaluated by PCR, and ultrastructural damage was observed by transmission electron microscopy. The most resistant among the tested organisms was C. antarcticus both in terms of colony formation and DNA preservation. Besides, results clearly demonstrate that DNA was well detectable in all the tested organisms even when microorganisms were dead. This high resistance provides support for the use of DNA as a possible biosignature during the next exploration campaigns. Implication in planetary protection and contamination during long-term space travel are put forward.

Antibiotic-Resistant Acinetobacter baumannii Increasing Success Remains a Challenge as a Nosocomial Pathogen

PubMed Central

Gonzalez-Villoria, Ana Maria; Valverde-Garduno, Veronica

2016-01-01

Antibiotic-resistant infectious bacteria currently imply a high risk and therefore constitute a strong challenge when treating patients in hospital settings. Characterization of these species and of particular strains is a priority for the establishment of diagnostic tests and preventive procedures. The relevance of Acinetobacter baumannii as a problematic microorganism in inpatient facilities, particularly intensive care units, has increased over time. This review aims to draw attention to (i) the historical emergence of carbapenem-resistant Acinetobacter baumannii, (ii) the current status of surveillance needs in Latin America, and (iii) recent data suggesting that A. baumannii continues to spread and evolve in hospital settings. First, we present synopsis of the series of events leading to the discovery and precise identification of this microorganism in hospital settings. Then key events in the acquisition of antibiotic-resistant genes by this microorganism are summarized, highlighting the race between new antibiotic generation and emergence of A. baumannii resistant strains. Here we review the historical development of this species as an infectious threat, the current state of its distribution, and antibiotic resistance characteristics, and we discuss future prospects for its control. PMID:26966582

Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle

PubMed Central

Rodriguez-Castaño, Gina P.; Caro-Quintero, Alejandro; Reyes, Alejandro; Lizcano, Fernando

2017-01-01

The “westernization” of global eating and lifestyle habits is associated with the growing rate of chronic diseases, mainly cardiovascular diseases, cancer, type 2 diabetes mellitus, and respiratory diseases. The primary prevention approach is to make nutritional and behavioral changes, however, there is another important determinant of our health that only recently has been considered and is the presence of beneficial microorganisms and their products in our gastrointestinal tract. Microorganisms living in our body can alter the fate of food, drugs, hormones, and xenobiotics, and recent studies point to the use of microorganisms that can counteract the harmful effects of certain compounds introduced or produced endogenously in our body. This review considers the effects of the western lifestyle on adiposity, glucose metabolism, oxidative markers and inflammation profile, emphasizes on the studies that have investigated bacterial strains and products of their metabolism that are beneficial under this lifestyle, and examines the screening strategies that recent studies are using to select the most promising probiotic isolates. In addition, we consider the relevance of studying the microbiota of metabolically healthy people under a western lifestyle for the understanding of the key components that delay the development of chronic diseases. PMID:28119734

New Proof-of-Concept in Viral Inactivation: Virucidal Efficacy of 405 nm Light Against Feline Calicivirus as a Model for Norovirus Decontamination.

PubMed

Tomb, Rachael M; Maclean, Michelle; Coia, John E; Graham, Elizabeth; McDonald, Michael; Atreya, Chintamani D; MacGregor, Scott J; Anderson, John G

2017-06-01

The requirement for novel decontamination technologies for use in hospitals is ever present. One such system uses 405 nm visible light to inactivate microorganisms via ROS-generated oxidative damage. Although effective for bacterial and fungal inactivation, little is known about the virucidal effects of 405 nm light. Norovirus (NoV) gastroenteritis outbreaks often occur in the clinical setting, and this study was designed to investigate potential inactivation effects of 405 nm light on the NoV surrogate, feline calicivirus (FCV). FCV was exposed to 405 nm light whilst suspended in minimal and organically-rich media to establish the virucidal efficacy and the effect biologically-relevant material may play in viral susceptibility. Antiviral activity was successfully demonstrated with a 4 Log 10 (99.99%) reduction in infectivity when suspended in minimal media evident after a dose of 2.8 kJ cm -2 . FCV exposed in artificial faeces, artificial saliva, blood plasma and other organically rich media exhibited an equivalent level of inactivation using between 50-85% less dose of the light, indicating enhanced inactivation when the virus is present in organically-rich biologically-relevant media. Further research in this area could aid in the development of 405 nm light technology for effective NoV decontamination within the hospital environment.

Microorganisms direct identification from blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Ferreira, L; Sánchez-Juanes, F; Porras-Guerra, I; García-García, M I; García-Sánchez, J E; González-Buitrago, J M; Muñoz-Bellido, J L

2011-04-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows a fast and reliable bacterial identification from culture plates. Direct analysis of clinical samples may increase its usefulness in samples in which a fast identification of microorganisms can guide empirical treatment, such as blood cultures (BC). Three hundred and thirty BC, reported as positive by the automated BC incubation device, were processed by conventional methods for BC processing, and by a fast method based on direct MALDI-TOF MS. Three hundred and eighteen of them yield growth on culture plates, and 12 were false positive. The MALDI-TOF MS-based method reported that no peaks were found, or the absence of a reliable identification profile, in all these false positive BC. No mixed cultures were found. Among these 318 BC, we isolated 61 Gram-negatives (GN), 239 Gram-positives (GP) and 18 fungi. Microorganism identifications in GN were coincident with conventional identification, at the species level, in 83.3% of BC and, at the genus level, in 96.6%. In GP, identifications were coincident with conventional identification in 31.8% of BC at the species level, and in 64.8% at the genus level. Fungaemia was not reliably detected by MALDI-TOF. In 18 BC positive for Candida species (eight C. albicans, nine C. parapsilosis and one C. tropicalis), no microorganisms were identified at the species level, and only one (5.6%) was detected at the genus level. The results of the present study show that this fast, MALDI-TOF MS-based method allows bacterial identification directly from presumptively positive BC in a short time (<30 min), with a high accuracy, especially when GN bacteria are involved. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms.

PubMed

Brandt, Kristian K; Amézquita, Alejandro; Backhaus, Thomas; Boxall, Alistair; Coors, Anja; Heberer, Thomas; Lawrence, John R; Lazorchak, James; Schönfeld, Jens; Snape, Jason R; Zhu, Yong-Guan; Topp, Edward

2015-12-01

Antibiotics play a pivotal role in the management of infectious disease in humans, companion animals, livestock, and aquaculture operations at a global scale. Antibiotics are produced, consumed, and released into the environment at an unprecedented scale causing concern that the presence of antibiotic residues may adversely impact aquatic and terrestrial ecosystems. Here we critically review the ecotoxicological assessment of antibiotics as related to environmental risk assessment (ERA). We initially discuss the need for more specific protection goals based on the ecosystem service concept, and suggest that the ERA of antibiotics, through the application of a mode of toxic action approach, should make more use of ecotoxicological endpoints targeting microorganisms (especially bacteria) and microbial communities. Key ecosystem services provided by microorganisms and associated ecosystem service-providing units (e.g. taxa or functional groups) are identified. Approaches currently available for elucidating ecotoxicological effects on microorganisms are reviewed in detail and we conclude that microbial community-based tests should be used to complement single-species tests to offer more targeted protection of key ecosystem services. Specifically, we propose that ecotoxicological tests should not only assess microbial community function, but also microbial diversity (‘species’ richness) and antibiotic susceptibility. Promising areas for future basic and applied research of relevance to ERA are highlighted throughout the text. In this regard, the most fundamental knowledge gaps probably relate to our rudimentary understanding of the ecological roles of antibiotics in nature and possible adverse effects of environmental pollution with subinhibitory levels of antibiotics.

Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lancaster, Andrew; Menon, Angeli; Scott, Israel

2014-03-26

Although as many as half of all proteins are thought to require a metal cofactor, the metalloproteomes of microorganisms remain relatively unexplored. Microorganisms from different environments are likely to vary greatly in the metals that they assimilate, not just among the metals with well-characterized roles but also those lacking any known function. Herein we investigated the metal utilization of two microorganisms that were isolated from very similar environments and are of interest because of potential roles in the immobilization of heavy metals, such as uranium and chromium. The metals assimilated and their concentrations in the cytoplasm of Desulfovibrio vulgaris strainmore » Hildenborough (DvH) and Enterobacter cloacae strain Hanford (EcH) varied dramatically, with a larger number of metals present in Enterobacter. For example, a total of 9 and 19 metals were assimilated into their cytoplasmic fractions, respectively, and DvH did not assimilate significant amounts of zinc or copper whereas EcH assimilated both. However, bioinformatic analysis of their genome sequences revealed a comparable number of predicted metalloproteins, 813 in DvH and 953 in EcH. These allowed some rationalization of the types of metal assimilated in some cases (Fe, Cu, Mo, W, V) but not in others (Zn, Nd, Ce, Pr, Dy, Hf and Th). It was also shown that U binds an unknown soluble protein in EcH but this incorporation was the result of extracellular U binding to cytoplasmic components after cell lysis.« less

Probiotics and clinical effects: is the number what counts?

PubMed

Bertazzoni, Elisa; Donelli, Gianfranco; Midtvedt, Tore; Nicoli, Jacques; Sanz, Yolanda

2013-08-01

Probiotics are defined as 'live microorganisms that when administered in adequate amounts confer health benefits on the host', underlining the need of microbial viability and the requirement of a suitable dose to obtain a health benefit. The dose and the administration regimen are critical issues for probiotics either ingested as foods claiming health benefits or used as drugs in clinics. In fact, regulatory authorities demand to guarantee consumers that a probiotic is effective in the recommended conditions of use and responds to its specific claims. Thus, a proper identification of probiotic strain(s), a definition of the amount of microorganisms surviving by the end of the product shelf-life, and a demonstration of their beneficial effects by appropriate human trials are required. The current knowledge on the effective dose of different probiotic strains used for several disorders is here reviewed.

Biological Production of a Hydrocarbon Fuel Intermediate Polyhydroxybutyrate (PHB) from a Process Relevant Lignocellulosic Derived Sugar (Poster)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, W.; Mittal, A.; Mohagheghi, A.

PHAs are synthesized by many microorganisms to serve as intracellular carbon storage molecules. In some bacterial strains, PHB can account for up to 80% of cell mass. In addition to its application in the packaging sector, PHB also has great potential as an intermediate in the production of hydrocarbon fuels. PHB can be thermally depolymerized and decarboxylated to propene which can be upgraded to hydrocarbon fuels via commercial oligomerization technologies. Cupriavidus necator is the microorganism that has been most extensively studied and used for PHB production on an industrial scale; However the substrates used for producing PHB are mainly fructose,more » glucose, sucrose, fatty acids, glycerol, etc., which are expensive. In this study, we demonstrate production of PHB from a process relevant lignocellulosic derived sugar stream, i.e., saccharified slurry from pretreated corn stover. The strain was first investigated in shake flasks for its ability to utilize glucose, xylose and acetate. In addition, the strain was also grown on pretreated lignocellulose hydrolyzate slurry and evaluated in terms of cell growth, sugar utilization, PHB accumulation, etc. The mechanism of inhibition in the toxic hydrolysate generated by the pretreatment and saccharification process of biomass, was also studied.« less

Methane producing bacteria: Immunological characterization: Progress report, April 1, 1984--June 30, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conway de Macario, E.; Macario, A.J.L.; Wolin, M.J.

1988-01-01

A major contribution of this research has been a significant advance of the immunology of methanogens and other archaebacteria (e.g., extreme halophiles). The foundations have been laid to begin the immunologic study of microbes which are non-methanogens themselves but are important for the fermentation process. This work helped to make clear that bacterial immunology goes beyond the study of pathogens for man, animals, or plants. Immunology can be applied successfully to the study of isolates of importance to understand evolution, phylogeny, ecology, bio-conversion systems, and to advance methanogenic biotechnology. Immunology holds considerable potential to aid in genetic and genetic engineeringmore » manipulations as well as in in situ handling of microbes relevant to methanogenesis. Thus, antibodies can help in the discovery of useful microbes, the generation of improved stains, the selection of desirable microorganisms, and in the monitoring and controlling of bioreactors. Immunogolic work in this new field should generate knowledge and devices relevant to areas such as Biological Energy Research, Ecology of Microorganisms, and Environmental (Sanitary) Engineering. In this regard, this work has contributed a comprehensive antiserum bank, a large panel of calibrated polyclonal antibody probes, and techniques for producing and utilizing these probes in the study of methanogens and related bacteria. 67 refs.« less

[Evaluation of mass spectrometry for the identification of clinically interesting yeasts].

PubMed

Galán, Fátima; García-Agudo, Lidia; Guerrero, Inmaculada; Marín, Pilar; García-Tapia, Ana; García-Martos, Pedro; Rodríguez-Iglesias, Manuel

2015-01-01

Identification of yeasts is based on morphological, biochemical and nutritional characteristics, and using molecular methods. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, a new method for the identification of microorganisms, has demonstrated to be very useful. The aim of this study is to evaluate this new method in the identification of yeasts. A total of 600 strains of yeasts isolated from clinical specimens belonging to 9 genera and 43 species were tested. Identification was made by sequencing of the ITS regions of ribosomal DNA, assimilation of carbon compounds (ID 32C), and mass spectrometry on a Microflex spectrometer (Bruker Daltonics GmbH, Germany). A total of 569 strains (94.8%) were identified to species level by ID 32C, and 580 (96.7%) by MALDI-TOF. Concordance between both methods was observed for 553 strains (92.2%), with 100% in clinically relevant species: C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and almost 100% in C. krusei. MALDI-TOF identified species requiring molecular methods: Candida dubliniensis, C. nivariensis, C. metapsilosis and C. orthopsilosis. Some irregularities were observed in the identification of arthroconidia yeast and basidiomycetes. MALDI-TOF is a rapid, effective and economic method, which enables the identification of most clinically important yeasts and the differentiation of closely related species. It would be desirable to include more species in its database to expand its performance. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Quantifying Glosair™ 400 efficacy for surface disinfection of American Type Culture Collection strains and micro-organisms recently isolated from intensive care unit patients.

PubMed

Herruzo, R; Vizcaíno, M J; Herruzo, I

2014-07-01

Microbial contamination of hospital surfaces may be a source of infection for hospitalized patients. We evaluated the efficacy of Glosair™ 400 against two American Type Culture Collection strains and 18 clinical isolates, placed on glass germ-carriers. Carriers were left to air-dry for 60 min and then exposed to a cycle before detection of any surviving micro-organisms. Antibiotic-susceptible Gram-negative bacilli were less susceptible (although not significantly) to this technique than resistant Gram-negative bacilli or Gram-positive cocci and yeasts (3, 3.4 and 4.6 log10 reduction, respectively). In conclusion, in areas that had not been cleaned, aerosolized hydrogen peroxide obtained >3 log10 mean destruction of patients' micro-organisms. Copyright © 2014 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

[Progress in synthetic biology of pinocembrin].

PubMed

Guo, Lei; Kong, Jianqiang

2015-04-01

Pinocembrin, belonging to flavanons, was isolated from various plants. Pinocembrin has a variety of pharmacological activities, such as neuroprotective effect, antimicrobial activity, and antioxidant efficacy. Pinocembrin was approved as class I drugs to its phase II clinical trial by CFDA in 2009, mainly used for the treatment of ischemic stroke. As a promising compound, the manufacturing technologies of pinocembrin, including chemical synthesis, extraction from plant and synthetic biology, have attracted many attentions. Compared with the first two technologies, synthetic biology has many advantages, such as environment-friendly and low-cost. Construction of biosynthetic pathway in microorganism offers promising results for large scale pinocembrin production by fermentation after taking lots of effective strategies. This article reviews some of recent strategies in microorganisms to improve the yield, with focus on the selection of appropriate the key enzyme sources, the supply of precursors and cofactors by microorganisms, the choice of substance and the level of the key enzyme expression.

Microbial Relevant Fouling in Membrane Bioreactors: Influencing Factors, Characterization, and Fouling Control

PubMed Central

Wu, Bing; Fane, Anthony G.

2012-01-01

Microorganisms in membrane bioreactors (MBRs) play important roles on degradation of organic/inorganic substances in wastewaters, while microbial deposition/growth and microbial product accumulation on membranes potentially induce membrane fouling. Generally, there is a need to characterize membrane foulants and to determine their relations to the evolution of membrane fouling in order to identify a suitable fouling control approach in MBRs. This review summarized the factors in MBRs that influence microbial behaviors (community compositions, physical properties, and microbial products). The state-of-the-art techniques to characterize biofoulants in MBRs were reported. The strategies for controlling microbial relevant fouling were discussed and the future studies on membrane fouling mechanisms in MBRs were proposed. PMID:24958297

The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace

PubMed Central

Roca, Ignasi; Espinal, Paula; Vila-Farrés, Xavier; Vila, Jordi

2012-01-01

During the past few decades Acinetobacter baumannii has evolved from being a commensal dweller of health-care facilities to constitute one of the most annoying pathogens responsible for hospitalary outbreaks and it is currently considered one of the most important nosocomial pathogens. In a prevalence study of infections in intensive care units conducted among 75 countries of the five continents, this microorganism was found to be the fifth most common pathogen. Two main features contribute to the success of A. baumannii: (i) A. baumannii exhibits an outstanding ability to accumulate a great variety of resistance mechanisms acquired by different mechanisms, either mutations or acquisition of genetic elements such as plasmids, integrons, transposons, or resistant islands, making this microorganism multi- or pan-drug-resistant and (ii) The ability to survive in the environment during prolonged periods of time which, combined with its innate resistance to desiccation and disinfectants, makes A. baumannii almost impossible to eradicate from the clinical setting. In addition, its ability to produce biofilm greatly contributes to both persistence and resistance. In this review, the pathogenesis of the infections caused by this microorganism as well as the molecular bases of antibacterial resistance and clinical aspects such as treatment and potential future therapeutic strategies are discussed in depth. PMID:22536199

Clinical impact of culture-positive preservation fluid on solid organ transplantation: A systematic review and meta-analysis.

PubMed

Oriol, Isabel; Sabé, N; Tebé, C; Veroux, M; Boin, I F S F; Carratalà, J

2018-04-01

Contamination of the preservation fluid (PF) used for donated organs is a potential source of post-transplant infection. However, the information on this issue is scarce. We therefore conducted a systematic review and meta-analysis to assess the incidence of culture-positive PF and its impact on solid organ transplant (SOT) recipients. Seventeen studies were identified and included. The overall incidence of culture-positive PF was 37% (95% CI: 27% to 49%), and the incidence of PF-related infections among SOT recipients with PF cultures that grew pathogenic microorganisms was 10% (95% CI: 7% to 15%). There were differences in the rates of infections due to pathogenic microorganisms between SOT recipients who received pre-emptive treatment and those who did not, but without statistical significance. The mortality rate among SOT recipients with PF-related infection was 35% (95% CI: 21% to 53%). In conclusion, although contamination of the PF of donated organs is frequent, the incidence of PF-related infection is relatively low. A closely clinical and microbiologic monitoring of the SOT recipient in case of culture-positive PF, regardless of the type of microorganism isolated might be do in order to establish a prompt diagnosis of PF-related infection. Copyright © 2017 Elsevier Inc. All rights reserved.

Bacteria and genetically modified bacteria as cancer therapeutics: Current advances and challenges.

PubMed

Nallar, Shreeram C; Xu, De-Qi; Kalvakolanu, Dhan V

2017-01-01

Bacteria act as pro- or anti- tumorigenic agents. Whole bacteria or cytotoxic or immunogenic peptides carried by them exert potent anti-tumor effects in the experimental models of cancer. The use of attenuated microorganism(s) e.g., BCG to treat human urinary bladder cancer was found to be superior compared to standard chemotherapy. Although the phase-I clinical trials with Salmonella enterica serovar Typhimurium, has shown limited benefits in human subjects, a recent pre-clinical trial in pet dogs with tumors reported some subjects benefited from this treatment strain. In addition to the attenuated host strains derived by conventional mutagenesis, recombinant DNA technology has been applied to a few microorganisms that have been evaluated in the context of tumor colonization and eradication using mouse models. There is an enormous surge in publications describing bacterial anti-cancer therapies in the past 15years. Vectors for delivering shRNAs that target oncogenic products, express tumor suppressor genes and immunogenic proteins have been developed. These approaches have showed promising anti-tumor activity in mouse models against various tumors. These can be potential therapeutics for humans in the future. In this review, some conceptual and practical issues on how to improve these agents for human applications are discussed. Copyright © 2016. Published by Elsevier Ltd.

In vitro activity of Aloe vera inner gel against microorganisms grown in planktonic and sessile phases.

PubMed

Cataldi, V; Di Bartolomeo, S; Di Campli, E; Nostro, A; Cellini, L; Di Giulio, M

2015-12-01

The failure of traditional antimicrobial treatments is becoming a worldwide problem. The use of Aloe vera is of particular interest for its role as curative agent and its efficacy in complementary therapies for a variety of illnesses. This study evaluated the antimicrobial activity of A. vera inner gel against a panel of microorganisms, Gram-positive and -negative bacteria, and Candida albicans. In addition to A. vera inner gel being used in the treatment of peptic ulcers, in dermatological treatments, and wound healing, it was also tested on the sessile phase of clinical Helicobacter pylori strains (including multi-drug-resistant strains) and on planktonic and sessile phase of Staphylococcus aureus/Pseudomonas aeruginosa clinical isolates from venous leg ulcers.A. vera inner gel expresses its prevalent activity against Gram-negative bacteria and C. albicans in respect to Gram-positive bacteria. The results of the A. vera antibiofilm activity showed a decrease of the produced biomass in a concentration-dependent-way, in each analyzed microorganism. The data obtained show that A. vera inner gel has both an antimicrobial and antibiofilm activity suggesting its potential use for the treatment of microbial infections, in particular for H. pylori gastric infection, especially in case of multi-drug-resistance, as well as for an effective wound dressing. © The Author(s) 2015.

Evaluation of Diuron Tolerance and Biotransformation by Fungi from a Sugar Cane Plantation Sandy-Loam Soil.

PubMed

Perissini-Lopes, Bruna; Egea, Tássia Chiachio; Monteiro, Diego Alves; Vici, Ana Cláudia; Da Silva, Danilo Grünig Humberto; Lisboa, Daniela Correa de Oliveira; de Almeida, Eduardo Alves; Parsons, John Robert; Da Silva, Roberto; Gomes, Eleni

2016-12-14

Microorganisms capable of degrading herbicides are essential to minimize the amount of chemical compounds that may leach into other environments. This work aimed to study the potential of sandy-loam soil fungi to tolerate the herbicide Herburon (50% diuron) and to degrade the active ingredient diuron. Verticillium sp. F04, Trichoderma virens F28, and Cunninghamella elegans B06 showed the highest growth in the presence of the herbicide. The evaluation of biotransformation showed that Aspergillus brasiliensis G08, Aspergillus sp. G25, and Cunninghamella elegans B06 had the greatest potential to degrade diuron. Statistical analysis demonstrated that glucose positively influences the potential of the microorganism to degrade diuron, indicating a cometabolic process. Due to metabolites founded by diuron biotransformation, it is indicated that the fungi are relevant in reducing the herbicide concentration in runoff, minimizing the environmental impact on surrounding ecosystems.

CRISPR-Cas Technologies and Applications in Food Bacteria.

PubMed

Stout, Emily; Klaenhammer, Todd; Barrangou, Rodolphe

2017-02-28

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.

DENTINE CARIES: ACID-TOLERANT MICROORGANISMS AND ASPECTS ON COLLAGEN DEGRADATION.

PubMed

Lager, Anders Hedenbjörk

2014-01-01

Dental caries is a common disease all over the world, despite the fact that it can be both effectively prevented and treated. It is driven by acids produced by oral microorganisms as a consequence of their metabolism of dietary carbohydrates. Given enough acid challenge, eventually the tooth enamel barrier will be broken down, and the carious lesion will extend into underlying hard tissue, forming a macroscopic cavity in the dentine. In comparison to biofilm on enamel, a dentine carious lesion provides a vastly different environment for the residing microorganisms. The environment influences the types and numbers of microorganisms that can colonize the dentine caries lesion. The overall aims for this thesis are to enumerate and further study microorganisms found in established dentine caries lesions and also to illuminate how host-derived proteolytic enzymes might contribute to this degradation, not only to better understand the caries process in dentine but also to find incitements for new methods to influence the natural progression of caries lesions. In Paper I, the numbers of remaining viable microorganisms after completed excavation using two excavation methods were investigated. Samples of carious dentine tissue were collected before and after excavation and cultivated on different agar media in different atmospheres. Analysis was performed by counting the number of colony-forming units (CFUs). Key findings: The number of remaining microorganisms after excavation was low for both methods, but some microorganisms always remained in the cavity floors even when the cavities were judged as caries free using normal clinical criteria. In Paper II, the acid tolerant microbiota in established dentine caries lesions was investigated. Samples were taken as in Paper I, but on three levels (superficial, center of lesion, floor of lesion after completed excavation). The samples were cultivated in anaerobic conditions on solid pH-selective agar media of different acidity. Key findings: Each investigated lesion harbored a unique microbiota in terms of both species composition and numbers of microorganisms. This indicates that various combinations of aciduric microorganisms can colonize, survive in and probably also propagate dentine carious lesions. We also found that solid pH-selective agars can be used successfully to select acid-tolerant microorganisms in caries lesions. This would preserve their phenotypic traits for further study. In Paper III, the relation between salivary levels of matrix metalloproteinase-8 (MMP-8), salivary levels of tissue inhibitor of MMP (TIMP-1), and the presence of manifest caries lesions in a large number of subjects was investigated. Saliva samples were collected and analyzed for concentrations of MMP-8, TIMP-1 and total protein using immunofluorometric assays, enzyme linked immunosorbent assays and Bradford assays, respectively. Key findings: Subjects with manifest caries lesions had significantly elevated levels of salivary MMP-8 compared to subjects without caries lesions. TIMP-1 was not significant in any case. In Paper IV, a new method for generating bioactive demineralized dentine matrix substrate (DDM) was developed using a dialysis system and two different demineralization approaches (acetic acid or EDTA). The generated DDM was subsequently analyzed for the presence of type 1 collagen, active MMP-8 and hydroxyproline (HYP) levels using SDS-PAGE, ELISA or immunofluorescence assay. Key findings: Both demineralization methods produced a substrate rich in collagen and with preserved MMP-8 activity. This report presents new knowledge on the composition of the acid tolerant dentine caries microbiota from three levels in dentine carious lesions and on the efficacy of operative caries removal on the numbers of viable microorganisms in the caries free cavity using two operative methods. Moreover, the basic mechanisms behind collagen degradation in the dentine caries process are studied from both a clinical and laboratory perspective. The report also provides a reference for further studies on dentine caries microbiology and dentine caries collagen degradation mechanisms, both of which are known only in part.

Phototherapy of adenoid disease in children

NASA Astrophysics Data System (ADS)

Naumov, Sergey A.; Chankov, Ivan I.; Volovodenko, Alexey V.; Khlusov, Igor A.; Vovk, Sergey M.; Tuchin, Valery V.

2004-08-01

The results presented testify to the high clinical effectiveness of therapy of adenoid disease based on photodynamic effects caused by combined action of physical (red light) and chemical factors (methylene blue) on pathogenic microorganisms. Original physiotherapy device and autonomous photostimulator of "Duny" Inc. were used. Clinical results have a good correlation with results of bacteriological and cell research conducted in vivo and in vitro.

Cross-sectional point prevalence survey to study the environmental contamination of nosocomial pathogens in intensive care units under real-life conditions.

PubMed

Wille, I; Mayr, A; Kreidl, P; Brühwasser, C; Hinterberger, G; Fritz, A; Posch, W; Fuchs, S; Obwegeser, A; Orth-Höller, D; Lass-Flörl, C

2018-01-01

In intensive care units (ICUs), inanimate surfaces and equipment may be contaminated by nosocomial pathogens, including multi-drug-resistant micro-organisms. To assess the degree of environmental contamination close to and distant from patients, and contamination of healthcare workers' (HCWs) hands with nosocomial pathogens under real-life conditions and to investigate potential transmission events. Over the course of three weeks, agar contact samples were taken close to and distant from patient areas and from HCWs' hands in eight ICUs of a tertiary care hospital in Innsbruck, Austria. Each ICU was visited once without announcement. Species identification and antimicrobial susceptibility testing were performed according to standard methods, and corresponding strains from patient, environment and hand samples were genotyped using pulsed-field gel electrophoresis. Among 523 samples, HCWs' hands were most frequently contaminated with potentially pathogenic bacteria (15.2%), followed by areas close to patients (10.9%) and areas distant from patients (9.1%). Gram-positive bacteria were identified most often (67.8%), with Enterococcus spp. being the most prevalent species (70% vancomycin sensitive and 30% vancomycin resistant) followed by Staphylococcus aureus, of which 64% were classified as meticillin-resistant Staphylococcus aureus. Molecular typing documented identical strains among patient, environment and hand isolates. This study found widespread contamination of the ICU environment with clinically relevant pathogens, including multi-drug-resistant micro-organisms, despite cleaning and disinfection. The bioburden might not be restricted to areas close to patients. The role of extended environmental disinfection of areas distant from patients in order to improve infection prevention needs further discussion. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Salivary protein adsorption and Streptococccus gordonii adhesion to dental material surfaces.

PubMed

Schweikl, Helmut; Hiller, Karl-Anton; Carl, Ulrich; Schweiger, Rainer; Eidt, Andreas; Ruhl, Stefan; Müller, Rainer; Schmalz, Gottfried

2013-10-01

The initial adhesion of microorganisms to clinically used dental biomaterials is influenced by physico-chemical parameters like hydrophobicity and pre-adsorption of salivary proteins. Here, polymethyl methacrylate (PMMA), polyethylene (PE), polytetrafluoroethylene (PTFE), silicone (Mucopren soft), silorane-based (Filtek Silorane) and methacrylate-based (Tetric EvoCeram) dental composites, a conventional glassionomer cement as well as cobalt-chromium-molybdenum (Co28Cr6Mo) and titanium (Ti6Al4V) were tested for adsorption of salivary proteins and adhesion of Streptococcus gordonii DL1. Wettability of material surfaces precoated with salivary proteins or left in phosphate-buffered saline was determined by the measurement of water contact angles. Amounts of adsorbed proteins were determined directly on material surfaces after biotinylation of amino groups and detection by horseradish peroxidase-conjugated avidin-D. The same technique was used to analyze for the binding of biotinylated bacteria to material surfaces. The highest amount of proteins (0.18μg/cm(2)) adsorbed to hydrophobic PTFE samples, and the lowest amount (0.025μg/cm(2)) was detected on silicone. The highest number of S. gordonii (3.2×10(4)CFU/mm(2)) adhered to the hydrophilic glassionomer cement surface coated with salivary proteins, and the lowest number (4×10(3)CFU/mm(2)) was found on the hydrophobic silorane-based composite. Hydrophobicity of pure material surfaces and the number of attached microorganisms were weakly negatively correlated. No such correlation between hydrophobicity and the number of bacteria was detected when surfaces were coated with salivary proteins. Functional groups added by the adsorption of specific salivary proteins to material surfaces are more relevant for initial bacterial adhesion than hydrophobicity as a physical property. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Dynamics of biofilm formation and the interaction between Candida albicans and methicillin-susceptible (MSSA) and -resistant Staphylococcus aureus (MRSA).

PubMed

Zago, Chaiene Evelin; Silva, Sónia; Sanitá, Paula Volpato; Barbugli, Paula Aboud; Dias, Carla Maria Improta; Lordello, Virgínia Barreto; Vergani, Carlos Eduardo

2015-01-01

Polymicrobial biofilms are an understudied and a clinically relevant problem. This study evaluates the interaction between C. albicans, and methicillin- susceptible (MSSA) and resistant (MRSA) S. aureus growing in single- and dual-species biofilms. Single and dual species adhesion (90 min) and biofilms (12, 24, and 48 h) were evaluated by complementary methods: counting colony-forming units (CFU mL-1), XTT-reduction, and crystal violet staining (CV). The secretion of hydrolytic enzymes by the 48 h biofilms was also evaluated using fluorimetric kits. Scanning electron microscopy (SEM) was used to assess biofilm structure. The results from quantification assays were compared using two-way ANOVAs with Tukey post-hoc tests, while data from enzymatic activities were analyzed by one-way Welch-ANOVA followed by Games-Howell post hoc test (α = 0.05). C. albicans, MSSA and MRSA were able to adhere and to form biofilm in both single or mixed cultures. In general, all microorganisms in both growth conditions showed a gradual increase in the number of cells and metabolic activity over time, reaching peak values between 12 h and 48 h (ρ<0.05). C. albicans single- and dual-biofilms had significantly higher total biomass values (ρ<0.05) than single biofilms of bacteria. Except for single MRSA biofilms, all microorganisms in both growth conditions secreted proteinase and phospholipase-C. SEM images revealed extensive adherence of bacteria to hyphal elements of C. albicans. C. albicans, MSSA, and MRSA can co-exist in biofilms without antagonism and in an apparent synergistic effect, with bacteria cells preferentially associated to C. albicans hyphal forms.

Pathogenetic aspects of uncomplicated urinary tract infection: recent advances.

PubMed

Fünfstück, R; Smith, J W; Tschäpe, H; Stein, G

1997-01-01

Urinary tract infections mostly are caused by Enterobacteriaceae; E. coli dominating in 80-90% for uncomplicated diseases. Microorganisms possessing the ability to colonize the uroepithelium (fimbriae/pili) and to cytotoxically damage cells and tissue (hemolysin) may initiate acute infection. Properties such as serum resistance, iron sequesteration, hydroxamate production and the presence of K-antigen are found in strains which persist in the host without initiating clinical symptoms. The ability of bacteria to adhere to cells of the epithelial boundary layer of the host organisms is of initial importance in the origin and progress of an infection. A variety of specific factors, e.g. glycolipids on the surface of the uroepithelium as well as cellular and humoral disorders of immunoreactions in the host determine the course of a disease. The immune response may ameliorate clinical symptoms and select urovirulent characteristics of the causative microorganism in recurrent diseases.

Targeting Unknowns Just Underfoot: Microbial Ecology and Community Genomics of C Cycling in Soil Informed and Enabled with DNA-SIP

NASA Astrophysics Data System (ADS)

Pepe-Ranney, C. P.; Campbell, A.; Buckley, D. H.

2015-12-01

Microorganisms drive biogeochemical cycles and because soil is a large global carbon (C) reservoir (soil contains more C than plants and the atmosphere combined), soil microorganisms are important players in the global C-cycle. Frustratingly, however, many soil microorganisms resist cultivation and soil communities are astoundingly complex. This makes soil microbiology difficult to study and without a solid understanding of soil microbial ecology, models of soil C feedbacks to climate change are under-informed. Stable isotope probing (SIP) is a useful approach for establishing identity-function connections in microbial communities but has been challenging to employ in soil due to the inadequate resolution of microbial community fingerprinting techniques. High throughput DNA sequencing improves SIP resolving power transforming it into a powerful tool for studying the soil C cycle. We conducted a DNA-SIP experiment to track flow of xylose-C, a labile component of plant biomass, and cellulose-C, the most abundant global biopolymer, through a soil microbial community. We could track 13C into microbial DNA even when added 13C amounted to less than 5% of native C and found Spartobacteria, Chloroflexi, and Planctomycetes taxa were among those that assimilated 13C cellulose. These lineages are cosmopolitan in soil but little is known of their ecophysiology. By profiling SSU rRNA genes across entire DNA-SIP density gradients, we assessed relative DNA atom % 13C per taxon in 13C treatments and found cellulose degraders exhibited signal consistent with a specialist lifestyle with respect to C preference. Further, DNA-SIP enriches DNA of targeted microorganisms (Verrucomicrobia cellulose degraders were enriched by nearly two orders of magnitude) and this enriched DNA can serve as template for community genomics. We produced draft genomes from soil cellulose degraders including microorganisms belonging to Verrucomicrobia, Chloroflexi, and Planctomycetes from SIP enriched DNA. This study demonstrates how DNA-SIP can be used to study microbial ecology and target guilds of microorganisms for community genomics. Improving our fundamental understanding of ecophysiology relevant to terrestrial C cycling is essential for tuning global C models.

Impact of microbial invasion of amniotic cavity and the type of microorganisms on short-term neonatal outcome in women with preterm labor and intact membranes.

PubMed

Cobo, Teresa; Vives, Irene; Rodríguez-Trujillo, Adriano; Murillo, Clara; Ángeles, Martina A; Bosch, Jordi; Vergara, Andrea; Gratacós, Eduard; Palacio, Montse

2017-05-01

The objective of this study was to evaluate the impact of microbial invasion of the amniotic cavity and the type of microorganisms on pregnancy and short-term neonatal outcomes in women with preterm labor. Prospective observational cohort study including women with preterm labor from 22.0 to 36.0 weeks. Microbial invasion of the amniotic cavity was defined based on amniotic fluid aerobic/anaerobic/mycoplasma cultures, and intra-amniotic inflammation on amniotic fluid interleukin-6 levels. Demographic data and pregnancy outcomes were compared among women exposed to microbial invasion of the amniotic cavity by Ureaplasma spp., women with microbial invasion of the amniotic cavity by other microorganisms, and a No-microbial invasion of the amniotic cavity/No-intra-amniotic inflammation group. The short-term neonatal outcome was evaluated in women delivering after 24.0 weeks. We included 228 women with preterm labor. Microbial invasion of the amniotic cavity occurred in 35% (80/228), 28% (22/80) being caused by Ureaplasma spp. Gestational age at admission and at delivery were significantly earlier and the rate of delivery at <24.0 weeks' gestation and of women who further developed clinical chorioamnionitis were significantly higher in women with microbial invasion of the amniotic cavity by microorganisms other than Ureaplasma spp. However, after 24 weeks, regardless of the microorganisms isolated, the short-term neonatal outcome was similar between women exposed to microbial invasion of the amniotic cavity and the No-microbial invasion of the amniotic cavity/No-intra-amniotic inflammation group when gestational age was considered. Microbial invasion of the amniotic cavity by microorganisms other than Ureaplasma spp. was associated with earlier gestational age at admission and at delivery, and a higher rate of preterm delivery <24.0 weeks and of women who developed clinical chorioamnionitis. However, we did not find differences in the short-term neonatal outcome between women exposed to microbial invasion of the amniotic cavity and the no-microbial invasion of the amniotic cavity/no-intra-amniotic inflammation group delivering after 24.0 weeks' gestation when adjusted by gestational age at delivery. © 2017 Nordic Federation of Societies of Obstetrics and Gynecology.

Fighting microbial infections: A lesson from amphibian skin-derived esculentin-1 peptides.

PubMed

Mangoni, Maria Luisa; Luca, Vincenzo; McDermott, Alison M

2015-09-01

Due to the growing emergence of resistance to commercially available antibiotics/antimycotics in virtually all clinical microbial pathogens, the discovery of alternative anti-infective agents, is greatly needed. Gene-encoded antimicrobial peptides (AMPs) hold promise as novel therapeutics. In particular, amphibian skin is one of the richest storehouses of AMPs, especially that of the genus Rana, with esculentins-1 being among the longest (46 amino acids) AMPs found in nature to date. Here, we report on the recently discovered in vitro and in vivo activities and mechanism of action of two derivatives of the N-terminal part of esculentin-1a and -1b peptides, primarily against two relevant opportunistic microorganisms causing a large number of life-threatening infections worldwide; i.e. the Gram-negative bacterium Pseudomonas aeruginosa and the yeast Candida albicans. Because of distinct advantages compared to several mammalian AMPs, the two selected frog skin AMP-derivatives represent attractive candidates for the development of new antimicrobial compounds with expanded properties, for both human and veterinary medicine. Copyright © 2015 Elsevier Inc. All rights reserved.

Evaluation of the antifungal activity and modulation between Cajanus cajan (L.) Millsp. leaves and roots ethanolic extracts and conventional antifungals

PubMed Central

Brito, Samara A.; Rodrigues, Fabíola F. G.; Campos, Adriana R.; da Costa, José G. M.

2012-01-01

Background: The use and investigation of natural products with antimicrobial activity from vegeral source have been reported by several researchers. Cajanus cajan (Fabaceae) is a multiple use specie mainly as human food. In popular medicine, diverse parts of the plant are used as sedative and to treat cough, hepatitis, and diabetes. Materials and Methods: This study shows the characterization of secondary metabolites present in ehtanolic extracts from leaves and roots of Cajanus cajan by phytochemical prospection. The evaluation of the antifungal activity was performed by the microdilution method, and from the subinhibitory concentrations (MIC 1/8) the modulatory activity of antifungical (fluconazole and ketoconazole) was analyzed by the direct contact assay against C. albicans ATCC40006, Candida krusei ATCC 6538 and Candida tropicalis ATCC 40042. Results: The results showed the presence of tannins, flavonoids, and alkaloids in both extracts as the clinically relevant antifungal activity. The modulatory potential is presented by the antifungal tested against yeasts. Conclusion: The extracts studied here have demonstrated to be a new therapeutic source to treat these microorganism-associated diseases. PMID:22701281

Evaluation of the antifungal activity and modulation between Cajanus cajan (L.) Millsp. leaves and roots ethanolic extracts and conventional antifungals.

PubMed

Brito, Samara A; Rodrigues, Fabíola F G; Campos, Adriana R; da Costa, José G M

2012-04-01

The use and investigation of natural products with antimicrobial activity from vegeral source have been reported by several researchers. Cajanus cajan (Fabaceae) is a multiple use specie mainly as human food. In popular medicine, diverse parts of the plant are used as sedative and to treat cough, hepatitis, and diabetes. This study shows the characterization of secondary metabolites present in ehtanolic extracts from leaves and roots of Cajanus cajan by phytochemical prospection. The evaluation of the antifungal activity was performed by the microdilution method, and from the subinhibitory concentrations (MIC 1/8) the modulatory activity of antifungical (fluconazole and ketoconazole) was analyzed by the direct contact assay against C. albicans ATCC40006, Candida krusei ATCC 6538 and Candida tropicalis ATCC 40042. The results showed the presence of tannins, flavonoids, and alkaloids in both extracts as the clinically relevant antifungal activity. The modulatory potential is presented by the antifungal tested against yeasts. The extracts studied here have demonstrated to be a new therapeutic source to treat these microorganism-associated diseases.

Diagnosis of Carrion’s Disease by Direct Blood PCR in Thin Blood Smear Negative Samples

PubMed Central

Tinco Valdez, Carmen; Pons, Maria J.; del Valle, Luis J.; Oré, Verónica Casabona; Michelena, Denisse Champin; Mayra, Jorge Bazán; Gavidea, Víctor Zavaleta; Vargas, Martha; Ruiz, Joaquim

2014-01-01

Bartonella bacilliformis is the etiologic agent of Carrion's disease. This disease has two well established phases, the most relevant being the so called Oroya Fever, in which B. bacilliformis infect the erythrocytes resulting in severe anemia and transient immunosuppression, with a high lethality in the absence of adequate antibiotic treatment. The presence of B. bacilliformis was studied in 113 blood samples suspected of Carrion’s disease based on clinical criteria, despite the absence of a positive thin blood smear, by two different PCR techniques (using Bartonella-specific and universal 16S rRNA gene primers), and by bacterial culture. The specific 16S rRNA gene primers revealed the presence of 21 B. bacilliformis and 1 Bartonella elizabethae, while universal primers showed both the presence of 3 coinfections in which a concomitant pathogen was detected plus Bartonella, in addition to the presence of infections by other microorganisms such as Agrobacterium or Bacillus firmus. These data support the need to implement molecular tools to diagnose Carrion’s disease. PMID:24651298

Effect of solid boundaries on a motile microorganism in a viscoelastic fluid

NASA Astrophysics Data System (ADS)

Karimi, Alireza; Li, Gaojin; Ardekani, Arezoo

2014-11-01

Microorganisms swimming in viscoelastic fluids are ubiquitous in nature; this includes biofilms grown on surfaces, Helicobacter pylori colonizing in the mucus layer covering the stomach and spermatozoa swimming through cervical mucus inside the mammalian female reproductive tract. Previous studies have focused on the locomotion of microorganisms in an unbounded viscoelastic fluid. However in many situations, microorganisms interact with solid boundaries and their hydrodynamic interaction is poorly understood. In this work, we numerically study the effect of solid boundaries on the swimming behavior of an archetypal low-Reynolds number swimmer, called ``squirmer,'' in a viscoelastic fluid. A Giesekus constitutive equation is used to model both viscoelasticity and shear-thinning behavior of the background fluid. We found that the time a neutral squirmer spends in the close proximity of the wall increases with polymer relaxation time and reaches a maximum at Weissenberg number of unity. A pusher is found to be trapped near the wall in a viscoelastic fluid, but the puller is less affected. This publication was made possible, in part, with support from NSF (Grant No. CBET-1150348-CAREER) and Indiana Clinical and Translational Sciences Institute Collaboration in Biomedical/Translational Research (Grant No. TR000006) from NIH.

Clinical relevance in anesthesia journals.

PubMed

Lauritsen, Jakob; Møller, Ann M

2006-04-01

The purpose of this review is to present the latest knowledge and research on the definition and distribution of clinically relevant articles in anesthesia journals. It will also discuss the importance of the chosen methodology and outcome of articles. In the last few years, more attention has been paid to evidence-based medicine in anesthesia. Several articles on the subject have focused on the need to base clinical decisions on sound research employing both methodological rigor and clinically relevant outcomes. The number of systematic reviews in anesthesia literature is increasing as well as the focus on diminishing the number of surrogate outcomes. It has been shown that the impact factor is not a valid measure of establishing the level of clinical relevance to a journal. This review presents definitions of clinically relevant anesthesia articles. A clinically relevant article employs both methodological rigor and a clinically relevant outcome. The terms methodological rigor and clinical outcomes are fully discussed in the review as well as problems with journal impact factors.

Septic implantation syndrome in dogs and cats: a distinct pattern of endophthalmitis with lenticular abscess.

PubMed

Bell, Cynthia M; Pot, Simon A; Dubielzig, Richard R

2013-05-01

To summarize the clinical and pathologic findings in a group of dogs and cats with progressive clinical ocular disease, which were diagnosed with suppurative endophthalmitis and lens capsule rupture. Twenty cats and forty-six dogs that underwent unilateral enucleation or evisceration for intractable uveitis and/or glaucoma. Biopsy submission requests and microscopic case material were evaluated for clinical and histological features, including history of ocular trauma, duration of ocular disease, pattern of inflammation, and the presence of intralenticular microorganisms. The median duration for cats and dogs was 6 and 5 weeks, respectively. A history of trauma was reported for four (20%) cats and 18 (39%) dogs. All confirmed cases of trauma-three in cats and 14 in dogs-were caused by a cat scratch. Microscopically, all cases had suppurative endophthalmitis centered on the lens, lens capsule rupture, cataract, and lenticular abscess. Infectious organisms were identified by Gram stain within the lens of 14 (70%) cats and 30 (65%) dogs. Gram-positive cocci were seen most commonly. Male cats were overrepresented as compared to females. There were no apparent gender, age or breed predilections in dogs. A unique pattern of slowly progressive or delayed-onset endophthalmitis with lens capsule rupture, lenticular abscess, and frequently intralenticular microorganisms is associated with traumatic penetration of the globe and lens capsule. The term Septic Implantation Syndrome (SIS) is favored in lieu of 'phacoclastic uveitis' to avoid confusion with phacolytic uveitis and to clearly implicate the role of intralenticular microorganisms in the pathogenesis. © 2012 American College of Veterinary Ophthalmologists.

Bacteriology of peritonsillar abscess: the changing trend and predisposing factors.

PubMed

Tsai, Yi-Wen; Liu, Yu-Hsi; Su, Hsing-Hao

2017-07-17

Peritonsillar abscess is the most common deep neck infection. The infectious microorganism may be different according to clinical factors. To identify the major causative pathogen of peritonsillar abscess and investigate the relationship between the causative pathogen, host clinical factors, and hospitalization duration. This retrospective study included 415 hospitalized patients diagnosed with peritonsillar abscess who were admitted to a tertiary medical center from June 1990 to June 2013. We collected data by chart review and analyzed variables such as demographic characteristics, underlying systemic disease, smoking, alcoholism, betel nut chewing, bacteriology, and hospitalization duration. A total of 168 patients had positive results for pathogen isolation. Streptococcus viridans (28.57%) and Klebsiella pneumoniae (23.21%) were the most common microorganisms identified through pus culturing. The isolation rate of anaerobes increased to 49.35% in the recent 6 years (p=0.048). Common anaerobes were Prevotella and Fusobacterium spp. The identification of K. pneumoniae increased among elderly patients (age>65 years) with an odds ratio (OR) of 2.76 (p=0.03), and decreased in the hot season (mean temperature>26°C) (OR=0.49, p=0.04). No specific microorganism was associated with prolonged hospital stay. The most common pathogen identified through pus culturing was S. viridans, followed by K. pneumoniae. The identification of anaerobes was shown to increase in recent years. The antibiotics initially selected should be effective against both aerobes and anaerobes. Bacterial identification may be associated with host clinical factors and environmental factors. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

New bacterial composition in primary and persistent/secondary endodontic infections with respect to clinical and radiographic findings.

PubMed

Tennert, Christian; Fuhrmann, Maximilian; Wittmer, Annette; Karygianni, Lamprini; Altenburger, Markus J; Pelz, Klaus; Hellwig, Elmar; Al-Ahmad, Ali

2014-05-01

The aim of the present study was to analyze the microbiota of primary and secondary/persistent endodontic infections of patients undergoing endodontic treatment with respect to clinical and radiographic findings. Samples from the root canals of 21 German patients were taken using 3 sequential sterile paper points. In the case of a root canal filling, gutta-percha was removed with sterile files, and samples were taken using sterile paper points. The samples were plated, and microorganisms were then isolated and identified morphologically by biochemical analysis and sequencing the 16S rRNA genes of isolated microorganisms. In 12 of 21 root canals, 33 different species could be isolated. Six (50%) of the cases with isolated microorganisms were primary, and 6 (50%) cases were endodontic infections associated with root-filled teeth. Twelve of the isolated species were facultative anaerobic and 21 obligate anaerobic. Monomicrobial infections were found for Enterococcus faecalis and Actinomyces viscosus. E. faecalis was most frequently isolated in secondary endodontic infections (33%). Moraxella osloensis was isolated from a secondary endodontic infection that had an insufficient root canal filling accompanied by a mild sensation of pain. A new bacterial composition compromising Atopobium rimae, Anaerococcus prevotii, Pseudoramibacter alactolyticus, Dialister invisus, and Fusobacterium nucleatum was recovered from teeth with chronic apical abscesses. New bacterial combinations were found and correlated to clinical and radiographic findings, particularly to chronic apical abscesses. M. osloensis was detected in root canals for the second time and only in German patients. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The effects of space relevant environmental factors on halophilic Archaea

NASA Astrophysics Data System (ADS)

Leuko, Stefan; Moeller, Ralf; Rettberg, Petra

Within the last 50 years, space technology has provided tools for transporting terrestrial (microbial) life beyond Earth's protective shield in order to study its responses to selected conditions of space. Microorganisms are ubiquitous and can be found in almost every environment on Earth. They thrive and survive in a broad spectrum of environments and are true masters in adapting to rapidly changing external conditions. Although microorganisms cannot actively grow under the harsh conditions of outer space or other known planets, some microorganisms might be able to survive for a time in space or other planets as dormant, inactive spores or in similar desiccation-resistant resting states, e.g., enclosed in halite crystals or biofilms. Halite crystals are the realm of halophilic Archaea as they have adapted to life at extreme salt concentrations. They can stay entrapped in such crystals for millions of years without losing viability and therefore the family Halobacteriaceae belongs to the group of microorganisms which may survive space travel or may even be found on other planets. Several members of this family have been utilized in space relevant experiments where they were exposed to detrimental environmental conditions such as UV-C radiation, vacuum, temperature cycles (+60(°) C and -25(°) C) and heavy iron bombardment (150 MeV He, 500 MeV Ar and 500 MeV Fe ions). The viability was evaluated by colony forming unit (cfu) counts as well as with the LIFE/DEAD kit. Results revealed that UV-C radiation (up to 1.000 J/m (2) ) has a considerable effect on the viability, whereas the other tested parameters inflict little damage onto the organisms. Repair of UV-C inflicted damage is efficient and several DNA damage repair genes are up-regulated following exposure. Halophilic archaea display a strong resistance against heavy iron bombardment, with dosages of up to 2.000 Gy 500 MeV Fe ions needed to establish a visible effect on the vitality. Genomic integrity after exposure was investigated by several different methods e.g. RAPD - PCR, a technique that elucidates damages within the genome by different amplification patterns. Overall experimental results indicate that halophilic Archaea are able to withstand the exposure to space related environmental factors for a considerable time. This work in combined with others will lead to a detailed understanding of the response of extraterrestrial conditions to halophilic Archaea for astrobiological considerations.

Artificial Cells, Blood Substitutes, and Immobilization Biotechnology. Volume 22, Number 3, 1994.

DTIC Science & Technology

1994-05-01

culture, microorganisms, enzymes, drugs, receptors, sorbents, immunosorbents and other biologically active molecules. (2) Artificial cells, microcapsules ...recombinant hemoglobin, and others. Chemistry, methods, in-vitro studies, in-vivo evaluations and clinical results. (4) Microencapsulation and other

Artificial Cells, Blood Substitutes, and Immobilization Biotechnology. Volume 22 Number 2, 1994.

DTIC Science & Technology

1994-05-01

culture, microorganisms, enzymes, drugs, receptors, sorbents, immunosorbents and other biologically active molecules. (2) Artificial cells, microcapsules ...recombinant hemoglobin, and others. Chemistry, methods, in-vitro studies, in-vivo evaluations and clinical results. (4) Microencapsulation and other

Artificial Cells, Blood Substitutes, and Immobilization Biotechnology, Volume 22 Number 4, 1994.

DTIC Science & Technology

1994-01-01

culture, microorganisms, enzymes, drugs, receptors, sorbents, immunosorbents and other biologically active molecules. (2) Artificial cells, microcapsules ...recombinant hemoglobin, and others. Chemistry, methods, in-vitro studies, in-vivo evaluations and clinical results. (4) Microencapsulation and other

Microbial Transformations of Selenium Species of Relevance to Bioremediation

PubMed Central

Eswayah, Abdurrahman S.; Smith, Thomas J.

2016-01-01

Selenium species, particularly the oxyanions selenite (SeO32−) and selenate (SeO42−), are significant pollutants in the environment that leach from rocks and are released by anthropogenic activities. Selenium is also an essential micronutrient for organisms across the tree of life, including microorganisms and human beings, particularly because of its presence in the 21st genetically encoded amino acid, selenocysteine. Environmental microorganisms are known to be capable of a range of transformations of selenium species, including reduction, methylation, oxidation, and demethylation. Assimilatory reduction of selenium species is necessary for the synthesis of selenoproteins. Dissimilatory reduction of selenate is known to support the anaerobic respiration of a number of microorganisms, and the dissimilatory reduction of soluble selenate and selenite to nanoparticulate elemental selenium greatly reduces the toxicity and bioavailability of selenium and has a major role in bioremediation and potentially in the production of selenium nanospheres for technological applications. Also, microbial methylation after reduction of Se oxyanions is another potentially effective detoxification process if limitations with low reaction rates and capture of the volatile methylated selenium species can be overcome. This review discusses microbial transformations of different forms of Se in an environmental context, with special emphasis on bioremediation of Se pollution. PMID:27260359

Risk of Adverse Health Effects Due to Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Oubre, Cherie; Castro, Sarah; Mehta, Satish; Pierson, Duane

2015-01-01

While preventive measures limit the presence of many medically significant microorganisms during spaceflight missions, microbial infection of crewmembers cannot be completely prevented. Spaceflight experiments over the past 50 years have demonstrated a unique microbial response to spaceflight culture, although the mechanisms behind those responses and their operational relevance were unclear. In 2007, the operational importance of these microbial responses was emphasized as the results of an experiment aboard STS-115 demonstrated that the enteric pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) increased in virulence in a murine model of infection. The experiment was reproduced in 2008 aboard STS-123 confirming this finding. In response to these findings, the Institute of Medicine of the National Academies recommended that NASA investigate this risk and its potential impact on the health of the crew during spaceflight. NASA assigned this risk to the Human Research Program. To better understand this risk, evidence has been collected and reported from both spaceflight analog systems and actual spaceflight. Although the performance of virulence studies during spaceflight are challenging and often impractical, additional information has been and continues to be collected to better understand the risk to crew health. Still, the uncertainty concerning the extent and severity of these alterations in host-microorganism interactions is very large and requires more investigation.

Salmonella and Campylobacter biofilm formation: a comparative assessment from farm to fork.

PubMed

Lamas, Alexandre; Regal, Patricia; Vázquez, Beatriz; Miranda, José M; Cepeda, Alberto; Franco, Carlos M

2018-02-09

It takes several steps to bring food from the farm to the fork (dining table), and contamination with food-borne pathogens can occur at any point in the process. Campylobacter spp. and Salmonella spp. are the main microorganisms responsible for foodborne disease in the EU. These two pathogens are able to persist throughout the food supply chain thanks to their ability to form biofilms. Owing to the high prevalence of Salmonella and especially of Campylobacter in the food supply chain and the huge efforts of food authorities to reduce these levels, it is of great importance to fully understand their mechanisms of persistence. Diverse studies have evaluated the biofilm-forming capacity of foodborne pathogens isolated at different steps of food production. Nonetheless, the principal obstacle of these studies is to reproduce the real conditions that microorganisms encounter in the food supply chain. While there are a wide number of Salmonella biofilm studies, information on Campylobacter biofilms is still limited. A comparison between the two microorganisms could help to develop new research in the field of Campylobacter biofilms. Therefore, this review evaluates relevant work in the field of Salmonella and Campylobacter biofilms and the applicability of the data obtained from these studies to real working conditions. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Tackling probiotic and gut microbiota functionality through proteomics.

PubMed

Ruiz, Lorena; Hidalgo, Claudio; Blanco-Míguez, Aitor; Lourenço, Anália; Sánchez, Borja; Margolles, Abelardo

2016-09-16

Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Many strains exert their beneficial effects after transiently colonizing the human gut, where they interact with the rest of the intestinal microorganisms and with the host mucosa. Indeed the human gut harbours a huge number of microorganisms also known as gut microbiota. Imbalances in the relative abundances of the individual components of the gut microbiota may determine the health status of the host and alterations in specific groups have been related to different diseases and metabolic disorders. Proteomics provide a set of high-throughput methodologies for protein identification that are extremely useful for studying probiotic functionality and helping in the assessment of specific health-promoting activities, such as their immunomodulatory activity, the intestinal colonization processes, and the crosstalk mechanisms with the host. Furthermore, proteomics have been used to identify markers of technological performance and stress adaptation, which helps to predict traits such as behaviour into food matrices and ability to survive passage through the gastrointestinal tract. The aim of this review is to compile studies in which proteomics have been used to assess probiotic functionality and to identify molecular players supporting their mechanisms of action. Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Molecular basis underlying the functional properties of probiotic bacteria responsible for the health promoting effects have been in the background for many years. Breakthrough of omics technologies in the probiotic and microbiota fields has had a very relevant impact in the elucidation of probiotic mechanisms and in the procedures to select these microorganisms, based on solid scientific evidence. It is unquestionable that, in the near future, the evolution of proteomic techniques will play a pivotal role in the generation of knowledge about the functions of probiotics and gut commensals, still a pending issue in the field of intestinal microbiomics. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of meteorites as habitats for terrestrial microorganisms: Results from the Nullarbor Plain, Australia, a Mars analogue site

NASA Astrophysics Data System (ADS)

Tait, Alastair W.; Wilson, Siobhan A.; Tomkins, Andrew G.; Gagen, Emma J.; Fallon, Stewart J.; Southam, Gordon

2017-10-01

Unambiguous identification of biosignatures on Mars requires access to well-characterized, long-lasting geochemical standards at the planet's surface that can be modified by theoretical martian life. Ordinary chondrites, which are ancient meteorites that commonly fall to the surface of Mars and Earth, have well-characterized, narrow ranges in trace element and isotope geochemistry compared to martian rocks. Given that their mineralogy is more attractive to known chemolithotrophic life than the basaltic rocks that dominate the martian surface, exogenic rocks (e.g., chondritic meteorites) may be good places to look for signs of prior life endemic to Mars. In this study, we show that ordinary chondrites, collected from the arid Australian Nullarbor Plain, are commonly colonized and inhabited by terrestrial microorganisms that are endemic to this Mars analogue site. These terrestrial endolithic and chasmolithic microbial contaminants are commonly found in close association with hygroscopic veins of gypsum and Mg-calcite, which have formed within cracks penetrating deep into the meteorites. Terrestrial bacteria are observed within corrosion cavities, where troilite (FeS) oxidation has produced jarosite [KFe3(SO4)2(OH)6]. Where terrestrial microorganisms have colonized primary silicate minerals and secondary calcite, these mineral surfaces are heavily etched. Our results show that inhabitation of meteorites by terrestrial microorganisms in arid environments relies upon humidity and pH regulation by minerals. Furthermore, microbial colonization affects the weathering of meteorites and production of sulfate, carbonate, Fe-oxide and smectite minerals that can preserve chemical and isotopic biosignatures for thousands to millions of years on Earth. Meteorites are thus habitable by terrestrial microorganisms, even under highly desiccating environmental conditions of relevance to Mars. They may therefore be useful as chemical and isotopic ;standards; that preserve evidence of life, thereby providing the possibility of universal context for recognition of microbial biosignatures on Earth, Mars and throughout the solar system.

Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria.

PubMed

Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Turroni, Francesca; Milani, Christian; Mangifesta, Marta; Ferrario, Chiara; Anzalone, Rosaria; Viappiani, Alice; van Sinderen, Douwe; Ventura, Marco

2017-02-01

The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome). In the current study, we assessed the resistome of the Bifidobacterium genus based on phenotypic and genotypic data of members that represent all currently recognized bifidobacterial (sub)species. Moreover, a comparison between the bifidobacterial resistome and gut metagenome data sets from adults and infants shows that the bifidobacterial community present at the first week following birth possesses a reduced AR arsenal compared to that present in the infant bifidobacterial population in subsequent weeks of the first year of life. Our findings reinforce the concept that the early infant gut microbiota is more susceptible to disturbances by antibiotic treatment than the gut microbiota developed at a later life stage. The spread of resistance to antibiotics among bacterial communities has represented a major concern since their discovery in the last century. The risk of genetic transfer of resistance genes between microorganisms has been extensively investigated due to its relevance to human health. In contrast, there is only limited information available on antibiotic resistance among human gut commensal microorganisms such as bifidobacteria, which are widely exploited by the food industry as health-promoting microorganisms or probiotic ingredients. In the current study, we explored the occurrence of antibiotic resistance genes in the genomes of bifidobacteria and evaluated their genetic mobility to other human gut commensal microorganisms. Copyright © 2017 American Society for Microbiology.

Microneedle Arrays Allow Lower Microbial Penetration Than Hypodermic Needles In Vitro

PubMed Central

Donnelly, Ryan F.; Singh, Thakur Raghu Raj; Tunney, Michael M.; Morrow, Desmond I. J.; McCarron, Paul A.; O’Mahony, Conor; Woolfson, A. David

2010-01-01

Methods In this study we determined, for the first time, the ability of microorganisms to traverse microneedle-induced holes using two different in vitro models. Results When employing Silescol® membranes, the numbers of Candida albicans, Pseudomonas aeruginosa and Staphylococcus epidermidis crossing the membranes were an order of magnitude lower when the membranes were punctured by microneedles rather than a 21G hypodermic needle. Apart from the movement of C. albicans across hypodermic needle-punctured membranes, where 40.2% of the microbial load on control membranes permeated the barrier over 24 h, the numbers of permeating microorganisms was less than 5% of the original microbial load on control membranes. Experiments employing excised porcine skin and radiolabelled microorganisms showed that the numbers of microorganisms penetrating skin beyond the stratum corneum were approximately an order of magnitude greater than the numbers crossing Silescol® membranes in the corresponding experiments. Approximately 103cfu of each microorganism adhered to hypodermic needles during insertion. The numbers of microorganisms adhering to MN arrays were an order of magnitude higher in each case. Conclusion We have shown here that microneedle puncture resulted in significantly less microbial penetration than did hypodermic needle puncture and that no microorganisms crossed the viable epidermis in microneedle—punctured skin, in contrast to needle-punctured skin. Given the antimicrobial properties of skin, it is, therefore, likely that application of microneedle arrays to skin in an appropriate manner would not cause either local or systemic infection in normal circumstances in immune-competent patients. In supporting widespread clinical use of microneedle-based delivery systems, appropriate animal studies are now needed to conclusively demonstrate this in vivo. Safety in patients will be enhanced by aseptic or sterile manufacture and by fabricating microneedles from self-disabling materials (e.g. dissolving or biodegradable polymers) to prevent inappropriate or accidental reuse. PMID:19756972

Primary Super-Infection of Hydatid Cyst—Clinical Setting and Microbiology in 37 Cases

PubMed Central

García, Moncef Belhassen; Lledías, Javier Pardo; Pérez, Inmaculada Galindo; Tirado, Virginia Velasco; Pardo, Lucia Fuentes; Bellvís, Luis Muñoz; Varela, Gonzalo; Sánchez, Miguel Cordero

2010-01-01

The clinical and microbiological characteristics of super-infected hydatid cysts are described. In our cohort, 7.3% of 503 patients had a super-infected cyst. Four patients developed severe sepsis, and two of them died. Escherichia coli, viridans group streptococci, and Enterococcus species in liver cysts and Aspergillus fumigatus in lung cysts were the microorganisms most frequent involved. PMID:20207859

Publications in anesthesia journals: quality and clinical relevance.

PubMed

Lauritsen, Jakob; Moller, Ann M

2004-11-01

Clinicians performing evidence-based anesthesia rely on anesthesia journals for clinically relevant information. The objective of this study was to analyze the proportion of clinically relevant articles in five high impact anesthesia journals. We evaluated all articles published in Anesthesiology, Anesthesia & Analgesia, British Journal of Anesthesia, Anesthesia, and Acta Anaesthesiologica Scandinavica from January to June, 2000. Articles were assessed and classified according to type, outcome, and design; 1379 articles consisting of 5468 pages were evaluated and categorized. The most common types of article were animal and laboratory research (31.2%) and randomized clinical trial (20.4%). A clinically relevant article was defined as an article that used a statistically valid method and had a clinically relevant end-point. Altogether 18.6% of the pages had as their subject matter clinically relevant trials. We compared the Journal Impact Factor (a measure of the number of citations per article in a journal) and the proportion of clinically relevant pages and found that they were inversely proportional to each other.

JPRS Report, Science & Technology. Japan: Economic Planning Agency Technology Forecast to the Year 2010.

DTIC Science & Technology

1991-11-17

are several concrete examples of how these affect application. (1) For the development and spread of solar photoelectric power generation, under the...technician in charge of each generator. In order to promote the installation of solar cells at various households and businesses, the relevant laws must be...products from microorganisms ’ Solar photoelectric power Communications satellites Skyscrapers Alone in 1st Tied for 1st 10 Years Ago Present !i

Marine microbial L-asparaginase: Biochemistry, molecular approaches and applications in tumor therapy and in food industry.

PubMed

Izadpanah Qeshmi, Fatemeh; Homaei, Ahmad; Fernandes, Pedro; Javadpour, Sedigheh

2018-03-01

The marine environment is a rich source of biological and chemical diversity. It covers more than 70% of the Earth's surface and features a wide diversity of habitats, often displaying extreme conditions, where marine organisms thrive, offering a vast pool for microorganisms and enzymes. Given the dissimilarity between marine and terrestrial habitats, enzymes and microorganisms, either novel or with different and appealing features as compared to terrestrial counterparts, may be identified and isolated. L-asparaginase (E.C. 3.5.1.1), is among the relevant enzymes that can be obtained from marine sources. This amidohydrolase acts on L-asparagine and produce L-aspartate and ammonia, accordingly it has an acknowledged chemotherapeutic application, namely in acute lymphoblastic leukemia. Moreover, L-asparaginase is also of interest in the food industry as it prevents acrylamide formation. Terrestrial organisms have been largely tapped for L-asparaginases, but most failed to comply with criteria for practical applications, whereas marine sources have only been marginally screened. This work provides an overview on the relevant features of this enzyme and the framework for its application, with a clear emphasis on the use of L-asparaginase from marine sources. The review envisages to highlight the unique properties of marine L-asparaginases that could make them good candidates for medical applications and industries, especially in food safety. Copyright © 2018 Elsevier GmbH. All rights reserved.

Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.

PubMed

Dong, Jun; Ding, Linjie; Wang, Xu; Chi, Zifang; Lei, Jiansen

2015-03-01

Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms.

Epidemiologically relevant antimicrobial resistance phenotypes in pathogens isolated from critically ill patients in a Brazilian Universitary Hospital

PubMed Central

de Carvalho, Rodolfo Henriques; Gontijo Filho, Paulo P.

2008-01-01

Antimicrobial resistance is a threat to public health worldwide and is associated with higher mortality and morbidity. Despite the extensive knowledge about this problem, drug resistance has continued to emerge, especially in intensive care units (ICUs). The objective of this study was to evaluate the frequencies of epidemiologically relevant resistance phenotypes in pathogens isolated from ventilator-associated pneumonia (VAP), bloodstream infections (BSI) and urinary tract infections (UTI) in patients admitted in the adult intensive care unit (AICU) of the Clinical Hospital of Federal University of Uberlândia, during an one year period. Additionally, at the period of the study, the antibiotic consumption in AICU was verified. Coagulase-negative staphylococci and S. aureus were the main agents of BSI (43.9%), with 60.0% of oxacilin-resistance for both microorganisms, Klebsiella-Enterobacter group predominated in UTI (23.4%), with resistance to third generation cephalosporins in 58.0% of the isolates; and, Pseudomonas aeruginosa in VAP (42.0%), with 72.0% of resistance to imipenem. Cephalosporins (49.6%), vancomycin (37.4%) and carbapenems (26.6%) were the most prescribed antibiotics in the unit. The comparison of the results with a publication of the NNIS program evidenced a worse situation in the studied hospital, mainly between Gram-negative, that had surpassed the percentile 90% elaborated by that system. Based on these results a reconsideration on the empirical use of antibiotics and on prevention and control of nosocomial infections practices is recommended. PMID:24031278

Feasibility of quantitatively diagnosing cornea infection using Raman spectroscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Bai, Yanru; Chen, Keren; Mishra, Arti; Beuerman, Roger; Liu, Quan

2017-02-01

Ocular infection is a serious eye disease that could lead to blindness without prompt and proper treatment. In pathology, ocular infection is caused by microorganisms such as bacteria, fungi or viruses. The essential prerequisite for the optimal treatment of ocular infection is to identify the microorganism causing infection early as each type of microorganism requires a different therapeutic approach. The clinical procedure for identifying the microorganism species causing ocular infection includes Gram staining (for bacteria)/microscopy (for fungi) and the culture of corneal surface scraping, or aqueous and vitreous smear samples taken from the surface of infected eyes. The culture procedure is labor intensive and expensive. Moreover, culturing is time consuming, which usually takes a few days or even weeks. Such a long delay in diagnosis could result in the exacerbation of patients' symptoms, the missing of the optimal time frame for initiating treatment and subsequently the rising cost for disease management. Raman spectroscopy has been shown highly effective for non-invasive identification of both fungi and bacteria qualitatively. In this study, we investigate the feasibility of identifying the microorganisms of ocular infection and quantifying the concentrations using Raman spectroscopy by measuring not only gram negative and gram positive bacteria but also infected cornea. By applying a modified orthogonal projection approach, the relative concentration of each bacteria species could be quantified. Our results indicate the great potential of Raman spectroscopy as an alternative tool for non-invasive diagnosis of ocular infection and could play a significantly role in future ophthalmology.

Human recombinant lysosomal enzymes produced in microorganisms.

PubMed

Espejo-Mojica, Ángela J; Alméciga-Díaz, Carlos J; Rodríguez, Alexander; Mosquera, Ángela; Díaz, Dennis; Beltrán, Laura; Díaz, Sergio; Pimentel, Natalia; Moreno, Jefferson; Sánchez, Jhonnathan; Sánchez, Oscar F; Córdoba, Henry; Poutou-Piñales, Raúl A; Barrera, Luis A

2015-01-01

Lysosomal storage diseases (LSDs) are caused by accumulation of partially degraded substrates within the lysosome, as a result of a function loss of a lysosomal protein. Recombinant lysosomal proteins are usually produced in mammalian cells, based on their capacity to carry out post-translational modifications similar to those observed in human native proteins. However, during the last years, a growing number of studies have shown the possibility to produce active forms of lysosomal proteins in other expression systems, such as plants and microorganisms. In this paper, we review the production and characterization of human lysosomal proteins, deficient in several LSDs, which have been produced in microorganisms. For this purpose, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, and Ogataea minuta have been used as expression systems. The recombinant lysosomal proteins expressed in these hosts have shown similar substrate specificities, and temperature and pH stability profiles to those produced in mammalian cells. In addition, pre-clinical results have shown that recombinant lysosomal enzymes produced in microorganisms can be taken-up by cells and reduce the substrate accumulated within the lysosome. Recently, metabolic engineering in yeasts has allowed the production of lysosomal enzymes with tailored N-glycosylations, while progresses in E. coli N-glycosylations offer a potential platform to improve the production of these recombinant lysosomal enzymes. In summary, microorganisms represent convenient platform for the production of recombinant lysosomal proteins for biochemical and physicochemical characterization, as well as for the development of ERT for LSD. Copyright © 2015 Elsevier Inc. All rights reserved.

Contaminants in blood cultures: importance, implications, interpretation and prevention.

PubMed

Dargère, S; Cormier, H; Verdon, R

2018-04-03

Despite the development of new microbiologic technologies, blood cultures (BCs) remain the first-line tool for the diagnosis of bloodstream infections. Their diagnostic value may be affected when a microorganism of questionable evidence is isolated-for example, coagulase-negative staphylococci, Bacillus spp., viridans group streptococci, Corynebacterium spp., Propionibacterium spp. and Micrococcus spp. Finally, making a correct diagnosis of pathogenicity (vs. contamination) is challenging. To review the current ways of dealing with the problem of BC contaminants (BCCs) and to provide practical suggestions to decrease BCC rates. PubMed electronic databases and existing reviews were searched up to December 2017 to retrieve relevant publications related to the topic. This review describes the burden of BCC and analyses the main current issues and controversies in interpreting the occurrence of potential BC contaminants. It focuses on the best-described approaches to decide whether BCC is present and discusses the different strategies of prevention in adults. Each institution should have an efficient policy to prevent BCC, emphasizing the importance of following guidelines for prescribing and collecting BCs. Training healthcare workers should focus on detrimental influence on patient care and highlight the work and costs due to contaminants. The accurate differentiation of a contaminant from a true pathogen relies on a multidisciplinary approach and the clinical judgement of experienced practitioners. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Activation, Impaired Tumor Necrosis Factor-α Production, and Deficiency of Circulating Mucosal-Associated Invariant T Cells in Patients with Scrub Typhus

PubMed Central

Won, Eun Jeong; Cho, Young-Nan; Jung, Hyun-Ju; Kwon, Yong-Soo; Kee, Hae Jin; Ju, Jae Kyun; Kim, Jung-Chul; Kim, Uh Jin; Jang, Hee-Chang; Jung, Sook-In; Kee, Seung-Jung; Park, Yong-Wook

2016-01-01

Background Mucosal-associated invariant T (MAIT) cells contribute to protection against certain microorganism infections. However, little is known about the role of MAIT cells in Orientia tsutsugamushi infection. Hence, the aims of this study were to examine the level and function of MAIT cells in patients with scrub typhus and to evaluate the clinical relevance of MAIT cell levels. Methodology/Principal Findings Thirty-eight patients with scrub typhus and 53 health control subjects were enrolled in the study. The patients were further divided into subgroups according to disease severity. MAIT cell level and function in the peripheral blood were measured by flow cytometry. Circulating MAIT cell levels were found to be significantly reduced in scrub typhus patients. MAIT cell deficiency reflects a variety of clinical conditions. In particular, MAT cell levels reflect disease severity. MAIT cells in scrub typhus patients displayed impaired tumor necrosis factor (TNF)-α production, which was restored during the remission phase. In addition, the impaired production of TNF-α by MAIT cells was associated with elevated CD69 expression. Conclusions This study shows that circulating MAIT cells are activated, numerically deficient, and functionally impaired in TNF-α production in patients with scrub typhus. These abnormalities possibly contribute to immune system dysregulation in scrub typhus infection. PMID:27463223

An Update on Candida tropicalis Based on Basic and Clinical Approaches

PubMed Central

Zuza-Alves, Diana L.; Silva-Rocha, Walicyranison P.; Chaves, Guilherme M.

2017-01-01

Candida tropicalis has emerged as one of the most important Candida species. It has been widely considered the second most virulent Candida species, only preceded by C. albicans. Besides, this species has been recognized as a very strong biofilm producer, surpassing C. albicans in most of the studies. In addition, it produces a wide range of other virulence factors, including: adhesion to buccal epithelial and endothelial cells; the secretion of lytic enzymes, such as proteinases, phospholipases, and hemolysins, bud-to-hyphae transition (also called morphogenesis) and the phenomenon called phenotypic switching. This is a species very closely related to C. albicans and has been easily identified with both phenotypic and molecular methods. In addition, no cryptic sibling species were yet described in the literature, what is contradictory to some other medically important Candida species. C. tropicalis is a clinically relevant species and may be the second or third etiological agent of candidemia, specifically in Latin American countries and Asia. Antifungal resistance to the azoles, polyenes, and echinocandins has already been described. Apart from all these characteristics, C. tropicalis has been considered an osmotolerant microorganism and this ability to survive to high salt concentration may be important for fungal persistence in saline environments. This physiological characteristic makes this species suitable for use in biotechnology processes. Here we describe an update of C. tropicalis, focusing on all these previously mentioned subjects. PMID:29081766

Negative correlation between phospholipase and esterase activity produced by Fusarium isolates.

PubMed

Ishida, K; Alviano, D S; Silva, B G; Guerra, C R; Costa, A S; Nucci, M; Alviano, C S; Rozental, S

2012-05-01

Fusarium species have emerged as one of the more outstanding groups of clinically important filamentous fungi, causing localized and life-threatening invasive infections with high morbidity and mortality. The ability to produce different types of hydrolytic enzymes is thought to be an important virulence mechanism of fungal pathogens and could be associated with the environment of the microorganism. Here, we have measured the production of two distinct lipolytic enzymes, phospholipase and esterase, by sixteen Fusarium isolates recovered from the hospital environment, immunocompromised patients' blood cultures, foot interdigital space scrapings from immunocompromised patients, and foot interdigital space scrapings from immunocompetent patients (4 isolates each). Fourteen of these 16 isolates were identified as Fusarium solani species complex (FSSC) and two were identified as F. oxysporum species complex (FOSC). Some relevant genus characteristics were visualized by light and electron microscopy such as curved and multicelled macroconidia with 3 or 4 septa, microconidia, phialides, and abundant chlamydospores. All Fusarium isolates were able to produce esterase and phospholipase under the experimental conditions. However, a negative correlation was observed between these two enzymes, indicating that a Fusarium isolate with high phospholipase activity has low esterase activity and vice versa. In addition, Fusarium isolated from clinical material produced more phospholipases, while environmental strains produced more esterases. These observations may be correlated with the different types of substrates that these fungi need to degrade during their nutrition processes.

Negative correlation between phospholipase and esterase activity produced by Fusarium isolates

PubMed Central

Ishida, K.; Alviano, D.S.; Silva, B.G.; Guerra, C.R.; Costa, A.S.; Nucci, M.; Alviano, C.S.; Rozental, S.

2012-01-01

Fusarium species have emerged as one of the more outstanding groups of clinically important filamentous fungi, causing localized and life-threatening invasive infections with high morbidity and mortality. The ability to produce different types of hydrolytic enzymes is thought to be an important virulence mechanism of fungal pathogens and could be associated with the environment of the microorganism. Here, we have measured the production of two distinct lipolytic enzymes, phospholipase and esterase, by sixteen Fusarium isolates recovered from the hospital environment, immunocompromised patients' blood cultures, foot interdigital space scrapings from immunocompromised patients, and foot interdigital space scrapings from immunocompetent patients (4 isolates each). Fourteen of these 16 isolates were identified as Fusarium solani species complex (FSSC) and two were identified as F. oxysporum species complex (FOSC). Some relevant genus characteristics were visualized by light and electron microscopy such as curved and multicelled macroconidia with 3 or 4 septa, microconidia, phialides, and abundant chlamydospores. All Fusarium isolates were able to produce esterase and phospholipase under the experimental conditions. However, a negative correlation was observed between these two enzymes, indicating that a Fusarium isolate with high phospholipase activity has low esterase activity and vice versa. In addition, Fusarium isolated from clinical material produced more phospholipases, while environmental strains produced more esterases. These observations may be correlated with the different types of substrates that these fungi need to degrade during their nutrition processes. PMID:22415116

Mucosal-associated invariant T cells are numerically and functionally deficient in patients with mycobacterial infection and reflect disease activity.

PubMed

Kwon, Yong-Soo; Cho, Young-Nan; Kim, Moon-Ju; Jin, Hye-Mi; Jung, Hyun-Ju; Kang, Jeong-Hwa; Park, Ki-Jeong; Kim, Tae-Jong; Kee, Hae Jin; Kim, Nacksung; Kee, Seung-Jung; Park, Yong-Wook

2015-05-01

Mucosal-associated invariant T (MAIT) cells contribute to protection against certain microorganism infections. The aims of this study were to examine the levels of MAIT cells in pulmonary tuberculosis (TB) and nontuberculous mycobacteria (NTM) lung disease patients, to evaluate the clinical relevance of MAIT cell levels, and to investigate the functions of MAIT cells. Patients with pulmonary TB (n = 35), NTM (n = 29), and healthy controls (n = 75) were enrolled in the study. MAIT cell levels and functions were measured by flow cytometry. Circluating MAIT cell levels were found to be reduced in TB and NTM patients. MAIT cell deficiency reflects a variety of clinical conditions. In particular, MAIT cell numbers were significantly correlated with sputum AFB positivity, extent of disease, hemoglobin levels, lymphocyte counts, CRP and ESR levels. MAIT cells in TB patients failed to produce interferon-γ irrespective of the mode of stimulation, whereas NTM patients displayed a defect in MR1-dependent signaling pathway. Notably, an elevated expression of programmed death-1 was also associated with MAIT cell deficiency in TB. This study shows that MAIT cells are numerically and functionally deficient in TB and NTM patients and these deficiencies could contribute to immune system dysreguation in mycobacterial infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bacterial Contamination During Diagnostic and Interventional Neuroangiography is a Frequent Finding: But Does It Matter? An Observational Study.

PubMed

Kabbasch, C; Dorn, F; Wenchel, H M; Krug, B; Mpotsaris, A; Liebig, T

2017-03-01

Bacterial contamination during angiographic procedures is a potential source of bacteremia. It is largely unknown whether it is clinically relevant. Our aim was to evaluate the incidence of contamination of liquids during catheter-based neuroangiographic examinations, the spectrum of microorganisms, a comparison of two different trolley-settings, and a follow-up of all patients with regard to clinical and lab signs of infection. A total of 170 patients underwent either diagnostic angiography (n = 111) or arterial neuroendovascular procedures (n = 59). To study the impact of airborne contamination of sterile liquids, we randomly assigned equal numbers of procedures to two distinct setups. Group A with standard open-surface bowls and group B with repetitive coverage of liquids throughout the procedure. Patient preparation was performed with utmost care. After each procedure, samples of the liquids were sent for microbiological evaluation. Patients were followed for signs of infection (fever, white blood cell count, C-reactive-protein). Of all samples, 25.3 % were contaminated. Contamination consisted of resident skin microbiota only and was more common with procedures (28.8 %) than with diagnostic angiography (23.4 %) and less common in uncovered (23.5 %) than in covered bowls (27.1 %). However, these differences were insignificant. None of the patients developed clinical or lab signs of infection. Contamination during diagnostic and interventional angiography does occur and cannot be avoided by intermittent coverage. Despite a surprisingly high incidence, our findings support the common strategy that antibiotic coverage is unnecessary in most patients undergoing arterial angiography as it lacks clinical impact. Airborne contamination does not appear to play a role.

Molecular methods for diagnosis of odontogenic infections.

PubMed

Flynn, Thomas R; Paster, Bruce J; Stokes, Lauren N; Susarla, Srinivas M; Shanti, Rabie M

2012-08-01

Historically, the identification of microorganisms has been limited to species that could be cultured in the microbiology laboratory. The purpose of the present study was to apply molecular techniques to identify microorganisms in orofacial odontogenic infections (OIs). Specimens were obtained from subjects with clinical evidence of OI. To identify the microorganisms involved, 16S rRNA sequencing methods were used on clinical specimens. The name and number of the clones of each species identified and the combinations of species present were recorded for each subject. Descriptive statistics were computed for the study variables. Specimens of pus or wound fluid were obtained from 9 subjects. A mean of 7.4 ± 3.7 (standard deviation) species per case were identified. The predominant species detected in the present study that have previously been associated with OIs were Fusobacterium spp, Parvimonas micra, Porphyromonas endodontalis, and Prevotella oris. The predominant species detected in our study that have not been previously associated with OIs were Dialister pneumosintes and Eubacterium brachy. Unculturable phylotypes accounted for 24% of the species identified in our study. All species detected were obligate or facultative anaerobes. Streptococci were not detected. Molecular methods have enabled us to detect previously cultivated and not-yet-cultivated species in OIs; these methods could change our understanding of the pathogenic flora of orofacial OIs. Copyright © 2012 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

The Emerging Microbe Project: Developing Clinical Care Plans Based on Pathogen Identification and Clinical Case Studies †

PubMed Central

O’Donnell, Lauren A.; Perry, Michael W.; Doup, Dane’t R.

2015-01-01

For many students in the health sciences, including doctor of pharmacy (PharmD) students, basic and clinical sciences often appear detached from each other. In the infectious disease field, PharmD students additionally struggle with mastering the diversity of microorganisms and the corresponding therapies. The objective of this study was to design an interdisciplinary project that integrates fundamental microbiology with clinical research and decision-making skills. The Emerging Microbe Project guided students through the identification of a microorganism via genetic sequence analysis. The unknown microbe provided the basis for a patient case that asked the student to design a therapeutic treatment strategy for an infected patient. Outside of lecture, students had two weeks to identify the pathogen using nucleotide sequences, compose a microbiology report on the pathogen, and recommend an appropriate therapeutic treatment plan for the corresponding clinical case. We hypothesized that the students would develop a better understanding of the interplay between basic microbiology and infectious disease clinical practice, and that they would gain confidence and skill in independently selecting appropriate antimicrobial therapies for a new disease state. The exercise was conducted with PharmD students in their second professional year of pharmacy school in a required infectious disease course. Here, we demonstrate that the Emerging Microbe Project significantly improved student learning through two assessment strategies (assignment grades and exam questions), and increased student confidence in clinical infectious disease practice. This exercise could be modified for other health sciences students or undergraduates depending upon the level of clinical focus required of the course. PMID:26753029

In vitro inhibition of commercial douche products against vaginal microflora.

PubMed Central

Pavlova, S I; Tao, L

2000-01-01

Recently, vaginal douching has been associated with many health risks in women. The aim of this study was to analyze the effect of commercial douche products against various vaginal microorganisms, including lactobacilli. Seven commercial douches were tested against eight Lactobacillus clinical isolates and three type strains from the American Type Culture Collection. BV-associated bacteria included six strains of five genera: Gardnerella, Mobiluncus, Mycoplasma, Peptostreptococcus, and Ureaplasma. Two isolates of group B Streptococcus, and three species of Candida were also tested. The minimal inhibition concentrations and minimal contact times for these products against vaginal microorganisms were determined in broth cultures. Four antiseptic-containing douche products showed a strong inhibitory effect against all vaginal microorganisms tested with a short contact time (less than 1 min). Three vinegar-containing douche products selectively inhibited vaginal pathogens associated with bacterial vaginosis, group B streptococcal vaginitis, and candidiasis, but not lactobacilli. The antimicrobial effects of the commercial douche products varied among different brands and microbial species tested. PMID:10805365

Prevalence of extended-spectrum beta-lactamases-producing microorganisms in nosocomial patients and molecular characterization of the shv type isolates

PubMed Central

de Oliveira, Caio Fernando; Salla, Adenilde; Lara, Valéria Maria; Rieger, Alexandre; Horta, Jorge André; Alves, Sydney Hartz

2010-01-01

The emergence of Extended-Spectrum Beta-Lactamase (ESBL)-producing microorganisms in Brazilian hospitals is a challenge that concerns scientists, clinicians and healthcare institutions due to the serious risk they pose to confined patients. The goal of this study was the detection of ESBL production by clinical strains of Escherichia coli and Klebsiella sp. isolated from pus, urine and blood of patients at Hospital Universitário Santa Maria, Rio Grande Sul, RS, Brazil and the genotyping of the isolates based on bla SHV genes. The ESBL study was carried out using the Combined Disc Method, while Polymerase Chain Reaction (PCR) was used to study the bla SHV genes. Of the 90 tested isolates, 55 (61.1%) were identified as ESBL-producing by the combined disk method. The bla SHV genes were found in 67.8% of these microorganisms. K. pneumoniae predominated in the samples, presenting the highest frequency of positive results from the combined disk and PCR. PMID:24031491

[EPIDEMIOLOGICAL, CLINICAL AND MICROBIOLOGICAL FINDINGS IN WOMEN WITH AEROBIC VAGINITIS].

PubMed

Dermendjiev, T; Pehlivanov, B; Hadjieva, K; Stanev, S

2015-01-01

Aerobic vaginitis (AV) is an alterarion of the normal lactobacillic flora accompanied by signs of inflammation, presence of mainly aerobic microorganisms from intestinal commensals or other aerobic pathogens. Clinical symptoms may vary by type and intensity and are marked by a high tendency for recurrence and chronification. Inflammation and ulcerations in AV could increase the risk of contracting HIV or other sexually transmitted infections. The aim is to study some epidemiological, clinical and microbiological features of the aerobic vaginitis in patients of the specialized Obstetric and Gynecological Clinic in Plovdiv, Bulgaria. In a retrospective research 4687 vaginal smears have been gathered in Microbiological laboratory at "St. George" Hospital - Plovdiv. We used clinical, microbiological and statistical methods. Information processing is performed by variation, alternative, correlation and graphical analysis using specialized package SPSS v13.0. The overall prevalence rate of AV in the studied population is 11.77%. The levels of prevalence of AV in pregnant and non-pregnant women are respectively 13.08% and 4.34%. The highest frequency of AV is in the age group 21-30 years (32.3%). The results show a marked association between Escherichia coli and the cases of AV (p < 0.001). AV is a common cause of vaginal symptoms in patients of specialized ambulatory outpatient. One in ten women with vaginal complaints suffers from AV Streptococcus agalactiae and Escherichia coli are most often isolated aerobic microorganisms.

Healthcare professionals' agreement on clinical relevance of drug-related problems among elderly patients.

PubMed

Bech, Christine Flagstad; Frederiksen, Tine; Villesen, Christine Tilsted; Højsted, Jette; Nielsen, Per Rotbøll; Kjeldsen, Lene Juel; Nørgaard, Lotte Stig; Christrup, Lona Louring

2018-02-01

Background Disagreement among healthcare professionals on the clinical relevance of drug-related problems can lead to suboptimal treatment and increased healthcare costs. Elderly patients with chronic non-cancer pain and comorbidity are at increased risk of drug related problems compared to other patient groups due to complex medication regimes and transition of care. Objective To investigate the agreement among healthcare professionals on their classification of clinical relevance of drug-related problems in elderly patients with chronic non-cancer pain and comorbidity. Setting Multidisciplinary Pain Centre, Rigshospitalet, Copenhagen, Denmark. Method A pharmacist performed medication review on elderly patients with chronic non-cancer pain and comorbidity, identified their drug-related problems and classified these problems in accordance with an existing categorization system. A five-member clinical panel rated the drug-related problems' clinical relevance in accordance with a five-level rating scale, and their agreement was compared using Fleiss' κ. Main outcome measure Healthcare professionals' agreement on clinical relevance of drug related problems, using Fleiss' κ. Results Thirty patients were included in the study. A total of 162 drug related problems were identified, out of which 54% were of lower clinical relevance (level 0-2) and 46% of higher clinical relevance (level 3-4). Only slight agreement (κ = 0.12) was found between the panellists' classifications of clinical relevance using a five-level rating scale. Conclusion The clinical pharmacist identified drug related problems of lower and higher clinical relevance. Poor overall agreement on the severity of the drug related problems was found among the panelists.

The importance of guidelines in the development and application of probiotics.

PubMed

Reid, Gregor

2005-01-01

Probiotics, defined as "Live microorganisms which when administered in adequate amounts confer a health benefit on the host" have many attributes including the lack of adverse side effects associated with their use. While probiotics have proven benefits, the optimism associated with their use is counterbalanced by the fact that many so-called "probiotic" products are unreliable in content and unproven clinically. Therefore much remains to be done to gain the acceptance of the broader medical community. Recognition of the obvious product inequality and the lack of any regulatory guidelines lead to the development of Operating Standards in 2002 (FAO/WHO), that would ensure product safety, reliability and a level playing field for all companies producing probiotic products. The guidelines constitute a set of parameters required for a product/strain to be termed "probiotic" and also the clinically relevant steps to be followed to move probiotics closer to being embraced by the medical community. These include i) implementation of Guidelines for use of probiotics; ii) phase I, II and III clinical trials to prove health benefits that are as good as or better than standard prevention or treatments for a particular condition or disease; iii) Good Manufacturing Practice and production of high quality products; iv) studies to identify mechanism of action in vivo; v) informative/ precise labelling; vi) development of probiotic organisms that can carry vaccines to hosts and/or anti- viral probiotics; vii) expansion of proven strains to benefit the oral cavity, nasopharynx, respiratory tract, stomach, vagina, bladder and skin as well as for cancer, allergies and recovery from surgery/ injury.

[In vitro antibacterial activity of Curcuma longa (Zingiberaceae) against nosocomial bacteria in Montería, Colombia].

PubMed

Méndez Álvarez, Nelson; Angulo Ortíz, Alberto; Contreras Martínez, Orfa

2016-09-01

Bacterial resistance is a growing health problem worldwide that has serious economic and social impacts, compromising public health, and the therapeutic action of current antibiotics. Therefore, the search for new compounds with antimicrobial properties is relevant in modern studies, particularly against bacteria of clinical interest. In the present study, in vitro antibacterial activity of the ethanol extract and essential oil of Curcuma longa (Zingiberaceae) was evaluated against nosocomial bacteria, using the microdilution method. Escherichia coli strains, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus sp. were used, Salmonella sp. and Bacillus sp., isolated from nosocomial infections in a hospital in the city of Monteria and reference strains of S. aureus ATCC 43300, S. aureus ATCC 29213, S. aureus ATCC 25923, P. aeruginosa ATCC 27853, E. coli ATCC 25922 and K. pneumonia ATCC 700603. The ethanol extract antibacterial profile was more efficient at higher concentrations (1 000 ppm), obtaining significant percentages of reduction of more than 50 % against K. pneumoniae ATCC 700603 and a clinical isolate of E. coli; while compared to Bacillus clinical isolate, was more active than the essential oil. For the rest of microorganisms, the reduction percentages obtained at a concentration of 1 000 ppm varied between 17 and 42 % with ethanolic extract, and 8 to 43 % with essential oil. At concentrations of 100 and 500 ppm antibacterial activity of the extracts was lower. The results indicated that the ethanolic extract and essential oil of C. longa rhizomes have active compounds with antibacterial properties that could be used in future research as a therapeutic alternative for the treatment of infections caused by nosocomial pathogens.

Identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product ET-743

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schofield, Michael M.; Jain, Sunit; Porat, Daphne

Ecteinascidin 743 (ET-743, Yondelis) is a clinically approved chemotherapeutic natural product isolated from the Caribbean mangrove tunicate Ecteinascidia turbinata. Researchers have long suspected that a microorganism may be the true producer of the anti-cancer drug, but its genome has remained elusive due to our inability to culture the bacterium in the laboratory using standard techniques. Here, we sequenced and assembled the complete genome of the ET-743 producer, Candidatus Endoecteinascidia frumentensis, directly from metagenomic DNA isolated from the tunicate. Analysis of the ~631 kb microbial genome revealed strong evidence of an endosymbiotic lifestyle and extreme genome reduction. Phylogenetic analysis suggested thatmore » the producer of the anti-cancer drug is taxonomically distinct from other sequenced microorganisms and could represent a new family of Gammaproteobacteria. The complete genome has also greatly expanded our understanding of ET-743 production and revealed new biosynthetic genes dispersed across more than 173 kb of the small genome. The gene cluster’s architecture and its preservation demonstrate that the drug is likely essential to the interactions of the microorganism with its mangrove tunicate host. In conclusion, taken together, these studies elucidate the lifestyle of a unique, and pharmaceutically-important microorganism and highlight the wide diversity of bacteria capable of making potent natural products.« less

Identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product ET-743

DOE PAGES

Schofield, Michael M.; Jain, Sunit; Porat, Daphne; ...

2015-07-21

Ecteinascidin 743 (ET-743, Yondelis) is a clinically approved chemotherapeutic natural product isolated from the Caribbean mangrove tunicate Ecteinascidia turbinata. Researchers have long suspected that a microorganism may be the true producer of the anti-cancer drug, but its genome has remained elusive due to our inability to culture the bacterium in the laboratory using standard techniques. Here, we sequenced and assembled the complete genome of the ET-743 producer, Candidatus Endoecteinascidia frumentensis, directly from metagenomic DNA isolated from the tunicate. Analysis of the ~631 kb microbial genome revealed strong evidence of an endosymbiotic lifestyle and extreme genome reduction. Phylogenetic analysis suggested thatmore » the producer of the anti-cancer drug is taxonomically distinct from other sequenced microorganisms and could represent a new family of Gammaproteobacteria. The complete genome has also greatly expanded our understanding of ET-743 production and revealed new biosynthetic genes dispersed across more than 173 kb of the small genome. The gene cluster’s architecture and its preservation demonstrate that the drug is likely essential to the interactions of the microorganism with its mangrove tunicate host. In conclusion, taken together, these studies elucidate the lifestyle of a unique, and pharmaceutically-important microorganism and highlight the wide diversity of bacteria capable of making potent natural products.« less

Oral cavity infection: an adverse effect after the treatment of oral cancer in aged individuals.

PubMed

Pan, Jie; Zhao, Jun; Jiang, Ning

2014-01-01

The immune compromised patients after treatment of oral cancer may have a chance of infection by drug-resistant opportunistic microbes. We investigated the occurrence of opportunistic microorganisms in aged individuals receiving follow-up examinations after treatment of oral cancer in China. These patients were used as test group and the respective age grouped healthy individuals as control group. In this study, the oral cavity microorganisms such as bacteria and yeast were taken for the analysis. After the screening of representative microorganisms, their aptitude of pervasiveness against drugs was studied. Here, we used antimicrobial agents which are common in clinical practice. We also performed studies to investigate the presence of toxin genes in methicillin-resistant S. aureus (MRSA). The results indicate that the prevalence of drug-resistant microbes was more pronounced in oral cancer patients after initial treatment above 70 years old. The oxacillin resistance of S. aureus isolate confirms that the prevalence of MRSA is increasing in accordance to age-factor and immune compromise in elderly patients. This study reveals the occurrence of drug-resistant opportunistic microorganisms in oral cavity after treatment for oral cancer in aged individuals. Special attention should be directed to MRSA during the treatment of oral cancer, and to realize the fact of immune compromise in elderly patients.

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast

PubMed Central

Díaz-Nieto, Leonardo M.; D´Alessio, Cecilia

2016-01-01

Culex pipiens is the most cosmopolitan mosquito of the Pipiens Assemblage. By studying the nature of interactions between this species and microorganisms common to its breeding environment we can unravel important pitfalls encountered during development. We tested the survival rate of larval stages, pupae and adults of a Cx. pipiens colony exposed to a variety of microorganisms in laboratory conditions and assessed the transmission to offspring (F1) by those organisms that secured development up to adulthood. Three complementary experiments were designed to: 1) explore the nutritional value of yeasts and other microorganisms during Cx. pipiens development; 2) elucidate the transstadial transmission of yeast to the host offspring; and 3) to examine the relevance of all these microorganisms in female choice for oviposition-substratum. The yeast Saccharomyces cerevisiae proved to be the most nutritional diet, but despite showing the highest survival rates, vertical transmission to F1 was never confirmed. In addition, during the oviposition trials, none of the gravid females was attracted to the yeast substratum. Notably, the two native bacterial strains, Klebsiella sp. and Aeromonas sp., were the preferred oviposition media, the same two bacteria that managed to feed neonates until molting into 2nd instar larvae. Our results not only suggest that Klebsiella sp. or Aeromonas sp. serve as attractants for oviposition habitat selection, but also nurture the most fragile instar, L1, to assure molting into a more resilient stage, L2, while yeast proves to be the most supportive diet for completing development. These experiments unearthed survival traits that might be considered in the future development of strategies of Cx. pipiens control. These studies can be extended to other members of the Pipiens Assemblage. PMID:27055276

Formation of 2,4-D bound residues in soils: New insights into microbial metabolism.

PubMed

Botero, Liliana Rocío; Mougin, Chistian; Peñuela, Gustavo; Barriuso, Enrique

2017-04-15

The microbial contribution to the formation of bound residues in soils is studied by characterizing the metabolic activity of three microorganisms (Trametes versicolor, Fusarium solani and Ralstonia eutropha) on 14 C-2,4-dichlorophenoxyacetic acid (2,4-D) during incubation in synthetic liquid media and soil. A fractionation protocol was applied to quantify the 14 C-2,4-D that was incorporated into the biomass among biomolecular-like fractions. Successive fractionation of microbial biomass was implemented to break up and quantify the methanol/dichloromethane fraction (corresponding to the 14 C-lipid-like fraction), the trichloroacetic acid fraction (or hydrolysed 14 C-polysaccharide-like fraction) and the acid hydrolysable fraction (or the hydrolysed 14 C-protein-like fraction). Relevant differences in the 2,4-D degradation and biomass radioactivity distribution among the three microorganisms were found. The 14 C-protein-like fraction was the most consistent biomass fraction for reflecting the pesticide use capacity of the microorganisms under liquid and soil conditions. 2,4-D and its metabolite 4-chlorophenol were detected in methanol/dichloromethane and trichloroacetic acid fractions of the biomass of microorganisms exhibiting a low capacity to mineralize 2,4-D, thus proving that the microbial participation in the formation of bound residues while conserving the initial pesticide structure under natural soil conditions may be intimately associated with the lipid- and polysaccharide-like constituents. The fractionation protocol differentiates between 14 C that is incorporated into biomass as a biomolecular constituent and the pesticide or its metabolites that accumulate in the biomass and thus correspond to the stricto sensu definition of bound residues. Copyright © 2017 Elsevier B.V. All rights reserved.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

[The hypothesis of infectious etiology for idiopathic nervous system diseases: from the postulates of Koch to the criteria of Hill].

PubMed

Bélec, L

1999-01-01

The evaluation of the hypothesis of an infectious etiology to some neurological diseases comprises four different situations. First, numerous neurological diseases have an obvious infectious etiology (encephilitis, meningoencephilitis). Second, some neurological disorders were primarily suspected to be have an infectious etiology, but the causative microorganism was discovered either longtime after the princeps description of the disease (neurologic Whipple disease, due to Tropheryma whippelii), or at the same time (tropical spastic para-paresis secondary to HTLV-I infection). Third, for other neurological diseases, an infectious etiology that was not suspected at time of their anatomoclinic descriptions, was further demonstrated in the context of a generally complex physiopathology (Guillain-Barré syndrome and infection by Campylobacter jejuni). Finally, some idiopathic neurological diseases could be related to well known or yet unknown microorganisms, in association with some environmental factors, and with a particular genetic or acquired susceptibility of the host. The evaluation of an infectious etiology to these idiopathic neurological disorders must be envisioned according to 3 possibilities: 1) generally, the neurological disease is well defined, but its etiology remains unknown and an infectious hypothesis could be relevant (multiple sclerosis, post-polio syndrome, amyotrophic lateral sclerosis); 2) sometimes, a microorganism that is not associated with a known disease, and then qualified as "orphelin", could be associated with neurological disorders (spumaretrovirus); 3) finally, a new neurological disease could be associated with a known or yet unknown microorganism, directly or indirectly. In conclusion, some idiopathic neurological diseases could have an infectious etiology, with physiopathologic, diagnostic, prophylactic (vaccination) and therapeutic (use of anti-infectious drugs) consequences.

New member of the hormone-sensitive lipase family from the permafrost microbial community.

PubMed

Petrovskaya, Lada E; Novototskaya-Vlasova, Ksenia A; Gapizov, Sultan Sh; Spirina, Elena V; Durdenko, Ekaterina V; Rivkina, Elizaveta M

2017-07-04

Siberian permafrost is a unique environment inhabited with diverse groups of microorganisms. Among them, there are numerous producers of biotechnologically relevant enzymes including lipases and esterases. Recently, we have constructed a metagenomic library from a permafrost sample and identified in it several genes coding for potential lipolytic enzymes. In the current work, properties of the recombinant esterases obtained from this library are compared with the previously characterized lipase from Psychrobacter cryohalolentis and other representatives of the hormone-sensitive lipase family.

Incidental findings in multislice computed tomography prior to transcatheter aortic valve implantation: frequency, clinical relevance and outcome.

PubMed

Trenkwalder, Teresa; Lahmann, Anna Lena; Nowicka, Magdalena; Pellegrini, Costanza; Rheude, Tobias; Mayr, N Patrick; Voss, Stephanie; Bleiziffer, Sabine; Lange, Rüdiger; Joner, Michael; Kasel, Albert M; Kastrati, Adnan; Schunkert, Heribert; Husser, Oliver; Hadamitzky, Martin; Hengstenberg, Christian

2018-02-21

Multislice computed tomography (MSCT) has emerged as the mainstay in patients planned for transcatheter aortic valve implantation (TAVI). Incidental findings (IF) in MSCT are common. However, the exact incidence, clinical relevance and further consequences of IF are unclear and it is controversial whether IF adversely affect patients' outcome. We analyzed MSCT data of 1050 patients screened for TAVI between January 2011 and December 2014. Median follow-up of patients was 20 months. In total, 3194 IF were identified, which were classified into clinically non-relevant IF (2872, 90%) and clinically relevant IF (322, 10%). In 25% of patients (258/1050) at least one clinically relevant IF was present. Age (80 ± 7 vs. 80 ± 7 years; p = 0.198) and EuroSCORE II (3.6% [2.1-5.7] vs. 3.6% [2.1-5.9]; p = 0.874) was similar between patients with and without a clinically relevant IF. TAVI was performed less frequently in patients with a clinically relevant IF (76% vs. 85%; p < 0.001), with more patients receiving surgical aortic valve replacement in that group (14% vs. 11%; p = 0.042), possibly due to the high rate of incidental aneurysms of the ascending aorta (n = 48). If TAVI was performed mortality did not differ (30-days: 4% vs. 3%; p = 0.339, 1-year: 11% vs. 14%; p = 0.226) between patients with and without a clinically relevant IF. Our study is the largest study to analyze prevalence, clinical relevance and therapeutic consequences of IF during screening for TAVI. IF in pre-procedural MSCT are common and clinically relevant in one-quarter of patients. However, these findings had no impact on overall mortality.

Dose imprecision and resistance: free-choice medicated feeds in industrial food animal production in the United States.

PubMed

Love, David C; Davis, Meghan F; Bassett, Anna; Gunther, Andrew; Nachman, Keeve E

2011-03-01

Industrial food animal production employs many of the same antibiotics or classes of antibiotics that are used in human medicine. These drugs can be administered to food animals in the form of free-choice medicated feeds (FCMF), where animals choose how much feed to consume. Routine administration of these drugs to livestock selects for microorganisms that are resistant to medications critical to the treatment of clinical infections in humans. In this commentary, we discuss the history of medicated feeds, the nature of FCMF use with regard to dose delivery, and U.S. policies that address antimicrobial drug use in food animals. FCMF makes delivering a predictable, accurate, and intended dose difficult. Overdosing can lead to animal toxicity; underdosing or inconsistent dosing can result in a failure to resolve animal diseases and in the development of antimicrobial-resistant microorganisms. The delivery of antibiotics to food animals for reasons other than the treatment of clinically diagnosed disease, especially via free-choice feeding methods, should be reconsidered.

Bioremediation strategies for chromium removal: Current research, scale-up approach and future perspectives.

PubMed

Fernández, Pablo M; Viñarta, Silvana C; Bernal, Anahí R; Cruz, Elías L; Figueroa, Lucía I C

2018-05-28

Industrial applications and commercial processes release a lot of chromium into the environment (soil, surface water or atmosphere) and resulting in serious human diseases because of their toxicity. Biological Cr-removal offers an alternative to traditional physic-chemical methods. This is considered as a sustainable technology of lower impact on the environment. Resistant microorganisms (e.g. bacteria, fungi, and algae) have been most extensively studied from this characteristic. Several mechanisms were developed by microorganisms to deal with chromium toxicity. These tools include biotransformation (reduction or oxidation), bioaccumulation and/or biosorption, and are considered as an alternative to remove the heavy metal. The aim of this review is summarizes Cr(VI)-bioremediation technologies oriented on practical applications at larger scale technologies. In the same way, the most relevant results of several investigations focused on process feasibility and the robustness of different systems (reactors and pilot scale) designed for chromium-removal capacity are highlighted. Copyright © 2018. Published by Elsevier Ltd.

Gut immunity in Lepidopteran insects.

PubMed

Wu, Kai; Yang, Bing; Huang, Wuren; Dobens, Leonard; Song, Hongsheng; Ling, Erjun

2016-11-01

Lepidopteran insects constitute one of the largest fractions of animals on earth, but are considered pests in their relationship with man. Key to the success of this order of insects is its ability to digest food and absorb nutrition, which takes place in the midgut. Because environmental microorganisms can easily enter Lepidopteran guts during feeding, the innate immune response guards against pathogenic bacteria, virus and microsporidia that can be devoured with food. Gut immune responses are complicated by both resident gut microbiota and the surrounding peritrophic membrane and are distinct from immune responses in the body cavity, which depend on the function of the fat body and hemocytes. Due to their relevance to agricultural production, studies of Lepidopteran insect midgut and immunity are receiving more attention, and here we summarize gut structures and functions, and discuss how these confer immunity against different microorganisms. It is expected that increased knowledge of Lepidopteran gut immunity may be utilized for pest biological control in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Plasma membrane microorganization of LR73 multidrug-resistant cells revealed by FCS

NASA Astrophysics Data System (ADS)

Winckler, Pascale; Jaffiol, Rodolphe; Cailler, Aurélie; Morjani, Hamid; Jeannesson, Pierre; Deturche, Régis

2011-03-01

Tumoral cells could present a multidrug resistance (MDR) to chemotherapeutic treatments. This drug resistance would be associated to biomechanisms occurring at the plasma membrane level, involving modification of membrane fluidity, drug permeability, presence of microdomains (rafts, caveolae...), and membrane proteins overexpression such as Pglycoprotein. Fluorescence correlation spectroscopy (FCS) is the relevant method to investigate locally the fluidity of biological membranes through the lateral diffusion of a fluorescent membrane probe. Thus, we use FCS to monitor the plasma membrane local organization of LR73 carcinoma cells and three derived multidrug-resistant cancer cells lines. Measurements were conducted at the single cell level, which enabled us to get a detailed overview of the plasma membrane microviscosity distribution of each cell line studied. Moreover, we propose 2D diffusion simulation based on a Monte Carlo model to investigate the membrane organisation in terms of microdomains. This simulation allows us to relate the differences in the fluidity distributions with microorganization changes in plasma membrane of MDR cells.

Pathogenic marine microbes influence the effects of climate change on a commercially important tropical bivalve.

PubMed

Turner, Lucy M; Alsterberg, Christian; Turner, Andrew D; Girisha, S K; Rai, Ashwin; Havenhand, Jonathan N; Venugopal, M N; Karunasagar, Indrani; Godhe, Anna

2016-08-31

There is growing evidence that climate change will increase the prevalence of toxic algae and harmful bacteria, which can accumulate in marine bivalves. However, we know little about any possible interactions between exposure to these microorganisms and the effects of climate change on bivalve health, or about how this may affect the bivalve toxin-pathogen load. In mesocosm experiments, mussels, Perna viridis, were subjected to simulated climate change (warming and/or hyposalinity) and exposed to harmful bacteria and/or toxin-producing dinoflagellates. We found significant interactions between climate change and these microbes on metabolic and/or immunobiological function and toxin-pathogen load in mussels. Surprisingly, however, these effects were virtually eliminated when mussels were exposed to both harmful microorganisms simultaneously. This study is the first to examine the effects of climate change on determining mussel toxin-pathogen load in an ecologically relevant, multi-trophic context. The results may have considerable implications for seafood safety.

Acanthamoeba castellanii is not be an adequate model to study human adenovirus interactions with macrophagic cells

PubMed Central

Cateau, Estelle; Leveque, Nicolas; Kaaki, Sihem; Beby-Defaux, Agnès; Rodier, Marie-Hélène

2017-01-01

Free living amoebae (FLA) including Acanthamoeba castellanii, are protozoa that feed on different microorganisms including viruses. These microorganisms show remarkable similarities with macrophages in cellular structures, physiology or ability to phagocyte preys, and some authors have therefore wondered whether Acanthamoeba and macrophages are evolutionary related. It has been considered that this amoeba may be an in vitro model to investigate relationships between pathogens and macrophagic cells. So, we intended in this study to compare the interactions between a human adenovirus strain and A. castellanii or THP-1 macrophagic cells. The results of molecular and microscopy techniques following co-cultures experiments have shown that the presence of the adenovirus decreased the viability of macrophages, while it has no effect on amoebic viability. On another hand, the viral replication occurred only in macrophages. These results showed that this amoebal model is not relevant to explore the relationships between adenoviruses and macrophages in in vitro experiments. PMID:28591183

Enzyme leaps fuel antichemotaxis

PubMed Central

Jee, Ah-Young; Dutta, Sandipan; Cho, Yoon-Kyoung

2018-01-01

There is mounting evidence that enzyme diffusivity is enhanced when the enzyme is catalytically active. Here, using superresolution microscopy [stimulated emission-depletion fluorescence correlation spectroscopy (STED-FCS)], we show that active enzymes migrate spontaneously in the direction of lower substrate concentration (“antichemotaxis”) by a process analogous to the run-and-tumble foraging strategy of swimming microorganisms and our theory quantifies the mechanism. The two enzymes studied, urease and acetylcholinesterase, display two families of transit times through subdiffraction-sized focus spots, a diffusive mode and a ballistic mode, and the latter transit time is close to the inverse rate of catalytic turnover. This biochemical information-processing algorithm may be useful to design synthetic self-propelled swimmers and nanoparticles relevant to active materials. Executed by molecules lacking the decision-making circuitry of microorganisms, antichemotaxis by this run-and-tumble process offers the biological function to homogenize product concentration, which could be significant in situations when the reactant concentration varies from spot to spot. PMID:29255047

Sea ice, extremophiles and life on extra-terrestrial ocean worlds

NASA Astrophysics Data System (ADS)

Martin, Andrew; McMinn, Andrew

2018-01-01

The primary aim of this review is to highlight that sea-ice microbes would be capable of occupying ice-associated biological niches on Europa and Enceladus. These moons are compelling targets for astrobiological exploration because of the inferred presence of subsurface oceans that have persisted over geological timescales. Although potentially hostile to life in general, Europa and Enceladus may still harbour biologically permissive domains associated with the ice, ocean and seafloor environments. However, validating sources of free energy is challenging, as is qualifying possible metabolic processes or ecosystem dynamics. Here, the capacity for biological adaptation exhibited by microorganisms that inhabit sea ice is reviewed. These ecosystems are among the most relevant Earth-based analogues for considering life on ocean worlds because microorganisms must adapt to multiple physicochemical extremes. In future, these organisms will likely play a significant role in defining the constraints on habitability beyond Earth and developing a mechanistic framework that contrasts the limits of Earth's biosphere with extra-terrestrial environments of interest.

Steroid 11-Alpha-Hydroxylation by the Fungi Aspergillus nidulans and Aspergillus ochraceus.

PubMed

Ríos, Lidia Ortega-de Los; Luengo, José M; Fernández-Cañón, José M

2017-01-01

Steroids are a group of natural compounds derived from the cyclopentane-perhydro-phenantrene nucleus that have a great interest for the pharmaceutical industries as a consequence of their physiological effects. Among their functions are anti-inflammatory, immunosuppressive, or contraceptive activities. Nowadays, microbial transformation of steroid precursors is winning relevance opposite to the chemical synthesis, since it allows for decreasing time, expenses, and environmental pollution. Pharmaceutical industry tends to use cholesterol and phytosterols as starting materials due to their low cost. Aspergillus ochraceus and Aspergillus nidulans, a fungus whose biochemistry and genetics are well known, have been chosen because of their capacity of 11-α-hydroxylation over some steroids which confers on them their anti-inflammatory properties. We have cloned the genes encoding the 11-α-hydroxylase enzymatic activities with the aim to introduce them in other microorganisms, such as Mycobacterium smegmatis, used in the industry to split the side chain of phytosterols, and thus creating recombinant microorganisms able to generate useful steroids from cheap precursors in just one-step fermentation.

Adhesion of Photoactive Microalgae to Surfaces is Switchable by Light

NASA Astrophysics Data System (ADS)

Bäumchen, Oliver; Kreis, Christian; Le Blay, Marine; Linne, Christine; Makowski, Marcin

The natural habitats of many microorganisms are confined geometries, such as the interstitial space of rocks and soil, where interactions with interfaces and surfaces are of paramount importance. We performed in vivo force spectroscopy experiments on the unicellular biflagellated microalga Chlamydomonas, a prime model organism in cell- and microbiology, and discovered that the flagella-mediated adhesion to surfaces can be switched on and off by light. Time-resolved micropipette experiments show that the light-switchable adhesiveness of the flagella is a completely reversible process that is based on a redistribution of adhesion-promoting flagella-membrane proteins within seconds. Light-switchable adhesion enables the cell to regulate the transition between planktonic and surface-associated state, which possibly represents a significant biological advantage for photoactive microorganisms. In terms of the colonization of surfaces and the formation of biofilms, the findings might have immediate economic and environmental relevance in biotechnological settings, such as photo-bioreactors for the sustainable production of biofuels.

Microbially-induced Carbonate Precipitation for Immobilization of Toxic Metals.

PubMed

Kumari, Deepika; Qian, Xin-Yi; Pan, Xiangliang; Achal, Varenyam; Li, Qianwei; Gadd, Geoffrey Michael

2016-01-01

Rapid urbanization and industrialization resulting from growing populations contribute to environmental pollution by toxic metals and radionuclides which pose a threat to the environment and to human health. To combat this threat, it is important to develop remediation technologies based on natural processes that are sustainable. In recent years, a biomineralization process involving ureolytic microorganisms that leads to calcium carbonate precipitation has been found to be effective in immobilizing toxic metal pollutants. The advantage of using ureolytic organisms for bioremediating metal pollution in soil is their ability to immobilize toxic metals efficiently by precipitation or coprecipitation, independent of metal valence state and toxicity and the redox potential. This review summarizes current understanding of the ability of ureolytic microorganisms for carbonate biomineralization and applications of this process for toxic metal bioremediation. Microbial metal carbonate precipitation may also be relevant to detoxification of contaminated process streams and effluents as well as the production of novel carbonate biominerals and biorecovery of metals and radionuclides that form insoluble carbonates. Copyright © 2016 Elsevier Inc. All rights reserved.

De novo biosynthesis of anthocyanins in Saccharomyces cerevisiae.

PubMed

Eichenberger, Michael; Hansson, Anders; Fischer, David; Dürr, Lara; Naesby, Michael

2018-06-01

Anthocyanins (ACNs) are plant secondary metabolites responsible for most of the red, purple and blue colors of flowers, fruits and vegetables. They are increasingly used in the food and beverage industry as natural alternative to artificial colorants. Production of these compounds by fermentation of microorganisms would provide an attractive alternative. In this study, Saccharomyces cerevisiae was engineered for de novo production of the three basic anthocyanins, as well as the three main trans-flavan-3-ols. Enzymes from different plant sources were screened and efficient variants found for most steps of the biosynthetic pathway. However, the anthocyanidin synthase was identified as a major obstacle to efficient production. In yeast, this enzyme converts the majority of its natural substrates leucoanthocyanidins into the off-pathway flavonols. Nonetheless, de novo biosynthesis of ACNs was shown for the first time in yeast and for the first time in a single microorganism. It provides a framework for optimizing the activity of anthocyanidin synthase and represents an important step towards sustainable industrial production of these highly relevant molecules in yeast.

Effect of simulated microgravity on growth and production of exopolymeric substances of Micrococcus luteus space and earth isolates.

PubMed

Mauclaire, Laurie; Egli, Marcel

2010-08-01

Microorganisms tend to form biofilms on surfaces, thereby causing deterioration of the underlaying material. In addition, biofilm is a potential health risk to humans. Therefore, microorganism growth is not only an issue on Earth but also in manned space habitats like the International Space Station (ISS). The aim of the study was to identify physiological processes relevant for Micrococcus luteus attachment under microgravity conditions. The results demonstrate that simulated microgravity influences physiological processes which trigger bacterial attachment and biofilm formation. The ISS strains produced larger amounts of exopolymeric substances (EPS) compared with a reference strain from Earth. In contrast, M. luteus strains were growing faster, and Earth as well as ISS isolates produced a higher yield of biomass under microgravity conditions than under normal gravity. Furthermore, microgravity caused a reduction of the colloidal EPS production of ISS isolates in comparison with normal gravity, which probably influences biofilm thickness and stability as well.

Production and removal of superoxide anion radical by artificial metalloenzymes and redox-active metals

PubMed Central

Kawano, Tomonori; Kagenishi, Tomoko; Kadono, Takashi; Bouteau, François; Hiramatsu, Takuya; Lin, Cun; Tanaka, Kenichiro; Tanaka, Licca; Mancuso, Stefano; Uezu, Kazuya; Okobira, Tadashi; Furukawa, Hiroka; Iwase, Junichiro; Inokuchi, Reina; Baluška, Frantisek; Yokawa, Ken

2015-01-01

Generation of reactive oxygen species is useful for various medical, engineering and agricultural purposes. These include clinical modulation of immunological mechanism, enhanced degradation of organic compounds released to the environments, removal of microorganisms for the hygienic purpose, and agricultural pest control; both directly acting against pathogenic microorganisms and indirectly via stimulation of plant defense mechanism represented by systemic acquired resistance and hypersensitive response. By aiming to develop a novel classes of artificial redox-active biocatalysts involved in production and/or removal of superoxide anion radicals, recent attempts for understanding and modification of natural catalytic proteins and functional DNA sequences of mammalian and plant origins are covered in this review article. PMID:27066179

Diagnosis of Infectious Diseases: a Cytopathologist’s Perspective

PubMed Central

Powers, Celeste N.

1998-01-01

This review explores the role of the cytopathology laboratory in the detection and presumptive identification of microorganisms. Sample procurement by exfoliation, abrasion, and aspiration techniques, as well as a variety of cytopreparatory and staining methods, is reviewed. Emphasis is placed on the utility of fine-needle aspiration as a rapid, safe, and cost-effective diagnositic procedure. The role of rapid interpretation and specimen triage is also discussed. Cytomorphologic features and staining characteristics are presented for a spectrum of microorganisms potentially encountered in the cytopathology laboratory. Pitfalls in diagnosis and the usefulness of special stains and ancillary techniques are also evaluated. The importance of communication, collaboration, and clinical correlation is stressed. PMID:9564567

Comparison of clinical and microbiological features of vulvovaginitis in prepubertal and pubertal girls.

PubMed

Yilmaz, Ayse E; Celik, Nurullah; Soylu, Gul; Donmez, Ahsen; Yuksel, Cigdem

2012-07-01

Vulvovaginitisis the most common gynecological problem of childhood. The aim of the study was to determine and compare clinical and microbiological features of vulvovaginitis in prepubertal and adolescent girls. In this retrospective study, the records of patients who were diagnosed with vulvovaginitis between January 2005 and December 2010 in the pediatric outpatient clinic at Fatih University Hospital were retrieved. Information regarding age, symptoms, history of antibiotic use within 1 month prior to presentation, findings on urinalysis, serum antistreptolysin-O levels, and results of urine/vaginal cultures was collected. The records of 112 patients were evaluated, 72 of which were prepubertal (64.2%) and 40 were pubertal (35.7%) at the time of diagnosis. Thirty-eight prepubertal patients (52.7%) had a positive result on vaginal culture, the most commonly encountered microorganism being group A beta-hemolytic streptococcus (15.2%). Culture positivity rate in the pubertal group was 47.5% (19 patients), with Candida albicans being the most frequently isolated microorganism (27.5%). The etiopathogenesis and culture results differ between prepubertal and adolescent girls with vulvovaginitis, which should be taken into consideration in the treatment approach of this disorder. Copyright © 2012. Published by Elsevier B.V.

Infective endocarditis; report from a main referral teaching hospital in Iran

PubMed Central

Heydari, Behrooz; Karimzadeh, Iman; Khalili, Hossein; Shojaei, Esfandiar; Ebrahimi, Abdolrasool

2017-01-01

Background/Objective: The aim of the present preliminary study was to assess the demographic, clinical, paraclinical, microbiological, echocardiographic, and therapeutic profile as well as in-hospital outcome of patients with infective endocarditis at a referral center for various infectious diseases in Iran. Methods: Required demographic, clinical, plausible complications and paraclinical data were collected from patients’ medical charts. Echocardiographic findings were obtained by performing transthoracic and/or transesophageal echocardiography as clinically indicated. In addition, details of management modalities and in-hospital outcome of patients were recorded. Results: During a 3-year period, 55 patients with definite or possible diagnosis of Infective endocarditis were admitted to the ward. Twenty one (38.2%) patients were injection drug users. Staphylococcus aureus and S.epidermidis were the most commonly isolated microorganisms. Management modalities of Infective endocarditis included antimicrobial therapy alone (48 cases) and the combination of antimicrobial therapy and surgery (7 cases). Conclusion: The rate of negative blood culture in our cohort is high. S. aureus and S.epidermidis were the most commonly isolated microorganisms from positive blood cultures. Congestive heart failure was the most frequent infective endocarditis complication as well as indication for surgery. In-hospital mortality rate of patients was unexpectedly low. PMID:28496492

Comparison of 'time to detection' values between BacT/ALERT VIRTUO and BacT/ALERT 3D instruments for clinical blood culture samples.

PubMed

Congestrì, Francesco; Pedna, Maria Federica; Fantini, Michela; Samuelli, Michela; Schiavone, Pasqua; Torri, Arianna; Bertini, Stefania; Sambri, Vittorio

2017-09-01

The early detection of bacteraemia and fungemia is of paramount importance to guide antimicrobial therapy in septic patients. In this study the 'time to detection' (TTD) value for the new blood culture system BacT/ALERT VIRTUO (VIRTUO) was evaluated in 1462 positive clinical bottles and compared with the TTD for 1601 positive clinical bottles incubated in the BacT/ALERT 3D system (BTA-3D). The most representative microorganisms isolated from bottles incubated in both blood culture systems were divided into eight categories (in order of frequency): coagulase-negative staphylococci (CoNS), Escherichia coli, Enterobacteriaceae (other than E. coli), Staphylococcus aureus, Enterococcus spp, viridans group streptococci, Pseudomonas aeruginosa, and Candida spp. The comparison of TTD values for the two blood culture systems strongly indicated that growth of the first five groups listed above was detected earlier with VIRTUO than with BTA-3D (p < 0.05). The new VIRTUO blood culture system can reduce the TTD for more than 75% of isolated microorganisms. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Shell-vial culture and real-time PCR applied to Rickettsia typhi and Rickettsia felis detection.

PubMed

Segura, Ferran; Pons, Immaculada; Pla, Júlia; Nogueras, María-Mercedes

2015-11-01

Murine typhus is a zoonosis transmitted by fleas, whose etiological agent is Rickettsia typhi. Rickettsia felis infection can produces similar symptoms. Both are intracellular microorganisms. Therefore, their diagnosis is difficult and their infections can be misdiagnosed. Early diagnosis prevents severity and inappropriate treatment regimens. Serology can't be applied during the early stages of infection because it requires seroconversion. Shell-vial (SV) culture assay is a powerful tool to detect Rickettsia. The aim of the study was to optimize SV using a real-time PCR as monitoring method. Moreover, the study analyzes which antibiotics are useful to isolate these microorganisms from fleas avoiding contamination by other bacteria. For the first purpose, SVs were inoculated with each microorganism. They were incubated at different temperatures and monitored by real-time PCR and classical methods (Gimenez staining and indirect immunofluorescence assay). R. typhi grew at all temperatures. R. felis grew at 28 and 32 °C. Real-time PCR was more sensitive than classical methods and it detected microorganisms much earlier. Besides, the assay sensitivity was improved by increasing the number of SV. For the second purpose, microorganisms and fleas were incubated and monitored in different concentrations of antibiotics. Gentamicin, sufamethoxazole, trimethoprim were useful for R. typhi isolation. Gentamicin, streptomycin, penicillin, and amphotericin B were useful for R. felis isolation. Finally, the optimized conditions were used to isolate R. felis from fleas collected at a veterinary clinic. R. felis was isolated at 28 and 32 °C. However, successful establishment of cultures were not possible probably due to sub-optimal conditions of samples.

Evidence Report: Risk of Adverse Health Effects Due to Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Oubre, Cherie; Wallace, Sarah; Mehta, Satish; Pierson, Duane

2016-01-01

While preventive measures limit the presence of many medically significant microorganisms during spaceflight missions, microbial infection of crewmembers cannot be completely prevented. Spaceflight experiments over the past 50 years have demonstrated a unique microbial response to spaceflight culture, although the mechanisms behind those responses and their operational relevance were unclear. In 2007, the operational importance of these microbial responses was emphasized as the results of an experiment aboard STS-115 demonstrated that the enteric pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) increased in virulence in a murine model of infection. The experiment was reproduced in 2008 aboard STS-123 confirming this finding. In response to these findings, the Institute of Medicine of the National Academies recommended that NASA investigate this risk and its potential impact on the health of the crew during spaceflight. NASA assigned this risk to the Human Research Program. To better understand this risk, evidence has been collected and reported from both spaceflight analog systems and actual spaceflight including Mir, Space Shuttle, and ISS missions. Although the performance of virulence studies during spaceflight are challenging and often impractical, additional information has been and continues to be collected to better understand the risk to crew health. Still, the uncertainty concerning the extent and severity of these alterations in host-microorganism interactions is very large and requires more investigation as the focus of human spaceflight shifts to longer-duration exploration class missions.

Cold and Hot Extremozymes: Industrial Relevance and Current Trends

PubMed Central

Sarmiento, Felipe; Peralta, Rocío; Blamey, Jenny M.

2015-01-01

The development of enzymes for industrial applications relies heavily on the use of microorganisms. The intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. Extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. These microorganisms have developed unique mechanisms and molecular means to cope with extreme temperatures, acidic and basic pH, high salinity, high radiation, low water activity, and high metal concentrations among other environmental conditions. Extremophile-derived enzymes, or extremozymes, are able to catalyze chemical reactions under harsh conditions, like those found in industrial processes, which were previously not thought to be conducive for enzymatic activity. Due to their optimal activity and stability under extreme conditions, extremozymes offer new catalytic alternatives for current industrial applications. These extremozymes also represent the cornerstone for the development of environmentally friendly, efficient, and sustainable industrial technologies. Many advances in industrial biocatalysis have been achieved in recent years; however, the potential of biocatalysis through the use of extremozymes is far from being fully realized. In this article, the adaptations and significance of psychrophilic, thermophilic, and hyperthermophilic enzymes, and their applications in selected industrial markets will be reviewed. Also, the current challenges in the development and mass production of extremozymes as well as future prospects and trends for their biotechnological application will be discussed. PMID:26539430

Peatland Acidobacteria with a dissimilatory sulfur metabolism.

PubMed

Hausmann, Bela; Pelikan, Claus; Herbold, Craig W; Köstlbacher, Stephan; Albertsen, Mads; Eichorst, Stephanie A; Glavina Del Rio, Tijana; Huemer, Martin; Nielsen, Per H; Rattei, Thomas; Stingl, Ulrich; Tringe, Susannah G; Trojan, Daniela; Wentrup, Cecilia; Woebken, Dagmar; Pester, Michael; Loy, Alexander

2018-02-23

Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.

Multiple micro-predators controlling bacterial communities in the environment.

PubMed

Johnke, Julia; Cohen, Yossi; de Leeuw, Marina; Kushmaro, Ariel; Jurkevitch, Edouard; Chatzinotas, Antonis

2014-06-01

Predator-prey interactions are a main issue in ecological theory, including multispecies predator-prey relationships and intraguild predation. This knowledge is mainly based on the study of plants and animals, while its relevance for microorganisms is not well understood. The three key groups of micro-predators include protists, predatory bacteria and bacteriophages. They greatly differ in size, in prey specificity, in hunting strategies and in the resulting population dynamics. Yet, their potential to jointly control bacterial populations and reducing biomass in complex environments such as wastewater treatment plants is vast. Here, we present relevant ecological concepts and recent findings on micropredators, and propose that an integrative approach to predation at the microscale should be developed enabling the exploitation of this potential. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of the cytotoxicity of clinically relevant cobalt-chromium and alumina ceramic wear particles in vitro.

PubMed

Germain, M A; Hatton, A; Williams, S; Matthews, J B; Stone, M H; Fisher, J; Ingham, E

2003-02-01

Concern over polyethylene wear particle induced aseptic loosening of metal-on-polyethylene hip prostheses has led to renewed interest in alternative materials such as metal-on-metal and alumina ceramic-on-alumina ceramic for total hip replacement. This study compared the effects of clinically relevant cobalt-chromium and alumina ceramic wear particles on the viability of U937 histiocytes and L929 fibroblasts in vitro. Clinically relevant cobalt-chromium wear particles were generated using a flat pin-on-plate tribometer. The mean size of the clinically relevant metal particles was 29.5+/-6.3 nm (range 5-200 nm). Clinically relevant alumina ceramic particles were generated in the Leeds MkII anatomical hip simulator from a Mittelmieier prosthesis using micro-separation motion. This produced particles with a bimodal size distribution. The majority (98%) of the clinically relevant alumina ceramic wear debris was 5-20 nm in size. The cytotoxicity of the clinically relevant wear particles was compared to commercially available cobalt-chromium (9.87 microm+/-5.67) and alumina ceramic (0.503+/-0.19 microm) particles. The effects of the particles on the cells over a 5 day period at different particle volume (microm(3)) to cell number ratios were tested and viability determined using ATP-Lite(TM). Clinically relevant cobalt-chromium particles 50 and 5 microm(3) per cell reduced the viability of U937 cells by 97% and 42% and reduced the viability of L929 cells by 95% and 73%, respectively. At 50 microm(3) per cell, the clinically relevant ceramic particles reduced U937 cell viability by 18%. None of the other concentrations of the clinically relevant particles were toxic. The commercial cobalt-chromium and alumina particles did not affect the viability of either the U937 histiocytes or the L929 fibroblasts.Thus at equivalent particle volumes the clinically relevant cobalt-chromium particles were more toxic then the alumina ceramic particles. This study has emphasised the fact that the nature, size and volume of particles are important in assessing biological effects of wear debris on cells in vitro.

Final technical report for project titled Quantitative Characterization of Cell Aggregation/Adhesion as Predictor for Distribution and Transport of Microorganisms in Subsurface Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gu, April Z.; Wan, Kai-tak

This project aims to explore and develop enabling methodology and techniques for nano-scale characterization of microbe cell surface contact mechanics, interactions and adhesion quantities that allow for identification and quantification of indicative properties related to microorganism migration and transport behavior in porous media and in subsurface environments. Microbe transport has wide impact and therefore is of great interest in various environmental applications such as in situ or enhanced subsurface bioremediation,filtration processes for water and wastewater treatments and protection of drinking water supplies. Although great progress has been made towards understanding the identities and activities of these microorganisms in the subsurface,more » to date, little is known of the mechanisms that govern the mobility and transport of microorganisms in DOE’s contaminated sites, making the outcomes of in situ natural attenuation or contaminant stability enhancement unpredictable. Conventionally, movement of microorganisms was believed to follows the rules governing solute (particle) transport. However, recent studies revealed that cell surface properties, especially those pertaining to cell attachment/adhesion and aggregation behavior, can cause the microbe behavior to deviate from non-viable particles and hence greatly influence the mobility and distribution of microorganisms in porous media.This complexity highlights the need to obtain detailed information of cell-cell and cell-surface interactions in order to improve and refine the conceptual and quantitative model development for fate and transport of microorganisms and contaminant in subsurface. Traditional cell surface characterization methods are not sufficient to fully predict the deposition rates and transport behaviors of microorganism observed. A breakthrough of methodology that would allow for quantitative and molecular-level description of intrinsic cell surface properties indicative for cell-surface interactions is essential for the field. To tackle this, we have developed a number of new Bio-nanomechanical techniques, including reflection interference contrast microscopy (RICM) and bio-AFM (Atomic Force Microscopy), for cell adhesion-detachment measurement of the long-range surface interactions, in combination with mathematical modeling, which would allow us to characterize the mechanical behavior from single cell to multi-cell aggregate, critical thresholds for large scale coaggregation and transportation of cells and aggregates in the presence of long range inter-surface forces etc. Although some technical and mathematical challenges remain, the preliminary results promise great breakthrough potential. In this study, we investigated the cellular surface characteristics of representative bio-remediating microorganisms relevant to DOE IFRC (Integrated Field-Scale Subsurface Research Challenges) sites and their transport behaviors in porous media, aiming to draw a groundbreaking correlation between the micro-scale genetic and biological origin-based cell surface properties, the consequent mechanical adhesion and aggregation behaviors, and the macro-scale microbial mobility and retention in porous media, which are unavailable in the literature. The long-term goal is to significantly improve the mechanistic and quantitative understanding of microbial mobility, sorption, and transport within reactive transport models as needed to manipulate subsurface contaminant fate and transport predictions.« less

Microbial Response to Microgravity and Other Low Shear Environments

NASA Technical Reports Server (NTRS)

Nickerson, C.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

2004-01-01

Microbial existence and survival requires the ability to sense and respond to environmental changes, including changes in physical forces. This is because microbes inhabit an amazingly diverse range of ecological niches and therefore must constantly adapt to a wide variety of changing environmental conditions, including alterations in temperature, pH, nutrient availability, oxygen levels, and osmotic pressure gradients. Microbes sense their environment through a variety of sensors and receptors which serve to integrate the different signals into the appropriate cellular response(s) that is optimal for survival. While numerous environmental stimuli have been examined for their effect on microorganisms, effects due to changes in mechanical and/or physical forces are also becoming increasingly apparent. Recently, several important studies have demonstrated a key role for microgravity and the low fluid shear dynamics associated with microgravity in the regulation of microbial gene expression, physiology and pathogenesis. The mechanosensory response of microorganisms to these environmental signals, which are relevant to those encountered during microbial life cycles on Earth, may provide insight into their adaptations to physiologically relevant conditions and may ultimately lead to eludicidation of the mechanisms important for mechanosensory transduction in living cells. This review summarizes the recent and potential future research trends aimed at understanding the effect of changes in mechanical forces that occur in microgravity and other low shear environments on different microbial parameters. The results of these studies provide an important step towards understanding how microbes integrate information from multiple mechanical stimuli to an appropriate physiological response.

Antibacterial Effect of Copper on Microorganisms Isolated from Bovine Mastitis

PubMed Central

Reyes-Jara, Angelica; Cordero, Ninoska; Aguirre, Juan; Troncoso, Miriam; Figueroa, Guillermo

2016-01-01

The antimicrobial properties of copper have been recognized for several years; applying these properties to the prevention of diseases such as bovine mastitis is a new area of research. The aim of the present study was to evaluate in vitro the antimicrobial activity of copper on bacteria isolated from subclinical and clinical mastitis milk samples from two regions in Chile. A total of 327 microorganisms were recovered between March and September 2013, with different prevalence by sample origin (25 and 75% from the central and southern regions of Chile, respectively). In the central region, Escherichia coli and coagulase negative Staphylococci (CNS) were the most frequently detected in clinical mastitis cases (33%), while in the southern region S. uberis, S. aureus, and CNS were detected with frequencies of 22, 21, and 18%, respectively. Antibiotic susceptibility studies revealed that 34% of isolates were resistant to one or more antibiotics and the resistance profile was different between bacterial species and origins of isolation of the bacteria. The minimum inhibitory concentration of copper (MIC-Cu) was evaluated in all the isolates; results revealed that a concentration as low as 250 ppm copper was able to inhibit the great majority of microorganisms analyzed (65% of isolates). The remaining isolates showed a MIC-Cu between 375 and 700 ppm copper, and no growth was observed at 1000 ppm. A linear relationship was found between the logarithm of viable bacteria number and time of contact with copper. With the application of the same concentration of copper (250 ppm), CNS showed the highest tolerance to copper, followed by S. uberis and S. aureus; the least resistant was E. coli. Based on these in vitro results, copper preparations could represent a good alternative to dipping solutions, aimed at preventing the presence and multiplication of potentially pathogenic microorganisms involved in bovine mastitis disease. PMID:27199953

Unique blood culture for diagnosis of bloodstream infections in emergency departments: a prospective multicentre study.

PubMed

Dargère, S; Parienti, J-J; Roupie, E; Gancel, P-E; Wiel, E; Smaiti, N; Loiez, C; Joly, L-M; Lemée, L; Pestel-Caron, M; du Cheyron, D; Verdon, R; Leclercq, R; Cattoir, V

2014-11-01

Detection of microorganisms by blood cultures (BCs) is essential in managing patients with bacteraemia. Rather than the number of punctures, the volume of blood drawn is considered paramount in efficient and reliable detection of microorganisms. We performed a 1-year prospective multicentre study in adult emergency departments of three French university hospitals comparing two methods for BCs: a unique blood culture (UBC) collecting a large volume of blood (40 mL) and the standard method of multiple blood cultures (MBC). The performances of both methods for bacterial contamination and efficient microbial detection were compared, each patient serving as his own control. Amongst the 2314 patients included, three hundred were positive for pathogens (n=245) or contaminants (n=55). Out of the 245 patients, 11 were positive for pathogens by UBC but negative by MBC and seven negative by UBC but positive by MBC (p 0.480). In the subgroup of 137 patients with only two BCs, UBC was superior to MBC (p 0.044). Seven and 17 patients had contaminated BCs by UBC and MBC only, respectively (p 0.062). Considering the sums of pathogens missed and contaminants, UBC significantly outperformed MBC (p 0.045). Considering the complete picture of cost savings, efficient detection of microorganisms and decrease in contaminations, UBC offers an interesting alternative to MBC. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

Resistance profiles and risk factors of resistant microorganisms in bacteraemia of abdominal origin.

PubMed

Martín Jaramago, J; Armero Ibáñez, R; Camarena Miñana, J J; Morales Suárez-Varela, M

2017-11-01

The presence of resistant microorganisms is a major cause of failure in initial empirical antimicrobial therapy. The objectives of this study are to determine the resistance profile of microorganisms that cause bacteraemia of abdominal origin and to identify whether the previous use of antibiotics and the place of acquisition of bacteraemia are risk factors associated with the presence of resistant organisms. A clinical, observational, epidemiological, retrospective cohort study was conducted with all the adult patients admitted to a university hospital from 2011-2013. Antimicrobial resistance profiles were described and a 95% confidence interval chi-square test was used to determine whether the variables studied were risk factors in the isolation of resistant microorganisms. Of the 1245 patients with bacteraemia, 212 (17%) presented bacteraemia of abdominal origin. The resistance profile highlights the incidence of methicillin resistant Staphylococcus aureus (50%), coagulase-negative staphylococci resistant to linezolid (20.58%), enterococci resistant to vancomycin (3.12%), Escherichia coli resistant to third-generation cephalosporins (9.9%) and fluoroquinolones (35.64%), Klebsiella pneumoniae resistant to third-generation cephalosporins (8.33%), Pseudomonas aeruginosa resistant to fluoroquinolones and carbapenem (25% and 25% respectively) and Acinetobacter baumanii resistant to fluoroquinolones and carbapenem (100% and 100% respectively), Candida albicans resistant to fluconazole (11.11%), single Candida krusei isolate resistant to fluconazole and Candida parapsilosis resistant to echinocandins (12.5%). In our study, previous use of antibiotics had a statistically significant association with the isolation of resistant microorganisms (P=.013) but not the place of acquisition of bacteraemia (P=.239). Establishing the incidence of resistant organisms can improve empirical antimicrobial therapy in patients with bacteraemia of abdominal origin. Previous use of antibiotics was statistically significantly related to the isolation of resistant microorganisms. Copyright © 2017 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

Bactericidal activity of biomimetic diamond nanocone surfaces.

PubMed

Fisher, Leanne E; Yang, Yang; Yuen, Muk-Fung; Zhang, Wenjun; Nobbs, Angela H; Su, Bo

2016-03-17

The formation of biofilms on implant surfaces and the subsequent development of medical device-associated infections are difficult to resolve and can cause considerable morbidity to the patient. Over the past decade, there has been growing recognition that physical cues, such as surface topography, can regulate biological responses and possess bactericidal activity. In this study, diamond nanocone-patterned surfaces, representing biomimetic analogs of the naturally bactericidal cicada fly wing, were fabricated using microwave plasma chemical vapor deposition, followed by bias-assisted reactive ion etching. Two structurally distinct nanocone surfaces were produced, characterized, and the bactericidal ability examined. The sharp diamond nanocone features were found to have bactericidal capabilities with the surface possessing the more varying cone dimension, nonuniform array, and decreased density, showing enhanced bactericidal ability over the more uniform, highly dense nanocone surface. Future research will focus on using the fabrication process to tailor surface nanotopographies on clinically relevant materials that promote both effective killing of a broader range of microorganisms and the desired mammalian cell response. This study serves to introduce a technology that may launch a new and innovative direction in the design of biomaterials with capacity to reduce the risk of medical device-associated infections.

Natural product-based nanomedicine: recent advances and issues

PubMed Central

Watkins, Rebekah; Wu, Ling; Zhang, Chenming; Davis, Richey M; Xu, Bin

2015-01-01

Natural products have been used in medicine for many years. Many top-selling pharmaceuticals are natural compounds or their derivatives. These plant- or microorganism-derived compounds have shown potential as therapeutic agents against cancer, microbial infection, inflammation, and other disease conditions. However, their success in clinical trials has been less impressive, partly due to the compounds’ low bioavailability. The incorporation of nanoparticles into a delivery system for natural products would be a major advance in the efforts to increase their therapeutic effects. Recently, advances have been made showing that nanoparticles can significantly increase the bioavailability of natural products both in vitro and in vivo. Nanotechnology has demonstrated its capability to manipulate particles in order to target specific areas of the body and control the release of drugs. Although there are many benefits to applying nanotechnology for better delivery of natural products, it is not without issues. Drug targeting remains a challenge and potential nanoparticle toxicity needs to be further investigated, especially if these systems are to be used to treat chronic human diseases. This review aims to summarize recent progress in several key areas relevant to natural products in nanoparticle delivery systems for biomedical applications. PMID:26451111

Unraveling the resistance of microbial biofilms: has proteomics been helpful?

PubMed

Seneviratne, C Jayampath; Wang, Yu; Jin, Lijian; Wong, Sarah S W; Herath, Thanuja D K; Samaranayake, Lakshman P

2012-02-01

Biofilms are surface-attached, matrix-encased, structured microbial communities which display phenotypic features that are dramatically different from those of their free-floating, or planktonic, counterparts. Biofilms seem to be the preferred mode of growth of microorganisms in nature, and at least 65% of all human infections are associated with biofilms. The most notable and clinically relevant property of biofilms is their greater resistance to antimicrobials compared with their planktonic counterparts. Although both bacterial and fungal biofilms display this phenotypic feature, the exact mechanisms underlying their increased drug resistance are yet to be determined. Advances in proteomics techniques during the past decade have facilitated in-depth analysis of the possible mechanisms underpinning increased drug resistance in biofilms. These studies have demonstrated the ability of proteomics techniques to unravel new targets for combating microbial biofilms. In this review, we discuss the putative drug resistance mechanisms of microbial biofilms that have been uncovered by proteomics and critically evaluate the possible contribution of the new knowledge to future development in the field. We also summarize strategic uses of novel proteomics technologies in studies related to drug resistance mechanisms of microbial biofilms. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automatic microbial transfer

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Mills, S. M.

1973-01-01

Device can transfer metabolites or inhibitory agents to broth cultures of bacteria, in various stages of growth, for study. It also has application in transfer of other micro-organisms, such as yeasts, and could be useful in clinical and research laboratories. Device has been used for wide variety of purposes in experimental situations.

An Antibiotic Resource Program for Students of the Health Professions.

ERIC Educational Resources Information Center

Tritz, Gerald J.

1986-01-01

Provides a description of a computer program developed to supplement instruction in testing of antibiotics on clinical isolates of microorganisms. The program is a simulation and database for interpretation of experimental data designed to enhance laboratory learning and prepare future physicians to use computerized diagnostic instrumentation and…

Differential responses of nitrifying archaea and bacteria to methylene blue toxicity.

PubMed

Sipos, A J; Urakawa, H

2016-02-01

Methylene blue, a heterocyclic aromatic chemical compound used to treat fish diseases in the ornamental fish aquaculture industry, is believed to impair nitrification as a side effect. However, very little is known about the toxicity of methylene blue to nitrifying micro-organisms. Here, we report the susceptibility of six bacterial and one archaeal ammonia-oxidizing micro-organisms to methylene blue within the range of 10 ppb to 10 ppm. Remarkably high susceptibility was observed in the archaeal species Nitrosopumilus maritimus compared to the bacterial species. Ammonia oxidation by Nitrosopumilus maritimus was inhibited 65% by 10 ppb of methylene blue. Of the bacterial species examined, Nitrosococcus oceani was the most resistant to methylene blue toxicity. For similar inhibition of Nitrosococcus oceani (75% inhibition), one thousand times more methylene blue (10 ppm) was needed. The examination of single cell viability on Nitrosomonas marina demonstrated that methylene blue is lethal to the cells rather than reducing their single cell ammonia oxidation activity. The level of susceptibility to methylene blue was related to the cell volume, intracytoplasmic membrane arrangement and the evolutionary lineage of nitrifying micro-organisms. Our findings are relevant for effectively using methylene blue in various aquaculture settings by helping minimize its impact on nitrifiers during the treatment of fish diseases. In the future, resistant nitrifiers such as Nitrosococcus oceani may be purposely added to aquaculture systems to maintain nitrification activity during treatments with methylene blue. The susceptibility of six bacterial and one archaeal nitrifying micro-organisms to methylene blue was tested. Remarkably high susceptibility was observed in the archaeal species compared to the bacterial species. The level of resistance to methylene blue was related to the cell volume, cytomembrane system and the taxonomic position of the nitrifying micro-organisms. This may be significant in the design and management of engineered nitrification systems and the stability of the nitrification process in various ecosystems if these systems are exposed to harmful chemicals or toxins. © 2015 The Society for Applied Microbiology.

Microcosm Studies to Evaluate Aerobic Cometabolism of Low Concentrations of 1,4-Dioxane by Isobutane-utilizing Microorganisms in the Presence of Chlorinated Solvent Co-contaminants

NASA Astrophysics Data System (ADS)

Rolston, H. M.; Azizian, M.; Hyman, M. R.; Semprini, L.

2015-12-01

Due to its use as a stabilizer for chlorinated solvents, 1,4-dioxane (1,4D), a probable human carcinogen, is a common co-contaminant in solvent spills at industrial and military sites and landfills. Its persistence in large groundwater plumes at low concentrations makes it a relevant candidate for in-situ bioremediation via cometabolism. Microcosm studies are being performed to evaluate the capability of aerobic microorganisms to cometabolize mixtures of 1,4D and chlorinated solvents, such as trichloroethylene (TCE), 1,1,1-trichloroethane (1,1,1TCA), and 1,1-dichloroethene (1,1DCE), with isobutane as the primary substrate. Microcosms were constructed using aquifer solids from Fort Carson, Colorado, a site contaminated with 1,4D and TCE, to assess the isobutane uptake and transformation of 1,4D and chlorinated solvents by microorganisms native to the site. Additional microcosms were augmented with Rhodococcus rhodochrous, a bacterium shown to cometabolize 1,4D and chlorinated solvents. Results indicate that native microcosms cometabolized 1,4D upon stimulation with isobutane after a lag period of about 15 days. TCE was also transformed, but at significantly slower rates. The presence of 1,4D and TCE at 500 and 300 ppb, respectively, did not inhibit the growth of native microorganisms on isobutane, with isobutane uptake and 1,4D transformation occurring simultaneously. Bioaugmented microcosms transformed 1,4D immediately after inoculation with R. rhodochrous. Tests in bioaugmented microorganisms indicated that the presence of TCE at low concentrations inhibits but does not block the transformation of 1,4D. Results from the microcosms will be used to design field tests to be performed at Fort Carson. Additional microcosm studies will compare the stimulation of native and bioaugmented microcosms and the transformation of mixtures of 1,4D, 1,1,1TCA and 1,1DCE. Molecular methods will analyze the monoxygenase enzymes expressed in the native and bioaugmented microcosms.

Contemporary issues: diseases with a food vector.

PubMed

Archer, D L; Young, F E

1988-10-01

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine.

Contemporary issues: diseases with a food vector.

PubMed Central

Archer, D L; Young, F E

1988-01-01

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine. PMID:3069199

Introduction to Clinical Microbiology for the General Dentist.

PubMed

Rams, Thomas E; van Winkelhoff, Arie J

2017-04-01

Clinical oral microbiology may help dental professionals identify infecting pathogenic species and evaluate their in vitro antimicrobial susceptibility. Saliva, dental plaque biofilms, mucosal smears, abscess aspirates, and soft tissue biopsies are sources of microorganisms for laboratory testing. Microbial-based treatment end points may help clinicians better identify patients in need of additional or altered dental therapies before the onset of clinical treatment failure, and help improve patient oral health outcomes. Microbiological testing appears particularly helpful in periodontal disease treatment planning. Further research and technological advances are likely to increase the availability and clinical utility of microbiological analysis in modern dental practice. Copyright © 2016 Elsevier Inc. All rights reserved.

Laboratory diagnosis of peritonitis in patients on continuous ambulatory peritoneal dialysis.

PubMed Central

Ludlam, H A; Price, T N; Berry, A J; Phillips, I

1988-01-01

The clinical course and laboratory diagnosis of peritonitis in patients undergoing continuous ambulatory peritoneal dialysis was studied in 32 consecutive episodes. Peritonitis was associated with a failure in aseptic technique in eight episodes and with an exit-site infection in four episodes. Intraperitoneal vancomycin and ceftazidime were safe, effective, and convenient. Most patients administered their antibiotics at home, and symptoms usually resolved by day 4. Culture of the deposit obtained by centrifugation of 50 ml of effluent after leukocyte lysis provided the best rate of recovery (84% culture positive) but was technically demanding. Filtration of the same volume without leukocyte lysis was simple to perform and almost as effective. Enrichment was less satisfactory (65% culture positive) owing to the presence of antibiotic or infection with fastidious microorganisms. Culture of 50 ml of effluent after concentration by a commonly used laboratory technique, centrifugation without leukocyte lysis, performed poorly (59% culture positive at 48 h), as this method caused sequestration and death of microorganisms within the leukocytes. Culture of nearly 1 liter of effluent from 33 asymptomatic patients by the same techniques yielded no microorganisms. PMID:3183023

Microorganisms isolated from root canals presenting necrotic pulp and their drug susceptibility in vitro.

PubMed

Lana, M A; Ribeiro-Sobrinho, A P; Stehling, R; Garcia, G D; Silva, B K; Hamdan, J S; Nicoli, J R; Carvalho, M A; Farias, L de M

2001-04-01

The knowledge about causative agents involved in endodontic infections is increasing, especially due to the improvement of culture techniques for anaerobic bacteria, showing that these microorganisms are predominant in this pathology. In this study, 31 canals with pulp necrosis were microbiologically analyzed before and after manipulation. Obligate and facultative anaerobes, microaerophilic bacteria and yeasts were recovered from 24, 14, 5 and 2 clinical specimens, respectively. The most frequent genera were Prevotella, Fusobacterium, Lactobacillus, Streptococcus, Clostridium and Peptostreptococcus for bacteria and Candida and Saccharomyces for yeasts. Strong positive associations, using an odds ratio system, were found between Clostridium and Prevotella and between Peptostreptococcus and Fusobacterium. Even after the instrumentation and the use of Ca(OH)2, facultative anaerobes were detected in two root canals and yeasts in three. Microorganisms were isolated from seven canals at the end of the endodontic treatment: facultative anaerobes from five and yeasts from one. The microbiological evaluation of root canals with pulp necrosis suggests the presence of polymicrobial infections, mainly involving obligate anaerobes, and shows that the infection may persist after treatment.

Metal oxide nanoparticles as antimicrobial agents: a promise for the future.

PubMed

Raghunath, Azhwar; Perumal, Ekambaram

2017-02-01

Microbial infectious diseases are a global threat to human health. Excess and improper use of antibiotics has created antimicrobial-resistant microbes that can defy clinical treatment. The hunt for safe and alternate antimicrobial agents is on in order to overcome such resistant micro-organisms, and the birth of nanotechnology offers promise to combat infectious organisms. Over the past two decades, metal oxide nanoparticles (MeO-NPs) have become an attractive alternative source to combat microbes that are highly resistant to various classes of antibiotics. Their vast array of physicochemical properties enables MeO-NPs to act as antimicrobial agents through various mechanisms. Apart from exhibiting antimicrobial properties, MeO-NPs also serve as carriers of drugs, thus barely providing a chance for micro-organisms to develop resistance. These immense multiple properties exhibited by MeO-NPs will have an impact on the treatment of deadly infectious diseases. This review discusses the mechanisms of action of MeO-NPs against micro-organisms, safety concerns, challenges and future perspectives. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Endotoxins in Environmental and Clinical Samples Assessed by GC-Tandem MS

NASA Astrophysics Data System (ADS)

Szponar, Bogumila

Bacteria appeared on the Earth millions years before us and human evolution was triggered by the constant presence of pathogenic and symbiotic microorganisms in our surroundings. Interplay occurred between higher organism and microbial consortia residing in the host organs and on the epithelial surfaces; another natural space of bacteria-human interaction is the indoor environment where we spend the majority of our lifetime. Indoor microbial exposure affects our well-being and can result in respiratory symptoms, such as allergies and asthma, since both dead and live microorganisms and their cell constituents, including lipopolysaccharides (LPS, endotoxins), interact with our immune system. Thus, there is a demand for robust tools for qualitative and quantitative determination of the microbial communities that we are exposed to.

Understanding the Mechanism of Bacterial Biofilms Resistance to Antimicrobial Agents

PubMed Central

Singh, Shriti; Singh, Santosh Kumar; Chowdhury, Indrajit; Singh, Rajesh

2017-01-01

A biofilm is a group of microorganisms, that causes health problems for the patients with indwelling medical devices via attachment of cells to the surface matrix. It increases the resistance of a microorganism for antimicrobial agents and developed the human infection. Current strategies are removed or prevent the microbial colonies from the medical devices, which are attached to the surfaces. This will improve the clinical outcomes in favor of the patients suffering from serious infectious diseases. Moreover, the identification and inhibition of genes, which have the major role in biofilm formation, could be the effective approach for health care systems. In a current review article, we are highlighting the biofilm matrix and molecular mechanism of antimicrobial resistance in bacterial biofilms. PMID:28553416

Endocrine dysfunction in sepsis: a beneficial or deleterious host response?

PubMed Central

Gheorghiţă, Valeriu; Barbu, Alina Elena; Gheorghiu, Monica Livia; Căruntu, Florin Alexandru

2015-01-01

Sepsis is a systemic, deleterious inflammatory host response triggered by an infective agent leading to severe sepsis, septic shock and multi-organ failure. The host response to infection involves a complex, organized and coherent interaction between immune, autonomic, neuroendocrine and behavioral systems. Recent data have confirmed that disturbances of the autonomic nervous and neuroendocrine systems could contribute to sepsis-induced organ dysfunction. Through this review, we aimed to summarize the current knowledge about the endocrine dysfunction as response to sepsis, specifically addressed to vasopressin, copeptin, cortisol, insulin and leptin. We searched the following readily accessible, clinically relevant databases: PubMed, UpToDate, BioMed Central. The immune system could be regarded as a “diffuse sensory organ” that signals the presence of pathogens to the brain through different pathways, such as the vagus nerve, endothelial activation/dysfunction, cytokines and neurotoxic mediators and the circumventricular organs, especially the neurohypophysis. The hormonal profile changes substantially as a consequence of inflammatory mediators and microorganism products leading to inappropriately low levels of vasopressin, sick euthyroid syndrome, reduced adrenal responsiveness to ACTH, insulin resistance, hyperglycemia as well as hyperleptinemia. In conclusion, clinical diagnosis of this “pan-endocrine illness” is frequently challenging due to the many limiting factors. The most important benefits of endocrine markers in the management of sepsis may be reflected by their potential to be used as biomarkers in different scoring systems to estimate the severity of the disease and the risk of death. PMID:25763364

One-year surveillance of ESKAPE pathogens in an intensive care unit of Monterrey, Mexico.

PubMed

Llaca-Díaz, Jorge Martín; Mendoza-Olazarán, Soraya; Camacho-Ortiz, Adrian; Flores, Samantha; Garza-González, Elvira

2012-01-01

Bacterial species from the ESKAPE group (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) are frequently resistant to antibiotics. The purpose of this study was to monitor the incidence of ESKAPE pathogens at the intensive care unit (ICU) of a tertiary care hospital in Monterrey, Mexico. All clinically relevant organisms isolated from June 2011 to June 2012 were included. Identification and susceptibility testing was performed using panels from Sensititre. Resistance to oxacillin, for S. aureus, and the production of extended spectrum β-lactamases (ESBLs), for K. pneumonia, were determined as defined by the Clinical Laboratory Standards Institute. Also, the presence of vanA and vanB genes was determined in E. faecium vancomycin (VAN)-resistant isolates. The majority of pathogens (64.5%) isolated in the ICU unit were from the ESKAPE group. The organisms most frequently isolated were A. baumannii (15.8%) and P. aeruginosa (14.3%). A high resistance to carbapenems was detected for A. baumannii (75.3%) while 62% of S. aureus isolates were confirmed to be methicillin resistant. Of the K. pneumoniae isolates, 36.9% were ESBL producers. We detected three E. faecium VAN-resistant isolates, all of which contained the vanA gene. The presence of the ESKAPE group of pathogens is a major problem in the ICU setting. The results of this study support the implementation of special antimicrobial strategies to specifically target these microorganisms. Copyright © 2013 S. Karger AG, Basel.

21 CFR 1271.75 - How do I screen a donor?

Code of Federal Regulations, 2011 CFR

2011-04-01

...) Risk factors for, and clinical evidence of, relevant communicable disease agents and diseases... risk factors for and clinical evidence of relevant cell-associated communicable disease agents and... having either of the following: (1) A risk factor for or clinical evidence of any of the relevant...

Same Day Identification and Full Panel Antimicrobial Susceptibility Testing of Bacteria from Positive Blood Culture Bottles Made Possible by a Combined Lysis-Filtration Method with MALDI-TOF VITEK Mass Spectrometry and the VITEK2 System

PubMed Central

Machen, Alexandra; Drake, Tim; Wang, Yun F. (Wayne)

2014-01-01

Rapid identification and antimicrobial susceptibility testing of microorganisms causing bloodstream infections or sepsis have the potential to improve patient care. This proof-of-principle study evaluates the Lysis-Filtration Method for identification as well as antimicrobial susceptibility testing of bacteria directly from positive blood culture bottles in a clinical setting. A total of 100 non-duplicated positive blood cultures were tested and 1012 microorganism-antimicrobial combinations were assessed. An aliquot of non-charcoal blood culture broth was incubated with lysis buffer briefly before being filtered and washed. Microorganisms recovered from the filter membrane were first identified by using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight VITEK® Mass Spectrometry (VITEK MS). After quick identification from VITEK MS, filtered microorganisms were inoculated to VITEK®2 system for full panel antimicrobial susceptibility testing analysis. Of 100 bottles tested, the VITEK MS resulted in 94.0% correct organism identification to the species level. Compared to the conventional antimicrobial susceptibility testing methods, direct antimicrobial susceptibility testing from VITEK®2 resulted in 93.5% (946/1012) category agreement of antimicrobials tested, with 3.6% (36/1012) minor error, 1.7% (7/1012) major error, and 1.3% (13/1012) very major error of antimicrobials. The average time to identification and antimicrobial susceptibility testing was 11.4 hours by using the Lysis-Filtration method for both VITEK MS and VITEK®2 compared to 56.3 hours by using conventional methods (p<0.00001). Thus, the same-day results of microorganism identification and antimicrobial susceptibility testing directly from positive blood culture can be achieved and can be used for appropriate antibiotic therapy and antibiotic stewardship. PMID:24551067

Antimicrobial effect of 4 disinfectants on alginate, polyether, and polyvinyl siloxane impression materials.

PubMed

Al-Jabrah, Osama; Al-Shumailan, Yousef; Al-Rashdan, Manhal

2007-01-01

Dental impressions often carry microorganisms that may cause cross infection from patients to dental staff. The aim of the current study was to determine the effectiveness of 4 different disinfectant solutions on 3 commonly used impression materials--alginate, polyether, and polyvinyl siloxane--to establish a protocol for disinfection of these impression materials after clinical exposure and prior to handling in the dental laboratory. A total of 45 impressions were taken from the maxillary dentate arches of 15 dental staff participants at the Department of Dentistry, Prince Rashid Hospital, Irbid, Jordan. For each participant, 3 successive impressions were recorded in the different impression materials. For each impression, 6 specimens were dissected from 6 different locations and exposed to 6 different regimens: 1 was left untreated, 1 was immersed in sterile water for 10 minutes to serve as a control, and the remaining 4 specimens were exposed to 4 different disinfection treatments (Dimenol, Perform-ID, MD 520, and Haz-tabs). Serial dilutions of the suspension were carried out and counted by the Miles-Misra technique (inoculation on Columbia blood agar for quantification). The dilutions were aerobically incubated at 37 degrees C for 48 hours. The disinfectants were able to completely eliminate microorganisms carried by the impressions. For those undisinfected specimens, the results showed that untreated alginate impressions appear to carry more microorganisms (P < .05) than the other 2 rubber impression materials used in the study. For those specimens immersed in sterile water for 10 minutes (control group), the number of microorganisms eliminated was increased from 62% to 90% compared to those left untreated. Impression materials may act as a vehicle for the transfer of microorganisms from the patient's mouth to dental personnel. Impressions should be disinfected to eliminate the risk of cross contamination.

Same day identification and full panel antimicrobial susceptibility testing of bacteria from positive blood culture bottles made possible by a combined lysis-filtration method with MALDI-TOF VITEK mass spectrometry and the VITEK2 system.

PubMed

Machen, Alexandra; Drake, Tim; Wang, Yun F Wayne

2014-01-01

Rapid identification and antimicrobial susceptibility testing of microorganisms causing bloodstream infections or sepsis have the potential to improve patient care. This proof-of-principle study evaluates the Lysis-Filtration Method for identification as well as antimicrobial susceptibility testing of bacteria directly from positive blood culture bottles in a clinical setting. A total of 100 non-duplicated positive blood cultures were tested and 1012 microorganism-antimicrobial combinations were assessed. An aliquot of non-charcoal blood culture broth was incubated with lysis buffer briefly before being filtered and washed. Microorganisms recovered from the filter membrane were first identified by using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight VITEK® Mass Spectrometry (VITEK MS). After quick identification from VITEK MS, filtered microorganisms were inoculated to VITEK®2 system for full panel antimicrobial susceptibility testing analysis. Of 100 bottles tested, the VITEK MS resulted in 94.0% correct organism identification to the species level. Compared to the conventional antimicrobial susceptibility testing methods, direct antimicrobial susceptibility testing from VITEK®2 resulted in 93.5% (946/1012) category agreement of antimicrobials tested, with 3.6% (36/1012) minor error, 1.7% (7/1012) major error, and 1.3% (13/1012) very major error of antimicrobials. The average time to identification and antimicrobial susceptibility testing was 11.4 hours by using the Lysis-Filtration method for both VITEK MS and VITEK®2 compared to 56.3 hours by using conventional methods (p<0.00001). Thus, the same-day results of microorganism identification and antimicrobial susceptibility testing directly from positive blood culture can be achieved and can be used for appropriate antibiotic therapy and antibiotic stewardship.

[Increasing incidence of community-acquired pneumonia caused by atypical microorganisms].

PubMed

Tazón-Varela, M A; Alonso-Valle, H; Muñoz-Cacho, P; Gallo-Terán, J; Piris-García, X; Pérez-Mier, L A

2017-09-01

Knowing the most common microorganisms in our environment can help us to make proper empirical treatment decisions. The aim is to identify those microorganisms causing community-acquired pneumonia. An observational, descriptive and prospective study was conducted, including patients over 14 years with a clinical and radiographic diagnosis of community-acquired pneumonia during a 383 consecutive day period. A record was made of sociodemographic variables, personal history, prognostic severity scales, progress, and pathogenic agents. The aetiological diagnosis was made using blood cultures, detection of Streptococcus pneumoniae and Legionella pneumophila urinary antigens, sputum culture, influenza virus and Streptococcus pyogenes detection. Categorical variables are presented as absolute values and percentages, and continuous variables as their means and standard deviations. Of the 287 patients included in the study (42% women, mean age 66±22 years), 10.45% died and 70% required hospital admission. An aetiological diagnosis was achieved in 43 patients (14.98%), with 16 microorganisms found in 59 positive samples. The most frequently isolated pathogen was Streptococcus pneumonia (24/59, 41%), followed by gram-negative enteric bacilli, Klebsiella pneumonia, Escherichia coli, Serratia marcescens and Enterobacter cloacae isolated in 20% of the samples (12/59), influenza virus (5/59, 9%), methicillin-resistant Staphylococcus aureus (3/59, 5%), Pseudomonas aeruginosa (2/59, 3%), Moraxella catarrhalis (2/59, 3%), Legionella pneumophila (2/59, 3%), and Haemophilus influenza (2/59, 3%). Polymicrobial infections accounted for 14% (8/59). A high percentage of atypical microorganisms causing community-acquired pneumonia were found. Copyright © 2016 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España, S.L.U. All rights reserved.

Non-contact electromagnetic induction heating for eradicating bacteria and yeasts on biomaterials and possible relevance to orthopaedic implant infections: In vitro findings.

PubMed

Pijls, B G; Sanders, I M J G; Kuijper, E J; Nelissen, R G H H

2017-05-01

Infection of implants is a major problem in elective and trauma surgery. Heating is an effective way to reduce the bacterial load in food preparation, and studies on hyperthermia treatment for cancer have shown that it is possible to heat metal objects with pulsed electromagnetic fields selectively (PEMF), also known as induction heating. We therefore set out to answer the following research question: is non-contact induction heating of metallic implants effective in reducing bacterial load in vitro ? Titanium alloy cylinders (Ti6Al4V) were exposed to PEMF from an induction heater with maximum 2000 watts at 27 kHz after being contaminated with five different types of micro-organisms: Staphylococcus epidermidis; Staphylococcus aureus; Pseudomonas aeruginosa ; spore-forming Bacillus cereus; and yeast Candida albicans . The cylinders were exposed to incremental target temperatures (35°C, 45°C, 50°C, 55°C, 60°C, 65°C, 70°C) for up to 3.5 minutes. There was an average linear heating rate of 0.39°C per second up to the target temperature, and thereafter the target temperature was maintained until the end of the experiment. At 60°C and higher (duration 3.5 minutes), there was a 6-log reduction or higher for every micro-organism tested. At 60°C, we found that the shortest duration of effective induction heating was 1.5 minutes. This resulted in a 5-log reduction or higher for every micro-organism tested. Non-contact induction heating of a titanium disk is effective in reducing bacterial load in vitro . These promising results can be further explored as a new treatment modality for infections of metal orthopaedic implants. Cite this article : B. G. Pijls, I. M. J. G. Sanders, E. J. Kuijper, R. G. H. H. Nelissen. Non-contact electromagnetic induction heating for eradicating bacteria and yeasts on biomaterials and possible relevance to orthopaedic implant infections: In vitro findings. Bone Joint Res 2017;6:323-330. DOI: 10.1302/2046-3758.65.BJR-2016-0308.R1. © 2017 Pijls et al.

Application of compost for effective bioremediation of organic contaminants and pollutants in soil.

PubMed

Kästner, Matthias; Miltner, Anja

2016-04-01

Soils contaminated with hazardous chemicals worldwide are awaiting remediation activities; bioremediation is often considered as a cost-effective remediation approach. Potential bioapproaches are biostimulation, e.g. by addition of nutrients, fertiliser and organic substrates, and bioaugmentation by addition of compound-degrading microbes or of organic amendments containing active microorganisms, e.g. activated sludge or compost. In most contaminated soils, the abundance of the intrinsic metabolic potential is too low to be improved by biostimulation alone, since the physical and chemical conditions in these soils are not conducive to biodegradation. In the last few decades, compost or farmyard manure addition as well as composting with various organic supplements have been found to be very efficient for soil bioremediation. In the present minireview, we provide an overview of the composting and compost addition approaches as 'stimulants' of natural attenuation. Laboratory degradation experiments are often biased either by not considering the abiotic factors or by focusing solely on the elimination of the chemicals without taking the biotic factors and processes into account. Therefore, we first systemise the concepts of composting and compost addition, then summarise the relevant physical, chemical and biotic factors and mechanisms for improved contaminant degradation triggered by compost addition. These factors and mechanisms are of particular interest, since they are more relevant and easier to determine than the composition of the degrading community, which is also addressed in this review. Due to the mostly empirical knowledge and the nonstandardised biowaste or compost materials, the field use of these approaches is highly challenging, but also promising. Based on the huge metabolic diversity of microorganisms developing during the composting processes, a highly complex metabolic diversity is established as a 'metabolic memory' within developing and mature compost materials. Compost addition can thus be considered as a 'super-bioaugmentation' with a complex natural mixture of degrading microorganisms, combined with a 'biostimulation' by nutrient containing readily to hardly degradable organic substrates. It also improves the abiotic soil conditions, thus enhancing microbial activity in general. Finally, this minireview also aims at guiding potential users towards full exploitation of the potentials of this approach.

Laboratory procedure for estimating residue dynamics of xenobiotic contaminants in a freshwater food chain

USGS Publications Warehouse

Johnson, B. Thomas

1980-01-01

A laboratory method of measuring the accumulation, transfer, elimination, and degradation of xenobiotic contaminants is described for organisms in a freshwater food chain (microorganisms, filter-feeder, and fish). A flow-through diluter-system, 14C-labeled contaminants, gas and thin-layer chromatography, autoradiography, and liquid scintillation spectrometry are used in making residue determinations. Accumulation factors and various index values are developed for measuring and estimating potential accumulation of xenobiotic contaminants by aquatic organisms. The laboratory procedure is economical, simple, reproducible, and ecologically relevant.

Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations.

PubMed

Rösch, Petra; Harz, Michaela; Schmitt, Michael; Peschke, Klaus-Dieter; Ronneberger, Olaf; Burkhardt, Hans; Motzkus, Hans-Walter; Lankers, Markus; Hofer, Stefan; Thiele, Hans; Popp, Jürgen

2005-03-01

Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria.

Chemotaxonomic Identification of Single Bacteria by Micro-Raman Spectroscopy: Application to Clean-Room-Relevant Biological Contaminations

PubMed Central

Rösch, Petra; Harz, Michaela; Schmitt, Michael; Peschke, Klaus-Dieter; Ronneberger, Olaf; Burkhardt, Hans; Motzkus, Hans-Walter; Lankers, Markus; Hofer, Stefan; Thiele, Hans; Popp, Jürgen

2005-01-01

Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria. PMID:15746368

Antibacterial activity of Mediterranean Oyster mushrooms, species of genus Pleurotus (higher Basidiomycetes).

PubMed

Schillaci, Domenico; Arizza, Vincenzo; Gargano, Maria Letizia; Venturella, Giuseppe

2013-01-01

Extracts of the Mediterranean culinary-medicinal Oyster mushrooms Pleurotus eryngii var. eryngii, P. eryngii var. ferulae, P. eryngii var. elaeoselini, and P. nebrodensis were tested for their in vitro growth inhibitory activity against a group of bacterial reference strains of medical relevance: Staphylococcus aureus ATCC 25923, S. epidermidis RP62A, Pseudomonas aeruginosa ATCC 15442, and Escherichia coli ATCC10536. All of the Pleurotus species analyzed inhibited the tested microorganisms in varying degrees. The data included in this paper for P. nebrodensis and P. eryngii var. elaeoselinii are new reports.

Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects.

PubMed

Ho, Po-Yi; Lin, Jie; Amir, Ariel

2018-05-20

Most microorganisms regulate their cell size. In this article, we review some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics that they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and its molecular implementations, protein number regulation, and population growth, all in relation to size regulation. Finally, we discuss several future directions for developing understanding beyond phenomenological models of cell size regulation.

Mobile phone interference with medical equipment and its clinical relevance: a systematic review.

PubMed

Lawrentschuk, Nathan; Bolton, Damien M

2004-08-02

To conduct a systematic review of studies on clinically relevant digital mobile phone electromagnetic interference with medical equipment. MEDLINE and SUMSEARCH were searched for the period 1966-2004. The Cochrane Library and Database of Abstracts of Reviews of Effects were also searched for systematic reviews. Studies were eligible if published in a peer-reviewed journal in English, and if they included testing of digital mobile phones for clinically relevant interference with medical equipment used to monitor or treat patients, but not implantable medical devices. As there was considerable heterogeneity in medical equipment studied and the conduct of testing, results were summarised rather than subjected to meta-analysis. Clinically relevant electromagnetic interference (EMI) secondary to mobile phones potentially endangering patients occurred in 45 of 479 devices tested at 900 MHz and 14 of 457 devices tested at 1800 MHz. However, in the largest studies, the prevalence of clinically relevant EMI was low. Most clinically relevant EMI occurred when mobile phones were used within 1 m of medical equipment. Although testing was not standardised between studies and equipment tested was not identical, it is of concern that at least 4% of devices tested in any study were susceptible to clinically relevant EMI. All studies recommend some type of restriction of mobile phone use in hospitals, with use greater than 1 m from equipment and restrictions in clinical areas being the most common.

Recommendations for intra-abdominal infections consensus report

PubMed Central

Avkan-Oğuz, Vildan; Baykam, Nurcan; Sökmen, Selman; Güner, Rahmet; Agalar, Fatih; Alp, Emine; Doğrul, Ahmet; Turhan, Özge; Ağalar, Canan; Kurtaran, Behice; Geçim, İbrahim Ethem; Özaras, Reşat; Yılmaz, Gürdal; Akbulut, Ayhan; Koksal, İftihar

2016-01-01

Guidelines include the recommendations of experts from various specialties within a topic in consideration of data specific to each country. However, to date there has not been a guideline standardizing the nomenclature and offering recommendations for intra-abdominal infections (IAIs) in Turkey. This is mainly due to the paucity of laboratory studies regarding the clinical diagnosis and treatment of IAIs or the sensitivity of microorganisms isolated from patients with IAIs. However, due to the diversification of host characteristics and advancements in technological treatment methods, it has become imperative to ‘speak a common language’. For this purpose May 2015, a group of 15 experts in intra-abdominal infections, under the leadership of the Infectious Diseases and Clinical Microbiology Specialty Society of Turkey (EKMUD) and with representatives from the Turkish Surgical Association, Turkish Society of Colon and Rectal Surgery, Hernia Society, Turkish Society of Hepato-pancreato-biliary Surgery, and the Turkish Society of Hospital Infections and Control, was formed to analyze relevant studies in the literature. Ultimately, the suggestions for adults found in this consensus report were developed using available data from Turkey, referring predominantly to the 2010 guidelines for diagnosing and managing complicated IAIs in adults and children by the Infectious Diseases Society of America (IDSA) and the Surgical Infection Society. The recommendations are presented in two sections, from the initial diagnostic evaluation of patients to the treatment approach for IAI. This Consensus Report was presented at the EKMUD 2016 Congress in Antalya and was subsequently opened for suggestions on the official websites of the Infectious Diseases and Clinical Microbiology Specialty Society of Turkey and Turkish Surgical Association for one month. The manuscript was revised according to the feedback received. PMID:28149134

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus

PubMed Central

Stubbe, Dirk; De Cremer, Koen; Piérard, Denis; Normand, Anne-Cécile; Piarroux, Renaud; Detandt, Monique; Hendrickx, Marijke

2014-01-01

The rates of infection with Fusarium molds are increasing, and a diverse number of Fusarium spp. belonging to different species complexes can cause infection. Conventional species identification in the clinical laboratory is time-consuming and prone to errors. We therefore evaluated whether matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a useful alternative. The 289 Fusarium strains from the Belgian Coordinated Collections of Microorganisms (BCCM)/Institute of Hygiene and Epidemiology Mycology (IHEM) culture collection with validated sequence-based identities and comprising 40 species were used in this study. An identification strategy was developed, applying a standardized MALDI-TOF MS assay and an in-house reference spectrum database. In vitro antifungal testing was performed to assess important differences in susceptibility between clinically relevant species/species complexes. We observed that no incorrect species complex identifications were made by MALDI-TOF MS, and 82.8% of the identifications were correct to the species level. This success rate was increased to 91% by lowering the cutoff for identification. Although the identification of the correct species complex member was not always guaranteed, antifungal susceptibility testing showed that discriminating between Fusarium species complexes can be important for treatment but is not necessarily required between members of a species complex. With this perspective, some Fusarium species complexes with closely related members can be considered as a whole, increasing the success rate of correct identifications to 97%. The application of our user-friendly MALDI-TOF MS identification approach resulted in a dramatic improvement in both time and accuracy compared to identification with the conventional method. A proof of principle of our MALDI-TOF MS approach in the clinical setting using recently isolated Fusarium strains demonstrated its validity. PMID:25411180

Comparison of clinical diagnosis and microbiological test results in vaginal infections.

PubMed

Karaca, M; Bayram, A; Kocoglu, M E; Gocmen, A; Eksi, F

2005-01-01

Lower genital tract infections continue to be a problem due to the fact that the clinical diagnosis is usually inadequate, and subsequent care is suboptimal. This study aimed at evaluating the accuracy of clinical diagnosis by comparing it with microbiologic test results, and to determine the causative agents of vaginal infections. Sixty-seven nonpregnant women (18-45 years of age) with the clinical diagnosis of lower genital tract infection were enrolled in the study. Patients were not included if they had a history of vaginal infection during the previous three-month period or intrauterine device. The clinical diagnosis was based on the combinations of symptoms, direct observation of wet mount, homogeneous discharge, vaginal pH > 4.5, and detection of the amine odor after exposure of vaginal secretions to 10% KOH. Vaginal samples were taken with two cotton swabs, one was used for pH determination, and the second was utilized for microbiological tests. Gram staining and cultures with Sabouraud agar and chocolate agar were performed for microbiological diagnosis, and the results were compared. The clinical diagnoses included 26 (38.8%) candidiasis, 18 (26.8%) bacterial vaginosis, three (4.5%) trichomoniasis, and 20 (29.9%) mixed vaginal infections. Of the 26 patients with clinical diagnoses of candidiasis, 12 (46.1%) revealed Candiada albicans, nine (34.6) patients revealed microorganisms other than candida species, and five (19.2%) patients had no growth. Five (27.8%) bacterial vaginosis patients revealed Gardnarella vaginalis and 12 patients (66.6%) did not grow any microorganism. The overall rate of accurate clinical diagnoses confirmed by microbiological test results was 43.2%. Seventeen (43.6) of the 39 microbiological test results correlated with clinical diagnosis, and no growth was observed in 28 (41.8%) cultures. We conclude that the clinical diagnosis of vaginal infection is inadequate and should be confirmed with microbiological testing if the resources are avaliable.

Head-to-head comparison of Microflex LT and Vitek MS systems for routine identification of microorganisms by MALDI-TOF mass spectrometry in Chile

PubMed Central

García, Patricia; Braun, Stephanie; Ulloa, María Teresa; Lafourcade, Mónica; Montaña, Alisson; Miranda, Carolina; Acosta-Jamett, Gerardo; Weitzel, Thomas

2017-01-01

Background Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a new and revolutionary identification method for microorganisms and has recently been introduced into clinical microbiology in many industrialized countries in Europe and North America. Objectives Our study aimed to compare the performance and practicality of two commercial MALDI-TOF MS platforms in a head-to head manner at a routine laboratory in Chile. Methods During a five-month period in 2012–13, the diagnostic efficiency (correct identification rate) and agreement between Microflex LT (Bruker Daltonics) and Vitek MS (bioMérieux) was compared in a parallel manner to conventional identification including genotypic analysis for difficult-to-identify strains. The study included 804 microbial isolates: 252 Enterobacteriaceae, 126 non-fermenters, 36 other gram-negative rods, 279 gram-positive cocci, 32 gram-positive rods, 32 anaerobes, and 47 yeasts. Other relevant factors of the two devices such as user friendliness and connectivity were also evaluated and compared. Results Both systems correctly identified the vast majority (98%) of the isolates to the genus level. Vitek MS reached higher rates of identification to species and species complex level than Microflex LT (81% vs. 85% and 87% vs. 93%, respectively), which was mainly based on the higher performance among coagulase negative staphylococci and Candida isolates. The evaluation of user friendliness and other technical aspects showed only marginal differences, which slightly favored Vitek MS, mainly due to its ready-to-use supplies, easier connectivity and workflow integration, and availability of local technical support. Conclusions Both MALDI-TOF MS systems permitted fast and accurate identification of most microbial strains and showed a high level of user-friendliness. The observed differences were marginal and slightly favored Vitek MS, mainly due to practicality and connectivity issues within our setting. PMID:28542393

Microbiota and Neurological Disorders: A Gut Feeling

PubMed Central

Moos, Walter H.; Faller, Douglas V.; Harpp, David N.; Kanara, Iphigenia; Pernokas, Julie; Powers, Whitney R.; Steliou, Kosta

2016-01-01

Abstract In the past century, noncommunicable diseases have surpassed infectious diseases as the principal cause of sickness and death, worldwide. Trillions of commensal microbes live in and on our body, and constitute the human microbiome. The vast majority of these microorganisms are maternally derived and live in the gut, where they perform functions essential to our health and survival, including: digesting food, activating certain drugs, producing short-chain fatty acids (which help to modulate gene expression by inhibiting the deacetylation of histone proteins), generating anti-inflammatory substances, and playing a fundamental role in the induction, training, and function of our immune system. Among the many roles the microbiome ultimately plays, it mitigates against untoward effects from our exposure to the environment by forming a biotic shield between us and the outside world. The importance of physical activity coupled with a balanced and healthy diet in the maintenance of our well-being has been recognized since antiquity. However, it is only recently that characterization of the host–microbiome intermetabolic and crosstalk pathways has come to the forefront in studying therapeutic design. As reviewed in this report, synthetic biology shows potential in developing microorganisms for correcting pathogenic dysbiosis (gut microbiota–host maladaptation), although this has yet to be proven. However, the development and use of small molecule drugs have a long and successful history in the clinic, with small molecule histone deacetylase inhibitors representing one relevant example already approved to treat cancer and other disorders. Moreover, preclinical research suggests that epigenetic treatment of neurological conditions holds significant promise. With the mouth being an extension of the digestive tract, it presents a readily accessible diagnostic site for the early detection of potential unhealthy pathogens resident in the gut. Taken together, the data outlined herein provide an encouraging roadmap toward important new medicines and companion diagnostic platforms in a wide range of therapeutic indications. PMID:27274912

Microbiota and Neurological Disorders: A Gut Feeling.

PubMed

Moos, Walter H; Faller, Douglas V; Harpp, David N; Kanara, Iphigenia; Pernokas, Julie; Powers, Whitney R; Steliou, Kosta

2016-01-01

In the past century, noncommunicable diseases have surpassed infectious diseases as the principal cause of sickness and death, worldwide. Trillions of commensal microbes live in and on our body, and constitute the human microbiome. The vast majority of these microorganisms are maternally derived and live in the gut, where they perform functions essential to our health and survival, including: digesting food, activating certain drugs, producing short-chain fatty acids (which help to modulate gene expression by inhibiting the deacetylation of histone proteins), generating anti-inflammatory substances, and playing a fundamental role in the induction, training, and function of our immune system. Among the many roles the microbiome ultimately plays, it mitigates against untoward effects from our exposure to the environment by forming a biotic shield between us and the outside world. The importance of physical activity coupled with a balanced and healthy diet in the maintenance of our well-being has been recognized since antiquity. However, it is only recently that characterization of the host-microbiome intermetabolic and crosstalk pathways has come to the forefront in studying therapeutic design. As reviewed in this report, synthetic biology shows potential in developing microorganisms for correcting pathogenic dysbiosis (gut microbiota-host maladaptation), although this has yet to be proven. However, the development and use of small molecule drugs have a long and successful history in the clinic, with small molecule histone deacetylase inhibitors representing one relevant example already approved to treat cancer and other disorders. Moreover, preclinical research suggests that epigenetic treatment of neurological conditions holds significant promise. With the mouth being an extension of the digestive tract, it presents a readily accessible diagnostic site for the early detection of potential unhealthy pathogens resident in the gut. Taken together, the data outlined herein provide an encouraging roadmap toward important new medicines and companion diagnostic platforms in a wide range of therapeutic indications.

Current Features of Secondary (Acquired) Types of Immune Deficiency.

PubMed

Kovalchuk, Leonid V.; Pinegin, Boris V.

1999-12-01

Secondary (acquired) types of immune deficiencies (SID) take a leading place in practice of modern clinical immunology. The causes for SID development are extremely variable. Special attention is concerned with accumulating facts about target action of microorganisms, and first of all viruses, on certain processes in immune system. Damageable action of HIV-1 on cell elements expressing CD4 molecules is known in most precise manner. It is noteworthy that the search of real molecular defects, induced by microorganisms in immune system is required. It is not to be ruled out that the increased level of apoptosis of immune system cells is one of the causes of SID. The basis of it is disbalance between positive and negative activation processes of immunocompetent cells. Multiple factors may serve as apoptogens, including drugs (glucocorticoids etc.), xenobiotics, physical factors (radiation) and many others. In practice of clinical laboratories a certain spectrum of immunological investigations is recommended that allows to diagnose the degree of immunopathology. At present, in clinical practice these methods are focused around flow cytometry (immunophenotyping), immunodiffusion and immunoenzyme tests (determination of immunoglobulins, cytokines, other soluble components of immune system), tests of estimation of immunocompetent cell activation, proliferation and differentiation. As a prospective, some methods, based on identification of molecular defects in cells and soluble factors of immune system, may be taken into consideration.

Guidelines for the Detection of Rickettsia spp.

PubMed

Portillo, Aránzazu; de Sousa, Rita; Santibáñez, Sonia; Duarte, Ana; Edouard, Sophie; Fonseca, Isabel P; Marques, Cátia; Novakova, Marketa; Palomar, Ana M; Santos, Marcos; Silaghi, Cornelia; Tomassone, Laura; Zúquete, Sara; Oteo, José A

2017-01-01

The genus Rickettsia (Rickettsiales: Rickettsiaceae) includes Gram-negative, small, obligate intracellular, nonmotile, pleomorphic coccobacilli bacteria transmitted by arthropods. Some of them cause human and probably also animal disease (life threatening in some patients). In these guidelines, we give clinical practice advices (microscopy, serology, molecular tools, and culture) for the microbiological study of these microorganisms in clinical samples. Since in our environment rickettsioses are mainly transmitted by ticks, practical information for the identification of these arthropods and for the study of Rickettsia infections in ticks has also been added.

The use of newly developed real-time PCR for the rapid identification of bacteria in culture-negative osteomyelitis.

PubMed

Kobayashi, Naomi; Bauer, Thomas W; Sakai, Hiroshige; Togawa, Daisuke; Lieberman, Isador H; Fujishiro, Takaaki; Procop, Gary W

2006-12-01

We report a case of a culture-negative osteomyelitis in which our newly developed real-time polymerase chain reaction (PCR) could differentiate Staphylococcus aureus from Staphylococcus epidermidis. This is the first report that described the application of this novel assay to an orthopedics clinical sample. This assay may be useful for other clinical culture-negative cases in a combination with a broad-spectrum assay as a rapid microorganism identification method.

Dose Imprecision and Resistance: Free-Choice Medicated Feeds in Industrial Food Animal Production in the United States

PubMed Central

Love, David C.; Davis, Meghan F.; Bassett, Anna; Gunther, Andrew; Nachman, Keeve E.

2011-01-01

Background Industrial food animal production employs many of the same antibiotics or classes of antibiotics that are used in human medicine. These drugs can be administered to food animals in the form of free-choice medicated feeds (FCMF), where animals choose how much feed to consume. Routine administration of these drugs to livestock selects for microorganisms that are resistant to medications critical to the treatment of clinical infections in humans. Objectives In this commentary, we discuss the history of medicated feeds, the nature of FCMF use with regard to dose delivery, and U.S. policies that address antimicrobial drug use in food animals. Discussion FCMF makes delivering a predictable, accurate, and intended dose difficult. Overdosing can lead to animal toxicity; underdosing or inconsistent dosing can result in a failure to resolve animal diseases and in the development of antimicrobial-resistant microorganisms. Conclusions The delivery of antibiotics to food animals for reasons other than the treatment of clinically diagnosed disease, especially via free-choice feeding methods, should be reconsidered. PMID:21030337

Mucin-Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications.

PubMed

Rokhsefat, Sana; Lin, Aifeng; Comelli, Elena M

2016-06-01

The mucus layer and gut microbiota interplay contributes to host homeostasis. The mucus layer serves as a scaffold and a carbon source for gut microorganisms; conversely, gut microorganisms, including mucin degraders, influence mucin gene expression, glycosylation, and secretion. Conjointly they shield the epithelium from luminal pathogens, antigens, and toxins. Importantly, the mucus layer and gut microbiota are established in parallel during early postnatal life. During this period, the development of gut microbiota and mucus layer is coupled with that of the immune system. Developmental changes of different mucin types can impact the age-dependent patterns of intestinal infection in terms of incidence and severity. Altered mucus layer, dysbiotic microbiota, and abnormal mucus-gut microbiota interaction have the potential for inducing systemic effects, and accompany several intestinal diseases such as inflammatory bowel disease, colorectal cancer, and radiation-induced mucositis. Early life provides a pivotal window of opportunity to favorably modulate the mucus-microbiota interaction. The support of a health-compatible mucin-microbiota maturation in early life is paramount for long-term health and serves as an important opportunity for clinical intervention.

Frequency of bacetrial content finding in persistant periapical lesions

PubMed Central

Grgurević, Joško; Tambić Andrašević, Arjana; Prpić Mehičić, Goranka; Kuzmac, Sania; Jukić, Silvana

2017-01-01

Objectives To determine the percentage of persistant apical lesions positive for bacterial nucleic acids, to detect microorganisms difficult to cultivate in persistant apical lesions by PCR and relate them to endodontic failure, clinical symptoms and diabetes mellitus. Materials and methods The samples of persistent apical lesions were collected during apicoectomy. Bacterial ubiquitous primer 16S rRNA was used to detect 16S ribosomal RNA in 36 samples. A species–specific PCR was performed with primers targeted to the bacterial 16S rRNA genes of Prevotella Nigrescens, Pseudoramibacter alactolyticus, and Propionobacterium propionicum. Results Six samples (16.67%) were positive for bacterial ribosomal RNA. Pseudoramibacter alactolyticus was detected in three samples. Propionibacterium propionicum and Prevotella nigrescens were detected in one sample each. The prevalence of infection of such lesions with P. intermedia, P. propionicum and P. alactolyticus is low. Conslusion The study we conducted gave insufficient data about extraradicular infection and its connection with diabetes mellitus and clinical symptoms. Conclusions Apical lesions persisting after endodontic treatment could harbor microorganisms other than Actinomyces and Propionicum species. PMID:29225362

5-Fluorouracil sensitivity varies among oral micro-organisms.

PubMed

Vanlancker, Eline; Vanhoecke, Barbara; Smet, Rozel; Props, Ruben; Van de Wiele, Tom

2016-08-01

5-Fluorouracil (5-FU), a commonly used chemotherapeutic agent, often causes oral mucositis, an inflammation and ulceration of the oral mucosa. Micro-organisms in the oral cavity are thought to play an important role in the aggravation and severity of mucositis, but the mechanisms behind this remain unclear. Although 5-FU has been shown to elicit antibacterial effects at high concentrations (>100 µM), its antibacterial effect at physiologically relevant concentrations in the oral cavity is unknown. This study reports the effect of different concentrations of 5-FU (range 0.1-50 µM) on the growth and viability of bacterial monocultures that are present in the oral cavity and the possible role in the activity of dihydropyrimidine dehydrogenase (DPD), an enzyme involved in 5-FU resistance. Our data showed a differential sensitivity among the tested oral species towards physiological concentrations of 5-FU. Klebsiellaoxytoca, Streptococcus salivarius, Streptococcus mitis, Streptococcus oralis, Pseudomonas aeruginosa and Lactobacillus salivarius appeared to be highly resistant to all tested concentrations. In contrast, Lactobacillusoris, Lactobacillus plantarum, Streptococcus pyogenes, Fusobacterium nucleatum and Neisseria mucosa showed a significant reduction in growth and viability starting from very low concentrations (0.2-3.1 µM). We can also provide evidence that DPD is not involved in the 5-FU resistance of the selected species. The observed variability in response to physiological 5-FU concentrations may explain why certain microbiota lead to a community dysbiosis and/or an overgrowth of certain resistant micro-organisms in the oral cavity following cancer treatment.

Challenges and Opportunities of Airborne Metagenomics

PubMed Central

Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

2015-01-01

Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. PMID:25953766

Treatment of Fungal Bioaerosols by a High-Temperature, Short-Time Process in a Continuous-Flow System▿

PubMed Central

Jung, Jae Hee; Lee, Jung Eun; Lee, Chang Ho; Kim, Sang Soo; Lee, Byung Uk

2009-01-01

Airborne fungi, termed fungal bioaerosols, have received attention due to the association with public health problems and the effects on living organisms in nature. There are growing concerns that fungal bioaerosols are relevant to the occurrence of allergies, opportunistic diseases in hospitals, and outbreaks of plant diseases. The search for ways of preventing and curing the harmful effects of fungal bioaerosols has created a high demand for the study and development of an efficient method of controlling bioaerosols. However, almost all modern microbiological studies and theories have focused on microorganisms in liquid and solid phases. We investigated the thermal heating effects on fungal bioaerosols in a continuous-flow environment. Although the thermal heating process has long been a traditional method of controlling microorganisms, the effect of a continuous high-temperature, short-time (HTST) process on airborne microorganisms has not been quantitatively investigated in terms of various aerosol properties. Our experimental results show that the geometric mean diameter of the tested fungal bioaerosols decreased when they were exposed to increases in the surrounding temperature. The HTST process produced a significant decline in the (1→3)-β-d-glucan concentration of fungal bioaerosols. More than 99% of the Aspergillus versicolor and Cladosporium cladosporioides bioaerosols lost their culturability in about 0.2 s when the surrounding temperature exceeded 350°C and 400°C, respectively. The instantaneous exposure to high temperature significantly changed the surface morphology of the fungal bioaerosols. PMID:19201954

Treatment of fungal bioaerosols by a high-temperature, short-time process in a continuous-flow system.

PubMed

Jung, Jae Hee; Lee, Jung Eun; Lee, Chang Ho; Kim, Sang Soo; Lee, Byung Uk

2009-05-01

Airborne fungi, termed fungal bioaerosols, have received attention due to the association with public health problems and the effects on living organisms in nature. There are growing concerns that fungal bioaerosols are relevant to the occurrence of allergies, opportunistic diseases in hospitals, and outbreaks of plant diseases. The search for ways of preventing and curing the harmful effects of fungal bioaerosols has created a high demand for the study and development of an efficient method of controlling bioaerosols. However, almost all modern microbiological studies and theories have focused on microorganisms in liquid and solid phases. We investigated the thermal heating effects on fungal bioaerosols in a continuous-flow environment. Although the thermal heating process has long been a traditional method of controlling microorganisms, the effect of a continuous high-temperature, short-time (HTST) process on airborne microorganisms has not been quantitatively investigated in terms of various aerosol properties. Our experimental results show that the geometric mean diameter of the tested fungal bioaerosols decreased when they were exposed to increases in the surrounding temperature. The HTST process produced a significant decline in the (1-->3)-beta-d-glucan concentration of fungal bioaerosols. More than 99% of the Aspergillus versicolor and Cladosporium cladosporioides bioaerosols lost their culturability in about 0.2 s when the surrounding temperature exceeded 350 degrees C and 400 degrees C, respectively. The instantaneous exposure to high temperature significantly changed the surface morphology of the fungal bioaerosols.

Morphology and rheology in filamentous cultivations.

PubMed

Wucherpfennig, T; Kiep, K A; Driouch, H; Wittmann, C; Krull, R

2010-01-01

Because of their metabolic diversity, high production capacity, secretion efficiency, and capability of carrying out posttranslational modifications, filamentous fungi are widely exploited as efficient cell factories in the production of metabolites, bioactive substances, and native or heterologous proteins, respectively. There is, however, a complex relationship between the morphology of these microorganisms, transport phenomena, the viscosity of the cultivation broth, and related productivity. The morphological characteristics vary between freely dispersed mycelia and distinct pellets of aggregated biomass, every growth form having a distinct influence on broth rheology. Hence, the advantages and disadvantages for mycelial or pellet cultivation have to be balanced out carefully. Because of the still inadequate understanding of the morphogenesis of filamentous microorganisms, fungal morphology is often a bottleneck of productivity in industrial production. To obtain an optimized production process, it is of great importance to gain a better understanding of the molecular and cell biology of these microorganisms as well as the relevant approaches in biochemical engineering. In this chapter, morphology and growth of filamentous fungi are described, with special attention given to specific problems as they arise from fungal growth forms; growth and mass transfer in fungal biopellets are discussed as an example. To emphasize the importance of the flow behavior of filamentous cultivation broths, an introduction to rheology is also given, reviewing important rheological models and recent studies concerning rheological parameters. Furthermore, current knowledge on morphology and productivity in relation to the environom is outlined in the last section of this review. Copyright 2010 Elsevier Inc. All rights reserved.

Biofilms in drinking water and their role as reservoir for pathogens.

PubMed

Wingender, Jost; Flemming, Hans-Curt

2011-11-01

Most microorganisms on Earth live in various aggregates which are generally termed "biofilms". They are ubiquitous and represent the most successful form of life. They are the active agent in biofiltration and the carriers of the self-cleaning potential in soils, sediments and water. They are also common on surfaces in technical systems where they sometimes cause biofouling. In recent years it has become evident that biofilms in drinking water distribution networks can become transient or long-term habitats for hygienically relevant microorganisms. Important categories of these organisms include faecal indicator bacteria (e.g., Escherichia coli), obligate bacterial pathogens of faecal origin (e.g., Campylobacter spp.) opportunistic bacteria of environmental origin (e.g., Legionella spp., Pseudomonas aeruginosa), enteric viruses (e.g., adenoviruses, rotaviruses, noroviruses) and parasitic protozoa (e.g., Cryptosporidium parvum). These organisms can attach to preexisting biofilms, where they become integrated and survive for days to weeks or even longer, depending on the biology and ecology of the organism and the environmental conditions. There are indications that at least a part of the biofilm populations of pathogenic bacteria persists in a viable but non-culturable (VBNC) state and remains unnoticed by the methods appointed to their detection. Thus, biofilms in drinking water systems can serve as an environmental reservoir for pathogenic microorganisms and represent a potential source of water contamination, resulting in a potential health risk for humans if left unnoticed. Copyright © 2011 Elsevier GmbH. All rights reserved.

Surviving space flight: case study on MELiSSA's CIII nitrifying compartment

NASA Astrophysics Data System (ADS)

Ilgrande, Chiara; Lasseur, Christophe; Mastroleo, Felice; Paille, Christel; Leys, Natalie; Morozova, Julia; Ilyin, Vyacheslav; Clauwaert, Peter; Christiaens, Marlies E. R.; Lindeboom, Ralph E. F.; Vlaeminck, Siegfried; Prat, Delphine; Arroyo, Jose M. C.; Conincx, Ilse; Van Hoey, Olivier; Roume, Hugo; Udert, Kai; Sas, Benedikt

2016-07-01

Space synthetic biology offers key opportunities for long-term space missions. Planets mining, terraformation, space medicine and Life Support technologies would all benefit from an integrative biological approach. However, space is a harsh environment for life: microgravity, temperature, UV and cosmic radiation can affect the health and functionality of microorganisms and plants, possibly preventing the optimal performance of the systems. The European Space Agency's Life Support System (MELiSSA) has been developed as a model for future long term Space missions and Space habitation. MELiSSA is a 5 compartment artificial ecosystem with microorganisms and higher, that aims at completely recycling gas, liquid and solid waste. In this study, the survival and functional activity after Lower Earth Orbit conditions of microbial nitrogen conversions, relevant for MELiSSA's CIII compartment, was tested. Synthetic communities containing Nitrosomonas europeae, Nitrosomonas ureae, Nitrobacter winogradskyi, Nitrospira moscoviensis and Cupriavidus pinatubonensis were exposed to the Lower Earth Orbit conditions of the International Space Station (ISS) for 7 days. Nitrosomonas europeae, Nitrobacter winogradskyi, Cupriavidus pinatubonensis, and three mixed communities (a urine nitrification sludge, a sludge containing aerobic ammonia oxidizing bacteria and anammox bacteria (OLAND), and an aquaculture sludge containing ammonia oxidizing archaea) were exposed to Lower Earth Orbit conditions for 44 days. Survival after both space flights was demonstrated because nitritation, nitratation, denitrification and anammox activity could be restored at a rate comparable to ground storage conditions. Our results validate the potential survival feasibility and suggest future space applications for N-related microorganisms.

Cold atmospheric plasma activity on microorganisms. A study on the influence of the treatment time and surface

NASA Astrophysics Data System (ADS)

Xaplanteris, C. L.; Filippaki, E. D.; Christodoulakis, J. K.; Kazantzaki, M. A.; Tsakalos, E. P.; Xaplanteris, L. C.

2015-08-01

The second half of the 20th century can be characterized and named as the `plasma era', as the plasma gathered scientific interest because of its special physical behaviour. Thus, it was considered as the fourth material state and the plasma physics began to form consequently. In addition to this, many important applications of plasma were discovered and put to use. Especially, in last few decades, there has been an increased interest in the use of cold atmospheric plasma in bio-chemical applications. Until now, thermal plasma has been commonly used in many bio-medical and other applications; however, more recent efforts have shown that plasma can also be produced at lower temperature (close to the environment temperature) by using ambient air in an open space (in atmospheric pressure). However, two aspects remain neglected: firstly, low-temperature plasma production with a large area, and secondly, acquiring the necessary knowledge and understanding the relevant interaction mechanisms of plasma species with microorganisms. These aspects are currently being investigated at the `Demokritos' Plasma Laboratory in Athens, Greece with radio frequency (27.12 MHz and it integer harmonics)-driven sub-atmospheric pressure plasma (100 Pa). The first aspect was achieved with atmospheric plasma being produced at a low temperature (close to the environment temperature) and in a large closed space systems. Regarding the plasma effect on living microorganisms, preliminary experiments and findings have already been carried out and many more have been planned for the near future.

Diverse microbial species survive high ammonia concentrations

NASA Astrophysics Data System (ADS)

Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

2012-04-01

Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

Clinical relevance of findings in trials of CBT for depression.

PubMed

Lepping, P; Whittington, R; Sambhi, R S; Lane, S; Poole, R; Leucht, S; Cuijpers, P; McCabe, R; Waheed, W

2017-09-01

Cognitive behavioural therapy (CBT) is beneficial in depression. Symptom scores can be translated into Clinical Global Impression (CGI) scale scores to indicate clinical relevance. We aimed to assess the clinical relevance of findings of randomised controlled trials (RCTs) of CBT in depression. We identified RCTs of CBT that used the Hamilton Rating Scale for Depression (HAMD). HAMD scores were translated into Clinical Global Impression - Change scale (CGI-I) scores to measure clinical relevance. One hundred and seventy datasets from 82 studies were included. The mean percentage HAMD change for treatment arms was 53.66%, and 29.81% for control arms, a statistically significant difference. Combined active therapies showed the biggest improvement on CGI-I score, followed by CBT alone. All active treatments had better than expected HAMD percentage reduction and CGI-I scores. CBT has a clinically relevant effect in depression, with a notional CGI-I score of 2.2, indicating a significant clinical response. The non-specific or placebo effect of being in a psychotherapy trial was a 29% reduction of HAMD. Copyright © 2017. Published by Elsevier Masson SAS.

Drug development in neuropsychopharmacology.

PubMed

Fritze, Jürgen

2008-03-01

Personalized medicine is still in its infancy concerning drug development in neuropsychopharmacology. Adequate biomarkers with clinical relevance to drug response and/or tolerability and safety largely remain to be identified. Possibly, this kind of personalized medicine will first gain clinical relevance in the dementias. The clinical relevance of the genotyping of drug-metabolizing enzymes as suggested by drug licensing authorities for the pharmacokinetic evaluation of medicinal products needs to be proven in sound clinical trials.

Evaluation of Antibacterial Activity of Three Selected Fruit Juices on Clinical Endodontic Bacterial Strains

PubMed Central

Behera, Subasish; Khetrapal, Prashant; Punia, Sandhya Kapoor; Agrawal, Deepak; Khandelwal, Minal; Lohar, Jitendra

2017-01-01

Introduction: The increasing problem of antibiotic drug resistance by pathogenic microorganisms in the past few decades has recently led to the continuous exploration of natural plant products for new antibiotic agents. Many consumable food materials have good as well as their bad effects, good effect includes their antibacterial effects on different microorganisms present in the oral cavity. Recently, natural products have been evaluated as source of antimicrobial agent with efficacies against a variety of microorganisms. Methodology: The present study describes the antibacterial activity of three selected fruit juices (Apple, Pomegranate and Grape) on endodontic bacterial strains. Antimicrobial activity of fruit juices were tested by wel l diffusion assay by an inhibition zone surrounding the well. The aim of the study was to evaluate the antibacterial activity of three fruit juises on different endodontic strains. Result: Agar well diffusion method was adopted for determining antibacterial potency. Antibacterial activity present on the plates was indicated by an inhibition zone surrounding the well containing the fruit juice. The zone of inhibition was measured by measuring scale in millimeter. Comparision between antibacterial efficacy of all three fruit juices against Enterococcus feacalis and Streptococcus mutans was observed with significant value of P ≤ 0.05. Conclusion: The results obtained in this study clearly demonstrated a significant antimicrobial effect of apple fruit juice against Enterococcus fecalis and Streptococcus mutans. However, preclinical and clinical trials are needed to evaluate biocompatibility & safety before apple can conclusively be recommended in endodontic therapy, but in vitro observation of apple effectiveness appears promising. PMID:29284967

Antimicrobial efficacy of 0·05% cetylpyridinium chloride mouthrinses.

PubMed

Sreenivasan, P K; Haraszthy, V I; Zambon, J J

2013-01-01

This study evaluated the antimicrobial activity of two commercially available 0·05% cetylpyridinium chloride (CPC) mouthrinses with or without alcohol and examined its antimicrobial activity on oral bacterial species including fresh clinical isolates compared to a chlorhexidine mouthrinse and a control fluoride mouthrinse without CPC. Two different approaches were used to evaluate antimicrobial activity. First, the minimum inhibitory concentration (MIC) was determined for each mouthrinse against a panel of 25 micro-organisms including species associated with dental caries, gingivitis and periodontitis. Second, supragingival dental plaque obtained from 15 adults was incubated with the four mouthrinses to evaluate antimicrobial activity on micro-organisms in oral biofilms. Both CPC mouthrinses exhibited lower MIC's, that is, greater antimicrobial activity, against oral Gram-negative bacteria especially periodontal pathogens and species implicated in halitosis such as Aggregatibacter actinomycemcomitans, Campylobacter rectus, Eikenella corrodens, Porphyromonas gingivalis, Prevotella intermedia and Solobacterium moorei than the control mouthrinse. Ex-vivo tests on supragingival plaque micro-organisms demonstrated significantly greater antimicrobial activity by the CPC mouthrinses (>90% killing, P < 0·001) and the chlorhexidine rinse (>98% killing, P < 0·05) compared to the control fluoride mouthrinse. Whilst the chlorhexidine mouthrinse was most effective, mouthrinses containing 0·05% CPC formulated with or without alcohol demonstrated broad-spectrum antimicrobial activity against both laboratory strains and supragingival plaque bacteria compared to a control mouthrinse without CPC. These in vitro and ex-vivo studies provide a biological rationale for previous clinical studies demonstrating the efficacy of CPC mouthrinses in reducing supragingival plaque and plaque-associated gingivitis. © 2012 The Society for Applied Microbiology.

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine

PubMed Central

Contreras, Alejandra V.; Cocom-Chan, Benjamin; Hernandez-Montes, Georgina; Portillo-Bobadilla, Tobias; Resendis-Antonio, Osbaldo

2016-01-01

It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput (HT) technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, HT data, bioinformatics, and systems biology. PMID:28018236

Direct identification of pathogens from positive blood cultures using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry.

PubMed

Rodríguez-Sánchez, B; Sánchez-Carrillo, C; Ruiz, A; Marín, M; Cercenado, E; Rodríguez-Créixems, M; Bouza, E

2014-07-01

In recent years, matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved a rapid and reliable method for the identification of bacteria and yeasts that have already been isolated. The objective of this study was to evaluate this technology as a routine method for the identification of microorganisms directly from blood culture bottles (BCBs), before isolation, in a large collection of samples. For this purpose, 1000 positive BCBs containing 1085 microorganisms have been analysed by conventional phenotypic methods and by MALDI-TOF MS. Discrepancies have been resolved using molecular methods: the amplification and sequencing of the 16S rRNA gene or the Superoxide Dismutase gene (sodA) for streptococcal isolates. MALDI-TOF predicted a species- or genus-level identification of 81.4% of the analysed microorganisms. The analysis by episode yielded a complete identification of 814 out of 1000 analysed episodes (81.4%). MALDI-TOF identification is available for clinicians within hours of a working shift, as oppose to 18 h later when conventional identification methods are performed. Moreover, although further improvement of sample preparation for polymicrobial BCBs is required, the identification of more than one pathogen in the same BCB provides a valuable indication of unexpected pathogens when their presence may remain undetected in Gram staining. Implementation of MALDI-TOF identification directly from the BCB provides a rapid and reliable identification of the causal pathogen within hours. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

[Periodontal microbiota and microorganisms isolated from heart valves in patients undergoing valve replacement surgery in a clinic in Cali, Colombia].

PubMed

Moreno, Sandra; Parra, Beatriz; Botero, Javier E; Moreno, Freddy; Vásquez, Daniel; Fernández, Hugo; Alba, Sandra; Gallego, Sara; Castillo, Gilberto; Contreras, Adolfo

2017-12-01

Periodontitis is an infectious disease that affects the support tissue of the teeth and it is associated with different systemic diseases, including cardiovascular disease. Microbiological studies facilitate the detection of microorganisms from subgingival and cardiovascular samples. To describe the cultivable periodontal microbiota and the presence of microorganisms in heart valves from patients undergoing valve replacement surgery in a clinic in Cali. We analyzed 30 subgingival and valvular tissue samples by means of two-phase culture medium, supplemented blood agar and trypticase soy agar with antibiotics. Conventional PCR was performed on samples of valve tissue. The periodontal pathogens isolated from periodontal pockets were: Fusobacterium nucleatum (50%), Prevotella intermedia/ nigrescens (40%), Campylobacter rectus (40%), Eikenella corrodens (36.7%), Gram negative enteric bacilli (36.7%), Porphyromonas gingivalis (33.3%), and Eubacterium spp. (33.3%). The pathogens isolated from the aortic valve were Propionibacterium acnes (12%), Gram negative enteric bacilli (8%), Bacteroides merdae (4%), and Clostridium bifermentans (4%), and from the mitral valve we isolated P. acnes and Clostridium beijerinckii. Conventional PCR did not return positive results for oral pathogens and bacterial DNA was detected only in two samples. Periodontal microbiota of patients undergoing surgery for heart valve replacement consisted of species of Gram-negative bacteria that have been associated with infections in extraoral tissues. However, there is no evidence of the presence of periodontal pathogens in valve tissue, because even though there were valve and subgingival samples positive for Gram-negative enteric bacilli, it is not possible to maintain they corresponded to the same phylogenetic origin.

Biodegradation of dispersed oil in Arctic seawater at -1°C.

PubMed

McFarlin, Kelly M; Prince, Roger C; Perkins, Robert; Leigh, Mary Beth

2014-01-01

As offshore oil and gas exploration expands in the Arctic, it is important to expand the scientific understanding of arctic ecology and environmental impact to mitigate operational risks. Understanding the fate of oil in arctic seawater is a key factor for consideration. Here we report the chemical loss due to the biodegradation of Alaska North Slope (ANS) crude oil that would occur in the water column following the successful dispersion of a surface oil slick. Primary biodegradation and mineralization were measured in mesocosms containing Arctic seawater collected from the Chukchi Sea, Alaska, incubated at -1°C. Indigenous microorganisms degraded both fresh and weathered oil, in both the presence and absence of Corexit 9500, with oil losses ranging from 46-61% and up to 11% mineralization over 60 days. When tested alone, 14% of 50 ppm Corexit 9500 was mineralized within 60 days. Our study reveals that microorganisms indigenous to Arctic seawater are capable of performing extensive biodegradation of chemically and physically dispersed oil at an environmentally relevant temperature (-1°C) without any additional nutrients.

Biochemical and Molecular Mechanisms of Plant-Microbe-Metal Interactions: Relevance for Phytoremediation

PubMed Central

Ma, Ying; Oliveira, Rui S.; Freitas, Helena; Zhang, Chang

2016-01-01

Plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. Plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. Some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (PGPMs), may alleviate metal phytotoxicity and stimulate plant growth indirectly via the induction of defense mechanisms against phytopathogens, and/or directly through the solubilization of mineral nutrients (nitrogen, phosphate, potassium, iron, etc.), production of plant growth promoting substances (e.g., phytohormones), and secretion of specific enzymes (e.g., 1-aminocyclopropane-1-carboxylate deaminase). PGPM can also change metal bioavailability in soil through various mechanisms such as acidification, precipitation, chelation, complexation, and redox reactions. This review presents the recent advances and applications made hitherto in understanding the biochemical and molecular mechanisms of plant–microbe interactions and their role in the major processes involved in phytoremediation, such as heavy metal detoxification, mobilization, immobilization, transformation, transport, and distribution. PMID:27446148

Cyclic Dinucleotides in Oral Bacteria and in Oral Biofilms.

PubMed

Gürsoy, Ulvi K; Gürsoy, Mervi; Könönen, Eija; Sintim, Herman O

2017-01-01

Oral cavity acts as a reservoir of bacterial pathogens for systemic infections and several oral microorganisms have been linked to systemic diseases. Quorum sensing and cyclic dinucleotides, two "decision-making" signaling systems, communicate to regulate physiological process in bacteria. Discovery of cyclic dinucleotides has a long history, but the progress in our understanding of how cyclic dinucleotides regulate bacterial lifestyle is relatively new. Oral microorganisms form some of the most intricate biofilms, yet c-di-GMP, and c-di-AMP signaling have been rarely studied in oral biofilms. Recent studies demonstrated that, with the aid of bacterial messenger molecules and their analogs, it is possible to activate host innate and adaptive immune responses and epithelial integrity with a dose that is relevant to inhibit bacterial virulence mechanisms, such as fimbriae and exopolysaccharide production, biofilm formation, and host cell invasion. The aim of this perspective article is to present available information on cyclic dinucleotides in oral bacteria and in oral biofilms. Moreover, technologies that can be used to detect cyclic dinucleotides in oral biofilms are described. Finally, directions for future research are highlighted.

Biodegradation of Dispersed Oil in Arctic Seawater at -1°C

PubMed Central

McFarlin, Kelly M.; Prince, Roger C.; Perkins, Robert; Leigh, Mary Beth

2014-01-01

As offshore oil and gas exploration expands in the Arctic, it is important to expand the scientific understanding of arctic ecology and environmental impact to mitigate operational risks. Understanding the fate of oil in arctic seawater is a key factor for consideration. Here we report the chemical loss due to the biodegradation of Alaska North Slope (ANS) crude oil that would occur in the water column following the successful dispersion of a surface oil slick. Primary biodegradation and mineralization were measured in mesocosms containing Arctic seawater collected from the Chukchi Sea, Alaska, incubated at −1°C. Indigenous microorganisms degraded both fresh and weathered oil, in both the presence and absence of Corexit 9500, with oil losses ranging from 46−61% and up to 11% mineralization over 60 days. When tested alone, 14% of 50 ppm Corexit 9500 was mineralized within 60 days. Our study reveals that microorganisms indigenous to Arctic seawater are capable of performing extensive biodegradation of chemically and physically dispersed oil at an environmentally relevant temperature (−1°C) without any additional nutrients. PMID:24416211

[Scientific substantiation of perfection of sanitary bacteriological monitoring in drinking water use].

PubMed

Rakhmanin, Iu A; Zhuravlev, P V; Aleshnia, V V; Panasovets, O P; Artemova, T Z; Zagaĭnova, A V; Gipp, E K

2014-01-01

Criterion of the epidemic safety of drinking water is the absence of pathogenic and potentially pathogenic microorganisms. Currently, water quality control is performed in terms of the index of total coliform bacteria (TCB). TCB index oriented to the labile lactose sign has not sufficient relevance in the determination of the degree of the epidemic danger in the water use in relation to Salmonella and potentially pathogenic microorganisms. The frequency of detection of GCB in standard quality of drinking water as well as the application of the methodology for the assessment of the microbial risk of the occurrence of bacterial intestinal infections with the use of integral index--GCB, provide the most reliable prediction of risk in the occurrence of water-caused intestinal infections and more objectively reflect the epidemiological importance of drinking water in their distribution among the population. Proceeding from the data obtained, it is advisable to carry out the quality control of drinking water with the use of the broader indicator index GCB- detected from basic signs of the Enterobacteriaceae family--glucose fermentation and oxidase test and oxidase test.

Synthesis, Characterization, and Antimicrobial Activity of a Novel Trisazo Dye from 3-Amino-4H-thieno[3,4-c][1]benzopyran-4-one.

PubMed

Tsemeugne, Joseph; Sopbué Fondjo, Emmanuel; Tamokou, Jean-de-Dieu; Rohand, Taoufik; Ngongang, Arnaud Djintchui; Kuiate, Jules Roger; Sondengam, Beibam Luc

2018-01-01

A new trisazo dye has been synthesized by coupling the diazonium ion of 3-amino-4H thieno[3,4-c][1]benzopyran-4-one with 2- tert -butyl-4-methoxyphenol. The newly prepared trisazo dye was characterized by its physical, elemental, and spectroscopic data. 2D-NMR (COSY, HSQC, and HMBC) techniques were used to secure the structural assignments. The new trisazo dye (compound 7 ) along with precursors 3 , 4 , and 6 was screened by microdilution susceptibility assay for antibacterial and antifungal activities towards eight bacterial strains and three yeasts selected on the basis of their relevance as human pathogens. The results showed that compound 7 (MIC = 2-128  μ g/mL) was the most active as compared with its precursors. The most resistant microorganisms were V. cholerae NB2 and V. cholerae SG24, whereas the most sensitive microorganism was C. neoformans. The overall results of this study indicated that compound 7 had the greatest potential value against both yeasts and multidrug-resistant bacteria, so further investigation is warranted.

Development of a process for efficient use of CO2 from flue gases in the production of photosynthetic microorganisms.

PubMed

González-López, C V; Acién Fernández, F G; Fernández-Sevilla, J M; Sánchez Fernández, J F; Molina Grima, E

2012-07-01

A new methodology to use efficiently flue gases as CO(2) source in the production of photosynthetic microorganisms is proposed. The CO(2) is absorbed in an aqueous phase that is then regenerated by microalgae. Carbonated solutions could absorb up to 80% of the CO(2) from diluted gas reaching total inorganic carbon (TIC) concentrations up to 2.0 g/L. The pH of the solution was maintained at 8.0-10.0 by the bicarbonate/carbonate buffer, so it is compatible with biological regeneration. The absorption process was modeled and the kinetic parameters were determined. Anabaena sp. demonstrated to tolerate pH (8.0-10.0) and TIC (up to 2.0 g/L) conditions imposed by the absorption step. Experiments of regeneration of the liquid phase demonstrated the feasibility of the overall process, converting CO(2) into organic matter. The developed process avoids heating to regenerate the liquid whereas maximizing the efficiency of CO(2) use, which is relevant to achieve the commercial production of biofuels from microalgae. Copyright © 2012 Wiley Periodicals, Inc.

Life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals.

PubMed

Orell, Alvaro; Navarro, Claudio A; Arancibia, Rafaela; Mobarec, Juan C; Jerez, Carlos A

2010-01-01

Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes. Copyright © 2010 Elsevier Inc. All rights reserved.

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes.

PubMed

Vorapreeda, Tayvich; Thammarongtham, Chinae; Laoteng, Kobkul

2016-07-01

Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.

Thermophilic xylanases: from bench to bottle.

PubMed

Basit, Abdul; Liu, Junquan; Rahim, Kashif; Jiang, Wei; Lou, Huiqiang

2018-01-17

Lignocellulosic biomass is a valuable raw material. As technology has evolved, industrial interest in new ways to take advantage of this raw material has grown. Biomass is treated with different microbial cells or enzymes under ideal industrial conditions to produce the desired products. Xylanases are the key enzymes that degrade the xylosidic linkages in the xylan backbone of the biomass, and commercial enzymes are categorized into different glycoside hydrolase families. Thermophilic microorganisms are excellent sources of industrially relevant thermostable enzymes that can withstand the harsh conditions of industrial processing. Thermostable xylanases display high-specific activity at elevated temperatures and distinguish themselves in biochemical properties, structures, and modes of action from their mesophilic counterparts. Natural xylanases can be further improved through genetic engineering. Rapid progress with genome editing, writing, and synthetic biological techniques have provided unlimited potential to produce thermophilic xylanases in their natural hosts or cell factories including bacteria, yeasts, and filamentous fungi. This review will discuss the biotechnological potential of xylanases from thermophilic microorganisms and the ways they are being optimized and produced for various industrial applications.

Co-culture microorganisms with different initial proportions reveal the mechanism of chalcopyrite bioleaching coupling with microbial community succession.

PubMed

Ma, Liyuan; Wang, Xingjie; Feng, Xue; Liang, Yili; Xiao, Yunhua; Hao, Xiaodong; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan

2017-01-01

The effect of co-culture microorganisms with different initial proportions on chalcopyrite bioleaching was investigated. Communities were rebuilt by six typical strains isolated from the same habitat. The results indicated, by community with more sulfur oxidizers at both 30 and 40°C, the final copper extraction rate was 19.8% and 6.5% higher, respectively, than that with more ferrous oxidizers. The variations of pH, redox potential, ferrous and copper ions in leachate also provided evidences that community with more sulfur oxidizers was more efficient. Community succession of free and attached cells revealed that initial proportions played decisive roles on community dynamics at 30°C, while communities shared similar structures, not relevant to initial proportions at 40°C. X-ray diffraction analysis confirmed different microbial functions on mineral surface. A mechanism model for chalcopyrite bioleaching was established coupling with community succession. This will provide theoretical basis for reconstructing an efficient community in industrial application. Copyright © 2016 Elsevier Ltd. All rights reserved.

Inactivation of Lactobacillus rhamnosus GG by fixation modifies its probiotic properties.

PubMed

Markowicz, C; Kubiak, P; Grajek, W; Schmidt, M T

2016-01-01

Probiotics are microorganisms that have beneficial effects on the host and are safe for oral intake in a suitable dose. However, there are situations in which the administration of living microorganisms poses a risk for immunocompromised host. The objective of this study was to evaluate the influence of several fixation methods on selected biological properties of Lactobacillus rhamnosus GG that are relevant to its probiotic action. Fixation of the bacterial cells with ethanol, 2-propanol, glutaraldehyde, paraformaldehyde, and heat treatment resulted in a significant decrease of alkaline phosphatase, peroxidase, and β-galactosidase activities. Most of the fixation procedures reduced bacterial cell hydrophobicity and increased adhesion capacity. The fixation procedures resulted in a different perception of the bacterial cells by enterocytes, which was shown as changes in gene expression in enterocytes. The results show that some procedures of inactivation allow a fraction of the enzymatic activity to be maintained. The adhesion properties of the bacterial cells were enhanced, but the response of enterocytes to fixed cells was different than to live bacteria. Inactivation allows maintenance and modification of some of the properties of the bacterial cells.

Synthesis, Characterization, and Antimicrobial Activity of a Novel Trisazo Dye from 3-Amino-4H-thieno[3,4-c][1]benzopyran-4-one

PubMed Central

Tsemeugne, Joseph; Rohand, Taoufik; Ngongang, Arnaud Djintchui; Sondengam, Beibam Luc

2018-01-01

A new trisazo dye has been synthesized by coupling the diazonium ion of 3-amino-4H thieno[3,4-c][1]benzopyran-4-one with 2-tert-butyl-4-methoxyphenol. The newly prepared trisazo dye was characterized by its physical, elemental, and spectroscopic data. 2D-NMR (COSY, HSQC, and HMBC) techniques were used to secure the structural assignments. The new trisazo dye (compound 7) along with precursors 3, 4, and 6 was screened by microdilution susceptibility assay for antibacterial and antifungal activities towards eight bacterial strains and three yeasts selected on the basis of their relevance as human pathogens. The results showed that compound 7 (MIC = 2–128 μg/mL) was the most active as compared with its precursors. The most resistant microorganisms were V. cholerae NB2 and V. cholerae SG24, whereas the most sensitive microorganism was C. neoformans. The overall results of this study indicated that compound 7 had the greatest potential value against both yeasts and multidrug-resistant bacteria, so further investigation is warranted. PMID:29484208

Diagnostic accuracy of semi-quantitative and quantitative culture techniques for the diagnosis of catheter-related infections in newborns and molecular typing of isolated microorganisms.

PubMed

Riboli, Danilo Flávio Moraes; Lyra, João César; Silva, Eliane Pessoa; Valadão, Luisa Leite; Bentlin, Maria Regina; Corrente, José Eduardo; Rugolo, Ligia Maria Suppo de Souza; da Cunha, Maria de Lourdes Ribeiro de Souza

2014-05-22

Catheter-related bloodstream infections (CR-BSIs) have become the most common cause of healthcare-associated bloodstream infections in neonatal intensive care units (ICUs). Microbiological evidence implicating catheters as the source of bloodstream infection is necessary to establish the diagnosis of CR-BSIs. Semi-quantitative culture is used to determine the presence of microorganisms on the external catheter surface, whereas quantitative culture also isolates microorganisms present inside the catheter. The main objective of this study was to determine the sensitivity and specificity of these two techniques for the diagnosis of CR-BSIs in newborns from a neonatal ICU. In addition, PFGE was used for similarity analysis of the microorganisms isolated from catheters and blood cultures. Semi-quantitative and quantitative methods were used for the culture of catheter tips obtained from newborns. Strains isolated from catheter tips and blood cultures which exhibited the same antimicrobial susceptibility profile were included in the study as positive cases of CR-BSI. PFGE of the microorganisms isolated from catheters and blood cultures was performed for similarity analysis and detection of clones in the ICU. A total of 584 catheter tips from 399 patients seen between November 2005 and June 2012 were analyzed. Twenty-nine cases of CR-BSI were confirmed. Coagulase-negative staphylococci (CoNS) were the most frequently isolated microorganisms, including S. epidermidis as the most prevalent species (65.5%), followed by S. haemolyticus (10.3%), yeasts (10.3%), K. pneumoniae (6.9%), S. aureus (3.4%), and E. coli (3.4%). The sensitivity of the semi-quantitative and quantitative techniques was 72.7% and 59.3%, respectively, and specificity was 95.7% and 94.4%. The diagnosis of CR-BSIs based on PFGE analysis of similarity between strains isolated from catheter tips and blood cultures showed 82.6% sensitivity and 100% specificity. The semi-quantitative culture method showed higher sensitivity and specificity for the diagnosis of CR-BSIs in newborns when compared to the quantitative technique. In addition, this method is easier to perform and shows better agreement with the gold standard, and should therefore be recommended for routine clinical laboratory use. PFGE may contribute to the control of CR-BSIs by identifying clusters of microorganisms in neonatal ICUs, providing a means of determining potential cross-infection between patients.

[Identification of mycobacteria by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry--using reference strains and clinical isolates of Mycobacterium].

PubMed

Niitsuma, Katsunao; Saito, Miwako; Koshiba, Shizuko; Kaneko, Michiyo

2014-05-01

Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) method is being played an important role for the inspection of clinical microorganism as a rapid and the price reduction. Mass spectra obtained by measuring become points of identification whether the peak pattern match any species mass spectral pattern. We currently use MALDI-TOF MS for rapid and accurate diagnosis of inactivated reference and clinical isolates of Mycobacterium because of the improved pretreatment techniques compared with former inspection methods that pose a higher risk of infection to the operator. The identification matching rate of score value (SV) peak pattern spectra was compared with that of conventional methods such as strain diffusion/amplification. Also, cultures were examined after a fixed number of days. Compared with the initial inspection technique, the pretreatment stage of current MALDI-TOF MS inspection techniques can improve the analysis of inactivated acid-fast bacteria that are often used as inspection criteria strains of clinical isolates. Next, we compared the concordance rate for identification between MALDI-TOF MS and conventional methods such as diffusion/amplification by comparison of peak pattern spectra and evaluated SV spectra to identify differences in the culture media after the retention period. In examination of 158 strains of clinical isolated Mycobacterium tuberculosis complex (MTC), the identification coincidence rate in the genus level in a matching pattern was 99.4%, when the species level was included 94.9%. About 37 strains of nontuberculous mycobacteria (NTM), the identification coincidence rate in the genus level was 94.6%. M. bovis BCG (Tokyo strain) in the reference strain was judged by the matching pattern to be MTC, and it suggested that they are M. tuberculosis and affinity species with high DNA homology. Nontuberculous mycobacterial M. gordonae strain JATA 33-01 shared peak pattern spectra, excluding the isolates, with each clinically isolated strain. However, the mass spectra of six M. gordonae clinical isolates suggested polymorphisms with similar mass-to-charge ratios compared with those of the reference strains. The peak pattern spectra of the clinical isolates and reference strains, excluding the NTM M. gordonae strain JATA33-01, were consistent with the peak pattern characteristics of each isolate. However, a comparison between the peak patterns of the reference strains and those of the six clinically isolated M. gordonae strains revealed a similar mass-to-charge ratio, which may indicate few polymorphisms. The SV spectrum of the improved inspection technique showed no fidelity, but it was acceptable after days of culture as indicated by the decrease in SV (0.3 degree). Also, the reproducibility of this method was good, but no difference was observed from the SV of the improved inspection technique, which decreased by approximately 0.3 because of the number of days of culture storage. In addition, expansion of the database and dissemination of regional specificity by genotype analysis of clinical isolates was relevant to the accumulated data, as expected. In future studies, the relevance and regional specificity of clinical isolates by genotype analysis can be determined by stacking the solid media and database penetration.

Co-colonisation with Aspergillus fumigatus and Pseudomonas aeruginosa is associated with poorer health in cystic fibrosis patients: an Irish registry analysis.

PubMed

Reece, Emma; Segurado, Ricardo; Jackson, Abaigeal; McClean, Siobhán; Renwick, Julie; Greally, Peter

2017-04-21

Pulmonary infection is the main cause of death in cystic fibrosis (CF). Aspergillus fumigatus (AF) and Pseudomonas aeruginosa (PA) are the most prevalent fungal and bacterial pathogens isolated from the CF airway, respectively. Our aim was to determine the effect of different colonisation profiles of AF and PA on the clinical status of patients with CF. A retrospective analysis of data from the Cystic Fibrosis Registry of Ireland from 2013 was performed to determine the effect of intermittent and persistent colonisation with AF or PA or co-colonisation with both microorganisms on clinical outcome measures in patients with CF. Key outcomes measured included forced expiratory volume in one second (FEV 1 ), number of hospitalisations, respiratory exacerbations and antimicrobials prescribed, and complications of CF, including CF related diabetes (CFRD) and allergic bronchopulmonary aspergillosis (ABPA). The prevalence of AF and PA colonisation were 11% (5% persistent, 6% intermittent) and 31% (19% persistent, 12% intermittent) in the Irish CF population, respectively. Co-colonisation with both pathogens was associated with a 13.8% reduction in FEV 1 (p = 0.016), higher levels of exacerbations (p = 0.042), hospitalisations (p = 0.023) and antimicrobial usage (p = 0.014) compared to non-colonised patients and these clinical outcomes were comparable to those persistently colonised with PA. Intermittent and persistent AF colonisation were not associated with poorer clinical outcomes or ABPA. Patients with persistent PA had a higher prevalence of CFRD diagnosis (p = 0.012). CF patients co-colonised with AF and PA had poor clinical outcomes comparable to patients persistently colonised with PA, emphasising the clinical significance of co-colonisation with these microorganisms.

Clinical Marine Toxicology: A European Perspective for Clinical Toxicologists and Poison Centers

PubMed Central

Schmitt, Corinne; de Haro, Luc

2013-01-01

Clinical marine toxicology is a rapidly changing area. Many of the new discoveries reported every year in Europe involve ecological disturbances—including global warming—that have induced modifications in the chorology, behavior, and toxicity of many species of venomous or poisonous aquatic life including algae, ascidians, fish and shellfish. These changes have raised a number of public issues associated, e.g., poisoning after ingestion of contaminated seafood, envenomation by fish stings, and exposure to harmful microorganism blooms. The purpose of this review of medical and scientific literature in marine toxicology is to highlight the growing challenges induced by ecological disturbances that confront clinical toxicologists during the everyday job in the European Poison Centers. PMID:23917333

Free software to analyse the clinical relevance of drug interactions with antiretroviral agents (SIMARV®) in patients with HIV/AIDS.

PubMed

Giraldo, N A; Amariles, P; Monsalve, M; Faus, M J

Highly active antiretroviral therapy has extended the expected lifespan of patients with HIV/AIDS. However, the therapeutic benefits of some drugs used simultaneously with highly active antiretroviral therapy may be adversely affected by drug interactions. The goal was to design and develop a free software to facilitate analysis, assessment, and clinical decision making according to the clinical relevance of drug interactions in patients with HIV/AIDS. A comprehensive Medline/PubMed database search of drug interactions was performed. Articles that recognized any drug interactions in HIV disease were selected. The publications accessed were limited to human studies in English or Spanish, with full texts retrieved. Drug interactions were analyzed, assessed, and grouped into four levels of clinical relevance according to gravity and probability. Software to systematize the information regarding drug interactions and their clinical relevance was designed and developed. Overall, 952 different references were retrieved and 446 selected; in addition, 67 articles were selected from the citation lists of identified articles. A total of 2119 pairs of drug interactions were identified; of this group, 2006 (94.7%) were drug-drug interactions, 1982 (93.5%) had an identified pharmacokinetic mechanism, and 1409 (66.5%) were mediated by enzyme inhibition. In terms of clinical relevance, 1285 (60.6%) drug interactions were clinically significant in patients with HIV (levels 1 and 2). With this information, a software program that facilitates identification and assessment of the clinical relevance of antiretroviral drug interactions (SIMARV ® ) was developed. A free software package with information on 2119 pairs of antiretroviral drug interactions was designed and developed that could facilitate analysis, assessment, and clinical decision making according to the clinical relevance of drug interactions in patients with HIV/AIDS. Copyright © 2016 Elsevier Inc. All rights reserved.

Finding New Enzymes from Bacterial Physiology: A Successful Approach Illustrated by the Detection of Novel Oxidases in Marinomonas mediterranea

PubMed Central

Sanchez-Amat, Antonio; Solano, Francisco; Lucas-Elío, Patricia

2010-01-01

The identification and study of marine microorganisms with unique physiological traits can be a very powerful tool discovering novel enzymes of possible biotechnological interest. This approach can complement the enormous amount of data concerning gene diversity in marine environments offered by metagenomic analysis, and can help to place the activities associated with those sequences in the context of microbial cellular metabolism and physiology. Accordingly, the detection and isolation of microorganisms that may be a good source of enzymes is of great importance. Marinomonas mediterranea, for example, has proven to be one such useful microorganism. This Gram-negative marine bacterium was first selected because of the unusually high amounts of melanins synthesized in media containing the amino acid l-tyrosine. The study of its molecular biology has allowed the cloning of several genes encoding oxidases of biotechnological interest, particularly in white and red biotechnology. Characterization of the operon encoding the tyrosinase responsible for melanin synthesis revealed that a second gene in that operon encodes a protein, PpoB2, which is involved in copper transfer to tyrosinase. This finding made PpoB2 the first protein in the COG5486 group to which a physiological role has been assigned. Another enzyme of interest described in M. mediterranea is a multicopper oxidase encoding a membrane-associated enzyme that shows oxidative activity on a wide range of substrates typical of both laccases and tyrosinases. Finally, an enzyme very specific for l-lysine, which oxidises this amino acid in epsilon position and that has received a new EC number (1.4.3.20), has also been described for M. mediterranea. Overall, the studies carried out on this bacterium illustrate the power of exploring the physiology of selected microorganisms to discover novel enzymes of biotechnological relevance. PMID:20411113

Detection of bovine mastitis pathogens by loop-mediated isothermal amplification and an electrochemical DNA chip.

PubMed

Kawai, Kazuhiro; Inada, Mika; Ito, Keiko; Hashimoto, Koji; Nikaido, Masaru; Hata, Eiji; Katsuda, Ken; Kiku, Yoshio; Tagawa, Yuichi; Hayashi, Tomohito

2017-12-22

Bovine mastitis causes significant economic losses in the dairy industry. Effective prevention of bovine mastitis requires an understanding of the infection status of a pathogenic microorganism in a herd that has not yet shown clinical signs of mastitis and appropriate treatment specific for the pathogenic microorganism. However, bacterial identification by culture has drawbacks in that the sensitivity may be low and the procedure can be complex. In this study, we developed a genetic detection method to identify mastitis pathogens using a simple and highly sensitive electrochemical DNA chip which can specifically detect bacterial DNA in milk specimens. First, we selected microorganisms belonging to 12 families and/or genera associated with mastitis for which testing should be performed. Next, we optimized the conditions for amplifying microorganism DNA by loop-mediated isothermal amplification (LAMP) using 32 primers and the use of a DNA chip capable of measuring all pathogens simultaneously. Sample detection could be completed in just a few hours using this method. Comparison of the results obtained with our DNA chip method and those obtained by bacterial culture verified that when the culture method was set to 100%, the total positive concordance rate of the DNA chip was 85.0% and the total negative concordance rate was 86.9%. Furthermore, the proposed method allows both rapid and highly sensitive detection of mastitis pathogens. We believe that this method will contribute to the development of an effective mastitis control program.

Detection of bovine mastitis pathogens by loop-mediated isothermal amplification and an electrochemical DNA chip

PubMed Central

KAWAI, Kazuhiro; INADA, Mika; ITO, Keiko; HASHIMOTO, Koji; NIKAIDO, Masaru; HATA, Eiji; KATSUDA, Ken; KIKU, Yoshio; TAGAWA, Yuichi; HAYASHI, Tomohito

2017-01-01

Bovine mastitis causes significant economic losses in the dairy industry. Effective prevention of bovine mastitis requires an understanding of the infection status of a pathogenic microorganism in a herd that has not yet shown clinical signs of mastitis and appropriate treatment specific for the pathogenic microorganism. However, bacterial identification by culture has drawbacks in that the sensitivity may be low and the procedure can be complex. In this study, we developed a genetic detection method to identify mastitis pathogens using a simple and highly sensitive electrochemical DNA chip which can specifically detect bacterial DNA in milk specimens. First, we selected microorganisms belonging to 12 families and/or genera associated with mastitis for which testing should be performed. Next, we optimized the conditions for amplifying microorganism DNA by loop-mediated isothermal amplification (LAMP) using 32 primers and the use of a DNA chip capable of measuring all pathogens simultaneously. Sample detection could be completed in just a few hours using this method. Comparison of the results obtained with our DNA chip method and those obtained by bacterial culture verified that when the culture method was set to 100%, the total positive concordance rate of the DNA chip was 85.0% and the total negative concordance rate was 86.9%. Furthermore, the proposed method allows both rapid and highly sensitive detection of mastitis pathogens. We believe that this method will contribute to the development of an effective mastitis control program. PMID:29093278

Microorganism-induced exacerbations in atopic dermatitis: a possible preventive role for vitamin D?

PubMed

Benetti, Cecilia; Piacentini, Giorgio L; Capristo, Carlo; Boner, Attilio L; Peroni, Diego G

2015-01-01

Atopic dermatitis (AD) is a common skin disease characterized by a complex pathogenesis not completely understood despite numerous studies to date. The clinical patterns result from interactions between genetic disorders determining abnormalities in the epidermis differentiation complex, modification of the cutaneous barrier, and dysfunction of immune responses. Several studies have shown that an alteration of the skin barrier combined with immune dysfunction is important for the onset, maintenance, and risk of exacerbations of the disease. In recent years, new aspects regarding the pathogenesis of the disease, such as the effects of vitamin D (VD) on immunity at the skin level and the role of certain microorganisms (particularly Staphylococcus and Malassezia species) on eczema exacerbations, have been evaluated. This article provides an overview of the evidences supporting the link between VD (deficiency) and microorganisms (skin colonization/sensitization) in AD pathogenesis, based on comprehensive review of the literature. By considering different aspects of disease, it might be possible to improve our understanding, particularly in those patients refractory to conventional treatments. An electronic research strategy was used to search in Medline Pub-Med Library using as research words AD, exacerbation, VD, Staphylococcus aureus (SA), and Malassezia. The results were downloaded and analyzed for systematic review. Few studies actually consider the relationship between VD deficiency (VDD), AD, and SA and Malassezia, but many suggest a correlation between these factors. VDs play a major role against microorganisms in the development of AD and should be considered when treating patients.

Clinicomanometric factors associated with clinically relevant esophagogastric junction outflow obstruction from the Sandhill high-resolution manometry system.

PubMed

Song, B G; Min, Y W; Lee, H; Min, B-H; Lee, J H; Rhee, P-L; Kim, J J

2018-03-01

Integrated relaxation pressure (IRP) is a key metric for diagnosing esophagogastric junction outflow obstruction (EGJOO). However, its normal value might be different according to the manufacturer of high-resolution manometry (HRM). This study aimed to investigate optimal value of IRP for diagnosing EGJOO in Sandhill HRM and to find clinicomanometric variables to segregate clinically relevant EGJOO. We analyzed 262 consecutive subjects who underwent HRM between June 2011 and December 2016 showing elevated median IRP (> 15 mm Hg) but did not satisfy criteria for achalasia. Clinically relevant subjects were defined as follows: (i) subsequent HRM met achalasia criteria during follow-up (early achalasia); (ii) Eckardt score was decreased at least two points without exceeding a score of 3 after pneumatic dilatation (variant achalasia); and (iii) significant passage disturbance on esophagogram without structural abnormality (possible achalasia). Seven subjects were clinically relevant, including two subjects with early achalasia, four subjects with variant achalasia, and one subject with possible achalasia. All clinically relevant subjects had IRP 20 mm Hg or above. Among subjects (n = 122) with IRP 20 mm Hg or more, clinically relevant group (n = 7) had significantly higher rate of dysphagia (100% vs 24.3%, P < .001) and compartmentalized pressurization (85.7% vs 21.7%, P = .001) compared to clinically non-relevant group (n = 115). Our results suggest that IRP of 20 mm Hg or higher could segregate clinically relevant subjects showing EGJOO in Sandhill HRM. Additionally, if subjects have both dysphagia and compartmentalized pressurization, careful follow-up is essential. © 2017 John Wiley & Sons Ltd.

Microbial Forensics: A Scientific Assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keim, Paul

2003-02-17

Microorganisms have been used as weapons in criminal acts, most recently highlighted by the terrorist attack using anthrax in the fall of 2001. Although such ''biocrimes'' are few compared with other crimes, these acts raise questions about the ability to provide forensic evidence for criminal prosecution that can be used to identify the source of the microorganisms used as a weapon and, more importantly, the perpetrator of the crime. Microbiologists traditionally investigate the sources of microorganisms in epidemiological investigations, but rarely have been asked to assist in criminal investigations. A colloquium was convened by the American Academy of Microbiology inmore » Burlington, Vermont, on June 7-9, 2002, in which 25 interdisciplinary, expert scientists representing evolutionary microbiology, ecology, genomics, genetics, bioinformatics, forensics, chemistry, and clinical microbiology, deliberated on issues in microbial forensics. The colloquium's purpose was to consider issues relating to microbial forensics, which included a detailed identification of a microorganism used in a bioattack and analysis of such a microorganism and related materials to identify its forensically meaningful source--the perpetrators of the bioattack. The colloquium examined the application of microbial forensics to assist in resolving biocrimes with a focus on what research and education are needed to facilitate the use of microbial forensics in criminal investigations and the subsequent prosecution of biocrimes, including acts of bioterrorism. First responders must consider forensic issues, such as proper collection of samples to allow for optimal laboratory testing, along with maintaining a chain of custody that will support eventual prosecution. Because a biocrime may not be immediately apparent, a linkage must be made between routine diagnosis, epidemiological investigation, and criminal investigation. There is a need for establishing standard operating procedures and training to meet these initial challenges so as minimize disturbance of the evidence. While epidemiology and forensics are similar sciences with similar goals when applied to biocrimes, forensics has additional and more stringent requirements. Maintaining a chain of custody on evidentiary samples is one example of an extra requirement imposed on an investigation of a biocrime. Another issue is the intent in microbial forensics to identify a bioattack organism in greatest detail. If possible, forensic investigations will strive to identify the precise strain and substrain, rather than just to the species level, which might be sufficient in an epidemiological investigation. Although multiple groups have developed lists of bioterrorism target pathogens, these lists are too narrow. An expansion of microorganisms relevant to food and water threats should be considered. Computerized networks should be established to track infectious disease outbreaks in real time. These systems could alert public health and agricultural officials to the existence of a potential bioattack earlier than simply waiting for a report of a suspicious cluster of similar patients. Once a biocrime is suspected, a wide variety of methods are available to identify the microorganism used in the bioattack and to analyze features that might lead to the source of the event. A multi-pronged approach to such an investigation may be preferable, using many available methods-ranging from genomics to sequencing to physiology to analysis of substances in the sample. Microbial forensics will be most effective if there is sufficient basic scientific information concerning microbial genetics, evolution, physiology, and ecology. Strain subtyping analysis will be difficult to interpret if we do not understand some of the basic evolutionary mechanisms and population diversity of pathogens. Phenotypic features associated with evidentiary pathogens also may provide investigative leads, but full exploitation of these features can only be accomplished if we understand basic principles that control microbial physiology. Finally, the more precise and refined a microbial forensic system becomes, the more proper guidelines for handling and storage will be defined. Thus, improper dissemination or use of the pathogens will be reduced and inadvertent release will be minimized. An additional outcome of establishing these guidelines or rules is that the legitimate investigator will be protected to pursue research without unnecessary intrusion. Colloquium participants identified a variety of needs and directions in the following areas: sample handling and collection, detection, research direction, data access, QA/QC, and education. General recommendations are provided for direction or insight for the scientific community, law enforcement community, legal community, and the public.« less

Applications of Flow Cytometry to Clinical Microbiology†

PubMed Central

Álvarez-Barrientos, Alberto; Arroyo, Javier; Cantón, Rafael; Nombela, César; Sánchez-Pérez, Miguel

2000-01-01

Classical microbiology techniques are relatively slow in comparison to other analytical techniques, in many cases due to the need to culture the microorganisms. Furthermore, classical approaches are difficult with unculturable microorganisms. More recently, the emergence of molecular biology techniques, particularly those on antibodies and nucleic acid probes combined with amplification techniques, has provided speediness and specificity to microbiological diagnosis. Flow cytometry (FCM) allows single- or multiple-microbe detection in clinical samples in an easy, reliable, and fast way. Microbes can be identified on the basis of their peculiar cytometric parameters or by means of certain fluorochromes that can be used either independently or bound to specific antibodies or oligonucleotides. FCM has permitted the development of quantitative procedures to assess antimicrobial susceptibility and drug cytotoxicity in a rapid, accurate, and highly reproducible way. Furthermore, this technique allows the monitoring of in vitro antimicrobial activity and of antimicrobial treatments ex vivo. The most outstanding contribution of FCM is the possibility of detecting the presence of heterogeneous populations with different responses to antimicrobial treatments. Despite these advantages, the application of FCM in clinical microbiology is not yet widespread, probably due to the lack of access to flow cytometers or the lack of knowledge about the potential of this technique. One of the goals of this review is to attempt to mitigate this latter circumstance. We are convinced that in the near future, the availability of commercial kits should increase the use of this technique in the clinical microbiology laboratory. PMID:10755996

The effect of probiotics on CD4 counts among people living with HIV: a systematic review.

PubMed

Miller, H; Ferris, R; Phelps, B R

2016-06-01

Probiotics are defined by the WHO as 'live microorganisms which when administered in adequate amounts confer a health benefit on the host'. Ongoing research has shown probiotics provide benefits to humans, including protection and restoration of the gastrointestinal and other mucosal tracts. As human immunodeficiency virus (HIV) activates gut-associated lymphoid tissue (GALT), several studies have investigated the effect of probiotics on CD4 cell count and related outcomes among those living with HIV. These studies are summarised here. Manuscripts were identified using the search terms 'probiotics', 'synbiotics', 'HIV', and 'CD4', and were reviewed for relevance and inclusion of CD4 count as an immunologic endpoint. Bibliographies of relevant manuscripts were also reviewed for additional studies matching inclusion and exclusion criteria. The search yielded 91 results; 13 included relevant outcomes. Seven of these studies produced beneficial CD4 outcomes, while the remaining 6 reported on insignificant beneficial or negative CD4 outcomes. The studies summarised here collectively suggest that daily consumption of probiotics over a prolonged period of time may improve CD4 count in people living with HIV.

Lactobacillemia: an emerging cause of infection in both the immunocompromised and the immunocompetent host.

PubMed Central

Antony, S. J.

2000-01-01

The bacterium, lactobacillus, is found in the mucosal surfaces of the mouth and the gastrointestinal and genitourinary tracts. There have been increasing reports of the micro-organism being a cause of serious infection in immunocompromised individuals. This article reviews the clinical presentation, laboratory characteristics and treatment of patients with lactobacillemia. PMID:10800296

Natural Clostridium botulinum Type C Toxicosis in a Group of Cats

PubMed Central

Elad, D.; Yas-Natan, E.; Aroch, I.; Shamir, M. H.; Kleinbart, S.; Hadash, D.; Chaffer, M.; Greenberg, K.; Shlosberg, A.

2004-01-01

Clinical signs of botulism were observed in a group of eight cats, four of which died, after being fed pelican carrion. Clostridium botulinum type C was isolated from one cat. The microorganism and its toxin were found in the pelican. This is apparently the first report of natural botulism in cats. PMID:15528757

[Infrastructure and adherence to hand hygiene: challenges to patient safety].

PubMed

Bathke, Janaína; de Cunico, Priscila Almeida; Maziero, Eliane Cristina Sanches; Cauduro, Fernanda Leticia Frates; Sarquis, Leila Maria Mansano; de Cruz, Elaine Drehmer Almeida

2013-06-01

Considering the importance of hands in the chain of transmission of microorganisms, this observational research investigated the material infrastructure and compliance of hand hygiene in an intensive care unit in the south of Brazil in 2010. The data was collected by direct non-participant observation and through the use of self-administered questionnaires to be completed by the 39 participants, which was analyzed with the assistance of the chi2 Test, descriptive statistics and quantitative discourse analysis. Although health professionals overestimate compliance rates, recognize the practice as relevant to the prevention of infection and refer there are no impeding factors, of the 1,277 opportunities observed, compliance was 26% and significantly lower before patient contact and the use of aseptic procedures than after patient contact: infrastructure was shown to be deficient. The results indicate risk to patient safety, and thus, the planning of corrective actions to promote hand washing is relevant.

Myasthenia gravis and infectious disease.

PubMed

Gilhus, Nils Erik; Romi, Fredrik; Hong, Yu; Skeie, Geir Olve

2018-01-25

Myasthenia gravis (MG) is an autoimmune disease with muscular weakness as the only symptom, and often with immunosuppressive treatment. All these aspects could have relevance for the risk of infections as well as their prophylactic and curative treatment. This is a review article, where Web of Science has been searched for relevant key words and key word combinations. Full papers were selected first by title and then by abstract. MG can be triggered and worsened by infections. No virus or other pathogen has been proven to have a specific link to MG. Treatment with immunosuppressive drugs and thymectomy implies a slightly increased risk for infections. Infections should be actively treated, but a few antibiotics are avoided due to potential interference with neuromuscular transmission. Hospitalization and intensive care may be necessary during infections because of MG deterioration and risk of insufficient respiration. Vaccinations are generally recommended in MG, but live microorganisms should be avoided if possible in immunosuppressed patients.

The Effect of Pistacia atlantica Var. mutica Mouthwash on Dental Plaque Bacteria and Subgingival Microorganisms: a Randomized and Controlled Triple-blind Study.

PubMed

Arami, S; Mojaddadi, M A; Pourabbas, R; Chitsaz, M T; Delazar, A; Mobayen, H

2015-09-01

Dental plaque is a well-documented etiologic factor for periodontal diseases. While chlorhexidine (CHX) is the gold-standard agent for treating dental plaques, undesirable side effects are often found after continuous use of the mouthwash. Therefore, this single-center, randomized, triple-blinded and clinical trial was undertaken to evaluate the efficacy of Pistacia atlantica Var. mutica extract mouthwash on de novo dental plaque bacteria and subgingival microorganisms compared to CHX on a total of 28 patients. The mean aerobic plaque bacterial count of patients at baseline was 2.17 × 10(6). After 4 days of treatment, there were statistically significant decreases in the mean aerobic bacteria in the patients who received P. atlantica and/or CHX (7.25 × 10(4), p = 0.006) and (9.91 × 10(3), p = 0.002), respectively, compared to the patients who received the placebo (6.26 × 10(5)). This study showed that P. atlantica mouthwash is effective against gingival microorganisms. Because of its reduced side effects, P. atlantica mouthwash may be a good alternative choice for patients. © Georg Thieme Verlag KG Stuttgart · New York.

Pelvic inflammatory disease.

PubMed

Soper, David E

2010-08-01

Pelvic inflammatory disease (PID) is an infection-caused inflammatory continuum from the cervix to the peritoneal cavity. Most importantly, it is associated with fallopian tube inflammation, which can lead to infertility, ectopic pregnancy, and chronic pelvic pain. The microbial etiology is linked to sexually transmitted microorganisms, including Chlamydia trachomatis, Neisseria gonorrheae, Mycoplasma genitalium, and bacterial vaginosis-associated microorganisms, predominantly anaerobes. Pelvic pain and fever are commonly absent in women with confirmed PID. Clinicians should consider milder symptoms such as abnormal vaginal discharge, metrorrhagia, postcoital bleeding, and urinary frequency as potential symptoms associated with the disease, particularly in women at risk of sexually transmitted infection. The diagnosis of PID is based on the findings of lower genital tract inflammation associated with pelvic organ tenderness. The outpatient treatment of mild-to-moderate PID should include tolerated antibiotic regimens with activity against the commonly isolated microorganisms associated with PID and usually consists of an extended spectrum cephalosporin in conjunction with either doxycycline or azithromycin. Clinically severe PID should prompt hospitalization and imaging to rule out a tuboovarian abscess. Parenteral broad-spectrum antibiotic therapy with activity against a polymicrobial flora, particularly gram-negative aerobes and anaerobes, should be implemented. Screening for and treatment of Chlamydia infection can prevent PID.

Bacterial Hyaluronidase Promotes Ascending GBS Infection and Preterm Birth

PubMed Central

Vornhagen, Jay; Quach, Phoenicia; Boldenow, Erica; Merillat, Sean; Whidbey, Christopher; Ngo, Lisa Y.; Adams Waldorf, K. M.

2016-01-01

ABSTRACT Preterm birth increases the risk of adverse birth outcomes and is the leading cause of neonatal mortality. A significant cause of preterm birth is in utero infection with vaginal microorganisms. These vaginal microorganisms are often recovered from the amniotic fluid of preterm birth cases. A vaginal microorganism frequently associated with preterm birth is group B streptococcus (GBS), or Streptococcus agalactiae. However, the molecular mechanisms underlying GBS ascension are poorly understood. Here, we describe the role of the GBS hyaluronidase in ascending infection and preterm birth. We show that clinical GBS strains associated with preterm labor or neonatal infections have increased hyaluronidase activity compared to commensal strains obtained from rectovaginal swabs of healthy women. Using a murine model of ascending infection, we show that hyaluronidase activity was associated with increased ascending GBS infection, preterm birth, and fetal demise. Interestingly, hyaluronidase activity reduced uterine inflammation but did not impact placental or fetal inflammation. Our study shows that hyaluronidase activity enables GBS to subvert uterine immune responses, leading to increased rates of ascending infection and preterm birth. These findings have important implications for the development of therapies to prevent in utero infection and preterm birth. PMID:27353757

Emerging Technologies for the Clinical Microbiology Laboratory

PubMed Central

Buchan, Blake W.

2014-01-01

SUMMARY In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory. PMID:25278575

Trustworthiness and relevance in web-based clinical question answering.

PubMed

Cruchet, Sarah; Boyer, Célia; van der Plas, Lonneke

2012-01-01

Question answering systems try to give precise answers to a user's question posed in natural language. It is of utmost importance that the answers returned are relevant to the user's question. For clinical QA, the trustworthiness of answers is another important issue. Limiting the document collection to certified websites helps to improve the trustworthiness of answers. On the other hand, limited document collections are known to harm the relevancy of answers. We show, however, in a comparative evaluation, that promoting trustworthiness has no negative effect on the relevance of the retrieved answers in our clinical QA system. On the contrary, the answers found are in general more relevant.

Studies on the antimicrobial activity and brine shrimp toxicity of Zeyheria tuberculosa (Vell.) Bur. (Bignoniaceae) extracts and their main constituents

PubMed Central

Bastos, Maria Lysete A; Lima, Maria Raquel F; Conserva, Lucia M; Andrade, Vânia S; Rocha, Eliana MM; Lemos, Rosangela PL

2009-01-01

Background Due to the indiscriminate use of antimicrobial drugs, the emergence of human pathogenic microorganisms resistant to major classes of antibiotics has been increased and has caused many clinical problems in the treatment of infectious diseases. Thus, the aim of this study was to evaluate for the first time the in vitro antimicrobial activity and brine shrimp lethality of extracts and isolated compounds from Zeyheria tuberculosa (Vell.) Bur., a species used in Brazilian folk medicine for treatment of cancer and skin diseases. Methods Using the disc diffusion method, bioautography assay and brine shrimp toxicity test (Artemia salina Leach), we studied the antimicrobial activity and lethality of extracts and isolated compounds against three microorganisms strains, including Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) bacteria and yeasts (Candida albicans). Results In this study, the extracts inhibited S. aureus (8.0 ± 0.0 to 14.0 ± 0.0 mm) and C. albicans (15.3 ± 0.68 to 25.6 ± 0.4 mm) growth. In the brine shrimp test, only two of them showed toxic effects (LC50 29.55 to 398.05 μg/mL) and some extracts were non-toxic or showed weak lethality (LC50 705.02 to > 1000 μg/mL). From these extracts, four flavones [5,6,7,8-tetramethoxyflavone (1), 5,6,7-trimethoxyflavone (2), 4'-hydroxy-5,6,7,8-tetramethoxyflavone (3), and 4'-hydroxy-5,6,7-trimethoxyflavone (4)] were isolated through bioassay-guided fractionation and identified based on the 1D and 2D NMR spectral data. By bioautography assays, compounds 1 [S. aureus (16.0 ± 0.0 mm) and C. albicans (20.0 ± 0.0 mm)] and 3 [S. aureus (10.3 ± 0.6 mm) and C. albicans (19.7 ± 0.6 mm)] inhibited both microorganisms while 2 inhibited only S. aureus (11.7 ± 0.6 mm). Compound 4 did not restrain the growth of any tested microorganism. Conclusion Our results showed that extracts and isolated flavones from Z. tuberculosa may be particularly useful against two pathogenic microorganisms, S. aureus and C. albicans. These results may justify the popular use this species since some fractions tested had antimicrobial activity and others showed significant toxic effects on brine shrimps. However, in order to evaluate possible clinical application in therapy of infectious diseases, further studies about the safety and toxicity of isolated compounds are needed. PMID:19450272

Identification of Lama glama as Reservoirs for Acinetobacter lwoffii

PubMed Central

Ledesma, Martín M.; Díaz, Ailén M.; Barberis, Claudia; Vay, Carlos; Manghi, Marcela A.; Leoni, Juliana; Castro, Marisa S.; Ferrari, Alejandro

2017-01-01

South American Camelids have an increasing relevance in local economies, worldwide. These animals are bred for their meat, fur and as companion and therapy animals. Thus, their sanitary status should be well-established. According to the OIE (World Organization for Animal Health), respiratory infections mainly produced by Pasteurella spp. have been reported for camelids. It has been stated that this microorganism causes a mild disease, although many authors report it is an important cause of mortality among alpacas. Nevertheless, the incidence of infection by Pasteurella spp. in camelids still needs to be investigated. The aim of the present study was to analyze the occurrence of nasopharyngeal colonization of Lama glama by respiratory bacteria, and to assess the usefulness of serological tests for clinical diagnosis. The colonization was studied by culture techniques carried out with material taken by nasopharyngeal swabs. Bacterial isolates were first phenotypically characterized and then identified by MALDI/TOF-MS. The presence of specific serum antibodies was studied by ELISA and Western blot. In the present work Pasteurella spp. was not found. Nevertheless, we report for the first time, the colonization of L. glama by bacteria of the Acinetobacter lwoffii, at a reliable level in 19.4% of the animals. Acinetobacter species are found in different environmental sources, as well as vegetables, animals, and humans, and their role in infections has recently gained relevance. The results presented herein contribute to a better understanding of the respiratory microbiota in camelids, and increase the knowledge about environmental distribution of Acinetobacter non-baumanii species. Given that these respiratory bacteria might be the cause of infection among cattle, and even humans, this report highlights the need for further research. PMID:28303121

Microbial endocrinology: Why the intersection of microbiology and neurobiology matters to poultry health.

PubMed

Villageliu, Daniel N; Lyte, Mark

2017-08-01

The union of microbiology and neurobiology has led to a revolution in the way we view the microbiome. Now recognized as important symbionts, the microorganisms which inhabit multiple niches in mammalian and avian (chicken) hosts, such as the intestinal tract and skin, serve and influence many important physiological functions. The realization that the gut microbiome serves as a kind of "microbial organ" has important implications for many areas of biology. In this paper advances in the field of microbial endocrinology which may hold relevance for the poultry industry are examined. © 2017 Poultry Science Association Inc.

[THE CLINICAL AND EPIDEMIOLOGICAL CHARACTERISTICS OF MALARIA CONCURRENT WITH OTHER INFECTIONS AND INVASIONS].

PubMed

Kondrashin, A V; Tokmalaev, A K; Morozov, E N; Morozova, L F

2016-01-01

The present review considers malaria infection concurrent with different species of helminths, bacterial and viral infections, as well as mixed malaria pathogens in the subtropical and tropical countries of the world, causing the clinical picture and epidemiological situation to be different. Malaria co-infections with different pathogenic micro-organisms, such as HIV, tuberculosis, viral hepatitides, and others, affect almost one third of the planet's population. It is known that people who are at risk for malaria may be also at risk for other parasitic and infectious diseases, most commonly helminthisms.

Clinical presentation, diagnosis and treatment of vulvovaginitis in girls: a current approach and review of the literature.

PubMed

Beyitler, İlke; Kavukcu, Salih

2017-04-01

Vulvovaginitis is the most common cause of gynecological complaints in children and young girls. Some of the factors which cause vulvovaginitis include hypoestrogenism, the anatomical proximity of rectum and delicate vulvar skin and vaginal mucosa. We made a literature search with Pubmed, Medline and Cochrane database from January 2002 to May 2015 in English language using the key words vulvovaginitis, children, clinical, diagnosis and treatment. Vulvovaginitis in girls is usually caused by non-specific factors and hygiene measures, bioyoghurt and avoidance of chemical irritants are generally useful. Weight control if necessary and prevention of voiding dysfunction are effective. Vaginal flora is important in girls and results should be interpreted with clinical features to decide whether an isolated microorganism is part of the normal microflora or is the cause of symptomatic vulvovaginitis. Specific treatment is generally considered in case of a detected pathogen microorganism. Isolation of a sexually transmitted organism requires further investigation. Persistent disease may not always indicate a foreign body but it must be taken into account. Girls and parents are encouraged psychologically in all steps of evaluation, diagnosis and treatment. Probiotics, nanotechnology and petroleum jelly are other important treatment options used in vulvovaginitis. In this review, we present current approach to the presentation and management of vulvovaginitis in childhood. This disorder requires a comprehensive evaluation in all steps of diagnosis, differential diagnosis and treatment.

The Challenging Diagnosis of Non-Community-Acquired Pneumonia in Non-Mechanically Ventilated Subjects: Value of Microbiological Investigation.

PubMed

Messika, Jonathan; Stoclin, Annabelle; Bouvard, Eric; Fulgencio, Jean-Pierre; Ridel, Christophe; Muresan, Ioan-Paul; Boffa, Jean-Jacques; Bachmeyer, Claude; Denis, Michel; Gounant, Valérie; Esteso, Adoracion; Loi, Valeria; Verdet, Charlotte; Prigent, Hélène; Parrot, Antoine; Fartoukh, Muriel

2016-02-01

Early recognition and an attempt at obtaining microbiological documentation are recommended in patients with non-community-acquired pneumonia (NCAP), whether hospital-acquired (HAP) or health care-associated (HCAP). We aimed to characterize the clinical features and microbial etiologies of NCAP to assess the impact of microbiological investigation on their management. This was a prospective 1-y study in a university hospital with 141 non-mechanically ventilated subjects suspected of having HAP (n = 110) or HCAP (n = 31). Clinical criteria alone poorly identified pneumonia (misdiagnosis in 50% of cases). Microbiological confirmation was achievable in 80 subjects (57%). Among 79 microorganisms isolated, 28 were multidrug-resistant aerobic Gram-negative bacilli and group III Enterobacteriaceae and 6 were methicillin-resistant Staphylococcus aureus. Multidrug-resistant aerobic Gram-negative bacilli accounted for one third of the microorganisms in early-onset HAP and for 50% in late-onset HAP. Methicillin-resistant S. aureus was most often recovered from subjects with HCAP. Inappropriate empirical antibiotics were administered to 36% of subjects with confirmed pneumonia. Forty subjects were admitted to the ICU, 13 (33%) of whom died. Overall, 39 subjects (28%) died in the hospital. Integrating the microbiological investigation in the complex clinical diagnostic workup of patients suspected of having NCAP is mandatory. Respiratory tract specimens should be obtained whenever possible for appropriate management. Copyright © 2016 by Daedalus Enterprises.

Efficacy of antimicrobial photodynamic therapy in the disinfection of acrylic denture surfaces: A systematic review.

PubMed

Varela Kellesarian, Sergio; Abduljabbar, Tariq; Vohra, Fahim; Malmstrom, Hans; Yunker, Michael; Varela Kellesarian, Tammy; Romanos, Georgios E; Javed, Fawad

2017-03-01

The aim of the present systematic review was to assess the efficacy of antimicrobial photodynamic therapy (aPDT) in the disinfection of acrylic denture surfaces. IN order to address the focused question: "Is aPDT more effective in decontaminating denture surfaces compared with traditional denture-disinfection techniques?" an electronic search without time or language restrictions was conducted up to November 2016 in indexed databases using different key words. The exclusion criteria included qualitative and/or quantitative reviews, case reports, case series, commentaries, letters to the editor, interviews, and updates. A total of 14 studies were included and processed for data extraction, out of which 1 study was a randomized clinical trial and 13 studies were performed in vitro. Results from 12 experimental studies reported that aPDT was effective in reducing bacteria and/or yeast cultured in single or multispecies biofilm growth on acrylic resin specimens. One experimental study reported selective microorganism reduction on acrylic resin after aPDT. One clinical randomized control trial reported that aPDT presented similar microorganism reduction compared with oral antifungal medication for the disinfection of denture surfaces. The role of aPDT in the disinfection of acrylic resin surfaces is unclear. From a clinical perspective further randomized control trials are needed to assess the efficacy of aPDT in the disinfection of acrylic resin surfaces. Copyright © 2016 Elsevier B.V. All rights reserved.

Reflections on relevance: Psychotherapy and Psychosomatics in 2004.

PubMed

Balon, Richard

2005-01-01

Relevance of an article is a highly desirable yet hardly predictable quality at the time of its publication. Article relevance is frequently measured by the impact factor of the journal where the article is published. Furthermore, impact factor, citation index and citation analysis are used as a measure of research progress and scientific wealth of a nation. The wisdom and significance of this approach to relevance is debatable and thus discussed here. In 2004, Psychotherapy and Psychosomatics published a variety of articles which, in the author's view, are clinically relevant. Several selected clinically relevant issues reviewed in this article include: the conceptualization of fibromyalgia as a stress disorder; the psychosocial impact and psychosocial interventions in cancer; the impact of alexithymia on patient care; the possible relationship between depression and nutrition (namely intake of folate and pyridoxal phosphate); the significance of hypercoagulability in panic-like anxiety; the questionable value of single isomer drugs, and the relevance and adequacy of clinimetrics versus psychometrics in clinical research. The reviewed issues seem to be relevant to clinical practice, research or both, but also to our critical thinking, and the critical review of the developments in psychiatry and psychology. Copyright 2005 S. Karger AG, Basel.

Challenges and opportunities of airborne metagenomics.

PubMed

Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

2015-05-06

Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans.

PubMed

Quatrini, Raquel; Jedlicki, Eugenia; Holmes, David S

2005-12-01

Commercial bioleaching of copper and the biooxidation of gold is a cost-effective and environmentally friendly process for metal recovery. A partial genome sequence of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans is available from two public sources. This information has been used to build preliminary models that describe how this microorganism confronts unusually high iron loads in the extremely acidic conditions (pH 2) found in natural environments and in bioleaching operations. A. ferrooxidans contains candidate genes for iron uptake, sensing, storage, and regulation of iron homeostasis. Predicted proteins exhibit significant amino acid similarity with known proteins from neutrophilic organisms, including conservation of functional motifs, permitting their identification by bioinformatics tools and allowing the recognition of common themes in iron transport across distantly related species. However, significant differences in amino acid sequence were detected in pertinent domains that suggest ways in which the periplasmic and outer membrane proteins of A. ferrooxidans maintain structural integrity and relevant protein-protein contacts at low pH. Unexpectedly, the microorganism also contains candidate genes, organized in operon-like structures that potentially encode at least 11 siderophore systems for the uptake of Fe(III), although it does not exhibit genes that could encode the biosynthesis of the siderophores themselves. The presence of multiple Fe(III) uptake systems suggests that A. ferrooxidans can inhabit aerobic environments where iron is scarce and where siderophore producers are present. It may also help to explain why it cannot tolerate high Fe(III) concentrations in bioleaching operations where it is out-competed by Leptospirillum species.

"Who owns your poop?": insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies.

PubMed

Hawkins, Alice K; O'Doherty, Kieran C

2011-10-07

While the social, ethical, and legal implications of biobanking and large scale data sharing are already complicated enough, they may be further compounded by research on the human microbiome. The human microbiome is the entire complement of microorganisms that exists in and on every human body. Currently most biobanks focus primarily on human tissues and/or associated data (e.g. health records). Accordingly, most discussions in the social sciences and humanities on these issues are focused (appropriately so) on the implications of biobanks and sharing data derived from human tissues. However, rapid advances in human microbiome research involve collecting large amounts of data on microorganisms that exist in symbiotic relationships with the human body. Currently it is not clear whether these microorganisms should be considered part of or separate from the human body. Arguments can be made for both, but ultimately it seems that the dichotomy of human versus non-human and self versus non-self inevitably breaks down in this context. This situation has the potential to add further complications to debates on biobanking. In this paper, we revisit some of the core problem areas of privacy, consent, ownership, return of results, governance, and benefit sharing, and consider how they might be impacted upon by human microbiome research. Some of the issues discussed also have relevance to other forms of microbial research. Discussion of these themes is guided by conceptual analysis of microbiome research and interviews with leading Canadian scientists in the field.

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

PubMed Central

Royo-Llonch, Marta; Ferrera, Isabel; Cornejo-Castillo, Francisco M.; Sánchez, Pablo; Salazar, Guillem; Stepanauskas, Ramunas; González, José M.; Sieracki, Michael E.; Speich, Sabrina; Stemmann, Lars; Pedrós-Alió, Carlos; Acinas, Silvia G.

2017-01-01

Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms. PMID:28790980

Long-term effects of sulfidized silver nanoparticles in sewage sludge on soil microflora.

PubMed

Kraas, Marco; Schlich, Karsten; Knopf, Burkhard; Wege, Franziska; Kägi, Ralf; Terytze, Konstantin; Hund-Rinke, Kerstin

2017-12-01

The use of silver nanoparticles (AgNPs) in consumer products such as textiles leads to their discharge into wastewater and consequently to a transfer of the AgNPs to soil ecosystems via biosolids used as fertilizer. In urban wastewater systems (e.g., sewer, wastewater treatment plant [WWTP], anaerobic digesters) AgNPs are efficiently converted into sparingly soluble silver sulfides (Ag 2 S), mitigating the toxicity of the AgNPs. However, long-term studies on the bioavailability and effects of sulfidized AgNPs on soil microorganisms are lacking. Thus we investigated the bioavailability and long-term effects of AgNPs (spiked in a laboratory WWTP) on soil microorganisms. Before mixing the biosolids into soil, the sludges were either anaerobically digested or directly dewatered. The effects on the ammonium oxidation process were investigated over 140 d. Transmission electron microscopy (TEM) suggested an almost complete sulfidation of the AgNPs analyzed in all biosolid samples and in soil, with Ag 2 S predominantly detected in long-term incubation experiments. However, despite the sulfidation of the AgNPs, soil ammonium oxidation was significantly inhibited, and the degree of inhibition was independent of the sludge treatment. The results revealed that AgNPs sulfidized under environmentally relevant conditions were still bioavailable to soil microorganisms. Consequently, Ag 2 S may exhibit toxic effects over the long term rather than the short term. Environ Toxicol Chem 2017;36:3305-3313. © 2017 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. © 2017 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc. on behalf of SETAC.

"Who owns your poop?": insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies

PubMed Central

2011-01-01

Background While the social, ethical, and legal implications of biobanking and large scale data sharing are already complicated enough, they may be further compounded by research on the human microbiome. Discussion The human microbiome is the entire complement of microorganisms that exists in and on every human body. Currently most biobanks focus primarily on human tissues and/or associated data (e.g. health records). Accordingly, most discussions in the social sciences and humanities on these issues are focused (appropriately so) on the implications of biobanks and sharing data derived from human tissues. However, rapid advances in human microbiome research involve collecting large amounts of data on microorganisms that exist in symbiotic relationships with the human body. Currently it is not clear whether these microorganisms should be considered part of or separate from the human body. Arguments can be made for both, but ultimately it seems that the dichotomy of human versus non-human and self versus non-self inevitably breaks down in this context. This situation has the potential to add further complications to debates on biobanking. Summary In this paper, we revisit some of the core problem areas of privacy, consent, ownership, return of results, governance, and benefit sharing, and consider how they might be impacted upon by human microbiome research. Some of the issues discussed also have relevance to other forms of microbial research. Discussion of these themes is guided by conceptual analysis of microbiome research and interviews with leading Canadian scientists in the field. PMID:21982589

Production of bulk chemicals via novel metabolic pathways in microorganisms.

PubMed

Shin, Jae Ho; Kim, Hyun Uk; Kim, Dong In; Lee, Sang Yup

2013-11-01

Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing 'big' biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources. Copyright © 2012 Elsevier Inc. All rights reserved.

Diagnostic value of clinical tests for degenerative rotator cuff disease in medical practice.

PubMed

Lasbleiz, S; Quintero, N; Ea, K; Petrover, D; Aout, M; Laredo, J D; Vicaut, E; Bardin, T; Orcel, P; Beaudreuil, J

2014-06-01

To assess the diagnostic value of clinical tests for degenerative rotator cuff disease (DRCD) in medical practice. Patients with DRCD were prospectively included. Eleven clinical tests of the rotator cuff have been done. One radiologist performed ultrasonography (US) of the shoulder. Results of US were expressed as normal tendon, tendinopathy or full-thickness tear (the reference). For each clinical test and each US criteria, sensitivity, specificity, negative predictive value and positive predictive value, accuracy, negative likelihood ratio (NLR) and positive likelihood ratio (PLR) were calculated. Clinical relevance was defined as PLR ≥2 and NLR ≤0.5. For 35 patients (39 shoulders), Jobe (PLR: 2.08, NLR: 0.31) and full-can (2, 0.5) test results were relevant for diagnosis of supraspinatus tears and resisted lateral rotation (2.42, 0.5) for infraspinatus tears, with weakness as response criteria. The lift-off test (8.50, 0.27) was relevant for subscapularis tears with lag sign as response criteria. Yergason's test (3.7, 0.41) was relevant for tendinopathy of the long head of the biceps with pain as a response criterion. There was no relevant clinical test for diagnosis of tendinopathy of supraspinatus, infraspinatus or subscapularis. Five of 11 clinical tests were relevant for degenerative rotator cuff disease. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Viability of 3h grown bacterial micro-colonies after direct Raman identification.

PubMed

Mathey, R; Dupoy, M; Espagnon, I; Leroux, D; Mallard, F; Novelli-Rousseau, A

2015-02-01

Clinical diagnostics in routine microbiology still mostly relies on bacterial growth, a time-consuming process that prevents test results to be used directly as key decision-making elements for therapeutic decisions. There is some evidence that Raman micro-spectroscopy provides clinically relevant information from a limited amount of bacterial cells, thus holding the promise of reduced growth times and accelerated result delivery. Indeed, bacterial identification at the species level directly from micro-colonies at an early time of growth (6h) directly on their growth medium has been demonstrated. However, such analysis is suspected to be partly destructive and could prevent the further growth of the colony needed for other tests, e.g. antibiotic susceptibility testing (AST). In the present study, we evaluated the effect of the powerful laser excitation used for Raman identification on micro-colonies probed after very short growth times. We show here, using envelope integrity markers (Syto 9 and Propidium Iodide) directly on ultra-small micro-colonies of a few tens of Escherichia coli and Staphylococcus epidermidis cells (3h growth time), that only the cells that are directly impacted by the laser lose their membrane integrity. Growth kinetics experiments show that the non-probed surrounding cells are sometimes also affected but that the micro-colonies keep their ability to grow, resulting in normal aspect and size of colonies after 15h of growth. Thus, Raman spectroscopy could be used for very early (<3h) identification of grown micro-organisms without impairing further antibiotics susceptibility characterization steps. Copyright © 2014 Elsevier B.V. All rights reserved.

Polymicrobial Infective Endocarditis: Clinical Features and Prognosis

PubMed Central

García-Granja, Pablo Elpidio; López, Javier; Vilacosta, Isidre; Ortiz-Bautista, Carlos; Sevilla, Teresa; Olmos, Carmen; Sarriá, Cristina; Ferrera, Carlos; Gómez, Itziar; Román, José Alberto San

2015-01-01

Abstract To describe the profile of left-sided polymicrobial endocarditis (PE) and to compare it with monomicrobial endocarditis (ME). Among 1011 episodes of left-sided endocarditis consecutively diagnosed in 3 tertiary centers, between January 1, 1996 and December 31, 2014, 60 were polymicrobial (5.9%), 821 monomicrobial (81.7%), and in 123 no microorganism was detected (12.2%). Seven patients (0.7%) were excluded from the analysis because contamination of biologic tissue could not be discarded. The authors described the clinical, microbiologic, echocardiographic, and outcome of patients with PE and compared it with ME. Mean age was 64 years SD 16 years, 67% were men and 30% nosocomial. Diabetes mellitus (35%) were the most frequent comorbidities, fever (67%) and heart failure (43%) the most common symptoms at admission. Prosthetic valves (50%) were the most frequent infection location and coagulase-negative Staphylococci (48%) and enterococci (37%) the leading etiologies. The most repeated combination was coagulase-negative Staphylococci with enterococci (n = 9). Polymicrobial endocarditis appeared more frequently in patients with underlying disease (70% versus 56%, P = 0.036), mostly diabetics (35% versus 24%, P = 0.044) with previous cardiac surgery (15% versus 8% P = 0.049) and prosthetic valves (50% versus 37%, P = 0.038). Coagulase-negative Staphylococci, enterococci, Gram-negative bacilli, anaerobes, and fungi were more frequent in PE. No differences on age, sex, symptoms, need of surgery, and in-hospital mortality were detected. Polymicrobial endocarditis represents 5.9% of episodes of left-sided endocarditis in our series. Despite relevant demographic and microbiologic differences between PE and ME, short-term outcome is similar. PMID:26656328

Microbiological diagnosis and antimicrobial sensitivity profiles in diseased free-living raptors.

PubMed

Vidal, Anna; Baldomà, Laia; Molina-López, Rafael A; Martin, Marga; Darwich, Laila

2017-08-01

Free-living raptors (birds of prey) can act as reservoirs of potentially zoonotic agents, but they also can be affected by microorganisms as target hosts. In this retrospective study, microbiological results (n = 663) and antibiotic sensitivity profiles (n = 108) of bacterial isolates were analysed from diseased free-living raptors. Sixty-nine percent of cases (n = 457) yielded bacteria: 58% were in pure culture and 42% were of different species. Remarkably, samples from necropsies (47%) had higher percentage of pure isolations than those obtained from clinical (31%) samples (P < 0.001). Among bacterial isolates, Escherichia coli was the most common agent (35%), principally recovered from necropsied birds with clinical signs of septicaemia or respiratory disorders. Pseudomonas aeruginosa (7%) was isolated from birds with systemic infection and from oral lesions, especially in nocturnal raptors (P < 0.001). Staphylococcus spp. (5%), mainly Staphylococcus aureus, was found to be the most prevalent cause of pododermatitis (35%) and Staphylococcus hyicus was isolated from conjunctivitis (18.2%). Interestingly, 8% of samples with lesions compatible with avian tuberculosis were positive to the Mycobacterium avium complex. The most frequent fungi associated with pneumonic lesions and ingluvitis were Aspergillus spp. and Candida spp., respectively. More than 50% of the 108 isolates (34 different bacterial spp.) demonstrated resistance to clindamycin, ampicillin, tetracycline, cefuroxime, enrofloxacin and trimethoprim/sulphamethoxazole. Among the E. coli strains, 71% (27/38) presented a multidrug-resistance pattern to >3 antimicrobials. Detection in wildlife of antimicrobial-resistant pathogens that might be significant at the animal-human-ecosystem interface is of great relevance under the 'One Health' approach.

Effects of xylitol on xylitol-sensitive versus xylitol-resistant Streptococcus mutans strains in a three-species in vitro biofilm.

PubMed

Marttinen, Aino M; Ruas-Madiedo, Patricia; Hidalgo-Cantabrana, Claudio; Saari, Markku A; Ihalin, Riikka A; Söderling, Eva M

2012-09-01

We studied the effects of xylitol on biofilms containing xylitol-resistant (Xr) and xylitol-sensitive (Xs) Streptococcus mutans, Actinomyces naeslundii and S. sanguinis. The biofilms were grown for 8 and 24 h on hydroxyapatite discs. The viable microorganisms were determined by plate culturing techniques and fluorescence in situ hybridization (FISH) was performed using a S. mutans-specific probe. Extracellular cell-bound polysaccharides (EPS) were determined by spectrofluorometry from single-species S. mutans biofilms. In the presence of 5 % xylitol, the counts of the Xs S. mutans decreased tenfold in the young (8 h) biofilm (p < 0.05) but no effect was seen in the mature (24 h) biofilm. No decrease was observed for the Xr strains, and FISH confirmed these results. No differences were detected in the EPS production of the Xs S. mutans grown with or without xylitol, nor between Xr and Xs S. mutans strains. Thus, it seems that xylitol did not affect the EPS synthesis of the S. mutans strains. Since the Xr S. mutans strains, not inhibited by xylitol, showed no xylitol-induced decrease in the biofilms, we conclude that growth inhibition could be responsible for the decrease of the counts of the Xs S. mutans strains in the clinically relevant young biofilms.

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection.

PubMed

Barreda-García, Susana; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Lobo-Castañón, María Jesús

2018-01-01

Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed. Graphical Abstract Expanding the analytical toolbox for the detection of DNA sequences specific of pathogens with isothermal helicase dependent amplification (HDA).

A controlled comparison of the BacT/ALERT® 3D and VIRTUO™ microbial detection systems.

PubMed

Totty, H; Ullery, M; Spontak, J; Viray, J; Adamik, M; Katzin, B; Dunne, W M; Deol, P

2017-10-01

The performance of the next-generation BacT/ALERT® VIRTUO™ Microbial Detection System (VIRTUO™, bioMérieux Inc., Hazelwood, MO) was compared to the BacT/ALERT® 3D Microbial Detection System (3D, bioMérieux Inc., Durham, NC) using BacT/ALERT® FA Plus (FA Plus), BacT/ALERT® PF Plus (PF Plus), BacT/ALERT® FN Plus (FN Plus), BacT/ALERT® Standard Aerobic (SA), and BacT/ALERT® Standard Anaerobic (SN) blood culture bottles (bioMérieux Inc., Durham, NC). A seeded limit of detection (LoD) study was performed for each bottle type in both systems. The LoD studies demonstrated that both systems were capable of detecting organisms at nearly identical levels [<10 colony-forming units (CFU) per bottle], with no significant difference. Following LoD determination, a seeded study was performed to compare the time to detection (TTD) between the systems using a panel of clinically relevant microorganisms inoculated at or near the LoD with 0, 4, or 10 mL of healthy human blood. VIRTUO™ exhibited a faster TTD by an average of 3.5 h, as well as demonstrated a significantly improved detection rate of 99.9% compared to 98.8% with 3D (p-value <0.05).

Stachybotrys: relevance to human disease.

PubMed

Terr, A I

2001-12-01

Recent public concern about the danger of environmental fungi has focused attention on one particular mold, Stachybotrys. The purpose of this review is to examine and critique the published literature on Stachybotrys for objective scientific and clinical evidence of disease caused by the presence of this fungal organism in the environment. Data were obtained from all published research and reviews of Stachybotrys indexed in MEDLINE since 1966. The publications used for this review were those that contained information about human health effects of this microorganism. The critique of these publications is the author's. Stachybotrys is a minor component of the indoor mycoflora, found on certain building material surfaces in water-damaged buildings, but airborne spores are present in very low concentrations. Published reports fail to establish inhalation of Stachybotrys spores as a cause of human disease even in water-damaged buildings. A possible exception may be mycotoxin-caused pulmonary hemorrhage/hemosiderosis in infants, although scientific evidence to date is suggestive but not conclusive. Based on old reports ingestion of food prepared from Stachybotrys-contaminated grains may cause a toxic gastroenteropathy. No convincing cases of human allergic disease or infection from this mold have been published. The current public concern for adverse health effects from inhalation of Stachybotrys spores in water-damaged buildings is not supported by published reports in the medical literature.

Specific Identification and Targeted Characterization of Bifidobacterium lactis from Different Environmental Isolates by a Combined Multiplex-PCR Approach

PubMed Central

Ventura, Marco; Reniero, Roberto; Zink, Ralf

2001-01-01

The species Bifidobacterium lactis, with its main representative strain Bb12 (DSM 10140), is a yoghurt isolate used as a probiotic strain and is commercially applied in different types of yoghurts and infant formulas. In order to ensure the genetic identity and safety of this bacterial isolate, species- and strain-specific molecular tools for genetic fingerprinting must be available to identify isolated bifidobacteria or lactic acid bacteria from, e.g., various clinical environments of relevance in medical microbiology. Two opposing rRNA gene-targeted primers have been developed for specific detection of this microorganism by PCR. The specificity of this approach was evaluated and verified with DNA samples isolated from single and mixed cultures of bifidobacteria and lactobacilli (48 isolates, including the type strains of 29 Bifidobacterium and 9 Lactobacillus species). Furthermore, we performed a Multiplex-PCR using oligonucleotide primers targeting a specific region of the 16S rRNA gene for the genus Bifidobacterium and a conserved eubacterial 16S rDNA sequence. The specificity and sensitivity of this detection with a pure culture of B. lactis were, respectively, 100 bacteria/ml after 25 cycles of PCR and 1 to 10 bacteria/ml after a 50-cycle nested-PCR approach. PMID:11375192

Bacterial vaginosis-associated microflora isolated from the female genital tract activates HIV-1 expression.

PubMed

Al-Harthi, L; Roebuck, K A; Olinger, G G; Landay, A; Sha, B E; Hashemi, F B; Spear, G T

1999-07-01

Alteration of cervicovaginal microbial flora can lead to vaginosis, which is associated with an increased risk of HIV-1 transmission. We recently characterized a soluble HIV-inducing factor (HIF) from the cervicovaginal lavage (CVL) samples of women. The goals of this study were to determine the effect of cervicovaginal microflora on HIV-1 expression and to elucidate the relationship between HIF activity and microflora. Physiologically relevant microorganisms, Mycoplasma, diphtheroid-like bacteria, Gardnerella vaginalis, Streptococcus agalactiae, and Streptococcus constellatus, cultured from the CVL of a representative woman with a clinical condition of bacterial vaginosis and possessing HIF activity, induced HIV-1 expression. The magnitude of virus induction varied widely with the greatest stimulation induced by diphtheroid-like bacteria and Mycoplasma. The transcriptional induction by Mycoplasma was mediated by activation of the KB enhancer, an activation mechanism shared with HIF. Also as with HIF, Mycoplasma induced AP-1 dependent transcription. Polymerase chain reaction (PCR)-based speciation showed that the isolate was M. hominis. Our data indicate that bacterial vaginosis-associated microflora can enhance HIV-1 transcription and replication and identify M. hominis as a potential source for HIF activity. The virus-enhancing activities associated with the microflora and HIF may increase genital tract viral load, potentially contributing to HIV transmission.

An insight into the ecology, diversity and adaptations of Gordonia species.

PubMed

Sowani, Harshada; Kulkarni, Mohan; Zinjarde, Smita

2018-08-01

The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.

Prevalence of microorganisms and immunoglobulins in children with tonsillar hypertrophy and adenoiditis.

PubMed

Miramontes, Henrique Prestes; Fagundes, Djalma José; Jurgielewicz, Julia Coelho Lima E; Miramontes Neto, Haroldo Prestes; Oliveira, Renan Gianotto de; Oliveira, Gustavo Gianotto de; Souza, Maria Rosa Machado de

2014-07-01

 Benign idiopathic tonsillar hypertrophy (HBI) may affect a child's quality of life and sleep. Several studies have sought to relate the clinical features of HBI with the infectious and/or immunologic changes that occur.  To increase the knowledge of the etiology of HBI.  From 2012 to 2013 we conducted a retrospective observational study of 101 children with HBI who underwent tonsillectomies at Ambulatory ENT General Hospital of the East Zone of São Paulo City, a region with a poor socioeconomic population. Preoperative serologic results were available to confirm mononucleosis, cytomegalovirus, anti-streptolysin O (ASLO) and immunoglobulins. The mean patient age was 5.8 years (55% male, 45% female). Using the Mann-Whitney U test, we identified significant gender differences in the parameters of immunoglobulins (Ig) M (IgM), IgA, and IgE. Forty-seven percent of the patients had increased ASLO levels, and 37% had increased IgE levels.  An evaluation of a patient's serologic parameters and laboratory results may be relevant to the etiology and prevention of HBI. Based on the results obtained from the study sample, the identification of etiologic agents and causative factors remain a public health challenge that affects the quality of life of children.

Antimicrobial and Antiproliferative Activity of Bauhinia forficata Link and Cnidoscolus quercifolius Extracts commonly Used in Folk Medicine.

PubMed

Alves, Erika P; de F Lima, Rennaly; de Almeida, Carolina M; Freires, Irlan A; Rosalen, Pedro L; Ruiz, Ana Ltg; Granville-Garcia, Ana F; Godoy, Gustavo P; Pereira, Jozinete V; de Brito Costa, Edja Mm

2017-08-01

Bauhinia forficata and Cnidoscolus quercifolius plants are commonly used in folk medicine. However, few studies have investigated their therapeutic potential. Herein, we evaluated the antimicrobial activity of B. forficata and C. quercifolius extracts against microorganisms of clinical relevance and their antiproliferative potential against tumor cells. The following tests were performed: Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC)/minimum fungicidal concentration (MFC), inhibition of biofilm adhesion, and effects on cell morphology. Antiproliferative tests were carried out with human keratinocytes and six tumor lines. Bauhinia forficata showed antimicrobial activity only against C. albicans with MIC of 15.62 ug/mL and MFC higher than 2000 ug/mL. It also inhibited biofilm adhesion and caused alterations in cell morphology. Cnidoscolus quercifolius showed no significant activity (MIC > 2.0 mg/mL) against the strains. Bauhinia forficata and C. quercifolius extracts showed cytostatic activity against the tumor cells. Bauhinia forficata has promising anti-Cand/da activity and should be further investigated for its therapeutic potential. The use of medicinal plants in the treatment of infectious processes has an important function nowadays, due to the limitations of the use of synthetic antibiotics available, related specifically to the microbial resistance emergence.

High Levels of Soluble C5b-9 Complex in Dialysis Fluid May Predict Poor Prognosis in Peritonitis in Peritoneal Dialysis Patients.

PubMed

Mizuno, Masashi; Suzuki, Yasuhiro; Higashide, Keiko; Sei, Yumi; Iguchi, Daiki; Sakata, Fumiko; Horie, Masanobu; Maruyama, Shoichi; Matsuo, Seiichi; Morgan, B Paul; Ito, Yasuhiko

2017-01-01

We searched for indicators to predict the prognosis of infectious peritonitis by measuring levels of complement proteins and activation products in peritoneal dialysis (PD) fluid (PDF) of patients at early stages of peritonitis. We retrospectively analyzed the relationship between the levels of sC5b-9, C3 and C4 in PDF and the subsequent clinical prognosis. We measured levels of sC5b-9, C3 and C4 in PDF on days 1, 2 and 5 post-onset of peritonitis in 104 episodes of infectious peritonitis in PD patients from 2008 and retrospectively compared levels with clinical outcomes. Further analysis for the presence of causative microorganisms or to demonstrate bacterial culture negative peritonitis was performed and correlated with change of levels of sC5b-9 in PDF. When PD patients with peritonitis were divided into groups that either failed to recover from peritonitis and were finally withdrawn from PD (group 1; n = 25) or recovered (group 2; n = 79), levels of sC5b-9, C3 and C4 in PDF were significantly higher in group 1 patients compared to those in group 2 on day5. Analysis of microorganisms showed significantly higher sC5b-9 levels in PDF of peritonitis cases caused by culture negative peritonitis in group 1 compared with group 2 when we analyzed for individual microorganisms. Of note, on day5, the sC5b-9 levels in PDF were similarly high in peritonitis caused by fungi or other organisms. Our results suggested that levels of complement markers in PDF, especially sC5b-9, have potential as surrogate markers to predict prognosis of PD-related peritonitis.

Evaluation of BACTEC 9240 blood culture system by using high-volume aerobic resin media.

PubMed Central

Schwabe, L D; Thomson, R B; Flint, K K; Koontz, F P

1995-01-01

The BACTEC 9240 blood culture system (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) is one of three automated, continuous-monitoring systems that is widely used in clinical laboratories. The BACTEC 9240 was compared with the BACTEC NR 660 for the detection of organisms and bacteremic episodes; time to detection of positive cultures; number of false-positive and false-negative cultures; and time needed to load, process, and perform quality control functions by using high-volume aerobic media. Blood specimens (5,282) were inoculated in equal volumes (5 to 10 ml per bottle) into BACTEC Plus Aerobic/F (9240 system) and BACTEC Plus NR26 (660 system) bottles. Clinically significant isolates were detected in 6.6% of cultures, representing 348 microorganisms and 216 bacteremic episodes. Two hundred forty-eight microorganisms were detected by both systems, 48 by the 9240 only and 52 by the 660 only (P = not significant). Of the bacteremic episodes, 158 were detected by both systems, 27 by the 9240 only and 31 by the 660 only (P = not significant). Analysis of data by month revealed equivalent recovery rates for both systems, with the exception of a 30-day period at one study site during which the 660 system detected significantly more microorganisms. Following a proprietary hardware design retrofit of the 9240 instrument, detection rates were again equivalent for the remaining three months at this study site. Positive cultures detected by both systems were detected an average of 4.3 h faster by the 9240 system (21 versus 25.3 h). The numbers of false-positive cultures for the 9240 and 660 systems were 40 (1.0%) and 9 ( < 1.0%), respectively.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7494044

Propolis--based chitosan varnish: drug delivery, controlled release and antimicrobial activity against oral pathogen bacteria.

PubMed

Franca, Juçara R; De Luca, Mariana P; Ribeiro, Tatiana G; Castilho, Rachel O; Moreira, Allyson N; Santos, Vagner R; Faraco, André A G

2014-12-12

Dental caries is the most prevalent oral disease in several Asian and Latin American countries. It is an infectious disease and different types of bacteria are involved in the process. Synthetic antimicrobials are used against this disease; however, many of these substances cause unwarranted undesirable effects like vomiting, diarrhea and tooth staining. Propolis, a resinous substance collected by honeybees, has been used to control the oral microbiota. So, the objective of this study was to develop and characterize sustained-release propolis-based chitosan varnish useful on dental cariogenic biofilm prevention, besides the in vitro antimicrobial activity. Three formulations of propolis - based chitosan varnish (PCV) containing different concentrations (5%, 10% and 15%) were produced by dissolution of propolis with chitosan on hydro-alcoholic vehicle. Bovine teeth were used for testing adhesion of coatings and to observe the controlled release of propolis associated with varnish. It was characterized by infrared spectroscopy, scanning electron microscopy, casting time, diffusion test in vitro antimicrobial activity and controlled release. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were tested for the main microorganisms involved in the cariogenic biofilm through the microdilution test in 96-well plates. The formulations presented a tooth surface adherence and were able to form films very fast on bovine tooth surface. Also, propolis-based chitosan varnishes have shown antimicrobial activity similar to or better than chlorhexidine varnish against all oral pathogen bacteria. All microorganisms were sensitive to propolis varnish and chitosan. MIC and MBC for microorganisms of cariogenic biofilme showed better results than chlorhexidine. Propolis active components were released for more than one week. All developed formulations turn them, 5%, 10% and 15% propolis content varnish, into products suitable for clinical application on dental caries prevention field, deserving clinical studies to confirm its in vivo activity.

Advanced Effect of Moringa oleifera Bioconversion by Rhizopus oligosporus on the Treatment of Atopic Dermatitis: Preliminary Study

PubMed Central

Hur, Sang-sun; Choi, Suk-won; Lee, Dong-ryul; Park, Jong-hwan

2018-01-01

This study was conducted to determine if topical application of Moringa oleifera extracts and its bioconversion product fermented by Rhizopus oligosporus has therapeutic properties enhancement for treatment of atopic dermatitis. Rhizopus oligosporus (KCCM 11232P) was used to ferment Moringa leaves' extracts in this study. Comparison of organic acids and flavonols in Moringa simple extracts and their fermented product by HPLC analysis revealed that concentration of organic acids and flavonols of bioconversion product was lower than that of hot water extracts. The fermentation process is used as a nutrient for isolation of each component by microorganisms and growth of microorganisms. The results demonstrated that MF extracts effectively reduced clinical features based on macrography, scratching count, and severity scores, as well as model's serum IgE level, including histopathological analyses. PMID:29576799

Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters.

PubMed

Lokker, Cynthia; Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Walter, Stephen D

2011-01-01

Clinical Queries filters were developed to improve the retrieval of high-quality studies in searches on clinical matters. The study objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters. Forty practicing physicians, presented with standardized treatment and diagnosis questions and one question of their choosing, entered search terms which were processed in a random, blinded fashion through PubMed alone and PubMed Clinical Queries. Participants rated search retrievals for applicability to the question at hand and satisfaction. For treatment, the primary outcome of retrieval of relevant articles was not significantly different between the groups, but a higher proportion of articles from the Clinical Queries searches met methodologic criteria (p=0.049), and more articles were published in core internal medicine journals (p=0.056). For diagnosis, the filtered results returned more relevant articles (p=0.031) and fewer irrelevant articles (overall retrieval less, p=0.023); participants needed to screen fewer articles before arriving at the first relevant citation (p<0.05). Relevance was also influenced by content terms used by participants in searching. Participants varied greatly in their search performance. Clinical Queries filtered searches returned more high-quality studies, though the retrieval of relevant articles was only statistically different between the groups for diagnosis questions. Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval.

Oral microbial and respiratory status of persons with mental retardation/intellectual and developmental disability: an observational cohort study.

PubMed

Binkley, Catherine J; Haugh, Gilbert S; Kitchens, Dinah H; Wallace, Debra L; Sessler, Daniel I

2009-11-01

The objective of this study was to determine the prevalence of select microorganisms in oral biofilms and to investigate relationships between oral and respiratory status in persons with mental retardation/intellectual and developmental disabilities (IDD). We conducted a 6-month-long observational cohort study with 63 persons with IDD. Oral examinations, oral sampling, and medical record reviews were performed at baseline and then monthly. Polymerase chain reaction (PCR) was used to analyze all baseline oral samples for the presence of Streptococcus pneumoniae, Methicillin-resistant Staphylococcus aureus (MRSA), Prevotella melaninogenica, and Candida albicans. PCR analyses were also performed on participants' samples collected in the month before being diagnosed with a respiratory infection. All subjects had P. melaninogenica detected by PCR in their oral samples. Fifty-five percent (35 of 63) of participants had S. pneumoniae, MRSA, and C. albicans in their oral samples at baseline. No dental decay was detected clinically, oral hygiene was fair, and dysphagia was common. During the 6 months of the study, there were 22 respiratory infections (35% of participants)-12 pneumonias, 7 sinusitis, 1 bronchitis, and 1 upper respiratory tract infection. Participants with microorganisms in their baseline samples were significantly more likely to develop any respiratory infection and those who had poor oral status were significantly more likely to develop pneumonia. Almost 60% of participants who developed respiratory infections had the same microorganism detected in the sample collected in the month before infection as had been detected in their baseline sample. Potentially pathogenic microorganisms in the oral cavity and poor oral status significantly increased the risk of developing respiratory infections, including pneumonia, in persons with IDD. The results suggest that colonization with these microorganisms may persist despite routine tooth brushing. Meticulous comprehensive oral hygiene of the oral cavity may be needed to reduce oropharyngeal microbial load.

Evaluation of the VITEK 2 System for Identification and Antimicrobial Susceptibility Testing of Medically Relevant Gram-Positive Cocci

PubMed Central

Ligozzi, Marco; Bernini, Cinzia; Bonora, Maria Grazia; de Fatima, Maria; Zuliani, Jessica; Fontana, Roberta

2002-01-01

A study was conducted to evaluate the new VITEK 2 system (bioMérieux) for identification and antibiotic susceptibility testing of gram-positive cocci. Clinical isolates of Staphylococcus aureus (n = 100), coagulase-negative staphylococci (CNS) (n = 100), Enterococcus spp. (n = 89), Streptococcus agalactiae (n = 29), and Streptococcus pneumoniae (n = 66) were examined with the ID-GPC identification card and with the AST-P515 (for staphylococci), AST-P516 (for enterococci and S. agalactiae) and AST-P506 (for pneumococci) susceptibility cards. The identification comparison methods were the API Staph for staphylococci and the API 20 Strep for streptococci and enterococci; for antimicrobial susceptibility testing, the agar dilution method according to the procedure of the National Committee for Clinical Laboratory Standards (NCCLS) was used. The VITEK 2 system correctly identified to the species level (only one choice or after simple supplementary tests) 99% of S. aureus, 96.5% of S. agalactiae, 96.9% of S. pneumoniae, 92.7% of Enterococcus faecalis, 91.3% of Staphylococcus haemolyticus, and 88% of Staphylococcus epidermidis but was least able to identify Enterococcus faecium (71.4% correct). More than 90% of gram-positive cocci were identified within 3 h. According to the NCCLS breakpoints, antimicrobial susceptibility testing with the VITEK 2 system gave 96% correct category agreement, 0.82% very major errors, 0.17% major errors, and 2.7% minor errors. Antimicrobial susceptibility testing showed category agreement from 94 to 100% for S. aureus, from 90 to 100% for CNS, from 91 to 100% for enterococci, from 96 to 100% for S. agalactiae, and from 91 to 100% for S. pneumoniae. Microorganism-antibiotic combinations that gave very major errors were CNS-erythromycin, CNS-oxacillin, enterococci-teicoplanin, and enterococci-high-concentration gentamicin. Major errors were observed for CNS-oxacillin and S. agalactiae-tetracycline combinations. In conclusion the results of this study indicate that the VITEK 2 system represents an accurate and acceptable means for performing identification and antibiotic susceptibility tests with medically relevant gram-positive cocci. PMID:11980942

Clinical relevance of diagnosing COPD by fixed ratio or lower limit of normal: a systematic review.

PubMed

van Dijk, Wouter D; Gupta, Nisha; Tan, Wan C; Bourbeau, Jean

2014-02-01

Different spirometric criteria in diagnosing COPD have been advocated by different groups, debilitating adequate diagnosis and treatment of COPD. We reviewed the clinical relevance of fixed ratio and lower limit of normal (LLN) in diagnosing COPD and explored if modifying factors may affect their clinical relevance. Two reviewers independently searched PubMed and Embase for papers that compared both criteria on any clinically relevant outcome, published before June 1st, 2012, without any language restriction. Two reviewers independently extracted the study characteristics, including study design, population characteristics and diagnostic criteria used, and summarized the results of clinical relevance. Study quality was assessed by scoring forms for bias and level of evidence. Of 394 studies retrieved, 11 studies were included, with a median of 1,258 participants. Although both criteria appeared related with various clinically relevant outcomes, we were unable to prefer one criterion over the other, with various performances of the criteria for different outcomes. Should the criteria disagree on diagnosis, an alternative diagnosis should be suspected, in particular in those (elderly) with less severe airflow limitation for whom the LLN appears a better criterion. The fixed ratio appears to perform better in subjects with more severe airflow limitation. In diagnosing COPD, severity of airflow limitation appears an important factor for choosing whether the fixed ratio or LLN. Disagreement between the criteria is suggestive for an alternative diagnosis. Future studies on clinical relevance should further reveal the criterion of choice, in order to improve adequate diagnosis and consequent treatments.

Field comparison of real-time polymerase chain reaction and bacterial culture for identification of bovine mastitis bacteria.

PubMed

Koskinen, M T; Wellenberg, G J; Sampimon, O C; Holopainen, J; Rothkamp, A; Salmikivi, L; van Haeringen, W A; Lam, T J G M; Pyörälä, S

2010-12-01

Fast and reliable identification of the microorganisms causing mastitis is important for management of the disease and for targeting antimicrobial treatment. Methods based on PCR are being used increasingly in mastitis diagnostics. Comprehensive field comparisons of PCR and traditional milk bacteriology have not been available. The results of a PCR kit capable of detecting 11 important etiological agents of mastitis directly from milk in 4h were compared with those of conventional bacterial culture (48h). In total, 1,000 quarter milk samples were taken from cows with clinical or subclinical mastitis, or from clinically healthy quarters with low somatic cell count (SCC). Bacterial culture identified udder pathogens in 600/780 (77%) of the clinical samples, whereas PCR identified bacteria in 691/780 (89%) of the clinical samples. The PCR analysis detected major pathogens in a large number of clinical samples that were negative for the species in culture. These included 53 samples positive for Staphylococcus aureus by PCR, but negative by culture. A total of 137 samples from clinical mastitis, 5 samples from subclinical mastitis, and 1 sample from a healthy quarter were positive for 3 or more bacterial species in PCR, whereas culture identified 3 or more species in 60 samples from clinical mastitis. Culture identified a species not targeted by the PCR test in 44 samples from clinical mastitis and in 9 samples from subclinical mastitis. Low SCC samples provided a small number of positive results both in culture (4/93; 4.3%) and by PCR (7/93; 7.5%). In conclusion, the PCR kit provided several benefits over conventional culture, including speed, automated interpretation of results, and increased sensitivity. This kit holds much promise as a tool to complement traditional methods in identification of pathogens. In conventional mastitis bacteriology, a sample with 3 or more species is considered contaminated, and resampling of the cow is recommended. Further study is required to investigate how high sensitivity of PCR and its quantitative features can be applied to improve separation of relevant udder pathogens from likely contaminants in samples where multiple species are detected. Furthermore, increasing the number of species targeted by the PCR test would be advantageous. Copyright © 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Fecal Microbiota Transplantation Inhibits Multidrug-Resistant Gut Pathogens: Preliminary Report Performed in an Immunocompromised Host.

PubMed

Biliński, Jarosław; Grzesiowski, Paweł; Muszyński, Jacek; Wróblewska, Marta; Mądry, Krzysztof; Robak, Katarzyna; Dzieciątkowski, Tomasz; Wiktor-Jedrzejczak, Wiesław; Basak, Grzegorz W

2016-06-01

Colonization of the gastrointestinal tract with multidrug-resistant (MDR) bacteria is a consequence of gut dysbiosis. We describe the successful utilization of fecal microbiota transplantation to inhibit Klebsiella pneumoniae MBL(+) and Escherichia coli ESBL(+) gut colonization in the immunocompromised host as a novel tool in the battle against MDR microorganisms. ClinicalTrials.gov identifier NCT02461199.

Molecular and cellular insights into Zika virus-related neuropathies.

PubMed

Zhou, Kai; Wang, Long; Yu, Di; Huang, Hesuyuan; Ji, Hong; Mo, Xuming

2017-06-01

Zika virus (ZIKV), a relatively elusive Aedes mosquito-transmitted flavivirus, had been brought into spotlight until recent widespread outbreaks accompanied by unexpectedly severe clinical neuropathies, including fetal microcephaly and Guillain-Barré syndrome (GBS) in the adult. In this review, we focus on the underlying cellular and molecular mechanisms by which vertically transmitted microorganisms reach the fetus and trigger neuropathies.

[Utility of MALDI-TOF MS for the identification of anaerobic bacteria].

PubMed

Zárate, Mariela S; Romano, Vanesa; Nievas, Jimena; Smayevsky, Jorgelina

2014-01-01

The analysis by MALDI-TOF MS (Matrix-assited laser desorption/ionization time-of-flight mass spectrometry) has become a reference method for the identification of microorganisms in Clinical Microbiology. However, data on some groups of microorganisms are still controversial. The aim of this study is to determine the utility of MALDI-TOF MS for the identification of clinical isolates of anaerobic bacteria. One-hundred and six anaerobic bacteria isolates were analyzed by MALDI-TOF MS and by conventional biochemical tests. In those cases where identification by conventional methodology was not applicable or in the face of discordance between sequencing methodologies, 16 S rRNA gene sequence analysis was performed. The conventional method and MALDI-TOF MS agreed at genus and species level by 95.3 %. Concordance in gram-negative bacilli was 91.4% and 100% among gram-positive bacilli; there was also concordance both in the 8 isolates studied in gram-positive cocci and in the single gram-negative cocci included. The data obtained in this study demonstrate that MALDI-TOF MS offers the possibility of adequate identification of anaerobic bacteria. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Ultrastructural study of ehrlichial organisms in the large colons of ponies infected with Potomac horse fever.

PubMed

Rikihisa, Y; Perry, B D; Cordes, D O

1985-09-01

Potomac horse fever is characterized by fever, anorexia, leukopenia, profuse watery diarrhea, dehydration, and high mortality. An ultrastructural investigation was made to search for any unusual microorganisms in the digestive system, lymphatic organs, and blood cells of ponies that had developed clinical signs after transfusion with whole blood from horses naturally infected with Potomac horse fever. A consistent finding was the presence of rickettsial organisms in the wall of the intestinal tract of these ponies. The organisms were found mostly in the wall of the large colon, but fewer organisms were found in the small colon, jejunum, and cecum. The organisms were also detected in cultured blood monocytes. In the intestinal wall, many microorganisms were intracytoplasmic in deep glandular epithelial cells and mast cells. Microorganisms were also found in macrophages migrating between glandular epithelial cells in the lamina propria and submucosa. The microorganisms were round, very pleomorphic, and surrounded by a host membrane. They contained fine strands of DNA and ribosomes and were surrounded by double bileaflet membranes. Their ultrastructure was very similar to that of the genus Ehrlichia, a member of the family Rickettsiaceae. The high frequency of detection of the organism in the wall of the intestinal tract, especially in the large colon, indicates the presence of organotrophism in this organism. Infected blood monocytes may be the vehicle for transmission between organs and between animals. The characteristic severe diarrhea may be induced by the organism directly by impairing epithelial cell functions or indirectly by perturbing infected macrophages and mast cells in the intestinal wall or by both.

Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR.

PubMed

Dalla-Costa, Libera M; Morello, Luis G; Conte, Danieli; Pereira, Luciane A; Palmeiro, Jussara K; Ambrosio, Altair; Cardozo, Dayane; Krieger, Marco A; Raboni, Sonia M

2017-09-01

Sepsis is the leading cause of death in intensive care units (ICUs) worldwide and its diagnosis remains a challenge. Blood culturing is the gold standard technique for blood stream infection (BSI) identification. Molecular tests to detect pathogens in whole blood enable early use of antimicrobials and affect clinical outcomes. Here, using real-time PCR, we evaluated DNA extraction using seven manual and three automated commercially available systems with whole blood samples artificially contaminated with Escherichia coli, Staphylococcus aureus, and Candida albicans, microorganisms commonly associated with BSI. Overall, the commercial kits evaluated presented several technical limitations including long turnaround time and low DNA yield and purity. The performance of the kits was comparable for detection of high microorganism loads (10 6 CFU/mL). However, the detection of lower concentrations was variable, despite the addition of pre-processing treatment to kits without such steps. Of the evaluated kits, the UMD-Universal CE IVD kit generated a higher quantity of DNA with greater nucleic acid purity and afforded the detection of the lowest microbial load in the samples. The inclusion of pre-processing steps with the kit seems to be critical for the detection of microorganism DNA directly from whole blood. In conclusion, future application of molecular techniques will require overcoming major challenges such as the detection of low levels of microorganism nucleic acids amidst the large quantity of human DNA present in samples or differences in the cellular structures of etiological agents that can also prevent high-quality DNA yields. Copyright © 2017 Elsevier B.V. All rights reserved.

Insights from clinical research completed during the west Africa Ebola virus disease epidemic

PubMed Central

Rojek, Amanda; Horby, Peter; Dunning, Jake

2018-01-01

The west Africa Ebola virus disease (EVD) epidemic was extraordinary in scale. Now that the epidemic has ended, it is a relevant time to examine published studies with direct relevance to clinical care and, more broadly, to examine the implications of the clinical research response mounted. Clinically relevant research includes literature detailing risk factors for and clinical manifestations of EVD, laboratory and other investigation findings in patients, experimental vaccine and therapeutic clinical trials, and analyses of survivor syndrome. In this Review, we discuss new insights from patient-oriented research completed during the west Africa epidemic, identify ongoing knowledge gaps, and suggest priorities for future research. PMID:28461209

Are there clinical signs and symptoms of infection to indicate the presence of multidrug-resistant bacteria in venous ulcers?

PubMed

Dos Santos, Silvana de Lima Vieira; Martins, Marlene Andrade; do Prado, Marinésia Aparecida; Soriano, José Verdú; Bachion, Maria Márcia

2017-12-01

The selection of topical and systemic therapies for the treatment of venous ulcers with signs of infection is challenging and should be accompanied by specific precautionary measures to protect against cross-contamination in the presence of multidrug-resistant microorganisms. However, there are still no clinical indicators for this situation, and confirmation of resistant strains occurs through culture and sensitivity, which can take up to 14 days. During this period, protective measures may no longer be taken, contributing to the spread of these pathogens. This study aimed to analyze the relationship between clinical signs and symptoms of infection in venous ulcers and the presence of antimicrobial-resistant Staphylococcus aureus and/or Pseudomonas spp. A cross-sectional study was developed including 69 patients with 98 venous ulcers. Clinical observation protocol was applied to detect infection indicators established by the European Wound Management Association and microbiological analysis of samples of the lesions. Fisher's exact test and χ 2 were used for analyses (P < 0.05). Two indicators of infection predominated (f >70%): discoloration of the opaque type and/or dark brick red and increased exudate volume; 31 (31.6%) ulcer samples showed positive culture for the bacteria studied. There was no relationship between signs and symptoms of infection and the presence of multidrug-resistant microorganisms. Taking into account the percentage of lesions with resistant strains, for safe care, contact precautionary measures should be implemented in the treatment rooms, in addition to standard precautions. Copyright © 2017 Society for Vascular Nursing, Inc. Published by Elsevier Inc. All rights reserved.

Molecular epidemiology of an outbreak of clinical mastitis in sheep caused by Mannheimia haemolytica.

PubMed

Omaleki, Lida; Browning, Glenn F; Allen, Joanne L; Markham, Philip F; Barber, Stuart R

2016-08-15

The aetiology and epidemiology of outbreaks of clinical mastitis in sheep under extensive pastoral conditions are incompletely understood. The objective of this study was to conduct a detailed investigation of a clinical mastitis outbreak that affected more than 10% of 230 at-risk ewes on a sheep and grain producing property in south east Australia during drought conditions in 2009. Milk samples were collected aseptically from all affected ewes and plated on sheep blood agar for bacterial identification. M. haemolytica was isolated from 80% of the samples that yielded cultivable microorganisms and thus was the main microorganism responsible for the outbreak. Analysis of the restriction endonuclease cleavage patterns of the isolates using pulsed field gel electrophoresis revealed some evidence of clonality, suggesting the possibility of horizontal transmission, but there was also considerable diversity between the clusters of closely related isolates. Multilocus sequence typing of the M. haemolytica isolates revealed most of the isolates belonged to ST1 with no association between the PFGE and MLST fingerprints of the isolates. Resistance to neomycin, streptomycin and sulphafurazole was detected in some of the isolates, but they were all susceptible to penicillin, ampicillin, ceftiofur, amoxycillin/clavulanic acid, ciprofloxacin, tetracycline, erythromycin and trimethoprim. This is the first published record of a comparison of the strains of M. haemolytica involved in a clinical mastitis outbreak in sheep and demonstrates the importance of this pathogen in sheep production systems, particularly during adverse climatic conditions and increased stocking rate. Copyright © 2016 Elsevier B.V. All rights reserved.

Silicon nitride grids are compatible with correlative negative staining electron microscopy and tip-enhanced Raman spectroscopy for use in the detection of micro-organisms.

PubMed

Lausch, V; Hermann, P; Laue, M; Bannert, N

2014-06-01

Successive application of negative staining transmission electron microscopy (TEM) and tip-enhanced Raman spectroscopy (TERS) is a new correlative approach that could be used to rapidly and specifically detect and identify single pathogens including bioterrorism-relevant viruses in complex samples. Our objective is to evaluate the TERS-compatibility of commonly used electron microscopy (EM) grids (sample supports), chemicals and negative staining techniques and, if required, to devise appropriate alternatives. While phosphortungstic acid (PTA) is suitable as a heavy metal stain, uranyl acetate, paraformaldehyde in HEPES buffer and alcian blue are unsuitable due to their relatively high Raman scattering. Moreover, the low thermal stability of the carbon-coated pioloform film on copper grids (pioloform grids) negates their utilization. The silicon in the cantilever of the silver-coated atomic force microscope tip used to record TERS spectra suggested that Si-based grids might be employed as alternatives. From all evaluated Si-based TEM grids, the silicon nitride (SiN) grid was found to be best suited, with almost no background Raman signals in the relevant spectral range, a low surface roughness and good particle adhesion properties that could be further improved by glow discharge. Charged SiN grids have excellent particle adhesion properties. The use of these grids in combination with PTA for contrast in the TEM is suitable for subsequent analysis by TERS. The study reports fundamental modifications and optimizations of the negative staining EM method that allows a combination with near-field Raman spectroscopy to acquire a spectroscopic signature from nanoscale biological structures. This should facilitate a more precise diagnosis of single viral particles and other micro-organisms previously localized and visualized in the TEM. © 2014 The Society for Applied Microbiology.

Systematic screening of plant extracts from the Brazilian Pantanal with antimicrobial activity against bacteria with cariogenic relevance.

PubMed

Brighenti, F L; Salvador, M J; Delbem, Alberto Carlos Botazzo; Delbem, Ádina Cleia Bottazzo; Oliveira, M A C; Soares, C P; Freitas, L S F; Koga-Ito, C Y

2014-01-01

This study proposes a bioprospection methodology regarding the antimicrobial potential of plant extracts against bacteria with cariogenic relevance. Sixty extracts were obtained from ten plants--(1) Jatropha weddelliana, (2) Attalea phalerata, (3) Buchenavia tomentosa, (4) Croton doctoris, (5) Mouriri elliptica, (6) Mascagnia benthamiana, (7) Senna aculeata, (8) Unonopsis guatterioides, (9) Allagoptera leucocalyx and (10) Bactris glaucescens--using different extraction methods - (A) 70° ethanol 72 h/25°C, (B) water 5 min/100°C, (C) water 1 h/55°C, (D) water 72 h/25°C, (E) hexane 72 h/25°C and (F) 90° ethanol 72 h/25°C. The plants were screened for antibacterial activity at 50 mg/ml using the agar well diffusion test against Actinomyces naeslundii ATCC 19039, Lactobacillus acidophilus ATCC 4356, Streptococcus gordonii ATCC 10558, Streptococcus mutans ATCC 35688, Streptococcus sanguinis ATCC 10556, Streptococcus sobrinus ATCC 33478 and Streptococcus mitis ATCC 9811. The active extracts were tested to determine their minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), cytotoxicity and chemical characterization. Forty-seven extracts (78%) were active against at least one microorganism. Extract 4A demonstrated the lowest MIC and MBC for all microorganisms except S. gordonii and the extract at MIC concentration was non-cytotoxic. The concentrated extracts were slightly cytotoxic. Electrospray ionization with tandem mass spectrometry analyses demonstrated that the extract constituents coincided with the mass of the terpenoids and phenolics. Overall, the best results were obtained for extraction methods A, B and C. The present work proved the antimicrobial activity of several plants. Particularly, extracts from C. doctoris were the most active against bacteria involved in dental caries disease. © 2014 S. Karger AG, Basel.

Volcaniclastic habitats for early life on Earth and Mars: A case study from ˜3.5 Ga-old rocks from the Pilbara, Australia

NASA Astrophysics Data System (ADS)

Westall, Frances; Foucher, Frédéric; Cavalazzi, Barbara; de Vries, Sjoukje T.; Nijman, Wouter; Pearson, Victoria; Watson, Jon; Verchovsky, Alexander; Wright, Ian; Rouzaud, Jean-Noel; Marchesini, Daniele; Anne, Severine

2011-08-01

Within the context of present and future in situ missions to Mars to investigate its habitability and to search for traces of life, we studied the habitability and traces of past life in ˜3.5 Ga-old volcanic sands deposited in littoral environments an analogue to Noachian environments on Mars. The environmental conditions on Noachian Mars (4.1-3.7 Ga) and the Early Archaean (4.0-3.3 Ga) Earth were, in many respects, similar: presence of liquid water, dense CO 2 atmosphere, availability of carbon and bio-essential elements, and availability of energy. For this reason, information contained in Early Archaean terrestrial rocks concerning habitable conditions (on a microbial scale) and traces of past life are of relevance in defining strategies to be used to identify past habitats and past life on Mars. One such example is the 3.446 Ga-old Kitty's Gap Chert in the Pilbara Craton, NW. Australia. This formation consists of volcanic sediments deposited in a coastal mudflat environment and is thus a relevant analogue for sediments deposited in shallow water environments on Noachian Mars. Two main types of habitat are represented, a volcanic (lithic) habitat and planar stabilized sediment surfaces in sunlit shallow waters. The sediments hosted small (<1 μm in size) microorganisms that formed colonies on volcanic particle surfaces and in pore waters within the volcanic sediments, as well as biofilms on stabilised sediment surfaces. The microorganisms included coccoids, filaments and rare rod-shaped organisms associated with microbial polymer (EPS). The preserved microbial community was apparently dominated by chemotrophic organisms but some locally transported filaments and filamentous mat fragments indicate that possibly photosynthetic mats formed nearby. Both microorganisms and sediments were silicified during very early diagenesis. There are no macroscopic traces of fossilised life in these volcanic sediments and sophisticated instrumentation and specialized sample preparation techniques are required to establish the biogenicity and syngenicity of the traces of past life. The fact that the traces of life are cryptic, and the necessity of using sophisticated instrumentation, reinforces the challenges and difficulties of in situ robotic missions to identify past life on Mars. We therefore recommend the return of samples from Mars to Earth for a definitive search for traces of life.

Identifying Opportunities for Vertical Integration of Biochemistry and Clinical Medicine.

PubMed

Wendelberger, Karen J.; Burke, Rebecca; Haas, Arthur L.; Harenwattananon, Marisa; Simpson, Deborah

1998-01-01

Objectives: Retention of basic science knowledge, as judged by National Board of Medical Examiners' (NBME) data, suffers due to lack of apparent relevance and isolation of instruction from clinical application, especially in biochemistry. However, the literature reveals no systematic process for identifying key biochemical concepts and associated clinical conditions. This study systematically identified difficult biochemical concepts and their common clinical conditions as a critical step towards enhancing relevance and retention of biochemistry.Methods: A multi-step/ multiple stakeholder process was used to: (1) identify important biochemistry concepts; (2) determine students' perceptions of concept difficulty; (3) assess biochemistry faculty, student, and clinical teaching scholars' perceived relevance of identified concepts; and (4) identify associated common clinical conditions for relevant and difficult concepts. Surveys and a modified Delphi process were used to gather data, subsequently analyzed using SPSS for Windows.Results: Sixteen key biochemical concepts were identified. Second year medical students rated 14/16 concepts as extremely difficult while fourth year students rated nine concepts as moderately to extremely difficult. On average, each teaching scholar generated common clinical conditions for 6.2 of the 16 concepts, yielding a set of seven critical concepts and associated clinical conditions.Conclusions: Key stakeholders in the instructional process struggle to identify biochemistry concepts that are critical, difficult to learn and associated with common clinical conditions. However, through a systematic process beginning with identification of concepts and associated clinical conditions, relevance of basic science instruction can be enhanced.

Sarcoid-like lesions in Paracoccidioidomycosis: immunological factors*

PubMed Central

de Medeiros, Vanessa Lucília Silveira; Arruda, Lúcia

2013-01-01

The clinical presentation of paracoccidioidomycosis is spectral. Spontaneous cure, state of latency or active disease with different levels of severity can occur after the hematogenous dissemination. The morphology and number of skin lesions will depend on the interaction of host immunity, which is specific and individual, and fungus virulence. Some individuals have natural good immunity, which added to the low virulence of the fungus maintain the presence of well-marked granulomas with no microorganism and negative serology for a long time, making the diagnosis a challenge. Factors inherent to the fungus, however, may modulate the immune response and modify the clinical picture over the time. We present a sarcoidosis-like clinical presentation and discuss the immunological factors involved. PMID:23539015

[Thoracic nocardiosis - a clinical report].

PubMed

Vale, Artur; Guerra, Miguel; Martins, Daniel; Lameiras, Angelina; Miranda, José; Vouga, Luís

2014-01-01

Nocardia genus microorganisms are ubiquitous, Gram positive aerobic bacterias, responsible for disease mainly in immunocompromised hosts, with cellular immune response commitment. Inhalation is the main form of transmition and pulmonary disease is the most frequent presentation. Dissemination may occur by contiguity and also via hematogenous. The clinical and imaging presentation is not specific, and diagnosis is obtained after identification of Nocardia bacteria in biological samples. Since there are no reliable studies that indicate the best therapeutic option, treatment should be individualized and based on antimicrobial susceptibility testing. Surgical drainage should also be considered in all patients. The authors present a clinical case of a patient with thoracic nocardiosis, and make a short literature review on the theme.

Recombinant microorganisms for increased production of organic acids

DOEpatents

Yi, Jian [East Lansing, MI; Kleff, Susanne [East Lansing, MI; Guettler, Michael V [Holt, MI

2012-02-21

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

Recombinant microorganisms for increased production of organic acids

DOEpatents

Yi, Jian; Kleff, Susanne; Guettler, Michael V

2013-04-30

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

Retention of knowledge and perceived relevance of basic sciences in an integrated case-based learning (CBL) curriculum

PubMed Central

2013-01-01

Background Knowledge and understanding of basic biomedical sciences remain essential to medical practice, particularly when faced with the continual advancement of diagnostic and therapeutic modalities. Evidence suggests, however, that retention tends to atrophy across the span of an average medical course and into the early postgraduate years, as preoccupation with clinical medicine predominates. We postulated that perceived relevance demonstrated through applicability to clinical situations may assist in retention of basic science knowledge. Methods To test this hypothesis in our own medical student cohort, we administered a paper-based 50 MCQ assessment to a sample of students from Years 2 through 5. Covariates pertaining to demographics, prior educational experience, and the perceived clinical relevance of each question were also collected. Results A total of 232 students (Years 2–5, response rate 50%) undertook the assessment task. This sample had comparable demographic and performance characteristics to the whole medical school cohort. In general, discipline-specific and overall scores were better for students in the latter years of the course compared to those in Year 2; male students and domestic students tended to perform better than their respective counterparts in certain disciplines. In the clinical years, perceived clinical relevance was significantly and positively correlated with item performance. Conclusions This study suggests that perceived clinical relevance is a contributing factor to the retention of basic science knowledge and behoves curriculum planners to make clinical relevance a more explicit component of applied science teaching throughout the medical course. PMID:24099045

Does the choice of display system influence perception and visibility of clinically relevant features in digital pathology images?

NASA Astrophysics Data System (ADS)

Kimpe, Tom; Rostang, Johan; Avanaki, Ali; Espig, Kathryn; Xthona, Albert; Cocuranu, Ioan; Parwani, Anil V.; Pantanowitz, Liron

2014-03-01

Digital pathology systems typically consist of a slide scanner, processing software, visualization software, and finally a workstation with display for visualization of the digital slide images. This paper studies whether digital pathology images can look different when presenting them on different display systems, and whether these visual differences can result in different perceived contrast of clinically relevant features. By analyzing a set of four digital pathology images of different subspecialties on three different display systems, it was concluded that pathology images look different when visualized on different display systems. The importance of these visual differences is elucidated when they are located in areas of the digital slide that contain clinically relevant features. Based on a calculation of dE2000 differences between background and clinically relevant features, it was clear that perceived contrast of clinically relevant features is influenced by the choice of display system. Furthermore, it seems that the specific calibration target chosen for the display system has an important effect on the perceived contrast of clinically relevant features. Preliminary results suggest that calibrating to DICOM GSDF calibration performed slightly worse than sRGB, while a new experimental calibration target CSDF performed better than both DICOM GSDF and sRGB. This result is promising as it suggests that further research work could lead to better definition of an optimized calibration target for digital pathology images resulting in a positive effect on clinical performance.

Dominance of Saccharomyces cerevisiae in alcoholic fermentation processes: role of physiological fitness and microbial interactions.

PubMed

Albergaria, Helena; Arneborg, Nils

2016-03-01

Winemaking, brewing and baking are some of the oldest biotechnological processes. In all of them, alcoholic fermentation is the main biotransformation and Saccharomyces cerevisiae the primary microorganism. Although a wide variety of microbial species may participate in alcoholic fermentation and contribute to the sensory properties of end-products, the yeast S. cerevisiae invariably dominates the final stages of fermentation. The ability of S. cerevisiae to outcompete other microbial species during alcoholic fermentation processes, such as winemaking, has traditionally been ascribed to its high fermentative power and capacity to withstand the harsh environmental conditions, i.e. high levels of ethanol and organic acids, low pH values, scarce oxygen availability and depletion of certain nutrients. However, in recent years, several studies have raised evidence that S. cerevisiae, beyond its remarkable fitness for alcoholic fermentation, also uses defensive strategies mediated by different mechanisms, such as cell-to-cell contact and secretion of antimicrobial peptides, to combat other microorganisms. In this paper, we review the main physiological features underlying the special aptitude of S. cerevisiae for alcoholic fermentation and discuss the role of microbial interactions in its dominance during alcoholic fermentation, as well as its relevance for winemaking.

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

PubMed Central

O'Sullivan, Daniel J.; Giblin, Linda; McSweeney, Paul L. H.; Sheehan, Jeremiah J.; Cotter, Paul D.

2012-01-01

The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors. PMID:23346082

Study of Transport Characteristics of Motile Microorganisms Using Micro-Scale Devices

NASA Astrophysics Data System (ADS)

Parashar, R.; Scheibe, T. D.; Plymale, A.; Hu, D.; Kelly, R.; Frederick, J. M.; Yang, X.; Sund, N. L.

2016-12-01

Accurate numerical models of microbial transport are needed to support design and evaluation of bioremediation implementations. A sequence of micro-scale experiments using advanced microfluidics and imaging techniques was conducted to quantify the movement patterns of individual microbes and their interactions with solid surfaces in unobstructed medium and simple pore geometries. The set of bacteria studied encompasses strictly anaerobic, facultatively anaerobic, fermentative, and facultatively autotrophic species, with capacities to reduce a range of metals and radionuclides, as well as nitrate, using a variety of electron donors, including acetate, lactate, carbohydrates, and molecular hydrogen. Motion of motile microorganisms recorded over time provides results that can be analyzed to determine the character and several statistical attributes of microbial motion. Individual tracks on the order of several seconds to a few minutes in duration are characterized to provide information on 1) the length (distance in microns) of microbial runs, 2) velocity distributions along individual trajectories, and 3) the angle between the directions of sequential runs. Analysis of the microbial trajectories elucidates parameters related to dynamics of their motion. Comparison of these parameters with those of a classical Brownian motion yields crucial information on selection of appropriate model to account for microbial motility in relevant applications.

Synergistic effect of chickpea plants and Mesorhizobium as a natural system for chromium phytoremediation.

PubMed

Velez, Pilar A; Talano, Melina A; Paisio, Cintia E; Agostini, Elizabeth; González, Paola S

2017-09-01

The presence of chromium in soils not only affects the physiological processes of plants but also the microbial rhizosphere composition and metabolic activities of microorganisms. Hence, the inoculation of plants with Cr(VI)-tolerant rhizospheric microorganisms as an alternative to reduce Cr phytotoxicity was studied. In this work, chickpea germination was reduced by Cr(VI) concentrations of 150 and 250 mg/L (6 and 33%, respectively); however lower Cr(VI) concentrations negatively affected the biomass. On the other hand, its symbiont, Mesorhizobium ciceri, was able to grow and remove different Cr(VI) concentrations (5-20 mg/L). The inoculation of chickpea plants with this strain exposed to Cr(VI) showed a significantly enhanced plant growth. In addition, inoculated plants accumulated higher Cr concentration in roots than those noninoculated. It is important to note that Cr was not translocated to shoots independently of inoculation. These results suggest that Mesorhizobium's capability to remove Cr(VI) could be exploited for bioremediation. Moreover, chickpea plants would represent a natural system for phytoremediation or phytostabilization of Cr in situ that could be improved with M. ciceri inoculation. This strategy would be considered as a phytoremediation tool with great economic and ecological relevance.

The application of food safety interventions in primary production of beef and lamb: a review.

PubMed

Adam, K; Brülisauer, F

2010-07-31

The production of safe red meat depends on effective control of pathogenic microorganisms at all stages of the "farm-to-fork" chain. Eight microorganisms have been selected as the focus of the PathogenCombat project: Shiga toxin producing Escherichia coli (STEC), Mycobacterium avium subspecies paratuberculosis (Map), Listeria monocytogenes, Campylobacter jejuni, Penicillium nordicum, invasive variants of Saccharomyces cerevisiae, hepatitis E virus and tick borne encephalitis virus. The need and potential for coordinated control of the selected food-borne pathogens by on-farm interventions is assessed using a decision tree and a review of the relevant scientific literature. Control measures to reduce the carriage of these pathogens in ruminants prior to slaughter are reviewed with reference to the current regulations and guidelines relating to the primary production. From the eight pathogens investigated, two (STEC and Map), are likely to be effectively controlled by interventions at farm level and the applicable interventions are described and discussed. Ruminants are the main reservoir for these two pathogens; hence a reduction of carriage in livestock should directly reduce human exposure through the consumption of beef and lamb. Copyright 2009 Elsevier B.V. All rights reserved.

Epilactose production by 2 cellobiose 2-epimerases in natural milk.

PubMed

Krewinkel, Manuel; Gosch, Maria; Rentschler, Eva; Fischer, Lutz

2014-01-01

It was reported recently that cellobiose 2-epimerases (CE) from various aerobic microorganisms convert lactose to epilactose in defined buffer systems. In this study, we showed that CE from 2 mesophilic microorganisms, Flavobacterium johnsoniae and Pedobacter heparinus, were capable of converting lactose to prebiotic epilactose not only in buffer but also in a complex milk system. First, the 2 enzymes were separately cloned, recombinantly expressed in Escherichia coli, and purified by column chromatography. The production of F. johnsoniae CE was carried out in a stirred-tank reactor, indicating that future upscaling is possible. The bioconversions of milk lactose were carried out at an industrially relevant low temperature of 8°C to avoid undesired microbial contaminations or chemical side reactions. Both enzymes were reasonably active at this low temperature, because of their origin from mesophilic organisms. The enzymes showed different operational stabilities over a 24-h time-course. A conversion yield of about 30 to 33% epilactose was achieved with both enzymes. No side products were detected other than epilactose. Therefore, CE may introduce an added value for particular dairy products by in situ production of the prebiotic sugar epilactose. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Cellulase recycling in biorefineries--is it possible?

PubMed

Gomes, Daniel; Rodrigues, Ana Cristina; Domingues, Lucília; Gama, Miguel

2015-05-01

On a near future, bio-based economy will assume a key role in our lives. Lignocellulosic materials (e.g., agroforestry residues, industrial/solid wastes) represent a cheaper and environmentally friendly option to fossil fuels. Indeed, following suitable processing, they can be metabolized by different microorganisms to produce a wide range of compounds currently obtained by chemical synthesis. However, due to the recalcitrant nature of these materials, they cannot be directly used by microorganisms, the conversion of polysaccharides into simpler sugars being thus required. This conversion, which is usually undertaken enzymatically, represents a significant part on the final cost of the process. This fact has driven intense efforts on the reduction of the enzyme cost following different strategies. Here, we describe the fundamentals of the enzyme recycling technology, more specifically, cellulase recycling. We focus on the main strategies available for the recovery of both the liquid- and solid-bound enzyme fractions and discuss the relevant operational parameters (e.g., composition, temperature, additives, and pH). Although the efforts from the industry and enzyme suppliers are primarily oriented toward the development of enzyme cocktails able to quickly and effectively process biomass, it seems clear by now that enzyme recycling is technically possible.

Metabolic regulation in solventogenic clostridia: regulators, mechanisms and engineering.

PubMed

Yang, Yunpeng; Nie, Xiaoqun; Jiang, Yuqian; Yang, Chen; Gu, Yang; Jiang, Weihong

2018-02-22

Solventogenic clostridia, a group of important industrial microorganisms, have exceptional substrate and product diversity, capable of producing a series of two-carbon and even long-chain chemicals and fuels by using various substrates, including sugars, cellulose and hemicellulose, and C1 gases. For the sake of in-depth understanding and engineering these anaerobic microorganisms for broader applications, studies on metabolic regulation of solventogenic clostridia had been extensively carried out during the past ten years, based on the rapid development of various genetic tools. To date, a number of regulators that are essential for cell physiological and metabolic processes have been identified in clostridia, and the relevant mechanisms have also been dissected, providing a wealth of valuable information for metabolic engineering. Here, we reviewed the latest research progresses on the metabolic regulation for chemical production and substrate utilization in solventogenic clostridia, by focusing on three typical Clostridium species, the saccharolytic C. acetobutylicum and C. beijerinckii, as well as the gas-fermenting C. ljungdahlii. On this basis, future directions in the study and remodeling of clostridial regulation systems, were proposed for effective modification of these industrially important anaerobes. Copyright © 2018 Elsevier Inc. All rights reserved.

Neutrophil Apoptosis: Relevance to the Innate Immune Response and Inflammatory Disease

PubMed Central

Fox, Sarah; Leitch, Andrew E.; Duffin, Rodger; Haslett, Christopher; Rossi, Adriano G.

2010-01-01

Neutrophils are the most abundant cell type involved in the innate immune response. They are rapidly recruited to sites of injury or infection where they engulf and kill invading microorganisms. Neutrophil apoptosis, the process of programmed cell death that prevents the release of neutrophil histotoxic contents, is tightly regulated and limits the destructive capacity of neutrophil products to surrounding tissue. The subsequent recognition and phagocytosis of apoptotic cells by phagocytic cells such as macrophages is central to the successful resolution of an inflammatory response and it is increasingly apparent that the dying neutrophil itself exerts an anti-inflammatory effect through modulation of surrounding cell responses, particularly macrophage inflammatory cytokine release. Apoptosis may be delayed, induced or enhanced by micro-organisms dependent on their immune evasion strategies and the health of the host they encounter. There is now an established field of research aimed at understanding the regulation of apoptosis and its potential as a target for therapeutic intervention in inflammatory and infective diseases. This review focuses on the physiological regulation of neutrophil apoptosis with respect to the innate immune system and highlights recent advances in mechanistic understanding of apoptotic pathways and their therapeutic manipulation in appropriate and excessive innate immune responses. PMID:20375550

In vitro antimicrobial activities of metabolites from vaginal Lactobacillus strains against Clostridium perfringens isolated from a woman's vagina.

PubMed

Amin, Mansour; Moradi Choghakabodi, Parastoo; Alhassan Hamidi, Mohammad; Najafian, Mahin; Farajzadeh Sheikh, Ahmad

2017-01-01

More than 50 different species of bacteria may live in a woman's vagina, with lactobacilli being the predominant microorganism found in healthy adult females. Lactobacilli are relevant as a barrier to infection and are important in the impairment of colonization by pathogens, owing to competitive adherence to adhesion sites in the vaginal epithelium and their capacity to produce antimicrobial compounds. The aim of the present study was to demonstrate the inhibitory capability of Lactobacillus metabolites against Clostridium perfringens, an anaerobic Gram-positive bacterium. These bacteria were isolated from vaginal swabs by using culture-dependent approaches, and the bacteriostatic effect of Lactobacillus metabolites, extracted from different isolates, was assessed using a modified E test. Among the 100 vaginal swabs, 59 (59%) samples showed the presence of Lactobacillus strains and only one sample contained C. perfringens. Lactobacillus metabolites demonstrated the significant potency of in vitro activity against C. perfringens, with minimal inhibitory concentration values ranging from 15.6 μg/mL to 31.2 μg/mL. This study suggests that women without vaginal Lactobacillus strains may be susceptible to nonindigenous and potentially harmful microorganisms. Copyright © 2016. Published by Elsevier Taiwan LLC.

Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

PubMed Central

Moreira, Cristiana; Vasconcelos, Vitor; Antunes, Agostinho

2013-01-01

Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins. PMID:24189276

Detecting clinically relevant new information in clinical notes across specialties and settings.

PubMed

Zhang, Rui; Pakhomov, Serguei V S; Arsoniadis, Elliot G; Lee, Janet T; Wang, Yan; Melton, Genevieve B

2017-07-05

Automated methods for identifying clinically relevant new versus redundant information in electronic health record (EHR) clinical notes is useful for clinicians and researchers involved in patient care and clinical research, respectively. We evaluated methods to automatically identify clinically relevant new information in clinical notes, and compared the quantity of redundant information across specialties and clinical settings. Statistical language models augmented with semantic similarity measures were evaluated as a means to detect and quantify clinically relevant new and redundant information over longitudinal clinical notes for a given patient. A corpus of 591 progress notes over 40 inpatient admissions was annotated for new information longitudinally by physicians to generate a reference standard. Note redundancy between various specialties was evaluated on 71,021 outpatient notes and 64,695 inpatient notes from 500 solid organ transplant patients (April 2015 through August 2015). Our best method achieved at best performance of 0.87 recall, 0.62 precision, and 0.72 F-measure. Addition of semantic similarity metrics compared to baseline improved recall but otherwise resulted in similar performance. While outpatient and inpatient notes had relatively similar levels of high redundancy (61% and 68%, respectively), redundancy differed by author specialty with mean redundancy of 75%, 66%, 57%, and 55% observed in pediatric, internal medicine, psychiatry and surgical notes, respectively. Automated techniques with statistical language models for detecting redundant versus clinically relevant new information in clinical notes do not improve with the addition of semantic similarity measures. While levels of redundancy seem relatively similar in the inpatient and ambulatory settings in the Fairview Health Services, clinical note redundancy appears to vary significantly with different medical specialties.

The Effects of Clinically Relevant Multiple-Choice Items on the Statistical Discrimination of Physician Clinical Competence.

ERIC Educational Resources Information Center

Downing, Steven M.; Maatsch, Jack L.

To test the effect of clinically relevant multiple-choice item content on the validity of statistical discriminations of physicians' clinical competence, data were collected from a field test of the Emergency Medicine Examination, test items for the certification of specialists in emergency medicine. Two 91-item multiple-choice subscales were…

Microorganisms with Claimed Probiotic Properties: An Overview of Recent Literature

PubMed Central

Fijan, Sabina

2014-01-01

Probiotics are defined as live microorganisms, which when administered in adequate amounts, confer a health benefit on the host. Health benefits have mainly been demonstrated for specific probiotic strains of the following genera: Lactobacillus, Bifidobacterium, Saccharomyces, Enterococcus, Streptococcus, Pediococcus, Leuconostoc, Bacillus, Escherichia coli. The human microbiota is getting a lot of attention today and research has already demonstrated that alteration of this microbiota may have far-reaching consequences. One of the possible routes for correcting dysbiosis is by consuming probiotics. The credibility of specific health claims of probiotics and their safety must be established through science-based clinical studies. This overview summarizes the most commonly used probiotic microorganisms and their demonstrated health claims. As probiotic properties have been shown to be strain specific, accurate identification of particular strains is also very important. On the other hand, it is also demonstrated that the use of various probiotics for immunocompromised patients or patients with a leaky gut has also yielded infections, sepsis, fungemia, bacteraemia. Although the vast majority of probiotics that are used today are generally regarded as safe and beneficial for healthy individuals, caution in selecting and monitoring of probiotics for patients is needed and complete consideration of risk-benefit ratio before prescribing is recommended. PMID:24859749

A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM).

PubMed

Iwasaki, Yuki; Abe, Takashi; Wada, Kennosuke; Wada, Yoshiko; Ikemura, Toshimichi

2013-11-20

With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.

Antibiosis of vineyard ecosystem fungi against food-borne microorganisms.

PubMed

Cueva, Carolina; Moreno-Arribas, M Victoria; Bartolomé, Begoña; Salazar, Óscar; Vicente, M Francisca; Bills, Gerald F

2011-12-01

Fermentation extracts from fungi isolated from vineyard ecosystems were tested for antimicrobial activities against a set of test microorganisms, including five food-borne pathogens (Staphylococcus aureus EP167, Acinetobacter baumannii (clinically isolated), Pseudomonas aeruginosa PAO1, Escherichia coli O157:H7 (CECT 5947) and Candida albicans MY1055) and two probiotic bacteria (Lactobacillus plantarum LCH17 and Lactobacillus brevis LCH23). A total of 182 fungi was grown in eight different media, and the fermentation extracts were screened for antimicrobial activity. A total of 71 fungi produced extracts active against at least one pathogenic microorganism, but not against any probiotic bacteria. The Gram-positive bacterium S. aureus EP167 was more susceptible to antimicrobial fungi broth extracts than Gram-negative bacteria and pathogenic fungi. Identification of active fungi based on internal transcribed spacer rRNA sequence analysis revealed that species in the orders Pleosporales, Hypocreales and Xylariales dominated. Differences in antimicrobial selectivity were observed among isolates from the same species. Some compounds present in the active extracts were tentatively identified by liquid chromatography-mass spectrometry. Antimicrobial metabolites produced by vineyard ecosystem fungi may potentially limit colonization and spoilage of food products by food-borne pathogens, with minimal effect on probiotic bacteria. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Diagnostic Evasion of Highly-Resistant Microorganisms: A Critical Factor in Nosocomial Outbreaks.

PubMed

Zhou, Xuewei; Friedrich, Alexander W; Bathoorn, Erik

2017-01-01

Highly resistant microorganisms (HRMOs) may evade screening strategies used in routine diagnostics. Bacteria that have evolved to evade diagnostic tests may have a selective advantage in the nosocomial environment. Evasion of resistance detection can result from the following mechanisms: low-level expression of resistance genes not resulting in detectable resistance, slow growing variants, mimicry of wild-type-resistance, and resistance mechanisms that are only detected if induced by antibiotic pressure. We reviewed reports on hospital outbreaks in the Netherlands over the past 5 years. Remarkably, many outbreaks including major nation-wide outbreaks were caused by microorganisms able to evade resistance detection by diagnostic screening tests. We describe various examples of diagnostic evasion by several HRMOs and discuss this in a broad and international perspective. The epidemiology of hospital-associated bacteria may strongly be affected by diagnostic screening strategies. This may result in an increasing reservoir of resistance genes in hospital populations that is unnoticed. The resistance elements may horizontally transfer to hosts with systems for high-level expression, resulting in a clinically significant resistance problem. We advise to communicate the identification of HRMOs that evade diagnostics within national and regional networks. Such signaling networks may prevent inter-hospital outbreaks, and allow collaborative development of adapted diagnostic tests.

Field Ionization Mass Spectrometric Rapid Diagnosis of Infectious Diseases

DTIC Science & Technology

1975-10-01

microorganisms following extraction. We also planned to examine artificial growth media.for changes in chemical composition following short periods of...patients suffering from infectious diseases, particularly, infec- tious hepatitis and mononucleosis . LI. 4 ’V iiN II. Carry out the same type of...analytical chemi- stry determines quantitatively one constituent at a time. When applied I to clinical diagnosis of metabolic disorders, from hormone

[Bacteremia associated with mycotic aneurysm of the transversal aortic arch and myocarditis caused by Salmonella enteritidis].

PubMed

Martínez-Martínez, L; Mesa, E; Rodríguez, J E; Sánchez, M P; Ugarte, J; Algora Weber, A; Dámaso, D; Daza, R M; Mendaza, P

1989-02-01

A 60-year-old male with diabetes mellitus had Salmonella enteritidis bacteremia associated with mycotic aneurysm of the transverse aortic arc and myocarditis. Antibiotic therapy with ampicillin and chloramphenicol was ineffective despite the fact that the microorganism was sensitive in vitro to those antimicrobials, and the patient had a progressive clinical deterioration which culminated in death.

Risk of Adverse Health Effects Due to Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Oubre, Cherie; Wallace, Sarah; Mehta, Satish; Pierson, Duane

2016-01-01

Numerous spaceflight experiments have been conducted to investigate alterations in microbial responses resulting from culture during spaceflight and spaceflight-analogs. However, recent studies investigating spaceflight-associated alterations in microbial virulence have initiated the review and production of evidence to better understand the impact these alterations would have on the incidence of infectious disease during a spaceflight exploration mission. The preponderance of evidence indicates that alterations in microbial gene expression and phenotype (including virulence) are occurring; however, the clinical implications of such changes are still unclear. Greater knowledge is required including a better understanding of the mechanism behind unique spaceflight-associated microbial responses to determine how this environmental stimulus impacts various microorganisms, their diversity and concentration in the spacecraft and crew microbiome, their impact on the vehicle and crew, and their resistance to current mitigation and antibiotic regimens. This knowledge will enable us to determine requirements, guidelines, and processes for design and monitoring of the next generation vehicles.

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling

PubMed Central

Magennis, E. Peter; Fernandez-Trillo, Francisco; Sui, Cheng; Spain, Sebastian G.; Bradshaw, David; Churchley, David; Mantovani, Giuseppe; Winzer, Klaus; Alexander, Cameron

2014-01-01

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms, for diagnostic or anti-infective applications, but which can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerisation of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms which produced them. This ‘bacteria-instructed synthesis’ can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the ‘instructing’ cell types. We further expand on the bacterial redox chemistries to ‘click’ fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualisation of pathogens. PMID:24813421

Osteomyelitis: a descriptive study.

PubMed

Prieto-Pérez, Laura; Pérez-Tanoira, Ramón; Petkova-Saiz, Elizabet; Pérez-Jorge, Concepción; Lopez-Rodriguez, Cristina; Alvarez-Alvarez, Beatriz; Polo-Sabau, Jorge; Esteban, Jaime

2014-03-01

To analyze the incidence and clinical-microbiological characteristics of osteomyelitis (OM) in a tertiary Spanish hospital. All cases diagnosed with OM between January 2007 and December 2010 were retrospectively reviewed. The variables examined include epidemiological characteristics, risk factors, affected bone, radiographic changes, histology, microbiological culture results, antibiotic treatment, and the need for surgery. Sixty-three cases of OM were diagnosed. Twenty-six patients (41.3%) had acute OM whereas 37 patients (58.7%) were classified as chronic OM. OM may result from haematogenous or contiguous microbial seeding. In this group, 49 patients (77.8%) presented with OM secondary to a contiguous source of infection and 14 patients had hematogenous OM (22.2%). Staphylococcus aureus was the most commonly found microorganism. OM mainly affected patients with risk factors related to the presence of vascular diseases. Antibiotic treatment must be guided by susceptibility patterns of individual microorganisms, although it must be performed together with surgery in most of the cases.

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling

NASA Astrophysics Data System (ADS)

Magennis, E. Peter; Fernandez-Trillo, Francisco; Sui, Cheng; Spain, Sebastian G.; Bradshaw, David J.; Churchley, David; Mantovani, Giuseppe; Winzer, Klaus; Alexander, Cameron

2014-07-01

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms for diagnostic or anti-infective applications, but that can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerization of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms that produced them. This ‘bacteria-instructed synthesis’ can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the ‘instructing’ cell types. We further expand on the bacterial redox chemistries to ‘click’ fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualization of pathogens.

[The microbiology laboratory: a key participant in transplantation].

PubMed

Pérez, José L; Pumarola, Tomàs

2007-04-01

Together with organ rejection, infectious complications are still the most important cause of morbidity and mortality in organ transplant recipients. Many infectious complications have an exogenous origin, including those produced by organ-transmitted pathogens, whereas others are caused by latent microorganisms that become reactivated in the recipient. Accurate pre-transplantation assessment of the organ donor as well as the recipient can prevent some infectious complications or reduce their detrimental effects during the post-transplant period. A wide range of primary and opportunistic microorganisms can affect transplant recipients, and a detailed description of these pathogens is beyond the scope of this study. However, the importance of microbiology laboratories in centers with transplant programs and the need for integration and active participation of clinical microbiologists in multidisciplinary transplant teams should be emphasized. The work of these professionals is a key requisite to establish accurate diagnoses of infectious complications, which will benefit the patient and optimize the expenditure of resources.

Medical Entomology: A Reemerging Field of Research to Better Understand Vector-Borne Infectious Diseases.

PubMed

Laroche, Maureen; Bérenger, Jean-Michel; Delaunay, Pascal; Charrel, Remi; Pradines, Bruno; Berger, Franck; Ranque, Stéphane; Bitam, Idir; Davoust, Bernard; Raoult, Didier; Parola, Philippe

2017-08-15

In the last decade, the Chikungunya and Zika virus outbreaks have turned public attention to the possibility of the expansion of vector-borne infectious diseases worldwide. Medical entomology is focused on the study of arthropods involved in human health. We review here some of the research approaches taken by the medical entomology team of the University Hospital Institute (UHI) Méditerranée Infection of Marseille, France, with the support of recent or representative studies. We propose our approaches to technical innovations in arthropod identification and the detection of microorganisms in arthropods, the use of arthropods as epidemiological or diagnostic tools, entomological investigations around clinical cases or within specific populations, and how we have developed experimental models to decipher the interactions between arthropods, microorganisms, and humans. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Ozone and caries: a review of the literature.

PubMed

Burke, F J Trevor

2012-05-01

Ozone, either in gaseous form or as ozonated water, has been available for use as a treatment for dental caries for a decade. This paper reviews the literature on the subject by examining the findings of publications in the peer review literature. Eighteen papers were identified by a literature search. From the review of these, it was concluded that, while some laboratory studies and some short duration clinical studies have suggested that ozone may be effective in the treatment of root caries or killing of oral micro-organisms, the clinical evidence for the use of ozone in treatment of caries is not compelling.

Impact of a novel teaching method based on feedback, activity, individuality and relevance on students' learning.

PubMed

Edafe, Ovie; Brooks, William S; Laskar, Simone N; Benjamin, Miles W; Chan, Philip

2016-03-20

This study examines the perceived impact of a novel clinical teaching method based on FAIR principles (feedback, activity, individuality and relevance) on students' learning on clinical placement. This was a qualitative research study. Participants were third year and final year medical students attached to one UK vascular firm over a four-year period (N=108). Students were asked to write a reflective essay on how FAIRness approach differs from previous clinical placement, and its advantages and disadvantages. Essays were thematically analysed and globally rated (positive, negative or neutral) by two independent researchers. Over 90% of essays reported positive experiences of feedback, activity, individuality and relevance model. The model provided multifaceted feedback; active participation; longitudinal improvement; relevance to stage of learning and future goals; structured teaching; professional development; safe learning environment; consultant involvement in teaching. Students perceived preparation for tutorials to be time intensive for tutors/students; a lack of teaching on medical sciences and direct observation of performance; more than once weekly sessions would be beneficial; some issues with peer and public feedback, relevance to upcoming exam and large group sizes. Students described negative experiences of "standard" clinical teaching. Progressive teaching programmes based on the FAIRness principles, feedback, activity, individuality and relevance, could be used as a model to improve current undergraduate clinical teaching.

Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes?

PubMed

Marmeisse, Roland; Kellner, Harald; Fraissinet-Tachet, Laurence; Luis, Patricia

2017-09-01

Eukaryotic microorganisms from diverse environments encompass a large number of taxa, many of them still unknown to science. One strategy to mine these organisms for genes of biotechnological relevance is to use a pool of eukaryotic mRNA directly extracted from environmental samples. Recent reports demonstrate that the resulting metatranscriptomic cDNA libraries can be screened by expression in yeast for a wide range of genes and functions from many of the different eukaryotic taxa. In combination with novel emerging high-throughput technologies, we anticipate that this approach should contribute to exploring the functional diversity of the eukaryotic microbiota. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biomass growth restriction in a packed bed reactor

DOEpatents

Griffith, William L.; Compere, Alicia L.

1978-01-01

When carrying out continuous biologically catalyzed reactions with anaerobic microorganisms attached to a support in an upflow packed bed column, growth of the microorganisms is restricted to prevent the microorganisms from plugging the column by limiting the availability of an essential nutrient and/or by the presence of predatory protozoa which consume the anaerobic microorganisms. A membrane disruptive detergent may be provided in the column to lyse dead microorganisms to make them available as nutrients for live microorganisms.

Microorganism immobilization

DOEpatents

Compere, Alicia L.; Griffith, William L.

1981-01-01

Live metabolically active microorganisms are immobilized on a solid support by contacting particles of aggregate material with a water dispersible polyelectrolyte such as gelatin, crosslinking the polyelectrolyte by reacting it with a crosslinking agent such as glutaraldehyde to provide a crosslinked coating on the particles of aggregate material, contacting the coated particles with live microorganisms and incubating the microorganisms in contact with the crosslinked coating to provide a coating of metabolically active microorganisms. The immobilized microorganisms have continued growth and reproduction functions.

Evaluation of the Broad-Range PCR/ESI-MS Technology in Blood Specimens for the Molecular Diagnosis of Bloodstream Infections.

PubMed

Jordana-Lluch, Elena; Giménez, Montserrat; Quesada, M Dolores; Rivaya, Belén; Marcó, Clara; Domínguez, M Jesús; Arméstar, Fernando; Martró, Elisa; Ausina, Vicente

2015-01-01

Rapid identification of the etiological agent in bloodstream infections is of vital importance for the early administration of the most appropriate antibiotic therapy. Molecular methods may offer an advantage to current culture-based microbiological diagnosis. The goal of this study was to evaluate the performance of IRIDICA, a platform based on universal genetic amplification followed by mass spectrometry (PCR/ESI-MS) for the molecular diagnosis of sepsis-related pathogens directly from the patient's blood. A total of 410 whole blood specimens from patients admitted to Emergency Room (ER) and Intensive Care Unit (ICU) with clinical suspicion of sepsis were tested with the IRIDICA BAC BSI Assay (broad identification of bacteria and Candida spp.). Microorganisms grown in culture and detected by IRIDICA were compared considering blood culture as gold standard. When discrepancies were found, clinical records and results from other cultures were taken into consideration (clinical infection criterion). The overall positive and negative agreement of IRIDICA with blood culture in the analysis by specimen was 74.8% and 78.6%, respectively, rising to 76.9% and 87.2% respectively, when compared with the clinical infection criterion. Interestingly, IRIDICA detected 41 clinically significant microorganisms missed by culture, most of them from patients under antimicrobial treatment. Of special interest were the detections of one Mycoplasma hominis and two Mycobacterium simiae in immunocompromised patients. When ICU patients were analyzed separately, sensitivity, specificity, positive and negative predictive values compared with blood culture were 83.3%, 78.6%, 33.9% and 97.3% respectively, and 90.5%, 87.2%, 64.4% and 97.3% respectively, in comparison with the clinical infection criterion. IRIDICA is a promising technology that offers an early and reliable identification of a wide variety of pathogens directly from the patient's blood within 6h, which brings the opportunity to improve management of septic patients, especially for those critically ill admitted to the ICU.

There's an App for That? Highlighting the Difficulty in Finding Clinically Relevant Smartphone Applications.

PubMed

Wiechmann, Warren; Kwan, Daniel; Bokarius, Andrew; Toohey, Shannon L

2016-03-01

The use of personal mobile devices in the medical field has grown quickly, and a large proportion of physicians use their mobile devices as an immediate resource for clinical decision-making, prescription information and other medical information. The iTunes App Store (Apple, Inc.) contains approximately 20,000 apps in its "Medical" category, providing a robust repository of resources for clinicians; however, this represents only 2% of the entire App Store. The App Store does not have strict criteria for identifying content specific to practicing physicians, making the identification of clinically relevant content difficult. The objective of this study is to quantify the characteristics of existing medical applications in the iTunes App Store that could be used by emergency physicians, residents, or medical students. We found applications related to emergency medicine (EM) by searching the iTunes App Store for 21 terms representing core content areas of EM, such as "emergency medicine," "critical care," "orthopedics," and "procedures." Two physicians independently reviewed descriptions of these applications in the App Store and categorized each as the following: Clinically Relevant, Book/Published Source, Non-English, Study Tools, or Not Relevant. A third physician reviewer resolved disagreements about categorization. Descriptive statistics were calculated. We found a total of 7,699 apps from the 21 search terms, of which 17.8% were clinical, 9.6% were based on a book or published source, 1.6% were non-English, 0.7% were clinically relevant patient education resources, and 4.8% were study tools. Most significantly, 64.9% were considered not relevant to medical professionals. Clinically relevant apps make up approximately 6.9% of the App Store's "Medical" Category and 0.1% of the overall App Store. Clinically relevant apps represent only a small percentage (6.9%) of the total App volume within the Medical section of the App Store. Without a structured search-and-evaluation strategy, it may be difficult for the casual user to identify this potentially useful content. Given the increasing adoption of devices in healthcare, national EM associations should consider curating these resources for their members.

A randomized trial comparing INR monitoring devices in patients with anticoagulation self-management: evaluation of a novel error-grid approach.

PubMed

Hemkens, Lars G; Hilden, Kristian M; Hartschen, Stephan; Kaiser, Thomas; Didjurgeit, Ulrike; Hansen, Roland; Bender, Ralf; Sawicki, Peter T

2008-08-01

In addition to the metrological quality of international normalized ratio (INR) monitoring devices used in patients' self-management of long-term anticoagulation, the effectiveness of self-monitoring with such devices has to be evaluated under real-life conditions with a focus on clinical implications. An approach to evaluate the clinical significance of inaccuracies is the error-grid analysis as already established in self-monitoring of blood glucose. Two anticoagulation monitors were compared in a real-life setting and a novel error-grid instrument for oral anticoagulation has been evaluated. In a randomized crossover study 16 patients performed self-management of anticoagulation using the INRatio and the CoaguChek S system. Main outcome measures were clinically relevant INR differences according to established criteria and to the error-grid approach. A lower rate of clinically relevant disagreements according to Anderson's criteria was found with CoaguChek S than with INRatio without statistical significance (10.77% vs. 12.90%; P = 0.787). Using the error-grid we found principally consistent results: More measurement pairs with discrepancies of no or low clinical relevance were found with CoaguChek S, whereas with INRatio we found more differences with a moderate clinical relevance. A high rate of patients' satisfaction with both of the point of care devices was found with only marginal differences. A principal appropriateness of the investigated point-of-care devices to adequately monitor the INR is shown. The error-grid is useful for comparing monitoring methods with a focus on clinical relevance under real-life conditions beyond assessing the pure metrological quality, but we emphasize that additional trials using this instrument with larger patient populations are needed to detect differences in clinically relevant disagreements.

Distribution and clinical determinants of time-to-positivity of blood cultures in patients with neutropenia.

PubMed

Lambregts, Merel M C; Warreman, Eva B; Bernards, Alexandra T; Veelken, Hendrik; von dem Borne, Peter A; Dekkers, Olaf M; Visser, Leo G; de Boer, Mark G

2018-02-01

Blood cultures (BCs) are essential in the evaluation of neutropenic fever. Modern BC systems have significantly reduced the time-to-positivity (TTP) of BC. This study explores the probability of bacteraemia when BCs have remained negative for different periods of time. All adult patients with neutropenia and bacteraemia were included (January 2012-February 2016). Predictive clinical factors for short (≤16 hours) and long (>24 hours) TTP were determined. The residual probability of bacteraemia was estimated for the scenario of negative BC 24 hours after collection. The cohort consisted of 154 patients, accounting for 190 episodes of bacteraemia. Median age of 61 years, 60.5% were male. In 123 (64.7%) episodes, BC yielded a single Gram-positive micro-organism and in 49 (25.8%) a Gram-negative micro-organism (median TTP 16.7, 14.5 hours respectively, P < .01). TTP was ≤24 hours in 91.6% of episodes. Central line-associated bacteraemia was associated with long TTP. The probability of bacteraemia if BC had remained negative for 24 hours was 1%-3%. The expected TTP offers guidance in the management of patients with neutropenia and suspected bacteraemia. The knowledge of negative BC can support a change in working diagnosis, and impact clinical decisions as soon as 24 hours after BC collection. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Sensitivity and Predictive Value of 15 PubMed Search Strategies to Answer Clinical Questions Rated Against Full Systematic Reviews

PubMed Central

Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

2012-01-01

Background Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. Objective To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. Methods We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed’s Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. Results The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%–25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P < .001 compared with unfiltered queries) and positive predictive values of 20%–30% (P < .001 compared with unfiltered queries). This benefit was consistent for most clinical questions. Searches based on related articles retrieved about a third of the relevant studies. Conclusions The Clinical Queries narrow filter, along with well-formulated queries based on the PICO framework, provided the greatest aid in retrieving relevant clinical trials within the 2 first PubMed pages. These results can help clinicians apply effective strategies to answer their questions at the point of care. PMID:22693047

Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews.

PubMed

Agoritsas, Thomas; Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

2012-06-12

Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed's Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%-25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P < .001 compared with unfiltered queries) and positive predictive values of 20%-30% (P < .001 compared with unfiltered queries). This benefit was consistent for most clinical questions. Searches based on related articles retrieved about a third of the relevant studies. The Clinical Queries narrow filter, along with well-formulated queries based on the PICO framework, provided the greatest aid in retrieving relevant clinical trials within the 2 first PubMed pages. These results can help clinicians apply effective strategies to answer their questions at the point of care.

Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

DOE PAGES

Hausmann, Bela; Knorr, Klaus-Holger; Schreck, Katharina; ...

2016-03-25

A cryptic sulfur cycle and effectively competes with methanogenic degradation pathways sustains dissimilatory sulfate reduction in peatlands. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16–174 nmol cm –3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (greater than or equalmore » to0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. The most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.« less

Microbiota dynamics and diversity at different stages of industrial processing of cocoa beans into cocoa powder.

PubMed

Lima, Lídia J R; van der Velpen, Vera; Wolkers-Rooijackers, Judith; Kamphuis, Henri J; Zwietering, Marcel H; Nout, M J Rob

2012-04-01

We sampled a cocoa powder production line to investigate the impact of processing on the microbial community size and diversity at different stages. Classical microbiological methods were combined with 16S rRNA gene PCR-denaturing gradient gel electrophoresis, coupled with clone library construction, to analyze the samples. Aerobic thermoresistant spores (ThrS) (100°C; 10 min) were also isolated and characterized (identity, genetic diversity, and spore heat resistance), in view of their relevance to the quality of downstream heat-treated cocoa-flavored drinks. In the nibs (broken, shelled cocoa beans), average levels of total aerobic microorganisms (TAM) (4.4 to 5.6 log CFU/g) and aerobic total spores (TS) (80°C; 10 min; 4.3 to 5.5 log CFU/g) were significantly reduced (P < 0.05) as a result of alkalizing, while fungi (4.2 to 4.4 log CFU/g) and Enterobacteriaceae (1.7 to 2.8 log CFU/g) were inactivated to levels below the detection limit, remaining undetectable throughout processing. Roasting further decreased the levels of TAM and TS, but they increased slightly during subsequent processing. Molecular characterization of bacterial communities based on enriched cocoa samples revealed a predominance of members of the Bacillaceae, Pseudomonadaceae, and Enterococcaceae. Eleven species of ThrS were found, but Bacillus licheniformis and the Bacillus subtilis complex were prominent and revealed great genetic heterogeneity. We concluded that the microbiota of cocoa powder resulted from microorganisms that could have been initially present in the nibs, as well as microorganisms that originated during processing. B. subtilis complex members, particularly B. subtilis subsp. subtilis, formed the most heat-resistant spores. Their occurrence in cocoa powder needs to be considered to ensure the stability of derived products, such as ultrahigh-temperature-treated chocolate drinks.

Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture.

PubMed

Simmons, Christopher W; Reddy, Amitha P; Vandergheynst, Jean S; Simmons, Blake A; Singer, Steven W

2014-01-01

The use of ionic liquids (ILs) to disrupt the recalcitrant structure of lignocellulose and make polysaccharides accessible to hydrolytic enzymes is an emerging technology for biomass pretreatment in lignocellulosic biofuel production. Despite efforts to reclaim and recycle IL from pretreated biomass, residual IL can be inhibitory to microorganisms used for downstream fermentation. As a result, pathways for IL tolerance are needed to improve the activity of fermentative organisms in the presence of IL. In this study, microbial communities from compost were cultured under high-solids and thermophilic conditions in the presence of 1-ethyl-3-methylimidazolium-based ILs to enrich for IL-tolerant microorganisms. A strain of Bacillus coagulans isolated from an IL-tolerant community was grown in liquid and solid-state culture in the presence of the ILs 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) or 1-ethyl-3-methylimidazolium chloride ([C2mim][Cl]) to gauge IL tolerance. Viability and respiration varied with the concentration of IL applied and the type of IL used. B. coagulans maintained growth and respiration in the presence of 4 wt% IL, a concentration similar to that present on IL-pretreated biomass. In the presence of both [C2mim][OAc] and [C2mim][Cl] in liquid culture, B. coagulans grew at a rate approximately half that observed in the absence of IL. However, in solid-state culture, the bacteria were significantly more tolerant to [C2mim][Cl] compared with [C2mim][OAc]. B. coagulans tolerance to IL under industrially relevant conditions makes it a promising bacterium for understanding mechanisms of IL tolerance and discovering IL tolerance pathways for use in other microorganisms, particularly those used in bioconversion of IL-pretreated plant biomass. © 2013 American Institute of Chemical Engineers.