Microbiological Material Research Articles

Statistical characterisation of bio-aerosol background in an urban environment

In this paper we statistically characterise the bio-aerosol background in an urban environment. To do this we measure concentration levels of naturally occurring microbiological material in the atmosphere over several days. Naturally occurring bio-aerosols can be considered as noise, as they mask the presence of signals coming from biological material of interest (such as an intentionally released biological agent). Analysis of this ‘biobackground’ was undertaken in the 1–10 μm size range and a 3–9% contribution was found to be biological in origin – values which are in good agreement with other studies reported in the literature. A model based on the physics of turbulent mixing and dispersion was developed and validated against this analysis. The Gamma distribution (the basis of our model) is shown to comply with the scaling laws of the concentration moments of our data, which enables us to universally characterise both biological and non-biological material in the atmosphere. An application of this model is proposed to build a framework for the development of novel algorithms for bio-aerosol detection and rapid characterisation.

Electrochemistry of Escherichia coli JM109: Direct electron transfer and antibiotic resistance

In this study, the cyclic voltammetry (CV) and square wave voltammetry (SWV) techniques were used to investigate the extracellular electron transfer from Escherichia coli JM109. It was demonstrated that the formal redox potential of direct electron transfer between electrode and an E. coli JM109 cell in aerobic buffer corresponds to −0.42 V vs. Ag/AgCl. Based on the electroactivity of bacterial cells, the electrochemical system for definition of sensitivity of microbiological material to antibiotics cefepime, ampicillin, amikacin, and erythromycin was proposed. The results obtained indicate that with electrochemical methods it is possible to provide screening of potential drugs for bacterial diseases. The electrochemical method allows estimating the degree of E. coli JM109 cells resistance to antibiotics within 2–5 h using disposable screen-printed graphite electrodes.

Clinical laboratory waste management in Shiraz, Iran

Clinical laboratories are significant generators of infectious waste, including microbiological materials, contaminated sharps, and pathologic wastes such as blood specimens and blood products. Most waste produced in laboratories can be disposed of in the general solid waste stream. However, improper management of infectious waste, including mixing general wastes with infectious wastes and improper handling or storage, could lead to disease transmission. The aim of this study was to assess waste management processes used at clinical laboratories in Shiraz, Iran. One hundred and nine clinical laboratories participated In this cross sectional study, Data collection was by questionnaire and direct observation. Of the total amount of waste generated, 52% (by weight) was noninfectious domestic waste, 43% was non-sharps infectious waste and 5% consisted of sharps. There was no significant relationship between laboratory staff or manager education and the score for quality of waste collection and disposal at clinical laboratories. Improvements in infectious waste management processes should involve clearer, more uniformly accepted definitions of infectious waste and increased staff training.

Effects of Asian Sand Dust on Mucin Gene Expression and Activation of Nasal Polyp Epithelial Cells

Asian sand dust (ASD) contains a variety of chemical and microbiological materials such as lipopolysaccharide (LPS) and beta-glucan that can cause inflammation. The increase in the atmospheric concentration of ASD has been associated with asthma severity and adverse effects on respiratory function. The aim of this study was to evaluate the effect of ASD on the inflammatory process and mucin gene expression in nasal epithelial cells. Primary nasal polyp epithelial cells were exposed to ASD for 72 hours, and then the supernatants were collected. To determine the activation of the epithelial cells, IL-6, IL-8, and granulocyte-macrophage colony-stimulating factor were measured. In addition, the potential cytotoxic effects of ASD on the epithelial cells were evaluated. Quantitative reverse-transcription polymerase chain reaction for MUC4, MUC5AC, MUC5B, and MUC8 mRNA expression, in the nasal epithelial cells, was performed. ASD stimulated the production of chemical mediators in a time-dependent manner. The cytokine production was highest at 100 micrograms/mL of ASD. MUC4 and MUC5B mRNA expression was significantly increased at 10 and 50 micrograms/mL of ASD. Atomospheric exposure to various chemical species and microbiological materials carrying ASD may affect upper airway inflammation through the production of inflammatory cytokines and mucin.

Development and validation of stable reference materials for food microbiology using Bacillus cereus and Clostridium perfringens spores

To develop a new type of microbiological Reference Materials (RMs), displaying long-term stability at room temperature. The purpose was to produce and validate two batches of RMs for the enumeration of Bacillus cereus and Clostridium perfringens. The RMs were based on spores of B. cereus and Cl. perfringens, adsorbed on calcium carbonate pellets. Two batches of 1000 units were manufactured and validated in compliance with ISO guide 35. After verification of their homogeneity, the stability of the 'RM-B. cereus' and 'RM-Cl. perfringens' batches was proven during at least 36 and 9 months, respectively, at room temperature. The validation study was completed by international collaborative trial involving 12 laboratories, allowing the validation of the assigned values. The methodology developed in this work enabled to produce easy-to-handle and cost-effective RMs, displaying an unprecedented stability at room temperature, a good homogeneity and a precise and validated assigned value. This study revealed new paths for the development of stable microbiological RMs. Overcoming the intrinsic instability of the living cells makes it possible to produce valuable tools for the quality assurance of microbiology laboratories.

Staphylococcus aureus isolated from patients with recurrent furunculosis carrying Panton-Valentine leukocidin genes represent agr specificity group IV

Recurrent furunculosis (RF) caused by Staphylococcus aureus presents a difficult clinical problem and causes significant morbidity. The study aim was to characterise agr groups and detect toxin genes among S.aureus strains isolated from RF patients. Microbiological material was obtained from evacuated furuncules of 44 RF patients. Nasal swabs were obtained from both the RF patients and the controls (150 healthy volunteers with no history of RF). All strains were screened for the presence of lukS/lukF-PV, tst, sea, seb, sec, sed, eta, and etb genes. Moreover, agr specificity groups (I-IV) were identified. Antibiotic-susceptibility tests were performed by disk diffusion method and methicillin susceptibility was verified by mecA gene amplification. The investigated strains were resistant to penicillin, clindamycin, erythromycin, and tetracycline. All showed susceptibility to methicillin. Thirty-five of 44 strains tested were positive for leukocidin lukS/lukF-PV genes and 12/44 for enterotoxin seb gene. The coexistence of PVL genes and seb gene concerned 7/44 strains. The remaining toxin genes were not found. Forty-three strains belonged to agr specificity group IV including all strains with lukS/lukF-PV genes. Nasal carriage of S. aureus was observed in 27/44 (61.3%) RF patients and in 43/150 (28.6%) controls (p = 0.001). In all RF subjects, nasal strains did not differ from those isolated from furuncules in terms of lukS/lukF-PV gene status and agr specificity. To the best of our knowledge, it is the first study that shown such a predominance of agr group IV strains in RF patients.

An approach to integrated data assessment in a proficiency test on the enumeration of Escherichia coli

To develop appropriate statistical approaches to plan and evaluate proficiency tests for the enumeration of Escherichia coli, addressing, in particular, a possible but frequently unavoidable lack of test sample homogeneity. Each of 50 laboratories analysed two samples of a stabilized suspension of E. coli in duplicate, using various media, inoculation methods, and incubation times and conditions. In parallel, the E. coli suspension was tested by the organiser for homogeneity and stability. Escherichia coli counts followed a log-normal distribution. After eliminating, by Youden analysis, two data sets that were considered outliers and eight data sets for underperformance of the laboratories (substantial lack of repeatability), the standard deviation of the mean was about 0·06 log(10) units. There was no evidence of bimodality of the data. Lack of homogeneity of distribution of bacteria had a strong effect on measurement uncertainty, in addition to laboratory bias and method repeatability. The homogeneity decreases during storage of the individual test vials; this effect could be modelled by the known kinetics of inactivation of micro-organisms. The results were confirmed by Monte Carlo simulations. By a tailored analysis of proficiency testing data, it is possible to distinguish the effect of lack of homogeneity, laboratory bias and method repeatability, on the measurement uncertainty. A statistic tool is provided to solve problems related to lack of stability of microbiological test material and to separate the effects of sample inhomogeneity from the performance of the individual laboratory.

Understanding patterns of use and scientific opportunities in the emerging global microbial commons

Rapidly growing global networking has induced and supported an increased interest in the life sciences in such general issues as health, climate change, food security and biodiversity. Therefore, the need to address and share research data and materials in a systematic way emerged almost simultaneously. This movement has been described as the so-called global research commons. Also in microbiology, where the sharing of microbiological materials is a key issue, microbial commons is attracting attention. Microbiology is currently facing great challenges with the advances of high throughput screening and next-generation whole genome sequencing. Furthermore, the exploration and use of microorganisms in agriculture and food production are increasing so as to safeguard global food and feed production. Further to several meetings on the subject, a special issue of Research in Microbiology is dedicated to Microbial Research Commons with a series of reviews elaborating its major pay-offs and needs in basic and applied microbiology. This paper gives an introduction to these articles covering a range of topics. These include the role of public culture collections and biological resource centers and legal aspects in the exchange of materials, microbial classification, an internet-based platform for data-sharing, applications in agriculture and food production, and challenges in metagenomics and extremophile research.

Microbiological material exchanges among scientists

Traditionally, biologists exchange scientific materials with other scientists to enable the independent confirmation of their research. For example, in microbiology, cultures of bacteria and other microorganisms and viruses are commonly sent to other laboratories upon request. Apart from this, it is a requirement of the International Code of Nomenclature for Prokaryotes, that culture type strains of a novel bacterial species be deposited in ‘at least two different publically accessible service collections in different countries from which the subcultures must be available’ to ensure their availability to all other scientists who may wish to study them. However, special challenges have recently been encountered in transporting such strains in order to meet such needs. This paper discusses the use of material exchanges and the challenges in this field.

A common basis for facilitated legitimate exchange of biological materials proposed by the European Culture Collections' Organisation

Being charged with the task of accessioning and supplying of living microbiological material, microbial culture collections are institutions that play a central role between the interests of a variety of user communities. On the one side are the providers of living microbiological material, such as individual scientists, institutions and countries of origin and on the other side are the various kinds of recipients/users of cultures of microorganisms from academia and industry. Thus, providing access to high quality biological material and scientific services while at the same time observing donor countries' rights, intellectual property rights, biosafety and biosecurity aspects poses demanding challenges. E.g. donor countries rights relate to Article 15 of the Convention on Biological Diversity: "Contracting parties …. recognize the sovereign rights of states over their natural resources …. shall facilitate access to resources … and not impose restrictions that run counter to the aims of the Convention. Access to natural resources shall be by mutually agreed terms and subject to prior informed consent ..." The use of a proposed standard contract by culture collections is discussed as a way of contractually safeguarding the existing research commons, while observing the new rights established in the Convention on Biological Diversity as well as other existing and new legislation impacting on the accessibility of living microbial material.

A common basis for facilitated legitimate exchange of biological materials proposed by the European Culture Collections' Organisation

Being charged with the task of accessioning and supplying of living microbiological material, microbial culture collections are institutions that play a central role between the interests of a variety of user communities. On the one side are the providers of living microbiological material, such as individual scientists, institutions and countries of origin and on the other side are the various kinds of recipients/users of cultures of microorganisms from academia and industry. Thus, providing access to high quality biological material and scientific services while at the same time observing donor countries' rights, intellectual property rights, biosafety and biosecurity aspects poses demanding challenges. E.g. donor countries rights relate to Article 15 of the Convention on Biological Diversity: Contracting parties …. recognize the sovereign rights of states over their natural resources …. shall facilitate access to resources … and not impose restrictions that run counter to the aims of the Convention. Access to natural resources shall be by mutually agreed terms and subject to prior informed consent ... The use of a proposed standard contract by culture collections is discussed as a way of contractually safeguarding the existing research commons, while observing the new rights established in the Convention on Biological Diversity as well as other existing and new legislation impacting on the accessibility of living microbial material.

Novel freeze-substitution electron microscopy provides new aspects of virulent Mycobacterium tuberculosis with visualization of the outer membrane and satisfying biosafety requirements

Transmission electron microscopy (TEM) of virulent bacteria is usually performed following chemical fixation (CF) with aldehyde fixatives such as glutaraldehyde because of the biosafety problem. However, CF may alter sample ultrastructure. In this study, we used a rapid-freeze substitution (RFS) sandwich method without pre-embedding in agar. TEM images obtained using this method were completely different from those of conventional chemically fixed samples; the bacilli cytoplasm of the RFS preparations was filled evenly with numerous ribosomes, and there was no positional variation of electron density that was obvious in those obtained with CF samples. The sandwich method is suitable for microbiological materials without expensive devices and can be easily performed in a biosafety cabinet. In future, this method coupled with novel labeling techniques may help localize structural and functional molecules throughout a bacterial cell.

The Effects of Microbial Materials Adhered to Asian Sand Dust on Allergic Lung Inflammation

Asian sand dust (ASD) containing microbiological materials, sulfate (SO(4)(2)), and nitrate (NO(3)(-) ) derived from air pollutants in East China, reportedly cause adverse respiratory health effects. ASD aggravates ovalbumin (OVA)-associated experimental lung eosinophilia. In this study, the toxic materials adsorbed onto ASD were excluded by heat treatment at 360 degrees C for 30 min. The effects of nonheated ASD or heated ASD (H-ASD) toward the allergic lung inflammation were compared in murine lungs. ICR mice were administered intratracheally with normal saline (control), H-ASD, ASD, OVA, OVA + H-ASD, and OVA + ASD, four times at 2-week intervals. ASD only increased neutrophils in bronchoalveolar lavage fluids (BALFs) along with pro-inflammatory mediators, such as keratinocyte chemoattractant (KC). H-ASD and ASD enhanced eosinophil recruitment induced by OVA in the alveoli and in the submucosa of the airway, which has a goblet cell proliferation in the bronchial epithelium. The two ASDs synergistically increased interleukin-5 (IL-5), monocyte chemotactic protein-3 (MCP-3), and eotaxin, which were associated with OVA, in BALF. The enhancing effects were much greater in ASD than in H-ASD. The two ASDs induced the adjuvant effects to specific IgE and IgG1 production by OVA. In the in vitro study using RAW264.7 cells, ASD increased the expression of Toll-like receptor 2 (TLR 2) mRNA but not TLR4 mRNA. H-ASD caused no expression of either TLR mRNA. These results suggest that the aggravated lung eosinophilia by ASD may be due to activation of Th2-associated immune response via the activation of TLR2 by microbial components adhered to ASD.

Comparação entre dois meios de coleta e transporte para estudo da microbiota conjuntival de indivíduos normais

To compare the microbiological profile of normal microbiota of healthy people obtained from conjunctival smear using dry swab in Stuart's transport medium and wet swab transported in test tube sealed with cotton. A prospective study with random samples, performed at the Departments of Ophthalmology and Pathology of Santa Casa Misericórdia de São Paulo, in August of 2006. Eighty normal eyes of 40 healthy individuals were analyzed. Samples were collected in the right eye with a dry swab and stored in Stuart's medium, where all microbiological material is kept immersed in the medium and the tube is hermetically sealed. In the left eye, the conjunctival material was collected using a swab embedded in saline solution 0.9%, and stored in dry and sterile test tubes sealed with cotton. The samples were analyzed within 2 hours at most after collection. Out of 40 samples collected with wet swab and transported in dry tube, bacteria were observed in 10 (25%), whereas of 40 samples collected with dry swab and transported in Stuart's medium, 12 (30%) had bacteria. The results of the microbiological profile of normal conjunctival microbiota using dry swab in Stuart's medium were statistically similar (p=0.85) to those obtained in wet swab in dry tube for spreading performed within 2 hours after collection of conjunctival specimen.

Micromammals as palaeoenvironmental indicators of the southern African Quaternary

Micromammals from archaeological cave sites have provided considerable information on environmental (vegetational and climatic) conditions during the Quaternary in southern Africa. The material basis is jaws of small mammals below 150 g mass. An underlying principle of palaeoenvironmental reconstruction is that each taxon carries with it, or can be said to represent, a more or less detailed suite of environmental information. More explicitly, members of a given taxon may be known to inhabit certain habitats, aspects of which may include vegetation, landform and climate, and to have certain biological or ecological characteristics. Palaeoenvironmental interpretation borrows extensively from ecology and biology, both for methods and data. For this reason, it is opportune to re-consider the validity of some previous assumptions in the light of significant improvements in understanding of modern processes as well as the constraints implicit in palaeoecological studies. With knowledge has come increased difficulty in extracting reliable information. Advances in identification of modern taxa, especially at the species level, make it more difficult to equate identifications based on bones with those based on microbiological material. The development of the field of taphonomy has greatly impacted on interpretation of fossil samples. The environmental correlates of mean individual size, life-history adaptations of species richness and diversity are harder to separate from the suite of factors now known to be involved but are still worth investigating. Currently, micromammal studies can probably be characterised as being in an intermediate, rather conservative, phase of development but can be expected to progress once more information and understanding from modern ecological studies is incorporated into palaeo studies.

Training program on microbiological test collection material methods at a teaching hospital: investment and result assessment

This study aimed at evaluating the results, direct costs and investment of a training program on microbiological test material collection at a teaching hospital. Test collections that did not follow the established criteria (failure) were considered as the result measure. Variable and absorption costing were used to calculate direct costs and investments, respectively. Of the 11,893 collected materials, failures were evidenced in 59 (0.5%). Direct cost corresponded to R$ 154.10 and R$ 2,431.29 was invested in training. These findings revealed that the evidenced number of anomalies (failures) represented a low percentage in relation to the total collected material for microbiological exams. Therefore, this should not be considered a critical point that justifies the continuity of the training and, consequently, the investment.

From an idea to a vision: There’s plenty of room at the bottom

Many workers in nanotechnology cite Richard Feynman’s after-dinner speech, “There’s plenty of room at the bottom,” which was given by him on December 29, 1959, to be the birthday of theoretical nanotechnology. This attribution is misleading because there is no direct link from Feynman’s talk to today’s micromachines. We discuss the historical background of Feynman’s talk, the state of the art in 1959, and Feynman’s motivation. We conclude that Feynman was not interested in building miniaturized versions of existing macroscopic machines, but wished to construct microbiological machines and tools that would enable scientists to mimic microbiological materials.

Filter paper strip kit: a cost-effective transport media

This study was undertaken to discover a feasible transport media for the transportation of ocular microbiological material from the periphery to the central laboratory. A total of 94 cases of ocular infection with clinical diagnosis of conjunctivitis and keratitis were studied. In all cases, two representative microbiological samples were collected, and sent by filter paper strip (FPS) kit as well as by direct culture technique. The isolated organisms by both the methods were analysed. Of the total 94 cases studied, bacteria were isolated in 48 cases by direct culture and in 45 cases by FPS kit, whereas, fungus were isolated in 13 cases by each method. FPS kit appears to be an alternative, feasible, and cost-effective technique for transportation of ocular microbiological material from periphery to the central laboratory.

An assessment of risk associated with the photography of microbiological materials

This study investigated risks associated with the photography of materials that are a potential source of infection, the extent to which medical illustrators are aware of these risks, the relevant government regulations and guidance, and whether recommended control measures are adopted. To seek information about current practice, a questionnaire was sent to randomly selected Medical Illustration Units across the United Kingdom. The data indicated that a significant proportion of medical illustrators routinely photograph materials that could be a source of infection, but that a high percentage know little about the specific regulations and guidance which govern the handling of such materials. Apparent deficiencies in safety procedures currently applied in photographing microbiological materials were identified; recommendations that address these problems at little or no cost are proposed.

Committee on Microbiological and Extraneous Materials

Committee on Microbiological and Extraneous Materials