The microbiology of foods,

Errata slip inserted.

Diagnostic microbiology : a textbook for the isolation and identification of pathogenic microorganisms /

Mode of access: Internet.

Real-time PCR in the microbiology laboratory

Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types. However, conventional PCR was already an essential tool in the research laboratory. Real-time PCR has catalysed wider acceptance of PCR because it is more rapid, sensitive and reproducible, while the risk of carryover contamination is minimised. There is an increasing number of chemistries which are used to detect PCR products as they accumulate within a closed reaction vessel during real-time PCR. These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail. It is not only the technology that has changed with the introduction of real-time PCR. Accompanying changes have occurred in the traditional terminology of PCR, and these changes will be highlighted as they occur. Factors that have restricted the development of multiplex real-time PCR, as well as the role of real-time PCR in the quantitation and genotyping of the microbial causes of infectious disease, will also be discussed. Because the amplification hardware and the fluorogenic detection chemistries have evolved rapidly, this review aims to update the scientist on the current state of the art. Additionally, the advantages, limitations and general background of real-time PCR technology will be reviewed in the context of the microbiology laboratory.

Validation of assembled nucleic acid-based tests in diagnostic microbiology laboratories

Medical microbiology and virology laboratories use nucleic acid tests (NAT) to detect genomic material of infectious organisms in clinical samples. Laboratories choose to perform assembled (or in-house) NAT if commercial assays are not available or if assembled NAT are more economical or accurate. One reason commercial assays are more expensive is because extensive validation is necessary before the kit is marketed, as manufacturers must accept liability for the performance of their assays, assuming their instructions are followed. On the other hand, it is a particular laboratory's responsibility to validate an assembled NAT prior to using it for testing and reporting results on human samples. There are few published guidelines for the validation of assembled NAT. One procedure that laboratories can use to establish a validation process for an assay is detailed in this document. Before validating a method, laboratories must optimise it and then document the protocol. All instruments must be calibrated and maintained throughout the testing process. The validation process involves a series of steps including: (i) testing of dilution series of positive samples to determine the limits of detection of the assay and their linearity over concentrations to be measured in quantitative NAT; (ii) establishing the day-to-day variation of the assay's performance; (iii) evaluating the sensitivity and specificity of the assay as far as practicable, along with the extent of cross-reactivity with other genomic material; and (iv) assuring the quality of assembled assays using quality control procedures that monitor the performance of reagent batches before introducing new lots of reagent for testing.

The microbiology of the eye

Infection of the external structures of the eye is one of the commonest types of eye disease worldwide. In addition, although relatively impermeable to microorganisms, infection within the eye can result from trauma, surgery or systemic disease. This article reviews the general biology of viruses, bacteria, fungi and protozoa and the major ocular infections that they cause. In addition, the effectiveness of the various antimicrobial agents in controlling ocular disease is discussed. Because of changes in the normal ocular flora, continuous monitoring of the microbiology of the eye will continue to be important in predicting future types of eye infection. Basic research is also needed into the interactions of microbes at the ocular surface. There is increasing microbial resistance to the antimicrobial agents used to treat ocular infections and hence, new antimicrobial agents will continue to be needed together with new methods of drug delivery to increase the effectiveness of existing antimicrobial agents.

The use of analysis of variance (ANOVA) in applied microbiology

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the number of replications required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the DF of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for each error term of the ANOVA. Finally, it is important to consider the design of the experiment because this determines the appropriate ANOVA to use. Some of the most common experimental designs used in the biosciences and their relevant ANOVAs are discussed by. If there is doubt about which ANOVA to use, the researcher should seek advice from a statistician with experience of research in applied microbiology.

Statistical analysis in microbiology:statnotes

This book is aimed primarily at microbiologists who are undertaking research and who require a basic knowledge of statistics to analyse their experimental data. Computer software employing a wide range of data analysis methods is widely available to experimental scientists. The availability of this software, however, makes it essential that investigators understand the basic principles of statistics. Statistical analysis of data can be complex with many different methods of approach, each of which applies in a particular experimental circumstance. Hence, it is possible to apply an incorrect statistical method to data and to draw the wrong conclusions from an experiment. The purpose of this book, which has its origin in a series of articles published in the Society for Applied Microbiology journal ‘The Microbiologist’, is an attempt to present the basic logic of statistics as clearly as possible and therefore, to dispel some of the myths that often surround the subject. The 28 ‘Statnotes’ deal with various topics that are likely to be encountered, including the nature of variables, the comparison of means of two or more groups, non-parametric statistics, analysis of variance, correlating variables, and more complex methods such as multiple linear regression and principal components analysis. In each case, the relevant statistical method is illustrated with examples drawn from experiments in microbiological research. The text incorporates a glossary of the most commonly used statistical terms and there are two appendices designed to aid the investigator in the selection of the most appropriate test.

Food Microbiology Laboratory Overview of food analysis

Introduction to microorganisms and foodborne diseases. Activities in a Food Microbiology Laboratory.

Microbiology of chronic suppurative otitis media at Queen Elizabeth Central Hospital, Blantyre, Malawi: A cross-sectional descriptive study

Background Chronic suppurative otitis media (CSOM) is still a significant health problem in developing countries. Therefore, it was pertinent to determine the local Malawian microbiology in order to guide adequate treatment, avoid complications, and provide records for future reference. Aim The study sought to determine the CSOM-causing microorganisms at Queen Elizabeth Central Hospital in Blantyre, Malawi, and establish their relationship signs and symptoms, and with the demographic pattern of the study. Methods This was a hospital-based cross-sectional descriptive study carried out at the ENT outpatient clinic and the Microbiology Department of Queen Elizabeth Central Hospital.The sample comprised 104 patients with unilateral or bilateral active CSOM, who met the inclusion criteria. All patients were evaluated through a detailed history and clinical examination. Pus samples from draining ears were collected by aspiration with a sterile pipette. The specimens were immediately sent for microbiological analysis. Data were analyzed using SPSS.version 20. Results The study found that Proteus mirabilis , Pseudomonas aeruginosa , and Staphylococcus aureus were the most prevalent aerobic bacteria, while Bacteroides spp. and Peptostreptococcus spp. were the commonest anaerobic bacteria causing CSOM. These CSOM-causing microorganisms were predominant among males aged 18 years and below. Some CSOMcausing microorganisms were—significantly more so than the others— characteristically associated with each of the following clinical features: quantity of pus drainage, mode of onset, otalgia, hearing loss, location of tympanic membrane perforation, and mucosal appearance.

A microbiology study of the surgical site infection, at a hospital in northern Portugal

Surgical site infections (SSIs) remain a major clinical problem in terms of morbidity, mortality, time spent in hospital and overall direct and indirect costs. Objectives: To measure the prevalence of the SSI, by type of surgery and microbiologically characterization, in adult patients undergoing surgery during 2015 at a public hospital in northern Portugal. Methods: A prospective study, attended by 609 adult patients, undergoing surgery. The sociodemographic and clinical data of the population, as well as the surgical procedure and microbiological study were analyzed using Microsoft Access 2013. Results: In the sample of 609 adults undergoing surgery, it was found that 62.89% of surgical wound were cleaned, 15.8% were clean-contaminated, 8.70% were contaminated and 9.36% infected. About 62.52% of the intervened patients had antibiotic prophylaxis prior to surgery. Out of all surgeries, 33.3% were laparoscopic. The percentage of SSI was 5.74%; In these positive cases, only 3.61% was identiied the responsible bacteria. The urgent surgeries have more infections when compared to the programmed ones. In colon surgery the number of infections was 60% after cholecystectomy (22.86%). In hernioplasty, infection occurred in only 2.86% of the patients. The most isolated bacteria was Escherichia coli with 59%, in which 30% are -producing-lactamases of extended spectrum, followed by Pseudomonas aeruginosa (13.6%) and Serratia marcescens (13.6%). The mortality rate was 14.8%. Pseudomonas aeruginosa was isolated in 3 of 4 patients who died. Conclusions: The most microorganisms belong to the group of Gram-negative and are usually linked to infections associated with health care.

"The post-antibiotic apocalypse" and the "war on superbugs": catastrophe discourse in microbiology, its rhetorical form and political function

Discourses evoking an antibiotic apocalypse and a war on superbugs are emerging just at a time when so-called "catastrophe discourses" are undergoing critical and reflexive scrutiny in the context of global warming and climate change. This article combines insights from social science research into climate change discourses with applied metaphor research based on recent advances in cognitive linguistics, especially with relation to "discourse metaphors." It traces the emergence of a new apocalyptic discourse in microbiology and health care, examines its rhetorical and political function and discusses its advantages and disadvantages. It contains a reply by the author of the central discourse metaphor, "the post-antibiotic apocalypse," examined in the article.

Huambo Microbiology Laboratory : economical and financial viability

Mestrado em Finanças