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.

Bacteriologic investigation of the effects of sodium hypochlorite and chlorhexidine during the endodontic treatment of teeth with apical periodontitis

SIQUEIRA JR. et al. Bacteriologic investigation of the effects of sodium hypochlorite and chlorhexidine during the endodontic treatment of teeth with apical periodontitis. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod., v. 104, n. 1, p. 122-130, 2007.

Desinfeção aplicada aos cones de guta-percha

Introdução: Ao longo do tempo o Tratamento Endodôntico Não Cirúrgico tem sido das áreas da Medicina Dentária que mais tem evoluído. Todos os passos do tratamento têm sido revistos de forma a aumentar a taxa de sucesso. O controlo microbiológico é crucial para que o tratamento seja um sucesso a curto, médio e longo prazo. A assepsia deve ser mantida em todas as fases deste tratamento para que este seja um sucesso. Objetivo: Ao longo do meu percurso académico pude concluir que a fase da descontaminação dos cones, aquando a obturação (fase final do Tratamento Endodôntico Não Cirúrgico) era desvalorizada, o que me levou a efetuar uma revisão bibliográfica de modo a poder melhorar os meus conhecimentos e técnica. Material e Métodos: Para a elaboração deste trabalho foi realizada uma pesquisa bibliográfica recorrendo aos seguintes motores de busca: B-on, PubMed, Scielo e ScienceDirect, com as seguintes palavras-chave: “decontamination in endodontics”;” disinfection in endodontics”; “root canal irrigants”; “endodontics microbiology”; “Candida albicans“; “Enterococcus faecalis”; “sodium hypochlorite ”; “alcohol”; “contamination during Obturation”; “clorohexidine”; “filling materials endodontics”; “termoplastic gutta-percha”; “obturation material”; “Mineral Trioxide Aggregate”; “resilon”; “resin cement”; “resin material for root canal obturation”; “resin sealer”; “root canal”; “root canal sealing”; “root canal filling materials”; “condensation in endodontics”; “lateral condensation”; “gutta-percha”; “microlekeage”; “system B”; “fluid filtration model”;“dye penetration”. Como critério de inclusão estabeleceu-se que os artigos deveriam ser em Português, Inglês ou Espanhol e publicados entre 1995 e 2015. Dos resultados apresentados foram utilizados 110 artigos, pesquisados entre Maio de 2015 e 20 de Outubro de 2015. Foram ainda consultados livros de referência nestes mesmos locais. Conclusão: a presença de bactérias e os seus subprodutos no sistema tridimensional de canais está diretamente implicado com o insucesso do Tratamento Endodôntico. A descontaminação dos cones de guta-percha, é, portanto, um processo importante no Tratamento Endodôntico pois impede que os cones sejam colocados nos canais radiculares, estando contaminados por microorganismos que inviabilizam o tratamento efetuado. A submersão dos cones durante um minuto em clorohexidina a 2% ou hipoclorito a 5,25% está indicado e comprovado como um processo eficiente de desinfeção dos cones.

Bacteriologic investigation of the effects of sodium hypochlorite and chlorhexidine during the endodontic treatment of teeth with apical periodontitis

SIQUEIRA JR. et al. Bacteriologic investigation of the effects of sodium hypochlorite and chlorhexidine during the endodontic treatment of teeth with apical periodontitis. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod., v. 104, n. 1, p. 122-130, 2007.

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

Novel biomaterials for regeneration of periapical bone defects in endodontic and implant therapy

Endodontic-related periapical bone defects are a common occurrence in the global populations. Considering the number of root canal treatments performed annually, new strategies and new biomaterials for the management of these bone defects will be important and highlight the need for continued research and development in endodontic field. The present PhD thesis have several objectives and is divided into two main sections: one focused on in vitro and laboratory research and the other on clinical in vivo investigations. The first part, focused on laboratory and in vitro research, investigated 2 main topics: • the microbial communities of apical periodontitis to evaluate the predominant bacterial using 16sr DNA-targeted Nanopore sequencing; • the physical-chemical properties of innovative premixed calcium-silicate based bioceramic sealers for endodontic therapy; The second part, focused on in vivo clinical studies, investigated 2 main topics: • the clinical application of premixed calcium-silicate-based sealers. Ethical committee approval was obtained in 2 separate in vivo studies. The first one is a prospective cohort study with a two-year follow-up where the test group was compared with a control group (considered the gold standard). The second is a pilot prospective cohort study with a 12-month follow-up which set the foundation for a subsequent randomized investigation. Thanks to these investigations, we validated a new technique that innovatively associates a warm obturation technique with calcium-silicate-based sealers. Historically, these sealers were only used with cold techniques. This investigation highlights the possibility for wider utilization and improvements in endodontic techniques. • The outcome of 2 different types of implants characterized by different surface treatments and placed with different techniques. The marginal bone level and periodontal parameters were evaluated with a follow-up of 4 and 10 years. This Ph.D thesis is based on a compilation of published papers I have done during my three-year PhD program.

Changes In The Bacterial Community Of Soil From A Neutral Mine Drainage Channel.

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.

The Cratylia Mollis Seed Lectin Induces Membrane Permeability Transition In Isolated Rat Liver Mitochondria And A Cyclosporine A-insensitive Permeability Transition In Trypanosoma Cruzi Mitochondria.

Previous results provided evidence that Cratylia mollis seed lectin (Cramoll 1,4) promotes Trypanosoma cruzi epimastigotes death by necrosis via a mechanism involving plasma membrane permeabilization to Ca(2+) and mitochondrial dysfunction due to matrix Ca(2+) overload. In order to investigate the mechanism of Ca(2+) -induced mitochondrial impairment, experiments were performed analyzing the effects of this lectin on T. cruzi mitochondrial fraction and in isolated rat liver mitochondria (RLM), as a control. Confocal microscopy of T. cruzi whole cell revealed that Cramoll 1,4 binding to the plasma membrane glycoconjugates is followed by its internalization and binding to the mitochondrion. Electrical membrane potential (∆Ψm ) of T. cruzi mitochondrial fraction suspended in a reaction medium containing 10 μM Ca(2+) was significantly decreased by 50 μg/ml Cramoll 1,4 via a mechanism insensitive to cyclosporine A (CsA, membrane permeability transition (MPT) inhibitor), but sensitive to catalase or 125 mM glucose. In RLM suspended in a medium containing 10 μM Ca(2+) this lectin, at 50 μg/ml, induced increase in the rate of hydrogen peroxide release, mitochondrial swelling, and ∆Ψm disruption. All these mitochondrial alterations were sensitive to CsA, catalase, and EGTA. These results indicate that Cramoll 1, 4 leads to inner mitochondrial membrane permeabilization through Ca(2+) dependent mechanisms in both mitochondria. The sensitivity to CsA in RLM characterizes this lectin as a MPT inducer and the lack of CsA effect identifies a CsA-insensitive MPT in T. cruzi mitochondria.

Hypertrophic Adenoid Is A Major Infection Site Of Human Bocavirus 1.

Human bocavirus 1 (HBoV1) is associated with respiratory infections worldwide, mainly in children. Similar to other parvoviruses, it is believed that HBoV1 can persist for long periods of time in humans, probably through maintaining concatemers of the virus single-stranded DNA genome in the nuclei of infected cells. Recently, HBoV-1 was detected in high rates in adenoid and palatine tonsils samples from patients with chronic adenotonsillar diseases, but nothing is known about the virus replication levels in those tissues. A 3-year prospective hospital-based study was conducted to detect and quantify HBoV1 DNA and mRNAs in samples of the adenoids (AD), palatine tonsils (PT), nasopharyngeal secretions (NPS), and peripheral blood (PB) from patients undergoing tonsillectomy for tonsillar hypertrophy or recurrent tonsillitis. HBoV1 was detected in 25.3% of the AD samples, while the rates of detection in the PT, NPS, and PB samples were 7.2%, 10.5%, and 1.7%, respectively. The viral loads were higher in AD samples, and 27.3% of the patients with HBoV had mRNA detectable in this tissue. High viral loads and detectable mRNA in the AD were associated with HBoV1 detection in the other sample sites. The adenoids are an important site of HBoV1 replication and persistence in children with tonsillar hypertrophy. The adenoids contain high HBoV1 loads and are frequently positive for HBoV mRNA, and this is associated with the detection of HBoV1 in secretions.

Culturable Bacterial Diversity From A Feed Water Of A Reverse Osmosis System, Evaluation Of Biofilm Formation And Biocontrol Using Phages.

Biofilm formation on reverse osmosis (RO) systems represents a drawback in the application of this technology by different industries, including oil refineries. In RO systems the feed water maybe a source of microbial contamination and thus contributes for the formation of biofilm and consequent biofouling. In this study the planktonic culturable bacterial community was characterized from a feed water of a RO system and their capacities were evaluated to form biofilm in vitro. Bacterial motility and biofilm control were also analysed using phages. As results, diverse Protobacteria, Actinobacteria and Bacteroidetes were identified. Alphaproteobacteria was the predominant group and Brevundimonas, Pseudomonas and Mycobacterium the most abundant genera. Among the 30 isolates, 11 showed at least one type of motility and 11 were classified as good biofilm formers. Additionally, the influence of non-specific bacteriophage in the bacterial biofilms formed in vitro was investigated by action of phages enzymes or phage infection. The vB_AspP-UFV1 (Podoviridae) interfered in biofilm formation of most tested bacteria and may represent a good alternative in biofilm control. These findings provide important information about the bacterial community from the feed water of a RO system that may be used for the development of strategies for biofilm prevention and control in such systems.

Does The Reciproc File Remove Root Canal Bacteria And Endotoxins As Effectively As Multifile Rotary Systems?

To evaluate the effectiveness of Reciproc for the removal of cultivable bacteria and endotoxins from root canals in comparison with multifile rotary systems. The root canals of forty human single-rooted mandibular pre-molars were contaminated with an Escherichia coli suspension for 21 days and randomly assigned to four groups according to the instrumentation system: GI - Reciproc (VDW); GII - Mtwo (VDW); GIII - ProTaper Universal (Dentsply Maillefer); and GIV -FKG Race(™) (FKG Dentaire) (n = 10 per group). Bacterial and endotoxin samples were taken with a sterile/apyrogenic paper point before (s1) and after instrumentation (s2). Culture techniques determined the colony-forming units (CFU) and the Limulus Amebocyte Lysate assay was used for endotoxin quantification. Results were submitted to paired t-test and anova. At s1, bacteria and endotoxins were recovered in 100% of the root canals investigated (40/40). After instrumentation, all systems were associated with a highly significant reduction of the bacterial load and endotoxin levels, respectively: GI - Reciproc (99.34% and 91.69%); GII - Mtwo (99.86% and 83.11%); GIII - ProTaper (99.93% and 78.56%) and GIV - FKG Race(™) (99.99% and 82.52%) (P < 0.001). No statistical difference were found amongst the instrumentation systems regarding bacteria and endotoxin removal (P > 0.01). The reciprocating single file, Reciproc, was as effective as the multifile rotary systems for the removal of bacteria and endotoxins from root canals.