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On the complexity of the pulmonary microbiology in cystic fibrosis: thoughts of a clinician.

The pulmonary microbiology is a dominant element in cystic fibrosis and the main cause of death. Contemporary consensus accords an exclusive role in this to a single microorganism, Pseudomonas aeruginosa. The evidence convincingly shows that the microbiology consists of a multiplicity of species living in perpetual interaction and in a variety of forms--planktonic, sessile, anaerobic--and in organized communities as microcosms, biofilms and ecosystem. This compound microbiology, the essence of the pulmonary disease, is of necessity exposed to constant influence both from without (the air) and within (via the blood), leading to a perpetual state of flux with consequent impact on the clinical course. It is perhaps significant that to date, most or all microbiologic studies were probably conducted, classically, with inert instruments (glass? plastic?), whereas in real life the CF microbiology lives in "test-tubes" of live mucosa with which it maintains a permanent "cross-talk." The difference to microbial life between these two media may well be very important. It therefore justifies study and may be far-reaching in its effect. There is persuasive argument to strive for a novel holistic view of the totality of the complex microbiology of CF, and to initiate fresh concepts, strategies and methods.

Anti-Bacterial Agents↗

[Nosocomial infections in Germany. Microbiological diagnosis, preventive antibiotics and antibiotic therapy].

BACKGROUND: The NIDEP-study (Nosocomial Infections in Germany-Prevalence and Prevention) is the first large multicenter survey to examine the prevalence of nosocomial infections (NI) in Germany. This part of the NIDEP-study describes the frequency and quality of the microbiological diagnosis, antimicrobial chemoprophylaxis and therapy in representative German hospitals. PATIENTS AND METHOD: Prevalence of nosocomial infections in 14 966 patients of 72 randomly selected representative German hospitals was determined. Frequency, nature and results of the microbiological diagnosis, antimicrobial chemoprophylaxis and therapy were recorded simultaneously. RESULTS: The total prevalence rate of nosocomial infections was 3.5%. The most common infections were urinary tract infections (42.1%), lower respiratory tract infections (20.6%), postoperative wound infections (15.8%), and septicemia (8.3%). Microbiological evaluation was done in 56.5% of the patients with infections. Only five of the 49 hospitals with less than 400 beds and only nine of the 23 hospitals with more than 400 beds had their own microbiological department. Antimicrobial chemotherapy was administered in 17.7% of the patients. In 35.1% of the patients who were treated with antibiotics, no clinical diagnosis of infection was made, criteria for nosocomial infections were not fulfilled or microbiological evaluation was not established. Antimicrobial chemoprophylaxis was done in one third of the patients. Prophylaxis was missed in 20.6% of patients with colorectal operations, 60.1% of appendectomies, 48% of vaginal hysterectomies, and 35.5% of total hip replacements. On the other hand antimicrobial chemoprophylaxis was frequently administered in clean procedures without increased risk of postoperative wound infections. CONCLUSION: Insufficient microbiological evaluation, inadequate perioperative antimicrobial chemoprophylaxis and administration of chemotherapy without documented infection were detected in representative German hospitals.

Anti-Bacterial Agents↗

["Control of symbiosis" or "microbiological therapy"--an immunological therapy principle?].

"Flora modulation" or "microbiologic therapy"-- an immunologic method of treatment? "Microbiologic therapy" includes the methods of quantitative measurement of the intestinal "microbial flora", the oral or parenteral application of microbial pharmaceutics and the preparation of autovaccines from excretions of the treated persons. Initially a "flora modulation" was supposed to be the mechanism of "microbiologic therapy". After the failure of this hypothesis, some physicians claim the "microbiologic therapy" to be a special form of immunomodulation or -stimulation. Most influential in this immunologic foundation of "microbiologic therapy" was the "Institut für Mikroökologie" in Herborn, Germany. A detailed analysis of the available publications however reveals, that all methods of "microbiological therapy" are based on theoretically untenable presumptions. Furthermore, up to now there is no scientific evidence for the effectiveness of this form of therapy.

Adjuvants, Immunologic↗

The role of microbiological testing in systems for assuring the safety of beef.

The use of microbiological testing in systems for assuring the safety of beef was considered at a meeting arranged by the International Livestock Educational Foundation as part of the International Livestock Congress, TX, USA, during February, 2000. The 11 invited participants from industry and government research organizations concurred in concluding that microbiological testing is necessary for the implementation and maintenance of effective Hazard Analysis Critical Control Point (HACCP) systems, which are the only means of assuring the microbiological safety of beef; that microbiological testing for HACCP purposes must involve the enumeration of indicator organisms rather than the detection of pathogens; that the efficacy of process control should be assessed against performance criteria and food safety objectives that refer to the numbers of indicator organisms in product; that sampling procedures should allow indicator organisms to be enumerated at very low numbers; and that food safety objectives and microbiological criteria are better related to variables, rather than attributes sampling plans.

Animals↗

Waterborne diseases prevention: evaluation of inspection scoring system for water sites according to water microbiological tests during the Athens 2004 pre-Olympic and Olympic period.

STUDY OBJECTIVES: To evaluate the inspection grading system for water sites implemented during the Athens 2004 Olympic inspection programme. DESIGN: The relation between the standardised inspections results of 716 water supply systems and 289 public swimming pools, and microbiological test results of 2358 samples collected during inspections was examined. SETTING: Athens, Thessaloniki, Patra, Volos, and Iraklio, Greece. Inspections and sampling conducted during a two year period before the 2004 Olympics. MAIN RESULTS: Swimming pools unsatisfactory inspection grading results were significantly associated with positive water microbiological test results (relative risk = 2.5, p<0.05). One of the six violations of swimming pools and five of the seven violations of water supply systems designated as "critical" water safety hazards in the inspection reports were significantly associated with positive microbiological test results. The receiver operating characteristic analysis identified the unsatisfactory score designed in the swimming pools standardised inspection report, as the ideal score (-15), in adequately producing positive microbiological test results (sensitivity 13.2%, specificity 89%). CONCLUSIONS: This study shows the utility of standardised inspection grading systems in waterborne diseases prevention planning and implementation strategies of policy makers and regulators. Future water quality assessment should be based on the implementation of a robust standardised inspection system and reduce the need of microbiological tests.

Data Collection↗

Cost analysis in a clinical microbiology laboratory.

The use of models for business management and cost control in public hospitals has led to a need for microbiology laboratories to know the real cost of the different products they offer. For this reason, a catalogue of microbiological products was prepared, and the costs (direct and indirect) for each product were analysed, along with estimated profitability. All tests performed in the microbiology laboratory of the "Virgen de la Concha" Hospital in Zamora over a 2-year period (73192 tests) were studied. The microbiological product catalogue was designed using homogeneity criteria with respect to procedures used, workloads and costs. For each product, the direct personnel costs (estimated from workloads following the method of the College of American Pathologists, 1992 version), the indirect personnel costs, the direct and indirect material costs and the portion of costs corresponding to the remaining laboratory costs (capital and structural costs) were calculated. The average product cost was 16.05 euros. The average cost of a urine culture (considered, for purposes of this study, as a relative value unit) reached 13.59 euros, with a significant difference observed between positive and negative cultures (negative urine culture, 10.72 euros; positive culture, 29.65 euros). Significant heterogeneity exists, both in the costs of different products and especially in the cost per positive test. The application of a detailed methodology of cost analysis facilitates the calculation of the real cost of microbiological products. This information provides a basic tool for establishing clinical management strategies.

Cost Control↗

Predictive microbiology.

Predictive microbiology is based upon the premise that the responses of populations of microorganisms to environmental factors are reproducible, and that by considering environments in terms of identifiable dominating constraints it is possible, from past observations, to predict the responses of those microorganisms. Proponents claim that predictive microbiology offers many benefits to the practice of food microbiology, and there is growing interest internationally. This review considers the origins, benefits and approaches to predictive microbiology and critically considers limitations and potential solutions. It is suggested that the traditional delineation between kinetic and probabilistic models is artificial, and that the two approaches represent the opposite ends of a spectrum of modelling needs. It is concluded: that despite the complexity of many food systems predictive modelling can be successfully applied; that strategies based on predictive models can simplify problems and allow useful predictions and analyses to be made; that the full potential of the technique has not yet been realised; and that "predictive microbiology" may be seen as providing a rational framework for understanding the microbial ecology of food.

Bacteria↗

A microbiological view of sterile service production.

The primary purpose of a Sterile Services Department is the prevention of infection. A specific guide to Good Manufacturing Practice (GMP) has been published by the Institute of Sterile Service Management to assist managers to ensure that the final products are of the nature and quality intended. The testing and monitoring of machinery, such as autoclaves, has an obvious microbiological relevance but other practices, such as expire dates and presterilization of used items, are of dubious microbiological advantage and can act against the main aim. GMP recommendations on environmental controls have received disproportionate attention to the remainder of the document, particularly relating to packing rooms. The standard should not be seen as a primarily microbiological measure but as a sensible control to limit the ingress of unwanted dust, flies and people and provide basic ventilation. Tests indicate that the standard for particle counts can be achieved without structural alteration in some departments. Microbiological counts are similar to those within operating theatres and additional protective clothing is of no apparent advantage. Process failure is the main cause of risks to the patient, and other practices, although both relevant and important, should not be given a false microbiological significance as these can detract and distract attention from the main issue.

Air Microbiology↗

Risk factors contributing to microbiological contamination of shallow groundwater in Kampala, Uganda.

A study of water quality variation in shallow protected springs in Kampala was undertaken over a 12-month period to assess the causes of microbiological contamination. The microbiological quality of water was assessed using thermotolerant coliforms and faecal streptococci. Sanitary inspections and hazard assessments were undertaken to identify faecal sources (hazards), contaminant pathways and contributory factors. Data were collected on rainfall and population as additional factors potentially exerting an influence on microbiological quality. Initial analysis of the data showed a significant relationship between median level of contamination and rainfall, in particular to short-term rainfall events. Total sanitary risk score showed a significant relationship with median level of contamination, but population density may be a confounding factor. The raw microbiological data were transformed into five water quality targets: <1 and < or =10 cfu 100ml(-1) for faecal streptococci; and <1, < or =10 and < or=50 cfu 100 ml(-1) for thermotolerant coliforms. The presence of individual risk factors as well as variables for rainfall and population density were analysed with respect to failure to meet these water quality targets using contingency tables. Logistic regression models were developed for each of the five water quality targets. The analysis strongly suggested that there is rapid recharge of the springs after rainfall and this leads to microbiological contamination. On-site sanitation was less important than other sources of faecal matter, which was consistent with a low sanitation coverage in the study area. The study suggested that improving sanitary completion and local environmental hygiene was more important than controlling on-site sanitation in improving the quality of these springs.

Enterobacteriaceae↗

Computerization in microbiology.

Computerization of the clinical microbiology laboratory is finally coming of age. Operations and functions easily adapted from other clinical laboratories have already been implemented in the microbiology laboratory, e.g., fiscal, clerical, and other administrative housekeeping chores. Similarly, storage, retrieval, and analysis of banks of data easily collected and filed have also been successfully accomplished in microbiology for several years. The more challenging problems of computerization still deserve and require the attention of microbiologists. These problems lie in the smooth sequential formulation and transmission of clinical microbiological test results from the laboratory to clinical records; the manipulation of relevant data by the computer prospectively for the detection and prediction of nosocomial infections or miniepidemics; and the development of programed lessons and examinations for computerized instruction, retraining, and examination of technologists and other individuals interested in microbiology.

Clinical Laboratory Techniques↗

Predictive food microbiology for the meat industry: a review.

Predictive food microbiology (PFM) is an emerging multidisciplinary area of food microbiology. It encompasses such disciplines as mathematics, microbiology, engineering and chemistry to develop and apply mathematical models to predict the responses of microorganisms to specified environmental variables. This paper provides a critical review on the development of mathematical modelling with emphasis on modelling techniques, descriptions, classifications and their recent advances. It is concluded that the role and accuracy of predictive food microbiology will increase as understanding of the complex interactions between microorganisms and food becomes clearer. However the reliance of food microbiology on laboratory techniques and skilled personnel to determine process and food safety is still necessary.

Animals↗

Role of the clinical microbiology laboratory in infection control--a Danish perspective.

Clinical microbiology laboratories in Denmark are located in hospitals and staffed by clinical microbiologists who are clinically trained medical doctors. Each county has its own clinical microbiology unit, serving a population of 0.3-0.6 million. The responsibilities of clinical microbiology unit cover many different aspects of infection control. They include detection of outbreaks of hospital-acquired infections, screening for multi-resistant organisms, advice to clinicians about disinfection, sterilization and isolation procedures, and the rational use of antibiotics. Clinical microbiologists work closely with infection control nurses. Together they form the infection control team, which is the executive part of the local infection control committee. The infection control team is also the main body responsible for the development of guidelines, which are approved by the regional infection control committee. The local microbiology laboratories work in close contact with the National Department of Hospital Hygiene and other reference laboratories at the State Serum Institute. The present structure of infection control was established 25 years ago. The main aim at that time was to decentralize infection control and establish facilities as close to clinicians and patients as practically possible. This has solved most basic problems related to infection control, and compliance by clinicians has been fairly good. However, the present organization will not meet future requirements for standardization and documentation of quality. Currently a national standard for infection control is being prepared. It consists of a main standard defining requirements for the management system and 12 subsidiary standards defining requirements for specific areas of infection control. Adoption of the standard will undoubtedly require additional resources for infection control at a local level, and some organizational changes may also be needed. Infection control should be maintained as an integrated part of clinical microbiology.

Cross Infection↗

Advisory Committee on Dangerous Pathogens (ACDP). Seminar on microbiological risk assessment, 28 January 1997.

Microbiological risk assessment is an area of growing importance and significant potential, where the underlying science, software systems and databases are developing to the point of real and useful application. It is also an area where the developing science is posing as many questions as it is presenting answers. Key issues emerging from the day included: the need for more sophisticated management of uncertainty, which is much more relevant to microbiological risk analysis than to other applications; the need for global surveillance systems with better compatibility and appropriate peer review; considered assessment of the impact of new molecular-based diagnostic and screening techniques; the explosion of relevant information available, particularly on the Internet, which makes computer literacy essential both to professionals and 'laymen'; and the appearance of software systems which are either tailored for microbiological application or have the potential for this use. The closely associated issues of risk communication and perception also emerged as being vital to the effective application of microbiological risk management to public health issues. Overall, the majority of participants considered the event to have been valuable and stimulating and thought that it would lead to improvements in the use of microbiological risk assessment. The Advisory Committee on Dangerous Pathogens is committed to taking this topic forward and will be both taking up the messages from this seminar and encouraging development of suitable databases and software systems.

Bacterial Infections↗

Determination of aerial microbiological contamination in scholastic sports environments.

AIMS: To assess the microbiological indoor air quality (IAQ) of high school and college gyms during physical training lessons and to evaluate the effective microbiological exposure of students. METHODS AND RESULTS: Air samples from 11 high school and college gyms of Pavia, Italy were collected. Total bacterial counts, total fungal counts and characterization of fungal taxa were determined. Air quality was evaluated using three microbiological contamination indices: the global index of microbiological contamination per m3 (GIMC per m3), the index of mesophilic bacterial contamination (IMC) and the amplification index (AI). CONCLUSIONS: This work testifies that air contamination in indoor gyms is always superior to that of the outdoor environment. Nevertheless, students are exposed to relatively low concentrations of airborne micro-organisms. The highest values of fungal counts and GIMC per m3 (>14,661) were observed between April and October when the central heating systems were switched off. The lowest fungal counts were detected in modern buildings equipped with forced ventilation systems. From qualitative aeromycological studies, 45 fungal taxa were identified, and different potentially allergenic species were isolated. SIGNIFICANCE AND IMPACT OF THE STUDY: The standardization of air sampling methods and the correct evaluation of aeromicrobiological results allow the classification of indoor air healthiness. The proposed microbiological contamination indices together with the characterization of airborne fungal taxa are useful tools for detailed description of IAQ.

Air Microbiology↗

Microbiological standards and handling codes for chilled and frozen foods. A review.

The usefulness of microbiological standards for frozen foods is now a controversy in the trade and scientific literature. Most reviewers have given arguments both for and against, and have concluded that they should be applied with great caution. Such standards have the advantage of putting questions of safety on a convenient numerical basis. Canadian workers have reported that promulgation of standards has invariably raised the hygienic level of the products controlled. Bacteriological standards have often been associated with the question of safety to the consumer. Everyone recognizes that food poisoning bacteria are a potential danger in any food. But many have argued that the history of food poisoning outbreaks from frozen foods is excellent and that there is no need for standards; on the other hand, proponents of standards have pointed to the incomplete investigation and reporting of outbreaks, and have argued that there may be more outbreaks than we realize. They have pointed to laboratory studies that have shown grossly mishandled precooked frozen foods to be truly dangerous. Some have proposed that pathogens should be absent from foods; but others have questioned that a microbiological standard can accomplish this end. Some pathogens, such as Salmonella or Staphylococcus have been shown to be so ubiquitous that their presence in some commercial foods is unavoidable. Also, sampling and analytical methods have been described as inadequate to guarantee that pathogens present will be detected. Some have argued that control at the source is a better way-through inspections of the plant operation, by enforcement of handling codes, or by processing procedures such as pasteurization, which would be more certain to result in a pathogen-free food.A most important part of any of the proposed standards is a "total count" of viable aerobic bacteria. English workers have found that foods causing poisoning outbreaks usually had total viable counts above 10 million per gram. On the other hand, these same workers found Salmonella on meats with very low total viable count. The assumption by many that low total count indicates safety has been shown to be not always true. Furthermore, high counts of nonpathogenic organisms, such as psychrophilic saprophytes would have no public health significance. The relation between bacterial level and quality is open to less controversy. Some authorities have pointed to bacterial level as a measure of sanitation, adequacy of refrigeration, or speed of handling. Others have indicated that to determine which of these factors caused a high count would be impossible with only a total count on the product as a guide. Some investigators have said a high count affects flavor adversely before actual spoilage is evident, and this may be a factor in competition on today's market. It is well established that initial bacterial level will affect the shelf-life of a chilled product. Methods of analysis are more nearly adequate for counts than for pathogens, but they need improvement, and should be clearly specified as part of any bacteriological standard. Foods with high count could sometimes be brought into compliance merely by storing them for a sufficient period frozen, or by heating them slightly. This has been cited by some authors as a disadvantage of bacteriological standards. The enterococci and the coliform group (except Escherichia coli) have been shown to be ubiquitous and therefore should not be used alone to indicate fecal contamination. Although E. coli has greater significance, its source should be determined each time it is found. Various reviewers have expressed the need for caution in the application of standards. The principal precautionary arguments we have found are as follows:1) A single set of microbiological standards should not be applied to foods as a miscellaneous group, such as "frozen foods" or "precooked foods."2) Microbiological standards should be applied first to the more hazardous types of foods on an individual basis, after sufficient data are accumulated on expected bacterial levels, with consideration of variations in composition, processing procedures, and time of frozen storage.3) When standards are chosen, there should be a definite relation between the standard and the hazard against which it is meant to protect the public.4) Methods of sampling and analysis should be carefully studied for reliability and reproducibility among laboratories, and chosen methods should be specified in detail as part of the standard.5) Tolerances should be included in the standard to account for inaccuracies of sampling and analysis.6) At first, the standard should be applied on a tentative basis to allow for voluntary compliance before becoming a strictly enforced regulation.7) Microbiological standards will be expensive to enforce.8) If standards are unwisely chosen they will not stand in courts of law.

Canada↗

Infectious disease physicians rate microbiology services and practices.

Recent years have seen increasing emphasis on cost containment and quality improvement in clinical laboratory activities. Modifying those activities to enhance clinical relevance is one strategy that should be satisfying to both laboratory scientists and administrators. This guest commentary describes one approach to quality improvement--the use of user surveys to identify areas for improvement. As an initial attempt to define such areas in clinical diagnostic microbiology, infectious disease specialists, targeted for their particular interest and expertise in microbiology laboratory results, were polled and their responses were analyzed. Some of these data have been presented previously (E. J. Baron, D. P. Francis, and K. M. Peddecord, abstr. C-170, p. 520, in Abstracts of the 94th General Meeting of the American Society for Microbiology, 1994; K. M. Peddecord, E. J. Baron, D. P. Francis, and A. S. Benenson, abstr. C-172, p. 520, in Abstracts of the 94th General Meeting of the American Society for Microbiology, 1994; K. M. Peddecord, E. J. Baron, D. P. Francis, and J. A. Drew, Am. J. Clin. Pathol. 105:58-64, 1996). The discussion includes our recommendations for the use of these survey responses, and their limitations, as stimuli to initiate reexamination of certain microbiology laboratory practices in the interest of developing more cost-effective and clinically relevant protocols.

Bacteremia↗

There must be a prokaryote somewhere: microbiology's search for itself.

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.

Archaea↗

[Quality assessment program of the Spanish Society of Infectious Diseases and Clinical Microbiology. Analysis of results. 2005].

Quality assurance of the analytical processes performed at the clinical microbiology laboratory is mandatory and should be carried out by using external and internal quality control activities. External quality assessment programs allow intercomparison within laboratories, detection of errors, and evaluation of the suitability of some reagents or diagnostic kits for the purpose for which they were designed; these activities are also useful for continuous education. The program launched 15 years ago by the Spanish Society of Infectious Diseases and Clinical Microbiology is based on sending typified materials along with a clinical and microbiological case related to these control materials. The spectrum of the samples is broad, including bacteriology (monthly and three-monthly), serology, mycology, parasitology, mycobacteria, virology, and molecular microbiology. After receiving the results from the participants, the program organization delivers an individual certificate comparing the results with those of a reference laboratory. Additionally, a report is generated by analyzing all the results sent by the participants; laboratories are also sent review articles on the subject of each assessment as a tool for continuous education in clinical microbiology. In this article, the most relevant conclusions and lessons from the 2005 assessments are presented.

Clinical Laboratory Techniques↗