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PubMed1999

Immunochemical detection and isolation of DNA from metabolically active bacteria.

Most techniques used to assay the growth of microbes in natural communities provide no information on the relationship between microbial productivity and community structure. To identify actively growing bacteria, we adapted a technique from immunocytochemistry to detect and selectively isolate DNA from bacteria incorporating bromodeoxyuridine (BrdU), a thymidine analog. In addition, we developed an immunocytochemical protocol to visualize BrdU-labeled microbial cells. Cultured bacteria and natural populations of aquatic bacterioplankton were pulse-labeled with exogenously supplied BrdU. Incorporation of BrdU into microbial DNA was demonstrated in DNA dot blots probed with anti-BrdU monoclonal antibodies and either peroxidase- or Texas red-conjugated secondary antibodies. BrdU-containing DNA was physically separated from unlabeled DNA by using antibody-coated paramagnetic beads, and the identities of bacteria contributing to both purified, BrdU-containing fractions and unfractionated, starting-material DNAs were determined by length heterogeneity PCR (LH-PCR) analysis. BrdU-containing DNA purified from a mixture of DNAs from labeled and unlabeled cultures showed >90-fold enrichment for the labeled bacterial taxon. The LH-PCR profile for BrdU-containing DNA from a labeled, natural microbial community differed from the profile for the community as a whole, demonstrating that BrdU was incorporated by a taxonomic subset of the community. Immunocytochemical detection of cells with BrdU-labeled DNA was accomplished by in situ probing with anti-BrdU monoclonal antibodies and Texas red-labeled secondary antibodies. Using this suite of techniques, microbial cells incorporating BrdU into their newly synthesized DNA can be quantified and the identities of these actively growing cells can be compared to the composition of the microbial community as a whole. Since not all strains tested could incorporate BrdU, these methods may be most useful when used to gain an understanding of the activities of specific species in the context of their microbial community.

Antibodies, Monoclonal↗
PubMed1993

Value of bacterial antigen detection in the diagnostic yield of transthoracic needle aspiration in severe community acquired pneumonia.

BACKGROUND: Transthoracic needle aspiration (TNA) with an ultrathin needle is a safe and highly specific procedure for obtaining a diagnosis in bacterial pneumonias, but its sensitivity is at best 70%. A study was performed to assess whether Streptococcus pneumoniae and Haemophilus influenzae type b antigen detection by latex agglutination from the TNA sample enhanced the diagnostic yield. METHODS: Blood cultures, TNA with an ultrathin needle (culture, Gram stain, and latex agglutination), serological tests, and pneumococcal antigen detection in the urine by counterimmunoelectrophoresis were performed in samples from 18 of 23 consecutive patients with severe community acquired pneumonia. RESULTS: The causative organism was identified in 16 cases (88%): S pneumoniae (10 cases), S pneumoniae plus H influenzae (two cases), Legionella pneumophila (three cases), and Mycoplasma pneumoniae (one case). The investigation of antigens by latex agglutination in the pulmonary aspirate increased the diagnostic yield of TNA from 50% to 78% and provided a rapid diagnosis (in less than two hours) with therapeutic implications in seven cases. Its effectiveness was not modified by prior antibiotic therapy. CONCLUSIONS: A latex agglutination test on the pulmonary aspirate enhances the diagnostic yield of TNA in severe community acquired pneumonia.

Adult↗
PubMed2000

A novel method for collecting and detecting amoxycillin in urine: a tool for testing antibiotic compliance in the community.

Assessing compliance to prescribed antibiotics in community studies of respiratory tract infections is difficult. We describe a simple method for collecting and detecting amoxycillin in urine using urine dip-sticks in conjunction with a bioassay. Urine was collected at timed intervals from eight healthy volunteers following oral amoxycillin administration. Dip-sticks inoculated with urine collected 1 and 8 h after antibiotic resulted in mean zones of inhibition of 1.75 and 1.37 cm, respectively. Amoxycillin activity remained demonstrable 14 days after inoculation of dip-sticks with urine. Dip-sticks inoculated with urine from control subjects who had not taken amoxycillin did not cause inhibition.

Amoxicillin↗
PubMed2006

The community and phylogenetic diversity of biological soil crusts in the Colorado Plateau studied by molecular fingerprinting and intensive cultivation.

We studied the bacterial communities in biological soil crusts (BSCs) from the Colorado Plateau by enrichment and cultivation, and by statistically analyzed denaturing gradient gel electrophoresis (DGGE) fingerprinting of environmental 16S rRNA genes, and phylogenetic analyses. Three 500-m-long transects, tens of km apart, consisting of 10 equally spaced samples each, were analyzed. BSC communities consistently displayed less richness (10-32 detectable DGGE bands per sample) and Shannon diversity (2.1-3.3) than typical soil communities, with apparent dominance by few members. In spite of some degree of small-scale patchiness, significant differences in diversity and community structure among transects was detectable, probably related to the degree of crust successional maturity. Phylogenetic surveys indicated that the cyanobacterium Microcoleus vaginatus was dominant, with M. steenstrupii second among phototrophs. Among the 48 genera of nonphototrophs detected, Actinobacteria (particularly Streptomyces spp.) were very common and diverse, with 18 genera and an average contribution to the total 16S rDNA amplificate of 11.8%. beta-Proteobacteria and Bacteriodetes contributed around 10% each; Low-GC Gram-positives, alpha-Proteobacteria, Thermomicrobiales, and Acidobacteria were common (2-5%). However, the second largest contribution was made by deep-branching unaffiliated alleles (12.6%), with some of them representing candidate bacterial divisions. Many of the novel strains isolated are likely new taxa, and some were representatives of the phylotypes detected in the field. The mucoid or filamentous nature of many of these isolates speaks for their role in crust formation.

Alleles↗
PubMed2004

Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries.

We analyzed bacterioplankton community structure in Tillamook Bay, Oregon and its tributaries to evaluate phylogenetic variability and its relation to changes in environmental conditions along an estuarine gradient. Using eubacterial primers, we amplified 16S rRNA genes from environmental DNA and analyzed the PCR products by length heterogeneity polymerase chain reaction (LH-PCR), which discriminates products based on naturally occurring length differences. Analysis of LH-PCR profiles by multivariate ordination methods revealed differences in community composition along the estuarine gradient that were correlated with changes in environmental variables. Microbial community differences were also detected among different rivers. Using partial 16S rRNA sequences, we identified members of dominant or unique gene fragment size classes distributed along the estuarine gradient. Gammaproteobacteria and Betaproteobacteria and members of the Bacteroidetes dominated in freshwater samples, while Alphaproteobacteria, Cyanobacteria and chloroplast genes dominated in marine samples. Changes in the microbial communities correlated most strongly with salinity and dissolved silicon, but were also strongly correlated with precipitation. We also identified specific gene fragments that were correlated with inorganic nutrients. Our data suggest that there is a significant and predictable change in microbial species composition along an estuarine gradient, shifting from a more complex community structure in freshwater habitats to a community more typical of open ocean samples in the marine-influenced sites. We also demonstrate the resolution and power of LH-PCR and multivariate analyses to provide a rapid assessment of major community shifts, and show how these shifts correlate with environmental variables.

Bacteria↗
PubMed2006

Plant community responses to experimental warming across the tundra biome.

Recent observations of changes in some tundra ecosystems appear to be responses to a warming climate. Several experimental studies have shown that tundra plants and ecosystems can respond strongly to environmental change, including warming; however, most studies were limited to a single location and were of short duration and based on a variety of experimental designs. In addition, comparisons among studies are difficult because a variety of techniques have been used to achieve experimental warming and different measurements have been used to assess responses. We used metaanalysis on plant community measurements from standardized warming experiments at 11 locations across the tundra biome involved in the International Tundra Experiment. The passive warming treatment increased plant-level air temperature by 1-3 degrees C, which is in the range of predicted and observed warming for tundra regions. Responses were rapid and detected in whole plant communities after only two growing seasons. Overall, warming increased height and cover of deciduous shrubs and graminoids, decreased cover of mosses and lichens, and decreased species diversity and evenness. These results predict that warming will cause a decline in biodiversity across a wide variety of tundra, at least in the short term. They also provide rigorous experimental evidence that recently observed increases in shrub cover in many tundra regions are in response to climate warming. These changes have important implications for processes and interactions within tundra ecosystems and between tundra and the atmosphere.

Arctic Regions↗
PubMed2006

A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities.

A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-positive signals of approximately 5% after protocol optimization and a marginal loss of correct positive signals. Subsequent microarray analysis of sediment-related community RNA from four different German river sites suggested low diversity for the groups targeted but indicated distinct differences in community composition. The results were supported by parallel fluorescence in situ hybridization in combination with sensitive catalyzed reporter deposition (CARD-FISH). In comparisons of the data of different sampling sites, specific detection of populations with relative cellular abundances down to 2% as well as a correlation of microarray signal intensities and population size is suggested. Our results demonstrate that DNA microarray technology allows for the fast and efficient precharacterization of complex bacterial communities by the use of standard single-cell hybridization probes and the direct detection of environmental rRNA, also in methodological challenging habitats such as heterogeneous lotic freshwater sediments.

Bacteria↗
PubMedDate not supplied

Control of hypertension in the population. Strategies in affluent and developing countries.

Control of hypertension in population. Strategies in affluent and developing countries. The control of hypertension encompasses primary prevention, early detection and adequate treatment of high blood pressure. Primary prevention involves action at the population level to reduce obesity, alcohol and salt consumption, and to increase physical activity. The management of hypertension involves diagnostic work-up, assessment of overall cardiovascular disease risk, non-pharmacological and pharmacological treatment. The majority of community control programmes emphasized detection and treatment, rather than primary prevention. There are limitations to pharmacological treatment of hypertension, as shown by various studies, where a significant proportion of hypertensives have not been controlled by the treatment applied. In addition, the blood pressure-cardiovascular risk relationship is continuous and progressive and, even within the conventionally defined "normotensive" range, complications occur with escape control. Developing countries will encounter the problem of prohibitive costs of care and drug treatment for hypertension. Therefore greater emphasis must be put on primary prevention in population control of hypertension.

Antihypertensive Agents↗
PubMed2005

Screening clinical breast examination: how often does it miss lethal breast cancer?

BACKGROUND: Although most American women regularly receive screening clinical breast examination (CBE), little is known about CBE accuracy in community practice. We sought to estimate the rate of cancer detection (sensitivity) of screening CBE performed by community-based clinicians on women who ultimately died of breast cancer, as well as to identify factors associated with accurate detection. SUBJECTS AND METHODS: We evaluated CBE accuracy among asymptomatic female health plan enrollees in five states (WA, OR, CA, MA, and MN) who received a CBE within 1 year of breast cancer diagnosis and who died of breast cancer within 15 years of diagnosis (N = 485). Sensitivity was estimated as the proportion whose exam was abnormal. Bivariate and logistic regression analyses identified patient characteristics associated with cancer detection. RESULTS: An abnormality was noted on screening CBE in one of five women who ultimately succumbed to breast cancer (sensitivity = 21.6%; 95% confidence interval [CI] = 18.1% to 25.6%). The odds of a true-positive screening CBE (sensitivity) were decreased among women using estrogen (odds ratio [OR] = 0.23; 95% CI = 0.07 to 0.80), receiving a Pap smear during the same visit as CBE (OR = 0.45; 95% CI = 0.27 to 0.72), and with increasing chronic disease comorbidity (P(trend) = .08). CONCLUSION: Screening CBE as performed in the community may be insufficiently sensitive to detect most lethal breast cancers. Low sensitivity of screening CBE in community practice may be partly attributable to its performance alongside time-consuming clinical tasks such as Pap smear screening or chronic illness care.

Adult↗
PubMed2000

A trans-cultural comparison of four psychiatric case-finding instruments in a Welsh community.

BACKGROUND: Case-finding instruments have been developed for different purposes and in different cultural settings. Four instruments designed to detect psychiatric morbidity in community-based populations were studied in order to compare the performance of instruments from differing sources in a common setting. METHODS: The study was undertaken in a Welsh primary care setting. The Revised Clinical Interview Schedule (CIS-R) was used to define caseness. The instruments studied were the General Health Questionnaire (GHQ), the Mental Health Index (MHI), the Self Reporting Questionnaire (SRQ), and the Shona Symptom Questionnaire (SSQ). Performance was assessed by standard test indices, kappa values, and receiver operating curve analysis. The content of the four instruments was also compared. RESULTS: Sixty-nine adults completed the study. The prevalence of CIS-R caseness in this sample was 45%. No significant differences in case-recognition were found and all instruments had misclassification rates of 10% or less. The instruments showed wide variation in content. Half the items were unique to a single instrument and only three items (sleep, unhappiness and decision making) were shared by three instruments. The most frequent symptom within the total sample, and among cases, was the Zimbabwean concept of 'thinking too much'. CONCLUSIONS: Etic instruments (SRQ and SSQ) performed as well as emic ones (GHQ and MHI) in this setting, despite the wide variation in instrument structure.

Adult↗
PubMedDate not supplied

Epidemiological investigations on viral hepatitis in preschool and school communities. Note III. Sources of infection for HBsAg carriers and former viral hepatitis patients.

HBsAg carriers and viral hepatitis B patients detected in preschool and school communities as well as members of their families were subjected to thorough epidemiological investigations. The source of infection was represented by the community in 33.3% of the preschool children and in 26.5% of the schoolchildren and by the family in 10% of the former and 29.4% of the latter.

Adolescent↗
PubMed2003

Evaluation of a PCR assay for detection of Streptococcus pneumoniae in respiratory and nonrespiratory samples from adults with community-acquired pneumonia.

Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, but it is undoubtedly underdiagnosed. We used a nested PCR assay (targeting the pneumolysin gene) to detect S. pneumoniae DNA in multiple sample types from 474 adults with community-acquired pneumonia and 183 control patients who did not have pneumonia. Plasma or buffy coat samples were PCR positive in only 6 of the 21 patients with positive blood cultures for S. pneumoniae and in 12 other patients (4 of whom had no other laboratory evidence of S. pneumoniae infection). Buffy coat samples from two control patients (neither having evidence of S. pneumoniae infection), but no control plasma samples, were PCR positive. Although pneumococcal antigen was detected in the urine from 120 of 420 (29%) patients, only 4 of 227 (2%) urine samples tested were PCR positive. Overall, 256 of 318 (81%) patients had PCR-positive sputum samples, including 58 of 59 samples from which S. pneumoniae was cultured. Throat swab samples from 229 of 417 (55%) patients were PCR positive and, in those who produced sputum, 96% also had positive PCR results from sputum. Throat swabs from 73 of 126 (58%) control patients were also PCR positive. We conclude that the pneumolysin PCR assay adds little to existing diagnostic tests for S. pneumoniae and is unable to distinguish colonization from infection when respiratory samples are tested.

Adult↗
PubMed2004

Racial influence on biochemical disease-free survival in men treated with external-beam radiotherapy for localized prostate cancer.

BACKGROUND: We retrospectively analyzed the clinical characteristics and outcomes of various racial and ethnic groups who underwent radiotherapy alone for localized or locally advanced prostate cancer. METHODS: From April 1987 to January 1998, 964 patients underwent full-dose, external-beam radiotherapy alone for localized or locally advanced prostate cancer and were included in the study. The patients' medical records were reviewed for pertinent information. RESULTS: Of the 964 patients, 810 were non-Hispanic white, 86 were African-American, 54 were Hispanic, and 14 were Asian. The most significant difference between groups was in the proportion of patients who presented with initial PSA levels > 20 ng/ml. More than 20% of men in all minority groups presented with a serum PSA > 20 ng/ml, compared to only 11% of whites (p = 0.0012). Similarly, 14% of minorities presented with Gleason scores > or = 8 compared to only 11% of whites (p = 0.0265). Hispanic and Asian patients exhibited a higher incidence of Gleason score > or = 8 prostate cancer. When comparing the time intervals of 1995-1998 vs. 1987-1994, the number of men presenting for EBRT with PSA levels < 10 ng/ml increased to 74% from 57% for Caucasians (p < 0,001), 71% from 40% for African Americans (p = 0.012), 67% from 49% for Hispanics (p = 0.1 18), and no change (50%) for Asians. CONCLUSIONS: The number of African-American patients presenting with favorable characteristics (PSA < 10 ng/ml) is increasing. These findings suggest that the message of screening and early detection may be reaching the African-American community. Continued diligence in screening and early detection may improve prostate cancer outcome for other minority populations.

Black or African American↗
PubMed1993

Detection of alcoholism in schizophrenia using the MAST.

The classification accuracy of the Michigan Alcoholism Screening Test (MAST) for detecting alcoholism in a community sample of 75 schizophrenic outpatients was assessed, as a replication and extension of Searles et al. (1990). The criterion diagnosis of alcohol use disorder was based on the convergence of ratings from multiple sources. The MAST classified 85% of the sample correctly, and item-based analyses showed that various subsets were equally effective, indicating a high degree of redundancy among MAST items. Differences between our sample and that of Searles et al. influenced the choice of MAST items for optimal detection and classification, and males were consistently classified more correctly than females. These results suggest that the construction of a brief and accurate detection instrument for alcohol use among schizophrenic patients may be possible, although attention to subpopulation differences will be required.

Adult↗
PubMed2004

Assessment of depression prevalence in rural Uganda using symptom and function criteria.

BACKGROUND: We sought to assess the prevalence of major depression in a region of sub-Saharan Africa severely affected by HIV, using symptom and functional criteria as measured with locally validated instruments. METHOD: Six hundred homes in the Masaka and Rakai districts of southwest Uganda were selected by weighted systematic random sampling. A locally validated version of the depression section of the Hopkins Symptom Check List (DHSCL) and a community-generated index of functional impairment were used to interview 587 respondents. RESULTS: Of respondents, 21% were diagnosed with depression using three of the five DSM-IV criteria (including function impairment) compared with 24.4% using symptom criteria alone. Increased age and lower educational levels are associated with a greater risk for depression; however, a gender effect was not detected. CONCLUSIONS: Most community-based assessments of depression in sub-Saharan Africa based on the DSM-IV have used symptom criteria only. We found that expanding criteria to more closely match the complete DSM-IV is feasible, thereby making more accurate assessments of prevalence possible. This approach suggests that major depression and associated functional impairment are a substantial problem in this population.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

Development of a cancer prevention and early detection program for nurses working with African Americans.

BACKGROUND: Many health care institutions expect nurses to assume leadership roles in the provision of cancer education and screening. However, all too often, nurses lack the knowledge and skills needed to effectively inform, screen, and counsel their clients. The challenges may be compounded when they are expected to provide cancer care to clients from cultural, racial, and ethnic backgrounds different from their own. METHOD: The Cancer Prevention and Early Detection Program for Nurses Working with African Americans was developed to help fill this void. The program provides nurses with theoretical, clinical, and practical information regarding cancer prevention and early detection for use within clinical and community settings. RESULTS AND CONCLUSIONS: The Cancer Prevention and Early Detection Program for Nurses Working with African Americans enhanced participants' abilities to provide cancer education, screening, and follow up, and it heightened their sensitivity and understanding of issues and trends influencing cancer prevention and early detection among African Americans.

Adult↗
PubMed2004

Mounting a community-randomized trial: sample size, matching, selection, and randomization issues in PRISM.

This paper discusses some of the processes for establishing a large cluster-randomized trial of a community and primary care intervention in 16 local government areas in Victoria, Australia. The development of the trial in terms of design factors such as sample size estimates and the selection and randomization of communities to intervention or comparison is described. The intervention program to be implemented in Program of Resources, Information and Support for Mothers (PRISM) was conceived as a whole community approach to improving support for all mothers in the first 12 months after birth. A cluster-randomized trial was thus the design of choice from the outset. With a limited number of communities available, a matched-pair design with eight pairs was chosen. Sample size estimates, adjusting for the cluster randomization and the pair-matched design, showed that with eight pairs, on average, 800 women from each community would need to respond to provide sufficient power to determine a 3% reduction in the prevalence of maternal depression 6 months after birth-a reduction deemed to be a worthwhile impact of the intervention to be reliably detected at 80% power. The process of selecting suitable communities and matching them into pairs required careful collection of data on numbers of births, size of the local government areas (LGAs), and an assessment of the capacity of communities to implement the intervention. Ways of dealing with boundary issues associated with potential contamination are discussed. Methods for the selection of feasible configurations of sets of pairs and the ultimate allocation to intervention or comparison are provided in detail. Ultimately, all such studies are a balancing act between selecting the minimum number of communities to detect a meaningful outcome effect of an intervention and the maximum size budget and other resources allow.

Adult↗
PubMed2005

Legionella species diversity in an acidic biofilm community in Yellowstone National Park.

Legionella species are frequently detected in aquatic environments, but their occurrence in extreme, acidic, geothermal habitats has not been explored with cultivation-independent methods. We investigated a predominately eukaryotic algal mat community in a pH 2.7 geothermal stream in Yellowstone National Park for the presence of Legionella and potential host amoebae. Our analyses, using PCR amplification with Legionella-specific primers targeting 16S rRNA genes, detected four known Legionella species, as well as Legionella sequences from species that are not represented in sequence databases, in mat samples and cultivated isolates. The nonrandom occurrence of sequences detected at lower (30 degrees C) and higher (35 to 38 degrees C) temperatures suggests that natural thermal gradients in the stream influence Legionella species distributions in this mat community. We detected only one sequence, Legionella micdadei, from cultivated isolates. We cultured and sequenced partial 18S rRNA gene regions from two potential hosts, Acanthamoeba and Euglena species.

Acanthamoeba↗