Biomic

BACKGROUND: The purpose of this study was to objectively compare methodological approaches that might be utilized in designing an antimicrobial resistance (AMR) surveillance program in beef feedlot cattle. Specifically, four separate comparisons were made to investigate their potential impact on estimates for prevalence of AMR. These included investigating potential differences between 2 different susceptibility testing methods (broth microdilution and disc diffusion), between 2 different target bacteria (non-type-specific E...

BACKGROUND: Several macroevolutionary hypotheses propose a synchrony between climatic changes and variations in the structure of faunal communities. Some of them focus on the importance of the species ecological specialization because of its effects on evolutionary processes and the resultant patterns. Particularly, Vrba's turnover pulse hypothesis and resource-use hypothesis revolve around the importance of biome inhabitation. In order to test these hypotheses, we used the Biomic Specialization Index, which is based on the number of biomes occupied by each species, and evaluated the changes in the relative importance of generalist and specialist rodents in more than forty fossil sites from the Iberian Plio-Pleistocene...

This study compared the Biomic automated well reader results to the MicroScan WalkAway results for reading MicroScan antimicrobial susceptibility and identification panels at four different sites. Routine fresh clinical isolates and quality control (QC) organisms were tested at each study site. A total of 46,176 MicroScan panel drug-organism combinations were read. The Biomic category agreement for 3,117 Gram-negative bacteria was 98.4%, with 1.4% minor and 0.2% major discrepancies. The Biomic category agreement for 5,233 Gram-positive bacteria was 98...

The gut microbiota, the intestinal mucosa and the host immune system are among the large biological networks involved in the development of inflammatory bowel disease (IBD), which includes Crohn disease (CD) and ulcerative colitis (UC). Host genetics and environmental factors can significantly modulate the interactive relationships among these biological systems and influence predilection toward IBD. High monozygotic twin discordance rates and the rapid rise in the prevalence of IBD indicate that environmental influences may be as important or even more important in their pathogenesis than genetic susceptibility...

The resource-use hypothesis proposed by E.S. Vrba predicts that specialist species have higher speciation and extinction rates than generalists because they are more susceptible to environmental changes and vicariance. In this work, we test some of the predictions derived from this hypothesis on the 197 extant and recently extinct species of Ruminantia (Cetartiodactyla, Mammalia) using the biomic specialization index (BSI) of each species, which is based on its distribution within different biomes. We ran 10000 Monte Carlo simulations of our data in order to get a null distribution of BSI values against which to contrast the observed data...

Tuberculosis is one of the most deadly infectious diseases. The situation is worsening because of co-infection with HIV and increased occurrence of drug resistance. Although the BCG vaccine has been in use for 90 years, protection is insufficient; new vaccine candidates are therefore needed. 12 potential vaccines have gone into clinical trials. Ten are aimed at prevention of tuberculosis and, of these, seven are subunit vaccines either as adjuvanted or viral-vectored antigens. These vaccines would be boosters of BCG-prime vaccination...

We evaluated all Candida spp. isolates obtained from patients admitted to two tertiary care hospitals between 1999 and 2003 in the city of São Paulo, Brazil. The in vitro activities of fluconazole (FCZ) and voriconazole were determined by the agar disk diffusion test using the Clinical and Laboratory Standards Institute M44-A guidelines. The inhibition zone diameters were read and interpreted automatically by the BIOMIC(®) image-analysis plate reader system. We tested a total of 4,625 strains, including 2,393 strains of C...

BACKGROUND: We utilized results from the ARTEMIS DISK Global Antifungal Surveillance Program to evaluate the species distribution and fluconazole and voriconazole susceptibilities of yeast isolates from clinical specimens in South Korea from 2001 to 2007. METHODS: Data were collected on 5,665 yeast isolates from all body sites at three locations. All investigators tested clinical yeast isolates using the CLSI M44-A disk diffusion method. Test plates were automatically read and results were recorded using the BIOMIC image analysis plate reader system (Giles Scientific, USA)...

No new vaccine has been licensed for tuberculosis (TB) for more than three-quarters of a century, and no new drug has been licensed for half a century. One major drawback has been the attrition caused by the lack of a reliable biological indicator (biomarker) to predict toxicity and efficacy early in the development pipeline. This review portrays the landscape of biomarker discovery for TB in the context of drug and vaccine development using emerging global biomics platforms. The time is ripe to move from single markers for correlates of protection to a biosignature comprising a well-defined set of robust indicators in TB that can accelerate rapid screening and early selection of potential drug and vaccine candidates...

The rate of in vitro resistance to various antimicrobials in 179 consecutive isolates of Salmonella spp., which included serogroups D (109), B (52), C1 (10) and C2 (8) isolated from children, was investigated. Production of extended-spectrum beta-lactamase (ESBL) was studied in ampicillin-resistant isolates. Antimicrobial susceptibilities were determined by disk diffusion tests and by BIOMIC video reader system. Overall resistance rates to ampicillin and amoxicillin/clavulanate were 26.3% and 10.6%, respectively...

The late Paleozoic earth experienced alternation between glacial and non-glacial climates at multiple temporal scales, accompanied by atmospheric CO2 fluctuations and global warming intervals, often attended by significant vegetational changes in equatorial latitudes of Pangaea. We assess the nature of climate-vegetation interaction during two time intervals: middle-late Pennsylvanian transition and Pennsylvanian-Permian transition, each marked by tropical warming and drying. In case study 1, there is a catastrophic intra-biomic reorganization of dominance and diversity in wetland, evergreen vegetation growing under humid climates...

The Biomic V3 microbiology system identifies bacteria by reading the color of colonies selected by the user. For CHROMagar orientation, Biomic results agreed with conventional methods for 94% of the strains assayed. For CHROMagar MRSA, Biomic correctly identified 100% of the strains tested and did not misidentify two methicillin-susceptible Staphylococcus aureus strains growing on the plates.

BACKGROUND: This paper tests Vrba's resource-use hypothesis, which predicts that generalist species have lower specialization and extinction rates than specialists, using the 879 species of South American mammals. We tested several predictions about this hypothesis using the biomic specialization index (BSI) for each species, which is based on its geographical range within different climate-zones. The four predictions tested are: (1) there is a high frequency of species restricted to a single biome, which henceforth are referred to as stenobiomic species, (2) certain clades are more stenobiomic than others, (3) there is a higher proportion of biomic specialists in biomes that underwent through major expansion-contraction alternation due to the glacial-interglacial cycles, (4) certain combinations of inhabited biomes occur more frequently among species than do others...

Fluconazole in vitro susceptibility test results for 205,329 yeasts were collected from 134 study sites in 40 countries from June 1997 through December 2005. Data were collected for 147,776 yeast isolates tested with voriconazole from 2001 through 2005. All investigators tested clinical yeast isolates by the CLSI M44-A disk diffusion method. Test plates were automatically read and results recorded with a BIOMIC image analysis system. Species, drug, zone diameter, susceptibility category, and quality control results were collected quarterly...

The ARTEMIS Global Antifungal Susceptibility Program provides the collection of epidemiological data and the results of the fluconazole and voriconazole susceptibility testing of yeast isolates. Participating in this study, a total of 7318 clinical yeast isolates were tested from different geographical areas in Hungary in the period 2001 to 2003. The species isolated most frequently was C. albicans (68.8%), followed by C. glabrata (11.8%), C. tropicalis (5.7%) and C. krusei (4.6%). Isolates of C. albicans, C...

A Native American-Indian female presenting with anemia and thrombocytosis was diagnosed with myelodysplastic syndrome (MDS, refractory anemia). Over the course of 5 years she developed cytopenias and periods of leukocytosis with normal bone marrow (BM) blast counts, features of an unclassifiable MDS/MPS syndrome. The patient ultimately progressed to acute myelogenous leukemia (AML, FAB M2) and had a normal karyotype throughout her course. The episodes of leukocytosis were associated with infectious complications...

Fluconazole in vitro susceptibility test results for 140,767 yeasts were collected from 127 participating investigators in 39 countries from June 1997 through December 2003. Data were collected on 79,343 yeast isolates tested with voriconazole from 2001 through 2003. All investigators tested clinical yeast isolates by the CLSI (formerly NCCLS) M44-A disk diffusion method. Test plates were automatically read and results were recorded with the BIOMIC Vision Image Analysis System. Species, drug, zone diameter, susceptibility category, and quality control results were collected quarterly via e-mail for analysis...

The interaction between the human body and nutrition is an extremely complex process involving multi-organ physiology with molecular mechanisms on all levels of regulation (genes, gene expression, proteins, metabolites). Only with the recent technology push have nutritional scientists been able to address this complexity. Both the challenges and promises that are offered by the merge of 'biomics' technologies and mechanistic nutrition research are huge, but will eventually evolve in a new nutrition research concept: nutritional systems biology...

A plethora of new 'omics such as transcriptomics, proteomics, metabolomics (or metabonomics), pharmacogenomics, physiomics and cytomics are upon us, but can histochemistry be an 'omic? To be an 'omic a technique must take a 'global' and 'holistic' view of biology that addresses biological complexity head-on by synthesising multiparameter data into predictive models. Thus to be an 'omic, a histochemical technique should be as inclusive as possible in identifying as many targets as possible with equal likelihood and sensitivity of detection...

In vitro susceptibilities of 290 isolates of Candida spp to fluconazole were evaluated by a new NCCLS M44-P agar disk diffusion method that was read and interpreted automatically by the BIOMIC image-analysis plate reader system. Disk test results were compared to results obtained by a modified NCCLS M27-A broth microdilution method using RPMI-1640 supplemented with 2% dextrose. Overall agreement between both methods was 90.0%. Category agreement between the broth and disk test results for susceptible, susceptible dose-dependent and resistant disk results were 99...