Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity.
01 Nov 1988-Journal of Clinical Microbiology (American Society for Microbiology)-Vol. 26, Iss: 11, pp 2465-2466
TL;DR: An index of discrimination for typing methods is described, based on the probability of two unrelated strains being characterized as the same type, which may be used to compare typing methods and select the most discriminatory system.
Abstract: An index of discrimination for typing methods is described, based on the probability of two unrelated strains being characterized as the same type. This index may be used to compare typing methods and select the most discriminatory system.
Citations
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TL;DR: Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages and Criteria for their evaluation and application and the interpretation of their results are proposed.
771 citations
Cites methods from "Numerical index of the discriminato..."
...Hunter and Gaston’s modification of Simpson’s index of diversity and fixed confidence intervals are important parameters used for making a decision on strain identity or diversity [86]....
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...It can be expressed as a probability using Simpson’s index of diversity [85,86]....
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TL;DR: Evidence that M. tuberculosis genotype influences clinical disease phenotype is provided and a significant interaction between host and bacterial genotypes and the development of tuberculosis is demonstrated for the first time.
Abstract: The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM) and 237 Vietnamese adults with uncomplicated pulmonary tuberculosis. The host genotype of tuberculosis cases was also compared with the genotype of 392 cord blood controls from the same population. Isolates of M. tuberculosis were genotyped by large sequence polymorphisms. The hosts were defined by polymorphisms in genes encoding Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP) and Toll-like receptor-2 (TLR-2). We found a significant protective association between the Euro-American lineage of M. tuberculosis and pulmonary rather than meningeal tuberculosis (Odds ratio (OR) for causing TBM 0.395, 95% confidence intervals (C.I.) 0.193-0.806, P = 0.009), suggesting these strains are less capable of extra-pulmonary dissemination than others in the study population. We also found that individuals with the C allele of TLR-2 T597C allele were more likely to have tuberculosis caused by the East-Asian/Beijing genotype (OR = 1.57 [95% C.I. 1.15-2.15]) than other individuals. The study provides evidence that M. tuberculosis genotype influences clinical disease phenotype and demonstrates, for the first time, a significant interaction between host and bacterial genotypes and the development of tuberculosis.
484 citations
Additional excerpts
...strains belonging to the j type [52]....
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TL;DR: It is determined that S. aureus likely has a primarily clonal population structure and that spa typing can singly index genetic variation with 88% direct concordance with the microarray and can correctly assign isolates to phylogenetic lineages.
Abstract: Strain typing of microbial pathogens has two major aims: (i) to index genetic microvariation for use in outbreak investigations and (ii) to index genetic macrovariation for use in phylogenetic and population-based analyses. Until now, there has been no clear indication that one genetic marker can efficiently be used for both purposes. Previously, we had shown that DNA sequence analysis of the protein A gene variable repeat region (spa typing) provides a rapid and accurate method to discriminate Staphylococcus aureus outbreak isolates from those deemed epidemiologically unrelated. Here, using the hypothesis that the genetic macrovariation within a low-level recombinogenic species would accurately be characterized by a single-locus marker, we tested whether spa typing could congruently index the extensive genetic variation detected by a whole-genome DNA microarray in a collection of 36 isolates, which was recovered from 10 countries on four continents over a period of four decades, that is representative of the breadth of diversity within S. aureus. Using spa and coa typing, pulsed-field gel electrophoresis (PFGE), and microarray and multilocus enzyme electrophoresis (MLEE) data in molecular epidemiologic and evolutionary analyses, we determined that S. aureus likely has a primarily clonal population structure and that spa typing can singly index genetic variation with 88% direct concordance with the microarray and can correctly assign isolates to phylogenetic lineages. spa typing performed better than MLEE, PFGE, and coa typing in discriminatory power and in the degree of agreement with the microarray at various phylogenetic depths. This study showed that genetic analysis of the repeat region of protein A comprehensively characterizes both micro- and macrovariation in the primarily clonal population structure of S. aureus.
483 citations
Cites background from "Numerical index of the discriminato..."
...calculates the probability that any two isolates will have different genotypes (14)....
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TL;DR: The widespread distribution of the nontuberculous mycobacteria in the environment, coupled with their ability to degrade and metabolize a variety of complex hydrocarbons including pollutants, suggests that NTM may be agents of nutrient cycling.
Abstract: A majority of the Mycobacterium species, called the nontuberculous mycobacteria (NTM), are natural inhabitants of natural waters, engineered water systems, and soils. As a consequence of their ubiquitous distribution, humans are surrounded by these opportunistic pathogens. A cardinal feature of mycobacterial cells is the presence of a hydrophobic, lipid-rich outer membrane. The hydrophobicity of NTM is a major determinant of aerosolization, surface adherence, biofilm-formation, and disinfectant- and antibiotic resistance. The NTM are oligotrophs, able to grow at low carbon levels [>50 microg assimilable organic carbon (AOC) l(-1)], making them effective competitors in low nutrient, and disinfected environments (drinking water). Biofilm formation and oligotrophy lead to survival, persistence, and growth in drinking water distribution systems. In addition to their role as human and animal pathogens, the widespread distribution of NTM in the environment, coupled with their ability to degrade and metabolize a variety of complex hydrocarbons including pollutants, suggests that NTM may be agents of nutrient cycling.
483 citations
Cites methods from "Numerical index of the discriminato..."
...Calculations of indices of discrimination for all three methods of DNA fingerprinting (Hunter and Gaston 1988) show that they provide the discrimination for source tracking....
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TL;DR: A method for determining confidence intervals for a commonly used index of diversity facilitates the comparison of the genetic population structure of microorganisms isolated from different environments and improves the objective assessment of the discriminatory power of typing techniques.
Abstract: We describe here a method for determining confidence intervals for a commonly used index of diversity. This approach facilitates the comparison of the genetic population structure of microorganisms isolated from different environments and improves the objective assessment of the discriminatory power of typing techniques.
472 citations
Cites background from "Numerical index of the discriminato..."
...The index of diversity D, as defined by Simpson (5) and lately utilized for the assessment of the discriminatory power of typing techniques (2, 6), is an unbiased estimate of the true diversity of a population based on a sample of n individuals....
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References
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TL;DR: In this article, the authors define and examine a measure of concentration in terms of population constants, and examine the relationship between the characteristic and the index of diversity when both are applied to a logarithmic distribution.
Abstract: THE 'characteristic' defined by Yule1 and the 'index of diversity' defined by Fisher2 are two measures of the degree of concentration or diversity achieved when the individuals of a population are classified into groups. Both are defined as statistics to be calculated from sample data and not in terms of population constants. The index of diversity has so far been used chiefly with the logarithmic distribution. It cannot be used everywhere, as it does not always give values which are independent of sample size ; it cannot do so, for example, when applied to an infinite population of individuals classified into a finite number of groups. Williams3 has pointed out a relationship between the characteristic and the index of diversity when both are applied to a logarithmic distribution. The present purpose is to define and examine a measure of concentration in terms of population constants.
10,077 citations
TL;DR: DNA typing methods appear to offer important potential advantages over phenotyping methods, and provide a base for further epidemiologic studies and for further development of techniques, such as the use of cloned probes for studies of DNA homology.
Abstract: Methods are described for extraction of DNA from the yeast form of Candida spp., followed by digestion and electrophoresis of DNA fragments. The resulting gel patterns (greater than 100 bands) were used to type Candida isolates. Four intense bands identified, three of which are present in each isolate (6 to 7, 3.7 or 4.2, and 2.5 to 3 kilobases), appear to be DNA encoding the rRNA. The methods proved to be both simple and reproducible. The patterns were shown to be stable through several hundred doublings from multiple single colonies. A survey of isolates showed that, on the basis of similarity of gel patterns, several Candida species could be sorted into mutually exclusive groups, and subgroups could be created. Analyses of this survey suggested the possible epidemiologic and taxonomic applications of these methods. DNA typing methods appear to offer important potential advantages over phenotyping methods. The methods provide a base for further epidemiologic studies and for further development of techniques, such as the use of cloned probes for studies of DNA homology. Images
387 citations
TL;DR: By using a simple system, it was possible to differentiate up to 512 isolates of C. albicans according to their susceptibility to the killer effect of nine selected killer yeasts, and the use of this method as an epidemiological marker in the case of presumptive nosocomial infections due to C.Albicans is reported.
Abstract: The killer effect of 37 species of Candida, Cryptococcus, Hansenula, Pichia, Rhodotorula, Saccharomyces, and Trichosporon on 100 Candida albicans isolates of human and animal origin was studied. All of the C. albicans cultures were sensitive to one or more killer yeasts. The factors affecting the killer phenomenon on C. albicans were investigated for realizing a simple system for the differentiation of the 100 C. albicans isolates. By using this system, it was possible to differentiate up to 512 isolates of C. albicans according to their susceptibility to the killer effect of nine selected killer yeasts. The use of this method as an epidemiological marker in the case of presumptive nosocomial infections due to C. albicans is also reported.
203 citations
TL;DR: A new method of typing Candida albicans based on immunoblotting is described, which was much more sensitive than the serotyping and morphotyping methods and lacked the phenotypic variability of the biotyping procedure previously used to define the outbreak.
68 citations
TL;DR: A total of 126 Candida albicans strains were enzymatically evaluated by the API ZYM system, and four enzymologically based groups of C. al bicans are recognized.
Abstract: A total of 126 Candida albicans strains were enzymatically evaluated by the API ZYM system. Four enzymatically based groups of C. albicans are recognized.
49 citations