This chapter describes two key strategies for the discovery of new antibacterial agents and illustrates the critical role played by genomics in each. The first approach is genomic target-based screening. Comparative genomics and bioinformatics are used to identify novel, selective ...

Genome sequencing, the determination of the complete complement of DNA in an organism, is revolutionizing all aspects of the biological sciences. Genome sequences make available for scientific scrutiny the complete genetic capacity of an organism. With respect to microbes, this mea ...

Microbial pathogens possess a repertoire of virulence determinants that make unique contributions to bacterial fitness during infection. In this chapter, we focus on the recent progress and adaptations of signature-tagged mutagenesis (STM) by PCR instead of hybridization. This ...

Recent advances in gene-amplification technology and molecular phylogenetics have provided the means of detecting and classifying bacteria directly from their natural habitats without the need for culture. These techniques have revolutionized environmental microbio ...

Isolates of bacterial species that are indistinguishable in genotype are assigned as a clone, with the implication that they are descended from the same recent ancestor. Clones are difficult to define with precision since bacteria are not truly asexual, and recombinational replaceme ...

Bacterial taxonomy comprises systematics (theory of classification), nomenclature (formal process of naming), and identification. There are two basic approaches to classification. Similarities may be derived between microorganisms by numerical taxonomic methods bas ...

Methods for isolation of small plasmids (usually cloning vehicles) from genetically characterized strains of Enterobacteriaceae (Escherichia coli and Salmonella) are well established (1–3). This chapter seeks to complement them by describing reliable basic methods for det ...

This chapter describes a simple method of making DNA probes with a nonisotopic label. The development of this type of new technology has, for example, created novel ways of detecting and identifying pathogenic microorganisms, which has led to a re-evaluation of methodological approaches ...

Antibiotic resistance is not an absolute property. Even within a single species, strains can exhibit different degrees of antibiotic resistance. When a bacterium is tested for resistance, it should be compared, quantitatively with a standard. This standard may be the resistance of a wild- ...

Plasmids are extra-chromosomal molecules of deoxyribonucleic acid (DNA) capable of autonomous replication. Such molecules have been identified in many bacterial genera and usually exist as covalently closed circular (CCC) molecules. Plasmids range in size from less than one meg ...

Traditional methods for the identification of some bacterial species can be time consuming and often necessitate the isolation of pure cultures before further characterization may be undertaken. Advances in molecular biology have allowed the identification of bacterial spec ...

Polymerase chain reaction (PCR) can be used to identify microorganisms in at least two basic ways. The first method depends on a knowledge of DNA sequence unique to the organism under study and provides a specific means of identifying that organism. This method is discussed elsewhere in this volu ...

DNA probes are being used increasingly to detect and identify microorganisms, particularly pathogenic bacteria in a variety of areas. These include medicine, the food industry, and the environment. Various strategies have been used to develop DNA probes for specific bacteria that inc ...

Bacteriophages (phages) are viruses that infect bacteria. Susceptibility to infection by particular phages varies between strains within a species, and this property can be exploited to construct highly discriminatory schemes for the type identification of strains in epidemi ...

Bacteriocins are proteins produced by bacteria which are lethal for other members of the same species and, occasionally, for other species. In general, bacteriocins are active in very low concentrations against specific strains. This property has been widely utilized for the identifi ...

Polyacrylamide gel electrophoresis (PAGE) of proteins has been used increasingly during the past decade in the examination of bacteria for both comparative purposes and in the study of their protein biochemistry at the molecular level. The most popular of the techniques employed, disc ...

Lipopolysaccharide (LPS), traditionally termed somatic antigen or O-antigen, forms an integral part of the outer membrane of Gram-negative bacteria. In general, LPS consists of essentially three parts: 1. A hydrophobic portion, lipid A,

The cell envelope of Gram-negative bacteria comprises an inner and an outer membrane separated by a layer of peptidoglycan (Fig. 1). The inner membrane is the site of biochemical reactions involved in respiration and oxidative phosphorylation, and the synthesis of structural membrane c ...

Pyrolysis of microorganisms yields complex mixtures of products that can be analyzed quantitatively by mass spectrometry (MS). The resulting mass spectra represent transient bacterial “fingerprints” that can be compared mathematically for relatedness. The method has poten ...

Mass spectrometry (MS) is a chemical analytical technique that can yield data in the form of a spectrum of peaks of differing relative intensities and over a range of mass-to-charge (m/z) values. Such data permit calculation of molecular weight and molecular structure. The technique has been us ...