Identification of bacteria

Starr, M.P., Stolp, H., Triiper, H.G., Balows, A. and Schlegel, H.G. 1981 The Prokaryotes A Handbook on Habitats, Isolation, and Identification of Bacteria. Vol. 1. Berlin, Springer-Verlag. Turban-Just, S. in preparation Biogene Dekomposition von Knochenprotein. Ph.D. dissertation, Miinchen. 

Voordouw G, JK Voordouw, RR Karkhoff-Schweiser, PM Eedorak, DWS Westlake (1991) Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl Environ Microbiol 57 3070-3078. 

CULTURAL, SEROLOGICAL, AND GENETIC METHODS FOR IDENTIFICATION OF BACTERIA... 

The prompt identification of bacteria that are animal pathogens is important to veterinarians maintaining the health of pets, livestock, and poultry.14 It is also important to physicians if the animal pathogens are transmissible to humans. In animal husbandry, information on the species found in specialized microbial habitats, such as the bovine rumen, can even be used to improve the efficiency of feed conversion.15... 

In this chapter a variety of conventional and rapid methods that are currently used for the identification of bacteria (Table 1.1) will be discussed. 

The identification of bacteria has traditionally required the establishment of a pure culture before any other steps are taken. Pure cultures of bacteria may sometimes be obtained from blood and spinal fluid, which are normally sterile, or from extreme environments like hot springs. However, because there are few such situations in nature, individual bacteria must generally be isolated from other cells and grown for one to five days to obtain pure cultures before identification. Some pathogenic bacteria are obligate intracellular parasites that are difficult or impossible to grow outside their mammalian host cells 37 for these, pure cultures are not feasible. 

TABLE 1.1 Methods for Identification of Bacteria and Some Recent Examples Using Them... 

Two principal types of nucleic acid-based methods, nucleic acid hybridization and polymerase chain reaction (PCR), are commonly used for the rapid identification of bacteria. A few other nucleic acid-based methods will also be mentioned. 

DNA,83 which produces one million or more copies of amplified DNA in a short time. For identification of bacteria, PCR can be used to amplify DNA either after extraction from a sample or after lysis of the cells.83,84 Methods using washing, filtration, or magnetic beads with specific antibodies can be used to collect bacterial cells for PCR.85,86 PCR can be modified for the detection of bacteria from various sources32 and can even amplify DNA from dead cells.87... 

Bergeron, M. G. Ouellette, M. Preventing antibiotic resistance through rapid genotypic identification of bacteria and of their antibiotic resistance genes in the clinical microbiology laboratory. J. Clin. Microbiol. 1998, 36, 2169-2172. 

Busse, H. J. Denner, E. B. M. Lubitz, W. Classification and identification of bacteria Current approaches to an old problem overview of methods used in bacterial systematics. J. Biotechnol. 1996, 47, 3-38. 

Manz, W. Szewzyk, U. Ericsson, P. Amann, R. Schleifer, K. H. Stenstrom, T. A. In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl. Environ. Microbiol. 1993,59, 2293-2298. 

Krishnamurthy, T. Ross, P. L. Rapid identification of bacteria by direct matrix-assisted laser desorption/ionization mass spectrometric analysis of whole cells. Rapid Commun. Mass Spectrom. 1996,10,1992-1996. 

Sasser, M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Technical Note 101, MIDI, Inc., 2001. Available at http //www.midilabs.com. 

Metastable atom bombardment (MAB) is a novel ionization method for mass spectrometry invented by Michel Bertrand s group at the University of Montreal, Quebec, Canada, and described by Faubert et al.38 For the identification of bacteria by MS, MAB has a number of significant advantages relative to more familiar ionization techniques. Electron ionization (El) imparts so much excess energy that labile biomolecules break into very small fragments, from which the diagnostic information content is limited since all... 

As noted above, whole-cell MALDI-TOF MS was intended for rapid taxonomic identification of bacteria. Neither the analysis of specific targeted bacterial proteins, nor the discovery of new proteins, was envisioned as a routine application for which whole cells would be used. An unknown or target protein might not have the abundance or proton affinity to facilitate its detection from such a complex mixture containing literally thousands of other proteins. Thus, for many applications, the analysis of proteins from chromatographically separated fractions remains a more productive approach. From a historical perspective, whole-cell MALDI is a logical extension of MALDI analysis of isolated cellular proteins. After all, purified proteins can be obtained from bacteria after different levels of purification. Differences in method often reflect how much purification is done prior to analysis. With whole-cell MALDI the answer is literally none. Some methods attempt to combine the benefits of the rapid whole cell approach with a minimal level of sample preparation, often based on the analysis of crude fractions rather... 

Anhalt, J. P. Fenselau, C. Identification of bacteria using mass spectrometry. Anal. Client. 1975,47,219-225. 

Helm, D. Labischinski, H. Schallehn, G. Naumann, D. Classification and identification of bacteria by Fourier-transform infrared spectroscopy. J. Gen. Microbiol. 1991,137, 69-79. 

Dworzanski, J. R Snyder, A. P. Chen, R. Zhang, H. Wishart, D. Li, L. Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring. Anal. Chem. 2004,76,2355-2366. 

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