Return to index

The Environmental Reporter
January 2008 Volume 6 | Issue 1

Hello,

I hope that you are doing well. This month we have an article by Dr. Michael Berg summarizing an article that discusses the importance of environmental monitoring for hospital-acquired Legionellosis and another article by Dr. Michelle Seidl discussing bacterial taxonomy. I hope you find them interesting and useful.

With best wishes,
Dave Gallup




New Study Shows the Importance of Environmental Monitoring for Hospital-acquired Legionellosis
By Dr. Michael Berg, EMLab P&K Senior Molecular Biologist

Legionnaire's disease and pontiac fever are caused by Legionella bacteria, which are commonly found in community water and hospital water systems. We have previously discussed Legionella bacteria in a focus article of the Environmental Reporter issue in January 2007. A new study spearheaded by the University of Pittsburgh School of Medicine and published in the July 2007 issue of the journal Infection Control and Hospital Epidemiology, has now determined that environmental monitoring of hospital water systems can help predict the risk of hospital-acquired Legionella pneumonia. The study also questions the current policy of the Centers for Disease Control (CDC) not to recommend routine environmental monitoring.

This new study evaluated samples for water systems of 20 hospitals across the country from 2000 to 2002. Water samples from at least 10 separate locations at each facility were tested multiple times over the two-year period for a total of 676 environmental samples. The study also included Legionella tests of urine and/or sputum samples from 633 patients in 12 of the 20 hospitals. The researchers found that 14 (70%) of the hospital water systems tested positive for Legionella species, and that 6 (43%) of those had high-level colonization of the water systems (30% or more of the distal outlets tested positive). Hospital-acquired Legionella pneumonia was identified in 4 hospitals, all of which had a high-level colonization with L. pneumopohila serogroup 1. The authors of the article conclude from this new study that environmental surveillance for Legionella should be part of a proactive strategy for prevention of hospital-acquired legionnaire's disease.

References:
1. Stout J., et al. (2007). Role of environmental surveillance in determining the risk of hospital-acquired legionellosis: a national surveillance study with clinical correlations. Infection Control and Hospital Epidemiology 28 (7): 818-824.




Bacterial Taxonomy
By Dr. Michelle Seidl, EMLab P&K Mycologist

Taxonomy is one of the oldest sciences and bacterial taxonomy dates back to the 1700's when M?ler first acknowledged bacteria in a classification scheme. That was a century after they were first observed by Anton van Leeuwenhoek, using his personally designed monocular (single lens) microscope. Their existence had been hypothesized since the Middle Ages or even earlier, but it took the clever invention of Leeuwenhoek to observe and name these entities. Early on in bacterial taxonomy, two problems existed in the classification systems. First, morphological features, such as cell shape, were heavily used in grouping organisms together. The cells are simple in shape, similar in size and therefore provide very little data. More recent schemes rely heavily on other characteristics, such as physiological or molecular. Secondly, the 'pure culture technique' that revolutionized microbiology, was not developed until the second half of the 19th century. A natural development of the pure culture technique was the establishment of "type strains" of species. These are deposited into repositories referred to as culture collections. Type strains can be obtained from culture collections and used as reference strains for direct comparisons with new isolates.

The three separate but interrelated areas of taxonomy are: classification, nomenclature and identification. Classification is the arrangement of organisms into taxonomic groups (taxa) and is comprised of various ranks (see Fig. 1). In 1866, Ernst Haeckel (in his General Morphology of Organisms) first created a Kingdom for microorganisms. He placed all microscopic organisms into Kingdom Protista, while everything else was either in Kingdom Plantae or Animalia. As new techniques developed, a dichotomy was found where some Protista had a nucleus and others were lacking such a structure in their cells. As a result, Kingdom Monera was created for prokaryotes and Protista remained for single-celled eukaryotes. With molecular techniques, we now know Monera is made up of two domains: the bacteria and archaea.

Taxonomic rank Example
Kingdom Bacteria
Phylum/Division Proteobacteria
Class Gammaproteobacteria
Order Enterobacteriales
Family Enterobacteriaceae
Genus Escherichia
Species coli
Fig. 1. Taxonomic ranks for the common bacterium species E. coli.

Nomenclature is the assignment of names to taxa according to international rules. In reference to any organism, their official name consists of two parts: the genus and the species (or specific epithet) and should always be italicized. For bacteria, the key reference is Bergey's manual (Holt, et al. 1994). When a new bacterial species is discovered, an adequate description consists of overall similarities including biochemical, physiological, genetic and morphological characteristics, as well as any feature that sets this new taxon apart from other closely related species. Officially a species can be divided into two or more subspecies based on minor but consistent phenotypic variations. This is the lowest taxonomic rank that has official standing in nomenclature and should also be italicized when used. Levels below the subspecies have no official standing in nomenclature but often have great practical usefulness. These are often used to indicate groups of strains that can be distinguished by some special character, i.e. distinctive antigenic properties (serovar or serotype), pathogenic properties for certain hosts (pathovar or pathotype), ability to be lysed by certain bacteriophages (phagovar or phagotype), special biochemical or physiological parameters (biovar or biotype), distinctive morphological features (morphovar or morphotype).

The concept of a bacterial species is less definitive than for higher organisms. As expected, bacteria being prokaryotic, differ considerably from more complex organisms. Sexuality is not used in species definitions because few bacteria undergo conjugation (a temporary union of two bacteria in which genetic material is transferred). In addition, morphological features alone are not very useful because most bacterial species are too simple morphologically to provide much useful taxonomic information. Consequently, morphological features fill a less important role in bacterial taxonomy. A bacterial species is regarded as a collection of strains that share many features in common and possess one or more unique characters, which sets it apart from other strains or different species. What then is a strain? A strain encompasses descendents of a single isolation in pure culture and is usually made up of a succession of cultures, ultimately derived from an initial single colony. One strain of a species is designated as the type strain. This type strain serves as the name-bearer strain of the species and is the permanent example or reference specimen for this species. This has great importance for classification at the species level because a species consists of the type strain and all other strains that are considered to be sufficiently similar to it as to warrant inclusion within that species. The level of DNA homology exhibited among a group of strains has also been used as a basis for defining species and compares degree of genetic relatedness among strains.

For practical reasons, classification and nomenclature should remain stable because changes create confusion, particularly at the genus and species levels, and result in costly modifications of identification schemes, textbooks, etc. However, classifications have never remained static because new information is continually being generated. Genetic studies have resolved many instances of confusion concerning which strains belong to a given species and molecular work is increasingly being used for establishing new species and resolving taxonomic problems at the species level.

Above the level of species, there is no general agreement on the definition of a genus in bacterial taxonomy and considerable subjectivity is involved. Genetic relatedness has offered hope for greater objectivity and has proved useful in this regard. At classification levels above genus, the relationships are even less stable. For example, in the 8th edition of Bergey's manual, the methanogens consisted of 1 family and 3 genera. Authorities for this group later proposed that 3 orders were required for the circumscription of these organisms.

Identification is the process of determining that an isolate belongs to one of the established, named taxa. A bacterial species is defined by the similarities among its members. Properties such as chemical compositions, biochemical reactions, cellular structures, genetic characteristics and immunological features are used for identification of bacterial species. Identifying a species and determining its limitations presents the most challenging aspects of biological classification for any type of organism. The major treatise for bacteria since it's first publication in 1923 is Bergey's Manual of Determinative Bacteriology. This is used for identification and has extensive keys and information for various groups. Currently the 9th edition has become somewhat dated in that new molecular information has been accumulating at a rapid rate. Another useful tool for identifying bacteria is the print or online edition of The Prokaryotes, which has updated information on the isolation and identification of bacteria (see Dworkin et al. 2007).

In addition, informal (also referred to as vernacular) groups defined by common descriptive names are often used, yet these have no official standing in nomenclature. Over the years certain problems have resulted from using informal names within bacterial taxonomy. One ambiguous example is the term 'bacillus' which is defined as rod-shaped bacteria and is also a genus name. Common names can be problematical as in 'pneumococcus' for Streptomyces pneumoniae and 'meningococcus' for Neisseria meningitides.

In general terms, the classification of bacteria has primarily been based on morphology (cocci, bacilli, spiral and pleomorphic) and staining (Gram positive, Gram negative and Acid fast). Other useful features have been oxygen requirements (whether anaerobic or aerobic), spore formation, culture properties, antigenic properties, biochemical reactions, and DNA based properties (G+C content, ribosomal gene sequences, protein sequences and total gene sequences). Another fairly recent breakthrough in bacterial classification was the discovery of micropaleontological evidence indicating that microorganisms existed during the Precambrian period. The discovery of fossil microbes in early sedimentary rocks is interesting but divulges very little about the phylogeny of prokaryotic organisms. The fossil record is very incomplete, yet scientists have put forth various phylogenetic schemes. With recent molecular techniques, a record of bacterial evolution appears to exist in the amino acid sequence of bacterial proteins and in the nucleotide sequences of bacterial DNA and RNA.

One cannot leave the subject of bacterial taxonomy without a brief discussion of Archaea. Carl Woese and George Fox (1977) first identified this additional prokaryotic group of living organisms as being a distinct lineage, based on 16S rRNA. Originally, this group was referred to as Archaebacteria and the remaining prokaryotes as Eubacteria, but the work of Woese and Fox, as well as additional RNA and DNA sequence analyses, has determined these two groups represent fundamentally different lineages. As mentioned above, Kingdom Monera has been divided into Archaea and Bacteria (see Fig. 2). As new data comes in, additional bacterial groups are surveyed and data is interpreted, the taxonomy of this diverse group will continue to change as updates are applied.

Phylogenetic tree

Fig. 2. A phylogenetic tree based on rRNA data, showing the separation of Bacteria, Archaea, and Eucaryota.
Source: Wikipedia, Archaea

References:
1. Bergey, D. H., Krieg, Noel R., Holt, John G. 1989. Bergey's Manual of Systematic Bacteriology. Baltimore: Williams & Wilkins.

2. Boone, David R., Castenholz, Richard W., Garrity, George M., Brenner, Don J., Krieg, Noel R., Staley, James R. (Eds.). 2005. Bergey's Manual of Systematic Bacteriology. 2nd edition. New York: Springer Verlag.

3. Dworkin, Martin, Falkow, S., Rosenberg, E., Schleifer, K.-H, Stackebrandt, E. (Eds.). 2007. The Prokaryotes. Vols. 1-7. Version eReference. 3rd edition. ISBN 978-0-387-30740-4.

4. Holt, John G., Krieg, Noel R., Sneath, Peter H. A., Staley, James T., Willims, Stanley T., (eds.). 1994. Bergey's Manual of Determinative Bacteriology, 9th edition. Baltimore: Williams and Wilkins.

5. Krieg, Noel R., Holt John G. (eds.). 1989. Bergey's Manual of Systematic Bacteriology. Baltimore: Williams and Wilkins.

6. Woese, C., Fox, G. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74(11):5088-5090.


The data and other information contained in this newsletter are provided for informational purposes only and should not be relied upon for any other purpose. EMLab P&K hereby disclaims any liability for any and all direct, indirect, punitive, incidental, special or consequential damages arising out of the use or interpretation of the data or other information contained in, or any actions taken or omitted in reliance upon, this newsletter. Images included in this newsletter are property of EMLab P&K, unless otherwise specified.

EMLab P&K: When quality and accuracy are critical.