Bacterial Infections

Classification (taxonomy) of Bacteria :

Earlier in the course we talked about the various taxonomic categories:

Kingdom
Phylum (called Divisions in plant biology)
Class
Order (called Sections in bacterial taxonomy)
Family
Genus
Species

These are listed in decending order from most inclusive [Kingdom] to least inclusive [Species].

Bacteria are currently divided into 4 Divisions (phyla) which are in turn divided into 7 Classes based on differences in cell wall characteristics. The classes are divided into a total of 33 Sections (rather than orders). The bacteria belong to the Kingdom Monera (Kingdom Procaryotae) , which currently includes the:

true bacteria ( Eubacteria ) - includes all of the bacteria of medical significance
blue-green algae ( Cyanobacteria ) - photosynthetic algae-like organisms (not true algae)
archaea ( Archeobacteria ) - primitive inhabitants of extreme environments

The bacteria of medical significance (those that cause human disease) are included in these groups:

Gram negative rods ( Enterobacteria and others)
Obligate intracellular parasites ( Ricckettsia and Chlamydia)
Gram negative curved rods ( vibrios, Helicobacter, Campylobacter, and others)
Gram negative cocci ( Neisseria and others )
Gram positive rods ( Bacillus, Clostridium, and others )
Gram positive cocci ( Staphylococcus, Streptococcus, and others )
Acid fast rods ( Mycobacterium, Nocardia )
Spirochetes ( Treponema, Borellia, and others )
Mycoplasmas (tiny bacteria that lack a cell wall)

In the above list, the italicized words are genera (plural of genus). Genus and species names are always italicized (or underlined) to indicate that they are scientific names. The genus name is always capitalized, and the species name is never capitalized.

In biology, species may be further subdivided into sub-species. Bacterial sub-species are called strains and are designated by names, numbers, letters, or combinations of letters and numbers (eg. Escherichia coli strain 0157-H7 is the strain that has recently caused a number of human deaths). Strains are simply subgroups that have characteristics that differ in some important way from other subgroups of the same species. In some groups (eg. the genus Salmonella ), the term serovar is used to designate a serologically distinct strain. We'll talk more about serology when we talk about antigen-antibody reactions.

Some of the characteristics of bacteria that are employed in their classification and identification are:

morphology - cell shape and size
staining reactions - especially gram staining reaction
metabolism - biochemical reactions
growth characteristics including colony size, shape, and color
environmental requirements - eg. oxygen tolerance, temperature tolerance, etc.
serologic reactions - antigen-antibody reactions
phage typing - using bacteriophages to identify bacterial strains
DNA hybridization - to determine closeness of relationship between various bacteria
base sequence of nucleic acids
protein types - determined by polyacrylamide gel electrophoresis [ PAGE ]
lipid types
other characteristics

Classical determinative bacteriology is largely based upon the first five types of characteristics listed above. Bacteria are identified to species by determining their cell size, shape, staining characteristics, environmental requirements and metabolic characteristics. The substrates that a bacterium can utilize as energy sources, and the by-products that are produced when it utilizes those substrates are the basis for the metabolic characterization of bacteria.

The "bible" of bacterial identification is a book called Bergey's Manual of Determinative Bacteriology. Bergey is long dead, but the American Society for Microbiology continues to revise and publish the book. It is currently in its ninth edition.

Taxonomy of Bacteria

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Clinical bacteria are grouped into five categories based on gram stain appearance under the light microscope. Two groups have a general rounded shape and stain either red or blue, the cocci. Two groups have a general rod-like shape and stain either red or blue, the bacilli. By far the largest group numerically is the gram negative bacilli group. Gram negative organisms have thinner cell walls and the cell wall composition is different from that of gram positive organisms. This difference accounts for general differences in how both virulence factors and antigentic determinants are expressed. This difference also accounts for some general distinctions in susceptibility to antibiotic drugs. Thus the gram stain is considered by many as the single most important characteristic of clinical bacteria. However the gram stain itself is not used for the identification of organisms. One rare exception would of course be a gram stain of GNID in urethral discharge.

Bacterial Classifications and Terms

Descriptive terms are used to broadly categorize clinical bacteria in several useful ways.

They are categorized according to their gram stain characteristics as described above.

They are classified taxonomically as to genera and species. An inclusive alphabetical list would be useful to indicate the scope of the numbers of kinds of organisms encompassed within the field of clinical bacteriology. The names of the clinical bacteria in such a list often describe distinctive characteristics, as for example Mycobacterium, which has mycolic acids within the cell wall. The names have sometimes been problematic. Since 1974 there has been a proliferation of new names. Names of some genera of clinical bacteria have changed more than once. Some genera have two names until concensus is reached. Sometimes taxa* are defined predominantly based on DNA homology, sometimes not. But, now with reliably routine methods of genome sequencing, the taxonomic similarities and dissimilarities which distinguish clinical bacteria can also be based on DNA code; classifications may become more clear and less subject to change.*sing. taxon, pl. taxa

Clinical bacteria are categorized based on whether they require strict anaerobic conditions for growth. If they do, they are called anaerobes, as for example Fusobacterium sp. If they do not, the term facultative is generally used. Facultative means that they are flexible and can grow in both conditions, as for example E coli. Very few organisms strictly require aerobic conditions for growth. So in most cases an organism is said to be either an anaerobe or a facultative organism. Anaerobes account for 5-10% of all clinical infections

Clinical bacteria are categorized according to which region of the body they inhabit as part of normal flora or from which part they are frequently isolated or cause disease, as for example the family Enterobacteriaceae, which includes many familiar gram negative enteric bacilli.. Sources such as the cerebrospinal fluid and blood should never harbor any bacterial organisms and therefore any and all organisms from these sources are considered dangerous and are indications for antimicrobial therapy.

Clinical bacteria are classified according to how dangerous they are. Pathogens are always likely to cause disease. Organisms which cause disease only when they have a special opportunity to gain entrance inside the body are called opportunistic, as for example Bacteroides fragilis, or Clostridium difficile. Some organisms such as the Streptococcus viridans group can gain entry into the bloodstream and quietly become entrenched on the mitral valves of the heart causing a problem only after a long period as a cumulative effect. Some pathogens proactively create portals of entry. These organisms are called invasive, as for example, Salmonella enteritidis, or strains of Streptococcus pyogenes, the sensationalised, "flesh eating," bacteria.

Perhaps a useful system of categorization would give an indication of the probability of infection by a particular organism. True, the CDC publishes a weekly report entitled MMWR and also publishes yearly figures on the incidence of infection of the various disease causing agents including bacteria which are thorough and authoritative. And it would be irresponsible for health care professionals to ignore a given bacterial agent simply because its incidence were very low. If for example a particular organism is only seen in the tropics, it may be of interest to someone considering visiting a tropical venue or to someone who has visited such a venue or to a health care professional serving the needs of such persons. But to Mary and John Q. Public for whom the names of the clinical bacteria are just a list of strange latin binomials, the important questions are, "Which are relevant, how are they significant, and what would be the probability that they would personally affect Mary and John?" So for proper perspective of relative incidence and probability, we have included various anecdotes which even health professionals may find humorous. If a given impression is grossly misleading, let us know. Upon completion, there will have been two or three intentional misstatements just to see whether you are awake or asleep at the wheel.

# posted by Pat O'Connor @ 10:48 AM