Clinical bacteria for which the gram stain is not applicable
This fifth group is small in number. These organisms are rarely, if ever, seen in the routine clinical laboratory but, when they are present, they are pathogenic. As a consequence there are methods other than gram staining with which to detect or confirm their presence.

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.