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Table of Contents

General Introduction
Vibrio, Aeromonas and Plesiomonas
Campylobacter and Helicobacter
Pseudomonas and Moraxella
Haemophilus, Pasteurella and Actinobacillus
Bordetella and Francisella
Mycobacterium Tuberculosis
Other Mycobacteria
Treponema, Borrelia and Leptospira
Rickettsia and Cocxiella
Other Important Bacteria

General Introduction

Bacteria (singular bacterium) are ubiquitous, mostly free-living organisms often single celled and reproduce by binary fission. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Superficially, bacteria appear to be relatively simple forms of life; in fact, they are sophisticated and highly adaptable.

Humans and most animals carry millions of bacteria mostly in the gut and on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, though many are beneficial, particularly the ones in the gut. However, several species of bacteria are pathogenic and cause several infectious diseases.

In developed countries, 90 percent of documented infections in hospitalized patients are caused by bacteria. These cases probably reflect only a small percentage of the actual number of bacterial infections occurring in the general population, and usually represent the most severe cases. In developing countries, a variety of bacterial infections often exert a devastating effect on the health of the inhabitants. Malnutrition, parasitic infections, and poor sanitation are a few of the factors contributing to the increased susceptibility of these individuals to bacterial pathogens.

(Reference Baron S, editor. Galveston (TX): University of Texas Medical Branch at Galveston; 1996.)

Bacteriology is the branch of biology that studies the morphology, ecology, genetics, biochemistry, identification, classification, and characterization of bacteria.

Antony van Leeuwenhoek is largely regarded as the father of Bacteriology having discovered protsista and bacteria, which at the time he named them animalcules.

My work, which I've done for a long time, was not pursued in order to gain the praise I now enjoy, but chiefly from a craving after knowledge, which I notice resides in me more than in most other men. And therewithal, whenever I found out anything remarkable, I have thought it my duty to put down my discovery on paper, so that all ingenious people might be informed thereof.
Antonie van Leeuwenhoek, in a letter dated 12 June 1716.

He (Antony) was the first even to think of looking and certainly, the first with the power to see. Using his own deceptively simple, single-lensed microscopes, he did not merely observe, but conducted ingenious experiments, exploring and manipulating his microscopic universe with a curiosity that belied his lack of a map or bearings. Leeuwenhoek was a pioneer, a scientist of the highest calibre.
Nick Lane, 2015.


The Family Micrococcaceae consists of Gram-positive cocci, which may be aerobic or anaerobic, and are arranged in tetrads or clusters. Micrococcaceae consists of four genera, Staphylococcus, Micrococcus, Planococcus, and Stomatococcus.

The genus Staphylococcus consists of 32 species, most of which are animal pathogens or commensals. The bacteria belonging to this genus are aerobic and facultative anaerobic, catalase positive, oxidase negative, and are arranged in clusters, pairs, or tetrads.

Staphylococcus aureus

Staphylococcus aureus is the most important human pathogencausing diseases ranging from superficial skin lesions like folliculitis to deep-seated abscess and various pyogenic infections like endocarditis, osteomyelitis, etc. The bacterium also causes toxin-mediated diseases, such as food poisoning, toxic shock syndrome (TSS), and staphylococcal scalded skin syndrome (SSSS).

Staphylococci have the following characteristics:


Staphylococcus species can grow on several types of cultures including Mueller Hinton agar, nutrient agar, blood agar or MacConkey agar.
On nutrient agar, Staphylococcus aureus produces round convex well defined colonies about 2-4mm in diameter. The colonies have asmooth shiny surface.
On blood agar, Staphylococcus aureus produces clear zones of hemolysis surrounding the colonies.
On MacConkey agar, Staphylococcus aureus produces small pink colonies due to lactose fermentation.

Staphylococcus aureus is slsectively grown on Mannitol salt agar or milk agar or glycerol monoacetate agar. Most strains of Staphylococcus aureus ferment mannitol resulting in acid production which gives rise to yellow zones around the colonies.

Staphylococcus aureus produces turbidity in liquid media with no pigment observed

Biochemical tests

Staphylococcus aureus is:

Most staphylococcus strains can withstand moist heat at 60℃ for 30 minutes but die beyond 30 minutes. They are also killed rapidly by disinfectatnts and aniline dyes such as Crystal violet.


S. aureus are pyogenic (pus producing) bacteria that cause localized lesions in contrast to streptococci that are spreading in nature. Staphylococci adhere to the damaged skin, mucosa, or tissue surfaces. Diseases and conditions caused by Staphylococcus aureus include:


The toxins produced by Staphylococcus aureus include toxic shock syndrome toxin, enterotoxin, exfoliative toxin, leukocidins, and hemolysins. These toxins can cause staphylococcal food poisoning, staphylococcal toxic shock syndrome, and staphylococcal scalded skin syndrome.

Hospital-acquired S. aureus infections

This is the most common cause of hospital-acquired infections. Certain strains of S. aureus causing hospital infections are known as hospital strains. These strains are usually resistant to penicillin, methicillin, and other routinely used antibiotics.

Diagnosis and Treatment

The presense of Staphylococcus aureus can be achieved through several techniques.

When antimicrobial therapy is needed, the duration and mode of therapy are largely dependent on the infection type as well as other factors. In general, penicillin remains the drug of choice if isolates are sensitive (MSSA, or methicillin sensitive S. aureus strains) and vancomycin for MRSA strains.

Other Staph species

Staphylococcus epidermidis
Infection occurs in immunocompromised hosts, such as those suffering from Neutropenia, particularly in association with intravenous catheters and other prosthetic devices, such as heart valves. It can also cause sepsis in neonates, osteomyelitis, wound infections, vascular graft infections, and mediastinitis.

Staphylococcus saprophyticus
is associated with urinary tract infection by endogenous spread in colonized women. It adheres to the epithelial cells lining the urogenital tract causing dysuria, pyuria, and hematuria. In males, it causes urethritis, catheter-associated urinary tract infections, prostatitis in the older ages, and rarely, sepsis and endocarditis.

Streptococcus and Enterococcus

Streptococci are aerobic and facultatively anaerobic Grampositive cocci, arranged in pairs, or chains. The enterococci are facultative anaerobes. They require complex nutrients for their growth.

Streptococcus species are part of the normal flora in humans and animals. They are nonmotile, nonsporing spherical or ovoid cocci with a hyaluronic acids capsule. They are catalase negative (which differentiates them from Staphylococcus) and are relatively difficult to culture, they require enriched media such as blood agar for them to grown.

Some of the major species of importance include:

Streptococcus pyogenes

S. pyogenes is the most important human pathogen causing:
1. Pyogenic infections, such as bacterial pharyngitis and cellulitis.
2. Toxin-mediated diseases, such as scarlet fever and toxic shock syndrome.
3. Immunologic diseases, such as acute glomerulonephritis (AGN) and rheumatic fever.

Characterization of S. pyogenes

Gram positive cocci about 0.6-1µm in diameter and arranged in long chains. Some strains produce a capsule during the first 2-4 hours of growth. The capsule contains hyaluronic acid which is chemically similar to the host's connective tissue so it renders the bacteria non-antigenic.

S. pyogenes can grow on blood agar producing small white colonies with a clear zone of hemolysis.

Addition of crystal violet to blood agar makes the media highly selective for this bacteria because it inhibits the other gram positive bacteria.

Biochemical reactions

S. pyogenes shows following biochemical reactions:

Physcial and Chemical Agents

Streptococci are killed by heating at 54℃ for 30 minutes and by most common disinfectants.

Capsule: The cell wall of the Streptococcus is surrounded by a capsule. The capsule is nonantigenic and weakly antiphagocytic. It acts like a barrier between the complement proteins bound to the bacteria and the phagocytic cells, thereby preventing phagocytosis of the bacteria.


S. pyogenes produces toxins such as Streptococcal pyrogenic exotoxins, Hemolysins, Streptolysin O, Streptolysin S and Pyrogenic exotoxins which are associated with the pathogencity of various diseases including Scarlet fever and Streptococcal toxic shock syndrome.

Streptococcus agalactiae

S. agalactiae are found as normal flora in the genitourinary tract and lower gastrointestinal tract.

S. agalactiae in pregnant women can cause urinary tract infection particularly immediately after delivery. In nonpregnant women and in men, S. agalactiae can cause infections, such as osteomyelitis, arthritis, peritonitis, and skin infections.

Streptococcus equisimilis

S. equisimilis resembles S. pyogenes in fermenting trehalose but differs from it by not fermenting ribose. It causes upper respiratory tract infections and also pneumonia, osteomyelitis, endocarditis, brain abscess, and puerperal sepsis. S. equisimilis shows tolerance to treatment with penicillin; therefore patients may not respond to treatment with penicillin.

Streptococcus bovis and Streptococcus equinus are the nonenterococcal streptococci, which are associated with human infections, such as urinary tract infections and rarely endocarditis. They are susceptible to penicillins.

S. sanguis is the most common causative agent of bacterial endocarditis in individuals with preexisting heart lesions.

S. mutans is an important causative agent of dental caries. It splits dietary sucrose, producing acid and a dextran. The acid damages the dentine. The dextran binds together exfoliative epithelial cells, mucus, food debris, and bacteria to form dental plaques.


The enterococci are Gram-positive, spherical, oval, or coccobacillary and are arranged in pairs and short chains. Most of the species are nonmotile and noncapsulated. They grow at a temperature range of 35–37℃. Colonies on blood agar media are 1–2 mm in diameter and alpha-hemolytic (actually nonhemolytic; appearance of alpha-hemolysis is due to the production of the enzyme peroxidase rather than hemolysins). Some cultures are beta-hemolytic on agar containing rabbit, horse, or human blood but not on agar containing sheep blood.

Enterococci possess two important virulence factors: (a) aggregation substances and (b) carbohydrate adhesions. Aggregation substances are hair-like proteins that facilitate binding of bacteria to the epithelial cells. Carbohydrate adhesins facilitate binding of cocci to host cells gelatinase.

The enterococci are commonly found in gastrointestinal and genital tract of humans and animals. Enterococci are nonpathogenic.