Glossary, Bacteria

I. General Information II. Bacterial Types and Groups III. Growth Media IV. Technical Terms V. Online References

I. General Information
Disclaimer: Diagnosis of a particular health condition should be performed by a medical professional. This laboratory tests environmental samples only. Clinical samples should be directed to a medical testing facility. Bacteria can be separated into three basic groups with respect to their potential health effects. They are the following: Contaminant bacteria are found essentially everywhere in the environment. These bacteria usually exist without harming humans. An example of contaminant bacteria is Micrococcus.Opportunistic pathogens do not usually cause disease unless the individual is immunocompromised. Such a condition might include chronic illness, AIDS, cancer, and/or trauma. An example of an opportunistic pathogen is Pseudomonas aeruginosa.Pathogenic bacteria may be found in the environment, but with much less frequency than the contaminants and opportunistic pathogens. These bacteria cause disease and are usually not part of the human normal flora. Vibrio cholerea, the causative agent of cholera, is such an example.

II. Bacterial Types and Groups

These are brief descriptions for general informational purposes. More detailed and extensive information can be found from various sources, including those on the Internet. Acinetobacter (A-sin-ee-tow-back-tur)- Genus of Gram-negative bacilli that naturally occur in water, sewage, and soil. Common isolate: A. calcoaceticus

Actinomycetes (Ak-tin-no-my-seats)- Aerobic Gram-positive filamentous bacteria found in soil. Mostly thermophilic. Well known components of the micro-flora of composts. May be linked to respiratory problems in agricultural workers. Aerococcus (Air-o-kok-us)- A Gram-positive cocci widely present in the environment. Normally found in water, soil, dust, air, meat products, plants, and hospitals. May cause disease in lobsters, but are mainly opportunistic pathogens to humans. Aeromonas (Air-row-moan-us) These Gram-negative bacilli are members of the family Vibrionaceae. They can be found in both sewage and fresh water and likewise be pathogenic to fish and reptiles. In humans, these can be opportunistic pathogens that may lead to diarrhea and bacteremia. Common isolate: A. hydrophila Agrobacterium (Ag-row-back-teer-ee-um) Genus of Gram-negative bacilli that are found in the soil and considered a plant pathogen. Alcaligenes (Al-ka-lodge-uh-knees) Genus of Gram-negative bacilli that naturally occurs in the soil and water. Sometimes found within the intestinal tract of animals. May occasionally cause opportunistic infections. Common isolate: A. faecalis Arthrobacter (Arth-row-back-tur) Genus of Gram-positive aerobic rods commonly found in the soil. Can cause secondary infection in immunocompromised individuals. Bacillus (Ba-sill-us) Genus of Gram-positive spore forming bacilli which are widely distributed in the environment. They produce endospores making them highly resistant to environmental factors. In spore form they can remain viable for years in a harsh environment. Some species are considered pathogenic. Pathogenic isolates: B. anthracis (causative agent of anthrax) and B. cereus (causes food poisoning in foods such as rice, potatoes, and meats). Other common isolates include B. subtilis and B. megaterium. Brevibacterium (Brev-i-back-teer-ee-um) Genus of Gram-positive rods. These bacteria are considered non-pathogenic and have industrial applications such as the ripening of cheese. Hence they can be found in dairy products and also on the skin. Burkholderia (Burk-hol-deer-ee-uh) Genus of Gram-negative bacilli. Certain species were originally found to be plant pathogens (in onions). However, B. cepacia is now used in agriculture to promote growth. It can be pathogenic to humans, especially in patients with cystic fibrosis and animals, such as horses. Common isolates: B. cepacia and B. pseudomallei Citrobacter (Sit-row-back-tur) Genus belonging to the family Enterobacteriaceae. It is found in the feces of humans and animals and can be an opportunistic pathogen. Common isolate: C. freundii Corynebacterium (Co-rine-uh-back-teer-ee-um) Genus of Gram-positive irregular bacilli that can be isolated from the skin or mucous membranes of mammals. Some species are parasitic and may be pathogenic to humans. Pathogenic isolate: C. diphtheriae (causative agent of Diphtheria)

Curtobacterium (Ker-toe-back-teer-ee-um) Genus of Gram-positive coccobacilli which is pathogenic to plants and grouped into the genus Corynebacterium. Dermabacter (Der-ma-back-tur) Genus of Gram-positive bacilli found on human skin that can be associated with opportunistic infections. E. coli - see Escherichia Edwardsiella (Ed-ward-see-el-la)- This genus belonging to the family Enterobacteriaceae can be found in the intestines of coldblooded animals (i.e. reptiles). It can also be found in the environments of cold-blooded animals, mostly fresh water. It may be pathogenic for some animals, especially fish, but rarely infects humans. Enterobacter (In-ter-row-back-tur)- Gram-negative bacilli that belong to the family Enterobacteriaceae. There are many different species included in this genus and they can be found in a wide range of environments including water, sewage, soil, and on vegetables. Some species are part of the normal flora of the human intestinal tract. Some species are opportunistic pathogens causing infections involving the respiratory tract, urinary tract, and cutaneous wounds. Enterobacteriaceae (In-ter-row-back-teer-ee-ace-ee-aa)- This family consists of Gram-negative bacilli that can be found in the normal flora of human and animal intestinal tracts. When present in the environment they are usually in the form of fecal contaminants. Some members of this family are pathogenic to humans and animals and generally infect through ingestion. Enterococcus (In-ter-row-kok-us)- Gram-positive cocci that are normally found in the intestinal tracts of humans and animals. This species can be used as an indicator of fecal contamination. Enterococcus is considered an opportunistic pathogen, but can occasionally be implicated in causing symptoms related to mild food poisoning. Escherichia (Es-share-eek-ee-uh)- bacteria genus belonging to the family Enterobacteriaceae. E. coli is the most common isolate of this genus and is a part of the normal flora of the intestinal tract. It is, however, capable of causing illnesses ranging from mild food poisoning to severe kidney damage, and in few cases, even death. The pathogenic serovars (types) of E.coli are divided into four groups, whose identification usually require serological methods: Enterohemorrahagic E.coli - produces bloody diarrhea and can progress to kidney damage and death. E.coli O157:H7 is in this category. Enteroinvasive E.coli - causes watery diarrhea with blood and mucus. Enteropathogenic E.coli - characterized by fever, vomiting, and diarrhea. Enterotoxigenic E.coli - characterized by watery diarrhea and dehydration.

More E. coli information can be found on our Sewage Screen \ E. coli page. Flavimonas oryzihabitans (Flav-i-moan-us or-rise-i-hab-i-tans)- Gram-negative bacillus that was renamed Pseudomonas oryzihabitans. It is found as an agent in nosocomial infections. Hafnia (Half-knee-uh)- Genus belonging to the family Enterobacteriaceae. Found in human and animal feces, soil, sewage, water, and dairy products. Can be an opportunistic pathogen of humans. Klebsiella (Kleb-see-el-uh)- Genus belonging to the family Enterobacteriaceae. Found in human feces, soil, water, grain, fruit, and vegetables. It is generally considered an opportunistic pathogen and is frequently isolated from nosocomial infections. Common isolate: K. pneumoniae Legionella (Lee-juhn-el-uh)- Genus of Gram-negative bacilli isolated from stagnant water, mud, and other environments where water can collect and remain undisturbed. This is responsible for Legionellosis and is primarily characterized by pneumonia. Common isolate: L. pneumophila Listeria (Li-steer-ee-uh)- Genus of Gram-positive bacilli found in soil, vegetation, and feces. It may also be part of the fecal flora of humans and animals. It is pathogenic in humans and animals and causes food poisoning from dairy, meats, fruits, and vegetables. Food-borne Listeriosis can range from being asymptomatic to more rare, serious infections and even death. Pathogenic isolate: L. monocytogenes (food poisoning) Micrococcus (Mike-row-kok-us) - Gram-positive cocci that are commonly found on skin and as a contaminant. Not generally considered pathogenic to humans or animals. Mycobacterium (My-co-back-teer-ee-um)- Genus of Gram-positive acid fast bacilli that can be found on decaying material in the soil. However, certain species have adapted to human, birds, and other animals. Mycobacterium are resistant to harsh environmental conditions due to their cell wall and may be found in a variety of places ranging from air droplets to the footpads of armadillos. Some species within this genus cause disease such as leprosy and tuberculosis. Pathogenic isolate: M. leprae (leprosy) and M. tuberculosis (tuberculosis) Myroides (My-roy-dees)- Gram-negative bacilli that were previously classified as Flavobacterium. It is an opportunistic pathogen and has been isolated from urine, wound, sputum, blood, and ear specimens. Possible opportunistic infections include those of the urinary tract and wounds. Common isolates: M. odoratum and M. odoratimimus Nocardia (No-car-dee-uh)- Genus of partially acid fast bacilli. They are naturally found in the soil and some species are opportunistic pathogens. Pathogenic isolates: N. asteroides and N. brasiliensis

Plesiomonas (Please-ee-oo-moan-us)- Member of the family Vibrionaceae. Found in aquatic animals and some mammals. Can occasionally cause opportunistic infections or diarrhea in humans. Proteus (Pro-tee-us)- Genus belonging to the family Enterobacteriaceae. It can be found in the intestines of humans and other mammals, manure, polluted water, and soil. Can be an opportunistic pathogen and thus cause disease in humans. Common isolate: P. vulgaris Pseudomonas (Sue-dough-moan-us)- These gram-negative bacilli are widely found in nature. They are especially prevalent in hot tubs and swimming pools due to the fluctuations in temperature and improper sanitation procedures. Some species such as P. aeruginosa and P. flourescens can be opportunistic pathogens to plants, humans, and animals. Disease states may range from mild skin infection and swimmers ear to corneal ulceration and vision loss due to microbial keratitis. The disease conditions may be exacerbated if the host is immunocompromised. More information is found on our Pseudomonas Screen page. Salmonella (Sal-moe-nel-uh)- This genus belongs to the family Enterobacteriaceae. They are part of the intestinal flora of birds and other animals such as pigs. Can be found in water, raw animal food products, and animal feces. Salmonella is spread through ingestion of contaminated foods and can cause a variety of diseases ranging from mild food poisoning to severe septicemia. Pathogenic isolates: S. typhi (Typhoid) and S. typhimurium (food poisoning) Serratia (Sir-ray-she-uh)- This genus belongs to the family Enterobacteriaceae. Can be found in environments such as on plants, soil, water, insects, rodents, and the digestive tract. Some species are major contributors to nosocomial infection and can also be pathogenic to animals. Shigella (She-g-el-uh)- This genus belongs to the family Enterobacteriaceae. It is found in the intestines of humans and also in polluted water. It is spread through ingestion and causes diarrhea, cramps, bloody stool, and fever. Pathogenic isolates: S. dysenteriae (bacillary dysentery) Staphylococcus (Staff-low-kok-us)- These Gram-positive cocci are found as normal flora of the skin and mucous membranes. Can also be isolated from dust, water, and food products. Several species are considered as opportunistic pathogens to humans and animals. The primary pathogenic species in the genus is S. aureus, which causes food poisoning. Stenotrophomonas (Sten-oh-troph-oh-moan-us)- Gram-negative bacilli. Some species have been implicated in opportunistic infection of humans. Streptococcus (Strep-toe-kok-us)- These Gram-positive cocci can be found as normal flora to the skin and mucous membranes. Most species are considered as opportunistic pathogens and some species may cause potentially severe diseases in humans and animals. For example, S. pyogenes can cause Rheumatic fever and S. pneumoniae can cause respiratory illness.

Streptomyces (Strep-toe-my-sees)- An Actinomycete commonly found in soil, but have also been isolated from mucous membranes, skin, and superficial wounds. They are used in the industrial and pharmaceutical industry. A few species have been found to cause opportunistic infections in humans. Common isolates: S. albus and S. griseus Thermoactinomyces (Thur-moe-ak-tin-o-my-sees)- An Actinomycete commonly found in nature. They are most prevalent in molding hay and cereal grains, and in decaying vegetable material and composting heaps where temperatures can reach 50 C. The spores produced are extremely resilient and can be found in soil and sediment core samples. It is generally considered a contaminant, but has been implicated to a human disease called Farmers lung. Thermomonospora (Thur-mom-uh-no-spore-uh)- An Actinomycete that is a common contaminant. It is found in soil, but more likely in manure, compost heaps, and overheated fodders where temperatures can reach 50 C. Vibrionaceae (Vib-ri-no-aa-cee-aa) Family of Gram-negative straight or curved rods.

III. Growth Media used

Blood agar- A general, non-selective bacterial growth media which differentiates bacteria based on their hemolytic activities. MacConkeys agar- A selective media used for the isolation of Gram-negative bacteria. It also differentiates between coliforms and non-coliforms. MEA (Malt Extract Agar)- An all purpose fungal media used to identify viable spores. This type of media is routinely used in our lab for fungal testing. R2A- An all-purpose growth media commonly used in heterotrophic plate counts. R2A is non-selective and non-differential. Our lab uses this type of media for our routine bacterial testing. TSA (Tryptic Soy Agar)- A general-purpose bacterial growth media. Most aerobic pathogenic and non-pathogenic bacteria will grow on this media. TSA is non-selective and non-differential.

IV. Technical Terms

Aerobic bacteria- require free oxygen to survive in a given environment. Anaerobic bacteria- grow in an environment devoid of oxygen.

Bacilli- elongated, rod shaped bacteria observable under a high powered microscope. Bacteria belonging to the Enterobacteriaceae family are bacillus shaped. Bacteremia - the presence of bacteria in the blood. Cocci- bacteria which are spherically shaped and observable under a high powered microscope. CFU- (colony forming unit) a unit of measure used to quantify bacteria in a given sample. Each CFU represents one bacterium. Coliform- group of Gram-negative bacilli from the Enterobacteriaceae family that produces gas via lactose fermentation. Their presence is commonly considered an indication of fecal contamination. E. coli. is an example of a coliform. Differential media- media that contains a substance or chemical that can distinguish between different types of bacteria. Endotoxin - a substance that is part of the outer cell wall of all gram-negative bacteria. Its toxic properties remain even after the bacteria is dead, making it easy to accumulate in dust or other matrices. Inhalation can cause activation of macrophages and other cells in the lung that result in inflammation. Fever, coughing, and other respiratory symptoms can occur. Fecal Coliform- A sub-group of coliforms. These bacteria are found almost exclusively in the fecal matter of humans and animals. Presence of these in the environment is consistent with fecal contamination. Genus- (plural, genera) The first part of the scientific name. For example, Homo sapiens is the scientific name for man. "Homo" is the genus name. The genus differentiates organisms from each other included within a family. Gram stain- A fundamental bacterial identification method which involves a multi-step staining procedure. The bacteria will generally fall into either the Gram-positive or Gram-negative category. The categories are defined by the resultant color of the bacterium at the end of the staining process. Gram-positive- stain a deep blue or purple color. Gram-negative- stain a pink to red color. Gram-negative bacilli- This category contains a broad range of bacterial specimens. Two main sub-categories may be considered: enteric and non-enteric. Common isolates: E. coli and P. aeruginosa Gram-negative cocci- Isolation from the environment is rare. Most bacteria in this group are considered pathogenic. Some examples include Neisseria (Gonorrhea) and Haemophilus (bacterial meningitis).

Gram-positive bacilli- These are considered environmental contaminants. They are found in air, swab, bulk, and soil samples. Some species within this group are considered pathogens and can be severe. Common isolates: Corynebacterium and Bacillus Gram-positive cocci- These are most frequently isolated from clinical samples. They are found as normal flora of the skin, mucous membranes, and other areas of humans and animals. These bacteria are considered mainly as opportunistic pathogens. Common isolates: Staphylococcus, Streptococcus, and Micrococcus Heterotrophic plate count (HPC)- a method that provides the count, Gram reaction, and morphology of the bacteria in a given sample. The HPC is useful in testing the efficacy of a disinfection or clean-up process and also can be used as supportive data to accompany other tests. Immunocompromised- a condition characterized by a decreased function of the immune system. Some examples include AIDS patients, transplant recipients, and the elderly. Media- a nutrient based substrate used to grow bacteria and fungi. Media is available in many different varieties and can range from very basic to highly selective and differentiating. Normal flora- the microorganisms that can be found on or in the body of healthy humans and animals. Nosocomial infection- an infection contracted as a result of a hospital stay. Pseudomonas screen- a procedure that specifically tests for Pseudomonas. It is commonly performed on recreational waters such as swimming pools and hot tubs. Selective media- media that contains a substance or chemical that inhibits the growth of certain microorganisms while permitting the growth of others. Septicemia- condition characterized by high levels of virulent microorganisms in the bloodstream. Serological test- tests which utilize antibody detection methods for disease diagnosis purposes. Species- the second part of the scientific name. For example, Homo sapiens is the scientific name for man. "sapiens" is the species name. The species classification helps to differentiate it from all other organisms included in a genus. Thermophilic growing best at high temperatures, above 45 C. Total coliform/E. coli test- This analysis provides a quantitative assessment of the coliforms and E. coli present in a given sample. The presence of these microorganisms is consistent with fecal contamination.

V. Online References and other information

Bacterial Infections and Mycoses - Karolinska Institutet. Good list of sites, both to comprehensive sites concerning particular groups of bacteria as well as to pages devoted to specific bacteria and infections. Species Filing Cabinet - Virtual Museum of Bacteria Bacteria in Indoor Air - Environmental Services Laboratory Airborne Pathogen Database : Bacteria - Aerobiological Engineering Series presented by the Penn State Architectural Engineering & Biology Departments Gram-negative Bacteria - Southern Illinois University Carbondale, Medical Microbiology course. Gram-negative Bacteria - MicroBioNet Gram-positive Bacteria - MicroBioNet A Web-Surfer's Guide to Bacteria Associated with Infections in Humans - derived from Oxford Textbook of Medicine Clinical Bacteria Lexicon of Microbiology Terms - Hardy Diagnostics Microbiology Glossary - University of Waterloo Environmental Microbiology department Glossary of Environment and Microbiology Terms - Alken Murray Corp Pseudomonas proliferates in warm, wet environments like hot tubs and swimming pools E. coli is an important marker for sewage contamination