Don's Home Health Germs - Pathogens
Related Pages: Common Cold | FLu | Disinfecting | Household germs | Traveler's diarrhea | Water Purification | Pandemics
Germs are generally microbes (living material too small to see) that cause diseases, also called Pathogens.


Structure: Viruses are basically raw genetic material, DNA or RNA with a protein coating (called a capsid). Viruses first attach themselves to healthy cells and then inject their genetic material into those cells. The viral genetic material takes over the cells' operation, forcing the repeated production of viral proteins and genetic material. Eventually, the accumulating viral particles cause the host cell to rupture. This burst sends out large numbers of viruses to repeat the cycle of infection. Viruses are not considered to be living organisms because they cannot reproduce outside of a living cell.

Types: parainfluenza, influenza, respiratory syncytial virus, HIV, rotavirus, ebola, hantavirus, variola

Reproduction: have to invade other cells and hijack their cellular machinery to reproduce.

Size: .01 - .3 µm

Diseases: mumps, measles, Common Cold, influenza (flu), rabies, hepatitis, poliomyelitis, smallpox, AIDS, polio, Ebola, viral pneumonia, Chickenpox, Dengue Fever, Ebola, Hepatitis (A, B, or C), Lassa Fever, Marburg, Meningitis, Poliomyelitis, Rubella (German Measles), Yellow Fever and certain types of cancer.
The influenza virus is a class of viruses containing RNA as its hereditary material. It replicates by entering a host cell and using this cell's resources to produce hundreds of copies of the viral RNA.

                                      Colds   Flu
    Days from infection to symptoms    2-3    1-4
Days contagious after symptoms start   2-3    5-7
                  Time to run course 1-2 wks 1-2 wks

See virus page for more.


Structure: Single-celled organisms without a nucleus and generally ony one chrosome. Many good bacteria live in our bodies, mostly in our digestive tract. Only 300 out of some 4,600 listed species are considered pathogens (disease causing).

All told, the microbes in your body outnumber your own cells by ten to one and can weigh as much as or more than your brain--about three pounds in an average adult.
  Your gut is where many of these good bacteria exist. Traditional estimates were that there from 500-1,000 species of microorganisms in your gut, but a 2007 study suggested there were over 35,000. However, it is probable that 99% of the bacteria come from about 30 or 40 species.
See Gut Microbiota in Health and Disease (

An imbalanced gut bacteria (more bad bacteria than good bacteria) or diminished bacteria in general (a sterilized gut) will affect your immune function, absorption of essential nutrients, and can promote a perfect environment for the development or maintenance of mental-emotional disorders and serious physical pathologies such as neurological diseases.

Research is now supporting that gut bacteria influences brain development and even behaviour. One study of interest shows that serotonin and dopamine are regulated by colonizing gut bacteria - so these substances (that are often related to depression etc.) don't develop normally in "bad" guts.
Source: Gut Health: The Key to our Overall Health and Immunity | K-W Homeopathic Medicine and Wellness Clinic

Gut bacteria help digest food, absorb nutrients, protect intestinal wals, regulate weight and ward off autoimmune diseases.
10-40% of children given broad-spectrum antibiotics develop diarrhea because gut microbes have been disturbed.
Source: Microbes: Small, Small World | National Geographic

Types: Escherichia coli (E. coli), salmonella, Bacillus, staphylococci, enterococci, Campylobacter, shigella and Vibrio parahaemolyticus, Cholera.
Vancomycin-resistant enterococci (VRE) and MRSA (Methicillin-Resistant Staphylococcus aureus) are a types of bacteria that have developed resistance to many antibiotics.

Serratia marcescens is a bacteria commonly found in homes and hospitals.
It causes infections in the urinary and respiratory tracts and in wounds and the eye.
It is common in the environment and shows up as a pink, pink-orange, or orange discoloration and slimy film feeding off phosphorus-containing materials or fatty substances such as soap and shampoo residue. Commonly found growing in bathrooms (especially on tile grout, shower corners, toilet water line, and basin or other damp environments.

Reproduction: Bacteria have ribosomes, tools necessary for copying DNA so bacteria can reproduce.

Size: .2 - 20 µm

Diseases: Cholera, diphtheria, leprosy, plague, some kinds of pneumonia, strep throat, tetanus, tuberculosis, anthrax, tooth decay, several sexually transmitted diseases, typhoid fever, Legionnaires' Disease, Lyme Disease, Meningitis, Pertussis (Whooping Cough), Strep Infections (Scarlet Fever, Rheumatic Fever, Invasive Strep), Tuberculosis, Typhus.

Parasites - Protozoans (protists)

Structure: Single-celled organisms, that may have more than one nucleus. There are 10,000 kinds of parasites, but only a few cause disease in humans

Types: Amoeba, Giardia, Coccidia, Plasmodium falciparum, Trypanosoma, Cryptosporidium, Babesiosis
Cryptosporidium is harder to kill.

Reproduction: Division

Size: 15-200 µm

Diseases: Malaria, Trypanosomiasis (African sleeping sickness), Amoebic Dysentery, Chagas' disease, giardiasis, leishmaniasis, and toxoplasmosis.

The time between being infected and developing symptoms is 7 - 14 days. The acute phase lasts 2 - 4 weeks.


Structure: Fungi and are generally multicellular, such as molds or mushrooms, but include single-celled yeasts. A single teaspoon of topsoil contains about 120,000 fungi.

Types: gonorrhoeae, Candida, Phytophthora infestans (Irish potato famine), yeast

Reproduction: Division, budding and germination from reproductive cells called spores

Size: 1-100 * µm

Diseases: ringworm, athlete's foot, candidiasis (Thrush) and some kinds of pneumonia, and jock itch

parasitic worms

Structure: multi-celled animals.

Types: Helminths. - flatworms or Platyhelminthes (flukes and tapeworms) and the roundworms or Nematoda.

Reproduction: eggs. Worms do not generally reproduce in the body.

Size: 50-100µm (eggs)

Diseases: Anisakiasis, Elephantiasis, Guinea Worm, Hookworm, River Blindness, Schistosomiasis, Tapeworm, Trichinosis

* Many fungi cells generally cling together so they are large enough to be seen.

An infectious agent composed of protein in a misfolded form.
Also referred to as transmissible spongiform encephalopathies (TSEs), they are a family of rare progressive neurodegenerative disorders that affect both humans and animals.
They are responsible for bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle. In humans, prions cause Creutzfeldt-Jakob Disease (CJD), variant Creutzfeldt-Jakob Disease (vCJD).

They are distinct from other pathogens which contain nucleic acids (either DNA, RNA)

CDC - Prion Diseases
Prion - Wikipedia See

Other Pathogenic Agents
Natural Toxins: Shellfish, Mushroom, Other

Some scientists now believe brain illnesses like mad cow disears are among a few diseases caused by an infectious agents called prions. Prions are not even DNA or RNA, but simply proteins.

Biosafety Risk Groups:
The National Institute of Health has created a list of Human etiologic agents (pathogens) that is categorized into 4 major risk groups. of the National Institutions of Health has created a list of Human etiologic agents (pathogens) that is categorized into 4 major risk groups.
Risk Group 1 (RG1) Agents that are not associated with disease in healthy adult humans.
e.g. Bacillus subtilis or Bacillus licheniformis
Risk Group 2 (RG2) Agents that are associated with human disease which is rarely serious and for which preventive or therapeutic interventions are often available.
e.g. Salmonella, E.coli, Cryptosporidium, Giardia, Streptococcus, Adenoviruses, Hepatitis, Measles, Mumps, Parainfluenza viruses types A, B, and C, Rhinoviruses, Coronaviruses, Staphylococcus aureus, Streptococcus pneumoniae, Herpes simplex, Acinetobacter, Chryseobacterium hominis, Moraxella osloensis, Dengue virus
Risk Group 3 (RG3) Agents that are associated with serious or lethal human disease for which preventive or therapeutic interventions may be available (high individual risk but low community risk)
e.g. Influenza viruses 1918-1919 H1N1 (1918 H1N1), human H2N2 Influenza (1957-1968), avian influenza H5N1, SARS, West Nile virus (WNV), HIV, Yellow fever virus, St. Louis encephalitis virus
Risk Group 4 (RG4) Agents that are likely to cause serious or lethal human disease for which preventive or therapeutic interventions are not usually available (high individual risk and high community risk)
e.g. Tick-born encephalitis virus complex, Ebola virus
See Risk Groups for the complete list.

The World Health Organization (WHO) has slightly different definitions. See Public Health Emergency page (

Biosafety Levels (BSL) prescribe procedures and levels of containment for the particular microorganism or material (including Research Involving Recombinant or Synthetic Nucleic Acid Molecules). Similar to Risk Groups, BSL are graded from 1 - 4.
Detailed descriptions of containment practices and biosafety levels can be found in the CDC-NIH Guidelines - Biosafety in Microbiological and Biomedical Laboratories.

A micron (µm) is 1/1000 of a millimeter, a nanometer nm is 1/1000 of a micron.
Diameter of human hair is 50-100 microns.
Viruses can be from 0.02-0.3 µm (100-300 nm)

  • Rhinovirus (Cold) - 0.02 microns
  • Hepatitis - 0.03 microns
  • Flu virus - 0.17 microns
  • Coronavirus - 0.12 microns
  • small polio virus is0.028 microns
  • chickenpox virus is .12 to .2 micron
  • smallpox virus (Poxvirus variola) at .14 to .3 micron
  • ebola is .8 to 1 micron
  • Coronavirus or Rhinovirus - Cold
  • Adenovirus - cold
  • whooping cough bacteria (Bordetella pertussis) is .2 to .3 micron
  • pneumonia bacteria (Mycoplasma pneumoniae) is .2 to .3 micron
  • bronchitis bacteria (Chlamydia pneumoniae) is .2 to .4 micron
  • meningitis bacteria (Haemophilus influenzae) is .2 to .3 micron
  • tuberculosis bacteria (Mycobacterium tuberculosis) is .2 to .6 micron
  • diphtheria bacteria (Corynebacteria diphtheria) is .3 to .8 micron
  • scarlet fever bacteria (Streptococcus pyogenes) is .6 to 1.0 micron
  • otitis media bacteria (Streptococcus pneumoniae) is .8 to 1.0 micron
  • anthrax bacteria (Bacillus anthracis) is 1.0 to 1.25 microns
Family Known germs Size range
Viruses Hepatitis A, Norwalk Virus, Rotavirus, Poliovirus ~0.02 - 0.2 microns
Bacteria E-coli (Escherichia coli), Salmonella (Salmonella typhimurium), Cholera (Vibrio cholerae) 0.2 - 5 microns
Protozoans Amoeobiasis (Entamoeba histolytica), Giardia lamblia (Giardia intestinalis), Cryptosporidium (Cryptosporidumparvum) 1 - 15 microns

Source: from and
Selection Card Bacteria EN Web at

Incidence in North America:
An article "Microbiology" in the Dec. 2003 Backpacker states:
An American Water study of treatment plants in 14 US states and one Canadian province in 1991 found:

Giardia          17% of samples
Cryptosporidium  27%
Standards have been raised since then.
A 2003 American Water study of six watersheds found:
Giardia          23%
Cryptosporidium   4%
However levels of cryptosporidium were so low your chance of ingesting an infectious dose is approximately 1 in 5,000.
However if your imune system is compromised because of Chemotherapy, AIDS or other reasons you should be more careful.

Studies showed that it took an average of 132 Cryto cysts to cause a problem.

However if your imune system is compromised because of Chemotherapy, AIDS or other reasons you should be more careful.

See more at water purification under recreation.

The increasing use of antimicrobials in humans, animals, and agriculture has resulted in many pathogens developing resistance to these powerful drugs. All major groups of pathogens viruses, fungi, parasites, and bacteria can become resistant to antimicrobials.

Viruses are generally avoided by increasing immunity with a vaccines before you get sick. A vaccine is a suspension of whole or parts of bacteria or viruses (live or inactivated) that have been engineered so that they don't make the immunized person sick but do induce an immune response and prevent disease.
Examples are the polio and flu vaccines.
Some viruses (e.g. HIV and Hepatitis) use "protease" (an enzyme that breaks down protein) to get into the cell. Drugs called protease inhibitors can be used to fight them.

Neuraminidase inhibitors are a class of antiviral drugs targeted at the influenza virus, which work by blocking the function of the viral neuraminidase protein. e.g Oseltamivir (Tamiflu®) and Zanamivir (Relenza®).

Antiviral treatment as early as possible is recommended for any patients with confirmed or suspected influenza who are hospitalized, seriously ill, or ill and at high risk of serious influenza-related complications, including young children, people 65 and older, people with certain underlying medical conditions and pregnant women.

Antibiotics are used for Bacterial Infections. Some antibiotics work by interfering with the bacteria's ability to build a cell wall (e.g. Penicillin). Antibiotics may also destroy the bacteria's ability to use nutrients or make proteins (e.g. erythromycin, azithromycin and clarithromycin). Still others stop the bacteria from making DNA (e.g. sulfas ( "sulfanilamides" or "sulfonamides"))

Eating and Drinking:
See Flu Recovery Diet

Flu Recovery Diet
Infectious agents and how they cause disease at
Pathogen survival
Traveler's diarrhea
Division of Microbiology and Infectious Diseases - DMID at the National Institute of Allergy and Infectious Diseases (NIAID) in the National Institutes of Health (NIH)
Your Kitchen Sponge is Covered With Bacteria -- Don't Bother Cleaning It - D-brief (DiscoverMagazine)
Microbes: Small, Small World | National Geographic
Bad Bug Book at the Center for Food Safety & Applied Nutrition at the FDA
Centers for Disease Control and Prevention
Orthomyxoviridae Influenza Viruses.
Emergency Water Essentials
water purification
Gut Health: The Key to our Overall Health and Immunity | K-W Homeopathic Medicine and Wellness Clinic
John and Amy's Influenza Page
Bacteria vs Viruses at
Cryptosporidium and Water: A Public Health Handbook | CDC

1. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 104: 13780-13785, 2007.

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last updated 11 Aug 2017