Monday, June 29, 2015

Pathogenic Microorganisms (edited for link formatting)

[Below, Gentle Readers, is the article I wrote on Friday. It was not meant to appear here. It was meant for the use of a paying client. It was written for publication overseas, so follows British spelling and punctuation rules rather than the American rules this site normally follows. Due to what may have been ordinary foul-ups in cyberspace, which are common enough, but we can't rule out the possibility that the foul-ups were deliberately created to allow someone to gank the text without paying for it, I've not received payment for the job. So, here's what I wrote. If the client just didn't want it, very well, it's still my intellectual property, which someone else may purchase and print if they like. If some hacker is trying to use it without paying, I can prove plagiarism.]

[About the references: In Word Documents, we use footnotes or endnotes. In Blogspot, we use links. Some of these links open pages that use up lots of memory and/or contain cookies, despite their academic respectability, and you might prefer to look up some of the references in print anyway; I didn't, but printed versions exist. So, each link is used only once. While footnotes are usually placed at the end of a paragraph that draws on a source, links are attached to keywords or names, sometimes at the beginning of the paragraph. A list of links appears in order at the end of the document.]

Pathogenic microorganisms are tiny living things that can cause diseases. Four types of pathogenic microorganisms are viruses, bacteria, fungi, and parasitic protozoa.
Viruses evolve fast because they reproduce only within living host cells of animals, plants, or even bacteria. They appear under an electron microscope to consist of 'an RNA or DNA core, a protein coat, and, in more complex types, a surrounding envelope.' Distinct shapes allow virologists to classify some viruses into families, genera, and species.
Nucleic acid from a virus and host cell can combine during the process of replication, allowing a virus to transfer nucleic acid from one host to another even if the second host belongs to a different species. This makes some viruses useful in genetic modification.
Not all viruses cause disease symptoms. Some viruses can be 'dormant' in a body for years without producing symptoms. While virus-related diseases like the 'common cold' produced by human rhinovirus, or the symptoms produced by Herpes simplex, are well known, researchers are still studying the many factors that seem to influence whether or not these viruses cause symptoms in a particular patient.
Virus Transmission
Some viruses, such as norovirus, can be transmitted through the air. Others seem to require more direct contact; human immunodeficiency virus (HIV, which causes AIDS) and Herpes simplex seem to be transmitted only through contact with certain body fluids from an infected person. For some viruses, the means of transmission and avoidance are not fully understood. There is debate about whether standing at a 'healthy distance' from other people, washing hands frequently, or both is most important in preventing infection with human rhinovirus.
Bacteria consist of a single cell that has a cell wall but lacks the nucleus and organelles observed in single cells from more complex organisms. A 'nucleoid' contains chromosomes (DNA); the cytoplasm in a bacterium also contains ribosomes and other 'inclusions'. Bacteria may also have appendages, often 'flagella' structures that help a bacterium swim. Senior classifies bacteria into eight groups based on their ability to photosynthesise, their shape, and their reaction to staining.
Although many bacteria have been given genus and species names, bacteriologists debate the definition of a bacterial species. Future scientists may eventually discard familiar species names such as Staphylococcus aureus and Lactobacillus acidophilus.
Bacterial 'growth' is measured as an increase in numbers rather than size. Bacteria reproduce by fission when the environment is favorable. Conditions favorable to bacterial growth vary but most bacteria associated with human diseases multiply at temperatures close to human body temperature.
Nutrition triggers reproduction in bacteria. Bacteria vary in their needs for oxygen, salt, and acidity, but most of the bacteria that infect humans thrive in environments similar to human bodies. While the Cyanobacteria or 'blue-green algae' live by independent photosynthesis, and some types of bacteria self-nourish through 'chemosynthesis' of specific chemicals, most bacteria need a variety of nutrients found in organic material. Researchers cultivate most bacteria in the laboratory on agar solutions.
Some bacteria, like Lactobacillus acidophilus, are so 'friendly' to humans that bacterial cultures are used to process food and even sold as digestive supplements. Others, like Staphylococcus aureus, may 'commonly colonise' humans 'without causing any problems' yet cause diseases that may become fatal to immune-deficient patients. A few, like Clostridium tetani, are associated with specific diseases.
Bacterial Transmission 
Some bacteria can be transmitted through the air. Some are transmitted by food, and may cause 'food poisoning'. Most bacteria that infect humans can also spread through contact with body fluids. Some can be transmitted by 'vector' species such as mosquitoes. A few hardy bacteria like Staphylococcus aureus can survive on nonliving surfaces, such as linens, long enough to infect others. Clostridium bacteria, which do not tolerate oxygen, are not airborne but can be transmitted through contact with soil where an infected person or animal deposited body fluids.
Fungi are a very large and diverse group of organisms traditionally placed in the plant kingdom. The three main types of fungi are single-cell organisms (yeasts), multi-cell filaments (moulds), and multi-cell filamentous organisms that form large fruiting bodies (mushrooms).
Mushrooms may be nutritious or toxic when consumed by humans but the fungi that form mushrooms are not considered genuine pathogens. They can, however, be allergens.
A few types of yeasts and moulds can infect humans, occasionally producing serious disease conditions. Most people who develop serious fungal infections have immune system impairments. Since fungi thrive in warm, damp environments, they are often associated with tropical countries, but outbreaks of histoplasmosis (infection by Histoplasma capsulatum) are reported among people who explore bat habitats as far north as southern Canada. Candidiasis (infection by an overgrowth of naturally occurring Candida albicans) and ringworm (infection by Tinea species) are reported worldwide. 
Fungal Infection Transmission 
Although fungus spores are airborne, most fungal infections are transmitted through direct contact with the fungus. Tinea infections often spread through contact with surfaces at spas, gyms, locker rooms, etc. Histoplasmosis can be transmitted either through skin contact with mould spores, or through inhaling airborne spores. Candidiasis can be transmitted through direct contact but usually becomes a problem only when the patient loses normal immunity, since Candida albicans is normally present in healthy human bodies.
Protozoa are relatively large, mobile, single-cell organisms that can be observed through a simple microscope. Although each protozoan consists of only one cell, some amoebae can be up to 1 mm in size, and protozoan cells have nuclei and various other structures similar to those found in animals; Yaeger describes their complexity as "more like an animal than like a single cell." Most protozoa pass through several stages, sometimes including "cyst" stages in which the organism is encased in a rigid wall and seems dormant until conditions permit it to emerge into a more active form. The most common form of reproduction is simple fission, but some forms of protozoan reproduction are considered sexual. Protozoa spend most of their lives in liquids, which may include tears, blood, and other liquids within larger organisms.
Most protozoans are harmless to humans. A few, such as Trichomonas vaginalisEntamoeba histolytica, and Giardia lamblia, can infect humans and cause diseases. 
Protozoan Transmission 
Protozoa are less easily transmitted than the smaller pathogens. They usually spread from one host to another by direct contact. This can be body-to-body contact (the usual route for Trichomonas vaginalis), contact with infected water or soil (the usual route for Entamoeba and Giardia), contact through vectors such as mosquitoes, or 'predator-prey' contact (eating infected organisms as food). 
How are pathogenic microorganisms treated and prevented? 
A variety of treatments have been developed and used, with varying degrees of success, to treat different types of infestation with pathogenic microorganisms. Antibiotics are effective against most bacterial infections (although resistant strains have emerged) because most bacteria reproduce asexually, evolve slowly, and tend to die out in a given habitat after some time in any case. Fungal infections can be harder to treat, and some viral infections still defy medical science despite recent breakthroughs with antiviral drugs. Clean, healthy humans with robust immune systems still enjoy better resistance and better chances of recovery from infection by pathogenic microorganisms.
The category of viruses includes both human rhinovirus, probably the least feared of all common pathogenic microorganisms, and human immunodeficiency virus, possibly the most feared. These two types of infection display the wide range of human responses to pathogenic microorganisms.
People infected with human rhinovirus may or may not bother to seek help. If they do seek help they may be told to get some rest, sip hot liquids, take aspirin, or just work through it. Most people's immune systems wipe out the virus in a day or two.
People infected with human immunodeficiency virus may carry and transmit the virus for years without knowing they have it. What 'awakens' the dormant virus and produces AIDS is not completely understood; however, when HIV begins replicating, it destroys the patient's natural immunity and prevents the patient from ever really fighting off the infection. Although today's antiviral drugs offer people with AIDS better prospects for a long active life than was imaginable in the 1980s, treatment for this disease remains costly and lasts a lifetime.
Rapid progress is being made in understanding and treating conditions caused by pathogenic microorganisms. Earlier detection and more effective treatments are possible today than were possible even ten years ago. Nevertheless, prevention remains the best cure.

References [all confirmed 26 June 2015]
1. Available from
2. Gelderblom, H. 'Structure and classification of viruses' in Medical Microbiology 4th edition, ed Baron S, University of Texas at Galveston, Galveston, 1996. Available from
3. University of California at Menlo Park, 1997, Introduction to the viruses. Available from
4. Lee, W, Lemanske, R, Evans, M, Vang, F, Pappas, T, Gangnon, R, Jackson, D, & Gern, J, 2012, 'Human rhinovirus species and season of infection determine illness severity', American Journal of Respiratory & Critical Care Medicine 2012 Nov 1; 186(9): 886–891. Available from
5. Liggett, S, Bochkov, Y, Pappas, T, Lemanske, R, Gern, J, Sengamalay, N, Zhao, X, Suc, Q, Fraser, C & Palmenberg, A, 2014, 'Genome sequences of Rhinovirus A isolates from Wisconsin pediatric respiratory studies', Genome Announcements March/April 2014, vol. 2. no. 2, e00200-14. Available from
6. Centers for Disease Control & Prevention 2015, HIV transmission. Available from
7. Public Health Agency of Canada 2011, Rhinovirus. Available from
8. Centers for Disease Control & Prevention 2015, Common colds: Protect yourself and others. Available from
9. Available from
10. Todar, K. Todar's Online Textbook of Bacteriology. Madison WI, 2012. Available from
11. Senior, K. 2014, How many types of bacteria are there? Available from
12. Cohan, FM 2002, 'What are bacterial species?', Annual Review of Microbiology 2002;56:457-87. Available from
13. University of California at Davis, Bacterial growth and reproduction. Available from
14. Scheffers, D, 2013, 'Bacterial reproduction and growth', Wiley Online Library, DOI: 10.1002/9780470015902.a0001419.pub2. Available from
15. Georgia Perimeter College, Bacterial growth. Available from'09WebPages/Web%20Chapter%20Notes/Ch6BacterialGrowth1-11-02revisions.htm.
16. Public Health England 2014, Staphylococcus aureus: guidance, data and analysis. Available from
17. Mayo Clinic Staff 2015, Staph infections: Causes. Available from
18. Centers for Disease Control & Prevention 2013, Tetanus: Causes and transmission. Available from
19. Society for General Microbiology 2015, 'Fungi', Microbiology online. Available from
20. Betz, B, 1990, 'Respiratory tract diseases in oyster mushroom cultivators', Pneumologie 1990 Feb;44 Suppl 1:339-40. Available from
21. Centers for Disease Control & Prevention 2015, 'Fungal diseases'. Available from 'Types of fungal diseases'. Available from 'Who gets fungal diseases?' Available from
22. Ericsson, C, Steffen, R, Panackal, A, Hajjeh, R, Cetron, M & Warnock, D, 2015, 'Fungal infections among returning travelers', Clinical Infectious Diseases, vol. 35, issue 9. Available from
23. Chiller, T, 2013, 'Histoplasmosis', in Centers for Disease Control & Prevention, Infectious diseases related to travel. Available from
24. Public Health Agency of Canada, 2014, Candida albicans: Pathogen safety data sheet. Available from
25. ABPI Schools 2015, Resources for schools. Available from
26. Yaeger, R. Medical Microbiology 4th edition, ed Baron S, University of Texas at Galveston, Galveston, 1996. Available from
27. Australian Society for Parasitology, 'Protozoan parasites', Para-site. Available from
28. Mayo Clinic Staff, 2015, Diseases and conditions: HIV/AIDS: Treatments and drugs. Available from