Saturday, January 26, 2008


Problem Statement
There are outbreaks of viral, fungal and protozoa diseases among platoons of army soldiers in Indonesia. Soldiers reported sick after 2 weeks of jungle warfare training. It is of concern to the ministry that there are also sporadic reports of avian flu in the nearby villages. In view of these outbreaks, you have been tasked to conduct a pre-mission briefing with blogs and poster to educate future batches of soldiers.

Environment in the tropical jungle:
1. High exposure to different kinds of virus, fungal and protozoa.
2. Dark and moist environment which allows growth of microorganisms.
3. High amounts of decay (leaf, dead plants and animals) which microorganisms can thrive in.
4. Indonesia is in tropical area. The environment is always warm and humid in its jungle.
5. Short supply of food and clean water.
6. poor hygiene conditions due to continuous training of the soldiers.
7. Source of food may come from jungle or nearby village. The food may be cook improperly to cause infection.Disease can be acquired from water, soil, animals, plants, and human to human interaction.

Possible fugal infection in tropical jungle in Indonesia

1. Superficial mycoses
Tinea versicolor or pityriasis versicolor

Description :

Tinea versicolor or pityriasis versicolor is a common skin infection caused by Malassezia furfur. This yeast is normally found on the human skin and only becomes troublesome under certain circumstances, such as a warm and humid environment. In tropical climate, the condition is more common than in temperate zones and as many as 40% of some apparently healthy populations may be affected.

Microscopic: tinea versicolor, "spaghetti and meatballs" appearance
Taken from

The development of disease is thought to follow a shift in the balance between the host and resident yeast flora. There are many factors contributing to this change. Infection is more prone to be caused by environmental risk factors and individual host susceptibility such as genetic susceptibility. Most of the transmission is through direct contact with the yeast.

Signs and Symptoms:
· Generally oval or irregularly-shaped spots of 1/4 to 1 inch in diameter, often merging together to form a larger patch
· Occasional fine scaling of the skin producing a very superficial ash-like scale
· Pale, dark tan, or pink in color, with a reddish undertone that can darken when the patient is overheated, such as in a hot shower or during/after exercise
· Sharp border
· commonly affect the back, underarm, upper arm, chest, lower legs, and neck. Occasionally it can also be present on the face.
· In people with dark skin tones, pigmentary changes such as hypopigmentation (loss of color) are common, while in those with lighter skin color, hyperpigmentation (increase in skin color) are more common. These discolorations have led to the term "sun fungus".

· Topical antifungal medications such as selenium sulfide, ketoconazole, clotrimazole, miconazole or terbinafine is applied to dry skin and washed off after 10 minutes, repeated daily for 2 weeks.
· Oral antifungal prescription only medications include ketoconazole or fluconazole in a single dose, or ketoconazole daily for 7 days, or itraconazole daily for 3-7 days. The single-dose regimens can be made more effective by having the patient exercise 1-2 hours after the dose, to induce sweating. The sweat is allowed to evaporate, and showering is delayed for a day, leaving a film of the medication on the skin.

Prevention:Infection may be reduced by intermittent application of topical agents (such as tea tree oil) or adding a small amount of anti-dandruff shampoo to water used for bathing.

2. Cutaneous mycoses

Dermatophytosis is caused by fungi in the genera Microsporum, Trichophyton and Epidermophyton. Belonging to pathogenic members of the keratinophilic (keratin digesting) soil fungi. Microsporum and Trichophyton are human and animal pathogens. Epidermophyton is a human pathogen.Dermatophytes grow best in warm and humid environments and are, therefore, more common in tropical and subtropical regions. The geographic distribution varies with the organism. M. canis, M. nanum, T. mentagrophytes, T. verrucosum and T. equinum occur worldwide. T. simii (found in monkeys) occurs only in Asia.

Transmission :
Infection occurs by contact with arthrospores (asexual spores formed in the hyphae of the parasitic stage) or conidia (sexual or asexual spores formed in the “free living” environmental stage). Infection usually begins in a growing hair or the stratum corneum of the skin. Dermatophytes do not generally invade resting hairs, since the essential nutrients they need for growth are absent or limited. Hyphae spread in the hairs and keratinized skin, eventually developing infectious arthrospores. Transmission between hosts usually occurs by direct contact with a symptomatic or asymptomatic host, or direct or airborne contact with its hairs or skin scales. Geophilic dermatophytes, such as M. nanum and M. gypseum, are usually acquired directly from the soil rather than from another host.

Signs and Symptoms:

Tinea capitis, tinea barbae and tinea faciei are generally treated with systemic antifungals. Topical lotions or shampoos are sometimes used to decrease shedding of fungi and spores. Tinea corporis can usually be treated with nonprescription antifungals. Prescription drugs may be required if the fungus infects the hairs and recrudescence occurs. Tinea manuum is usually treated with topical drugs and emollients.

Control of the disease in animals can prevent some cases of dermatophytosis in humans. Infected animals should be treated and the premises and fomites should be disinfected. Gloves and protective clothing should be used during contact with infected animals. Such contact should be avoided as much as possible. Similar measures can prevent infections with anthropophilic dermatophytes.

3. Subcutaneous mycoses

The fungi that cause subcutaneous mycoses normally reside in soil or vegetation. They enter the skin or subcutaneous tissue by traumatic inoculation with contaminated material. In general, the lesions become granulomatous and expand slowly from the area of implantation. Extension via the lymphatic draining the lesion is usually slow. These mycoses are usually confined to the subcutaneous tissues, but in rare cases they become systemic and produce life-threatening disease. Chromoblastomycosis is mainly caused by phialophora verrucosa, fonsecaea pedrosoi, Rhinocladiella aquaspersa, Fonsecaea compacta, and Cladophilophora carrionii.

Cladosporium (Cladophialophora) carrionii, magnified 475X. The C. carrionii fungus is a common cause of chromoblastomycosis infections, and is particularly prevalent in arid and semi-arid areas, most often in tropical and subtropical zones
Taken from

The organisms responsible for Chromoblastomycosis are found in the soil, endemic in the tropicas. They are introduced into tissues by trauma from eg :thorns or splinters. Transmission from person to person does not occur.

Signs and symptoms:
· a small red papule (skin elevation)
· Painless lesion
· Satellite lesion form if patient scratches
· Formation of cauliflower-like warty swellings which spread over the years
· Foul discharge may occur in secondary infection
· Nodular pattern becomes tumorous, large, rough and ulcerating
· Several complications may occur

Sugical excision with wide margins is the therapy of choice for small lesions. Chemotherapy with flucytosine or itraconazole may be efficacious for larger lesions. Local applied heat is also beneficial. Relapse is common.

There is no known preventative measure aside from avoiding the traumatic inoculation of fungi.

4. Endemic mycoses

Histoplasmosis, also known as Darling's disease, is caused by the dimorphic fungus Histoplasma capsulatum. This sexually reproducing fungal species is naturally found in the soil (often associated with avian and bat guano) and is endemic in tropical areas of the world. The fungus exists in a hyphal form in the soil and exists as small conidia in the human host. In C.albicans both the yeast and hyphal forms are important in virulence while in H.capsulatum (and other systemic mycoses) only the conididal form is associated with disease. Inhalation of the infectious propagules by normal healthy individuals usually results in a self limiting sub-clinical infection.

Asexual spores (conidia). Tuberculate macroconidia of Histoplasma capsulatum.
Taken from

Histoplasmosis can be transmissed through breathing in airborne spores. The initial infection often occurs without causing symptoms, and most persons usually will not develop subsequent disease, unless the exposure was heavy.
Long-term smokers and those with preexisting lung disease may be at higher risk for developing the disease.
People with severely damaged immune systems are vulnerable to a very serious disease known as progressive, disseminated histoplasmosis. Nationwide, about 5 percent of people with AIDS will develop histoplasmosis. In geographic areas where the fungus is common, people with AIDS are at higher risk for disseminated histoplasmosis.

Signs and symptoms:
· symptoms start within 3 to 17 days after exposure; the average is 12-14 days. Most affected individuals have clinically-silent manifestations and show no apparent ill effects.
· The acute phase of histoplasmosis is characterized by non-specific respiratory symptoms, often cough or flu-like. Chest X-ray findings are normal in 40-70% of cases.
· Chronic histoplasmosis cases can resemble tuberculosis; disseminated histoplasmosis affects multiple organ systems and is fatal unless treated.
· Severe infections can cause hepatosplenomegaly, lymphadenopathy, and adrenal enlargement.
· Lesions have a tendency to calcify as they heal.
· Ocular histoplasmosis damages the retina of the eyes. Scar tissue is left on the retina which can experience leakage, resulting in a loss of vision.

Antifungal medications are used to treat severe cases of acute histoplasmosis and all cases of chronic and disseminated disease. Typical treatment of severe disease first involves treatment with amphotericin B, followed by oral itraconazole. In many milder cases, simply itraconazole is sufficient. Asymptomatic disease is typically not treated. Past infection results in partial protection against ill effects if reinfected.

Avoid areas where disease is prominent.


Done be: Liu Qian and Dorene


Viral Infections

In the jungle environment, viral transmission can occur through soil, contaminated food or water, breathing in of viruses in the form of aerosals and by insect vectors such as mosquitoes e.g. dengue. The rate or speed of transmission of virus infections depends on factors that include population density, the number of susceptible individuals, the quality of health care and the weather. The following are some examples of Virus that can be found in the jungle envirnment.


Arboviruses are transmitted through arthropod vectors. Arthropods refer to the
insects, arachnids, crustaceans and others. The arthropods transmit the virus upon biting the host, allowing the virus to enter the bloodstream causing viraemia.

Avian influenza A

Influenza, commonly known as flu, is an infectious disease caused by RNA viruses of the family Orthomyxoviridae. Avian influenza is an infection caused by birds which are infected with flu viruses. These influenza viruses occur naturally among birds. Wild birds worldwide carry the viruses in their intestines, but usually do not get sick from them. Infected birds shed influenza virus in their saliva, nasal secretions, and feces. Susceptible birds become infected when they have contact with contaminated secretions or excretions from these infected birds. Influenza A viruses have also infected many different animals including ducks, chickens, pigs, whales, horses, and seals. However, certain subtypes of influenza A virus are specific to certain species, except for birds, which are hosts to all known subtypes of influenza.

Direct from birds or from avian virus-contaminated environments to people or through an intermediate host, such as a pig. The influenza viruses are transmitted from wild aquatic birds to domestic poultry giving rise to human influenza pandemics.

Signs and Symptoms:
Conjunctivitis, influenza-like illness symptoms, severe respiratory illness, nausea, vomiting and neurologic changes.
Treatment: Antiviral medication of oseltamivir is administered.
Prevention: Persons exposed to avian influenza A-infected or potentially infected poultry are recommended to follow good infection control practices including careful attention to hand hygiene and to use personal protective equipment. In addition, they should be vaccinated against seasonal influenza and should take influenza antiviral agents for prophylaxis. Exposed persons should be carefully monitored for symptoms that develop during and in the week after exposure to infected poultry or to potentially avian influenza-contaminated environments. Also, humans should avoid consumption of poultry from the nearby villages as they face a high risk of influenza infection.
Influenza Virus- Taken from

Chikungunya Virus

Chikungunya is an alphavirus in the Togaviridae family of viruses. It is a viral disease that is almost self limiting and rarely fatal. The symptoms are similar to those of dengue. However, unlike dengue, there is no hemorrhagic or shock syndrome form.

Spread through bites from Aedes aegypti and Culex mosquitoes.

Signs and Symptoms:
Fever which can reach 39°C, a petechial or maculopapular rash usually involving the limbs and trunk, and arthritis affecting multiple joints. The fever typically lasts for two days and then comes down abruptly. However, other symptoms, namely joint pain, intense headache, insomnia, vomiting, epitaxis and an extreme degree of prostration last for a variable period; usually for about 5 to 7 days.

Chloroquine is gaining ground as a possible treatment for the symptoms associated with chikungunya and as an antiviral agent to combat the Chikungunya virus.

Prevention :
Protection against any contact with the disease-carrying mosquitoes. These include using insect repellents with substances like DEET (N, N’-Diethyl-3-methylbenzamide), icaridin and PMD (p-menthane-3,8-diol). Mosquito nets can be used to protect those who may rest during the day. The effectiveness of such nets can be improved by treating them with permethrin (pyrethroid insecticide). Wearing bite-proof long sleeves and trousers also offers protection. In addition, garments can be treated with pyrethoids, a class of insecticides that often has repellent properties. Securing screens on windows and doors will help to keep mosquitoes out of the house. Mosquito coils can be used too. Mosquito control is also especially important by draining water from coolers, tanks, barrels, drums and buckets and emptying coolers when not in use etc.

Chikungunya Virus- Taken from

West Nile Virus

Arbovirus that spreads to people from the bite of the mosquito infected with the virus. The mosquitoes are active under warm conditions and temperate climates like Asia’s. Thus, the West Nile virus infection generally occurs under these conditions .

Mosquitoes get infected with West Nile virus by feeding on infected birds. Once infected with the virus, a mosquito will transmit the virus to other animals or birds when they take another blood meal.

Signs and Symptoms:
Most people infected with West Nile virus do not often become ill. If they do, they have mild illness with fever, headache, eye pain, muscle aches, joint pain, a rash on the trunk, swollen lymph nodes, nausea and vomiting. Symptoms of severe illness include extreme muscle weakness, inflammation of the brain (encephalitis), paralysis, and coma. Symptoms usually occur 3 to 15 days after an infected mosquito bites a person.

There is no specific treatment for West Nile virus infection. A physician may provide treatment to relieve the symptoms of the illness. In severe cases hospitalization may be required.

West Nile control is achieved through mosquito control, by elimination of mosquito breeding sites, larviciding active breeding areas and encouraging personal use of mosquito repellents containing DEET.

West Nile Virus- Taken from

It belongs to a family of viruses transmitted by mosquitos and ticks that cause some important diseases including dengue, yellow fever, tick-borne encephalitis virus, and Japanese encephalitis (JE) virus. It causes rare viral infections and it primarily occurs in tropical areas of the world.

Japanese encephalitis virus

Japanese encephalitis is a mosquito-borne viral disease. In subtropical and tropical regions, risk of infection is associated with the rainy season. In tropical areas, sporadic cases may occur at any time of the year. Disease is endemic and epidemic in Asia such Indonedia,Japan,Hong Kong, Malaysia. The Japanese encephalitis virus (JEV) infects the lumen of the endoplasmic reticulum and rapidly accumulates substantial amounts of viral proteins for the JEV.

The virus is transmitted by various mosquitoes of the genus Culex. It infects pigs, various wild birds and humans. Mosquitoes become infective after feeding on viraemic pigs or birds.

Signs and Symptoms:
Most infections are asymptomatic. Symptomatic ones begin clinically as a flu-like illness with headache, fever, and often gastrointestinal symptoms. Confusion and disturbances in behaviour also may occur. It may progress to encephalitis, and in one third of cases, the illness may be fatal. Another one third of cases survive with serious neurologic after effects such as paralysis or other forms of brain damage.

There is no specific treatment for Japanese encephalitis. Antibiotics are not effective against viruses, and no effective anti-viral drugs have been discovered.

Japanese Encephalitis vaccination and wear mosquito repellents containing DEET as an active ingredient. Main protection rests in taking all possible care against being bitten. The mosquitoes, which transmit Japanese B Encephalitis tend to bite mainly in the evening time though day biting in shady areas may also occur.

Dengue virus

The dengue virus causes dengue and dengue hemorrhagic fever. The dengue virus is composed of single-stranded RNA, and it has four serotypes, known as DEN-1, 2, 3, and 4.

The transmission cycle of dengue virus by the mosquito Aedes aegypti begins with a dengue-infected person. The person will have viremia that lasts for about five days. During the viremic period, an uninfected female Aedes aegypti mosquito bites the person and ingests blood that contains dengue virus. The mosquito then bites a susceptible person and transmits the virus to him or her, as well as to every other susceptible person the mosquito bites for the rest of its lifetime. The virus is inoculated into humans with the mosquito saliva. It localizes and replicates in various target organs, for example, local lymph nodes and the liver. The virus is then released from these tissues and spreads through the blood to infect white blood cells and other lymphatic tissues.

Signs and Symptoms:
Manifestation starts with a sudden onset of fever, with severe headache, muscle and joint pains (myalgias and arthralgias) and rashes. The dengue rash is characteristically bright red petechia and usually appears first on the lower limbs and the chest; in some patients, it spreads to cover most of the body. There may also be gastritis with some combination of associated abdominal pain, nausea, vomitting or diarrhoea.

The mainstay of treatment is supportive therapy. Increased oral fluid intake is recommended to prevent dehydration. Supplementation with intravenous fluids may be necessary to prevent dehydration and significant concentration of the blood if the patient is unable to maintain oral intake. A platelet transfusion is indicated in rare cases if the platelet level drops significantly (below 20,000) or if there are significant bleeding.

Mosquito control is the primary prevention of dengue. This can be done through the elimination or reduction the mosquito vector for dengue. Public spraying for mosquitoes is the most important aspect of this vector. Application of larvicides such as Abate® to standing water is more effective in the long term control of mosquitoes.

Dengue Virus. Taken from

Tick-borne encephalitis virus(TBEV)

TBE is an important infectious disease of in many parts of Europe, the former Soviet Union, and Asia, corresponding to the distribution of the ixodid tick reservoir. It is a human viral infectious disease involving the central nervous system. The virus can infect the brain (encephalitis), the membrane that surrounds the brain and spinal cord (meningitis) or both (meningoencephalitis).

It is transmitted by the bite of infected deer ticks or (rarely) through the non-pasteurized milk of infected cows.

Signs and Sympoms:
The incubation period of TBE is usually between 7 and 14 days and is asymptomatic. Fever, malaise, anorexia, muscle aches, headache, nausea, and/or vomiting follows after that.

Hospitalization and supportive care based on syndrome severity. Anti-inflammatory drugs, such as corticosteroids, may be considered under specific circumstances for symptomatic relief. Intubation and ventilatory support may be necessary. There are four main catgeories of treatment for TBE. Phosphrenyl, both a therapeutic and prophylactic agent for TBE, interferon treatment (like interferon for Hepatitis C), antibiotic treatment for possible tickborne coinfections and phytotherapy.

TBEV infection can be prevented by using insect repellents and protective clothing to prevent tick bites. A vaccine is available in some disease endemic areas.

Nipah virus

Nipah virus is a newly recognized zoonotic virus. Nipah is closely related to another newly recognized zoonotic virus, called Hendra virus. Both Nipah and Hendra are members of the virus family Paramyxoviridae. Certain species of fruit bats are the natural hosts of both Nipah and Hendra viruses

From animal to animal. Animal to human transmission is uncertain, but appears to require close contact with contaminated tissue or body fluids from infected animals. Nipah antibodies have been detected in pigs, other domestic and wild animals. Despite frequent contact between fruit bats and humans there is no serological evidence of human infection among bat carers.

Signs and Symptoms:
"Influenza-like" symptoms, high fever and muscle pains (myalgia). The disease may progress to inflammation of the brain (encephalitis) with drowsiness, disorientation, convulsions and coma.

No drug therapies have yet been proven to be effective in treating Nipah infection. Treatment relies on providing intensive supportive care. However, there is some evidence that early treatment with the antiviral drug, ribavirin, can reduce both the duration of feverish illness and the severity of disease.

Humans should avoid animals that are known to be infected and use appropriate personal protective equipment devices when it is necessary to come into contact with potentially infected animals.
Nipah virus. Taken from
Arthropod Cell Culture Systems. (2006). Mosquito Cell Lines. Retrieved January 20, 2008 from

eMedicine from WebMD. (2008). Viral Hemorrhagic Fevers. Retrieved January 22, 2008 from
Wikipedia, the free Encyclopedia. (2008). Tick-borne encephalitis viruses. Retrieved January 23, 2008 from
Wikipedia, the free Encyclopedia. (2008). West Nile Virus. Retrieved January 23, 2008 from
Done by Cassandrea Teng, Sasikala S. and Vinodhini Jayaram

Protozoal Diseases
These diseases are commonly found spread in the jungles and forests through sources such as water (from the river, lakes), food (from infected animals) and mosquitoes. Most of the diseases listed below are found in Indonesia forests whereas others are found worldwide.

• Diarrheal illness caused by the protozoa Giardia lamblia.
Description: Giardiasis is an infection of the small intestine caused by Giardia lamblia, a flagellate protozoan. This disease is prevalent among people in the jungles and forests.
Transmission: Infection usually occurs through ingestion of G. cysts in water (unfiltered drinking-water or recreational water, i.e. water in lakes, rivers, ponds, or streams that can be contaminated with feces from humans or animals) contaminated by the faeces of infected humans or animals.
Clinical signs & symptoms: Anorexia, nausea, chronic watery diarrhoea, abdominal cramps, bloating, frequent loose greasy stools, fatigue and weight loss.
Prevention: Avoid drinking unfiltered or recreational water. Boil water for longer periods, at least twenty minutes to destroy any heat-resistant cysts.
Treatment: Metronidazole or quinacrine hydrochloride.

Giardia lamblia

Taken from:

• Intestinal disease caused by the protozoa (amoeba) Entamoeba histolytica.
Description: In amebiasis, the commensal amoeba produces proteolytic enzymes that enable penetration of intestinal mucosa and invasion of other parts of the body. This produces flask-shaped ulcers “ameboma” in the liver, lungs & brain.
Transmission: Fecal-oral transmission occurs through ingestion of mature cyst through contaminated water (in this case, from lakes in the jungle).
Clinical signs & symptoms: Fulminating dysentery, diarrhea, weight loss, fatigue, abdominal pain, and amebomas.
Prevention: Avoid drinking untreated water and observe good hygiene practices such as hand-washing. Vegetables should be cooked before consumption as some villages use human feces as fertilizers for their crops.
Treatment: Metronidazole for the treatment of intestinal amebiasis or hepatic abscess. Asymptomatic patients are treated with a lumenal amoebicide i.e. paromomycin.

E. histolytica

Taken from:

• Diarrheal disease caused by the protozoa, Cryptosporidium parvum.
Description: This disease is caused by microscopic parasites of Cryptosporidium. The oocysts excyst in the small intestine of an infected person or animal, where the trophozoites attach to the gut wall. The parasite is protected by an outer shell that allows it to survive outside the body for long periods of time and makes it very resistant to chlorine-based disinfectants.
Life cycle of Cryptosporidium parvum:

Taken from:
Oocysts release sporozoites, which release trophozoites. Several stages ensue, with the formation of schizonts and merozoites. Finally, micrgametes and macrogametes form. They unite to produce a zygote, which differentiates into oocysts.
Transmission: Fecal-oral transmission of oocysts. Once an animal or person is infected, the parasite lives in the intestine and passes in the stool. Cryptosporidium is found in soil, water, or surfaces that have been contaminated with the infected human or animal feces e.g. recreational water contaminated with Cryptosporidium parvum.
Clinical signs & symptoms: Stomach cramps or pain, dehydration, nausea, vomiting, fever and weight loss.
Prevention: Avoid drinking unfiltered or recreational water. Purification of water supply such as filtration can help to remove any cysts in the water. These cysts are resistant to chlorination.
Treatment: Paromomycin is effective in reducing diarrhea.

• Blood-borne disease caused by the protozoa, Plasmodium falciparum and Plasmodium vivax.
Description: Plasmodium falciparum is dangerous because it digests the red blood cell's hemoglobin and also, it changes the adhesive properties of the cell it inhabits. This change in turn causes the cell to stick to the walls of blood vessels. It becomes especially dangerous when the infected blood cells stick to the capillaries in the brain, obstructing blood flow, a condition called cerebral malaria. P. vivax and P. falciparum are found predominantly in Southeast Asia.
The Life Cycle of Malaria Parasite:

Taken from:

The life cycle of the malaria parasite begins when an infected mosquito transmits malaria sporozoites to a new host. The sporozoites travel to the liver, invade hepatocytes and multiply thousands of times over the following two weeks before rupturing out of the liver into the blood stream. During the 1st 48 hours after infecting a erythrocyte, the parasite undergoes several phases of development.

First phase: Ring stage in which the parasite begins to metabolize hemoglobin.
Second phase: Trophozoite stage during which the parasite metabolizes most of the hemoglobin, gets larger, and prepares to reproduce more parasites.
Last stage: The parasite divides asexually to form a multinucleated schizont. The erythrocyte bursts open and the parasites are dispersed to infect more red blood cells.

Transmission: Plasmodium falciparum and Plasmodium vivax are transmitted by the bites of about 60 species of mosquitoes in the genus Anopheles.

Taken from:

Clinical signs & symptoms: Moderate to severe shaking chills, profuse sweating as body temperature falls, high fever, general feeling of unease and discomfort (malaise), headache, nausea, vomiting and diarrhea.
Prevention: Bednets, insecticides, and antimalarial drugs are effective. Apply mosquito repellent.
Treatment: Chloroquine, sulfadoxine-pyrimethamine (Fansidar®), mefloquine (Lariam®), atovaquone-proguanil (Malarone®) and quinine.

• Diarrheal disease caused by the protozoa, Cyclospora cayetanensis.
Description: Cyclosporaisis is endemic in tropical and sub-tropical regions, especially when the disease is in its best season for spreading. These warmer temperatures are needed to get oocysts to sporulate rapidly. The only hosts C. cayetanensis uses are humans. The protozoan lives out its lifecycle intracellularly within the host’s epithelial cells and gastrointestinal tract.
Transmission: Occurs through the oral-fecal route, and begins when a person ingests oocysts in fecally contaminated food or water.
Clinical signs & symptoms: Prolonged watery diarrhea, abdominal cramping, weight loss, anorexia, myalgia, and occasionally vomiting and/or fever.
Prevention: Avoid drinking water from river and lakes without boiling and add water sterilization tablets to the river water before drinking.
Treatment: Seven-day course of oral trimethoprim-sulfamethoxazole.

Cyclospora cayetanensis

Taken from:

• Disease caused by the protozoa, Toxoplasma gondii.
Description: The parasite infects most warm-blooded animals, including humans, but the primary host is the felid (cat) family. The cycle in the cat begins with ingestion of cysts in raw meat, e.g. mice. There is a possibility that T. gondii in the cat’s feces get passed on to intermediate hosts such as pig and lambs grazed in soil contaminated with infected cat feces. Human infection occurs from consuming under-cooked meat from these animals.
Transmission: By the ingestion of raw or partly cooked meat, especially pork, lamb, transmitted by contaminated cat feces, Drinking water contaminated with Toxoplasma gondii.
Clinical signs & Symptoms: Asymptomatic.
Prevention: Ensure that all food are cooked thoroughly and drink treated water.
Treatment: Combination of pyrimethamine and sulfadiazine, trisulfapyrimidines, spiramycin, clindamycin, trimethoprim sulfamethoxazole.

Toxoplasma gondii

Taken from:

• Disease caused by the protozoa, Balantidium coli.
Description: Balantidium coli is a species of ciliate protozoan. Cysts are the infective stage, responsible for transmission of balantidiasis. The host acquires cysts through ingestion of contaminated food or water. After ingestion, excystation occurs in the small intestine, and the trophozoites colonize the large intestine.
Transmission: Occurs through fecal-oral, person-to-person and water transmission. Hosts include pigs, wild boars, rats, primates (including humans), horses. Pigs are the most important reservoir hosts, though they show few symptoms. There is a possibility that the soldiers come into contact with the feces of an infected wild boar in the jungle or drinking of contaminated water.
Clinical signs & Symptoms: Persistent diarrhea, occasionally dysentery, abdominal pain, and weight loss
Prevention: Drink treated water and reduce contact with feces.
Treatment: Tetracycline with iodoquinol and metronidazole as alternatives.

Balantidium coli shown in wet mount

Taken from:


Levinson, W. (2006). Revise of Medical Microbiology and Immunology. USA: The McGraw-Hill Companies.

International Travel and Health. (2005). CHAPTER 5: Infectious Diseases of Potential Risk for Travellers. Retrieved January 19, 2008, from

Centre for Disease Control. (2004). Giardiasis. Retrieved January 19, 2008, from

Centre for Disease Control. (2007). Cryptosporidium Infections. Retrieved January 25, 2008, from

MayoClinic. (2006). Malaria. Retrieved January 25, 2008, from

MicroWorlds. (2001). What is Malaria? Retrieved January 24, 2008, from

K-State. (2007). Cyclospora cayetanensis. Retrieved January 25, 2008, from

Wikipedia. (2008). Toxoplasmosis. Retrieved January 25, 2008, from

Carlo Denegri Foundation. (2008). Balantidium coli. Retrieved January 24, 2008, from

MedicineNet. (2004). Definition of Balantidium. Retrieved January 25, 2008, from

Sodeman, W. J. (2002). Intestinal Protozoa: Amebas. Retrieved January 25, 2008, from

Medical Microbiology Lecture Notes

Done by: Sally and Shu Hui TG02

Sunday, December 9, 2007


Suspected Diagnosis 

Suspected Microorganisms 

Lab Investigations 

Khong Fay Seah 


  • Escherichia coli
  • Staphylococcus saprophyticus
  • Proteus mirabilis
  • Klebsielle pneumoniae
  • Enterobacter
  • Serratia
  • Pseudomonas aeruginosa
  • Morganella morganii
  • Enterococcus faecalis
  • Chlamydiae
  • Gram staining to classify the bacteria into gram-positive and gram-negative groups.
  • Urine culture on blood agar, MacConkey, EMB.
  • Antibiotic Susceptibility Test using ampicillin, cephalosporin, aminoglycosides, trimethoprim-sulfamethoxazole, norfloxacin, novobiocin, cefotaxime etc.
  • Biochemical Tests like TSI, Oxidase, Indole, Catalyse, Coaulase, Methyl Red an Urease etc.

Kwan Siew Yan

Enterocolitis (most likely the bacterial type)

  • Shigella species
  • Enteroinvasive E.Coli (EIEC)
  • Enterohermorrhagic E.coli (EHEC)
  • Salmonella species eg: S. enteritidis, S. typhimurium
  • Campylobacter jejuni
  • Vibro parahaemolyticus
  • Vibro cholerae
  • Clostridium difficile
  • C. perfringens
  • Yersinia species eg: Y. Enterocolitica
  • Bacillus cereus
  • Entamoeba histolytica
  • Stool culture to isolate and identify any parasites or bacteria
  • Microscopy with gram staining
  • Antibody Susceptibility Test
  • Biochemical Test like oxidase, catalase

Maisy Hong


  • Escherichia (E.) coli
  • Staphylococcus saprophyticus
  • Klebsiella
  • Enterococci bacteria
  • Proteus mirabilis
  • ureaplasma urealyticum
  • Mycoplasma hominis
  • Chlamydia
  • Mycoplasma
  • Corynebacterium
  • Pseudomonas aeruginosa
  • Urine culture
  • Antibiotic Susceptibility Test
  • Staining and Microscopy

Tong Wei Hong


  • Respiratory adenovirus
  • Rhinovirus
  • Histoplasma capsulatum
  • Cryptococcus neoformans
  • Pneumocystis jiroveci
  • Mycoplasma pneumoniae
  • Chlamydia pneumoniae
  • Streptococcus pneumoniae
  • Staphylococcus aureus
  • K.pneumoniae
  • P.aeruginosa
  • Haemophilus influenzae
  • Moraxella catarrhalis
  • Culture using chocolate, blood, Mannitol Salt agar etc.
  • Gram staining
  • EIA
  • Antibiotic Susceptibility Test using penicillin, vancomycin, doxycycline etc.
  • Other Biochemical Test like catalase, oxidase etc.

Wong Fei Hong

Wound Infection

  • Staphylococcus aureus
  • Enterococci Escherichia coli
  • Pseudomonas aeruginosa
  • Proteus mirabilis
  • Klebsiella pneumoniae
  • Proteus mirabilis
  • Enteric Gram negative bacilli
  • Beta-hemolytic streptococci
  • Streptococcus milleri
  • Streptococcus pyogenes
  • Gram-negative aerobes
  • Methicillin resistant Staphylococcus aureus
  • Culture of wound using blood agar, BAP, chocolate agar, Xylose Lysine Sodium Deoxycholate (XLD) and MacConkey agar etc.
  • Gram staining and microscopy
  • Biochemical Test like indole, methyl red, cytochrome oxidase, phenylalanine deaminase etc.
  • Others like fungal culture if necessary

Ong Fei Fei

UTI & probably vaginal infection

Causes Vaginal infection:

  • Yeast eg. Candida vulvovaginitis
  • Gardnerella vaginalis, Mobiluncus species, Mycoplasma hominis
  • Trichomonas eg. Trichomonas vaginalis
  • Neisseria Gonorrhoea
  • Chlamydia trachomatis

Causes UTI:

Most Frequent

  • Enterococci
  • Streptococcus agalactae(Group B Streptococcus)
  • Enterobacteriaceae
  • Pseudomonas
  • Streptococcus pyogens(Group A Streptococccus)
  • Streptococcus aureus
  • S.saprophyticus
  • Candida species.

Less frequent

  • Gardenerella vaginalitis
  • Ureaplasma urealyticum
  • Mycoplasma hominis
  • Mobiluncus
  • Leptospira
  • Mycobacterium species
  • Chlamydia trachomatis(males)

Other Associated with multisystem disease

  • Salmonella(with gastroenteritis)
  • Schistosoma haematobium
  • Crytococcus neoformans
  • Trichosporon beigelii
  • Trichomonas vaginalis
  • Aspergillus
  • Penicillium
  • Adenovirus
  • Herpes simplex virus
  • Wet Mount
  • Whiff's Test
  • Chlamydia Rapid Test
  • Gram staining
  • Antibiotic Susceptibility Test using Carbenicillin, Cinoxacin, Lomefloxacin, norfloxacin, or Loracarbef etc.

Learning Issues for this PBL:


  1. Prepare a Gram stain of these organisms.
  2. Study the morphological and staining characteristics.


Procedure for Gram staining:





Colour of Cells 


Crystal violet 

As Primary Stain.


It colours the cytoplasm violet regardless of cell type 

Flood the smear with crystal violet solution for 1 minute

Then rinse with water




As a mordant.


Iodine combines with crystal violet to form an insoluble complex inside the cell.


Complex resists decolourization 

Flood the smear above with iodine solution for 30 seconds.


Then rinse with water 



95% Ethanol 

As a decolourising agent.


The violet dye complex is retained by Gram positive cells, but is readily removed from Gram negative cells. 

Flood the smear with 95% ethanol for a few seconds e.g, until the violet colour disappears.

Then rinse with water. 

Gram positive appear violet, while gram negatives appear colourless


Safranin or Dilute carbol fuchsin 

As a counter stain.


Stain bacterial cells light pink or red.


Gram negatives that have been decolourized will absorb safranin, while Gram positives will not.

Flood the smear above with safranin solution for 1 min.

Then rinse with water and blot dry. 

Gram positives remain violet while Gram negatives appear pink/ red 


  1. Streak the nasal swab for the isolation of Staphylococcus aureus, Streptococcus pyogenes from the normal flora on each of BAP and Chocolate agar plates.
  2. Incubate in CO2 incubator at 37oC for 24 hours.
  3. Study and record the colony characteristics

  • MacConkey agar (MAC) - Klebsiella pneumonia, Escherichia coli

    A selective and differential media used to differentiate between Gram negative bacteria while inhibiting the growth of Gram positive bacteria. The addition of bile salts and crystal violet to the agar inhibits the growth of most Gram positive bacteria, making MacConkey agar selective. Lactose and neutral red are added to differentiate the lactose fermenters, which form pink colonies, from lactose nonfermenters that form clear colonies.

  • Enterococci- Gram-positive cocci

    Enterococci are facultative anaerobic organisms, i.e. they prefer the use of oxygen, but they can survive in the absence of oxygen. They typically exhibit gamma-hemolysis on sheep's blood agar.


  • Pseudomonas aeruginosa is a Gram-negative, aerobic, rod-shaped bacterium

    Pseudomonas aeruginosa bacterial culture on a Xylose Lysine Sodium Deoxycholate (XLD) agar plate.

    The xylose lysine agars were developed for the differentiation of pathogens from non-pathogens and to support the growth of the more fastidious enteric organisms. The basal XL Agar is nutritionally designed to permit the development of all species.

    Xylose Lysine Deoxycholate (XLD) contains deoxycholate as inhibitor of Gram-positive organisms and allows the growth and differentiation of enteric pathogens.

    The Phenol red indicator changes from red to yellow under acid conditions.

    A 0.25 percent concentration of sodium deoxycholate in XLD provides nearly complete inhibition of Gram-positive microorganisms.


  • Proteus mirabilis is a Gram-negative, facultatively anaerobic bacterium

    The micro-organism tests:

  • Indole negative and Nitrogen Reductase positive (no gas bubble produced)
  • Methyl Red positive and Vogues-Proskauer negative
  • Catalase positive and Cytochrome Oxidase negative
  • Phenylalanine Deaminase positive

    A sensitivity test, also called an antibiotic susceptibility test, is also done. The bacteria are tested against different antibiotics to determine which will treat the infection by killing the bacteria.

    • OTHERS:

    If the physician thinks the wound may be infected with a mold or yeast, a fungal culture is also done. The wound sample is spread on special culture plates that are treated to encourage the growth of mold and yeast. Different biochemical tests and stains are used to identify molds and yeast.


    Case 6 (Liu Qian)

    Patient: Ong Fei Fei (37,F)

    Key Points:

    • Complaints of fever, pain during urination and virginal discharge
    • Possible diagnosis: UTI

    Investigation of vaginal discharge in sexually active adult women should involve the collection of both endocervical and high vaginal swabs. Low vaginal swabs are to be avoided as they are likely to be contaminated with perineal/ faecal flora. High vaginal swabs (HVS) should be placed in transport medium to prevent drying and to allow the survival of anaerobes.

    Urinary Tract Infection:

    Urinary tract infection (UTI) is one of the most common sources of infection. It is important as it can cause troublesome and recurrent symptoms and may point to unsuspected anomalies of the urinary tract. Outcome of infection is of concern as it is associated with future complications including poor renal growth, recurrent adult pyelonephritis, impaired glomerular function, early hypertension and end-stage renal disease. The aim of management should be prompt diagnosis, rapid treatment and the detection of any underlying cause that might predispose to further infection or lead to long-term renal damage.

    Urinary tract is made up of two sections: the lower urinary tract and the upper urinary tract. Lower urinary tract contains the bladder and urethra. Upper urinary tract contains two kidneys and the tube that connects them, called the ureters. An infection occurs when bacteria stick to the walls of the urethra, multiplying and moving up the urethra to the bladder. The urethra is the tube that carries urine from the bladder to outside the body. If a lower urinary tract infection is not treated, the infection may spread up through the ureters, and into the kidneys.

    Different types of UTI:

    • Urethritis is an infection or inflammation of the urethra. This can be due to other things besides the organisms usually involved in UTI's. In particular, many sexually transmitted diseases (STD's) appear initially as urethritis.
    • Cystitis is an infection of the bladder and is the most common form of UTI. Cystitis can often occur at the same time as urethritis. It can be aggravated if the bladder does not empty completely when you urinate.
    • Ureteritis is infection of a ureter. This can occur if the bacteria entered the urinary tract from above or if the ureter-to-bladder valves don't work properly and allow urine to "reflux" from the bladder into the ureters.
    • Pyelonephritis is an infection of the kidney. This can happen with infection from above, or if reflux into the ureters is so bad that infected urine refluxes all the way to the kidney. Kidney infections can cause kidney damage or even failure if left untreated for an extended period of time.

    Vaginal discharge:

    The female genital tract has a complex microbial flora. Bacteria commonly present in large numbers include anaerobic streptococci, diphtheroids, coagulase negative staphylococci, and haemolytic streptococci. Other common commensals which can act as pathogens include Candida spp, Staphylococcus aureus, f haemolytic streptococci including Str agalactiae, and Actinomyces spp. In bacterial vaginosis the concentration of Gardnerella vaginalis, increases.

    White: Thick, white discharge is common at the beginning and end of your cycle. Normal white discharge is not accompanied by itching. If itching is present, thick white discharge can indicate a yeast

    Clear and stretchy: This is "fertile" mucous and means you are ovulating.

    Clear and watery: This occurs at different times of your cycle and can be particularly heavy after exercising.

    Yellow or Green: May indicate an infection, especially if thick or clumpy like cottage cheese or has a foul odor.

    Brown: May happen right after periods, and is just "cleaning out" your vagina. Old blood looks brown.

    Spotting Blood/Brown Discharge: This may occur when you are ovulating/mid-cycle. Sometimes early in pregnancy you may have spotting or a brownish discharge at the time your period would normally come. If you have spotting at the time of your normal period rather than your usual amount of flow, and you have had sex without using birth control, you should check a pregnancy test.

    Possible microoragnisms that can cause Vaginal discharge:

    • Yeast, also called Candida, a type of fungi that is part of the normal flora of human skin but can also cause infections.(eg:Candida vulvovaginitis)
    • Bacteria found in the female genital tract that is the cause of bacterial vaginosis.(eg: Gardnerella vaginalis, Mobiluncus species, Mycoplasma hominis)
    • Trichomonas, a type of protozoa, an organism made up of one cell (eg: Trichomonas vaginalis)
    • Neisseria Gonorrhoea
    • Chlamydia trachomatis

    Possible microoragnisms that can cause UTI:

    Most Frequent

    • Enterococci
    • Streptococcus agalactae(Group B Streptococcus)
    • Enterobacteriaceae
    • Pseudomonas
    • Streptococcus pyogens(Group A Streptococccus)
    • Streptococcus aureus
    • S.saprophyticus
    • Candida species.

    Less frequent

    • Gardenerella vaginalitis
    • Ureaplasma urealyticum
    • Mycoplasma hominis
    • Mobiluncus
    • Leptospira
    • Mycobacterium species
    • Chlamydia trachomatis(males)

    Other Associated with multisystem disease

    • Salmonella(with gastroenteritis)
    • Schistosoma haematobium
    • Crytococcus neoformans
    • Trichosporon beigelii
    • Trichomonas vaginalis
    • Aspergillus
    • Penicillium
    • Adenovirus
    • Herpes simplex virus

    Diagnosis Plan:

    Fever and pain during urination are the symptoms of Urinary Tract Infection. Virginal discharge is normally present. But a change in color or amount of discharge, accompanied by other symptoms, may indicate that you have an infection. So I suspect that the bacteria go from vaginal to the urethra and cause Urinary infection.


    Vaginal swabs were cultured both anaerobically and aerobically on the surface of freshly prepared brain heart infusion agar plate supplemented with vitamin K (0.5 mg/l) and Haemin (5mg/l), blood agar and chocolate agar plates. Additional Bacteroides Bile Esculin agar, Neomycin Vancomycin Chocolate agar plates were inoculated for anaerobic culture. Agar plates were examined after 48 hrs, 96 hrs and 7days and isolates were identified.

    To confirm Vaginitis, vaginial fluid pH, wet mount preparation, ad KOH microsopy should be done. The interpretation can follow Figure 1.

    Possible microoragnisms that can cause Vaginal discharge:

    Laboratory investigation 


    Yeast, also called Candida, a type of fungi that is part of the normal flora of human skin but can also cause infections.(eg:Candida vulvovaginitis)

    Examine the KOH preparation under the microscope ("Wet Mount"). Multiple strands of thread-like hyphae confirm the presence of yeast.

    Whiff" test : Positive



    Bacteria found in the female genital tract that is the cause of bacterial vaginosis.(eg: Gardnerella vaginalis, Mobiluncus species, Mycoplasma hominis)

    1. Test the pH. If >5.0, this suggests Gardnerella.
    2. Mix one drop of KOH with some of the discharge on a microscope slide. The release of a bad-smelling odor confirms Gardnerella.
    3. Vaginal epithelial cells studded with coccoid bacteria are "clue cells" signifying Gardnerella.
    4. Whiff" test : Negative

    Trichomonas, a type of protozoa, an organism made up of one cell (eg: Trichomonas vaginalis)

    Mix one drop of saline with some discharge ("Wet Mount"). Under the microscope, large (bigger than WBCs), moving micro-organisms with four flagella are trichomonads.

    Whiff" test : can be positive

    Additional test: DNA probe tests and Culture


    Neisseria Gonorrhoea

    N. Gonorrhoea should begin with a Gram stain. If intracellular gram-negative diplococci are present, N. Gonorrhoea infection is presumed and treatment should be initiated. Gonococcal cultures should confirm the diagnosis. It was inoculated onto modified Thayer-Martin medium.Cultures were examined following overnight incubation, and if they were negative on initial evaluation, they were examined again following an additional 24 and 48 h of incubation. Typical colonies containing gram-negative diplococci and giving a positive oxidase reaction were presumptively identified as N. gonorrhoeae.
    The identities of presumptive N. gonorrhoeae colonies were then con- firmed with fluorescein-conjugated monoclonal antibodies.


    Chlamydia trachomatis

    Chlamydia Rapid Test(commercial kit)


    Figure1: Possible microoragnisms that can cause Vaginal discharge and and Laboratory investigation respectively.


    If vaginitis is not confirmed, urine sample must be asked for further investigation.

    Urine culture is the most straightforward and simplest method to diagnosis urinary tract infection. Urine was cultures in both Blood agar and Macconkey agar. It was "dogma" that a finding of 105 colony-forming units per ml (CFU/ml) or more was "positive". In addition, urine microscopy must be done to quantify the WBC.

    Gram stain should be performed for the positive cultures to determine the Gram nature and morphology of the Bacteria. (eg: Gram positive Bacilli)

    To identify the type of bacteria, colonies are isolated from the plate and enzyme tests are done.


    After all, the antiicobial susceptibility test should be done to guide the treatment.

    Antimicobials usually tested for UTI

    • Enterobacteriaceae
      • Carbenicillin
      • Cinoxacin
      • Lomefloxacin,norfloxacin, or ofloxacin
      • Loracarbef
      • Nitrofurantoin
      • Sulfisoxazole
      • Trimethoprim
    • Pseudomonas aeruginosa and other non-enterobacteraceae
      • Carbenicillin
      • Ceftizoxine
      • Tetracycline
      • Lomefloxacin, norfloxacin, or ofloxacin
      • Sulfisoxazole
    • Staphylococci
      • Lomefloxacin, norfloxacin, or ofloxacin
      • Nitrofurantoin
      • Sulfisoxazole
      • Trimethoprim
    • Enterococci
      • Ciprofloxacin
      • Norfloxacin
      • Nitrofurantoin
      • Tetracycline
    • Streptococci
      • Norfloxacin
      • Nitrofurantoin