Micro Assignment 4 Anaerobes

Define the following terms

Obligate anaerobes – Obligate anaerobes are microorganisms that can only grow in the absence of oxygen. They lack the enzymes necessary to detoxify reactive oxygen species (ROS) generated during aerobic respiration, and exposure to oxygen can be toxic or lethal to them. Obligate anaerobes obtain energy by using alternative electron acceptors such as nitrate, sulfate, or carbon dioxide in anaerobic respiration, or by carrying out fermentation. They are often found in environments with low or no oxygen, such as deep soil, sediment, waterlogged areas, and the gastrointestinal tract of animals. Examples of obligate anaerobes include Clostridium species, Bacteroides species, and Peptostreptococcus species.

Facultative anaerobes – Facultative anaerobes are microorganisms that can survive and grow in both the presence and absence of oxygen. They have the ability to switch between aerobic respiration, which uses oxygen as an electron acceptor to generate energy, and anaerobic respiration or fermentation, which uses alternative electron acceptors in the absence of oxygen. In the presence of oxygen, facultative anaerobes use aerobic respiration to generate more ATP (energy) than anaerobic respiration or fermentation. However, when oxygen is limited or absent, they can switch to anaerobic respiration or fermentation to continue generating energy. Facultative anaerobes are found in a variety of environments, including soil, water, and the gastrointestinal tract of animals. Examples of facultative anaerobes include Escherichia coli, Salmonella species, and Staphylococcus aureus.

Microaerophilic –

Microaerophilic organisms are microorganisms that require low levels of oxygen to grow and survive. They are adapted to environments with low oxygen levels, typically ranging from 2-10% oxygen concentration. Microaerophiles are not able to survive in the absence of oxygen, but high levels of oxygen are toxic to them. They are often found in environments such as the gastrointestinal tract of animals, waterlogged soil, and aquatic habitats.

Microaerophilic bacteria use different strategies to cope with the low oxygen concentration in their environment, such as producing superoxide dismutase (SOD) and catalase enzymes to detoxify reactive oxygen species (ROS), and having special respiratory mechanisms to enable them to use oxygen efficiently. Examples of microaerophilic bacteria include Helicobacter pylori, Campylobacter jejuni, and Brucella species.

Polymicrobic – Polymicrobial refers to the presence of multiple different types of microorganisms in a particular environment or infection site. Polymicrobial infections can involve bacteria, viruses, fungi, or parasites, and they are often more complex and difficult to treat than infections caused by a single organism. Polymicrobial infections can arise when multiple microorganisms colonize the same niche and interact with each other, either cooperatively or competitively, to establish a stable community. For example, dental plaque is a polymicrobial community composed of multiple species of bacteria that interact with each other to form a biofilm on the surface of teeth. Similarly, chronic wounds and infections, such as diabetic foot ulcers, may be polymicrobial and involve a mixture of aerobic and anaerobic bacteria. Effective treatment of polymicrobial infections requires careful identification of the different microorganisms involved, as well as an understanding of their interactions and antibiotic susceptibility profiles.

Briefly discuss specimen collection guidelines for anaerobes, including what to avoid or reject:

Review media used for anaerobic culture and fill in the table below.

What are the optimal environmental conditions to grow anaerobes? Give ONE example of an anaerobic incubation system.

Anaerobic Gram-Negative Bacilli

Bacteroides fragilis

Clinical significance:

B. fragilis is the only anaerobe that is Indole ________________ and Bile Esculin ___________________.

Colonies appear _______________ on BBE agar.

Prevotella sp.

Prevotella sp. are normal flora of the _______________ and _______________.  However, it is a cause of ____________________ infections.

Colonies fluoresce ___________________ when seen under UV light. 

So do colonies of ______________________.  Which is ___________________ and cannot ferment carbohydrates (including glucose).  This is one way to tell these organisms apart.

Fusobacterium sp.

Gram stain _________________________

F. nucleatum most often associated with these types of infections: ______________________________

F. necrophorum most often associated with these types of infections: ____________________________

Fill in the results below to help differentiate F. nucleatum from F. necrophorum.

Anaerobic Gram-Positive Spore Formers (Clostridium sp)

Gram stain _____________________

Catalase _______________________

Produce true ______________________ (virulence factor)

Clostridium tetani Spore location _______________

Clinical significance:

Clostridium botulinum Spore location _______________

Clinical significance:

Clostridium perfringens Spore location _______________

Clinical significance:

Clostridium difficile Spore location _______________

Clinical significance:

Produces Toxin A, and ______________ and Toxin B a _______________.  These can be easily detected by ________________________, ________________________, and ________________________.

Anaerobic Gram-Positive Non-Spore Formers

Actinomyces israelii causes __________________ and resembles a _______________ on agar.

Bifidobacterium is normal flora of the _________________ and _______________.

Propionibacterium acnes is often found as a ____________________ in blood culture specimens.

Anaerobic Gram-Positive Cocci

Peptostreptococcus anaerobius

Clinical significance:

Anaerobic Gram-Negative Cocci

Includes the following genera:

V_________________

M_________________

A__________________

A__________________

N__________________

True or False:  These organisms are highly pathogenic and often isolated.

Mycobacterium

Mycobacterium are considered acid fast bacilli.  What does this mean?

Compare and contrast carbolfuchsin stain (with methods) and fluorochrome stains.  Which is better?  Why don’t we use it more often?

What is the preferred (most common) specimen type? And what is not recommended?

Mycobacterium specimens must be processed.  Briefly state the purpose of each step and any reagents needed.

1. Decontamination

• Digestion

• Centrifugation

Mycobacterium growth requirements:

               Lowenstein-Jensen media

               Middlebrook media

               Which species or group of species grow at the following temperatures?

                              30°C- 32°C   ____________________    ____________________

                              35°C – 37°C  _______________________

                              42°C – 45°C  _____________________

Mycobacterium tuberculosis

Causes_______________

People become infected when______________________________________________________

Why is treatment difficult?

Define the following terms and list one or two species that fall into these categories:

Nonchromogen

Photochromogen

Scotochromogen

The Mycobacterium avium-intracellulare complex is an ___________ pathogen, especially in those individuals with __________________.

Chlamydia, Mycoplasma, and Rickettsia

Chlamydiaceae

Chlamydiaceae are _____________________________ parasites.

Chlamydia trachomatis

Briefly discuss clinical significance (The PowerPoint may be more useful than the book for a summary. And no, you do not need to memorize the biovars, serovars, or serotypes):

Why are serological tests limiting?

Chlamydiophila psittaci causes _____________________

Define ornithosis:

Mycoplasma

Mycoplasma are the _____________________________ and do not have a _______________________.

Mycoplasma pneumoniae causes _____________________________ or more commonly called _____________________________.   Patients who have recovered may have non-specific _______ type antibodies which we refer to as cold ______________________.

Rickettsiaceae

Rickettsia rickettsii causes _____________________   Vectors: ______________ and _______________

Rickettsia akari causes _______________________  Vector: ___________________

Rickettsia prowazekii causes ____________________________  Vector: ___________________

AND causes ____________________________  Vector: ___________________

Rickettsia typhi causes__________________  Vector: ___________________

Coxiella burnetii causes __________________

Spirochetes

General Characteristics of Spirochetes

Shape and motility: distinctive helical or spiral shape, and they are highly motile

Spirochetes are gram-negative.  True or False

Why?

True. Spirochetes are gram-negative bacteria because they have a thin peptidoglycan layer in their cell wall, which is surrounded by an outer membrane containing lipopolysaccharides (LPS). When stained with Gram stain, the thin peptidoglycan layer does not retain the crystal violet stain, and as a result, they appear as red or pink under the microscope, indicating that they are gram-negative. Spirochetes have a distinctive helical or spiral shape, and they are highly motile due to the presence of endoflagella (also called axial filaments) that run along the length of the bacteria and allow them to move in a corkscrew-like motion.

Borrelia recurrentis

Causes louse-borne relapsing fever (LBRF).

Vector Pediculus humanus

Laboratory detection is performed using _________________ stained with _______________________.  They will appear ____________ color on the slide.

Borrelia recurrentis laboratory detection is performed using blood smears stained with Giemsa stain. The bacteria will appear as long, slender spirochetes with tightly coiled spirals, and will be a reddish-purple color on the slide.

Borrelia recurrentis causes a disease called louse-borne relapsing fever (LBRF). LBRF is characterized by a rash called erythema migrans.

The vector (genus) that transmits Borrelia recurrentis is Pediculus humanus, commonly known as the human body louse.

Various methods are used for the detection of Borrelia recurrentis. These include microscopic examination of blood smears, polymerase chain reaction (PCR), and serological tests such as enzyme-linked immunosorbent assay (ELISA) and immunofluorescence assay (IFA).

The gold standard for the detection of Borrelia recurrentis is microscopic examination of Giemsa-stained blood smears. However, PCR has higher sensitivity and specificity and is increasingly being used for diagnosis

Borrelia burgdorferi

Causes  ___Lyme disease____  Which is characterized by a rash called ________erythema migrans____.

Vector (genus)  ___Ixodes____

_Diagnostic_ methods are used for detection.  These include serological tests, polymerase chain reaction (PCR), and culture.

The gold standard for detection is _a two-tiered serological testing approach, which involves an initial enzyme immunoassay (EIA) followed by a Western blot test.

Borrelia burgdorferi causes Lyme disease, which is characterized by a rash called erythema migrans. The vector genus responsible for transmitting the bacteria is Ixodes. Diagnostic methods used for detection of Lyme disease include serological tests, polymerase chain reaction (PCR), and culture. The gold standard for detection is currently a two-tiered serological testing approach, which involves an initial enzyme immunoassay (EIA) followed by a Western blot test.

What is meant by two-tier testing?

Two-tier testing refers to a diagnostic testing approach used for the detection of Lyme disease, another bacterial infection caused by the spirochete Borrelia burgdorferi.

The two-tier test begins with a screening test called an enzyme immunoassay (EIA) or an indirect fluorescent antibody (IFA) test. If the result of the screening test is positive or indeterminate, a confirmatory test called a Western blot is performed to confirm the presence of specific antibodies to Borrelia burgdorferi.

The use of two tests improves the accuracy of the diagnosis of Lyme disease, as it reduces the likelihood of false positives that can occur with the use of a single test. However, two-tier testing may miss some cases of Lyme disease, particularly in the early stages of the infection.

It’s worth noting that two-tier testing is a specific approach used for the diagnosis of Lyme disease, and may not be applicable to other infections or diseases.

Source: Centers for Disease Control and Prevention. (2022). Lyme Disease Diagnosis. Retrieved from https://www.cdc.gov/lyme/diagnosistesting/index.html.

Treponema pallidum subspecies pallidum

Causes  ___syphilis___

Treponema pallidum subspecies pallidum causes syphilis, a sexually transmitted infection that can also be transmitted from mother to fetus during pregnancy. Syphilis can progress through several stages if left untreated, including primary syphilis, secondary syphilis, latent syphilis, and tertiary syphilis. The disease can cause a wide range of symptoms, from mild to severe, and can affect multiple organs, including the brain, heart, and nervous system.

Syphilis can be treated with antibiotics, and early diagnosis and treatment are important to prevent the progression of the disease and its complications.

Source: Centers for Disease Control and Prevention. (2022). Syphilis – CDC Fact Sheet (Detailed). Retrieved from https://www.cdc.gov/std/syphilis/stdfact-syphilis-detailed.htm.

Very briefly indicate what happens in each of the stages of syphilis:

Primary – Characterized by the appearance of a painless, firm, and round sore (called a chancre) at the site of infection, usually the genitals, anus, or mouth. The sore typically heals on its own within a few weeks.

Secondary – Occurs several weeks after the initial infection and is marked by a widespread rash that may appear on the trunk, limbs, palms, and soles of the feet. Other symptoms may include fever, swollen lymph nodes, sore throat, and patchy hair loss.

Tertiary (late) – A period of asymptomatic infection that can last for years. During this time, the bacteria are still present in the body and can be transmitted to others.

Latent – Occurs in a small percentage of untreated individuals and can lead to serious complications, such as cardiovascular syphilis, neurosyphilis, and gummatous syphilis.

Congenital -Occurs when a pregnant woman with syphilis passes the infection to her fetus during pregnancy. Congenital syphilis can cause serious health problems for the baby, including stillbirth, prematurity, low birth weight, and congenital abnormalities

Discuss the non-treponemal test for T. pallidum:

The non-treponemal test is a type of blood test used to detect the presence of antibodies against T. pallidum, the bacterium responsible for causing syphilis. This test is commonly used as a screening tool for syphilis and is often followed up with a confirmatory treponemal test if the non-treponemal test is positive.

The most commonly used non-treponemal tests are the Venereal Disease Research Laboratory (VDRL) test and the Rapid Plasma Reagin (RPR) test. Both tests work by detecting antibodies produced by the body in response to an infection with T. pallidum. The VDRL test and RPR test are similar in how they work, but the RPR test is often preferred because it is more sensitive and easier to use.

One limitation of the non-treponemal test is that it can produce false-positive results in certain situations. For example, people with autoimmune diseases or certain viral infections may produce antibodies that cross-react with the test and cause a false positive result. Therefore, a positive non-treponemal test should always be confirmed with a treponemal test, which is more specific to T. pallidum

Very briefly discuss the treponemal tests for T. pallidum and compare/contrast to the non-treponemal:

Treponemal tests are another type of blood test used to detect antibodies against T. pallidum. These tests detect antibodies that are specifically produced in response to the bacterium, unlike the non-treponemal tests that detect a broader range of antibodies.

Examples of treponemal tests include the Fluorescent Treponemal Antibody Absorption (FTA-ABS) test and the Treponema pallidum Particle Agglutination (TPPA) test. Treponemal tests are highly specific to T. pallidum and are used to confirm a positive non-treponemal test result.

However, treponemal tests have some limitations. They cannot distinguish between past and current infections, and a positive result may persist for years even after the infection has been treated. In addition, some people who have been vaccinated for syphilis may have positive treponemal test results.

In summary, treponemal tests are highly specific to T. pallidum, but they cannot distinguish between past and current infections and may produce false-positive results in certain situations. They are often used to confirm a positive non-treponemal test result.

T. pallidum subspecies pertenue causes ______yaws_______________

T. pallidum subspecies pertenue causes yaws, which is a tropical disease that affects the skin, bones, and joints. Yaws is a chronic infectious disease caused by the bacterium T. pallidum subspecies pertenue, which is transmitted through direct skin-to-skin contact with an infected person. It primarily affects children living in impoverished, tropical areas with poor sanitation and hygiene. Yaws causes skin lesions and bone deformities, which can lead to disability if left untreated.

T. pallidum subspecies endemicum causes ____bejel________

T. pallidum subspecies endemicum causes bejel, which is a chronic skin and bone disease that affects mainly children and young adults in arid and semi-arid regions.

Bejel is a chronic disease caused by T. pallidum subspecies endemicum, which is transmitted through close personal contact, such as sharing utensils or mouth-to-mouth contact. The disease primarily affects children and young adults living in arid and semi-arid regions with poor sanitation and hygiene. Bejel causes skin lesions, gummatous ulceration, and bone deformities, which can lead to disability if left untreated.

Source: T. pallidum, Subspecies Endemicum (Bejel) – Infectious Diseases – MSD Manual Professional Edition. (2022). Retrieved from https://www.msdmanuals.com/professional/infectious-diseases/spirochetes/t-pallidum-subspecies-endemicum-bejel

T. carateum causes ______pinta___________

T. carateum causes pinta, which is a chronic skin disease that mainly affects the poor and rural populations of Central and South America. Pinta is caused by T. carateum, which is transmitted through direct skin-to-skin contact with an infected person or through contact with contaminated fomites. The disease primarily affects the skin, causing hypopigmented or hyperpigmented lesions that can become scaly or crusted. Pinta is usually not life-threatening, but it can lead to social stigma and psychological distress if left untreated.

Source: Centers for Disease Control and Prevention. (2020). Pinta. Retrieved from https://www.cdc.gov/pinta/index.html.

Leptospira sp.

Leptospira sp. is a genus of bacteria that can cause leptospirosis, a disease that affects humans and animals worldwide.

Leptospirosis is a zoonotic disease that is primarily transmitted through contact with the urine of infected animals, particularly rats and other rodents. The disease can cause a wide range of symptoms, from mild flu-like illness to severe manifestations, such as liver and kidney failure. Leptospirosis can also lead to long-term health problems, such as kidney and liver damage, if left untreated.

Prevention of leptospirosis includes avoiding contact with contaminated water or soil, wearing protective clothing and footwear in high-risk areas, and implementing rodent control measures.

Source: World Health Organization. (2022). Leptospirosis. Retrieved from https://www.who.int/news-room/fact-sheets/detail/leptospirosis.

What species is a human pathogen? ______________________  It causes ­­­­­­­__________________ and the severe form is called _____________________________.

Treponema pallidum is a human pathogen. It causes syphilis, which is a sexually transmitted infection that can also be transmitted from mother to fetus during pregnancy.

Syphilis can progress through several stages if left untreated, with the most severe form known as tertiary syphilis, which can affect multiple organs and cause significant morbidity and mortality.

Source: Centers for Disease Control and Prevention. (2022). Syphilis – CDC Fact Sheet (Detailed). Retrieved from https://www.cdc.gov/std/syphilis/stdfact-syphilis-detailed.htm.