Use of Selective and Differential Media

There are many different types of media that are used in a microbiology laboratory. Generally speaking there are three types of media used; selective, differential, and supportive or nutritive.

Selective media are manufactured to support the growth of one type of microorganism while inhibiting the growth of another, in other words, it selectively grows one type of microorganism. It is not uncommon or this media to contain antimicrobials, dyes such as crystal violet, or even alcohol. Some of the more routine selective media types are EMB agar, mannitol salt agar, MAC, and a PEA agar.

Differential media is used to distinguish microorganisms from one another based on growth characteristics that are evident when growth is obtained. There are visible differences between microorganisms when growth is achieved. One fo the more common differential media used is the MacConkey agar. This differentiates between lactose fermenters and non-lactose fermenters.

Supportive media is used to support the growth of a wide range of microorganisms. They are typically non-selective because they want to achieve growth of a wide array of microorganisms. Some more common ones include the sheeps blood agar, as well as the chocolate agar. It has the added X and V factors to support the growth of Haemophilus influenzae.


Overview of the Immune System; Part One

The overall function of the immune system is to prevent or limit infection. It is essential for survival. Multiple organ systems, cells, and proteins are involved in the immune response. It is the most complex system that the human body has. The immune system is differentiated into two directions. Innate or non-specific immunity or Acquired (specific) immunity.

The Innate immune system consists of many components. The skin acts as a mechanical barrier and is typically the first line of defense against foreign substances. Mucous membranes consist of the bodies normal microbiota which compete with invading microbes. The mucous membranes are also lined with mucous and cilia which act in an elevator type motion to push foreign substances away. Physiological barriers such as temperature, pH and the complement system. The more acidic environment that a lower pH offers disrupts bacterial growth. Antimicrobial proteins and peptides are present in different epithelial locations in the body. Lysozymes are present in the tears and saliva and cleave the peptidoglycan cell wall present in bacteria. Secretory phospholipase A2 is present in the gut and can enter the bacterial cell and hydrolyze lipids in the cell membrane. Lectins target gram positive bacteria and forms pores in the membranes. Defensins integrate into the lipid and form pores which causes loss of membrane integrity. These defensins are present in PMNs (neutrophils) and lamellar bodies in the gut. Cathelicidins are present in neutrophils and macrophages in the lungs and intestines and distrupt membranes. Histatins are constitutively produced by the glands in the oral cavity and are active against pathogenic fungi.  Inflammation plays a huge role in the Innate immune system. Inflammation induces vasodilation and increase in capillary permeability causing an influx of immune cells like PMNs and macrophages. Inflammation can be observed by the four cardinal signs; rumor (redness), tumor (swelling), color (heat), and dolor (pain). The innate immune response is a rapid response.

Innate Immunity

The complement system recognizes features of microbial surfaces and marks them for destruction by coating them with C3b. There are three distinct pathways; the classical pathway, the lectin pathway, and the alternative pathway. All pathways generate a C3 convertase which cleaves C3, leaving C3b bound to the microbial surface and releasing C3a. In the classical pathway the activated C1s cleaves C4 to C4a and C4b which binds to the microbial surface. C4b then binds C2, which is cleaved by C1s to C2a and C2b forming the C4b2b complex. C4b2b on the microbial surface is an active C3 convertase which cleaves C3 to C3a and C3b. This results in opsonization of the bacterial surface by C3b. The C4b2b3b complex is an active C5 convertase leading to the development of the membrane-attack complex. Each complement component (C4a/b, C2a/b, C3a/b) have different functions, but that is another discussion for another time. The lectin pathway of complement activation is when mannose-binding lectin (MBL) and ficolins recognize and bind to carbohydrates on the pathogen surface. Ficolins are similar to MBLs, but have a different carbohydrate binding domain. MBLs bind with high affinity to mannose and fucose residues. Conversely ficolins bind oligosaccharides containing acetylated sugars. When MBL binds to a pathogen surface MBL-associated serine protease (MASP)-2 is activated and cleaves C4 and C2 similar to the classical pathway. The alternative pathway is an amplification loop for C3b formation that is accelerated by properdin (factor P) in the presence of pathogens. Properdin stabilizes the C3bBb complex. C3 undergoes spontaneous hydrolysis to C3(H20) which binds to factor B, allowing it to be cleaved by factor D into Ba and Bb. The C3(H20)Bb complex is essentially a C3 convertase which cleaves more C3 into C3a and C3b. C3b molecules result in opsonization of bacterial surfaces. Its important to recognize that all pathways lead to generation of a C5 convertase. C4b2a4b in the classical pathway, C4b2a3b in the lectin pathway, and C3b2Bb in the alternative pathway. C5 is cleaved into C5a/b that initiates the assembly of the terminal complement components. These are the terminal complement components that form the membrane-attack complex.


The membrane attack complex consists of an assembly of C6, C7, and C8. This complex undergoes a conformational change that results in polymerization of C9 which generates a large pore in the cell membrane. Host cells contain CD59 which prevents the assembly of the C9 molecules preventing the formation of the membrane-attack complex.

C3a, C4a, and C5a are unique in that these complement components are called anaphylatoxics. They initiate a local inflammatory response when systemic injection of these molecules occurs. They induce smooth muscle cell contraction and increased vascular permeability. They induce adhesion molecules and activate mast cells that invade and populate submucosal tissues to release inflammatory mediators such as histamine and TNF-a.

The Acquired or adaptive immune system is all about specificity. The Humoral branch of the acquired immune system is executed by the B lymphocytes that produce antibodies to specific antigens. The cell-mediated branch consists of antigen presenting cells (APC) such as the dendritic cells processing foreign substances and presenting proteins of those substances as antigens through the major histocompatibility complex (MHC) to CD8 T lymphocytes. These are cytotoxic T-cells that kill these foreign antigens. The acquired immune response is a slow response because it takes the body time to produce antibodies. An important aspect of the adaptive response is memory. Once antibodies have been produced to an antigen, these responses last and the time it takes to produce an antibody on subsequent exposures is rapidly decreased.

These two different systems work in conjunction to produce an adequate and sustained response. When foreign antigens are processed and expressed on the surface of APCs as MHC peptides, pro-inflammatory cytokines such as IL-12p70, IL-18, and IFN-a are secreted. These attract NK cells which primarily attack viruses as well as PMNs and macrophages that phagocytize these antigen peptides to destroy them. Adaptive immunity is also started with dendritic cells that also undergo antigen uptake and processing. This is also called the maturation signal. This signal is augmented by IFN-y and TNF-a secreted by macrophages and NK cells. These dendritic cells either present the antigen to B lymphocytes which are the antibody producers or they present the antigen to CD4/CD8 T-cell lymphocytes.

There are multiple classes of antibodies. IgD is typically expressed on B-cell lymphocytes during differentiation with IgM. IgD is also present in the serum in low concentrations. IgM is a pentamer and the largest immunoglobulin. It is the first antibody that is produced in the immune response. IgA is in high concentration in the mucosal linings, saliva, and tears. Typically part of first line defenses. IgG is present in high concentrations in the serum. IgG is unique in that it can cross the placenta. IgE is involved in allergic reactions. It binds to mast cells and basophils causing degranulation.


Streptococcus Identification and Work Up

Streptococcus is a genus of coccus gram positive bacteria. They typically grow in chains of pairs as cell division occurs along a single axis in this family of bacteria. Most species in the streptococcus genus are oxidase negative, catalase negative, and most are facultative anaerobes. Many streptococcal species are not intact pathogenic and are part of the commensal human microbiota of the skin, mouth, intestine and upper respiratory tract. However, certain streptococcus species are the pathogenic agent for many cases of pink eye, meningitis, bacterial pneumonia, endocarditis, erysipelas, and necrotizing fasciitis.


Species of Streptococcus are classified based on their hemolytic properties. Alpha-hemolytic species cause oxidation of the iron within the red cells, giving a greenish color to appear on the blood agar. The bacteria produces hydrogen peroxide which oxidizes the hemoglobin to biliverdin. This is also referred to as incomplete hemolysis or partial hemolysis. Beta-hemolytic streptococci cause complete degradation of the red cells, appearing as wide clear areas surrounding the bacterial colonies. Gamma-hemolytic species cause no hemolysis.

The beta-hemolytic species are further classified by the Lancefield grouping. This is a serotype classification that describes the specific carbohydrate present on the bacterial cell wall. There are serotypes for Lancefield groups A-V. For times sake, the only ones that will be discussed are Group A, and Group B.

Alpha-Hemolytic Strep

Strep pneumoniae, often referred to as pneumococcus is the leading cause of bacterial pneumonia. It can also be the etiological agent for otitis media, sinusitis, meningitis and peritonitis. The viridian’s group of alpha-hemolytic streptococci are a large group of commensal organisms. They possess no Lancefield antigens (carbohydrates) and can or can not be hemolytic.


Beta-Hemolytic Strep

Streptolysin which is an exotoxin is the enzyme produced by the strep species that causes complete hemolysis of the red cells in the media. There are two types of streptolysin; Streptolysin O (SLO) and Streptolysin S (SLS). Streptolysin O is an oxygen-sensitive (labile) cytotoxin which is secreted by most of the Group A Streptococcus (GAS) which interacts with cholesterol in the membrane of the red cells. Streptolysin S is an oxygen-stable cytotoxin also produced by GAS species that affects the innate immune system of the host. It works in preventing the host immune system from clearing the infection.


Group A Strep

Group A strep, otherwise known as S. pyogenes is the causative agent for strep infections, invasive and non-invasive. The most common infection is pharyngitis, otherwise known as strep throat, impetigo, and scarlet fever. All these infections are non-invasive. Invasive GAS infections include necrotizing fasciitis, pneumonia, and bacteremia (bacteria present in the blood). Complications can arise from GAS infections. Rheumatic fever is a disease that affects the joints, kidneys, and the heart valves. It is the consequence of an untreated strep A infection. Antibodies created by the immune system cross-react with proteins in the body which causes an immune-mediated attack on the hosts own cells. Essentially an acquired auto-immune disease. GAS is also implicated in pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS). Autoimmune antibodies affect the basal ganglia causing rapid onset of psychiatric, motor, sleep and other neurological symptoms, primarily in the pediatric population.

GAS is diagnosed by either an rapid strep test or by culture.

Group B Strep

GBS, otherwise known as S. agalactiae, causes pneumonia and more importantly meningitis in neonates and the elderly. The American Congress of Obstetricians and Gynecologists now recommends that all women between 35 and 37 weeks gestation to be tested for group B strep. Those who test positive should be given prophylactic antibiotics during labor. The bacteria can cause premature rupture of the membranes during pregnancy and can colonize and cross the placenta to infect the fetus.

Laboratory diagnosis and Workup

After initial culture and preliminary identification of beta-hemolytic streptococcus is suspected there are further identification tests to make an accurate diagnosis. The first is by Lancefield antigen determination. Commercially available Lancefield antisera is used for the differentiation of beta-hemolytic species. These usually come as small kits and are directed to Lancefield groups A, B, C, F, and G. Antigen detection is demonstrated by agglutination by specific antibodies that are provided.

The PYR test is a rapid colormetric method most often used to distinguish S. pyogenes from other beta-hemolytic species. The PYR tests for the presence of the enzyme pyrrolidonyl aminopeptidase. This enzyme hydrolyzes L-pyrrolidonyl-b-naphthylamide (PYR) to B-naphthylamide, which produces a red color when a specific reagent is added. The test can be performed on paper strips that contain dried chromogenic substrates for the pyrrolidonyl aminopeptidase. S. pyogenes is PYR positive and in the case of an unknown organism displaying S. pyogenes morphology plus being PYR positive, it is acceptable to presumptively identify as S. pyogenes.

Bacitracin susceptibility is another test that can be used to differentiate S. pyogenes from other beta-hemolytic strep species. S. pyogenes has an increased susceptibility to bacitracin. A pure culture must be obtained and streaked on a sheep blood agar plate. A small disk containing 0.04 U of bacitracin is placed on the plate and incubated overnight at 35 degrees celsius in 5% CO2. A zone of inhibition surrounding the disk indicates susceptibility.

With the introduction and advancement of nucleic acid detection and serological methods in the laboratory it is now getting easier and faster to detect strep species without relying on culturing and further confirmation testing. It should be important to note that this does not replace the use of a culture or any of the further testing mentioned above. Serological testing relies on antibodies to anti-streptolysin O and anti-DNase B. The antibody levels against streptolysin O rise within one week of infection and peak around 3-6 weeks. DNase B is a nuclease among many that S. pyogenes uses to escape neutrophil extracellular nets. DNase B is specific for S. pyogenes. The antibody levels to DNase B rise post two weeks infection and reach maximum titers at around 6-8 weeks.

The Optochin test is used to differentiate alpha-hemolytic streptococci. This is either S. pneumoniae or strep viridians. S. pneumoniae species are sensitive to the chemical ethylhydrocupreine hydrochloride, otherwise known as optochin. Optochin disks, sometimes called P disks can be obtained from a commercial vendor. A pure culture is obtain and incubated to allow growth overnight. When growth has occurred, a subculture is plated and a P disk is placed on the agar and incubated overnight at 35 degrees celsius with 5% CO2. The zone of inhibition is then measured and a zone greater than 14 mm indicates sensitivity and allows for the presumptive diagnosis of pneumococci.

The bile solubility test is usually used as confirmatory test for S. pneumoniae that distinguishes it from other alpha-hemolytic species. Sodium deoxycholate (Bile) will lyse the cell wall of pneumococcal species.



A urinalysis is exactly what the name entails. An analysis of a patients urine. A urinalysis is a fairly common test that may be ordered as part of an annual physical or part of diagnostic testing. It can be used as an evaluation of UTIs, Diabetes Mellitus, kidney disease, kidney stones, proteinuria, rhabdomyolysis, liver disease, or if a patient presents with particular symptoms such as abdominal pain, flank pain, painful urination, blood upon urination, and fever. Pregnancy testing is also part of a routine urinalysis if ordered.

The first step in an urinalysis is collection of the specimen from the patient. An optimal sample is an early morning sample, as it is the most concentrated produced during the day. There are no fasting requirements or medication schedule dosage changes unless otherwise directed by the patients ordering physician. 30-60 mL of urine is collected in a clean urine specimen cup through a clean catch method that should be explained to the patient upon request of sample.

There are different variants of urinalysis. One is the macroscopic observation of the urine. This is the direct visual observation which includes noting its quantity, clarity, and color. Urine is normally yellow and clear without any cloudiness. Abnormalities can mean different things and further analysis is needed.

Cloudy: Infection

Dark Yellow: Dehydration

Brown: Liver disease (caused by an accumulation of bilirubin)

Red: Blood (Indicates UTI, stones, tumors, renal trauma)

Orange/Tea Colored: Rhabdomyelitis (Breakdown of muscle)

Foamy: May suggest excess protein

It is important to note that certain medications taken for UTIs can change the color of the urine, Phenazopyridine in particular.

Macroscopic -Urinalysis

Dipstick chemical analysis is performed on a narrow plastic strip which has individual tests denoted with different colored squares. The entire strip is dipped into the urine sample and color changes of the squares are noted either by the technologist or by inserting it into an instrument to read it. Each square takes a specific amount of time to react so its important to allow the reaction to come to fruition before resulting. The color change of particular squares are compared to a reference guide and can point out abnormalities.

In no particular order the squares on the dipstick indicate;

Specific gravity (concentration of the urine)


Protein concentration

Glucose concentration

Presence of Ketones


Leukocyte esterase (Suggestive of WBC in urine)

Nitrite (Suggestive of bacteria in urine)




Dipsticks are convenient and are easy to interpret and cost-effective. Its important to keep in mind that dipsticks are qualitative and not quantitative in that they only suggest that there is an abnormality, they don’t quantify that abnormality. Further analysis is required for such results.

Microscopic analysis can detect cells, cellular debris, bacteria, crystals, and certain casts to confirm the dipstick results and further quantify analysis. Once the samples are received they must be centrifuged and discarding the supernatant. Epithelial cells may suggest inflammation or damage to the gallbladder and casts and cellular debris suggest inflammation of the kidneys and upper urinary tract. On very rare occasions tumor cells can be seen which are diagnostic for certain renal carcinomas and other urinary tract cancers.

If red cells are noted it could indicate either an infection, trauma, or stones. They can also indicate glomerulonephritis which is inflammation of the kidneys. Sometimes small amounts of red cells will be seen in healthy individuals.

Urine is considered a sterile body fluid therefore there should be no white blood cells or bacteria. Any amount of WBC or bacteria within the urine is considered abnormal and is suggestive of an UTI, cystitis, or pyelonephritis.

Identifying crystals if any is important and lend diagnostic information as to what is pathologically going on within the body.

Uric acid crystals can vary in size and shape, but usually resemble a rhomboid shape. These crystals are common in individuals with urate nephrolithiasis or acute urate nephropathy.


Cystine crystals are usually colorless hexagonally shaped and look similar to benzene rings (bringing it back to organic chemistry days). These occur in patients with cystinuria which is a genetic defect in renal cystine transport and in acidic urine (pH <6.0).


Struvite crystals are often described as having a coffin-lid appearance. These crystals are typically magnesium ammonium phosphate and are seen in alkaline urine (pH >7.0). Seen in patients with UTIs caused by urea-splitting bacteria (Proteus mirabilis) or in patients with infected calculi (struvite stones).


Calcium oxalate crystals are typically found in acidic urine and can take on multiple shapes. Some may look like colorless ovoids, biconcave discs, or even rods. Usually seen in patients with high dietary oxalate ingestion, patients with nephrolithiasis or those in ethylene glycol toxicity with renal failure.


These are some of the more common crystals that will be seen. Urinalysis isn’t flashy and isn’t always fun as it is someones urine, but it is an important part of routine testing to better deliver care to the patient.




Blood Draw Tube Colors and Order

The tube order may not seem like a big deal and may seem unnecessary to some, but it is very important to pay attention too. It also matters as to what type of needle is being used for the draw. If a butterfly needle is being used it is important to have a spit tube because with a butterfly there is air within the hose that connects the needle to the vacutainer. Its important to get this air out before filling any tubes used for patient testing. If a standard needle is being used, you typically don’t need the spit tube, but its good practice. The order still remains the same for each.

Light Blue: The typical tube for routine coagulation studies. The additive is sodium citrate (3.2% or 3.8%). Citrate is a anticoagulant which binds to calcium within the blood so the blood can’t clot. Calcium plays an important role in primary and secondary homeostasis. See my post on DIC for that information, in short it is used in the coagulation cascade. An important aspect of coagulation studies is that the light blue tube must, must be filled completely. There is a ratio of sodium citrate to whole blood and that must remain constant. The tube must be rejected if it is not filled completely.

Green or Mint Tubes: These tubes are used for chemistry studies. Often referred to as PST or plasma separator tubes. The additive in these tubes are sodium heparin, lithium heparin or ammonia heparin. The heparin, being an anticoagulant activates antithrombin, which blocks the coagulation cascade and produces a whole blood with plasma sample instead of a clotted blood and serum sample. When these tubes are centrifuged, the gel barrier moves upwards creating a barrier that separates the plasma from the red cells allowing the plasma to be aspirated directly for testing.

Gray Tube: The gray tube tops are typically used for glucose testing, ethanol levels or lactate level testing. The additive is potassium oxalate and sodium fluoride. Potassium oxalate is an anticoagulant which prevents clotting and the sodium fluoride is an anti-glycolytic which prevent the cells from using the glucose in the sample.

Lavender/Pink Tube: The lavender tube is typically used for hematological testing or for Hemoglobin A1C testing. The pink tube is used primarily for blood bank testing such as type and screen and cross-matching. The additives in the lavender and pink tubes are EDTA K2 or EDTA K3. The EDTA binds to calcium which blocks the coagulation cascade in the same way that citrate in the light blue tube does. Red cells, leukocytes, and platelets are in EDTA anticoagulated blood for 24 hours. Blood smears should be done within 3 hours of receiving the sample.

SST/Mustard Tube: Serum separator and clot activator that will separate the blood from the serum upon centrifugation. This tube is usually used to test for aldosterone, B12, ferritin and folate levels.

There are not all the different tubes that are used, but these are the most common tubes that I listed and the ones that a laboratory professional will most likely come across. Its important to understand the additive in each one to make sure that they are appropriate for the testing that needs to be done on the patient sample itself within the tube.

phb_Order of Blood Draw with labels72dpi