Staphylococcus saprophyticus- An Overview

Staphylococcus saprophyticus is a Gram-positive, coagulase-negative, non-hemolytic coccus that belongs to the genus Staphylococcus . It is a facultative anaerobe that can grow in different pH, osmolarity, and urea levels in urine . It is a part of the normal flora in humans and animals, colonizing the perineum, rectum, urethra, cervix, and gastrointestinal tract . It can also be found in environmental sources such as meat, dairy products, and marine waters .

Staphylococcus saprophyticus is an important cause of urinary tract infections (UTIs), especially in young sexually active females . It accounts for 10-20% of community-acquired UTIs and is the second most common uropathogen after Escherichia coli . It can also cause complications such as acute pyelonephritis, urethritis, epididymitis, and prostatitis . In rare cases, it can also cause bacteremia and sepsis.

Staphylococcus saprophyticus is different from other staphylococci by its resistance to novobiocin, a characteristic that is used for its identification . It also lacks the enzyme coagulase, which distinguishes it from Staphylococcus aureus . It has several virulence factors that enable it to adhere to uroepithelial cells, produce urease, form biofilms, and resist host defenses .

Staphylococcus saprophyticus was first isolated from humans by Shaw in 1951, and its association with UTIs was established by Torres Pereira in 1962. Since then, it has been recognized as a significant uropathogen that requires appropriate diagnosis and treatment. The treatment of choice for uncomplicated UTIs caused by S. saprophyticus is nitrofurantoin or trimethoprim-sulfamethoxazole. Prevention of UTIs caused by S. saprophyticus involves good hygiene practices, adequate hydration, and post-coital voiding.

Classification of different species of the genus Staphylococcus is based on various factors ranging from morphology, chemical properties, amino acid sequences, biochemical characteristics, and nucleotide sequences . Staphylococcus spp. are primarily classified on the basis of DNA–DNA hybridization where members of the same species demonstrate relative DNA-binding values of generally 70 percent or greater. Staphylococcal subspecies, in turn, have been identified on the basis of phenotypic characters and DNA relatedness, and ribotyping.

There are two known subspecies of S. saprophyticus; S. s. saprophyticus and S. s. bovis which are differentiated based on their colony diameter and nitrate reduction activity . S. s. saprophyticus is present as the normal flora in most primates and smaller terrestrial animals in the Order Scandentia. S. s. bovis, however, is found as the normal flora in domestic cattle like cows and pigs.

The taxonomic classification of S. saprophyticus is as follows:

• Domain: Bacteria
• Phylum: Firmicutes
• Class: Bacilli
• Order: Bacillales
• Family: Staphylococcaceae
• Genus: Staphylococcus
• Species: Staphylococcus saprophyticus
• Subspecies: S. s. saprophyticus and S. s. bovis

S. saprophyticus can be differentiated from other staphylococci primarily on the basis of cell wall composition, carbohydrate reaction pattern, and, to a lesser extent, on low acid production under anaerobic conditions, production of acetylmethylcarbinol, the failure to reduce nitrate, and resistance to novobiocin . It can also be identified by its ability to cause urinary tract infections in young sexually active females .

S. saprophyticus is a widely distributed bacterium that can be found in various natural and artificial environments. It is also a part of the normal flora in humans and animals, especially in the genitourinary and gastrointestinal tracts.

In humans, S. saprophyticus subsp. saprophyticus is present as the normal flora of the perineum, rectum, urethra, cervix, and gastrointestinal tract. It is also a common cause of urinary tract infections (UTIs), especially in young sexually active women. The exact physiological role of the bacterium as the normal flora is not yet known; however, it is assumed that it may be involved in the lipid metabolism of the skin and that it may serve as a primary barrier against invading microbial pathogens.

S. saprophyticus subsp. bovis, on the other hand, is found as the normal flora in domestic cattle like cows and pigs. It can also be transferred to humans by eating meat and dairy products derived from these animals.

Besides being a part of the human and animal microbiota, S. saprophyticus can also be isolated from other environmental sources like cheese, meat, raw milk, vegetables, and recreational waters. It has also been reported in marine environments, either in polluted or natural waters.

S. saprophyticus can survive and grow in different environmental conditions, such as varying pH, temperature, osmolarity, and urea concentration. It can also utilize various carbon sources for its metabolism. These factors enable the bacterium to adapt to diverse habitats and cause infections in susceptible hosts.

Cells of S. saprophyticus are gram-positive cocci, nonmotile, non-spore-forming with an average diameter of 0.8 to 1.2 µm . These occur predominantly in pairs or as loose aggregates of single cells as a result of their division in irregular planes. The cell membrane is made up of the typical lipid-protein bilayer consisting of phospholipids and different proteins that together act as a selective barrier and fulfill functions like electron transport, active transport, septum formation, and segregation of DNA. The cell wall is made up of peptidoglycan and teichoic acid that function to maintain the spherical shape of the cell. Like other coagulase-negative Staphylococci, S. saprophyticus also has fewer cell wall adhesions and cell-wall associated proteins. S. saprophyticus have hemagglutinin mediated by its cell wall-anchored or associated surface proteins that help the organism anchor to the urogenital cells. It also has abundant transporter systems to adapt to ever-changing pH, osmolarity, and concentration of urea in human urine.

Staphylococci produce different distinct colonies on a variety of commercial, selective, and nonselective agar media. The commonly used selective media include mannitol–salt agar, lipase–salt–mannitol agar, phenyl ethyl alcohol agar, Columbia colistin–nalidixic acid (CNA) agar, and Tryptic soy agar supplemented with egg yolk tellurite enrichment. These media inhibit the growth of gram-negative bacteria, but allow the growth of staphylococci and certain other gram-positive bacteria. The choice of media also depends on the source or sample of the infection. For food or other environmental specimens, Mannitol salt agar is used along with selective broth consisting of tryptone, nalidixic acid, and novobiocin. For human samples like urine, blood agar is used .

The cultural characteristics of S. saprophyticus on different media are as follows:

• Nutrient Agar (NA): Circular, cream-colored to white colonies of S. saprophyticus are observed on NA. The colonies are mostly 1mm in diameter with an entire margin. The colonies have raised elevation and a dense center with transparent borders. The anaerobic species of S. saprophyticus grow well under anaerobic conditions but grow very poorly under aerobic conditions.
• Mannitol Agar: Yellow-colored colonies indicating mannitol fermentation as the color of the media is converted from red to yellow. The colonies are 1-2 mm in diameter with an entire margin.
• Blood agar (BA): Creamy Bright white non-hemolytic colonies, around 5-8 mm in diameter are seen on BA. Some variants (50-60%) of the species might produce pigments .
• P agar: Smooth, glistening, and usually opaque colonies are seen which are raised to slightly convex, circular, usually entire, and 4.0 to 9.0 mm in diameter. Colony pigment is variable; however, most strains are not pigmented or have a slight yellow tint which increased in intensity with age.
• Thioglycolate medium: Growth occurs in both the aerobic and anaerobic portions of the thioglycolate medium. The growth in the anaerobic portion is usually dense or shows a gradient from dense to light growth in the deeper, more anaerobic, portion of the medium.

The biochemical characteristics of S. saprophyticus can be tabulated as follows:

These tests help to differentiate S. saprophyticus from other staphylococci and other gram-positive cocci.

• Catalase test: This test detects the presence of the enzyme catalase that breaks down hydrogen peroxide into water and oxygen. S. saprophyticus is catalase-positive, meaning it produces bubbles when exposed to hydrogen peroxide. This test helps to distinguish staphylococci from streptococci and enterococci, which are catalase-negative.
• Coagulase test: This test detects the presence of the enzyme coagulase that causes plasma to clot. S. saprophyticus is coagulase-negative, meaning it does not produce clots when mixed with plasma. This test helps to distinguish S. saprophyticus from S. aureus, which is coagulase-positive.
• Oxidase test: This test detects the presence of the enzyme oxidase that transfers electrons from a reduced substrate to an oxidized substrate. S. saprophyticus is oxidase-negative, meaning it does not change the color of the oxidase reagent when applied. This test helps to distinguish staphylococci from other gram-positive cocci like Micrococcus and Corynebacterium, which are oxidase-positive.
• Nitrate reduction test: This test detects the ability of bacteria to reduce nitrate to nitrite or nitrogen gas. S. saprophyticus is nitrate-negative, meaning it does not reduce nitrate in the medium. This test helps to distinguish S. saprophyticus from other coagulase-negative staphylococci like S. epidermidis and S. haemolyticus, which are nitrate-positive.
• Urease test: This test detects the presence of the enzyme urease that hydrolyzes urea to ammonia and carbon dioxide. S. saprophyticus is urease-positive, meaning it produces a pink color in the urea broth or agar due to alkalization of the medium. This test helps to distinguish S. saprophyticus from other staphylococci and other gram-positive cocci like Enterococcus and Streptococcus, which are urease-negative.
• D-serine deaminase test: This test detects the presence of the enzyme D-serine deaminase that deaminates D-serine to pyruvate and ammonia. S. saprophyticus is D-serine deaminase-positive, meaning it produces a yellow color in the D-serine broth due to acidification of the medium. This test helps to distinguish S. saprophyticus from other staphylococci and other gram-positive cocci like Enterococcus and Streptococcus, which are D-serine deaminase-negative.
• Lipase test: This test detects the presence of the enzyme lipase that hydrolyzes lipids to glycerol and fatty acids. S. saprophyticus is lipase-positive, meaning it produces a clear zone around the colonies on egg yolk agar due to lipid hydrolysis. This test helps to distinguish S. saprophyticus from other staphylococci and other gram-positive cocci like Enterococcus and Streptococcus, which are lipase-negative.
• Novobiocin resistance test: This test detects the resistance of bacteria to the antibiotic novobiocin. S. saprophyticus is novobiocin-resistant, meaning it grows well on agar containing novobiocin even at high concentrations (5 µg/ml). This test helps to distinguish S. saprophyticus from other coagulase-negative staphylococci like S. epidermidis and S. haemolyticus, which are novobiocin-sensitive.
• Mannitol fermentation test: This test detects the ability of bacteria to ferment mannitol and produce acid by-products. S. saprophyticus is mannitol-positive, meaning it produces a yellow color on mannitol salt agar due to acidification of the medium. This test helps to distinguish S. saprophyticus from other staphylococci like S. aureus and S. lugdunensis, which are also mannitol-positive, but can be differentiated by other tests like coagulase and clumping factor tests.
• Lactose fermentation test: This test detects the ability of bacteria to ferment lactose and produce acid by-products. S. saprophyticus is lactose-negative, meaning it does not produce a color change on lactose broth or agar due to lack of acidification of the medium. This test helps to distinguish S. saprophyticus from other gram-positive cocci like Enterococcus and Streptococcus, which are lactose-positive.
• Sucrose fermentation test: This test detects the ability of bacteria to ferment sucrose and produce acid by-products. S. saprophyticus is sucrose-negative, meaning it does not produce a color change on sucrose broth or agar due to lack of acidification of the medium. This test helps to distinguish S. saprophyticus from other gram-positive cocci like Enterococcus and Streptococcus, which are sucrose-positive.

Staphylococcus saprophyticus is a Gram-positive, coagulase-negative coccus that is a common cause of uncomplicated urinary tract infections (UTIs), especially in young sexually active females. It is also responsible for complications such as acute pyelonephritis, urethritis, epididymitis, and prostatitis. The ability of S. saprophyticus to cause infection can be attributed to various virulence factors that help the bacterium to adhere, invade, and persist in the urinary tract. Some of the virulence factors associated with infections caused by S. saprophyticus are:

• Surface proteins: Six different surface proteins are associated with the ability of S. saprophyticus to cause infections. Among them, two non-covalently surface-associated proteins are characterized so far. One of which is a protein associated with the surface of S. saprophyticus (Ssp) and another is the fibronectin-binding autolysin (Aas). Besides, four-cell wall-anchored proteins; the uro-adherence factor A (UafA), the collagen-binding serine-aspartate-repeat protein (SdrI), the uro-adherence factor B (UafB), and a surface protein F of S. saprophyticus have also been identified that aid in the attachment and colonization of the urogenital epithelium. These surface proteins result in hemagglutination, causing the bacteria to bind to fibronectin and human ureters as a result of their autolytic and adhesive properties .

• Enzymes: S. saprophyticus possesses the enzyme urease that leads to alkalization of the urine and thus may result in the formation of kidney and bladder stones. Besides, urease is also associated with the formation of urinary calculi that aids in the inflammation in the bladder and the dissemination of the bacteria to other organs. D-serine deaminase is another enzyme that supports the survival of the organism in the urinary tract. It is essential for the survival of the uropathogens in the urinary environment as it confers the tolerance of the organism to the toxic concentration of D-serine in the urine. The surface-associated lipase present on the cell wall forms fimbria-like surface appendages, helping the bacteria to maintain tight adherence to these surfaces .

• Biofilm formation: Some strains of S. saprophyticus are capable of forming biofilms around medical devices like catheters that might result in nosocomial or hospital-acquired infections. Biofilm formation provides protection to the bacteria as it works as a barrier against the immune cells as well as antimicrobial agents. The process of biofilm formation is assisted by the presence of fibrinogen-binding adhesions and several other enzymes .

About 20-40% of all UTIs occurring in middle-aged women are found to be caused due to S. saprophyticus. These infections are also common in women within a few days after having sex, which is why these infections are termed as ‘honeymoon cystitis’. Besides, complications like acute pyelonephritis, urethritis, epididymitis, and prostatitis are also found to be caused by S. saprophyticus. The pathogenesis of S. saprophyticus during urinary infection can be explained as follows:

1. Adhesion/ Attachment/ Colonization The gastrointestinal tract is found to be a major reservoir of S. saprophyticus which is assumed to be the route of entry to the urinary tract. Bacterial colonization of the bladder and ureter epithelium by S. Saphrophyticus occurs via several different types of adhesions. Various virulence factors like surface-proteins act as hemagglutinin and hemolysin and bind to the fibrinogen present on the surface of the urogenital cells.
   Other adhesins and wall-associated autolysins along with the enzyme lipase help maintain a tight adherence to the cell walls. The production of extracellular slime also prevents the attacks of immune cells to the colonizing bacteria.

2. Invasion Colonization of the urinary tract is the primary mode of infection by S. saprophyticus, but in some cases, invasive activities are seen where the infection ultimately leads to bacteremia. The enzyme urease helps to maintain the environment required for the growth of the organism while causing the formation of stones or calculi throughout the urinary tract. It is assumed that the urinary tract obstruction caused by a renal stone enables S. saprophyticus to reach the renal pelvis easily, and aggravate the tissue invasiveness of bacteria from the urinary tract. Although S. saprophyticus bacteremia from UTI is rare, obstructive nephrolithiasis is considered to be a predisposing factor for bacteremia from UTI.

Catheters-related infections In the case of catheter-related infection, the pathogenesis of the infection can be explained due to biofilm formation. The biofilm formation is supported by various cell-wall associated adhesions that adhere the bacteria to the abiotic surfaces. The accumulation of bacteria is then brought about by the production of the extracellular matrix or slime. The biofilm provides protection against the innate immune system and the antimicrobial agents, thus promoting the growth and colonization by the organism.

The most common and important clinical manifestation of S. saprophyticus infection is urinary tract infection (UTI), especially in young sexually active females . UTIs are characterized by inflammation of the lower urinary tract, such as the bladder and urethra, resulting in symptoms like:

• Hematuria (red blood cells in urine) and pyuria (white blood cells in urine)
• Dysuria (painful or difficult urination)
• Urinary frequency (urinating more often than usual) and urgency (feeling a strong need to urinate)
• Suprapubic pain (pain in the lower abdomen above the pubic bone)

These symptoms usually appear within a few days after sexual intercourse, which is why these infections are sometimes called `honeymoon cystitis`. The infection is usually limited to the lower urinary tract and can be treated with antibiotics.

However, if the infection is not treated promptly or adequately, it may spread to the upper urinary tract, such as the kidneys and ureters, causing a more serious condition called pyelonephritis . Pyelonephritis is an inflammation of the kidney tissue and renal pelvis that can lead to complications such as renal insufficiency, sepsis, and abscess formation. Patients with pyelonephritis may experience additional symptoms such as:

• Back or flank pain (pain in the side or back below the ribs)
• Nausea and vomiting
• Fever or chills

Pyelonephritis requires hospitalization and intravenous antibiotics to prevent further damage to the kidneys and other organs.

In rare cases, S. saprophyticus may also cause bacteremia (bacteria in the bloodstream), which can lead to sepsis (a life-threatening inflammatory response to infection) . Bacteremia may occur when the bacteria enter the bloodstream through a break in the skin or mucous membranes, or when they spread from an infected site such as the urinary tract. Bacteremia may cause symptoms such as:

• Low blood pressure (hypotension)
• Rapid heart rate (tachycardia)
• Confusion or altered mental status
• Organ failure

Bacteremia and sepsis are medical emergencies that require immediate attention and aggressive treatment with antibiotics and supportive care.

Other less common clinical manifestations of S. saprophyticus infection include urethritis (inflammation of the urethra), epididymitis (inflammation of the epididymis), prostatitis (inflammation of the prostate), and catheter-related infections . These conditions may cause symptoms such as:

• Urethral discharge or burning sensation
• Testicular pain or swelling
• Pelvic pain or difficulty urinating
• Biofilm formation on catheters or medical devices

These conditions may also require antibiotic treatment and removal of any foreign bodies that may facilitate bacterial growth .

The lab diagnosis of S. saprophyticus infection involves the following steps:

• Collection of clinical specimens: The most common specimen for S. saprophyticus infection is urine, which should be collected in a sterile container and transported to the laboratory as soon as possible. Other specimens, such as stool and blood, may also be collected in some cases.
• Microscopic examination: A direct microscopic examination of the urine sample may reveal the presence of gram-positive cocci resembling staphylococci. However, this is not a definitive test and requires confirmation by culture.
• Culture and isolation: The urine sample is inoculated on selective and differential media, such as mannitol salt agar or blood agar, and incubated at 35-37°C for 18-24 hours. S. saprophyticus produces yellow colonies on mannitol salt agar due to mannitol fermentation and non-hemolytic colonies on blood agar. The colonies are usually 1-2 mm in diameter with an entire margin.
• Identification and characterization: The isolated colonies are subjected to various biochemical and phenotypic tests to identify and differentiate S. saprophyticus from other staphylococci. The most important test is the novobiocin susceptibility test, which distinguishes S. saprophyticus from other coagulase-negative staphylococci by its resistance to novobiocin . Other tests include coagulase test, hemolysis test, nitrate reduction test, urease test, D-serine deaminase test, and pigment production test . A positive culture is indicated by greater than 100,000 colony-forming units per mL, with a sensitivity and specificity of more than 90%.
• Rapid identification kits and automated systems: Several commercial kits and systems are available that can identify S. saprophyticus within a few hours based on various factors, such as antibiotic susceptibility, enzyme production, immunological reactions, and cellular fatty acid analysis. These methods are more convenient and accurate than conventional methods but may be more expensive and require specialized equipment.

• Molecular diagnosis: Molecular methods are based on the detection and analysis of bacterial DNA or RNA using techniques such as polymerase chain reaction (PCR), DNA sequencing, restriction fragment length polymorphism (RFLP), or ribotyping . These methods are more sensitive and specific than phenotypic methods and can also provide information on the genetic diversity and epidemiology of S. saprophyticus strains. However, these methods are also more costly and complex and require skilled personnel and equipment.

  Treatment of Staphylococcus saprophyticus infection

Treatment with outpatient antibiotics is indicated in symptomatic or complicated UTIs and pyelonephritis caused by S. saprophyticus. The specific local resistance patterns are to be considered while choosing the appropriate antibiotic drug.

The drug of choice in the case of uncomplicated S. saprophyticus UTIs is nitrofurantoin (Macrobid) which is to be taken 100 mg orally twice daily for five days or seven days in complicated cases.

Trimethoprim-sulfamethoxazole (TMP-SMX) is another drug that is administered at a dosage of 160 mg/800 mg by mouth twice daily for three days given alternatively in uncomplicated cases.

Other antibiotics that have been shown to be effective against S. saprophyticus include ampicillin, ceftriaxone, and quinolones such as ciprofloxacin and norfloxacin. However, these drugs may have higher rates of resistance or adverse effects than nitrofurantoin or TMP-SMX.

Symptomatic treatment for pain and nausea should also be addressed, and in some cases, acute uncomplicated UTIs are unlikely to cause renal injury, which should also be treated.

Prevention of Staphylococcus saprophyticus infection

Because S. saprophyticus is mostly known to cause urinary tract infections, preventive methods for urinary tract infections can be applied to prevent the infections caused by S. saprophyticus. Some of the preventive measures are:

• Clean and cover wounds. If you have a cut or other wound, wash it immediately with soap and water to prevent infection. Keep the wound clean and covered with a sterile, dry bandage until it’s fully healed.
• Clean your hands. Clean your hands frequently with soap and warm water or an alcohol-based hand rub. This can help prevent the spread of staph bacteria from person to person or from contaminated surfaces.
• Avoid sharing personal items. Do not share towels, razors, clothing, or other items that may come into contact with your skin or mucous membranes. Staph bacteria can survive on these objects and transfer to your skin.
• Drink enough water. Drinking plenty of fluids can help flush out bacteria from your urinary tract and prevent them from multiplying and causing infection.
• Urinate after sexual intercourse. This can help remove any bacteria that may have entered your urethra during sex and prevent them from causing infection.
• Avoid foods that may be contaminated with S. saprophyticus. S. saprophyticus is a common gastrointestinal flora in pigs and cows and may be transferred to humans through eating these respective foods. It has also been found in cheese, meat, raw milk, and marine environments . Cook foods thoroughly and avoid cross-contamination between raw and cooked foods.
• Seek medical attention if you have symptoms of a UTI. If you experience dysuria, urinary frequency, urinary urgency, suprapubic pain, hematuria, or pyuria, you should consult your doctor for diagnosis and treatment. Early treatment can prevent complications such as pyelonephritis, bacteremia, or sepsis.

Because S. saprophyticus is mostly known to cause urinary tract infections, preventive methods for urinary tract infections can be applied to prevent the infections caused by S. saprophyticus. Some of the preventive measures are:

• Clean and cover wounds. If you have a cut or other wound, wash it immediately with soap and water to prevent infection. Keep the wound clean and covered with a sterile, dry bandage until it’s fully healed.
• Clean your hands. Clean your hands frequently with soap and warm water or an alcohol-based hand rub. This can help prevent the spread of staph bacteria from person to person or from contaminated surfaces.
• Avoid sharing personal items. Do not share towels, razors, clothing, or other items that may come into contact with your skin or mucous membranes. Staph bacteria can survive on these objects and transfer to your skin.
• Drink enough water. Drinking plenty of fluids can help flush out bacteria from your urinary tract and prevent them from multiplying and causing infection.
• Urinate after sexual intercourse. This can help remove any bacteria that may have entered your urethra during sex and prevent them from causing infection.
• Avoid foods that may be contaminated with S. saprophyticus. S. saprophyticus is a common gastrointestinal flora in pigs and cows and may be transferred to humans through eating these respective foods. It has also been found in cheese, meat, raw milk, and marine environments . Cook foods thoroughly and avoid cross-contamination between raw and cooked foods.
• Seek medical attention if you have symptoms of a UTI. If you experience dysuria, urinary frequency, urinary urgency, suprapubic pain, hematuria, or pyuria, you should consult your doctor for diagnosis and treatment. Early treatment can prevent complications such as pyelonephritis, bacteremia, or sepsis.

We are Compiling this Section. Thanks for your understanding.