UTI Microbiology

Microbiology of UTIs

• UTIs affect ~150 million people globally.
• UTIs are more common in females, with 60% of women getting a UTI in their life.
• UTIs are also common in pregnancy, transplant, and catheterized patients.

UTI Types

• Upper UTIs affect renal parenchyma (pyelonephritis) or ureters (ureteritis).
• Lower UTIs affect the urethra (urethritis), bladder (cystitis), or prostate (prostatitis).
• Uncomplicated UTIs occur in a "normal" urinary tract, a simple cystitis of short (1-5 day) duration.
• Complicated UTIs occur in a urinary tract with functional or structural abnormalities.

Normal Microbiota and UTIs

• The urinary bladder and upper urinary tract are normally sterile.
• In women, the flora is influenced by estrogen, and lactobacilli dominate vaginal microbiota during reproductive years.
• In men, the urethra is normally sterile.

• 1,000 bacteria/ml or 100 coliforms/ml of urine indicates infection.

Prevalence of UTIs

• Women are more prone to UTIs due to anatomical factors allowing bacteria quick access to the bladder.
• Poor hygiene and sexual intercourse are contributory factors for prevalence in women.
• Hormonal changes like menopause and estrogen loss can contribute negatively.
• UTIs in men are rare but are often more severe.
• Uncircumcised men are more prone to UTIs due to bacterial buildup in the extra fold of skin.
• Elderly men have an increased risk due to kidney stones or prostate problems.
• Any abnormality interfering with urine flow increases the risk of complicated UTIs.

Clinical Syndromes

• Cystitis is inflammation of the bladder presenting as dysuria, urinary frequency, urinary urgency & suprapubic pain
• Cystitis has an absence of fever and flank pain (lower abdominal pain).
• Acute cystitis may manifest pyuria.
• Cystitis is commonly caused by bacterial infection, especially gram-negative bacilli.
• Common risks for Cystitis include: sexual intercourse, history of UTIs, and use of diaphragms.

Proelonephritis

• Pyelonephritis is a complicated UTI extending up into the kidney.
• Untreated lower UTIs can easily ascend into the kidney.
• Cardinal symptoms of pyelonephritis are fever (>38°c), chills, and flank pain.
• Other symptoms can include nausea, vomiting, back pain, dysuria, and frequency.
• Pyelonephritis may lead to complications associated with bacteremia and kidney failure.

Other infection types

• Cervicitis is inflammation of the cervix which may be acute or chronic and caused by sexually transmitted bacterial infections exhibiting symptoms of dysuria, urgency, vaginal discharge and low back pain.
• Urethritis is inflammation of the urethra manifesting as dysuria with a discharge, often associated with sexually transmitted bacterial infections, but may also occur due to trauma, allergic, or chemical factors.
• Bacteriuria is the presence of detectable bacteria in the urine and may be symptomatic or asymptomatic.

UTI Causes and Transmission

• UTIs are ~95% due to bacterial infections, particularly E. coli (79%).
• Other members of enterobacteriaceae (mostly Klebsiella spp, Proteus spp) are implicated.
• Other causes include Pseudomonas, Enterococcus, & Staphylococcus.
• The type of pathogen is determined by host and exposure.
• Infection by Pseudomonas & Klebsiella is more common in hospital care.

Transmission Methods

• Bacteria mostly enter and cause UTI through the ascending route, entering the bladder via the urethra.
• Bacteria originate from gut commensals but may be introduced sexually or via external objects, colonizing the perianal region.
• Hematogenous route (bacteremia, via lymphatics reaching the kidneys) rarely.

Bacterial Profiles

• Common bacteria causing UTIs: Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis or Proteus vulgaris
• Other bacteria Group B streptococcus, Enterococcus faecalis, Staphylococcus species, and Lactobacillus.
• Lactobacillus may be ignored in asymptomatic non-pregnant women except in high counts and pure culture.

Escherichia Coli

• E. Coli is a gram negative rod that is a facultative anaerobe, capsulated, motile and does not form spores
• Lactose fermenting and reproduces by binary fission.
• Oxidase and urease negative

E. Coli Virulence Factors

• Bacterial adhesion of the urinary tract initiates infection
• Uropathogenic E. coli (UPEC) display pili at their surface, which help mediate adhesion
• Type 1 pili attach to uroepithelium and stimulate mechanisms leading to invasion and apoptosis
• Exfoliation of the uroepithelium occurs & exposes underlying cells to further UPEC invasion
• Bacteria reside in these cells and cause recurrent infections with the help of adhesins.
• Adhesins may also trigger internalization of bacteria inside host cells to protect themselves from antibiotics.

Entry into Urinal Cells

• UPEC invade urothelial cells & replicate within them
• Inside epithelial cells they are protected & can persist, dormant, for long periods
• This protects them from host defenses and antibiotic therapy and provides opportunity for recurrent infections.

E. Coli - Biofilms

• Bacterial adhesion to cell surfaces contributes to formation of biofilms
• Biofilms are extracellular, matrix-enclosed, microbial assemblies
• Adhere to biological or nonbiological surfaces, including indwelling catheters
• Offers a protective mode of growth allowing bacterial survival in hostile envrionments.
• Matrix-embedded bacterial aggregates are more resistant to host defenses or antibiotic treatments.

E. Coli - Pathogenesis

• Virulence factors like pili or fimbriae enable bacteria to ascend into the bladder and kidney
• Colonization is the first step in the development of UTI with pathogens attaching to uroepithelial cells via pili or fimbriae
• Bacterial attachment causes recruitment of toll-like receptors (TLR), transmembrane coreceptors that recognize pathogen-associated protein patterns
• TLR binding triggers a cytokine response generating a local inflammatory response and exfoliation leads to further spread & upper UTI.

E. Coli - Manifestation

• Most cases of E.coli are caused by Uropathogenic E. coli (UPEC).
• UPEC is part of the normal microbiota in the gut and can be introduced in females during back-front wiping after defecation. It can be transferred from anal intercourse to vaginal sex.
• The UPEC mostly causes acute simple cystitis: dysuria, urinary frequency, urinary urgency & suprapubic pain.
• Complicated UTI results in pyelonephritis with: fever (>38°c), chills, flank pain with/out nausea, vomiting, back pain, dysuria, and frequency.
• Shiga toxin-producing Escherichia coli (STEC): O157:H7 usually causes bloody diarrhea
• Shiga toxins lead to premature destruction of the red blood cells and damage to blood vessels causing clots.
• Clots can clog the filtering system in the kidneys leading to kidney failure & death, called hemolytic uremic syndrome (HUS).
• Signs of HUS: decreased frequency of urination, lethargy, paleness, CNS damage.

E. Coli - Diagonsis

• Diagnosis occurs by urine examination, microscopy and dipstick tests for esterase and nitrate.
• Urine can be cultured for pyelonephritis, if the patient is pregnant or is a child or for patients with structural abnormality
• Culture Media - CLED is used for lactose fermenting and and blood agar to observe growth.
• HUS diagnosed thru blood-thrombocytopenia and urinalysis checking for toxins.

Proteus Mirabilis

• Gram negative rods
• Facultative anaerobes
• Motile by peritrichous flagella (swarming motility)
• Non-capsulate and do not form spores
• Non-lactose fermenter with positive nitrite and produce urease and H2S but oxidase negative

Proteus Mirabilis - Transmission

• Widely distributed in nature in soil and water and are a member of enterobacteriaceae
• Migrate across media or devices using a type of group motility called swarming which is commonly associated with catheter UTI.
• Majority of UTIs occur from ascension of bacteria from the gastrointestinal tract but can also be transmitted in healthcare sites.

Proteus Mirabilis - Virulence

• P. mirabilis causes 90% of proteus infections in humans and produces at least four types of fimbriae for with urinary tract colonization
• Phenotype known as "swarm cell differentiation" facilitates ascendance into urinary tract via long flagellae
• Bladder inoculation with the "swarm" type of proteus in animal models increases the incidence of pyelonephritis and is visible in culture.
• Produces many other virulence factors, such as hemolysin and IgA protease, flagella, fimbriae and urease
• Urease hydrolyzes urea to ammonia and carbon dioxide causing alkaline urine which leads to struvite stones and bacteria proliferation
• Manifests commonly with long-term catheterization.

Pseudomonas Aeruginosa

• Gram negative rods, Strict aerobes, Survive in low nutrients with polar flagellar that is unable to ferment lactose
• Oxidase positive, without spore
• Can be identified via distinct pigment generation
• Common cause of nosocomial infections

Pseudomonas Aeruginosa - Virulence

• Consists of Endotoxins, causes sepsis and septic shock
• Consists of Exotoxins A, causes tissue necrosis and inhibits human protein synthesis
• and Pyocyanin pigment damaging cilia leading to pneumonia.
• Creates Biofilms that making it AMR and a Type III secretion system that transfers exotoxin directly into adjacent human cell and dodges neutralization.

Klebsiella Pneumoniae

• Member of Enterobacteriaceae
• Gram negative rods, Non motile, non sporing and ferments lactose.
• Can produce mucoid colonies
• Largely capsulated
• Oxidase negative
• Can be recognized via nitrite and Urease test.
• Facultative anaerobe and capsular polysaccharide antigens can be classified into 77 serotypes
• Common cause of LRTI especially among immunocompromised persons

Klebsiella Pneumoniae - Virulence

• Has a an enhanced iron intake accelerates growth which is facilitated by Siderophores
• It can adhere via fimbriae and has an antiphagocytic and hypermucoviscosity effect for liver abscess
• Manifests commonly with patients in hospitals and symptomatic of UTI

Staphylococcus Saprophyticus

• Gram-positive, Catalase and Urease positive.
• Coagulase and Nitrite test negative and does not cause hemolysis or move independently
• Resistant to novobiocin used to differentiate from other CNS.
• Occurrence: A common cause of uncomplicated UTIs, particularly in young sexually active females aged 16-25, where it causes up to 42% of all infections

• 40% of all young, sexually active women contain S. saprophyticus as part of their normal genitourinary flora

• Part of the normal flora and colonizes the GIT tract with general risk factors for history or sex.

Staphylococcus Saprophyticus - Virulence Factors

• Colonizes the bladder and ureter epithelium
• Hemagglutinins have the ability to dissolve lysis
• Creates lipase for adherence, and biofilms for for antibiotic resistance

Streptococcus Agalactiae

• Gram-positive coccus that is capsulated and non motile
• Can be identified via culture, which will be beta-hemolytic on blood agar Occurrence: common inhabitant of GIT and can cause severe infections

Group B Streptococcus - Transmission and Manifestation

• Normal vaginal inhabitant, and severe silent infections can occur
• Tranmission from mother during pregnancy, or from breast milk. Is asymptomatic and can be diagnosed by Gram stain.
• Manifestation is dependent on the person.

Sample Collection Recommendations

• Suprapubic aspiration of the bladder is the gold standard with contamination of flora.
• The best sample represents that of the flora in the bladder.
• First stream should not be collected to avoid contamination and should be done quickly.

Catheter-Associated Infections and Risk Factors

• Bacterial with those who are Catheter are at higher risk of infection.
• Symptomatic bacteriuria is at 10^3.
• Duration and Sex are common factors.

Treatment

• Culture before collection.
• Use an ongoing catheter to avoid culturing.

Pregnancy

• Untreated cases of pregnancy have higher likelihood preterm births, and perinatal death.
• The prevalence increases and is at a high prevalence in the first trimester.
• Check for low pregnancy with a culture for complicated UTls

Children

• Has common UTI that are caused by E.Coli.
• Can be tested with symptoms, and age and diagnosis