Urine Cultures

Urinary tract sterility

• Urine is a sterile body fluid in healthy individuals

• Upper tract: kidneys and ureters; lower tract: bladder and urethra

• Resistant to colonization/infection due to:

  • Flushing action of urine

  • Mucosal immunity

  • Antimicrobial peptides

• Presence of organisms may indicate:

  • Contamination (e.g. poor collection technique)

  • Colonization (e.g. catheterized patients)

  • True infection (e.g. ≥10⁵ CFU/mL with symptoms)

UTI epidemiology

• UTIs are among the most common bacterial infections leading to doctor visits

• Males: more common <1 year and >60 years (due to enlarged prostate)

• Females: higher incidence due to shorter urethra and GI/sexual transmission

• Risk increased by:

  • Diabetes

  • Renal disease

  • Structural abnormalities

  • Neurologic dysfunction affecting urine flow

UTI pathogenesis

• Bacteria invade the urinary tract via two routes:

  • Ascending route — most common (e.g. entry through urethra)

  • Hematogenous/descending route — less common (e.g. seeding from bloodstream)

• Host immune defenses typically eliminate invading organisms unless compromised

Types of urinary tract infections

• Urethritis – inflammation of the urethra

• Cystitis – inflammation of the bladder

• Pyelonephritis (upper UTI) – infection of the kidney(s); more severe

• Asymptomatic bacteriuria – presence of bacteria in urine without symptoms

Laboratory testing – UA with reflex to culture

• Recommend urinalysis (UA) with reflex to culture when infection is suspected

• UA findings that trigger reflex to culture:

  • Nitrites: positive (suggests presence of nitrate-reducing bacteria)

  • WBCs: pyuria (increased white cells)

  • Leukocyte esterase: positive (enzyme from WBCs)

  • RBCs may also be present

• Culture is performed only if UA meets predefined criteria

Urine specimen types

• Clean-catch midstream urine – most common outpatient method; minimizes contamination

• Straight catheterized urine – reduces contamination; used in pediatric or non-ambulatory patients

• Suprapubic bladder aspiration – sterile collection; used in infants or when contamination must be avoided

• Indwelling catheter (foley cath) – collected from catheter port, not the bag; higher risk of colonization

Urine specimen transport

• Collect in a sterile container

• Refrigerate and transport within 24 hours

• Boric acid transport tubes allow preservation unrefrigerated for up to 48 hours

Urine culture setup

• Thoroughly mix specimen before plating

• Use calibrated loop (0.01 mL or 0.001 mL) for colony count

• Streak for isolation and quantification

• Common media (varies by lab):

  • 5% sheep blood agar

  • MacConkey agar

  • CNA agar (for Gram-positive selection)

  • Chromagar (for differential ID)

• Incubate at 35–37°C for 18–24 hours

Urine culture interpretation

• 1 organism ≥ threshold CFU

  • ID and susceptibility

  • Threshold: ≥10⁵ CFU/mL (males), ≥10³ CFU/mL (sterile specimens)

• 2 organisms ≥ threshold CFU

  • ID and susceptibility of both

• 2 organisms with 1 predominant

  • ID and susceptibility of predominant

  • Describe secondary organism

• ≥3 organisms

  • Report as mixed flora

  • Suggest possible contamination

• Sterile specimens (suprapubic/cystoscopy)

  • ID and susceptibility for any growth

Common urinary pathogens

• Enterococci

• Streptococcus agalactiae (Group B Strep)

• Enterobacteriaceae (e.g., E. coli, Klebsiella, Proteus)

• Pseudomonas spp.

• Streptococcus pyogenes (Group A Strep)

• Staphylococcus aureus

• Staphylococcus saprophyticus

• Candida spp.

Anatomy and normal flora – genital tract

• Female anatomy: proximity of urethra, vagina, and anus increases risk of contamination and ascending infections

• Male anatomy: longer urethra and prostatic secretions offer some protection

• Normal flora – females:

  • Lactobacillus spp. (predominant in healthy vaginal flora)

  • Corynebacterium, Staphylococcus, Streptococcus, Candida (low levels)

• Normal flora – males:

  • Corynebacterium, Staphylococcus epidermidis, non-pathogenic Neisseria spp.

• Normal flora must be considered to distinguish colonization from infection in genital cultures

• Anaroebes

Normal genital flora

• Coagulase-negative staphylococci

• Corynebacterium spp.

• Anaerobes

• Lactobacillus spp. – predominant organism in healthy vagina

• Streptococci

• Enterobacteriaceae – more common in reproductive-age women

Genital infections and epidemiology

• Some infections arise from endogenous genital flora due to:

  • Damage to protective barriers

  • Use of medical instrumentation

  • Introduction of foreign bodies

• Most genital infections are sexually transmitted (STIs)

Genital conditions

Vaginitis

• Inflammation/irritation of vaginal mucosa

• Causes:

  • Bacterial vaginosis

  • Trichomonas vaginalis

  • Candida spp.

• Symptoms: itching, burning, foul odor, dysuria, abdominal pain

Genital conditions

Cervicitis

• Purulent discharge from endocervix

• Common pathogens:

  • Neisseria gonorrhoeae

  • Chlamydia trachomatis

  • HSV

  • HPV

Genital conditions

Pelvic Inflammatory Disease (PID)

• Complication of cervicitis

• Most often caused by C. trachomatis or N. gonorrhoeae

• Symptoms: vague and nonspecific; may include abdominal pain, discharge, fever, dyspareunia, dysuria, irregular bleeding

Genital conditions

Epididymitis

• Inflammation of the male epididymis

• Often a complication of Chlamydia trachomatis or Neisseria gonorrhoeae

• Symptoms: scrotal inflammation, testicular pain/tenderness, dysuria, chills, fever

Genital conditions

Urethritis

• Inflammation of the urethra

• Symptoms: dysuria, urethral discharge

• Gonococcal urethritis: Neisseria gonorrhoeae

• Nongonococcal urethritis (NGU):

  • Chlamydia trachomatis

  • Less common: Ureaplasma urealyticum, Mycoplasma genitalium, Trichomonas vaginalis, HSV

Pathogens causing genital tract infections

• Neisseria gonorrhoeae – urethritis, cervicitis, PID

• Chlamydia trachomatis – urethritis, cervicitis, PID

• Trichomonas vaginalis – vaginitis

• Gardnerella vaginalis – vaginitis, clue cells

• Treponema pallidum – syphilis

• Haemophilus ducreyi – chancroid/lesion

• Herpes simplex virus – herpes genitalis

• Human papilloma virus – genital and anal warts

• Candida spp. – vaginitis

• Listeria monocytogenes – neonatal infection

• Streptococcus agalactiae – neonatal infection

Genital specimen collection – culture setup

Cervix

• Swab: moistened with Stuart’s or Amies media

• Transport: within 24 hrs, room temp

• Media: BAP, Choc, MAC, MTM

Genital specimen collection – culture setup

Urethra

• Swab: Stuart’s or Amies media

• Transport: within 24 hrs, room temp

• Media: BAP, Choc, MAC, MTM

Genital specimen collection – culture setup

Vagina

• Swab: Stuart’s, Amies, or JEMBEC (Thayer martin with pill that generates CO2 and then sealed in bag) system

• Transport: within 24 hrs, room temp

• Media: BAP, Choc, MAC, MTM

• Can also perform Gram stain for bacterial vaginosis

Genital specimen collection – culture setup

Prostate

• Swab (Stuart’s or Amies) or sterile container

• Transport: swab within 24 hrs (RT); immediate if sterile container

• Media: BAP, Choc, MAC, MTM, CNA, thioglycolate (thio)

Special considerations – genital culture collection

• Use Dacron or Rayon swabs

• Avoid calcium alginate swabs – toxic to some organisms

Gonococci isolation:

• Transport in Modified Stuart’s or Amies charcoal media

• If delay >12 hours, inoculate directly to culture media

• Acceptable culture media:

  • Modified Thayer-Martin (MTM)

  • New York City (NYC) medium

  • JEMBEC plates (generate CO₂ atmosphere with tablet)

Genital smears

Gram stain

• Detects Neisseria gonorrhoeae in urethral specimens (GNDC, intracellular)

• Identifies clue cells in vaginal specimens (epithelial cells covered with bacteria)

• Used in Nugent scoring system for diagnosing bacterial vaginosis

Genital smears

Wet mount/prep

• Detects motile Trichomonas vaginalis

• Must be performed promptly after collection to preserve organism viability