WEEK 2: Microbiology of the urinary tract

Question 1

Urine is normally sterile- flushing of the urinary tract.
The anterior urethra inhabited by normal flora.

Outline them.

Answer 1

 Staphylococcus epidermidis
 Enterococcus faecalis
 Alpha-hemolytic Streptococci
 Lactobacillus spp.

Question 2

State the examples of Enteric bacteria, contaminants from the skin, vulva or rectum.

Answer 2

 E. coli
 Proteus
 Corynebacteria

Question 3

The epidemiology of UTI

A urinary tract infection (UTI) is an infection in any part of the urinary system.

State the 4 main parts of the urinary system.

Most infections involve what part of the urinary system?

What is Urinary tract infection (UTI) defined as in terms of significant bacteriuria?

State signs and symptoms of UTI.

Answer 3

 kidneys
 ureters
 bladder
 urethra

Most infections involve the lower urinary tract — the bladder and the urethra.

 Urinary tract infection (UTI) is defined as significant bacteriuria ( >105 organisms / ml) in the presence of a constellation of symptoms such as

 dysuria (painful urination)
 increased urinary frequency and urgency
 suprapubic discomfort
 costovertebral angle tenderness

Question 4

Who is bacterial infection most common among?

 Affect up to 150 million individuals annually.
 Occur in two general settings:
Which are?

State the common causes of hospital acquired UTI and community acquired UTI.

Answer 4

Most common bacterial infection among young, sexually active women.
 Affect up to 150 million individuals annually.
 Occur in two general settings: community-acquired and hospital (nosocomially)-acquired, associated with catheterization.
 Most common hospital-acquired infection- 35-40% of nosocomial infections
 Total annual direct and indirect cost due to UTIs in the US alone is estimated to be greater than US$ 1.6 billion

Hospital-Acquired UTI (HAUTI) Bacteria:
*Escherichia coli (E. coli): E. coli is a common cause of UTIs and is frequently implicated in HAUTIs, especially those associated with catheter use.

Enterococcus spp.: Enterococcus bacteria, particularly Enterococcus faecalis and Enterococcus faecium, can cause HAUTIs, often in patients with urinary catheters.

Pseudomonas aeruginosa: This opportunistic pathogen is known to cause infections in hospitalized patients, including UTIs associated with catheterization.

Klebsiella pneumoniae: This bacterium is associated with healthcare settings and can cause UTIs, particularly in patients with compromised immune systems.

Proteus mirabilis: Proteus mirabilis is known for its role in catheter-associated UTIs and can form biofilms, contributing to the persistence of infections.

Escherichia coli (E. coli): E. coli is the most common cause of community-acquired UTIs, particularly in women. It is a normal part of the intestinal flora but can cause infection when introduced into the urinary tract.

Staphylococcus saprophyticus: This bacterium is a common cause of community-acquired UTIs, especially in young women. It is less common in healthcare settings.

Klebsiella pneumoniae: While more commonly associated with healthcare settings, Klebsiella pneumoniae can also be a cause of community-acquired UTIs.

Enterococcus faecalis: While more prevalent in healthcare-associated infections, Enterococcus faecalis can occasionally be implicated in community-acquired UTIs.

Proteus mirabilis: Proteus mirabilis is capable of causing both hospital-acquired and community-acquired UTIs.

Question 5

Describe the trend of UTI’S and males and females and also according to age.

Answer 5

Epidemiology- Incidence and prevalence
Incidence

 Females: 1,200 cases per 100,000 persons annually
 Males: 30 cases per 100,000 persons annually
Gender
 Most prevalent in sexually active women.
 1 in 3 sexually active women develop a urinary tract infection before the age of 24 years.
 Women over age 65, or any women without estrogen

Age
 More common in boys up to 6 months of age- lack of circumcision, anatomical
and structural abnormalities
 Between 1 and 65 years of age, UTI predominantly occurs in female patients -
anatomy of the female urethra
 Over age 65, bacteriuria affects men and women roughly equally
Genetics
 Patients who do not secrete A,B, H blood group antigens are three to four times more likely to have recurrent UTIs

Question 6

State the risk factors of UTI’s according to age and gender.

Answer 6

Check slides

Question 7

Describe the different routes of UTI.

Answer 7

1.Hematogenous Route:
o Infection of the renal parenchyma by blood-borne organisms
o Gram positive organism, Staphylococcus aureus, Salmonella, Mycobacterium tuberculosis
o Infections with Gram negative bacilli rarely occur by the hematogenous route

2.Ascending Route:
o Fecal flora colonize the vaginal introitus and displace the normal flora
(diphtheroid, lactobacilli, coagulase-negative staphylococci, and streptococcal species).

Question 8

Describe the different Antibacterial Host Defenses in the Urinary tract.

Answer 8

 Urine flow and micturition
 Urine osmolality
 pH
 Organic acids
 Urinary inhibitors of bacterial adherence:
 Bladder mucopolysaccharides
 Secretory immunoglobulin A (SIgA)
 Inflammatory response (PMNs, and cytokines-IL, TNF,)
 Prostatic secretions
 Humoral and cell-mediated immunity

Question 9

Describe the Bacterial Virulence factors.

Answer 9

 Fimbrae / Pili
 Capsular antigens ie.. K1, K5 - Protects bacterium from
phagocytic engulfment
 Lipopolysaccharide - Endotoxin which is an integral part of
Gram-ve bacteria cell wall
 Flagella - Allow bacteria to ascend from bladder & initiate kidney
infection
 Alpha hemolysin (HlyA)
 Secreted autotransporter toxin (SAT)
 Cytotoxic necrotizing factor 1 (CNF1)
 Iron chelating factors & siderophores
 Secretion of urease
 Biofilm formation

Question 10

State the 3 main lower UTI diseases.

State the Upper UTI diseases.

Answer 10

Lower UTI: cystitis, urethritis, prostatitis

Upper UTI: pyelonephritis, intra-renal abscess, perinephric abscess (usually late complications of
pyelonephritis)

Question 11

Define complicated and uncomplicated UTI.

Answer 11

 Uncomplicated UTI – Infection in a structurally and neurologically normal urinary tract. Simple cystitis of short (1-5 day) duration.

 Complicated UTI – Infection in a urinary tract with functional or structural abnormalities (ex. indwelling catheters and renal calculi). Cystitis of long duration or hemorrhagic cystitis.

Question 12

Define urethritis.

Answer 12

Swelling and irritation (inflammation) of the urethral mucosa.

Common manifestation of sexually transmitted disease

Question 13

Outline causes of urethritis.

Answer 13

Causes
 Bacteria that cause Urinary tract infections (E. coli)
 Sexually transmitted diseases (Chlamydia
trachomatis, N. gonorrhoea, Mycoplasma
genitalium, Ureaplasma urealyticum,
Trichomonas vaginalis)
 Viruses - herpes simplex virus and cytomegalovirus.
 Sensitivity to the chemicals used in
spermicides or contraceptive jellies,
creams, or foams

Question 14

State Risks for urethritis.

Answer 14

Risks for urethritis
 Females in the reproductive years
 Males, ages 20 - 35
 Having many sexual partners
 High-risk sexual behaviour (such as anal sex without a condom)
 History of sexually transmitted diseases

Question 15

State the symptoms of urethritis in males.

Answer 15

In men
 Burning pain while urinating (dysuria)
 Discharge from penis
 Frequent or urgent urination
 Itching, tenderness, or swelling in penis or groin area
 Pain with intercourse or ejaculation
 Blood in the urine or semen

Question 16

State the symptoms of urethritis in females.

Answer 16

 Abdominal pain
 Burning pain while urinating
 Frequent or urgent urination
 Pelvic pain
 Vaginal discharge
 Fever (rare

Question 17

State the tests used for diagnosis of urethritis.

Answer 17

Tests
 Urinalysis and urine cultures
 Tests for gonorrhea, chlamydia, and other sexually transmitted illnesses
(STI

Question 18

Describe the treatment plan for urethritis.

What is the goal?

Answer 18

Treatment
The goals of treatment are to:
 Eliminate the cause of infection
 Improve symptoms
 Prevent the spread of infection

Antibiotics.
➢ Ceftriaxone / Azithromycin
➢ Doxycycline
➢ Metronidazole
Sexual partner must also be treated.
Urethritis caused by trauma or chemical irritants is treated by avoiding the source of injury or irritation.

Question 19

Prognosis
➢With the correct diagnosis and treatment, urethritis usually clears up without any complications.
➢Can lead to permanent damage to the urethra (urethral stricture) and other urinary organs in both men and women

State the complications of urethritis in males and females.

Answer 19

Complications
Men

Bladder infection (cystitis)
Epididymitis
Infection in the testicles (orchitis)
Prostate infection (prostatitis)
Urethral stricture

Women with urethritis
Bladder infection (cystitis)
Cervicitis
Pelvic inflammatory disease

Question 20

Define cystitis.

Answer 20

Cystitis is an inflammation of the mucous membrane of the bladder, caused by bacteria that enter the urethra and then the bladder.

The infection can spread to the kidneys.

Question 21

State some differential diagnosis associated with cystitis.

Answer 21

Differential diagnosis
Vulvo vaginitis
Pelvic inflammatory disease
(In males: Cystitis rare, associated with stones ,prostatitis or chronic urinary retention. Urethritis, prostatitis)

Question 22

State the risk factors for cystitis.

Answer 22

 Procedures that involve the urinary tract, e.g.,: urinary catheter inserted in your bladder
 Enlarged prostate, narrowed urethra, or anything that blocks the flow of urine.
 Loss of bowel control (bowel incontinence)
 Older age (especially in people who live in nursing homes)
 Pregnancy, Diabetes
 Problems fully emptying your bladder (urinary retention)
 Staying still (immobile) for a long period of time
Most cases are caused by Escherichia coli (E. coli),

Question 23

Most common cause of UTI
Caused by serogroups of E. coli such as :
➢ O (cell wall LPS) serotypes (e.g. O1, O2, O4,
O6, O7 and O75)
➢ K (capsular polysaccharide) serotypes (e.g.
K1, K2, K3, K5, K12 and K13).
 Type 1 fimbrae : Promote attachment to
epithelial cells within urinary tract
 P fimbrae: Encoded by pap (pyelonephritisassociated pili)
 Strongest association with acute disease
 ~90% UPEC strains causing acute
pyelonephritis & ~20% strains causing
asymptomatic bacteriuria express P fimbriae

 Gram Negative Rods
 Motile
 Capsules and fimbriae
 Hemolytic on blood agar
 Lactose fermenter
 Indole positive
 Citrate negative
 Urease Negative
 Catalase positive

Name the bacteria.

Answer 23

E.coli

Question 24

 Second most common cause of
cystitis in young women.
 Sexual intercourse promotes
colonization and infection.
 Alterations in the genital flora by
spermicides or candida infection
favor colonization by S.
saprophyticus.
 Anal intercourse may play a role in
infection in homosexual men

 Gram positive cocci
 Coagulase negative
 Non motile
 Catalase positive
 Lactose fermenter
 Novobiocin resistant

Name the bacteria.

Answer 24

Staphylococcus saprophyticus

Question 25

 Hospital associated UTI
 Develop plasmid mediated multi drug resistance.

▪ Capsulated Gram negative rods
 Non motile
 Large mucoid colonies
 Lactose fermenting
 Indole negative
 Citrate positive
 Urease positive
 Catalase positive

Name the bacteria.

Answer 25

Klebsiella spp.

Question 26

 Proteus mirabilis most frequent cause of UTI
 Secretion of urease :
➢ Hydrolysis of urea to ammonia & CO2 (pH >7, up
to 9)
➢ Alkaline urine- precipitates phosphate,
carbonate & magnesium
➢ Resulting in formation of Struvite stones &
eventually large Stag horn calculi (stones)

 Gram negative rods
 Motile-swarming growth
 Lactose nonfermenters
 Urease positive
 Indole positive (P.mirabilis –
negative)
 Citrate positive
 H2S production in SIM
medium
 Fishy/seminal odour

Name the bacteria.

Answer 26

Proteus

Question 27

 Nosocomial UTIs
 Gram-negative rods with (polar) flagella
 Not Enterobacteriaceae
 Natural habitat – outside environment i.e. soil,
water, moist surfaces
 Naturally resistant to many antibiotics - Due to ‘Rplasmid’
 P. aeruginosa form biofilms on surface of urinary
catheters
 Biofilms difficult to eradicate, resistant to
antimicrobial agents & host defense mechanisms
 Often lead to persistent & recurrent infections.

 Non lactose fermenting
 Mucoid colonies
 Musty ,earthy smell
 Catalase positive
 Oxidase positive
 Citrate positive
 H2S negative
 Indole Negative
 Pigment production-
-Pyocyanin and pyoverdin

Name the bacteria.

Answer 27

Pseudomonas aeruginosa

Question 28

Discuss the treatment of cystitis and uncomplicated UTI.

Answer 28

Treatment:
Cystitis and uncomplicated UTI
Short course treatment- 3days
 Amoxicillin
 Nitrofurantoin
 Fluoroquinolones-Ciprofloxacin
 Cephalosporins
 Trimethoprim-Sulfamethoxazole

Prophylactic therapy
Continuous
 First choice Trimethoprim 100 mg at night
 Second choices Nitrofurantoin 50 mg at night
Co-amoxiclav 250/125 mg at night

Question 29

Define pyelonephritis.

Etiology?

Answer 29

Pyelonephritis - urinary tract infection (UTI) that affects one or both kidneys.
* Caused by a bacterium or virus infecting the kidneys
* Escherichia coli is often the cause.
* Bacteria and viruses can move to the kidneys from the bladder or can be carried through the bloodstream from other parts of the body.

Question 30

State the risk factors for pyelonephritis.

Answer 30

Risk factors
* Structural, or anatomic, problem in the urinary tract
* Pregnant women and people with diabetes or a weakened immune system

Question 31

State some complications of pyelonephritis.

Answer 31

Complications
 Renal scarring
 Hypertension
 End stage Kidney disease

Question 32

State some investigations done to diagnose pyelonephritis.

Answer 32

➢ Urinalysis and Urine culture
➢ Digital rectal examination (DRE). swollen prostate obstructing the neck of
the bladder.
➢ Ultrasound -who do not respond to treatment within 72 hours.
➢ Computerized tomography (CT) scan - obstructions in the urinary tract.
➢ Voiding cystourethrogram (VCUG) - abnormalities of the inside of the
urethra and bladder -used to detect VUR in children.
➢ Dimercaptosuccinic acid (DMSA) scintigraphy. show the severity of kidney
infection or kidney damage, such as scarring

Question 33

Describe the treatment plan for pyelonephritis.

Answer 33

Pyelonephritis and complicated UTI (i.e. with associated
systemic toxicity)
First choices Co-amoxiclav 500/125mg 8-hourly x 10 days
Ciprofloxacin 500 mg 12-hourly
Second choices In seriously ill patients start i.v treatment, e.g.
Cefuroxime 750 mg 8-hourly 7-14 days
Gentamicin (Dose adjusted to renal function)
Most people with pyelonephritis do not have complications if
appropriately treated with antibiotics

Question 34

SUMMARY

Answer 34

❖UTIs are among the commonest bacterial infections, especially
in women.
❖Usually endogenously acquired, with colonizing bacteria
ascending the urinary tract from the periurethral area.
❖E. coli is the predominant pathogen; other Gram-negative rods
are also responsible, especially in hospitalized patients.
❖Structural or mechanical factors in the host, or catheterization,
predispose to infection.
❖ Bacterial attributes such as adhesions and capsular
polysaccharides important in the development of UTI. Specific
toxins are not implicated.
Summary…
❖Asymptomatic infection is common in pregnancy,elderly and in
children. Infection is recurrent in a significant proportion .
❖ Pyelonephritis has a more severe presentation than lower UTI,
with fever and loin pain; recurrent infection results in renal
damage.
❖ Short-course treatment with oral antibacterials is effective for
lower UTI; pyelonephritis needs longer treatment, with
systemically administered drugs.
❖Hospital-acquired UTI is often caused by multiple-resistant
Gram-negative bacteria, and treatment should be based on
the results of antibiotic susceptibility tests