Microbiology

of Urinary Tract Infections

By: Asnake S.(MSc, MPHE)

 Introduction
Bacteriuria is presence of bacteria in urine
Significant bacteriuria is when there is >105 bacteria/ml
Leading cause of morbidity and health care expenditures in
persons of all ages.
 Second most common infection following respiratory infections
An estimated 50 % of women report having had a UTI at
some point in their lives.
 In USA, 8.3 million office visits and more than 1 million
hospitalizations, for an overall annual cost > $1 billion.
 UTI may involve only the lower UT or both the upper and lower

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 Intro…. Cont’

• UTIs are common, especially among women

• UTIs in men are less common and primarily occur
after 50 years of age
• UTIs infection usually occur by ascending route
(urethra to bladder)
• UTIs infection is less common by haematogenous
spread (kidney)
• UTIs occur in two general settings:
– Community-acquired and
– Hospital (nosocomially) acquired

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 Defin… cont’

• Acute pyelonephritis is a syndrome characterized by

flank pain, tenderness, or both, and fever, often
associated with dysuria, urgency, and frequency
accompanied by significant bacteriuria and acute
infection in the kidney.
– These symptoms can happen in the absence of infection.
E.g. Renal infraction or Renal calculus

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 Definitions
Urethritis : Infection of anterior urethral tract
dysuria, urgency and frequency of micturition
Dysuria (burning pain on passing urine)
Urgency (the urgent need to pas urine)
Frequency of micturition
Cystitis is the syndrome involving dysuria,
frequency, urgency and occasionally
suprapubic tenderness
These symptoms may be related to only the lower
UT without affecting the upper
E.g. Gonorrhoea or chlamydial urethritis

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 Defn … cont’

Uncomplicated UTI refers to infection in a

structurally and neurologically normal urinary tract
Complicated UTI refers to infection in urinary tract
with functional or structural abnormalities, including
indwelling catheters and calculi
Infection in men, pregnant women, children and patients
who are hospitalized or in a health care associated settings
may be considered as complicated UTI.
 In patients with complicated infection, infecting
microorganisms are usually resistant to antimicrobial
agents.

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 Intro…. Cont’

• Urosepsis is a sepsis syndrome caused by UTI

– Includes clinical evidence of UTI plus two or more
of the following:
• Temperature > 380c or < 360c
• Heart rate >90 beats/min
• Respiratory rate >20/min
• White blood cell count > 12,000/mm3 or> 10% band
froms

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 Intro…. Cont’

• Chronic UTI mean persistence of the same

organism for months or years with relapses
after treatment
• Recurrence--- relapse vs reinfection?
• Is reinfection a chronic UTI? Discuss
• Pyuria: Presence of pus in urine (more than 10
cells/HPF)

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 Etiologies Of Urinary Tract Infections
Group Organisms
Escherichia coli
Klebsiella, Proteus and Pseudomonas
S. aureus, S. epidermidis and S. saprophyticus
Bacterial
Enterococci (Strept. faecalis)
Mycobacterium tuberculosis
Chlamydia trachomatis, Mycoplasma
Viral Rubella, Mumps and HIV?
Fungi Candida, Histoplasma capsulatum
Protozoa T. vaginalis
Helminths S. haematobium
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 Etiology…. Cont’
• Escherichia coli: the commonest urinary pathogen
causing 60-90 % of urinary infections
• Pseudomonas, Proteus, Klebsiella and S. aureus
are associated with hospital acquired infections
because their resistance to antibiotics favor their
selection in hospital patients (catheterization,
gynaecological surgery)
• Proteus infections are associated with renal stones
– Proteus produce a potent urease which act on
ammonia, rendering the urine alkaline
• S. saprohyticus infections are found in sexually active
young women

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 Etiology… cont’

• Candida urinary infection is usually found in diabetic

patients and immunosuppression
• Infection of the anterior urinary tract (urethritis) is
mainly caused by N. gonorrhoae, staphylococci,
streptococci and chlamydiae
• M. tuberculosis is carried in blood to kidney from
another site of infection (e.g. respiratory T.B.)

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 Pathogenesis of Urinary tract infection

• UTI occurs as a result of interaction of bacterial

virulence and host biologic and behavioral factors as
opposed to highly efficient host defence mechanisms
• Three possible ways to acquire UTIs
– Ascending
– Haematogenous
– Lymphatic pathways

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 Virulence factors of the UT pathogens

• Fimbriae enable adherence to urethral epithelium

• Capsular polysaccharide inhibit phagocytosis
• Haemolysin production by E. coli
• Membrane damaging toxin
• Production of urease enzyme (proteus spp.)

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 Healthy UT
• Bacterial colonization in urinary tract is prevented
by:
– pH of urine (acidic)
– Chemical content of urine
– Flushing mechanisms

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 Factors predispose to UTI
• Disruption of urine flow or complete emptying of
bladder
– Pregnancy
– Renal stones
– Tumor
– Prostate hypertrophy
– Strictures = narrowing of ureter
• Loss of neurologic control of bladder and sphincters
– Paraplegia (inability to move lower limb), and
– Multiple sclerosis serious progressive disease of the central
nervous system, occurring mainly in young adults and thought to
be caused by a malfunction of the immune system.

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 Factors predispose….. Cont’
– Multiple sclerosis (cont.) leads to the loss of myelin
in the brain or spinal cord and causes muscle
weakness, poor eyesight, slow speech, and some
inability to move
• Vesicouretral reflux (reflux of urine from bladder up
the ureter)
– Anatomic abnormalities in children
• Catheterization facilitate bacterial access to bladder
- During insertion bacteria access to bladder

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 Summary on risk factors to UTIs
Age Female Male
All ages Previous UTIs Lack of circumcision
Urologic instrumentation or surgery Urologic instrumentation or surgery
Urethral catheterization Urethral catheterization
UT obstruction, calculi UT obstruction, calculi
Neurogenic bladder Neurogenic bladder
Renal transplantation Renal transplantation
Adults Sexual intercorse Insertive rectal intercorse
Lack of urination after intercourse Vaginal colonization with E. coli in
partner
Spermicidal contraceptive jellis
Diaphragm use
Pregnancy
Lower socioeconomic group
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 Risk…. Cont’
Age Female Male
Spermicidal contraceptive jellis
Diaphragm use
Pregnancy
Lower socioeconomic group
Adults DM
cont’
Sickle cell diseases
Older age Functional or mental impairment Functional or mental impairment

Estrogen deficiency (loss of vaginal Prostatic enlargement

lactobacilli )
Bladder prolapse Condom catheter drainage

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 Clinical Features
• Acute lower UTIs (Urithritis and cystitis):
– Characterized by rapid onset of:
• Dysuria (burning pain on passing urine)
• Urgency (the urgent need to pas urine)
• Frequency of micturition
• Upper UTIs (Pyelonephritis):
• Fever
• Chills
• Dysuria
• Urgency
• Frequency of micturition

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 Acute Uncomplicated Cystitis

• Common in Sexually active young

women.
• Risk factors: anatomy and certain
behavioral factors, including
delays in micturition, sexual
activity, and the use of
diaphragms and spermicides
tract.
• Aggressive diagnostic work-ups
are unwarranted in young women
presenting with an uncomplicated
episode of cystitis.

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 Acute Uncomplicated Cystitis…. Cont’

• The microbiology is limited to a few pathogens.

– About 90% of UTIs are caused by Escherichia coli
– 5-20%are caused by coagulase-negative
Staphylococcus saprophyticus
– 5-12% are caused by other Enterobacteriaceae such
as Klebsiella and Proteus.
• Clinical Features:
– Dysuria, frequency, urgency, suprapubic pain,
hematuria.
– Fever >38oC, flank pain, costovertebral angle
tenderness, and nausea or vomiting suggest upper
tract infection.
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 Acute Uncomplicated Cystitis… cont’

Diagnosis: direct history and physical examination

Physical Examination: Temperature, abdominal exam,
assessment of CVA tenderness, pelvic exam.
H/o STD’s, new sexual partner, partner with urethral
symptoms, gradual onset.
Guidelines for treatment of acute cystitis recommend
empiric antibiotic treatment
 Unnecessary antibiotic use??
Clinical criteria for Diagnosis:
Dysuria, presence of > trace urine leukocytes, and presence
of nitrites or...
Dysuria and frequency in the absence of vaginal discharge.

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 Acute Uncomplicated Cystitis… cont’

• Urine Analysis: Evaluation of midstream urine for

pyuria.
– White blood cell casts in the urine are diagnosis of upper
tract infection.
• Urine Culture:
– Warranted in: Suspected complicated infection, persistent
symptoms following treatment, symptoms recur after
treatment.

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 Acute Uncomplicated Cystitis… cont’

Urine dipsticks:
Leukocyte esterase (pyuria), sensitivity 75-90%, specificity
95%
Nitrite (Enterobacteriacea), sensitivity 35-85%, specificity
95%, false positive with phenazopyridine, beets.
Microscopic evaluation for pyuria or a culture is indicated in
patient with negative leukocyte esterase that have urinary
symptoms.

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 Acute Uncomplicated Cystitis… cont’

• Antibiotic Susceptibility:
– E. coli
• 30% isolates resistance to ampicillin and sulfonamides
• Increasing of resistance to TMP-SMX
• Resistance to nitrofurantoin is <5%
• Resistance to fluoroquinolones <5%
– S. saprophyticus
• 3% resistant to TMP-SMX
• 0% resistant to nitrofurantoin
• 0.4% resistant to ciprofloxacin

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 Acute Uncomplicated Cystitis… cont’

• Treatment:
– Short course vs. prolonged tx
• Short course preferred except with beta-lactam agents
– TMP-SMX (160/800mg BID x 3) first-line tx if: no
allergy to the drug and no recent hospitalization.
– Nitrofurantoin (100mg BID x 5 days)
– Analgesia: Phenazopyridine 200mg TIDx2

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 Acute Urethral Syndrome
• Acute symptomatic women with dysuria and
frequency with a midstream culture containing < 105
CFU/mL.
• > 102 CFU/mL in women with acute symptomatic
pyuria = UTI
• Treatment as an uncomplicated UTI
– Mycoplasma genitalium
– Ureaplasma urealyticum

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 Acute Complicated Cystitis
• UTI when/with structural, functional or metabolic
abnormalities (polycystic, solitary, transplant kidney;
DM, CRF, indwelling catheter, neurogenic bladder) or
elderly, male, child, pregnant or h/o recurrent UTI)
– E. coli accounts for fewer than one third of complicated
cases.
• Clinically, the spectrum of complicated UTIs may
range from cystitis to urosepsis with septic shock.

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 Acute Complicated Cystitis….cont’

• Urine culture and susceptibility are necessary.

• These infections are usually associated with high-
count bacteriuria (> 10(5) CFU/mL).
• Etiologies: Proteus, Klebsiella, Pseudomonas,
Serratia, and Providencia, enterococci, staphylococci
and fungi and E. coli

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 Acute Complicated Cystitis….cont’

• Empiric therapy for these patients should include an

agent with a broad spectrum of activity against the
expected uropathogens: fluoroquinolone,
ceftazidime, cefepime, aztreonam,
imipenemcilastatin.
• Obtain Urine culture examination prior to Treatment
• Treatment for 7-14 days
• Follow-up urine culture should be performed within
14 days after treatment???

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 Recurrent Cystitis

• Up to 27% of young women with acute cystitis

develop recurrent UTIs.
• The causative organism should be identified by urine
culture.
• Relapse: infection with the same organism (multiple
relapses = complicated UTIs).
• Recurrence: infection with different organisms.

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 Recurrent Cystitis…. Cont’

• >3 UTI recurrences documented by urine culture

within one year can be managed using one of three
preventive strategies:
1. Acute self-treatment with a three-day course of standard
therapy.
2. Postcoital prophylaxis with one-half of a TMP-SMX
double-strength tablet (80/400 mg).
3. Continuous daily prophylaxis TMP-SMX one-half tablet
per day (40/200 mg); nitrofurantoin 50 to 100 mg per day;
norfloxacin 200 mg per day.

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 Pyelonephritis
• Acute pyelonephritis
– In severe form the kidney is somewhat enlarged,
and discrete, yellowish, raised abscesses are
apparent on the surface.
– The pahtogonomic histologic feature is supprative
necrosis or abscess formation within the renal
subsatance.

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 Pyelonephritis…. Cont’

• Chronic pyelonephritis
– Refers to pathologic changes in the kidney caused
by infection only
– However identical pathologic alterations are found
in several other entities such as chronic urinary
obstruction, analgesic nephropathy, hypokalemic
nephropathy, vascular diseases, uric acid
nephropathy.
– Pathologic descriptions can’t differentiate
between the changes produced by infection
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 Pyelonephritis…. Cont’

• Chronic pyelonephritis
– One or both kidney contain gross scars, but even
when involvement is bilateral, the kidneys are not
equally damaged
– This uneven scarring is useful in differentiating
chronic pyelonephritis from diseases that cause
symetrical contracted kidneys- e.g. chronic
glumeronephritis

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 Papillary necrosis

• Papillary necrosis from infection is an acute

complication of pyelonephrities, usually in the
presence DM, urinary tract obstruction, sickle cell
diseases, or analgesic abuse
• Can happen in the absence or presence of infection

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 Uncomplicated Pyelonephritis

• Suspect if:
– Cystitis-like illness and accompanying flank pain
– Severe illness with fever, chills, nausea, vomiting,
abdominal pain
– Gram-negative bacteremia.

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 Uncomplicated Pyelonephritis… cont’

• Diagnosis: Clinical, confirm with:

– Urine Analysis: pyuria and/or WBC casts
– Urine culture with > 105 CFU/mL (80%)
• Treatment: 14 days total
– Oral: TMP/SMX, fluoroquinolones
– IV: 3rd gen cephalosporin, aztreonam, quinolones,
aminoglycoside

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 Uncomplicated Pyelonephritis… cont’

• Patient with symptoms after 3 days of appropriate

antimicrobial treatment should be evaluated by renal
ultrasound for obstruction or abscess.
• UTI in Men
– At risk: Older men with prostatic disease, anal sex,
or partner colonized with uropathogens, etc
– Urine Culture: 103 CFU/mL sensitivity and
specificity 97%.
– Additional studies?
• Not necessary in young healthy men who have a single
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 UTI in Men… cont’

• Treatment:
– Uncomplicated cystitis:
• TMP/SMX or fluoroquinolones x 7 days
– Complicated cystitis:
• Fluoroquinolones x 7-14 days
– Bacterial prostatitis:
• Fluoroquinolone x 6-12 weeks

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 Catheter-Associated UTI
• Risk of bacteriuria is ~ 5%/day (long term catheter
bacteriuria is inevitable).
• 40% of nosocomial infections
• Most common source of gram-negative
bacteremia.
• Diagnosis: Urine culture 102 CFU/mL
– Microorganisms: E. coli, Proteus, Enterococcus,
Pseudomona, Enterobacter, Serratia, Candida

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 Catheter-Associated UTI
• Mild to moderate: oral quinolones10-14days
• Severe infection: IV/oral 14-21days
• Asymptomatic bacteriuria in pt with an indwelling
should not be Tx unless they are immunosuppressed,
have risk of bacterial endocarditis or pt who are
about to undergo urinary tract instrumentation.

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 Asymptomatic Bacteriuria
• Urine Culture: > 105 CFU/mL with no symptoms
• Three groups of pt with asymptomatic bacteruria
have been shown to benefit from treatment:
– Pregnant
– Renal transplant
– Pt who are about to undergo urinary tract procedures.

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 Pregnant patients
• Asymptomatic bacteriuria: two consecutive voided
urine specimens with isolation of the same bacterial
strain >10(5) or a single cath urine specimen.
– Nitrofurantoin 100mg BID x 5-7 days
– Amoxi/Clav 500mg BID or 250 TID x 7days
– Fosfomycin 3g PO x 1

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 Assignment
Post streptococcal glumerolonephritis

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 Thank you for
your attention!
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