Organisms causing urinary tract

infections

Dr. Nilanthi Senanayake

Senior Lecturer in Microbiology
Faculty of Medicine
University of Colombo
Objectives:
• list common organisms causing urinary tract infections
• Describe briefly the common characteristics of
enterobacteriaceae.
• Describe how Escherichia coli cause urinary tract infections
and Gastroenteritis and how they are diagnosed and treated.
• describe infections caused by Klebsiella, Proteus and other
Gram negative species and how they are diagnosed and
treated.
 Enterobacteriaceae
• Gram-negative non-spore forming bacilli.
– When motile, by peritrichous flagella.
• Primarily normal flora of gastrointestinal tract.
– E. coli>Klebsiella>Proteus>Enterobacter
• Free living, also transient colonizers of skin.
• Facultative anaerobes
• All ferment glucose
– all oxidase negative.
Enterobacteriaceae
• Able to grow in the presence of bile
– Primary isolation media include MacConkey agar.

• Differential selective media for specific organisms

including dyes and bile salts.
– Salmonella-Shigella (SS) medium,
– bismuth sulfite media

Commonly known as coliforms

 Classification
~30 genera, over 100 species.
–Escherichia –Proteus
–Klebsiella – Providencia
–Salmonella – Morganella
– Hafnia
–Shigella
– Serratia
– Edwardsiella
– Yersinia
– Citrobacter
– Erwinia
– Enterobacter
 Antigenic Structure
• O antigen - lipopolysaccharide (endotoxin).
• H antigens - Most are motile by flagella.
• K antigen - Capsule.
– (Vi for Salmonella)-
• Important serotypes can be differentiated by their O,
H and K antigens
• various outer membrane proteins.
• Pili - various antigen types, some encoded by plasmids
 Antigens of Enterobacteria
• Enterobacteria possess a variety of antigens
– Used in serotyping
– Particularly Salmonellae, Shigellae, and E.coli

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 Antigens of Enterobacteria
1. O antigens: found in the bacterial cell wall
- heat stable
2. K antigens: capsular polysaccharide antigens
- surround the cell wall and can therefore interfere
with detection of underlying O antigens (K antigens
can be heat-inactivated, enabling O antigens to be
detected)
- K antigens of some salmonellae, e.g. S. Typhi, are
called Vi antigens
3. H antigens: flagellar protein antigens
- possessed by motile enterobacteria
- heat labile (destroyed at 60–100 0C) 8
Opportunistic diseases - • Escherichia
Enterobacteriaceae • Klebsiella
• Urinary tract infections • Citrobacter
• Enterobacter
• Septicemia,
• Hafnia
• Wound infections • Morganella
• Pneumonia
• Providencia
• Meningitis
• Serratia

• Escherichia coli
• Gastrointestinal diseases • Salmonella
• Shigella
• Yersinia entercolitica
 MacConkey agar
Contains lactose and other sugars

Has an indicator to detect acid

production
Acidic pH – pink

Lactose fermenter – pink

Lactose non fermenter – no clour
change

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 Enterobacteriaceae
• Includes many bacterial genera

• Lactose fermenting
Escherichia Klebsiella
Enterobacter Citrobacter

• Non-lactose fermenting
Salmonella Shigella
Proteus Providencia
Serratia Edwardsiella
Morganella Hafnia
Yersinia
• Species can be identified by biochemical tests 13
Identification of enterobacteria –
Biochemical tests

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Identification of enterobacteria –

Analytical Profile Index (API 20E)

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 Escherichia coli
• Predominant commensal flora of the intestinal tract.
• Some strains may contain pathogenic mechanisms that can
cause disease
– Toxins
– Adhesins
• Also found in the environment
– In water, food
– Indicator of faecal contamination
• Coliform count
Escherichia coli
• Motile , fimbriated GNB
– Some may have a capsule.
• Antigenic structure
– “O” antigen
– “H” flagella antigen
– “K “ capsular antigen
• polysaccharide
• Grow well on most culture media
– Lactose fermenter in McConkey agar
Growth on McConkey agar
(A selective and indicator medium)

Lactose fermenter Lactose non fermenter

 Pathogenesis
• “O” and “K” antigens protects against complement and
phagocytes.
• Haemolysins
• Siderophores
– Able to utilize ferric ions host cells
E. Coli
 Clinical infections
• Urinary tract infections
– Community acquired
– Hospital acquired
• Gastroenteritis
• Septicaemia, meningitis
– Especially in neonates
– K1 antgen stains more common
• Wound infection
• Abscesses
E. coli urinary tract infections

• Most common cause of acute UTI

• Infection can be
– Community acquired
– Hospital acquired
• Infection is seen more in women
E. coli urinary tract infections

• Predisposing factors
– Stagnation of urine
– Urethral obstruction
• Strictures, prostate enlargement
– Congenital malformations
– Calculi
– Instrumentation
• Catheters, cystoscopy
Urinary tract infections
• Most infections are endogenous.
– hospital associated infections may be due to colonization
• Organism attaches to the uroepithelium
– E. coli species which cause UTI’s typically have fimbriae with a
receptor for epithelial cell antigens
• eg “P” antigen, mannose residues
• Following attachment organisms invade and multiply
Diagnosis & Treatment
• Signs and symptoms
• Dysuria, increased frequency,
• Lower abdominal pain
• Turbid urine
• Fever
• Specimens
– Mid stream urine
– Catheter specimens
– Clean catch specimen from neonates infants and small
children
 Diagnosis & Treatment
• Culture
– CLED medium
– Semi quantitative culture
– Culture - 1 µl of urine - > 100 colonies
– Significant bacteriuria – 105 cfu/ml of urine

• Treatment
– Oral antibiotic for uncomplicated UTI
• Cotrimoxazole, Nalidixic acid, Nitrofurantoin, Norfloxacin
– Hospital associated UTI may require parenteral broad spectrum
antibiotics
 Gastroenteritis
• Some E.coli may cause gastrointestinal disease.
• Severity can range from mild self limiting to severe
haemorrhagic colitis
• Associated with Haemolytic uraemic syndrome (HUS).
• Five groups associated with gastroenteritis
 E.coli causing gastrointestinal disease
1. Enteropathogenic E. coli (EPEC)
2. Enterotoxigenic E. coli (ETEC)
3. Entero-invasive E. coli (EIEC)
4. Entero-haemorrhagic E. coli (EHEC)
5. Entero-aggregative E. coli (EAggEC)
 1) Enteropathogenic E. coli (EPEC)
• Certain serotypes are commonly found associated with
infantile diarrhoea.
• There is a characteristic morphological lesions
– Organism adhere to the epithelium without invasion.
– Brush border microvilli are lost.
• Clinically: fever, diarrhea, vomiting and nausea usually with
non-bloody stools.
 2) Enterotoxigenic E. coli (ETEC)
• Produce a watery diarrhoea, fever, abdominal cramps and nausea.
– Also known as "traveler’s diarrhoea".
– important cause of diarrhea in children in resource-poor countries
• Two types of enterotoxins are produced.
a) Heat labile toxins (LT)
• A&B sub units
• Adenyl cyclase is activated with production of cyclic AMP and increased
secretion of water and ions.
• similar to cholera toxin.
b) Heat stable toxins (ST)
• guanylate cyclase is activated which inhibits ionic and water uptake from the
gut lumen.
 3) Entero-invasive E. coli (EIEC)

• Cause dysentery
– Blood and mucus diarrhoea
– indistinguishable clinically from shigellosis.
• After ingestion, binds to the epithelial cells and taken in by
endocytosis.
• Multiply within the cell and cause cell lysis and spread to other
epithelial cells
– Inflammation and necrosis leading to ulceration.
 4) Entero-haemorrhagic E. coli (EHEC)
• Associated with mild to severe haemorrhagic diarrhoea
• Also known as Verotoxigenic E. coli (VTEC).
• Haemorrhagic colitis
– characterized by bloody and copious diarrhea with few
leukocytes in afebrile patients.
• organisms can spread into the bloodstream producing systemic
hemolytic-uremic syndrome (HUS).
– haemolytic anaemia, thrombocytopenia and kidney failure.
• Outbreaks are often caused by contaminated food.
– Hamburger / vegetables
– These are mostly due to serotype O157: H7.
Verotoxin
• An enterotoxin similar to the shiga toxin.
• Mediated by a bacteriophage
• Antigenically there are two types of toxins
– VT1 & VT2
• A &B subunits
– B subunit bind to surface receptors and A subunit prevent protein synthesis.
• Binds to receptors on cell surfaces
– Eg. erythrocytes, kidney cells
 5) Entero-aggregative E. coli (EAggEC)

• Associated with diarrhoea in children, especially in

malnourished children.
• Affect the small intestines.
– Aggregate and adhere to the epithelium
 Diagnosis and treatment
• Stool specimen for culture
– Lactose fermenting Gram negative baciili
– Specific identification by biochemical tests
– Specific antisera for identification of seotypes
• EPEC diarrhoea in children under 2 years of age.
– Toxin detection
• ELISA
• PCR
• Gene detection

• Antibiotic treatment
– Generally not recommended
– May increase morbidity
 Klebsiella
• Commonly Klebsiella pneumoniae
– Rarely Klebsiella oxytoca
– Lactose fermenter
• Commensals of GI tract, but potential pathogen
in other areas
– Opportunistic infections
• UTI, Respiratory infections etc.
• Virulence factors
– Capsule - Give rise to thick mucoid colonies
– Adhesions
– Iron capturing ability
Mucoid colonies of
Klebsiella
pneumoniae
 Clinical significance of Klebsiella
• Urinary tract infections
• Causes pneumonia - (K. pneumoniae)
– mostly in immunocompromised hosts.
– Bronchopneumonia with abscess formation
• In severe infections lung damage may occur.
• A major cause of nosocomial infections such as septicemia and
meningitis
• wound infections, bacteremia, meningitis, etc
• Treatment
– K. pneumoniae is inherently resistant to ampicillin/amoxycillin

– But in UTI
• amoxycillin/clavulanic acid combination,
• Cotrimoxazole
• Nitrofurantoin

– Other infections
• 2nd or 3rd Gen cephalosporins
• Fluoroquinalones
 Proteus
• Commensals of GI tract, but potential pathogen in other
areas

• General characteristics:
– Able to “swarm” due to motility
– Progressive spread from the edge of the colony to cover the plate.
– Non lactose fermenter
 Proteus mirabilis
Gram-negative, Facultatively anaerobic bacterium
Non lactose fermenter
P. mirabilis produces a very distinct odour.
It shows swarming motility, and urease activity
P. mirabilis causes 90% of all 'Proteus' infections
Alkaline urine sample is a possible sign of P. mirabilis (Urease
hydrolyzes urea to ammonia (NH3 )
 Proteus mirabilis cont..
Bacterium has the ability to produce high levels of urease

Urease hydrolyzes urea to ammonia (NH3) and thus makes the urine more alkaline

If left untreated, the increased alkalinity can lead to the formation of crystals of calcium
carbonate and apatite

The bacteria can be found throughout the stones

Proteus can also cause wound infections, septicemia and pneumonias (HAP and VAP)
Swarming
of Proteus
 Proteus
• Urinary tract infections – P. mirabilis
– In children,
– Associated with renal calculi
– Produces urease – alkaline conditions can lead to formation of calculi in the
urinary tract.
– Treatment – cotrimoxazole, ampicillin effective
– Resistant to Nitrofurantoin
• Other infections

• P. vulgaris strains (OX-19, OX-K, OX-2) have common antigen with

Rickettsia (Weil-Felix test).
 Pseudomonas aeruginosa
Gram negative rods
Obligate Aerobes
Produce water soluble pigments (pyocianin – greenish blue )
Transmission via fecal contamination
 Pseudomonas aeruginosa cont..
An opportunistic human pathogen in immunocompromised patients
Also cause hospital acquired infections
Can survive in the environment, in disinfectant solutions
P. aeruginosa typically infects
– Pulmonary tract
– Urinary tract
– Burns (most common cause)
– Wounds

P. aeruginosa is naturally resistant to a large range of antibiotics

 Pseudomonas aeruginosa
Nutrient agar Blood agar
 Oxidase test

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 Enterobacteriaceae Pseudomonas spp
Gram negative Gram negative
Facultative anaerobes Obligate aerobes
Oxidase negative Oxidase positive

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 Enterobacter
Found as saphrophytes and occasionally in human faeces and respiratory
tract
Clinically important species
E. aerogenes
E .cloacae
E. sakazakii

Infections caused by Enterobacter,

1. urinary tract infections
2. Septicaemia
Occur mainly as hospital infections

LF
Share many features with Klebsiella but motile and ornithin positive
ONPG positive 50
 Serratia
• Serratia marcescens is the commonly encountered
pathogen

Pathogenesity

Usually found in environment but cause infections in hospital

patients
1. Urinary tract infections
2. Respiratory tract infections
3. Meningitis
4. Wound infections
5. Septicaemia
6. Endocarditis
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 Serratia
• Motile rods or cocco-bacilli
• Produce a non-diffusible
red pigment which is
prominent after cultures
are kept at room temperature
for few hours
• VP positive
• PPA negative
• No H2S
• GELATINASE POSITIVE
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 Citrobacter
• Citrobacter freundii is the commonest pathogenic species
• Citrobacter koseri can cause neonatal meningitis
• Increasingly isolated in hospital patients, specially patients
of specialised units who are seriously ill
Infections caused by Citrobacter
1. Ventilator-associated pneumonia
2. Septicaemia

Motile
Citrate positive
MR positive
Gas +
VP, PPA negative
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Lactose fermentation variable
 Edwardsiella
• Infections are related to trauma in aquatic
environments
• Can cause severe sepsis
• Edwardsiella tarda is the commonest clinical
isolate

– NLF
– Lysine decarboxylase positive
– Negative in VP, citrate, urease, PPA, ONPG
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 Hafnia
• Hafnia alvei is the only species
• Opportunistic pathogen can cause wound
infection, abscesses, UTIs, sepsis

• NLF
• VP positive
• Negative for urease, indole, PPA, citrate,
H2S

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 Enterococcus
Enterococcus faecalis, Enterococcus faecium

Gram positive cocci in chains

Forms small colonies
Most strains are non haemolytic
Facultative anaerobe
Habitat is the human colon, tolerant to bile acids and
salts
Urethra and female genital tract can be colonized
Can cause hospital acquired infections
Antibiotic resistant development is a problem
 Enterococcus faecalis
Gram stain Colony morphology
 Staphylococcus saprophyticus
Gram positive cocci in clusters
Facultative Anaerobe
Skin coloniser
Community acquired
Typically causes infection in young, healthy females

Catalase test - positive

Coagulase test - negative
 Staphylococcus saprophyticus

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 Candida infection
Risk factors for candiduria
Diabetes mellitus
Indwelling urinary catheters
Antibiotic use

Candiduria may clear spontaneously or may result in deep fungal

infections
The presence of Candida species in the urine usually represents
colonization and not infection
Not all patients with candiduria require treatment
 Candida
Yeast

Many species are harmless commensals in humans

When mucosal barriers are disrupted or the immune system is

compromised they can invade and cause disease, known as an
opportunistic infection

Found on mucosal surfaces (mouth, vagina) and in the gastrointestinal

tract, along with the skin

Can cause superficial and invasive infections

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 Candida
Budding yeast cells

Forms large, round,

white or cream colonies

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 Diagnosis of UTI
Urine microscopy
Pus cells

Urine culture

Blood culture in upper tract infection

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 Urine culture
Semiquantitative method

>105 colony forming units, pure growth is taken as significant

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 Management
Lower UTI
Urinary antiseptics – Nitrofurantoin
Oral therapy is sufficient in uncomplicated patients

Upper UTI
Needs systemic therapy

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