Explain brief anatomical structure and function of renal system Discuss about the most common pathogens that can cause urinary tract infections Discuss about the different laboratory diagnostic methods of urinary tract infection

The renal system, also known as the urinary system, produces, stores and eliminates urine
It consists of the kidneys, ureters, bladder and the urethra .
The kidneys make urine by filtering wastes and extra water from blood
Urine travels from the kidneys through two thin tubes called ureters and fills the bladder
When the bladder is full, a person urinates through the urethra to eliminate the waste

1. Microbiology of the Renal
System
HaftomL. (MSc, asst. pro., MedicalMicrobiology), Department
of MLS
May, 2024

2. Objectives
•Explain brief anatomical structure and function of renal
system
•Discuss about the most common pathogens that can
cause urinary tract infections
•Discuss about the different laboratory diagnostic methods
of urinary tract infection
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3. Introduction
•Therenalsystem,alsoknownasthe
urinarysystem,produces,storesand
eliminatesurine
•Itconsistsofthekidneys,ureters,
bladderandtheurethra.
•Thekidneysmakeurinebyfiltering
wastesandextrawaterfromblood
•Urinetravelsfromthekidneysthrough
twothintubescalleduretersandfills
thebladder
•Whenthebladderisfull,aperson
urinatesthroughtheurethrato
eliminatethewaste
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Figure. 1. structures of
the human urinary
system
Short in
female than
male

4. Normal Microbiota of the Urinary Systems
Normal urine is not sterile
Using culture techniques and genetic analysis,
So far, 35 different genera have been identified in the UT.
The most prevalent genera in urine are Lactobacillus,
Corynebacterium, Streptococcus, Actinomyces, and Staphylococcus
Onlylowerpartofdistalurethraandvaginahavearesident
bacterialflora
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5. Restoftheurinarytractisnormallysterile
Flushing effect of urine flow,
The presence of IgA antibody on the bladder wall,
Phagocytosisof microorganisms by polymorphs
on the bladder surface,
A mucin layer on the bladder wall prevents
bacterial adherence
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6. The human microbiome is critical in the maintenance of
health and development at different sites throughout the
body,
•but whether the urinary microbiota have a role similar to that of
bacterial communities at other mucosal sites requires further
investigation
Potential roles of the urinary microbiota
‒Produce antimicrobial compounds that
kill pathogens
‒Outcompete pathogens for common
resources
‒Create a barrier, blocking pathogen access
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7. Urinary Tract Infection
A urinary tract infection (UTI) is an infection that affects part of
the urinary tract. (caused by bacteria, parasite and fungi)
Classified by
•Site
•Cystitis (bladder)
•Pyelonephritis (kidney)
•Urethritis (urethra)
•Prostatitis (prostate)
•Severity
•Uncomplicated: Infection in a structurally and neurologically normal
urinary tract.
•Complicated: associated with factors that compromise the urinary tract
or host defence, catheter/instrumentation, pregnancy, diabetes,
obstruction, anatomic abnormality, transplant/immunosuppression. Often
polymicrobial.
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8. Cystitis
Cystitis is most often caused by a bacterial infection of the
bladder.
“cysto” refers to bladder, and “itis” refers to inflammation.
But it can also occur as a reaction to certain treatments or
irritants such as radiation treatment, hygiene sprays, or
spermicides.
Common symptoms of cystitis includedysuria(urination
accompanied by burning, discomfort, or pain),pyuria(pus
in the urine),hematuria(blood in the urine), and bladder
pain.

9. Continued
In women,bladder infectionsare more common because the
urethra is short and located in close proximity to the anus,
which can result in infections of the urinary tract by fecal
bacteria.
Bladder infections are also more common in the elderly because
the bladder may not empty fully, causing urine to pool; the
elderly may also have weaker immune systems that make them
more vulnerable to infection.

10. Nephritis (Pyelonephritis and
Glomerulonephritis)
Pyelonephritis an inflammation of the kidney, can be caused by
bacteria that have spread from other parts of the urinary tract
(such as the bladder).
The infection can become serious, potentially leading
tobacteremiaand systemic effects that can become life-
threatening
In addition,pyelonephritiscan develop from bacteria that travel
through the bloodstream to the kidney.

11. Continued
Common signs and symptoms include back pain (due to
the location of the kidneys), fever, and nausea or vomiting,
grosshematuria(visible blood in the urine), enlarged
kidney is sometimes palpable.
Urine test findings are similar to
those seen in cystitis, but
urinary WBC casts can be seen

12. Glomerulonephritisoccurs when the glomeruli of the nephrons are
damaged from inflammation.
The most well-characterized mechanism of glomerulo nephritis is the
post-streptococcal sequelae associated withStreptococcus
pyogenesthroat and skin infections.
AlthoughS.pyogenesdoesnotdirectlyinfecttheglomeruliofthe
kidney,immunecomplexesthatforminbloodbetweenS.
pyogenesantigensandantibodieslodgeinthecapillaryendothelialcell
junctionsoftheglomeruliandtriggeradamaginginflammatory
response.
Glomerulonephritiscanalsooccurinpatientswithbacterial
endocarditis(infectionandinflammationofhearttissue
Continued

13. Pathogenesis of UTIs
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Ascending : A UTI typically
starts with periurethral
contamination by a
uropathogen residing in the
gut,
Followed by colonization of
the urethra, and
Subsequent migration of the
pathogen to the bladder,
an event that requires
appendages such as
flagella and pili
Hematogeniousroute

14. •Introduction of bacteria into
the bladder does not
inevitably lead to sustained
and symptomatic infection.
The interplay of host,
pathogen, and
environmental factors
determines whether tissue
invasion and symptomatic
infection will ensue
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FIGURE 162-1 Pathogenesis of urinary tract infection. The
relationship among specific host, pathogen, and
environmental factors determines
the clinical outcome.

15. •Bacterial virulence factors include:
•Enable the uropathogens to adhere, colonize and adapt
to the nutritionally limited bladder environment; evade
immune surveillance; and persist
and disseminate in the urinary tract
•Fimbriae(pili): that facilitate colonization and
adherence to the periurethral areas, urethra and
bladder wall;
•Capsules: inhibits phagocytosis and these are
associated with the development of pyelonephritis.
•Toxin/enzyme
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16. Predisposing host/environmental factors
•Age
•Female sex
•Pregnancy
•Diabetes
•Immunosuppression
•UT instrumentation
•UT obstruction
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17. Epidemiology of urinary tract infections
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18. Pathogens Commonly Encountered in UTI
•Escherichia coli
•Klebsiellapneumoniae
•Proteus mirabilis
•Staphylococcus Spp. (Staphylococcus saprophyticus)
•Pseudomonas aeruginosa
•Enterococcus spp.
•CandidaSpp.
•Schistosomahaematobium
•Others: EnterobactorSpp., CiterobactorSpp.,
Acinetobactorbaumannii, Serraríamarcescens
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19. Escherichia coli
Isa straight gram-negative rod
Normal flora in human and animal
gastrointestinal tract.
Found in soil, water & vegetation.
Most are motile; some are
capsulated
Posses three antigens O, K, andH
antigens
UPEC Virulence factors:
Toxins
Pili (adhesive factors)
Siderophores
Hemolysin

20. •E.coli pathogenesis
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22. UPEC colonization of the
kidneys
Polymeric immunoglobulin receptor (PIGR)

23. Collection of Specimens
•Clean catch mid-stream specimen of urine
•Early morning sample preferred
•Catheter specimen
•Suprapubic aspiration
•Early transport to the lab essential (with in 30 min)
oSamples should be collected before antimicrobial therapy
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24. Sterile specimen container
Female patients
Instruction for collection of mid stream urine
Spread
labia, using
plain soap
or antiseptic
wipe front
to back, dry
with tissues
Retract
prepuce,
using plain
soap or
antiseptic
clean glans.
Dry with
tissues.
Male patients
Beginpassingurine
Stop flow in midstream
Pass several ml into pen
container without touching
rim
Stop flow before it ends
Recapcontainer
Send specimen to
laboratory immediately
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25. •How to collect urine from catheter/
•From bladder : supra pubic?
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26. Processing of Specimen
Uncentrifuged specimen inoculated on
CLED medium and count the CFU/ml of
urine.
Interpret/report with presence or
absence of significant bacteriuria in the
urine.
Centrifuged specimen used for
microscopic exam
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27. Concept of Significant Bacteriuria
•Up to 10
4
cfu/ml considered normal i.e. Insignificant
•10
5
cfu/ml and above considered to be Significant
•However, in acutely symptomatic females and with other types
of specimens (i.e., those obtained by catheterization or
suprapubic aspiration) from either sex, a more appropriate
threshold, particularly in the presence of pus cells and the
absence of epithelial cells, might be more than 10
2
cfu/ml.
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28. Smear: Gram-negative rods
Culture: Lactose-fermenting mucoid
colonies on macconkey agar and some
strains are hemolytic on blood agar .
Colonies are further identified by their
morphology & biochemical reactions
Biochemical reaction
Lactose positive (Ferment lactose)
Indole positive, Lysine decarboxylase
(LDC) positive.
Antibiotic susceptibility testing is also
performed.
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Identification

29. •Other tests too
Beta-glucuronidase (PGUA) positive (E. coli 0157 is PGUA
negative).
-Hydrogen sulphide …… negative.
-Indole and Methyl red,, Voges-Proskaue, Citraterate
(IMViC)…positive, positive, negative, negative (+ + --)
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30. Klebsiella pneumoniae
•The bacterial genusKlebsiellais
named in honor of his work
•Is aGram-negative, non-
motile,encapsulated,lactose-
fermenting,facultative anaerobic,
rod-shapedbacterium.
•It appears as a mucoid lactose
fermenter onMacConkey agar.
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31. The mucoid colonies of
Klebsiella pneumoniae
are evidence of the
bacterium’s heavy
capsule
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32. K. pneumoniae…
Similarly to UPEC, K. pneumoniae uses type 1 pili for
biofilm formation and bladder colonization
Utilizes environmental cues to regulate the expression
of its type 1 fimbriae.
For example, type 1 fimbria genes are expressed in
the UT but not in the GI tract or lungs.
Contribute to the invasion and biofilm formation in
the bladder during UTI in a mouse model
Neither type of fimbria is expressed while K.
pneumoniae is planktonic
type 3 fimbriaeare expressed during biofilm
formation on catheters
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33. •Other Klibsilla spp that cause UTI
•More biochemical tests
•And add citrate and other tests to differentiate from E. coli
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34. Proteus mirabilis
Gram-negative, facultativelyanaerobic, rod-shaped
It showsswarming motilityandureaseactivity.
Analkalineurinesample is a possible sign ofP.
mirabilis
P. mirabiliscauses 90% of allProteusinfections in
humans
It can be diagnosed in the lab due to characteristic
swarming motility, and inability to metabolizelactose
Produces a very distinct fishy odor.
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35. Catheter-associated UTI mediated by Proteus mirabilis
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36. Proteus mirabilis…
P. mirabilis infections can cause the formation of urinary
stones (urolithiasis) composed of
Magnesium ammonium phosphate
(struvite) and
Calcium phosphate (apatite)
These stones can block urinary flow and cause tissue
damage;
They can also become quite large (>1 cm2)
Eventually blocking urine flow through the catheter
Importantly, the accumulation of ammonia becomes toxic for
the uroepithelial cells, inducing direct tissue damage
Furthermore, urinary stones can act as a focal point for
other species of bacteria to establish UTI
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37. Swarming colony ofP. mirabilis.
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38. Urease test in the lab
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39. Staphylococcus saprophyticus
Gram-positive cocci in cluster,
catalase positive, coagulase-negative
2
nd
frequent causative agent of
uncomplicated lower UTI in young,
sexually active women
Most cases occur within 24 hours of sex,
Earning this infection the nickname “honeymoon cystitis”.
In females 17–27 years old
39

40. Mulugeta K. 40

41. •Novobiocin
•Talk relative s. epidermides
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42. Enterococcus faecalis
The enterococci are Gram-positive, facultatively anaerobic
oval cocci that form chains of various lengths;
•They are sturdy and versatile,
•With a particular ability to survive under harsh
conditions (including high salt concentrations) and
•At a wide range of temperatures (from 10°C to
>45°C).
•A leading cause of catheter-associated urinary tract
infection (CAUTI)
•Unlike streptococci and staphylococci,
•Most enterococci do not produce a set of potent pro-
inflammatory toxins,
•but they are equipped with many genes encoding adhesion proteins
that may mediate adherence to host tissues
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43. Enterococcus faecalis pathogenesis during CAUTIs
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44. E. faecalis…
•Difficult to treat because of drug resistance of many E.
faecalis isolates
•Recently, Enterococcus spp. have developed high-level
resistance to glycopeptides,
•Including vancomycin, which is considered to be one of the last lines of
defense against multidrug-resistant organisms
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45. Major routes of nosocomial
transmission of vancomycin-resistant
enterococci
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•physical proximity to patients who
are infected or colonized with VRE
•A long period of hospitalization
•The presence of a urinary catheter
•administration of multiple courses
of antibiotics

46. E. faecalis…
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Many antibiotics increase the density
of VRE organisms in the
gastrointestinal tract, which, in turn,
facilitates the spread of these
organisms through faecal
contamination of the
hospital environment

47. •Bile esculin test
•PYR
•Say group D
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48. Mulugeta K. 48
Pseudomonas aeruginosa
Gram-negative motile aerobic rods having very simple
growth requirement.
Found in human and animal intestine, water, soil and
moist environment in hospitals.
Primarily a nosocomial pathogen.
Invasive and toxigenic, produces infections in patients
with abnormal host defences.

49. Mulugeta K. 49
Laboratory diagnosis
Smear: Gram-negative rods.
Culture: Obligate aerobe, grows
readily on all routine media over
wide range of temperature(5 -42
O
C). Bluish-green pigmented large
colonies with characteristic “fruity”
odor on culture media.
Figure. Pseudomonas aeruginosa
colonies on cetrimideagar

50. Mulugeta K. 50
Biochemical reactions
Oxidase positive
Catalase positive
Citrate positive
Indole negative

51. Mulugeta K. 51
Genus Enterobacter
It is gram-negative lactose fermenting motile rods,
and found as a commensal in the intestinal tract of
humans and animals and moist environments.
Enterobacteraerogensis associated with urinary
tract infection, wound infection and septicaemia in
immuno-compromised and chronically debilitated
patients.

52. •Add some biochemical characteristics or leave it
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53. Mulugeta K. 53
Genus Citrobacter
It is gram-negative lactose fermenting motile
rods, and opportunistic pathogen.
Medical important species is Citrobacterfreundii.
Citrobacterfreundiiis associated with urinary
tract infection, wound infection and septicaemia in
immuno-compromised and chronically debilitated
patients.

54. •Add some biochemical characteristics or leave it
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55. Acinetobacterbaumannii
Gram negative bacillus
Strictly aerobic
Non-motile
Catalase positive
Associated with biofilms, antibiotic resistance
Not part of normal human flora
Environmental reservoirs
Soil, Fresh water, Vegetables, Animals, body lice, fleas,
ticks
Common nosocomial pathogen
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56. In the hospital…
•Environmental surface, ventilators, dialysis machines, air
ventilation systems, water sources, hands, contaminated
suction equipment
•Survives on inanimate surfaces for weeks
•Infections and outbreaks
•Intensive care unit and healthcare settings
•Compromised immune systems and risk
•Colonized and infected patients as point sources
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57. Laboratory diagnosis
•Gram stain: Gram negative bacilli
•Culture:
•MAC, Leeds Acinetobacteragar
•Ferment glucose, xylose, lactose
•Biochemical test: catalase positive,
oxidase negative
•PCR
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58. Fungal causes of UTI
GenusCandida
•Found in oropharynx, GIT, genitourinary tract, and skin of
human as a normal flora.
•Since these species of Candidaare the part of the normal
endogenous microbial flora, candidiasis is usually the
result of autoinfection during an immunologic disturbance.
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59. •Human infection (candidiasis)
•Opportunistic
•Cause disease in immunosuppressed persons
•Caused by the following species of the genus Candida,
namely, C.albicans, C.glabrata, C.tropicalis, C.parapsilosis,
and C.krusei
•C.albicans (> 50%) is the most common cause of infection.
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60. Candida species enter the upper UT
from the bloodstream (antegrade
infection) or
Ascend the UT from a focus of
candidal colonization at or near the
urethra (retrograde infection)
Candida species adhere poorly to
bladder mucosa
•but under conditions of urinary tract
obstruction, concomitant bacteriuria,
or profound immunosuppression,
invasion of the bladder wall, ureter,
and/or kidney
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61. Patients with fungal tract infection can develop
fungus balls that consist of masses of hyphae.
Fungus balls can grow to a large size and lead to
obstruction of the collecting system surgical
intervention or percutaneous drainage is required.
Laboratory Dx
Microscopy: Germ tube test
Serology: Ag/Ab
Culture: SDA
PCR
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62. •How to differentiate between different C. spp
•List/talk like germ tube test, chlamydophore on cornmeal agar
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63. Parasitic diseases as
Urinary Schistosomiasis, and
Trichomoniasis
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Parasitic UTI

64. Schistosomiasis is an endemic disease in tropical, and
subtropical areas.
The urinary schistosomiasis caused by Schistosoma
haematobium is common around 75 countries in South
America, Africa, and The Middle East region.
More than 200 million people are infected, and it is estimated
that more than 800 million people are under the risk of
infection (WHO Information, 2010).
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Urinary Schistosomiasis

65. Mulugeta K. 65
Life Cycle of S. hematobium

66. Theaccumulationofeggsundermucosacausesmucosal
hyperemiaandhematuria.
Theeggswhichpenetrateintothemucosaandmigrateintothe
urinarybladderareexcretedthroughbleedingtheurine
Schistosomiasisisalsoknownasapredisposingfactorfor
adenocarcinomaofthebladder.
Itisoneofthemostimportantreasonsofurinarybladder
carcinomaespeciallyinAfricaandTheMiddleEast
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67. Signs and Symptoms
Itchiness in the area where the helminth enters the body, followed by
fever, chills, diarrhea, and cough.
Urinary tract symptoms occur at a later date.
The disease manifestations occur when the eggs in the bladder
induce a massive granulomatous response that leads to leakage in
the blood vessels and blood in the urine.
Blood in the urine and, eventually, bladder obstruction can occur.
Adult flukes can live for many years and, by eluding the immune
defenses, cause chronic infection.
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68. Laboratory Diagnosis
The parasite is diagnosed by the detection of
Schistosoma eggs in the urine.
The most appropriate method to detect the eggs in
the urine is by examining the last part of the urine
which is centrifuged.
It is recommended that the eggs examined for at least
five different days microscopically if the urine sample
is negative taken from clinically suspicious conditions.
Additionally, antigen and antibody detection tests can
be used alternatively in suspicious conditions
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Egg ofS.
haematobium. Note the
pointed spine at the tip
(i.e. terminal spine)

69. •How schistosoma lead to bladder cancer?
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70. Viruses causing UTI
Rarely, viruses such as adenovirus, BK virus, and
cytomegalovirus can cause a hemorrhagic cystitis.
These viruses almost exclusively cause cystitis in
immunocompromised hosts such as those who have
undergone stem cell transplants.
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71. •Discuss in brief about the viruses
•CMV
•BK
•Like Adeno type 34, 35, 42, 49 that cause UTI
•Consider adding physical, chemical, and microscopic urine analysis
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72. Thankyou!!!
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