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Urinary tract infections


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Urinary Tract Infections
Lab Diagnosis

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Urinary tract infections

  1. 1. Urinary Tract Infections Dr. Kanwal Deep Singh Lyall
  2. 2. 1. Definition 2. Anatomical structure 3. Classification 4. Etiology 5. Pathogenesis 6. Sign & symptoms 7. Specimen collection & transport 8. Lab diagnosis & interpretation 9. AST 10. Treatment 11. References
  3. 3. • A spectrum of diseases caused by microbial invasion of GU tract that extends from renal cortex of the kidney to the urethral meatus • An extremely common medical problem • Commonest sample received
  4. 4. Urinary tract
  5. 5. Resident Microflora of Urethra • Coagulase-negative staphylococci (excluding S. saprophyticus) • Viridians & non-hemolytic streptococci • Lactobacilli • Diphtheroids (Corynebacterium spp.) • Nonpathogenic Neisseria spp. • Anaerobic cocci • Propionibacterium spp. • Anaerobic gram-negative bacilli • Commensal Mycobacterium spp. • Commensal Mycoplasma spp.
  6. 6. Classification of UTI
  8. 8. Upper urinary tract infections Acute pyelonephritis Enterobacteriaceae Staphylococcus aureus Subclinical pyelonephritis CONS Candida Mycobacterium Mycoplasma hominis
  9. 9. Lower urinary tract infections Acute bacterial cystitis E coli Klebsiella spp. Proteus Enterococci CONS Urethritis Acute urethral syndrome Chlamydia trachomatis Neisseria gonorrhoeae Ureaplasma urealyticum
  10. 10. Etiology
  11. 11. Most frequent • Enterobacteriaceae • Enterococci • Streptococcus agalacitiae (gp B strept.) • Pseudomonas • Streptococcus pyogenes (gp A strept.) • Staphylococcus aureus • Staphylococcus saprophyticus • Candida species
  12. 12. Less frequent • Gardnerella vaginalis • Ureaplasma urealyticum • Mycoplasma hominis • Mobiluncus • Leptospira • Mycobacterium species • Chlamydia trachomatis
  13. 13. Often associated with multisystem diseases • Schistosoma haematobium • Cryptococcus neoformans • Trichosporon beigelii • Trichomonas vaginalis • Aspergillus • Penicillium • Adenovirus • HSV
  14. 14. Pathogenesis
  15. 15. Risk factors for UTI Females Males All ages Previous UTI Uroligical instrumentation or surgery Urethral catheterization Urinary tract obstruction Neurogenic bladder Renal transplantation Lack of circumcision Uroligical instrumentation or surgery Urethral catheterization Urinary tract obstruction Neurogenic bladder Renal transplantation HomosexualsAdults Sexual intercourse Spermicidal contraceptive jellies Diaphragm use Pregnancy Lower socioeconomic group Diabetes Sickle cell trait in pregnancy HIV + Diabetes HIV+ Older age Estrogen deficiency Loss of vaginal lactobacilli Bladder prolapse Functional & mental impairment Prostatic enlargement Condom catheter drainage
  16. 16. Antibacterial host defenses in urinary tract • Urine (osmolality, pH, organic acids) • Urine flow & micturation • Urinary tract mucosa (bactericidal activity, cytokines) Urinary inhibitors of bacterial adherence 1. Tamm-Horsfall protein 2. Bladder mucopolysaccharide 3. Low-molecular-weight oligosaccharides 4. Secretory immunoglobulin A (SIgA) 5. lactoferrin Inflammatory response 1. PMNs 2. Cytokines Immune system 1. Humoral immunity 2. Cell-mediated immunity • Prostatic secretions
  17. 17. Uropathogenic strains • Not all E coli cause UTI • Serogroups O1, O2, O4, O6, O7,O8, O75, O150 & O18ab • Certain O,K & H serogroups also correlate with clinical severity
  18. 18. Recognized virulence factors include • Adhesins →pili or fimbriae • Nonfilamentous proteins in outer membrane • P fimbriae • K antigen (K1, K5, K12) • α & β hemolysins • Aerobactin • Siderphores • Endotoxins • Sat protein • Motility
  19. 19. • Proteus adhere produce→ → urease hydrolyze urea increases pH of→ → urine direct toxicity to kidney cells→ stimulates formation of kidney stones→ • Similar findings with Klebsiella spp. • S. saprophyticus adheres better than S.aureus or S. epidermidis • invade superficial epithelial cells → replicate large foci triggers host→ → response exfoliation of superficial cells→
  20. 20. Signs & Symptoms
  21. 21. 1. Urethritis 2. Cystitis 3. Pyelonephritis 4. Asymptomatic bacteriuria 5. Urethral syndrome Types of UTI & their clinical manifestations
  22. 22. Specimen collection & transport
  23. 23. Specimen Patient preparation Special instructions Clean voided mid stream urine Females: clean area with soap & water; hold labia apart & begin voiding in commode; after passing several ml, collect MSU Males: clean glans with soap & water, rinse with water, retract the foreskin, after passing several ml, collect MSU
  24. 24. Specimen Patient preparation Special instructions Suprapubic aspirate Disinfect skin Needle aspiration above the symphysis pubis through abdominal wall into full bladder
  25. 25. Specimen Patient preparation Special instructions Indwelling catheter (Foley) Disinfect catheter Collection port Aspirate 5-10ml of urine with needle & syringe
  26. 26. Specimen Patient preparation Special instructions Straight catheter (in & out) Clean urethral area (soap & water) & rinse with water Insert catheter Into bladder; allow 1st 15ml to pass; collect remainder
  27. 27. • 1st urine passed in morning → most concentrated • Renal failure/young child → few milliliters of urine • Label (date & time of collection, name & number) • Explain to patient • Deliver promptly • Delay unavoidable → store in refrigerator at 4°C • Or transport in refrigerated container • Or collection & transport in container with boric acid at a final bacteriostatic conc. 1.8% • Samples not so treated and delayed more than 5hrs should be discarded & doctor should be informed
  28. 28. Tuberculosis of urinary tract • 1st urine passed in the day (early morning urine; EMU) • 3 to 6 consecutive days • 3 complete EMU should be sent to laboratory • Individual specimens refrigerated pending process
  29. 29. Urethritis • Initial flow rather than the mid stream collected Prostatitis • Prostatic secretions • Urethral urine & MSU obtained before & after massage
  30. 30. Laboratory Examination of Urine
  31. 31. Urine specimen Wet film Culture Microscopy Gram stain Non-specific biochemical tests Gross examination BA MacConkey LF NLF Colony charc. H’lysis α,β,NHPin head, pin point Identification AST
  32. 32. Appearance Possible Cause Cloudy Urine has an unpleasant smell & contains WBCs •Bacterial urinary infection Red & cloudy Due to red cells •Urinary schistosomiais •Bacterial infection Brown & cloudy → Due to haemoglobin •Blackwater fever •Intravascular Haemolysis Yellow-brown, green brown → Due to bilirubin •Acute viral hepatitis •Obstructive jaundice Yellow-orange → Due to urobilin, i.e. oxidized urobilinogen •Haemolysis •Hepatocellular jaundice Milky-white→ Due to chyle •Bancroftian filariasis
  33. 33. Microscopy Examine wet preparation, 40X to detect • Pus cells • Red cells • Casts • Yeast cells • Trichomonas vaginalis motile trophozoites • Schistosoma haematobium eggs • Bacteria (freshly collected urine)
  34. 34. WBC Epithelial cells RBC Tyrosine crystals calcium oxalate "coffin-lid" triple phosphate Uric acid crystals Cholesterol crystals Cystine crystals
  35. 35. Hyaline castGranular cast Cellular cast RBC cast of glomerular pathology Spermatozoa WBC cast of pyelonephritis
  36. 36. S. haematobium Budding yeast bacteria and many white cells Trichomonas vaginalis Renal epithelial cells Transitional Epi cells
  37. 37. Examination of a gram stained smear • Both uncentrifuged & centrifuged specimens • 1 or more bacterial cells/OIF x at least 5 fields (uncentrifuged) ≥ 105 CFU/ml • If negative → smear sediment → bacterial cells indicate < 105 CFU/ml
  38. 38. Non-specific biochemical tests 1. Griess nitrite test 2. Leucocyte esterase test 3. Catalase test 4. Triphenyltetrazolium chloride (TTC) 5. Glucose test paper method
  39. 39. Urine specimen Wet film Culture Microscopy Gram stain Non-specific biochemical tests Gross examination
  40. 40. Culture the specimen Quantitative methods Semi quantitative methods Pour plate method Surface viable count By spreading method Standard loop method Filter paper method Dip-slide method Miles & Misra method
  41. 41. Standard loop method No. of CFUs x 1000 (0.001 ml loop) or x 100 ( 0.01 ml loop) = no. of bacteria/ml
  42. 42. Dip slide method
  43. 43. Urine specimen Wet film Culture Microscopy Gram stain Non-specific biochemical tests Gross examination BA MacConkey LF NLF Colony charc. H’lysis α,β,NHPin head, pin point Identification AST
  44. 44. MacConkey LF NLF LF •Enterobacter (M,indole-, citrate+) •E.coli (M,indole+, citrate-) •Klebsiella (NM,indole-,urease+,citrate+) LLF •Citrobacter (M) •Serratia (M) Contd.
  45. 45. NLF Oxidase - Oxidase + Motile MotileNon-Motile Non-Motile •Chrysobacterium meningosepticum •Empedobacter brevis •Spingobacterium multivorum •Spingobacterium spiritivorum •Spingobacterium thalpophilium •Shigella •Acinetobacter Contd.Contd.
  46. 46. NLF, Oxidase +, motile • Pseudomonas aeruginosa • Pseudomonas flurescens • Pseudomonas mendocina • Pseudomonas monteilli • Pseudomonas putida • Pseudomonas stutzeri • Burkholderia cepacia • Aeromonas • Plesiomonas
  47. 47. NLF, Oxidase –ve, motile • Edwardsiella tarda • Edwardsiella tostinae • Hafnia (variable motility) • Morganella morganii • Proteus mirabilis • Proteus penneri • Proteus vulgaris • Providentia stuartii • Providentia rettgerii
  48. 48. BA Haemolysis Colony characters βα NH Pin head size Pin point size Staphylococcus Streptococcus Contd.
  49. 49. Haemolysis β-haemolytic Strept pyogenes Strept agalactiae Staphylococcus aureus α-haemolytic Strept viridans Strept pneumniae NHS Enterococcus faecalis Enterococcus faecium Enterococcus durans Enterococcus avium Streptococcus mutans
  50. 50. Fungal culture
  51. 51. Wet mount/gram stain fungal cells or hyphae or fungal infection suspected→ Few drops of sediment Fungal bottle containing Emmons modification of SDA & SDA with actidione Incubate @ room t° upto 2wks BHIA x room t°x 4wks (Diamorphic fungi suspected) Low colony count as significant as high
  52. 52. Mycobacterium
  53. 53. Urine 50ml x 3600g x 30mnts 2ml sediment Decontamination x oxalic acid x 30mnts Inoculate BACTEC medium LJ medium Incubate x 37°C ≥ 6wks Growth + Confirmation by AFB smear Incubate x 37°C ≥ 6wks Growth + Confirmation by AFB smear
  54. 54. Interpretation
  55. 55. Significant bacteriuria • MSU most easily & commonly collected sample • Contaminants → very bacteria which cause UTI • Isolation not proof of UTI • Proof of UTI → demonstration of pathogens in freshly voided urine in No. > those likely to result from contamination • Edward Kass suggested that this number, taken to indicate significant bacteriuria, is about 105 /ml • In properly collected sample contamination accounts for less than 104 /ml & usually for less than 103 /ml
  56. 56. General interpretation guidelines for urine cultures Result Specific specimen type/ associated clinical condition, if known Workup ≥104 CFU/ml of a single potential pathogen or of each of two potential pathogens MSU/ Pyelonephritis, acute cystitis, asymptomatic bacteriuria or catheterized urines Complete ≥103 CFU/ml of a single potential pathogen MSU/symptomatic males or catheterized urines or acute urethral syndrome Complete ≥three organisms with no predominating organism MSU or catheterized urines None. Because of possible contamination, ask for another specimen Either two or three organisms with predominant growth of one organism type & <104 CFU/ml of other organisms MSU Complete workup for predominant organism. description of other organisms ≥102 CFU/ml of any number of organism Suprapubic aspirates complete
  57. 57. Oxoid Chromogenic UTI Clarity Agar • Chromogenic media → aid diagnosis • Distinguish b/w colonies of different species on a culture plate. • Good growth of the main UTI pathogens • Prevents swarming of Proteus • Coliforms dark blue/purple→ colonies • Enterococci blue/turquoise→ colonies • Improved recovery of S aureus • Correct presumptive identification of Citrobacter freundii • Results 16-24 hours • Ready poured plates • Or dehydrated culture medium
  58. 58. Automated screening methods Automated Principle Bioluminescence UTI screen Detects bacterial ATP utilizing enzymatic bioluminescent reaction of ATP with luciferin & lucifrase Photometry Vitek If significant no. of organisms present grow in medium to a→ detectable conc. Utilizing photometry Colorimetric particle filtration Bac-T-Screen Automated combination testing for both bacteria & WBCs by membrane filtration & detection utilizing Safranin O dye
  59. 59. Antimicrobial sensitivity testing
  60. 60. Urine specimen Wet film Culture Microscopy Gram stain Non-specific biochemical tests Gross examination BA MacConkey LF NLF Colony charc. H’lysis α,β,NHSPin head, pin point Identification AST
  61. 61. • CAUTI • HAI
  62. 62. • AST → Mueller-Hinton agar by Kirby-Bauer disc diffusion method • Antibiotics concentrated in urine → high-content test discs For OPD patients → oral drugs • e.g. amoxycillin or ampicillin (25μg), cephalexin (30μg), nalidixic acid (30μg), ciprofloxacin or norfloxacin (5μg), nitrofurantion (50μg), trimethoprim (2.5μg), co- amoxiclav (30μg) For patients in hospital → parenteral drugs • Sensitivity to cefuroxime (30μg), gentamycin (10μg), amikacin, netlimycin, pipracillin & ceftazidime may be tested
  63. 63. Enterobact eriaceae P aeruginosa & non- enterobact. Staph. Enterococci Strept. Carbenic. Lomeflox., Norflox., or Oflox. Nitrofuran. Trimethop. Carbenic. Ceftizoxime Tetracyc. Lomeflox., Norflox., or Oflox. Lomeflox., Norflox., or Oflox. Nitrofuran. Trimethop. Ciproflox. Norflox. Nitrofuran. Tetracyc. Norflox. Nitrofuran. Antomicrobials usually tested
  64. 64. Treatment
  65. 65. Drug Dose Duration of course Dose Duration of course dose Duration of course dose Trimetho prim 300mg daily 3days 300mg daily 7-14days 200mg 12hrly 4-6 weeks 100mg/ni ght Co- amoxycl av 250mg 8-hrly 3days 250- 500mg 8hrly 7-14days 250mg/ni ght Gentamy cin 3-5mg/kg i.v. daily 7-14days Ciproflox acin 250- 500mg 12hrly 3days 250mg 12hrly oral or 750mg 6-8hrly i.v. 7-14days start treatmen t i.v. in seriously ill patient 250mg 12hrly 4-6 weeks Cefalexin 7-14days 250mg/ni ght Erythrom ycin 250mg 6hrly 4-6 weeks Treatment of presumed UTI Treatment of presumed pyelonephritis Treatment of acute prostatitis Prophyla ctic or suppressi ve threaphy
  66. 66. References
  67. 67. • Mackie & McCartney practical medical microbiology • Bailey & Scott’s diagnostic microbiology • Mahon Manusalis textbook of diagnostic microbiology • Monica cheesbrough textbook of diagnostic microbiology • Mandel’s