Basic Laboratory Investigations

1. Dr. Iman M. Fawzy; MD. PhD.
Mansoura, Egypt

2. Urinalysis

3. COMPONENTS OF THE URINE
DIPSTICK
• Color:pale yellow to amber
• Specific gravity: 1.015–1.025
• pH: 4.5–8.0
• Protein: negative
• Glucose: negative
• Ketone: negative
• Bilirubin: negative
• Urobilinogen: 0.2–1.0
• Blood: negative
• Nitrite: negative
• Leukocytes (esterase): negative

4. COMPONENTS OF THE URINE
DIPSTICK

5. Microscopic Examination of Urine Sediment
Increased WBCs are seen in
Urinary tract disease (eg, cystitis, prostatitis)
Chronic pyelonephritis
Tuberculosis
Viral infection
Interstitial nephritis
Glomerulonephritis
WBC casts
Pyelonephritis (most common cause)
Acute glomerulonephritis
Interstitial nephritis
Lupus nephritis
URINE WHITE BLOOD CELLS
Normal Values: WBCs: 0–4/hpf

6. Microscopic Examination of Urine Sediment
Increased numbers of RBCs occur in
• Contamination during Menstrual cycle
• Glomeulo and Pyelonephritis
• Renal stones
• Cystitis (acute or chronic)
• Prostatitis
• Genitourinary tract malignancies
• Bleeding disorders
• Trauma
• Anticoagulant therapy overdose
RBC casts in
• Glomerulonephritis (acute and chronic)
• Renal infarction
• Severe pyelonephritis
• Congestive heart failure
• Renal vein thrombosis
URINE RED BLOOD CELLS
Normal Values: RBCs: 0–3/HPF

7. Microscopic Examination of Urine Sediment
GRANULAR CASTS
Acute tubular necrosis
Advanced glomerulonephritis
Pyelonephritis
Malignant nephrosclerosis
Fever (dehydration)
Hyaline casts
Glomerulonephritis, pyelonephritis
Malignant hypertension
Chronic renal disease
Diabetic nephropathy
Fever (dehydration)
Emotional stress
Strenuous exercise
WAXY CASTS
Chronic renal disease
Nephrotic syndrome
Localized nephron obstruction
Fatty casts
lipiduria e.g. nephrotic syndrome

8. Urinary sediment crystals
Acidic urine
• Uric acid crystal
• Amorphous urates
• Cholesterol crystals
Alkaline urine
• Triple phosphate
crystals
• Calcium phosphate
• Amorphous phosphates
ACID, NEUTRAL, OR SLIGHTLY ALKALINE URINE
Calcium oxalate

9. URINE COMPOSITION URINALYSIS: FINDINGS IN
COMMON DISEASE STATES.
Disease Protein RBC WBC Casts
Other Microscopic
Findings
Normal 0
0 or
Occ
0 or Occ 0 or Occ Hyaline casts
Fever
Trace or
1+
0 Occ 0 or Occ Granular, Hyaline casts
Eclampsia 3+-4+ 0 or 1+ 0 3+, 4+ Hyaline casts
DM v 0 0 0 or 1+ Glucose, ketones
AGM 2+-4+ 1+-4+ v 2+-4+
Blood; RBC, cellular,
granular, and hyaline casts
Nephrotic
syndrome
4+ 0 4+
Granular, waxy, hyaline,
and fatty casts
Chronic renal
failure
1+-2+
Occ or
1+
0 1+-3+
Granular, hyaline, and
broad casts
Pyelonephritis 1+-2+ 0 or 1+ 4+ 0 or 1+
WBC casts and hyaline
casts; many pus cells;
bacteria

10. Clinical Microbiology

11. Organisms may found in Urine
BACTERIA
Gram positive Gram negative
Staphylococcus Escherichia coli
saprophyticus Proteus species
Haemolytic streptococci Pseudomonas aeruginosa
Klebsiella strains
Mycobacterium tuberculosis
Leptospira interrogans
Chlamydia
Mycoplasma
Candida
PARASITES
Schistosoma haematobium,
Trichomonas vaginalis
Enterobius vermicularis
Wuchereria bancrofti
Onchocerca volvulus.

12. Organisms may found in CSF
BACTERIA
Gram positive Gram negative
Streptococcus pneumoniae Neisseria meningitidis
Streptococcus agalactiae (Group B) Haemophilus influenzae
Listeria monocytogenes Escherichia coli
Pseudomonas aeruginosa
Proteus specie
Mycobacterium tuberculosis
Treponema pallidum.

13. Organisms may found in CSF
VIRUSES
Coxsackieviruses
Echovirus
arboviruses.
herpes simplex 2 virus
varicella zoster virus
FUNGI
Cryptococcus neoformans (mainly in AIDS patients)
Aspergillus species.
PARASITES
Trypanosoma species and Naegleria fowleri
Toxoplasma gondii (mainly in AIDS patients).

14. Bacterial meningitis
Glucose (mg/dL):
Normal to ↓↓<40
mg/dL.
Protein (mg/dL) ↑↑ > 250 mg/dL.
WBCs (cells/µL)
>500 (usually >
1000). Early: May be <
100.
Cell differential:
Predominance of
Neutrophils (PMNs)
Culture: Positive
Opening Pressure ↑
Fungal meningitis
Glucose (mg/dL): <40 mg/dL (Low)
Protein (mg/dL)
(moderate to ↑↑) 25 -
500 mg/dL
WBCs (cells/µL)
Variable (10 -1000
cells/µL) <500cells/µL.
Cell differential:
Predominance of
Lymphocytes
Culture: Positive (fungal)
Opening Pressure Variable
TB meningitis
Glucose (mg/dL): <40 mg/dL (Low)
Protein (mg/dL)
(moderate to ↑↑50 -
500 mg/dL
WBCs (cells/µL)
Variable (10 -1000
cells/µL) <500cells/µL.
Cell differential:
Predominance of
Lymphocytes
Culture: Positive for AFB
Opening Pressure Variable
Viral meningitis
Glucose (mg/dL): Normal (> 40 mg/dL.)
Protein (mg/dL)
<100 mg/dL (moderate
↑)
WBCs (cells/µL) < 100 cells/µL.
Cell differential:
Early: neutrophils. Late:
lymphocytes.
Culture: Negative
Opening Pressure Usually normal

15. Blood Cultures
BACTERIA
Gram positive Gram negative
Staphylococcus aureus Salmonella Typhi
Viridans streptococci Other Salmonella serovars
Streptococcus pneumoniae Brucella species
Streptococcus pyogenes Haemophilus influenzae
Enterococcus faecalis Pseudomonas aeruginosa
Clostridium perfringens Klebsiella strains
Anaerobic streptococci Escherichia coli
Proteus species
Bacteroides fragilis
Neisseria meningitidis
Yersinia pestis
Mycobacterium tuberculosis (HIV-associated tuberculosis),
Leptospira species,
Borrelia species,
rickettsiae,
Bartonella bacilliformis.
FUNGI
Candidaalbicansandother yeasts, e.g. Cryptococcus neoformans, and occasionally Histoplasma
capsulatum and other fungi that cause systemic mycoses.

16. Throat culture
BACTERIA
Gram positive Gram negative
Streptococcus pyogenes Vincent’s organisms
Corynebacterium diphtheriae
Corynebacterium ulcerans
VIRUSES
Respiratory viruses
enteroviruses and herpes simplex virus type 1
FUNGI
Candida albicans and other yeasts.

17. pus, ulcer material and skin culture
BACTERIA
Gram positive Gram negative
Staphylococcus aureus Pseudonomas aeruginosa
Streptococcus pyogenes Proteus species
Enterococcus species Escherichia coli
Anaerobic streptococci Bacteriodes species
Other streptococci Klebsiella species
Clostridium perfringens Pasteurella species
and other clostridia
Actinomycetes
Actinomyces israeli
Also Mycobacterium tuberculosis
FUNGI
Histoplasma c. duboisii
Candida albicans
Fungi that cause mycetoma
PARASITES
Entamoeba histolytica

18. Effusions culture
SYNOVIAL FLUID
Gram positive Gram negative
Staphylococcus aureus Neisseria gonorrhoeae
Streptococcus pyogenes Neisseria meningitidis
Streptococcus pneumoniae Haemophilus influenzae
Anaerobic streptococci Brucella species
Actinomycetes Salmonella serovars
Escherichia coli
Pseudomonas aeruginosa
Proteus
Bacteroides
Mycobacterium tuberculosis

19. Effusions culture
PLEURAL AND PERICARDIAL FLUIDS
Bacterial
Gram positive Gram negative
Staphylococcus aureus Haemophilus influenzae
Streptococcus pneumoniae Bacteroides
Streptococcus pyogenes Pseudomonas aeruginosa
Actinomycetes Klebsiella strains
Other enterobacteria
Mycobacterium tuberculosis
fungi
Viruses especially coxsackie B virus

20. Effusions culture
ASCITIC FLUID
Gram positive Gram negative
Enterococcus species Escherichia coli
Streptococcus pneumoniae Klebsiella strains
Staphylococcus aureus Other enterobacteria
Streptococcus pyogenes Pseudomonas aeruginosa
Streptococcus agalactiae Bacteroides
Viridans streptococci
Clostridium perfringens
Mycobacterium tuberculosis
Candida species

21. Urogenital culture
URETHRAL SWABS
Neisseria gonorrhoeae
Chlamydia trachomatis (serovars D-K)
Ureaplasma
Mycoplasma
Trichomonas vaginalis.

22. Urogenital culture
CERVICAL SWABS
From non-puerperal women:
Neisseria gonorrhoeae,
Chlamydia trachomatis (serovars D-K),
Streptococcus pyogenes,
herpes simplex virus.
From women with puerperal sepsis or septic abortion:
Streptococcus pyogenes, other betahaemolytic streptococci,
Staphylococcus aureus,
Enterococcus species,
anaerobic cocci,
Clostridium perfringens,
Bacteroides,
Proteus, Escherichia coli and other coliforms,
Listeria monocytogenes.

23. Urogenital culture
VAGINAL SWABS
Trichomonas vaginalis
Candida species
Gardnerella vaginalis
anaerobes

24. Stool sample
BACTERIA
Gram positive Gram negative
Clostridium perfringens Shigella species
Clostridium difficile Salmonella serovars
Staphylococcus aureus Campylobacter species
Escherichia coli (toxin)
Vibrio cholerae 01, 0139
Other Vibrio species
Aeromonas species
Mycobacterium tuberculosis
VIRUSES
Rotaviruses, Adenoviruses, , Astrovirus, calcivirus
PARASITES
Entamoeba histolytica, Giardia lamblia

25. Sputum
BACTERIA
Gram positive Gram negative
Streptococcus pneumoniae Haemophilus influenzae
Staphylococcus aureus Klebsiella pneumoniae
Streptococcus pyogenes Pseudomonas aeruginosa
Proteus species
Yersina pestis
Moraxella catarrhalis
Mycobacterium tuberculosis
Mycoplasma pneumoniae
Legionella pneumophila.
FUNGI AND ACTINOMYCETES
Pneumocystis jiroveci, Blastomyces dermatitidis, Histoplasma capsulatum, Aspergillus
species, Candida albicans, Cryptococcus neoformans, and Nocardia species.
PARASITES
Paragonimus species

26. Serology

27. Widal test
negative Widal
absence of infection
by S typhi and para typhi
False negative
• the carrier state
• early treatment
• hidden organism in bone or
joints
• Technical errors
positive Widal
Typhoid fever
False positive in:
• previous immunization with
Salmonella antigen.
• cross-reaction with non-
typhoidal Salmonella.
• infection with
malaria, Brucella, other
Enterobacteriaceae, dysentry,
pneumonia, dengue, immune
diseases
• Technical errors
O antigen: 4 fold ↑ if repeated
Or O antigen >1:160, H> 1: 320 in endemic areas

28. Brucella antibody
negative
absence of infection by
Brucella infection
False negative
• B canis infection
• Technical errors
positive
• Brucella infection (except B
canis)
False positive in:
• infections with Francisella
tularensis, Yersinia
enterocolitica, salmonella,
Rocky Mountain spotted
fever; vaccinations for
cholera
• Technical errors
Positive titer ≥1:80
↑≥ 4-fold in serum specimens obtained >2 weeks apart.

29. C-reactive protein (CRP)
Positive titre: >6 mg/dL
Positive in:
• Inflammation
False positive in:
• High protein diet
• Smoking
• Aging
• Pregnancy or contraceptive use
• Metabolic syndrome (insulin resistance)
• Diabetes
• Elevated triglycerides
• Cancer

30. Rheumatoid factor (RF)
Positive titre: >8 mg/dL
Positive in:
• Rheumatoid arthritis (75-90%),
False positive in
• Other auto immune diseases
• Drugs: methyldopa, others.
• 1-4% of normal individuals, acute immune responses (eg, viral
infections, including infectious mononucleosis and viral
hepatitis), chronic bacterial infections
(tuberculosis, leprosy, subacute infective endocarditis), and chronic
active hepatitis
False negative:
• 20% of Rheumatoid arthritis

31. Antistreptolysin O titer (ASO)
Positive titre: >200 IU/mL
• Detects antibody to the antigen streptolysin O
produced by group A streptococci.
Titer rises to a peak at 4-6 weeks and may remain
elevated for 1 year.
Positive in:
• Streptococcal infection (eg, upper airway
infections, scarlet fever)
• post-streptococcal infection complication (eg,
glomerulonephritis and rheumatic fever).
False positive in
• Some bacterial infections.

32. Hepatitis A antibody (Anti-HAV)
Positive in:
• IgM: Acute hepatitis A
• IgG: convalescence from hepatitis A
IgM antibody is detectable within a week after
symptoms develop and persists for 6 months.
IgG appears 4 weeks later than IgM and persists
for years.

33. Hepatitis B surface antigen (HBsAg)
In hepatitis B virus infection
HBsAg is
• detectable 2-5 weeks before
onset of symptoms
• peaks at the time of onset of
clinical illness.
• persists for 1-5 months
• Declining with resolution of
clinical symptoms.
Positive in:
• Acute hepatitis B
• chronic hepatitis B (persistence
of HBsAg for >6 months, positive
HBcAb [total])
• HBsAg positive carriers.
.

34. HBV markers

35. Hepatitis B markers

36. Hepatitis C antibody (HCV-Ab)
Detects antibody to HCV
Positive in:
HCV infection
False positive:
autoimmune liver disease
Hypergammaglobulinemia
False negative:
immunosuppressed patients
long-term hemodialysis.

37. HCV
ANTI-HCV HCV RNA (PCR) INTERPRETATION
Negative Negative No infection
Positive Positive
HCV present (acute or chronic
infection)
Negative Positive
•Chronic infection in
immunosuppressed patient
•Early infection
Positive Negative
•Resolved infection
•Treated infection
•False-positive anti-HCV test

38. HIV antibody
• HIV antibody test is considered positive only
when confirmed by a Western blot analysis or
immunofluorescent antibody test (IFA).
Positive in:
• HIV infection

39. Toxoplasma antibodys
Toxo IgG
Toxo IgM
Positive in:
• IgM: Acute or congenital toxoplasmosis
• IgG: previous toxoplasma exposure
false-positive
• SLE, HIV infection, positive rheumatoid
factor, positive ANA.

40. AUTOANTIBODIES: ASSOCIATIONS WITH CONNECTIVE TISSUE
DISEASES
Disease Test Sensitivity, Specificity Other Disease
CREST Anti-centromere antibody CREST (70-90%, high)
Scleroderma (10-15%), Raynaud
disease (10-30%).
SLE
ANA SLE (>95%, low)
RA (30-50%), scleroderma (60%),
Sjogren (80%).
anti-ds-DNA SLE (60-70%, high) Lupus nephritis
Anti-Smith antibody (anti-
Sm)
SLE (30-40%, high)
Mixed connective
tissue disease
(MCTD)
Anti-ribonucleoprotein
antibody (RNP)
MCTD (95-100%, low)
Scleroderma (20-30%, low)
SLE (30%), Sjogren, RA (10%),
discoid lupus (20-30%).
Rheumatoid
arthritis (RA)
Rheumatoid factor (RF), Anti-
CCP
Rheumatoid arthritis (50-90%)
Other rheumatic diseases,
chronic infections, elderly
Scleroderma Anti-Scl-70 antibody Scleroderma (15-20%, high)
Sjogren syndrome Anti-SS-A/Ro antibody Sjogren syndrome (60-70%, low)
SLE (30-40%), RA (10%), subacute
cutaneous lupus, vasculitis.
Wegener
granulomatosis
Anti-neutrophil cytoplasmic
antibody (ANCA)
Wegener granulomatosis
(systemic necrotizing vasculitis)
(56-96%, high)
Crescentic glomerulonephritis or
other systemic vasculitis (eg,
polyarteritis nodosa).

41. Clinical Chemistry

42. Glucose
Hyperglycemia
Physiologic
hard physical activity,
strong emotions, e.g., fear.
Pathologic
• Diabetes Mellitus Type 1, 2
• Gestational diabetes
• Chronic renal failure
• Chronic pancreatitis
• Glucagonoma
• Hyperthyroidism
• Pancreatic cancer
• Pancreatitis
• Hypopituitarism, Hypothyroidism
Hypoglycemia
Physiologic
normal pregnancy (mild)
neonates born to diabetic mothers.
Pathologic
Liver necrosis, adrenal cortical
hypofunction,
hepatic failure.
Fasting blood glucose 70-110mg/dL
2 hours post prandial <200 mg/dL

43. Alanine aminotransferase
(ALT, SGPT, GPT)
Reference range: 10 - 46 U/L
Increased in:
Acute viral hepatitis
biliary tract obstruction
Liver cirrhosis
Drugs

44. Aspartate aminotransferase
(AST, SGOT, GOT)
Reference range: 10 - 40 U/L
Increased in:
Acute viral hepatitis
biliary tract obstruction (cholangitis, stone)
cirrhosis
Acute myocardial infarction
Progressive muscle disease
Hemolytic anemia
Drugs

45. ALT + AST
Viral Hepatitis
• ↑20-50 even 100 times
• Before clinical manifestations
• Peak: 7th-12th day  ↓  normal at 3th-5th
week.
• ALT>AST
Toxic hepatitis:
• as viral hepatitis
Infectious mononucleosis + liver involvement:
• ↑ ALT & AST up to 20 times

46. ALT + AST
Biliary obstruction:
• ALT & AST higher in extrahepatic and chronic
obstruction
Cirrhosis:
• ALT & AST: high normal  ↑5 times
• AST>ALT
Malignancy
• ALT & AST: normal  ↑5-10 times

47. Bilirubin
Dierct
RR: 0.1-0.3 mg/dL
Increased in:
Bile duct obstruction
Hepatitis
Cirrhosis
Intrahepatic cholestasis
Indirect
RR: 0.1-0.7 mg/dL
Increased in:
Crigler-Najjar syndrome
Gilbert's disease
Hemolytic anemia
Hemolytic disease of the
newborn
Hepatitis
Physiological jaundice
Transfusion reaction

48. Albumin
Reference range: 3.5-5.2g/dL
Increased in:
Dehydration
hemoconcentration.
Decreased in:
Decreased hepatic synthesis
chronic liver disease,
malnutrition,
malabsorption
Increased losses
nephrotic syndrome
burns
enteropathy

49. Total Protein
Reference range: 6.3 - 8.2 g/dl
Increased in:
marked dehydration.
Decreased in:
Protein-losing enteropathies
chronic liver disease
acute burns
nephrotic syndrome
severe dietary protein deficiency
malabsorption syndrome

50. Alkaline phosphatase
Reference range: 45 - 150 U/L
ALP is found in liver, bone, intestine, and placenta.
Liver
• bil obstruction
– extrahepatic : ↑↑ 3 times e.g. stone, cancer head of
pancreas)
– Intrahepatic ↑↑ < 3 times (drugs, invasion by cancer
tissue)
• Moderate ↑ to normal: parenchymal cells of
liver affected e.g. infectious hepatitis

51. Alkaline phosphatase
Bone
• Physiologic
– Children: growing bones
– Healing bone fracture
• ↑↑ 10-25 times: Paget
• Moderate ↑: Osteomalacia
• 2 times: Rickets
• Normal: Osteoporosis
Pregnancy: 3rd trimestre: 2-3 times

52. Creatinine
Reference range:
0.5-1.2 mg/dL
Increased in:
Acute or chronic renal
failure
urinary tract
obstruction
nephrotoxic drugs
Decreased in:
Reduced muscle
mass.

53. Creatinine clearance
Refernce range
• Men
– Range: 97-137 ml/min/1.73 m2
• Women
– Range: 88-128 ml/min/1.73 m2
Increased in:
High cardiac output
exercise
Decreased in:
Acute or chronic renal failure
decreased renal blood flow (shock, hemorrhage, dehydration, CHF).
Nephrotoxic drugs.

54. Uric acid
Increased in:
Decreased renal excretion of Uric Acid
Primary idiopathic Hyperuricemia
Chronic Renal Insufficiency
Dehydration or starvation ketosis
Drugs
Overproduction of Uric Acid
HGPRTase deficiency
Myeloproliferative disorder
Lymphoproliferative disorder
Chemotherapy
Decreased in:
Drugs
SIADH
Hemochromatosis
Protein or purine deficient diet
Reference Range:
Males: 3.4 to 7.0 mg/dL
Females 2.4–6.0 mg/dL

55. Urea
Reference Range: 20-40 mg/dl
Increased in:
intake of high-protein diet 12 hours before blood sampling
Renal failure (acute or chronic)
urinary tract obstruction
dehydration,
Nephrotoxic drugs (eg, gentamicin).
Decreased in:
Hepatic failure,
nephrotic syndrome,
Cachexia

56. Cholesterol
Reference Range:
Desirable: <200 mg/dL
Borderline: 200-239 mg/dL
High risk: >240 mg/dL
Increased in:
Primary hypercholesterolemia
Secondary disorders:
hypothyroidism, uncontrolled diabetes mellitus, nephrotic syndrome, biliary
obstruction, Drugs.
Decreased in:
Severe liver disease (acute hepatitis, cirrhosis)
malnutrition
malabsorption
familial (Gaucher disease, Tangier disease)
abetalipoproteinemia

57. Triglycerides
Reference Range:
Desirable: <150 mg/dL
Borderline: 150-199 mg/dL
High risk: 200-499 mg/dL
Very high risk: >500 mg/dL
Increased in:
Primary
DM
Hypothyroidism,
nephrotic syndrome
biliary tract obstruction
Drugs
Decreased in:
Tangier disease
Malabsorption
parenchymal liver disease
Drugs

58. Calcium
Reference Range: 8.5 - 10.3 mg/dL
Increased in:
Hyperparathyroidism,
malignancies secreting parathyroid hormone-related protein (PTHrP)
vitamin D excess,
Bone diseases
Familial
Drugs
Decreased in:
Hypoparathyroidism
vitamin D deficiency
Renal insufficiency
massive transfusion
hypoalbuminemia.

59. CSF glucose and protein
CSF glucose
Reference range: 50 - 80 mg/dL (or 60-70% of
the blood glucose).
CSF protein
Reference range: 15–45 mg/dL

60. Laboratory Hematology

61. Complete blood count
Reference range
(adult)
↑ ↓
WBC 4-11 X109/L
Infection
Leukemia
Some infections
BM failure
WBC differential
Neutrophils: 55-75%
Lymphocytes: 25-40%
Monocytes: 2-8%
Eosinophils: 1-4%
Basophils: 0-1%
Bacterial: Neutrophilia
Viral: Lymphocytosis
Some infections
BM failure
Hb
Male: 13.5-16 g/dL
Female: 12-15 g/dL
Dehydration
Polycythemia
Anemia
Bleeding
Platelets 150-450 X109/L
Some infections
Thrombocytosis
Bleeding
Thrombocytope
nia

62. Erythrocyte sedimentation rate (ESR)
Reference range: Male: <10 Female: <15 mm/h
↑ ↓
Anemia
increased fibrinogen
Increased abnormal proteins
Inflammation
Infection
Marked ↑↑
Collagen diseases
Malignancy
TB
Polycythemia
abnormal red cells, eg
spherocytosis
sickle cells
Cryoglobulins
low fibrinogen

63. PT (INR) and APTT
PT APTT EXAMPLES
10 - 13.5 seconds,
or
INR of 0.8-1.1
30 to 45
seconds
Reference ranges
↑ Normal
Liver disease, ↓vitamin K, ↓factor
VII,anticoagulation drug therapy
Normal ↑ ↓factor VIII, IX, or XI, von Willebrand disease
↑ ↑ ↓ factor I, II, V or X, severe liver disease, DIC

64. THANK YOU