Clinical Analysis Laboratory: 2018

Systematic Parasitology

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A) PROTOZOA

1. Intestinal protozoa
I) Amoebae. Entamoeba genus: E. histolytica. Iodamoeba and Blastocystis genera
II) Flagellates. Giardia genus. G. intestinalis
III) Ciliates. Balantidium genus. B. coli
IV) Coccidia and Microsporidia: Isospora genus: I. belli
Cryptosporidium genus: C. parvum
Cyclospora genus: C. Cayetanensis
Sarcocystes genus
Microsporidia order

2. Hematic protozoa
- Plasmodium genus: Malaria
- Babesia genus: Babesia spp.
- Leishmania genus: L. donovani, L. tropica, L. braziliensis, L. mexicana
- Trypanosoma genus: T. gambiense, T. rhodesiense, T. cruzi

3. Protozoa of tissue and other localizations
I) Tissue-based: Toxoplasma genus: T. gondii
Pneumocystis genus: P. carinii
II) Others: Trichomonas genus: T. vaginalis
Naegleria genus
Acanthamoeba genus

B) HELMINTHS

1. Platyhelminths: Trematodes
I) Trematodes of the lungs and digestive system. Fasciola genus. F. hepatica
II) Hematic trematodes. Schistosoma genus

2. Platyhelminths: Cestodes
I) Intestinal cestodes (parasitism by adult cestodes): Taenia genus. T. solium and T. saginata Dipylidium caninum, Hymenolepis nana, Diphyllobothrium latum
II) Tissue-based cestodes (parasitism during larval stages). Echinococcus genus. E. granulosus Hydatid cyst

3. Intestinal nematodes:
- with exclusively intestinal habitat: Enterobius vermicularis and Trichuris trichiura - with tissue migration of larvae: Ascaris lumbricoides, Strongyloides stercolaris, Ancylostoma duodenale and Necator americanus

4. Tissue-based nematodes
- Trichinella genus. T. spiralis. Trichinosis
- filaria that parasitize humans: Wuchereria, Brugia, Loa, Onchocerca, Mansonella genera
- filariasis: Dracunculus genus. D. medinensis

5. Arthropods of health interest: Arachnida: Acarina (mites, ticks); Araneida and Scorpionida Insecta: Diptera; Heteroptera; Siphonaptera; Anoplura

Systematic Virology

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1. Herpes viruses
Herpesviridae family.
- Alphaherpesvirinae sub-family: Simplex Virus genus: herpes simplex virus types 1 and 22
- Varicella zoster virus
- Betaherpesvirinae subfamily: Cytomegalovirus genus: cytomegalovirus
- Gammaherpesvirinae sub-family: Lymphocryptovirus genus: Epstein-Barr virus
- Other unclassified herpes viruses: human herpes virus types 6, 7 and 8

2. Respiratory viruses
- F. Orthomyxoviridae
- Influenza virus A and B genus. Influenza virus C genus
- F. Paramyxoviridae. Paramyxovirinae sub-family. Paramyxovirus genus: parainfluenza virus
- Pneumovirinae sub-family. Pneumovirus genus: syncytial respiratory virus
- F. Adenoviridae
- Mastadenovirus genus. Adenovirus
- F. Picornaviridae
- Rhinovirus genus: Rhinovirus
- F. Coronaviridae: Coronavirus genus: Human coronavirus
- F. Reoviridae
- Orthoreovirus genus: Rheovirus

3. Enterovirus
- F. Picornaviridae
- Enterovirus genus. Poliomyelitis virus
- Enterovirus, Coxsackie virus and ECHO virus

4. Viruses which cause gastroenteritis
- F. Reoviridae
- Rotavirus genus. Rotavirus
- F. Caliciviridae. Calicivirus genus. Human calicivirus and Norwalk virus
- F. Adenoviridae: Mastadenovirus genus. Adenovirus: serotypes 40 and 41
- Others: human coronavirus and astrovirus

5. Viral hepatitis
- F. Hepadnaviridae
- Orthohepadnavirus genus. Hepatitis B virus
- F. Flaviviridae. Hepatitis C genus: Hepatitis C virus
- F. Picornaviridae
- Hepatovirus genus: Hepatitis A virus
- Other unclassified viruses that cause hepatitis: hepatitis delta virus and hepatitis E

6. Mumps virus and exanthematic viruses
- F. Paramyxoviridae: Paramyxovirinae sub-family: Paramyxovirus genus. Mumps virus
- Morbillivirus genus. Measles virus
- F. Togaviridae
- Rubivirus genus. Rubella virus
- F. Parvoviridae: Parvovirus genus: Parvovirus B19
- F. Herpesviridae. Type 6 human herpes virus

7. Rabies virus, arbovirus and other viruses which cause zoonosis
- F. Rhabdoviridae. Lyssavirus genus. Rabies virus
- Arbovirus: F. Togaviridae. Alphavirus genus. Western equine encephalitis virus
- F. Flaviviridae. Flavivirus genus. Yellow fever virus and dengue virus
- F. Bunyaviridae. Bunyavirus genus. F. Reoviridae. Orbivirus and Coltivirus genera
- Other viruses which cause zoonosis: F. Arenaviridae. Arenavirus genus. Lymphocytic choriomeningitis virus and lassa fever virus
F. Filoviridae. Filovirus genus: Marburg and Ebola viruses. F. Bunyaviridae. Hantavirus genus. Hantaan virus

8. Retrovirus
- Oncovirinae sub-family. Group HTLVBLV genus. Human T-cell lymphotropic virus types 1 and 2
- Lentivirinae sub-family. Lentivirus genus. Human immune deficiency virus types 1 and 2

9. Oncogene DNA viruses
- F. Papovaviridae. Papillomavirus genus. Human papilloma virus. Epstein-Barr virus. Hepatitis B and C viruses

10. Non-conventional agents: Viroids and prions

Systematic Bacteriology

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1. Staphylococcus genus
- S. aureus
- S. epidermidis
- S. saprophyticus

2. Streptococcus genus and Enterococcus genus
- Streptococcus pyogens (S. pyogenes and S. agalactiae) and streptococci of the viridans group
- S. pneumoniae
- Enterococcus genus

3. Clostridium genus and Bacillus genus
- C. tetani
- C. botulinum
- C. perfringens
- C. difficile
- Bacillus genus: B. anthracis and B. cereus

4. Corynebacterium genus and Listeria genus
- C. diphteriae
- L. monocytogenes

5. Neisseria genus
- N. gonorrhoeae
- N. meningitidis

6. Enterobacteriaceae family
- Salmonella genus
- Shigella genus
- Escherichia genus: E. coli
- Yersinia genus: Y. enterocolítica and Y. pseudotuberculosis, Y. pestis

7. Vibrio genus, Campylobacter genus and Helicobacter genus
- V. cholerae, V. parahaemolyticus
- C. jejuni
- H. pylori

8. Haemophilus genus and Bordetella genus
- H. influenzae
- B. pertussis

9. Legionella genus
- L. pneumophila

10. Brucella genus and Francisella
- Brucella genus: Brucellosis
- Francisella genus: F. tularensis

11. Strict gram-negative aerobic bacteria and opportunistic anaerobic bacteria
- Pseudomonas genus
- opportunistic enterobacteria
- Moraxella genera
- Acinetobacter
- Aeromonas
- Plesiomonas

12. Strict opportunistic anaerobic bacteria
- Gram-negative bacteria: Veillonella, Bacteroides, Leptotrichia and Fusobacterium genera.
- Gram-positive bacteria: Propionibacterium, Eubacterium, Peptococcus and Peptostreptococcus genera.

13. Spirochaetes
- Treponema genus. T. pallidum
- Borrelia genus. B. burgdorferi
- Leptospira genus. L. interrogans

14. Mycobacterium genus, Nocardia genus and Actinomyces genus
- M. tuberculosis, M. leprae
- Atypical mycobacteria: Nocardia genus, Actinomyces genus

15. Mycoplasma genus and Ureaplasma genus
- M. pneumoniae
- Ureaplasma genus

16. Rickettsia genus and Coxiella genus
- Rickettsia genus: R. conori
- Coxiella genus: C. burnetii

17. Chlamydia genus
- C. trachomatis
- C. psittaci
- C. pneumoniae

Clinical Microbiology and Parasitology

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A. GENERAL MICROBIOLOGY:
1. Concept of medical microbiology and parasitology
2. Bacteria
3. Fungi
4. Viruses
5. Parasites: protozoa and helminths
6. Microbial genetics
7. Action of physical and chemical agents on microorganisms

B. PATHOGENY OF INFECTIOUS DISEASES AND MICROBIAL IMMUNOLOGY:
1. Interrelationship between host and microorganism
2. Non-specific defence mechanisms
3. Factors that determine pathogenic action
4. Specific defence mechanisms

C. BASIC PRINCIPLES IN THE DIAGNOSIS, EPIDEMIOLOGY AND PROPHYLAXIS OF INFECTIOUS DISEASES:
1. Laboratory diagnosis of infectious diseases
2. Epidemiology and prophylaxis of infectious diseases
3. Immunity to infection: Vaccines and serums

D. CHEMOTHERAPY:
1. Antibacterial and antifungal agents
2. Antiviral agents: antiparasitic agents

E. SYSTEMATIC BACTERIOLOGY

F. SYSTEMATIC MYCOLOGY
1. Superficial, cutaneous and subcutaneous mycosis
2. Systemic mycosis
3. Opportunistic mycosis

G. SYSTEMATIC VIROLOGY

H. SYSTEMATIC PARASITOLOGY

Clinical Genetics

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Clinical genetic testing refers to the laboratory analysis of DNA or RNA to aid in the diagnosis of disease. Genetic testing can provide definitive diagnosis as well as help predict the likelihood of developing a particular disease before symptoms even appear.
Genetic tests are performed on a sample of blood, hair, skin, amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue. For example, a procedure called a buccal smear uses a small brush or cotton swab to collect a sample of cells from the inside surface of the cheek.
Clinical geneticists must continually take account of new discoveries that alter clinical practice. They have an important role to play in public education and debates about ethical issues arising from new developments in the clinical application of genetic knowledge.

Clinical Hematology

Uses of hematology: aiding in diagnosing anemia, certain cancers of the blood, inflammatory diseases, and to monitor blood loss and infection. Back to Clinical Analysis Laboratory page

Common haematology tests:

White blood cell count (WBC)

Red blood cell count (RBC)

Platelet count (PLT)

Hematocrit red blood cell volume (HCT)

Hemoglobin concentration (HB) - the oxygen-carrying protein in red blood cells.

Differential white blood count (percentage of each type of WBC in the blood)

Red blood cell indices (measurements: MCV, MCHC)

International Normalized Ratio (INR)

Coagulation: - Prothrombin time (PT) - Partial Thromboplastin Time (PTT)

Markers in Clinical Immunology

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Tumoral markers:

AFP

CA 19-9

CA 125

CA 72-4 (TAG-72)

CA 15-3

Calcitonina

CEA

CYFRA 21-1

HCG total

NSE (Neuron specific enolase)

PSA/free PSA

S 100

SCC

Tyroglobulin TG/Antityroglobulin antibodies

Endocrine markers:

steroids

ACTH

ADH (vasopressin)

adiponectin

AFP (Alfa-feto protein) - pregnancy marker/triple test

seric and urinary aldosteron

androstendion

angiotensin II

cortisol (urinary, salivary, seric)

DHEA-S (dehidroepiandrosteron-sulphate)

dihydrotestosterone

estradiol

unconjugated estriol

E1 (estrone)

PIGF

free Beta-HCG

FSH (folicular stimulating hormone)

FT3 (Free Triiodotironin)

hipocretin (orexin) FT4 (Free Tiroxin)

total HCG (HCG+beta)

hGH

AMH (Anti-Mullerian hormone)

IGF-binding protein 3

IGF-I (Somatomedin C)

HOMA

Inhibin A and B

Insulin

Leptin

LH (lutenizing hormone)

preeclampsia markers

melatonin

Peptide C

Progesteron

intact proinsulin

prolactin

direct plasmatic renin

SHBG

T3 (Triiodotironin)

T4 (Total Tiroxin)

TBG

Testosterone

TSH

Viral markers:

Ag HBe

Ag HBs (screening)

Ag HBs quantitative

Anti-HAV

Anti-HAV-IgM

Anti-HBc

Anti-HBc-IgM

Anti-HBe

Anti-HBs (quantitative)

Anti-HCV

Anti-HCV (confirmation)

Anti-HD

Anti-HIV 1 (confirmation)

Anti-HIV 1+2

Anticorpi anti-HTLV (leucemia virus with adult T-cells)

Hepatitis E Virus - IgG, IgM antibodies (Westernblot)

Cardiac markers:

homocisteine

NT-proBNP

reactive protein C (hsCRP) highly sensitive

Troponin T

Anemia markers:

anti-eritropoietin antibodies

eritropoietin

ferritin

serum folates

trasnferin

vitamin B12

Autoimmune markers:

anti-thyroglobulin

Anti-TPO (Anti-tiroidperoxidase)

Bone markers:

PTH (intact parathormon)

osteocalcin

Other markers:

specific (many)

Clinical Immunology

The Immunology unit offers support to the various professionals from different medical specialities in the diagnosis, monitoring and progress of different diseases, including those of auto-immune, infectious, haemato-oncological, rheumatic and immunodeficiency origin. See markers in clinical immunology. Back to Clinical Analysis Laboratory page

ANTIBODIES

Detection of auto-antibodies by Indirect Immunofluorescence (IIF)

Detection of specific antibodies to neuronal antigens (immunoblot and IIF)

Detection of antibodies related to systemic autoimmune diseases (IIF, ELISA, multiplex and immunoblot)

Detection of antibodies related to organ-specific autoimmune diseases (IIF, ELISA and immunoblot)

INFECTIOUS SEROLOGY

Viral, bacterial and parasitic serology using chemiluminescence, multiplex and IIF

FLOW CYTOMETRY

Lymphocyte populations

Study of leukocyte antigens (PNH, leukemias)
HLA B27 antigen study
Fertility studies
Diagnosis of autoimmune haemolytic anaemia
Monitoring of the borrelia infection
Osteoporosis

IMMUNOCHEMISTRY

Quantification of immunoglobulins and plasmatic proteins

IMMUNOASSAY AND MULTIPLEX

Proteins related to inflammation

Peritoneal fluid

When you have abdominal pain and swelling, nausea, and/or fever and your healthcare practitioner suspects you have peritonitis or ascites.
A sample of peritoneal fluid is collected by a healthcare practitioner with a syringe and needle using a procedure called paracentesis.
To help diagnose the cause of peritonitis, an inflammation of the membrane lining the abdomen, and/or peritoneal fluid accumulation, where fluid builds up in the abdomen or around internal organs (called ascites)

Pericardial fluid

Pericardial fluid analysis: to evaluate and classify the type of fluid between the pericardium membranes to assist with diagnosis of infection or fluid balance disorder.
Specimen: Pericardial fluid collected in a red- or green-top (heparin) tube for glucose, a lavender-top (EDTA) tube for cell count, and sterile containers for microbiology specimens; fluid in a clear container for cytology. Ensure that there is an equal amount of fixative and fluid in the container for cytology.
Method: Spectrophotometry for glucose; automated or manual cell count, macroscopic examination of cultured organisms, and microscopic examination of specimen for microbiology and cytology; microscopic examination of cultured microorganisms.

Pleural fluid

In a pleural fluid analysis, the doctor will remove fluid from the pleural membrane area by inserting a needle into the chest cavity and suctioning the fluid into a syringe (thoracentesis). This also works as a common procedure to drain the excess fluid from the chest cavity. The fluid will then be tested to determine the cause.
Pleural biopsy involves taking a sample of tissue from the pleura. This can be done by inserting a small needle from outside the chest wall into the chest cavity.

Synovial fluid

helps diagnosing the cause of joint inflammation, pain and/or swelling

tested when one or more of the joints are swollen, red and/or painful

a synovial fluid sample is obtained by inserting a needle into the space between the bones at a joint

synovial fluid collection and analysis may be performed after fasting or at random

Saliva testing

Saliva testing is a diagnostic technique that involves laboratory analysis of saliva to identify markers of endocrine, immunologic, inflammatory, infectious, and other types of conditions.

Saliva is a useful biological fluid for assaying steroid hormones such as cortisol, genetic material like RNA, proteins such as enzymes and antibodies, and a variety of other substances, including natural metabolites, including saliva nitrite.

Saliva testing is used to screen for or diagnose numerous conditions and disease states, as well as for drug testing.

Salivary testing has even been used by the U.S. government to assess circadian rhythm shifts in astronauts before flight and to evaluate hormonal profiles of soldiers undergoing military survival training.

Amniotic fluid

To detect and diagnose certain birth defects, genetic diseases, and chromosomal abnormalities in a fetus, especially if prenatal screening tests are abnormal.

A sample (about 1 ounce) of amniotic fluid is obtained using a procedure called amniocentesis that involves inserting a thin needle through the belly and uterus into the amniotic sac.

Cerebrospinal fluid

CSF is formed by a combined process of plasma ultrafiltration and active secretion.
Mechanical and osmotic barriers exist between plasma and CSF and between CSF and brain.
Lumbar puncture is the preferred technique for CSF sampling.
Normal CSF should be clear, colorless, and free of clotted material.
CSF can be examined for presence of microbes using stains.
Additionally, the chemical composition of CSF can be examined; tests of interest include glucose, protein, lactate, enzymes, glutamine, specific amino acids, biogenic amines, and various drugs.

Urine samples

Type of urine sample How it is used
First morning sample Provides a concentrated sample of urine that contains the overnight
accumulation of metabolites. Useful for detection of proteins or
unusual analytes.
Random Convenient sample that can be collected at any time.
Most often used for routine screening tests.
Timed Typically 2 to 6 hours of urine output is collected to give a
representative sample; duration of collection depends on the
analytes.
24-hour Entire urine output for a 24-hour period is collected. Like a timed
urine, but used for metabolites whose excretion rates may vary with
time of day and full 24-hour collection is needed to be representative.

Bibliography

https://www.upf.edu/en/web/biolac/assignatures
https://en.wikipedia.org/wiki/Clinical_chemistry
https://www.corelaboratory.abbott/sal/learningGuide/ADD-00061345_ClinChem_Learning_Guide.pdf
https://www.ncbi.nlm.nih.gov/pubmed/10172035
https://labtestsonline.org/tests/amniotic-fluid-analysis
https://en.wikipedia.org/wiki/Saliva_testing
https://labtestsonline.org/tests/synovial-fluid-analysis
https://www.healthline.com/health/pleural-effusion#diagnosis
https://nursing.unboundmedicine.com/nursingcentral/view/Davis-Lab-and-Diagnostic-Tests/425127/all/Pericardial_Fluid_Analysis
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https://en.wikipedia.org/wiki/Automated_analyser

Blood collection tubes

TUBE ADDITIVE STOPPER COLOR SAMPLE COMMENT
None Red Serum Clotting requires at least 30 minutes at room temperature Silica clot activator Red/black Serum Silica speeds the clotting
process compared to no
activator
Thrombin Gray/yellow Serum Speeds clotting process
significantly to produce serum in
several minutes — used mostly
for urgent (STAT) testing Lithium Heparin Green Plasma Preferred plasma sample for
most chemistry tests — not
suitable when testing for lithium Sodium Heparin Green Plasma Used when testing for lithium—
not suitable when testing for
sodium
EDTA Lavender Plasma Occasionally used for some
chemistry tests and typically
used for Hematology
Potassium EDTA
in special plastic tube Tan or brown Plasma For blood lead testing;
tubes are certified to have very low levels of contamination by lead
Sodium fluoride/
potassium oxalate Gray Plasma For glucose testing — sodium
fluoride inhibits metabolism of
glucose by white blood cells

Samples analyzed

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FLUIDS TYPICALLY USED FOR CLINICAL CHEMISTRY TESTS:

Blood (whole blood, serum or plasma)
Urine
Cerebrospinal fluid (CSF)
Amniotic fluid
Saliva
Synovial fluid (fluid that is found in joint cavities)
Pleural fluid (from the sac surrounding the lungs)
Pericardial fluid (from the sac surrounding the heart)
Peritoneal fluid (also called ascitic fluid; from the abdomen)

Clinical biochemistry

Clinical biochemistry laboratory: Back to Clinical Analysis Laboratory page

Samples analyzed
Analytes examined

Analytes examined

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Analytes examined in the clinical biochemistry laboratory:

Electrolyte panel:

sodium

potassium

chloride

carbon dioxide

Basic metabolic panel:

sodium

potassium

chloride

carbon dioxide

glucose

creatinine

urea (blood urea nitrogen; BUN)

Comprehensive metabolic profile:

sodium

potassium

chloride

carbon dioxide

glucose

creatinine

urea

calcium

total protein

albumin

alanine aminotransferase (ALT)

aspartate aminotransferase (AST)

alkaline phosphatase (AlkP)

total bilirubin

Renal (kidney) function tests:

creatinine

blood urea nitrogen

Hepatic panel (liver profile):

total protein (serum)

albumin

globulins

A/G ratio (albumin-globulin)

protein electrophoresis

urine protein

bilirubin; direct; indirect; total

aspartate transaminase (AST)

alanine transaminase (ALT)

gamma-glutamyl transpeptidase (GGT)

alkaline phosphatase (ALP)

Lipid profile:

total cholesterol

LDL cholesterol

HDL cholesterol

triglycerides

Cardiac markers:

H-FABP

troponin

myoglobin

CK-MB

B-type natriuretic peptide (BNP)

Minerals:

calcium

magnesium

phosphate

potassium

Blood disorders:

iron

transferrin

TIBC

vitamin B12

vitamin D

folic acid

Miscellaneous:

glucose

C-reactive protein

glycated hemoglobin (HbA1c)

uric acid

arterial blood gases (H+, Pco2, Po2)

adrenocorticotropic hormone (ACTH)

toxicological screening and forensic toxicology (drugs and toxins)

neuron-specific enolase (NSE)

fecal occult blood test (FOBT)

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Common haematology tests:

Tumoral markers:

Endocrine markers:

Viral markers:

Cardiac markers:

Anemia markers:

Autoimmune markers:

Bone markers:

Other markers:

Electrolyte panel:

Basic metabolic panel:

Comprehensive metabolic profile:

Renal (kidney) function tests:

Hepatic panel (liver profile):

Lipid profile:

Cardiac markers:

Minerals:

Blood disorders:

Miscellaneous: