MICROBIOLOGY

Presented by
Alyazeed hussein, BSc
BACTERIOLOGY
Gram positive cocci
Staphylococci:
 Staphylococcus aureus: S.aureus as resident flora, primarily in the anterior nares.
 Isolated from abscesses, wound infections. Cause osteomyelitis in Children and adults.
 scalded skin syndrome (SSS) and toxic shock syndrome (TSS).
 Identifying characteristics:
 Gram-positive cocci arranged in clusters. Colonies are golden color- beta-hemolytic on
blood agar.
 Catalase and coagulase positive(catalase mediates the breakdown of hydrogen peroxide
into oxygen and water), coagulase enzyme convert fibrinogen to fibrin causes plasma to
clot.
 Tolerate the high salt concentration (7.5%) of mannitol salt agar (MSA): ferments
mannitol and produces yellow colonies vs other staphylococci.
 DNase test positive (S.aureus) vs other staph.
 Penicillin resistance is due to beta-lactamase production.
 Methicillin resistant S. aureus (MRSA) is resistant to β-lactam antibiotics because of
production of altered penicillin-binding proteins.
 Coagulase-negative staphylococci(GNS):
 are very common skin flora and are mostly nonpathogenic. However, they can cause
disease in immunosuppressed patients. This group of bacteria causes urinary tract
infections (UTIs) and is associated with infections of catheters.
 Characteristics:
 Gram-positive cocci arranged in clusters
 Colonies appear white to gray on blood agar and nonhemolytic.
 Catalase positive and coagulase negative.
 infections associated with indwelling device.
1. Staphylococcus epidermidis: coagulase negative staphylococci, novobiocin
sensitive.
2. S. saprophyticus: Significant only in UTIs, novobiocin resistant.
 Streptococci:
 General Characteristics:
 Catalase-negative, gram-positive cocci arranged in pairs and chains.
 Can be alpha- or beta-hemolytic, or gamma- nonhemolytic on blood agar.
 Lancefield grouping is based on a cell wall antigen:
1. Group A Streptococcus (S. pyogenes):
 (pharyngitis), pneumonia, otitis media (middle ear infections), rheumatic fever and
post-streptococcal
glomerulonephritis(ASO): anti-streptolysin O=exotoxin.
 Sensitive to bacitracin, colonies show a large zone of beta-hemolysis.
2. Group B Streptococcus (S. agalactiae):
 25% of all females carry the bacteria as normal vaginal flora.
 Neonates acquire infections during birth, resulting in meningitis.
 Colonies are beta-hemolysis on BA.
 CAMP test(Christie-Atkinson-Munch-Peterson) arrow head of hemolysis, resistant to
bacitracin.
3.Group D Streptococcus(E. faecalis):
 Positive for growth in 6.5% NaCl.
 Can be alpha-, beta-, or most commonly nonhemolytic.
 Vancomycin-resistant enterococci (VRE).
 Cause subacute bacterial endocarditis (SBE), UTI and abdominal
infections.

CAMP test
 Streptococcus pneumoniae:
 Normal flora of upper respiratory tract but can cause: Pneumonia and Meningitis.
 Gram-positive diplococci that are lancet shaped, and alpha hemolytic(green colonies).
 Grows on BA with 5-10% CO2.
 Sensitive to Optochin.
 Viridans streptococci: S. mutans, S. intermedius,
 Normal flora of the oral cavity, respiratory tract, and gastrointestinal (GI) tract mucosa.
 Major cause of bacterial endocarditis in people with damaged heart valves.
 Alpha-hemolytic colonies(green color),
 Sensitive to vancomycin.
 Note that! Coagulase test: differentiate S.aureus(positive) from other staphylococci(negative).
 Novobiocin disc: differentiate S.epidermidis (sensitive) from S.saprophyticus (resistant).
 Catalse test: differentiate staphylococci(positive) from streptococci(negative).
 Bacitracin disc: differentiate S.pyogenes(sensitive) from S. agalactiae (resistant).
 CAMP test: differentiate S. agalactiae (positive) from other streptococci (negative).
 Growth at (6.5% NaCl): E.faecalis(grow), other streptococci(inhibited).
 Vancomycin: Viridans (sensitive) vs Enterococci (resistant).
viridans pneumococci point

negative Positive Quellung test

negative positive Bile solubility test

resistant sensitive Optochin disc

negative positive Inulin fermentation

GRAM POSITIVE BACILLI
 Bacillus spp (Bacillus anthracis and Bacillus cereus).
 Gram positive bacilli, aerobic, Spores forming, McFadyean's reaction (polychrome MB stain for capsule
(protein).
 Bacillus anthracis: spread by inhalation(woolsorter’s disease), cause anthrax(skin, lungs and intestine), non-
hemolytic and non motile.
 Bacillus cereus: an important cause of food poisoning and occasionally wounds(beta-hemolytic and motile).
 Corynebacterium diphtheriae:
 Gram positive bacilli, pleomorphic (Chinese letters)
 Causes diphtheria(pseudomembrane at the back of the throat).
 Staining with methylene blue will reveal metachromatic granules(Loeffler agar).
 Black colonies on potassium tellurite.
 Catalase positive.
 Elek test uses antitoxin to detect toxin production.
 Listeria monocytogenes: listeriosis,
 Gram positive, non spore forming motile bacilli (tumbling motility). Can grow at refrigerated temp.
 Cause meningitis in neonates, pregnant women, and immunosuppressed patients.(food poisoning)
 Nocardia: found in immunocompromised patients with chronic pulmonary disorders. (obligate aerobe).
 Pleomorphic, beaded branching filaments, gram-positive bacilli, Partially acid-fast, non motile. catalase
positive.
GRAM NEGATIVE BACILLI
Enterobacteriaceae and others
 Enterobacteriaceae: Most medically important family of gram-negative bacilli.
 Enterobacteriaceae are facultative anaerobes and oxidase negative.
 MacConkey (MAC) agar: (selective and differential) Lactose-positive colonies are pink/red, and lactose-
negative colonies are colorless.
1. Escherichia coli: E.coli is normal GI flora, causes UTI (most common), appendicitis, endocarditis,
meningitis in newborns and food poisonmg. Lactose fermenter, indole positive, motile, produce green
metallic sheen on EMB.
 Enterohemorrhagic E. coli (EHEC): (0157:H7):
 hemorrhagic colitis and hemolytic uremic syndrome (HUS).
 Enteroinvasive E. coli (EIEC) causes bloody diarrhea.
 Enterotoxigenic E.coli (ETEC) produces severe epidemic(traveler diarrhea), mainly from drinking
contaminated water.
 Enteropathogenic E. coli (EPEC) causes a watery diarrhea(children).
2. Shigella dysenteriae : Causes shigellosis, (bacillary dysentery), characterized by abdominal pain,
fever, and diarrhea.
 Note that! All shigella spp are non lactose fermenter except S. sonnei(delayed lactose fermenter).
 Non motile.
 3. Klebsiella: K.pneumoniae, typically cause nosocomial UTIs and pneumonia, on MAC agar, the pink
colonies (LF) are very mucoid because of capsule production.
4. Salmonella: cause gastroenteritis, The majority of human cases of salmonellosis are due to S.typhi
(Typhoid fever), osteomyelitis in Sickle cell patient, suitable sample in the first week is blood for culturing.
 Transmitted through contaminated water and undercooked food, especially chicken and eggs,
 Non lactose fermenter Motile and H2S-positive colonies on SSA, XLD (black center) .
5. Proteus: (P.mirabilis and P.vulgaris), UTI, triple phosphate stone (alkaline urine).
 H2S positive, and motile (swarming phenomenon or spreading film, on blood agar), urease positive,
P.vulgaris is indole positive while P.mirabilis is indole negative.
6.Yersinia: Y.pestis causes bubonic plague (rodents), pneumonic plague, (bipolar staining > safety pin
like).
Y.enterocolitica causes enterocolitis (bloody diarrhea) in human, NLF, motile at 25°C but not at 37°C.
 Note that!! Salmonella is motile and produce H2S on SSA, while shigella is non motile and do not
produce H2S.
 E.coli, salmonella and shigella, faecal/oral rout of transmission.
7. Haemophilis: H.influanzae, Normal flora of upper respiratory tract, major
cause of meningitis in children. Cause pneumonia.
 Pleomorphic gram-negative coccobacilli (filamentous), catalase
and oxidase positive.
 Fastidious bacteria, need hemin (X factor) + NAD (V factor) >
Chocolate agar (with 5-10% CO2), transparent dew drops like colonies.
 Show satellitism phenomennon with staph on blood agar. Proteus swarming
• Blood agar provides only X factor.
• S. aureus provides V factor by breaking the RBCs.
8. Pseudomonas aeruginosa: obligate aerobes, oxidase positive, motile and non
fermentative(oxidize the glucose), grow at 42 C, green-blue colonies (pyocyanin pigment), fruity
odor (grapel ike). Causes burn wound infections. Important pathogen in immunocompromised
individuals. P.aeruginosa is resistant to a number of disinfectants and has been responsible for
serious nosocomial infections. It is especially associated with hospital environments(UTI) and
equipment.
9. Bordetella pertussis: It inhabits the mucous membranes of the respiratory tract of humans.
Causes pertussis(whooping cough). Grows on Bordet-Gengou media(they appear like mercury
droplets).
10. Pasteurella multocida: normal respiratory/GI flora of animals.
 Oxidase, catalase and indole positive.
 Humans acquire the bacteria from animal bites (cats and dogs) or by inhalation of dried animal
feces.
 Causes osteomyelitis, meningitis, joint infections.
11. Brucella spp: aerobic, undulant fever, I/C, from unpasteurized milk, contact infected goats,
cows. Serological test is primary means for the diagnosis.
12. Legionella pneumophila: aquatic: found in humidifiers, and air conditioning chillers.
legionellosis, which can be asymptomatic or mild to severe atypical pneumonia.
 grow on BCYE agar(Buffered charcoal yeast extract). Poor gram stain visualize with silver
stain.
13. Serratia spp: Opportunistic pathogen. Pneumonia & septicemia in immunosuppressed, motile,
NLF, citrate & VP positive. Produce red pigment when incubated at RT.
14.Vibrio cholerae: motile (comma shaped), glucose fermenter, oxidase positive.
 Cause GI disease: cholera, (rice-watery diarrhea), dehydration.
 Grow on Thiosulfate citrate bile salt sucrose agar (TCBS) > sucrose fermentation > yellow
colonies.
15. Campylobacter jejuni: Curved (S) shape, urease negative, major cause of food poisoning,
causing gastroenteritis, bloody diarrhea.
 Curved bacilli that may appear S-shaped on Gram stain, grow well at 42°C.
 They do not oxidize or ferment carbohydrates, catalase and oxidase positive.
16. Helicobacter pylori: Curved, Motile, oxidase, rapid urease, and catalase positive.
 H. pylori causes gastritis, peptic and duodenal ulcers and has been linked to stomach cancer.
Bacteria produce ammonia (via urease) to protect from gastric acid. Tests include: serum Abs,
fecal antigen detection & (urea breath test).
17. Bacteroides: strict anaerobe, normal flora in GI, peritonitis GI abscesses, make the vitamin K.
18. HACEK organisms (Haemophilus species, Actinobacillus actinomycetemcomitans, Cardiobacterium
hominis, Eikenella corrodens, and Kingella species) are gram-negative bacilli that are part of normal oral
flora and can infect heart valves. They are the most common gram-negative cause of endocarditis in
non-IV drug users.
GRAM NEGATIVE COCCI
 Neisseria spp
(Neisseria gonorrhoeae & Neisseria meningitidis). Normal flora of the upper respiratory tract except N.
gonorrhoeae. Kidney bean-shaped, gram-negative diplococci. Oxidase positive, fastidious, and grow best
in 5-10% CO2.
1.Neisseria gonorrhoeae: can be isolated from the urethra, cervix, anal canal, skin lesions, joints, and
blood: In males it causes acute urethritis, which is characterized by a pus containing urethral discharge
and dysuria and can also cause prostatitis and epididymitis.
 In females it causes urethral infections and cervicitis.
 Neonates may be infected during vaginal delivery, resulting in gonococcal ophthalmia neonatorum, a
severe conjunctivitis leading to blindness. Complications: ectopic pregnancy, sterility.
 N. gonorrhoeae is fastidious, requiring enriched media such as chocolate. It does not grow on BA.
 On direct Gram stain, N. gonorrhoeae often appears intracellular as will as extracellular.
 Selective media include Thayer-Martin(TM), New York City media(NYC),
 Superoxol, catalase, oxidase, and glucose positive.
2. Neisseria meningitidis: normal flora of the nasopharynx, spread by respiratory droplets, meningitis,
meningococcemia, leading to disseminated intravascular coagulation(DIC). Meningococcemia:
Waterhouse-Friderichsen syndrome (WFS), adrenal gland failure due to bleeding to adrenal
gland.
3. Moraxella catarrhalis: otitis media, sinusitis, pneumonia, does not use sucrose, glucose,
maltose, and lactose (unlike some Neisseria species).
Specimens: Cerebrospinal fluid (CSF), sputum, blood, and nasopharyngeal
swabs.
N.meninigitidis will grow on SBA incubated in increased CO2 and produce
bluish-gray colonies.
Catalase, oxidase, glucose, and maltose positive.

Meningococci Gonococci point

Utilize glucose and Utilize glucose only Carbohydrate utilization

maltose

negative Positive Superoxol(30%)

Capsulated No capsule Capsule

ANAEROBIC GRAM-POSITIVE SPORE-
FORMING BACILLI
1. Clostridium perfringens: cause gas gangrene (myonecrosis). food poisoning.
 Diabetics and patients with circulatory disorders are more prone to infection(black ulcer).
 Identifying characteristics: Produces a double zone of beta-hemolysis on SBA incubated
anaerobically. Spores are subterminal, non motile.
2. Clostridium tetani: Bacteria and spores gain entry into the host by puncture
wounds(contaminated soil), produce neurotoxin that affects the spinal cord (tetanus, lockjaw).
 Identifying characteristics: Gram-positive bacilli with round/terminal spores (tennis racket) and
motile.
3. Clostridium difficile:
Causes antibiotic associated pseudomembranous colitis and diarrhea.
 C.difficile is normal GI flora, motile.
 Identifying characteristics: Because C.difficile can be normal flora, stool cultures can sometimes
be too sensitive, also important to test isolates for toxin production.
4. Clostridium botulinum: food poisoning in adult, floppy baby syndrome (infant).
5. Actinomyces israelii: gram positive, beaded filaments (long & branched), not acid fast, yellow
sulfur granules (actinomycosis), abscesses in mouth, lung GI.
 Mycobacterium tuberculosis: nonmotile, non-spore-forming, obligate aerobes. Cell wall contain
mycolic acid (lipid).
 Tuberculosis : lungs and kidnyes. Spread by person-to-person contact via infected droplets.
 Culture media: Lowenstein-Jensen (LJ). Quantiferon Gold assay. Best test is sputum culture for
acid fact bacilli(Ziehl-Neelsen stain). Mycobacterium avium-intracellulare, they are a major
opportunistic pathogen in AIDS patients with low CD4 counts. Mycobacterium leprae: lepromatous
leprosy, grow at low temperatures. Annual employees testing, Mantoux skin test PPD.
 Spirochetes:
Treponema pallidum: Causes syphilis. Transmitted by sexual contact, direct blood transmission, or
transplacental (congenital syphilis), diagnosed by (VDRL & TPHA, FTA-ABS ).
1. Borrelia recurrentis: Causes epidemic relapsing fever, Diagnosis is based on observing bacteria
in the peripheral blood smear via the Giemsa stain.
 Leptospira: aerobic, hooked end (ice tongue shape), Leptospirosis Weil’s syndrome
(icterohemorrhagic fever), spirochetes can seen by darkfield microscopy. Carried in rodents, dogs,
fish, birds.
 Other atypical bacteria: 1. Chlamydia trachomatis: Obligate intracellular, causes trachoma,
urethritis and conjunctivitis, contain infective stage (elementary body) and metabolic active
stage(reticulate body).
2. Mycoplasma pneumoniae: lack a cell wall (amorphic), resistant to all antibiotics that inhibit cell wall
synthesis (e.g. beta-lactams, tracheobronchitis. Fired egg appearance on culture (Eaton agar).
 Minimum inhibitory concentration(MIC):
 The lowest concentration of antibiotic that inhibit the growth of bacteria as well as not harm to
patient(bacteriostatic).
 Minimum bactericidal concentration(MBC):
 The lowest concentration of antibiotic that kill the bacteria as well as not harm to patient
(bactericidal).
ANAEROBIC CULTURING
 Primary purpose medium
group D streptococci and enterococci Bile esculin agar (BEA)

determination of hemolytic reactions Blood agar (BA)

Isolation of Bordetella pertussis Bordet-Gengou agar

Type of media:
fastidious organisms Brain-heart infusion agar
A. Selective and differential:
MacCkonkey, Legionella spp. Buffered charcoal–yeast
B. Enriched and differential: extract agar (BCYE)
Blood agar. Campylobacter spp. Campy-blood agar and Skirrow agar
C. Enrichment: fastidious microorganisms such as Chocolate agar
Selenite F broth, alkaline pepton Haemophilus spp, Brucella spp and
water for Vibrio. Neisseria spp.
gram-positive cocci Columbia colistinnalidixic acid (CNA)
agar
Corynebacterium diphtheriae Cystine-tellurite blood agar

Corynebacterium spp. Loeffler medium

Antimicrobial sensitivity Mueller-Hinton Agar (MHA)
Primary purpose medium
differentiation of lactose fermenting MacConkey agar
and non–lactose fermenting
differentiation of lactose fermenting Eosin methylene blue (EMB) agar
and non–lactose fermenting
staphylococci Mannitol salt agar
Selective for Neisseria gonorrhoeae; New York City (NYC) agar

Salmonella and Shigella spp. Salmonella-Shigella (SS) agar

Enrichment of isolation of Selenite broth

Salmonella spp.
N. gonorrhoeae and N. meningitidis. Thayer-Martin agar (TM) (modified
Thayer Martin [MTM])

Vibrio spp. Thiosulfate citrate–bile salts (TCBS)

agar
Salmonella and Shigella spp. from Xylose lysine deoxycholate (XLD)
other gramnegative enteric bacilli agar
PARASITOLOGY
 Parasitic Disease Risk Factors:
 Contaminated food or water, Immunocompromised patients, travel to endemic regions.
 Parasitic Disease Characteristics:
 Diarrhea, Intestinal obstruction, weight loss, ulcers, anemia etc..
 Specimen Collection and Processing:
 Stool, urine, blood, tissue and sputum.
 Stool sample: should not mixed with urine(acidity),

.also stool specimens should not be frozen

 Liquid stool: trophozoite detection, formed stool: cyst and ova detection.
 Fresh sample is the best, otherwise use trichrome stain.

Techniques:
 Saline wet mounts are quick and easy to perform and will allow trophozoite motility and
helminth ova and larvae to be seen.
 Iodine wet mounts are useful for the staining and detection of ova and protozoan cysts in stool
samples.
 Formol ether concentration technique(FECT): for helminths and protozoa( 10% formalin).
 Flotation technique: zinc sulphate, for light eggs e.g. H.nana, not used for heavy eggs,
trematodes and operculated eggs.
 Modified acid-fast stain(cold) Kinyoun stain, is used to detect Cryptosporidium and Isospora.
 The cellophane (Scotch) tape method is used to collect Enterobius vermicularis (pinworm) eggs from the perirectal
area.
 EnteroTest (string test) is used to obtain duodenal contents: giardia(gelatin capsule).
 Types of specimen:
 Feces: Giardia, Cryptosporidium, Ascaris, Enterobius,
 Duodenal aspiration: Giardia, strongyloides.
 Blood: Plasmodium, Leishmania, Trypanosoma, and microfilariae.
 Skin: Onchocerca and Leishmania.
 Vaginal or urethral: Trichomonas.
 Eye scrapings: Acanthamoeba.
 Urine: Schistosoma and Trichomonas.
 Sputum: Paragonimus westermani, Ascaris and Strongyloides.

INTESTINAL PROTOZOA:
 Entamoeba histolytica:
 Of the amoebae the principal pathogen for humans, causes amoebic dysentery(flask shape ulcer).
 Cyst: infective stage, contain 1 to 4 nuclei vs Entamoeba coli 8 nuclei. (food and water).
 Trophozoites: one nuclus, motile by pseudopods, cytoplasm contain RBCs.
 Giardia lamblia (Giardia intestinalis):
 Causes mild to moderate diarrhea, Severe infections can lead to malabsorption (steatorrhea)
 Cyst: infective stage, ovale shaped contain 2 – 4 nuclei.
 Trophozoite: motile by 4 pairs of flagella (falling leaf motility) and pear shaped, with two nuclei on each side of a
central axostyle. (duodenal aspiration or biopsy).
 Balantidium coli:
 Is the only member of the ciliates known to infect humans.
 Fecal/oral route.
 Intestinal ulcers.
 Trophozoite: the cell membrane is covered with cilia, large, kidney-shaped macronucleus. A small,
spherical micronucleus is present adjacent to the macronucleus.
 Cyst: infective stage, spherical to ellipsoid in shape, single kidney-shaped macronucleus, often
with a small, spherical micronucleus, small vacuoles in the cytoplasm.
 Cryptosporidium parvum:
 Causes cryptosporidiosis, which is characterized by moderate to severe diarrhea.
 In patients with acquired immunodeficiency syndrome (AIDS) Cryptosporidium infections are an
important cause of death due to dehydration.
 Diagnosis: acid-fast oocysts in stool(modified acid fast stain, cold acid fast). In light infection
Sheather’s sugar flotation method used.
 Cystoisospora belli:
 Cause Cystoisosporiasis, diarrhea and malabsorption.
 Opportunistic infection (AIDS).
 The oocysts are the diagnostic forms observed in human fecal specimens. Immature oocysts
contain a single sporocyst, the mature oocysts that contain two sporocysts.
 Trichomonas vaginalis:
a sexually transmitted disease, causes vaginitis in women
(green frothy discharge).
 Trophozoites (An undulating membrane is present that
extends from the basal body) are the infective stage and
infect the epithelial or mucosal Lining of the vagina, urethra,
and prostate gland, trophozoites are highly motile by
flagella(Jerky motility) so easy to detect by wet preparation ,
found in urine and vaginal discharges.
 Note that!!! T,vaginalis have no cyst.
 Hemoflagellates:
 1.Trypansoma:
 Vector is tsetse fly (infective metacyclic trypomastigotes.
 Trypansoma brucei: causes African trypanosomiasis or sleeping sickness, and infection affects the
lymphatic system and CNS.
 gambiense and rhodesiense.
 Trypansoma cruzi: causes Chagas disease or American trypanosomiasis(chagoma), conjunctivitis,
edema of the face and legs, and heart muscle involvement leading to myocarditis.
2.Leishmania:
 leishmaniasis, sand fly is the vector, promastigote as an infective stage (Macrophages).
 Cutaneous leishmaniasis is characterized by skin and mucous membrane ulcers(L.tropica, L.major).
 Viscral leishmaniasis(kala-azar): Liver, spleen(L.donovani).
 Diagnosis: amastigote in the blood or tissue.
 Toxoplasma gondii:
 Cause toxoplasmosis.
 Infective stage is oocysts (water/food contaminated with cat feces or
transplacental.
 Oocyst release tachyzoites in the small intestine.
 Lab diagnosis: IgM & IgG.
 Plasmodium spp:
 Causes: Malaria.
 Tertian malaria: P.falciparum, P.vivax
and P.ovale
 Quartan malaria: P.malariae.
 Paroxysm: cold, hot, sweat.
 Transmitted by female anopheles
mosquito during blood
meal(sporozoites).
 Cerebral malariae caused by
P.falciparum.
 Diagnosis: Blood film is gold
standard.
 Unfixed Thick smears(qualitaitve),
 Fixed thin film, methanol(quantitation
and differentiation).
 P.malarie P.ovale P.vivax P.falciparm findings

All stages All stages All stages Ring stage and Blood
gametocytes, stages
Cytoadherance
phenomenon

rare rare occasionally Yes Multi-

infected
RBCs

Old RBCs, Young, Young, All ages, Age of

Normal size Reticulocytes, Reticulocytes, Normal size infected
enlarged enlarged RBCs

Band shape Oval shape, Amoeboid Banana or crescent Other

trophozoite Fimbriated end shape shape gametocyte
and rosette of RBCs trophozoite
shape shizont
 Babesiosis:
 caused by Babesia microti.
 transmitted by tick bite.
 laboratory diagnosis:
 Parasite in peripheral blood smears.

 Tiny ring stage resembling the ring stage of P.falciparum.

 Mature forms simulating rabbit ears.

 Extracellular forms may be seen, which is a distinctly

distinguishing feature from Plasmodium species

 Helminths: (nematodes, cestodes and trematodes).
Nematodes: (intestinal and tissue nematodes).
A. Intestinal nematodes:
1. Enterobius vermicularis(pinworm):
 most common “you may have had an infection as a child, or, if not,
may likely get it when you have children.”
 causes enterobiasis, characterized by itching and inflammation of
the anus, in school-age children.
 Eggs are infective stage(D-shaped).
 Gravid females migrate to the perianal region, where eggs are laid
during the late evening, sample is collected in the morning. (scotch
tape).
 Specimen collected early morning.
2.Trichuris trichiura(whip worm): colitis, abdominal pain and bloody
diarrhea.
 Eggs are the infective stage, American football or barrel-shaped
with bipolar plugs at each end.
 Cause rectal prolapse.
3.Ascaris lumbricoides: (pink earth-worm
like).
 Largest intestinal worm, ascariasis,
resulting in intestinal destruction and
obstruction.
 Eggs contain larvae 3 (embryonated) are
infective stages(ingestion).
 Larva migration through lung
(pneumonitis) termed Löeffler’s
pneumonia (eosinophilia). Adult pass from
anus, mouth or nose.
4. Strongyloides stercoralis: diarrhea and
abdominal pain.
 Infective stage: penetration of skin by
filariform larvae from contaminated soil.
 Diagnosis: motile rhabditiform larvae in
stool and duodenal aspiration, with short
buccal cavity vs hook worm(long).
 Baermann technique is used for larvae.
5.Hook worm:
 Necator americanus and Ancylostoma
duodenale.
 skin penetration(filariform larvae) creeping
eruption, cutaneous larvae migrance.
 Diagnosis: eggs or larvae in stool or duodenal
aspiration, positive occult blood, causes IDA.
Trematodes
6. Schistosoma: (S. mansoni, S. haematobium).
 S.haematobium: in the blood vessels around
the bladder. The eggs penetrate the bladder
and passed in the urine. Patients often
present with hematuria.
 S.mansoni: schistosomiasis, which is
characterized by abdominal pain and bloody
diarrhea.
 Infective stage: cercariae from contaminated
water.
 Diagnosis: S.haematobium, egg in urine with
terminal spine, S.mansoni, egg in stool with
lateral spine.
 Fasciola hepatica: fascioliasis:
 Hermaphroditic.
 Infective stage: ingestion of metacercaria in water plant.
 Egg: very large size, ovoid shape, and yellow-brown staining,
with operculum.
 Clonorchis sinensis, the Chinese liver fluke:
 ingesting the raw or poorly cooked flesh of several species of
freshwater fish (metacercaria).
 Egg: light yellow-brown, operculum and knob.
 Paragonimus westermani:
 Adult: coffee bean shape.
 Human infected by ingestion of raw or poorly cooked
crabmeat or crayfish (metacercaria).
 larvae then invade the lung tissue.
 Lab diagnosis: operculated egg but no knob, in stool or
respiratory specimens.
Cestodes (tape worms):
 Taenia saginata and T. Solium: cysticercosis:
 cause abdominal pain and mild diarrhea.
 Infection is by the ingestion of undercooked
beef (T. saginata) or pork (T. solium) that
contains the cysticercus larvae.
 Diagnosis: eggs:thick shell with radial
striations and (proglottid) mature gravid
segment in stool.
 The eggs of the two species are identical.
Species identification relies on proglottid,
T.saginata contain more uterine branches.
 Diphyllobothrium latum (Fish Tapeworm):
 Egg: the only operculated egg in cestodes.
 operculum at one end and a knoblike
thickening at the other end (abopercular
end)).
 Cause vit-B12 deficiency (megaloblastic
anemia).
 Hymenolepis nana (dwarf tapeworm):
 particularly in children.
 ingestion of food or water contaminated with
Hymenolepis eggs.
 laboratory diagnosis: egg, oval, small, bipolar filaments.
 Hymenolepis diminuta (rat/mouse worm):
 accidental ingestion of the infected insect by a human,
larvae are released.
 Lab diagnosis: egg spherical, larger than H.nana, no
bipolar filaments and there is distance b/w the embryo
and the egg shell.
 Dipylidium caninum:
 ingestion of dog or cat fleas that are infected with the
cysticercoid.
 Adult worm: proglottides segment possessing a double
genital pore (Dipylos means two gates).
 Lab diagnosis: egg packets contain 15 to 25 globular
eggs.
2. Echinococcus granulosus: (hydatid disease),
 Humans ingest eggs, which hatch and develop into
oncospheres. The oncospheres penetrate the intestinal
mucosa, enter the circulation, and progress to the liver. A
hydatid cyst begins to develop.
 The cysts contain protoscolices, which appear as hydatid sand
when the cyst begins to break down.
 Eggs cannot be differentiated from Taenia eggs.
 Diagnosis: hydatid cyst fluids and detecting antibodies in serum
and radiological examination (CT, MRI).
Filarial Nematodes and Filariasis
 Adults inhabit primarily the circulatory and lymphatic
channels, may also be found in muscles, connective
tissues.
 Three important species: Wuchereria bancrofti, Brugia
malayi, and Loa loa.
 (W. bancrofti and B. malayi) transmitted by mosquito,
Culex, and Anopheles+Aedes mosquitos respectively.
 Loa loa transmitted by tabanid flies.
 Lab diagnosis:
 microfilaria in blood smears (use the 10× objective) with a
regular periodicity: W. bancrofti and B. malayi are
nocturnal, whereas those of Loa loa are diurnal.
Microfilaria are ribbonlike, a prominent sheath surrounds
the microfilaria of the previous three species. Sheathed
spp can be differentiated by observing the size and the
pattern of extension of nuclei into the tail sections: W.
bancrofti: the nuclei do not extend to the tip of the tail. B.
malayi: two nuclei extend into the tail. Loa loa: an
uninterrupted column of nuclei extend into and to the tip of
the tail.
 Onchocerciasis: subcutaneous portion of the skin.
 Causative agent is Onchocerca volvulus.
 The Simulium black or buffalo fly is the vector.
 Fibrous nodules and lesions in the skin and eyes
are formed (dead microfilaria).
 Onchocerciasis is a leading cause of blindness
in the world (river blindness) wandering
microfilaria.
 Wrinkled and hyperpigmented skin, leopard skin
(mal morado).
 hanging groin: femoral and inguinal hernias.
 Dracunculus medinensis: AKA guinea worm, cause
Dracunculiasis.
 Human acquire infection by ingestion of infected
cyclop in drinking water.
 gravid females migrate to the subcutaneous,
larvae produced by the female from the skin
blister.
 From the subcutaneous tissue the worm is
winding slowly on a stick, after stimulate it by
placing a cold water on the ulcer.
 Trichinella spiralis: nematode cause Trichinosis.
 It results from the ingestion of raw or poorly cooked meat
(pork or pork products that contain encysted larvae).
 laboratory diagnosis: detecting the spiral larvae in muscle
tissue, first digesting the muscle fibers with trypsin.
MYCOLOGY
 Yeasts:
1. Candida albicans: normal flora of the mucous membranes lining the respiratory,
gastrointestinal, and female genital tracts.
 Cause: oral infection, vaginitis, nail infection, meningitis, lung diseases and UTIs.
 Culture characteristics: corn meal agar with Tween 80 produce chlamydospores.
 Germ tube test positive.
2. Cryptococcus neoformans: pulmonary infection, meningitis in immunocompromised patient.
 Diagnosis: Direct antigen test for cryptococcal antigen(Latex): Performed on CSF
specimens(sensitive).
 Indian ink stain: demonstrate the capsule.
3. Malassezia furfur: superficial mycoses, skin normal flora, a lipophilic yeast and grows on solid
media supplemented with olive oil, or glycerol monooleate, cause tinea versicolor (pityriasis),
altered skin pigmentation that may look lighter in color than the normal skin, Spherical to
elongated yeast-like cells can be easily seen microscopically (skin scraping + 10% KOH),
spaghetti and meatballs.
Dermatophytes: (Microsporum, Trichophyton, Epidermophyton) > dermatophytosis (tinea or
ringworm).
 They are keratinophilic fungi, Infect keratinized tissues (Kertinase) including skin, nail, and hair.
 Are three group:
1. Anthropophilic: isolated from human sources, include (T. rubrum, T. tonsurans, T. violaceum, M.
audouinii and E. floccosum).
2. Zoophilic: Animals are the primary reservoir, (M. canis, M. nanum, T. mentagrophytes, T.
verrucosum).
3. Geophilic: Soil is the primary reservoir of geophilic dermatophytes, (M. gypseum and T. Terrestre).
 Tinea corporis: AKA ringworm, infect skin only (T. rubrm, T. mentagrophytes, M. canis).
 Tinea capitis: scalp infection, inflammation, ulceration and hair loss, (M. canis,T. tonsurans, T.
schoenleinii).
 Tinea barbae: affect hair of beard, (T. rubrum, T. violaceum, M. canis).
 Tinea pedis: known as athlete foot, infect toe, (T. rubrum and T. mentagrophytes).
 Tinea unguium: AKA onychomycosis, infect the nails, (T. rubrum and T. mentagrophytes).
 Lab diagnosis: culture in Sabouraud dextrose agar (SDA) with chloramphenicol and cycloheximide.
Microsporum and Trichophyton spp. tend to produce two types of conidia, the macroconidia and the
microconidia, the conidia of Microsporum spp are fusiform (spindle) Epidermophyton only
macroconidia. The macroconidia of all three spp are multinucleated.
 Aspergillus spp: (A. niger, A. terreus and A. fumigatus, A. flavus).
 (aspergillosis), otomycosis, sinusitis, allergies, opportunistic fungi, hyaline mold, with
septate hyphae with 45-degree branching.
 Otomycosis, also known as mycotic otitis externa and fungal ear infection, is a superficial
chronic or subacute infection of the outer ear canal.
 Zygomycosis: Zygomycete, (Mucor, Rhizopus, and Absidia). Infect skin, lung, GI. Lab
diagnosis: presence of aseptate hyphae. Mucor hyphae with 90-degree branching.

Aspergillus flavus

Aspergillus
fumigatus

Aspergillus niger

Aspergillus terreus
 Opportunistic fungi:
 1. Fusarium spp: keratitis, endophthalmitis and systemic infections.

 Culture: colony morphology: Fusarium produces white, cottony wooly

colonies that quickly develop pink or violet centers.
 Microscopic appearance: They form septate hyphae, produce banana-
shaped or sickle shaped macroconidia with 3-5 septa.
2.Pneumocystis carinii: (Pneumocystis jirovecii).
 Do not produce hyphae, found in the lower respiratory tract.

 Pneumonia in immunocompromised patients (AIDS),(opportunistic).

 Diagnosis: bronchoalveolar lavage(lung).

 Dimorphic fungi:
 Acquired via inhalation.

 Cause systemic infections.

 Grow as yeast at 35-37°C, and as mold at 25-30°C.

 Require 3-7 weeks to grow.

 Systemic dimorphic fungi:

1. Blastomyces dermatitidis (blastomycosis).

2. Coccidioides immitis (Coccidioidomycosis).

3. Histoplasma capsulatum (histoplasmosis).

4. Paracoccidioides brasiliensis (paracoccidioidomycosis).

5. Sporothrix schenkii, (sporotrichosis).
VIROLOGY
 General Characteristics of Viruses:
 Viruses are obligate intracellular parasites unable to self-replicate. Once inside living cells, viruses induce the host cell
to synthesize virus particles.
 The genome is either DNA or RNA.
 Replicate by Assembly.
 Viral Structure:
 I . Virion is the entire viral particle.
 2. Capsid is the protein coat that encloses the genetic material.
 3. Capsomer is the protein subunit that makes up the capsid.
 4. Nucleocapsid is composed of the capsid and genetic material.
 5. The envelope vs (Naked viruses).
 Samples for viral culture must be placed into a viral transport medium (VTM).
 Upper respiratory tract infections: rhinovirus, influenza virus, parainfluenza virus, respiratory syncytial virus (RSV),
Epstein-Barr virus (EBY), and coronavirus.
 bronchitis can be caused by influenza virus, parainfluenza virus, Respiratory Syncytial Virus RSV(children), and
adenovirus.
 Cutaneous Infections: Caused by HSV-1, HSV-2, VZV,measles virus, rubella virus.
 Genital Infections (Urethritis, Cervicitis, etc.)
 l. Caused by HSV-2 and human papillomavirus
 2. Genital tract infections are typically sexually transmitted.
 Gastroenteritis
 Caused by a number of viruses, including rotaviruses: diarrhea with dehydration and runny nose
particularly young children.
 Neonatal infections are acquired in utero, during childbirth, or soon after childbirth.
 The infections can be caused by HSV, CMV, and rubella virus (TORCH profile).
 VIRAL IDENTIFICATION:
 Electron Microscopy: (poxvirus, light microscope).
 Cytopathic effect(CPE): changes of the infected cells:
 Enlarged cells > Cytomegalovirus (CMV).
 Inclusion bodies > Negri bodies (eosinophilic cytoplasmic inclusion) > rabies virus.
 syncytium-multinucleated cell > RSV.
 For intracellular viruses( immunofluorescence).
 Viral Isolation:
 Cell culture(tissue culture), (suitable host cells e.g. respiratory epithelium, neurons).
 Monkey kidney cells.
Thanks