SPECIMEN PROCESSING

Three sets of samples were taken, centrifuged at 3000rpm for 15 mts and the deposit was processed as follows

1. First set of sample was used for microscopic examination. a) 10% Potassium hydroxide (KOH) mount preparation, b) Gram’s stain procedure

c) Ziehl-Neelsen staining

d) Modified Ziehl-Neelsen staining, e) Toluidine blue O staining

f) Giemsa staining.

2. Second set of sample was inoculated onto solid media like blood agar, chocolate agar and MacConkey agar.

3. Third set of sample was inoculated onto two slants of Sabouraud’s dextrose agar (SDA) devoid of antibiotics and cycloheximide.

39 a) Microscopic Examination:

a) 10% KOH mount preparation was examined for the presence of septate or aseptate hyphal elements, conidial forms or yeast forms.

b)Gram positive or Gram negative organisms or yeast cells were looked for in Gram’s stain preparation.

c) Fixed smear was stained by acid fast staining and looked for any acid fast bacilli.

d) Modified acid fast staining was done for identifying Nocardia spp. e) Smear was stained with Toluidene blue and Giemsa stains and examined for the presence of trophozoites and cysts of Pneumocystis jirovecii.

b) Culture:

The centrifuged deposit of bronchoalveolar lavage was inoculated on MacConkey agar, blood agar and chocolate agar plates and incubated at 37ºC for 24 hrs. The two inoculated SDA slants were incubated at 25ºC and 37ºC for up to 4 weeks.[101]

Interpretation of Bacterial culture:

Bacterial culture plates were observed for growth at 24 hours. If there are < 10 colonies on the plate, that equates < 103 cfu/ml, between 10-100 colonies indicate 103-104 cfu/ml and 100-1000 colonies indicate 104-105

40

cfu/ml. The diagnostic threshold for bronchoalveolar lavage is ≥104cfu/ml.[12]

Bacterial isolates were identified by means of Gram’s staining, motility and biochemical reactions by standard microbiological techniques as recommended by Clinical and Laboratory Standards Institute (CLSI).

All bacterial isolates were preserved in 0.2 – 0.5 % semisolid Nutrient agar slopes at 4 – 5º C in refrigerator with periodic subculture every 2 months.[104]

Interpretation of Fungal culture:

Two SDA slants were inoculated and incubated at 25ºC and 37ºC for minimum of 4 weeks before reporting as negative. These slants were inspected daily during the first week and twice weekly during the next three weeks for growth.[70] Growth on the slants with presence of hyphal elements in 10% KOH preparation was regarded as significant fungal growth.

Identification of filamentous fungi was done by preparing Lacto Phenol Cotton Blue mount and studying the morphology of hyphae and conidial arrangement. In difficult, ambiguous cases where sporulation was inadequate, Riddle’s slide culture technique was performed.[47]

Lactophenol Cotton Blue stain:[69]

Place a drop of Lactophenol Cotton Blue Stain in the center of a clean slide. Remove a fragment of the fungus colony 2-3mm from the colony edge

41

using an inoculating or teasing needle. Place the fragment in the drop of stain and tease gently. Apply a coverslip. Do not push down or tap the cover slip as this may dislodge the conidia from the conidiophores. Examine the preparation under low and high, dry magnification for the presence of characteristic mycelia and fruiting structures.

Riddle’s slide culture technique:[47]

This was used to study the undisturbed morphological details of fungi, particularly the relationship between reproductive structures and mycelium. Procedure:

1. A round piece of filter paper was placed on the bottom of a sterile Petri dish. A pair of thin glass rods was placed on top of the filter paper to serve as supports for a 3 inch × 1 inch glass microscopic slide.

2. A small 1cm block of SDA previously poured into a Petridish was placed on the surface of the microscopic slide. The block was cut using a sterile scalpel.

3. A small portion of the fungal colony to be studied was inoculated onto three or four places in the margins of the agar block using a straight inoculating wire.

4. A coverslip was gently heated by passing it quickly through the flame of a Bunsen burner and immediately placed directly on the surface of the inoculated agar block.

42

5. A small amount of water was placed into the bottom of the petri dish to saturate the filter paper.

6. The Petridish was incubated at 30ºC for 3-5 days.

7. When a growth visually appeared to mature, the coverslip was gently lifted from the surface of the agar with a pair of forceps taking care not to disrupt the mycelium adhering to the bottom of the coverslip.

8. The coverslip was placed on a small drop of LPCB on a second glass slide. Likewise, the mycelium adhering to the surface of the original glass slide after the block was removed also was stained with LPCB and a fresh coverslip was overlaid.

9. The characteristic shape and arrangement of spores was observed microscopically.

In case of yeasts, identification and speciation was done by Gram’s stain morphology, germ tube test, morphology on corn meal agar, and biochemical tests by standard microbiological techniques as recommended by CLSI.

Gram’s stain

Gram positive oval budding yeasts cells with presence or absence of pseudohyphae.

43 Germ Tube test

A loopful of creamy white yeast like colony from SDA was taken and it was inoculated into 0.5ml of mammalian serum. It was incubated at 37ºC for one and a half to 2 hours. After incubation period, a loop full of this serum suspension was placed on a clean glass slide and covered with cover slip and focused under high power objective to see the characteristic germ tube formation .

Chromagar

A single colony from Sabourauds dextrose agar was taken and it was streaked on chromagar and incubated at 37°C for 48 hrs. After incubation period, the plates were observed for characteristic coloured colonies of candida.

Cornmeal agar

A single colony from Sabouraud’s dextrose agar was inoculated on to a plate of cornmeal agar containing 1%Tween 80 and trypan blue. Three parallel steaks were made about half an inch apart at a 45º angle to the culture medium. A sterile coverslip was placed over it and incubated at 30ºC for 48 hrs. After incubation the areas where the cuts into the agar were made were examined for the presence of blastoconidia, arthroconidia, pseudohyphae, hyphae or chlamydoconidia.[5]

44 Carbohydrate fermentation test[5]

A saline suspension of the yeast colonies was prepared. About 0.2ml of this suspension was inoculated on to the carbohydrate fermentation broth that contain Durham’s tube and different sugars at a concentration of 2%. The different sugars used were glucose, lactose, sucrose, maltose respectively. The tubes were incubated at room temperature for 7-10 days. After incubation period, the tubes were observed for acid and gas production.

Carbohydrate assimilation test[5]

Organisms from SDA were inoculated onto carbohydrate free medium either in nutrient agar or blood agar. A suspension of the yeast in saline or distilled water to a density equivalent to a McFarland No.4 standard was prepared. The saline suspension was swabbed on sterile

yeast nitrogen base agar plate.

The different carbohydrate disc used include glucose, lactose, sucrose, maltose, galactose, trehalose , raffinose. The disc were placed on to the surface of the agar approximately 30mm apart from each other. The plates were incubated at 30ºC for 24 to 48hrs.

After incubation, the plates were observed for the presence of a colour change around the carbohydrate containing discs or the presence of growth surrounding them. All fungal growths were preserved by suspending a small

45

inoculum of spores or conidia in sterile distilled water and kept in sterile cryo vials at room temperature.[70]*