Materials and Methods
The present study was conducted at the Parasitology Laboratory, Department of Microbiology, of our tertiary care referral centre.
a. Patients and clinical samples
During the 5 year study period (Feb 2007 to Dec 2012), a total of 355 patients including both HIV sero positive and non-HIV immunocompromised patients with pulmonary infection clinically suggestive of PCP attending to various OPD and/or admitted to our tertiary care centre were enrolled.
Among these 355 patients, 106 were HIV seropositive patients (n=106) and remaining 249 were non-HIV immunocompromised patients. These non-HIV immunocompromised patients were further subdivided into post-renal transplant (PRT) recipients (n=66), cancer patients on chemotherapy (n=84), patients with various primary immunodeficiencies, and autoimmune disorders (n=99). From these 355 patients, equal number (n=355) samples were obtained that included, 244 bronchoalveolar lavage (BAL) fluid and 111 induced sputum (IS).
Demographic profile, clinical characteristics, laboratory findings and radiological findings of each patient were collected prospectively during the course of study. The study was approved by the institute’s research and ethics committee.
b. Clinical Sample Processing and DNA extraction:
All the BAL fluid samples were directly centrifuged at 4000 rpm at 4oC for 10 min. However, sputum samples were first treated with 6.5 mM dithiothreitol (DTT), a mucolytic agent and then subjected to centrifugation. The pellet obtained was resuspended in 20% of the supernatant and 100 µl of this suspended pellet was used for preparation of smears.
For DNA extraction, 200 µl of pellet was lysed using 200 µl of a sample-specific lysis buffer (50 mM KCl, 15 mM Tris-HCl (pH 8.3) and 0.5% NP 40) [Lee et al 1993] containing 500 mg of proteinase K. DNA extraction was performed using Qiagen tissue kit (Qiagen, USA).
Smears were prepared from all the samples. Smears were stained using Grocott’s methenamine silver (GMS) staining. All the stained slides were examined by two experienced microbiologists independently without prior knowledge of PCR results.
Conventional PCR (c-PCR) assay:
c-PCR was performed using highly conserved region of mitochondrial large sub-unit ribosomal RNA (mtLSU rRNA) gene of P. jirovecii. The following set of published primers pAZ 102 E and pAZ 102 H (Wakefield et al 1990), were used that amplify a 346 bp region of the gene.
Real-time PCR (qPCR) assay:
DNA extracted from all the clinical samples were subjected to qPCR assay targeting the single copy gene Beta-tubulin gene.
The set of primers used were as described by Nahimana et al 2000 for c-PCR and Brancart et al 2005 for qPCR targeting Beta-tubulin gene. However, the probe used was with slight modification. The probe was FAM – MGB probe, with the product size of 74bp. The sequences of forward and reverse primers; and probe used were as follows F-(1186-5’) GATCCGAGACATGGTCGCTATT,...