Respiratory syncytial virus and influenza are the key viral pathogens in children <2 years hospitalized with bronchiolitis and pneumonia in Islamabad Pakistan.

Pneumonia remains a leading cause of morbidity and mortality in developing countries. Comprehensive surveillance data are needed to review the prevention and control strategies. We conducted active surveillance of acute lower respiratory infections among children aged <2 years hospitalized at two hospitals of Islamabad, Pakistan. Viral etiology was determined using real-time PCR on respiratory specimens collected during March 2011-April 2012. The overall mean age was 7.83 ± 5.25 months while no statistical difference between age or sex distribution of patients with positive and negative viral etiology (p > 0.05). The average weight of the study group was 6.1 ± 2.25 kg. ≥1 viral pathogens were detected in 75% cases. Major respiratory viruses included RSV-A: 44%, RSV-B: 23%, Influenza-A: 24.5%, Influenza-B: 7%, Adenovirus: 8.4% and HmPV: 5.2%. A single, dual or multiple viral pathogens were detected in 43%, 27% and 5.2% patients respectively. Common symptoms were cough (95%), apnoea (84%), fever (78%), wheeze (64.5%), nasal congestion (55%) and rhinorrhea (48%). Among the RSV positive cases, 2-6 months age group had highest detection rate for RSV-A (30%, n = 21/69) and RSV-B (20%, n = 14/69) while patients infected with Influenza-A were in 2.1-6 months age group (61%, 23/38). Statistically significant difference was observed between RSV-positive and negative cases for nutrition status (p = 0.001), cigarette/wood smoke exposure (p = 0.001) and concomitant clinical findings. Most patients had successful outcome on combination therapy with bronchodilators, inhaled steroids and antibiotics. Our findings underscore high burden of ALRI in Pakistan. Interventions targeting viral pathogens coupled with improved diagnostic approaches are critical for better prevention and control.

External Quality Assessment Scheme (IEQAS) in haematology at National Institute of Health, Islamabad, Pakistan.

OBJECTIVE: To document overall performance and improvement, if any, gained through participation in an International External Quality Assessment Scheme (IEQAS). STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: The Haematology Department, Public Health Laboratories Division, National Institute of Health, Islamabad, Pakistan, from January 1996 to December 2006. METHODOLOGY: Overall performance of blood parameters and parasite identification were analysed. Individual values were assessed against consensus value (mean + or - SD) and deviation index (DI) from the mean, whereas coefficients of variation (CV) were calculated for years 1996 to 2006. The results are expressed as percentage of accurate versus inaccurate results, deviation index (DI) and coefficient of variation (%CV). RESULTS: The laboratory achieved 87.74% of values within acceptable limits for haemoglobin, 72.03% for white blood count, 69.49% for platelet and 77.03% for reticulocyte estimation. Results were satisfactory, having DI values less than 3 for all four parameters. %CV values was found to be dependent on the type of test performed and varied among different parameters. Difficulty has been observed in identifying Plasmodium malariae and ovale. CONCLUSION: Participation in External Quality Assessment Schemes is extremely beneficial for the improvement of laboratory performance and quality of care. Evaluation of the survey results on a regular basis serves as a useful guide to assess overall performance of the laboratory. Standardization of analytical procedures, equipments and reagents, continuous monitoring of personnel competency and thorough investigation of discordant results significantly contributes to the delivery of quality diagnostic services.

Frequency of tuberculous cervical lymphadenitis detection at a single laboratory in islamabad.

OBJECTIVE: To determine the frequency of tuberculous cervical lymphadenitis and to evaluate the diagnostic efficacy of microscopy and conventional Lowenstein Jensen (LJ) culture technique in the diagnosis of cervical lymphadenitis caused by M. tuberculosis (MTB) Study Design: A descriptive, cross-sectional study. Place and Duration of the Study: Department of Mycobacteriology, Public Health Laboratories Division, National Institute of Health, Islamabad, from January 2003 to December 2004. PATIENTS AND METHODS: A total of 220 patients from Pakistan Institute of Medical Sciences (PIMS), Islamabad, Federal Government Services Hospital (FGSH), Islamabad and Rawalpindi General Hospital (RGH), Rawalpindi, presenting with enlarged cervical lymph nodes (for at least six months), pain/ weight loss and low grade fever were studied for the presence of MTB from 142 lymph node biopsies, 60 FNA samples and 18 discharge fluids/swabs. All the samples were examined at NIH by ZN staining smear and culture on conventional LJ medium as well as on Bactec 12B medium using Bactec 460 TB system. The drug susceptibility testing of the isolates was performed on Bactec 460 TB system. NAP test on Bactec 460-TB system, Accuprobe and biochemical tests were employed to identify the mycobacterial isolates. RESULTS: M. tuberculosis accounted for 173 out of 220 cases of cervical lymphadenopathy. Maximum incidence was found to be in the age group 10-30 years with male to female ratio of 1:1.7. Discharge sinuses and abscess formation were uncommon. Biopsy tissue samples gave the maximum yield of positive mycobacterial cultures as all 142 biopsy samples being positive while only 50% (30/60) of FNA and 5.5% (1/18) of discharge fluids/swabs were positive. All the isolates were identified as M. tuberculosis. No atypical mycobacteria were recovered from the samples examined. All isolates were found to be susceptible to first line anti-tuberculous drugs i.e. Streptomycin, Isoniazid, Rifampicin and Ethambutol (SIRE). CONCLUSION: Tuberculosis was the major cause of cervical lymphadenopathy in the referral area. Culture of the biopsy tissue from the affected lymph nodes is a method of choice for laboratory diagnosis of tuberculous cervical lymphadenopathy.

Prediction of clinical factors associated with pandemic influenza A (H1N1) 2009 in Pakistan.

BACKGROUND: Influenza is a viral infection that can lead to serious complications and death(s) in vulnerable groups if not diagnosed and managed in a timely manner. This study was conducted to improve the accuracy of predicting influenza through various clinical and statistical models. METHODOLOGY: A retrospective cross sectional analysis was done on demographic and epidemiological data collected from March 2009 to March 2010. Patients were classified as ILI or SARI using WHO case definitions. Respiratory specimens were tested by RT-PCR. Clinical symptoms and co-morbid conditions were analyzed using binary logistic regression models. RESULTS: In the first approach, analysis compared children (≤12) and adults (>12). Of 1,243 cases, 262 (21%) tested positive for A(H1N1)pdm09 and the proportion of children (≤12) and adults (>12) were 27% and 73% respectively. Four symptoms predicted influenza in children: fever (OR 2.849, 95% CI 1.931-8.722), cough (OR 1.99, 95% CI 1.512-3.643), diarrhea (OR 2.100, 95% CI 2.040-3.25) and respiratory disease (OR 3.269, 95% CI 2.128-12.624). In adults, the strongest clinical predictor was fever (OR 2.80, 95% CI 1.025-3.135) followed by cough (OR 1.431, 95% CI 1.032-2.815). In the second instance, patients were separated into two groups: SARI 326 (26%) and ILI 917 (74%) cases. Male to female ratio was 1.41∶1.12 for SARI and 2∶1.5 for ILI cases. Chi-square test showed that fever, cough and sore throat were significant factors for A(H1N1)pdm09 infections (p = 0.008). CONCLUSION: Studies in a primary care setting should be encouraged focused on patients with influenza-like illness to develop sensitive clinical case definition that will help to improve accuracy of detecting influenza infections. Formulation of a standard "one size fits all" case definition that best correlates with influenza infections can help guide decisions for additional diagnostic testing and also discourage unjustified antibiotic prescription and usage in clinical practice.

Molecular characterization of circulating respiratory syncytial virus (RSV) genotypes in Gilgit Baltistan Province of Pakistan during 2011-2012 winter season.

Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV genotypes detected in Pakistani children less than 2 years of age with acute respiratory tract infections (ARIs) in a tertiary care hospital in Gilgit Baltistan (GB) province during 2011-12 winter season. RSV was detected in 75 out of 105 children presenting with acute respiratory infection. Male infants between 2-6 months age made up the highest percentage of RSV positive cases. Epidemiological factors such as pre-maturity, mean weight, clinical features and diagnosis when compared between RSV positive and negative groups were found to be statistically insignificant. Phylogenetic analysis classified all 75 of the RSV strains into 71 strains of subgroups A and 4 strains of subgroup B, respectively. Strains belonging to subgroups A and B were further subdivided into NA1/GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (>90%). Both RSV-A and RSV-B isolates had two potential N-glycosylation sites in HVR2 of G protein and with heavy O-glycosylation of serine and threonine residues (G scores of 0.5-0.7). This report highlights the significance of RSV as a dominant viral etiologic agent of pediatric ARIs, and need for continued molecular epidemiological surveys for early detection of prevalent strains and newly emerging genotypes to understand epidemiology of RSV infections in various regions of Pakistan.

Molecular epidemiology of influenza A(H1N1)pdm09 viruses from Pakistan in 2009-2010.

BACKGROUND: In early 2009, a novel influenza A(H1N1) virus that emerged in Mexico and United States rapidly disseminated worldwide. The spread of this virus caused considerable morbidity with over 18000 recorded deaths. The new virus was found to be a reassortant containing gene segments from human, avian and swine influenza viruses. METHODS/RESULTS: The first case of human infection with A(H1N1)pdm09 in Pakistan was detected on 18(th) June 2009. Since then, 262 laboratory-confirmed cases have been detected during various outbreaks with 29 deaths (as of 31(st) August 2010). The peak of the epidemic was observed in December with over 51% of total respiratory cases positive for influenza. Representative isolates from Pakistan viruses were sequenced and analyzed antigenically. Sequence analysis of genes coding for surface glycoproteins HA and NA showed high degree of high levels of sequence identity with corresponding genes of regional viruses circulating South East Asia. All tested viruses were sensitive to Oseltamivir in the Neuraminidase Inhibition assays. CONCLUSIONS: Influenza A(H1N1)pdm09 viruses from Pakistan form a homogenous group of viruses. Their HA genes belong to clade 7 and show antigenic profile similar to the vaccine strain A/California/07/2009. These isolates do not show any amino acid changes indicative of high pathogenicity and virulence. It is imperative to continue monitoring of these viruses for identification of potential variants of high virulence or drug resistance.