Faisal Malik

Human papillomavirus infection in women with and without cervical cancer in Karachi, Pakistan.

Background:No data exist on the population prevalence of, or risk factors for, human papillomavirus (HPV) infection in predominantly Muslim countries in Asia.Methods:Cervical specimens were obtained from 899 married women aged 15–59 years from the general population of Karachi, Pakistan and from 91 locally diagnosed invasive cervical cancers (ICCs). HPV was detected using a GP5+/6+ PCR-based assay.Results:The prevalence of HPV in the general population was 2.8%, with no evidence of higher HPV prevalence in young women. The positivity of HPV was associated with womens lifetime number of sexual partners, but particularly with the age difference between spouses and other husbands’ characteristics, such as extramarital sexual relationships and regular absence from home. The HPV16/18 accounted for 24 and 88% of HPV-positive women in the general population and ICC, respectively.Conclusion:Cervical cancer prevention policies should take into account the low HPV prevalence and low acceptability of gynaecological examination in this population.

Characterizing Mycobacterium tuberculosis isolates from Karachi, Pakistan: drug resistance and genotypes

OBJECTIVES To study the prevalence, risk factors, and genotypes of drug-resistant Mycobacterium tuberculosis in Karachi. METHODS Pulmonary tuberculosis (TB) patients were recruited in a cross-sectional study (2006-2009). Drug susceptibility testing was performed for culture-positive cases (n=1004). Factors associated with drug resistance were evaluated using logistic regression analysis. Strains were typed using spoligotyping and mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR). The associations of genotype and drug resistance were explored using the Chi-square test. RESULTS Resistance rates - new and previously treated - were as follows: multidrug-resistant (MDR)-TB, 2.4% and 13.9%, respectively; rifampin (RIF) monoresistance, 0.1% and 0.6%, respectively; any isoniazid (INH) resistance, 8.9% and 28.5%, respectively; and INH monoresistance, 3.0% and 6.3%, respectively. Prior TB treatment was a risk factor for MDR-TB (adjusted odds ratio (AOR) 6.8, 95% confidence interval (CI) 3.5-13.1) and INH monoresistance (AOR 2.4, 95% CI 1.1-5.2). Additional risk factors included low socioeconomic status for INH monoresistance (AOR 3.3, 95% CI 1.7-6.5), and belonging to Balouchi (AOR 9.2, 95% CI 2.5-33.4), Sindhi (AOR 4.1, 95% CI 1.2-13.5), or Pakhtun (AOR 3.4, 95% CI 1.0-11.2) ethnicity for MDR-TB. Although Central Asian strain (55.6%) was the most prevalent genotype, MDR-TB was significantly associated with Haarlem (H) genogroup (crude OR 9.2, 95% CI 3.6-23.8). CONCLUSIONS An MDR-TB rate of 2.4% is reported in new patients. Low RIF monoresistance supports the use of RIF as a marker for MDR-TB in this population. The need to strengthen TB care in the identified at-risk groups is emphasized. Based on INH resistance rates, a review of national treatment/prevention regimens relying on INH is suggested.

Prevalence of multi-drug resistant tuberculosis in Karachi, Pakistan: identification of at risk groups

Multidrug-resistant tuberculosis (MDR-TB) is a possible threat to global tuberculosis control. Despite a disease prevalence of 263/100 000 population Pakistan lacks information on prevalence of drug resistant TB. Our objective was to estimate prevalence of MDR and associated risk factors in patients with pulmonary tuberculosis in Karachi. Six hundred and forty consenting adult patients were enrolled from field clinics from July 2006 to August 2008 through passive case finding. Prevalence of MDR-TB with 95% confidence interval (CI) was calculated with Epi-Info. Logistic Regression analyses were performed for risk factors associated with MDR. Overall MDR rate was 5.0%, 95% CI: 3.3-6.6% (untreated 2.3%, treated 17.9%). Mean age was 32.5 (+/-15.6) years and there were 292 (45.6%) females and 348 (54.4%) males. Factors independently associated with MDR were: female gender (OR 3.12; 95% CI: 1.40-6.91), and prior history of incomplete treatment (OR 10.1; 95% CI: 4.71-21.64). Ethnic groups at higher risk for MDR included Sindhis (OR 4.5; 95% CI: 1.42-14.71) and Pashtoons (OR 3.6, 95% CI: 1.12-11.62). This study reports an overall MDR rate of 5.0% in our study population. It further highlights the need for MDR prevention through re-focusing Directly Observed Treatment, Short-course DOTS delivery with emphasis on women and certain high risk sub groups.

Trends in Mycobacterium tuberculosis resistance, Pakistan, 1990-2007

OBJECTIVE To determine resistance trends including the emergence of extensive drug resistance (XDR) in Mycobacterium tuberculosis (MTB) isolates from Pakistan. METHODS This was a retrospective analysis of MTB isolates (January 1990-June 2007) collected from the four provinces of Pakistan. Standard methods were used to isolate MTB. Susceptibility against rifampin, isoniazid, streptomycin, ethambutol, ethionamide, capreomycin, cycloserine, and ciprofloxacin was tested using the agar proportion method, while susceptibility to pyrazinamide was determined using BACTEC. Resistance over the study period was assessed using Chi-square for trend analysis. RESULTS Resistance in 15343 MTB isolates showed a steady increase over the study period; a significant trend of increasing resistance was noted in three of the four provinces included in the study. XDR-tuberculosis was first seen in 1998; to date 22 XDR cases have been documented. MTB resistance was significantly lower (p<0.001) in patients under 5 and over 60 years of age, and significantly higher in males than females (p<0.001). MTB resistance was also higher in pulmonary than extrapulmonary isolates (p<0.001). CONCLUSION This study documenting a steady increase in resistance among MTB isolates and the emergence of XDR strains is concerning. The data highlight the need to ensure adequate treatment of cases in order to prevent a further increase in multidrug resistance within the country. The importance of developing systems for monitoring drug resistance through nationwide surveillance is emphasized.

Increasing Trend of Resistance to Penicillin, Tetracycline, and Fluoroquinolone Resistance in Neisseria gonorrhoeae from Pakistan (1992–2009)

Emergence and spread of drug resistant Neisseria gonorrhoeae is global concern. We evaluated trends of antimicrobial resistance in Neisseria gonorrhoeae over years 1992–2009 in Pakistan. Resistance rates were compared between years (2007–2009) and (1992–2006). Antimicrobial susceptibility testing was performed and interpreted according to Clinical Laboratory Standards Institute (CLSI) criteria using the disk diffusion methodology against penicillin, ceftriaxone, tetracycline and ofloxacin. Additional antibiotics tested in 100 strains isolated during 2007–2009, included cefotaxime, cefoxitin, cefuroxime, cefipime, ceftazidime, ceftizoxime, cefixime, cefpodoxime, spectinomycin and azithromycin. Neisseria gonorrhoeae ATCC 49226 was used as control. Chi-square for trend analysis was conducted to assess resistance trend over the study period. During study period significant increase in combined resistance to penicillin, tetracycline and ofloxacin was observed (P value <0.01). Resistance rates during the two study period also increased significantly (P value <0.01). Ceftriaxone resistance was not observed. None of the isolates were found to be resistant or with intermediate sensitivity to additional antibiotics. Our findings suggest that penicillin, ciprofloxacin, tetracycline should not be used in the empirical treatment of gonorrhea in Pakistan. Ceftriaxone and cefixime should be the first line therapy; however periodic MICs should be determined to identify emergence of strains with reduced susceptibility.

Fluoroquinolone resistance among Mycobacterium tuberculosis strains from Karachi, Pakistan: data from community-based field clinics.

ABSTRACT A fluoroquinolone (FQ) resistance rate of 5.9% is reported in 205 Mycobacterium tuberculosis isolates from patients presenting to field clinics in Karachi, Pakistan (2006 to 2009). FQ resistance among multidrug-resistant (MDR) strains was 11.1% (5/45), and it was 4.9% (5/103) in M. tuberculosis strains susceptible to all first-line agents. Spoligotyping of resistant strains did not show dominance of one strain type. Our data reflect considerable FQ-resistant M. tuberculosis isolates and the need to consider inclusion of FQ within first-line sensitivity testing in such settings.

Flaviviruses as a Cause of Undifferentiated Fever in Sindh Province, Pakistan: A Preliminary Report

Arboviral diseases are expanding worldwide, yet global surveillance is often limited due to diplomatic and cultural barriers between nations. With human encroachment into new habitats, mosquito-borne viruses are also invading new areas. The actual prevalence of expanding arboviruses is unknown in Pakistan due to inappropriate diagnosis and poor testing for arboviral diseases. The primary objective of this study was to document evidence of flavivirus infections as the cause of undifferentiated fever in Pakistan. Through a cooperative effort between the USA and Pakistan, patient exposure to dengue virus (DENV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) was examined in Sindh Province for the first time in decades. Initial results from the 2015 arbovirus season consisting of a cross-sectional study of 467 patients in 5 sites, DENV NS1 antigen was identified in 63 of the screened subjects, WNV IgM antibodies in 16 patients, and JEV IgM antibodies in 32 patients. In addition, a number of practical findings were made including (1) in silico optimization of RT-PCR primers for flavivirus strains circulating in the Middle East, (2) shipping and storage of RT-PCR master mix and other reagents at ambient temperature, (3) Smart phone applications for the collection of data in areas with limited infrastructure, and (4) fast and reliable shipping for transport of reagents and specimens to and from the Middle East. Furthermore, this work is producing a group of highly trained local scientists and medical professionals disseminating modern scientific methods and more accurate diagnostic procedures to the community.

Fluoroquinolone resistance in Mycobacterium tuberculosis isolates from Pakistan 2010–2014: Implications for disease control

INTRODUCTION Fluoroquinolones (FQ) are an essential component of current and new regimens for the treatment of tuberculosis (TB). The 2014 Global TB report indicates a FQ resistance rate of 17% amongst multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) tested in 2013. There is, however, a paucity of FQ-resistance data from high burden countries. In this study the trend of FQ-resistance amongst MDR-MTB and non-MDR-MTB is analyzed over a four-and-a-half-year period (January 2010-July 2014). METHODS This study was conducted at the Aga Khan University laboratory, a technical partner of the Pakistan National TB Program and part of the World Health Organization (WHO) Supra-national Laboratory Network for TB. The laboratory receives specimens from across the country through its peripheral collection units. MTB was isolated using standard methods. Susceptibility testing was performed using the agar proportion method with drug concentrations as recommended by Clinical Laboratory Institute Standards (CLSI). FQ susceptibilities were determined using ofloxacin (2μg/ml). MTB H37Rv was used as a control with each batch of susceptibility testing. MDR was defined as resistance to both isoniazid (0.2μg/ml) and rifampicin (1.0μg/ml). RESULTS During the study period 14,711 MTB strains were isolated. Of these, 6403 (43.5%) were MDR and 8308 were non-MDR. FQ resistance in MDR strains ranged between 54% and 58%. Amongst non-MDR MTB strains, FQ resistance increased from 214/2059 (10.3%) in 2010 to 180/1049 (17.1%) in 2014. The proportion of FQ mono-resistant TB strains averaged at 10.5% of the non-MDR isolates during this period. CONCLUSIONS FQ resistance in non-MDR-MTB strains with a considerable proportion of FQ mono-resistant strains in Pakistan is alarming. These data highlight the limited potential of empirical FQ usage for TB treatment in both MDR and non-MDR cases and the need to implement regular surveillance for FQ-resistance in MTB in the country. High FQ resistance amongst MTB isolates further emphasizes the importance of stewardship and the responsible use of FQs in particular, and antimicrobials in general in the country.

Human west nile virus disease outbreak in Pakistan, 2015–2016

Like most of the world, Pakistan has seen an increase in mosquito-transmitted diseases in recent years. The magnitude and distribution of these diseases are poorly understood as Pakistan does not have a nation-wide system for reporting disease. A cross-sectional study to determine which flaviviruses were causing of arboviral disease in Pakistan was instituted. West Nile virus (WNV) is a cause of seasonal fever with neurotropic findings in countries that share borders with Pakistan. Here, we describe the active and persistent circulation of WNV in humans in the southern region of Pakistan. This is the first report of WNV causing neurological disease in human patients in this country. Of 997 enrolled patients presenting with clinical features suggestive of arboviral disease, 105 were positive for WNV IgM antibodies, and 71 of these patients possessed WNV-specific neutralizing antibodies. Cross-reactivity of WNV IgM antibodies with Japanese encephalitis virus (JEV) occurred in 75 of these 105 patients. WNV co-infections with Dengue viruses were not a contributing factor for the severity of disease. Nor did prior exposure to dengue virus contribute to incidence of neurological involvement in WNV-infected patients. Patients with WNV infections were more likely to present with altered mental status, seizures, and reduced Glasgow Coma scores when compared with JEV-infected patients. Human WNV cases and vector numbers exhibited a temporal correlation with climate.

Fluoroquinolone consumption and -resistance trends in Mycobacterium tuberculosis and other respiratory pathogens: Ecological antibiotic pressure and consequences in Pakistan, 2009–2015

Objective/background: Fluoroquinolones (FQs) are important anti-tuberculous drugs for the treatment of multidrug-resistant (MDR) tuberculosis. Resistance to FQs leads to fewer options for treatment of tuberculosis (TB), and infection with such strains may also require longer treatment duration. Trends of resistance in Mycobacterium tuberculosis (MTB) are indicators of MTB-resistance evolution. Drivers of such resistance need to be understood and studied to inform preventive strategies. Methods: Here, we present FQ-resistance rates and trends in Pakistan from 2010 to 2015 and compare rates with FQ-consumption data and rates in other community pathogens. Results: Our results reveal a recent decrease in FQ-resistance rates in MTB, but an increase in resistance for Haemophilus influenzae and Shigella spp. Correlation of FQ resistance with FQ consumption at the population level was weak for MTB, although strong associations were noted for H. influenzae and Shigella spp. Conclusion: We discuss the possible reasons for the decrease in resistance rates in TB, putative drivers of resistance other than volume of FQ consumption, and the possible impact of the National Tuberculosis Programme and drug regulatory activities.